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Sample records for molecular conformational generation

  1. Parallel cascade selection molecular dynamics (PaCS-MD) to generate conformational transition pathway

    NASA Astrophysics Data System (ADS)

    Harada, Ryuhei; Kitao, Akio

    2013-07-01

    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

  2. Conformation, orientation and interaction in molecular monolayers: A surface second harmonic and sum frequency generation study

    SciTech Connect

    Superfine, R.; Huang, J.Y.; Shen, Y.R.

    1988-12-01

    We have used sum frequency generation (SFG) to study the order in a silane monolayer before and after the deposition of a coadsorbed liquid crystal monolayer. We observe an increase in the order of the chain of the silane molecule induced by the interpenetration of the liquid crystal molecules. By using second harmonic generation (SHG) and SFG, we have studied the orientation and conformation of the liquid crystal molecule on clean and silane coated glass surfaces. On both surfaces, the biphenyl group is tilted by 70{degree} with the alkyl chain end pointing away from the surface. The shift in the C-H stretch frequencies in the coadsorbed system indicates a significant interaction between molecules. 9 refs., 3 figs.

  3. Conformational Transitions in Molecular Systems

    NASA Astrophysics Data System (ADS)

    Bachmann, M.; Janke, W.

    2008-11-01

    Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

  4. Molecular mechanics conformational analysis of tylosin

    NASA Astrophysics Data System (ADS)

    Ivanov, Petko M.

    1998-01-01

    The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

  5. The effect of the structure and conformational dynamics on quenching of triplet states of porphyrins and their chemical dimers by molecular oxygen and on singlet oxygen generation

    NASA Astrophysics Data System (ADS)

    Ivashin, N. V.; Shchupak, E. E.; Sagun, E. I.

    2015-01-01

    Quantum-chemical calculations are performed to analyze the factors affecting rate constant k T of quenching of the lowest triplet state by molecular oxygen and quantum yield γΔ of singlet oxygen generation in chemical dimers of porphyrins bound by phenyl spacers at one of the meso positions (OEP)2-Ph, (TPP)2, and their Zn complexes. It is established that, for both types of dimers, the triplet excitation is localized on one of the macrocycles. The steric hindrance of macrocycles at the site of the phenyl ring of (OEP)2-Ph, (ZnOEP)2-Ph, and their monomeric analogues OEP-Ph and ZnOEP-Ph facilitates its rotation by 90° in the triplet state. The lowest triplet state energy in this ( U) conformation is lower than 7800 cm-1, which makes impossible electronic excitation energy transfer to molecular oxygen. The potential barrier of transformation to the U conformation is considerably lower for dimers than for monomers. Because of this, the rate of conformational transformations for dimers is higher and some of the (OEP)2-Ph and (ZnOEP)2-Ph molecules have time to transform into the new U conformation before diffusion collision with O2 molecules in solution. This leads to a noticeable decrease in γΔ in accordance with experimental data. It is shown that the behavior of k T in the series of the studied dimers, their monomeric analogues, and relative compounds corresponds to the model of dipole-dipole electronic excitation energy transfer 1(3M⋯3Σ{g/-}) → 1(1M0⋯1Δg) in collisional complexes.

  6. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    PubMed Central

    2009-01-01

    Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625

  7. Conformation effects on the molecular orbitals of serine

    NASA Astrophysics Data System (ADS)

    Wang, Ke-Dong; Ma, Peng-Fei; Shan, Xu

    2011-03-01

    This paper calculates the five most stable conformers of serine with Hartree—Fock theory, density functional theory (B3LYP), Møller—Plesset perturbation theory (MP4(SDQ)) and electron propagation theory with the 6-311++G(2d,2p) basis set. The calculated vertical ionization energies for the valence molecular orbitals of each conformer are in agreement with the experimental data, indicating that a range of molecular conformations would coexist in an equilibrium sample. Information of the five outer valence molecular orbitals for each conformer is explored in coordinate and momentum spaces using dual space analysis to investigate the conformational processes, which are generated from the global minimum conformer Ser1 by rotation of C2-C3 (Ser4), C1-C2 (Ser5) and C1-O2 (Ser2 and Ser3). Orbitals 28a, 27a and 26a are identified as the fingerprint orbitals for all the conformational processes. Project supported by the Doctoral Research Fund of Henan Normal University, China (Grant No. 525449).

  8. Molecular modeling of conformational properties of oligodepsipeptides.

    PubMed

    Zhang, Jiajing; King, Michael; Suggs, Laura; Ren, Pengyu

    2007-10-01

    A depsipeptide is a chemical structure consisting of both ester and amide bonds. Quantum mechanics calculations have been performed to investigate the conformational properties of a depsidipeptide in the gas and solution phases. Similar to an alanine dipeptide, the depsidipeptide exhibits a strong preference for the polyproline II (PPII) helical conformation. Meanwhile, due to the changes in the intramolecular interaction, the propensity for beta-sheets and alpha-helices diminishes while an unusual inclination for the (phi,psi) = (-150 degrees ,0 degrees ) conformation was observed. A molecular mechanics model has been developed for polydepsipeptides based on the quantum mechanical study. Both simulated annealing and replica exchange molecular dynamics simulations have been carried out on oligodepsipeptide sequences with alternating depsi and natural residues in solution. Novel helical structures have been indicated from the simulations. When glycine is used as the alternating natural amino acid residue, the PPII conformation of a depsi residue stabilizes the peptide into a right-handed helical structure while the alpha-helical conformation of the depsi residue favors an overall left-handed helical structure. The free energy analysis indicates that both the left- and the right-handed helices are equally likely to exist. When charged lysine is introduced as the alternating natural residue, however, it is found that the depsipeptide sequence prefers an extended conformation as in PPII. Our results indicate that the depsipeptide is potentially useful in designing protein mimetics with controllable structure, function, and chemistry. PMID:17877396

  9. Measuring the mechanical properties of molecular conformers

    PubMed Central

    Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

    2015-01-01

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules. PMID:26388232

  10. Generating static fluid spheres by conformal transformations

    SciTech Connect

    Loranger, Jonathan; Lake, Kayll

    2008-12-15

    We generate an explicit four-fold infinity of physically acceptable exact perfect fluid solutions of Einstein's equations by way of conformal transformations of physically unacceptable solutions (one way to view the use of isotropic coordinates). Special cases include the Schwarzschild interior solution and the Einstein static universe. The process we consider involves solving two equations of the Riccati type coupled by a single generating function rather than a specification of one of the two metric functions.

  11. Determining Geometrically Stable Domains in Molecular Conformation Sets.

    PubMed

    Romanowska, Julia; Nowiński, Krzysztof S; Trylska, Joanna

    2012-08-14

    Detecting significant conformational changes occurring in biomolecules is a challenging task, especially when considering tens to hundreds of thousands of conformations. Conformational variability can be described by dividing a biomolecule into dynamic domains, i.e., by finding compact fragments that move as coherent units. Typical approaches, based on calculating a dynamical cross-correlation matrix, are limited by their inability to reveal correlated rotations and anticorrelated motions. We propose a geometric approach for finding dynamic domains, where we compare traces of atomic movements in a pairwise manner, and search for their best superposition. A quaternion representation of rotation is used to simplify the complex calculations. The algorithm was implemented in a Java graphical program: Geometrically Stable Substructures (GeoStaS). The program processes PDB and DCD binary files with large structural sets for proteins, nucleic acids, and their complexes. We demonstrate its efficiency in analyzing (a) ensembles of structures generated by NMR experiments and (b) conformation sets from biomolecular simulations, such as molecular dynamics. The results provide a clear description of the molecular movements even for large biomolecules. Compared to a standard dynamic cross-correlation matrix, our algorithm detects the correlations in both translational and rotational motions. PMID:26592104

  12. Patterns and conformations in molecularly thin films

    NASA Astrophysics Data System (ADS)

    Basnet, Prem B.

    Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn

  13. Conformational analyses of periplanone analogs by molecular mechanics calculations.

    PubMed

    Shimazaki, K; Mori, M; Okada, K; Chuman, T; Goto, H; Osawa, E; Sakakibara, K; Hirota, M

    1991-04-01

    Conformational parameters of pheromonally active analogs (1 and 2) of periplanones, the sex pheromones of the American cockroach, were investigated by molecular mechanics calculations. They existed in several conformers with small energy differences. These results were supported by NMR analysis. The structural features of the conformers of the analogs were compared with X-ray structures of periplanones. PMID:24258922

  14. Conformational Analysis in 18-Membered Macrolactones Based on Molecular Modeling

    PubMed Central

    Belaidi, Salah; Harkati, Dalal

    2011-01-01

    Conformational analysis of 18-ring membered macrolactones has been carried out using molecular mechanics calculations and molecular dynamics. A high conformational flexibility of macrolactones was obtained, and an important stereoselectivity was observed for the complexed macrolides. For 18d macrolactone, which was presented by a most favored conformer with 20.1% without complex, it was populated with 50.1% in presence of Fe(CO)3. PMID:24052826

  15. Toward Focusing Conformational Ensembles on Bioactive Conformations: A Molecular Mechanics/Quantum Mechanics Study.

    PubMed

    Avgy-David, Hannah H; Senderowitz, Hanoch

    2015-10-26

    The identification of bound conformations, namely, conformations adopted by ligands when binding their target is critical for target-based and ligand-based drug design. Bound conformations could be obtained computationally from unbound conformational ensembles generated by conformational search tools. However, these tools also generate many nonrelevant conformations thus requiring a focusing mechanism. To identify such a mechanism, this work focuses on a comparison of energies and structural properties of bound and unbound conformations for a set of FDA approved drugs whose complexes are available in the PDB. Unbound conformational ensembles were initially obtained with three force fields. These were merged, clustered, and reminimized using the same force fields and four QM methods. Bound conformations of all ligands were represented by their crystal structures or by approximations to these structures. Energy differences were calculated between global minima of the unbound state or the Boltzmann averaged energies of the unbound ensemble and the approximated bound conformations. Ligand conformations which resemble the X-ray conformation (RMSD < 1.0 Å) were obtained in 91%-97% and 96%-98% of the cases using the ensembles generated by the individual force fields and the reminimized ensembles, respectively, yet only in 52%-56% (original ensembles) and 47%-65% (reminimized ensembles) as global energy minima. The energy window within which the different methods identified the bound conformation (approximated by its closest local energy minimum) was found to be at 4-6 kcal/mol with respect to the global minimum and marginally lower with respect to a Boltzmann averaged energy of the unbound ensemble. Better approximations to the bound conformation obtained with a constrained minimization using the crystallographic B-factors or with a newly developed Knee Point Detection (KPD) method gave lower values (2-5 kcal/mol). Overall, QM methods gave lower energy differences than

  16. Molecular dynamics studies of the conformation of sorbitol

    PubMed Central

    Lerbret, A.; Mason, P.E.; Venable, R.M.; Cesàro, A.; Saboungi, M.-L.; Pastor, R.W.; Brady, J.W.

    2009-01-01

    Molecular dynamics simulations of a 3 m aqueous solution of D-sorbitol (also called D-glucitol) have been performed at 300 K, as well as at two elevated temperatures to promote conformational transitions. In principle, sorbitol is more flexible than glucose since it does not contain a constraining ring. However, a conformational analysis revealed that the sorbitol chain remains extended in solution, in contrast to the bent conformation found experimentally in the crystalline form. While there are 243 staggered conformations of the backbone possible for this open-chain polyol, only a very limited number were found to be stable in the simulations. Although many conformers were briefly sampled, only eight were significantly populated in the simulation. The carbon backbones of all but two of these eight conformers were completely extended, unlike the bent crystal conformation. These extended conformers were stabilized by a quite persistent intramolecular hydrogen bond between the hydroxyl groups of carbon C-2 and C-4. The conformational populations were found to be in good agreement with the limited available NMR data except for the C-2–C-3 torsion (spanned by the O-2–O-4 hydrogen bond), where the NMR data supports a more bent structure. PMID:19744646

  17. ConfGen: a conformational search method for efficient generation of bioactive conformers.

    PubMed

    Watts, K Shawn; Dalal, Pranav; Murphy, Robert B; Sherman, Woody; Friesner, Rich A; Shelley, John C

    2010-04-26

    We describe the methodology, parametrization, and application of a conformational search method, called ConfGen, designed to efficiently generate bioactive conformers. We define efficiency as the ability to generate a bioactive conformation within a small total number of conformations using a reasonable amount of computer time. The method combines physics-based force field calculations with empirically derived heuristics designed to achieve efficient searching and prioritization of the ligand's conformational space. While many parameter settings are supported, four modes spanning a range of speed and quality trades-offs are defined and characterized. The validation set used to test the method is composed of ligands from 667 crystal structures covering a broad array of target and ligand classes. With the fastest mode, ConfGen uses an average of 0.5 s per ligand and generates only 14.3 conformers per ligand, at least one of which lies within 2.0 A root-mean-squared deviation of the crystal structure for 96% of the ligands. The most computationally intensive mode raises this recovery rate to 99%, while taking 8 s per ligand. Combining multiple search modes to "fill-in" holes in the conformation space or energy minimizing using an all-atom force field each lead to improvements in the recovery rates at higher resolutions. Overall, ConfGen is at least as good as competing programs at high resolution and demonstrates higher efficiency at resolutions sufficient for many downstream applications, such as pharmacophore modeling. PMID:20373803

  18. Molecular insight into conformational transmission of human P-glycoprotein

    NASA Astrophysics Data System (ADS)

    Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan

    2013-12-01

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

  19. Molecular insight into conformational transmission of human P-glycoprotein

    SciTech Connect

    Chang, Shan-Yan; Liu, Fu-Feng E-mail: ysun@tju.edu.cn; Dong, Xiao-Yan; Sun, Yan E-mail: ysun@tju.edu.cn

    2013-12-14

    P-glycoprotein (P-gp), a kind of ATP-binding cassette transporter, can export candidates through a channel at the two transmembrane domains (TMDs) across the cell membranes using the energy released from ATP hydrolysis at the two nucleotide-binding domains (NBDs). Considerable evidence has indicated that human P-gp undergoes large-scale conformational changes to export a wide variety of anti-cancer drugs out of the cancer cells. However, molecular mechanism of the conformational transmission of human P-gp from the NBDs to the TMDs is still unclear. Herein, targeted molecular dynamics simulations were performed to explore the atomic detail of the conformational transmission of human P-gp. It is confirmed that the conformational transition from the inward- to outward-facing is initiated by the movement of the NBDs. It is found that the two NBDs move both on the two directions (x and y). The movement on the x direction leads to the closure of the NBDs, while the movement on the y direction adjusts the conformations of the NBDs to form the correct ATP binding pockets. Six key segments (KSs) protruding from the TMDs to interact with the NBDs are identified. The relative movement of the KSs along the y axis driven by the NBDs can be transmitted through α-helices to the rest of the TMDs, rendering the TMDs to open towards periplasm in the outward-facing conformation. Twenty eight key residue pairs are identified to participate in the interaction network that contributes to the conformational transmission from the NBDs to the TMDs of human P-gp. In addition, 9 key residues in each NBD are also identified. The studies have thus provided clear insight into the conformational transmission from the NBDs to the TMDs in human P-gp.

  20. Molecular conformational space analysis using computer graphics: going beyond FRODO.

    PubMed

    Nilsson, O

    1990-12-01

    The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed. PMID:2282358

  1. Conformations of Low-Molecular-Weight Lignin Polymers in Water.

    PubMed

    Petridis, Loukas; Smith, Jeremy C

    2016-02-01

    Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures. PMID:26763657

  2. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation.

    PubMed

    Lupyan, Dmitry; Abramov, Yuriy A; Sherman, Woody

    2012-11-01

    The Cambridge Structural Database (CSD) offers an excellent data source to study small molecule conformations and molecular interactions. We have analyzed 130 small molecules from the CSD containing an intramolecular sulfur-oxygen distance less than the sum of their van der Waals (vdW) radii. Close S···O distances are observed in several important medicinal chemistry motifs (e.g. a carbonyl oxygen connected by a carbon or nitrogen linker to a sulfur) and are not treated well with existing parameters in the MMFFs or OPLS_2005 force fields, resulting in suboptimal geometries and energetics. In this work, we develop modified parameters for the OPLS_2005 force field to better treat this specific interaction in order to generate conformations close to those found in the CSD structures. We use a combination of refitting a force field torsional parameter, adding a specific atom pair vdW term, and attenuating the electrostatic interactions to obtain an improvement in the accuracy of geometry minimizations and conformational searches for these molecules. Specifically, in a conformational search 58 % of the cases produced a conformation less than 0.25 Å from the CSD crystal conformation with the modified OPLS force field parameters developed in this work. In contrast, 25 and 37 % produced a conformation less than 0.25 Å with the MMFFs and OPLS_2005 force fields, respectively. As an application of the new parameters, we generated conformations for the tyrosine kinase inhibitor axitinib (trade name Inlyta) that could be correctly repacked into three observed polymorphic structures, which was not possible with conformations generated using MMFFs or OPLS_2005. The improved parameters can be mapped directly onto physical characteristics of the systems that are treated inadequately with the molecular mechanics force fields used in this study and potentially other force fields as well. PMID:23053737

  3. Molecular Visualization of Conformation-Triggered Flow Instability

    NASA Astrophysics Data System (ADS)

    Xu, Hui; Shirvanyants, David; Beers, Kathryn L.; Matyjaszewski, Krzysztof; Dobrynin, Andrey V.; Rubinstein, Michael; Sheiko, Sergei S.

    2005-06-01

    A new type of flow fingering instability was observed in monolayer-thick polymer films as they spread on a solid substrate. Tracing the movement of individual molecules by atomic force microscopy enabled us to follow the development of the flow instability on the molecular level and to understand the underlying physical mechanism. The fingering instability was observed to be triggered by conformational changes of brushlike macromolecules in response to the pressure gradient driving the flow.

  4. Electrostatic Swelling and Conformational Variation Observed in High-Generation Polyelectrolyte Dendrimers

    SciTech Connect

    Butler, Paul D; Chen, Wei-Ren; Herwig, Kenneth W; Hong, Kunlun; Liu, Yun; Porcar, L.; Shew, Chwen-Yang; Smith, Gregory Scott; Chen, Hsin-Lung; Chen, Chun-Yu; Li, Xin; Liu, Emily

    2010-01-01

    A coordinated study combining small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) measurements was conducted to investigate the structural characteristics of aqueous (D2O) generation 7 and 8 (G7 & G8) PAMAM dendrimer solutions as a function of molecular protonation at room temperature. The change in intra-molecular conformation was clearly exhibited in the data analysis by separating the variation in the inter-molecular correlation. Our results unambiguously demonstrate an increased molecular size and evolved intra-molecular density profile upon increasing the molecular protonation. This is contrary to the existing understanding that in higher generation polyelectrolyte dendrimers, steric crowding stiffens the local motion of dendrimer segments exploring additional available intra-dendrimer volume and therefore inhibits the electrostatic swelling. Our observation is relevant to elucidation of the general microscopic picture of polyelectrolyte dendrimer structure, as well as the development of dendrimer-based packages with based on the stimuli-responsive principle.

  5. Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations

    PubMed Central

    Wang, Kai; Long, Shiyang; Tian, Pu

    2015-01-01

    Hierarchical organization of free energy landscape (FEL) for native globular proteins has been widely accepted by the biophysics community. However, FEL of native proteins is usually projected onto one or a few dimensions. Here we generated collectively 0.2 milli-second molecular dynamics simulation trajectories in explicit solvent for hen egg white lysozyme (HEWL), and carried out detailed conformational analysis based on backbone torsional degrees of freedom (DOF). Our results demonstrated that at micro-second and coarser temporal resolutions, FEL of HEWL exhibits hub-like topology with crystal structures occupying the dominant structural ensemble that serves as the hub of conformational transitions. However, at 100ns and finer temporal resolutions, conformational substates of HEWL exhibit network-like topology, crystal structures are associated with kinetic traps that are important but not dominant ensembles. Backbone torsional state transitions on time scales ranging from nanoseconds to beyond microseconds were found to be associated with various types of molecular interactions. Even at nanoseconds temporal resolution, the number of conformational substates that are of statistical significance is quite limited. These observations suggest that detailed analysis of conformational substates at multiple temporal resolutions is both important and feasible. Transition state ensembles among various conformational substates at microsecond temporal resolution were observed to be considerably disordered. Life times of these transition state ensembles are found to be nearly independent of the time scales of the participating torsional DOFs. PMID:26057625

  6. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

    PubMed Central

    Caves, L. S.; Evanseck, J. D.; Karplus, M.

    1998-01-01

    Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory. PMID:9541397

  7. Origin of molecular conformational stability: Perspectives from molecular orbital interactions and density functional reactivity theory

    SciTech Connect

    Liu, Shubin E-mail: schauer@unc.edu; Schauer, Cynthia K. E-mail: schauer@unc.edu

    2015-02-07

    To have a quantitative understanding about the origin of conformation stability for molecular systems is still an unaccomplished task. Frontier orbital interactions from molecular orbital theory and energy partition schemes from density functional reactivity theory are the two approaches available in the literature that can be used for this purpose. In this work, we compare the performance of these approaches for a total of 48 simple molecules. We also conduct studies to flexibly bend bond angles for water, carbon dioxide, borane, and ammonia molecules to obtain energy profiles for these systems over a wide range of conformations. We find that results from molecular orbital interactions using frontier occupied orbitals such as the highest occupied molecular orbital and its neighbors are only qualitatively, at most semi-qualitatively, trustworthy. To obtain quantitative insights into relative stability of different conformations, the energy partition approach from density functional reactivity theory is much more reliable. We also find that the electrostatic interaction is the dominant descriptor for conformational stability, and steric and quantum effects are smaller in contribution but their contributions are indispensable. Stable molecular conformations prefer to have a strong electrostatic interaction, small molecular size, and large exchange-correlation effect. This work should shed new light towards establishing a general theoretical framework for molecular stability.

  8. Frog: a FRee Online druG 3D conformation generator.

    PubMed

    Leite, T Bohme; Gomes, D; Miteva, M A; Chomilier, J; Villoutreix, B O; Tufféry, P

    2007-07-01

    In silico screening methods based on the 3D structures of the ligands or of the proteins have become an essential tool to facilitate the drug discovery process. To achieve such process, the 3D structures of the small chemical compounds have to be generated. In addition, for ligand-based screening computations or hierarchical structure-based screening projects involving a rigid-body docking step, it is necessary to generate multi-conformer 3D models for each input ligand to increase the efficiency of the search. However, most academic or commercial compound collections are delivered in 1D SMILES (simplified molecular input line entry system) format or in 2D SDF (structure data file), highlighting the need for free 1D/2D to 3D structure generators. Frog is an on-line service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions. Given the atomic constitution of the molecules and connectivity information, Frog can identify the different unambiguous isomers corresponding to each compound, and generate single or multiple low-to-medium energy 3D conformations, using an assembly process that does not presently consider ring flexibility. Tests show that Frog is able to generate bioactive conformations close to those observed in crystallographic complexes. Frog can be accessed at http://bioserv.rpbs.jussieu.fr/Frog.html. PMID:17485475

  9. Sampling Molecular Conformers in Solution with Quantum Mechanical Accuracy at a Nearly Molecular-Mechanics Cost.

    PubMed

    Rosa, Marta; Micciarelli, Marco; Laio, Alessandro; Baroni, Stefano

    2016-09-13

    We introduce a method to evaluate the relative populations of different conformers of molecular species in solution, aiming at quantum mechanical accuracy, while keeping the computational cost at a nearly molecular-mechanics level. This goal is achieved by combining long classical molecular-dynamics simulations to sample the free-energy landscape of the system, advanced clustering techniques to identify the most relevant conformers, and thermodynamic perturbation theory to correct the resulting populations, using quantum-mechanical energies from density functional theory. A quantitative criterion for assessing the accuracy thus achieved is proposed. The resulting methodology is demonstrated in the specific case of cyanin (cyanidin-3-glucoside) in water solution. PMID:27494227

  10. Conformational model of the Holliday junction transition deduced from molecular dynamics simulations

    PubMed Central

    Yu, Jin; Ha, Taekjip; Schulten, Klaus

    2004-01-01

    Homologous recombination plays a key role in the restart of stalled replication forks and in the generation of genetic diversity. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. In the presence of metal ions, the Holliday junction folds into the stacked-X structure that has two alternative conformers. Experiments have revealed the spontaneous transitions between these conformers, but their detailed pathways are not known. Here, we report a series of molecular dynamics simulations of the Holliday junction at physiological and elevated (400 K) temperatures. The simulations reveal new tetrahedral intermediates and suggest a schematic framework for conformer transitions. The tetrahedral intermediates bear resemblance to the junction conformation in complex with a junction-resolving enzyme, T7 endonuclease I, and indeed, one intermediate forms a stable complex with the enzyme as demonstrated in one simulation. We also describe free energy minima for various states of the Holliday junction system, which arise during conformer transitions. The results show that magnesium ions stabilize the stacked-X form and destabilize the open and tetrahedral intermediates. Overall, our study provides a detailed dynamic model of the Holliday junction undergoing a conformer transition. PMID:15613597

  11. Evolution of dendrimer conformational structure with generation number

    NASA Astrophysics Data System (ADS)

    Betancourt, Beatriz A. Pazmiño; Douglas, Jack F.

    2016-05-01

    We simulate the conformational structure of a coarse-grained model of dendrimer molecules in a good solvent as a function of generation number G and find that they evolve through substantially more complex structures than regular star polymers with increasing arms because of their hierarchical topological structure. As G increases, they evolve from 3-arm stars to branched polymers that geometrically resemble lattice animals, and then percolation clusters for G = 4 - 6 range. For larger G, the dendrimers become similar to porous particles, but the molecule segregates segregates into subdomains at G = 9, reflecting the branching complexity of the first dendrimer generation.

  12. Aripiprazole salts IV. Anionic plus solvato networks defining molecular conformation

    NASA Astrophysics Data System (ADS)

    Freire, Eleonora; Polla, Griselda; Baggio, Ricardo

    2014-06-01

    Five new examples of aripiprazole (arip) salts are presented, viz., the Harip phthalate [Harip+·C8H5O4-(I)], homophthalate [Harip+·C9H7O4-(II)] and thiosalicilate [Harip+·C7H4O2S-(III)] salts on one side, and two different dihidrogenphosphates, Harip+·H2PO4-·2(H3PO4)·H2O (IV) and Harip+·H2PO4-·H3PO4(V). Regarding the internal structure of the aripH+ cations, they do not differ from the already known moieties in bond distances and angles, while interesting differences in conformation can be observed, setting them apart in two groups: those in I, II and III present similar conformations to those in the so far reported arip salts presenting the same centrosymmetric R(8)22 dimeric synthon, but different to those in IV and V. In parallel, the anion (+ acid) groups define bulky systems of different dimensionality (1D in the former group, 2D in the latter). The correlation between arip molecular conformation and anionic network type is discussed. An interesting feature arises with the water solvato molecule in IV, disordered around an inversion center, in regard with its interaction with an (also disordered) phosphato O-H, in a way that an “orderly disordered” H-bonding scheme arises, complying with the S.G. symmetry requirements only on average.

  13. Molecular dynamics study on the electrostatic effect of protein conformation

    NASA Astrophysics Data System (ADS)

    Sook Kang, Nam; Kwang Shin, Jae; Hyeok Yoon, Jeong; Shik John, Mu

    1993-05-01

    In order to examine in detail the effect of ionizable residues on the stability of α-helical structures, we have performed molecular dynamics simulations on melittin under controlled pH using a macroscopic dielectric model. We simulated at + 3-charged, + 6-charged and totally uncharged states of melittin. From these calculations, we obtained various conformational properties such as helical content, torsion angle trajectories, temperature factors and end-to-end distances. The +3-charged state corresponding to the basic pH range showed the most stable structure. Our analysis concluded that the helix is least stable at neutral pH including six positively charged residues, and helicity increases as the pH approaches the basic range. In addition, our results showed qualitatively the differences in the hinge-bending flexibility of the α-helix according to the pH.

  14. Dynamic conformational ensembles regulate casein kinase-1 isoforms: Insights from molecular dynamics and molecular docking studies.

    PubMed

    Singh, Surya Pratap; Gupta, Dwijendra K

    2016-04-01

    Casein kinase-1 (CK1) isoforms actively participate in the down-regulation of canonical Wnt signaling pathway; however recent studies have shown their active roles in oncogenesis of various tissues through this pathway. Functional loss of two isoforms (CK1-α/ε) has been shown to activate the carcinogenic pathway which involves the stabilization of of cytoplasmic β-catenin. Development of anticancer therapeutics is very laborious task and depends upon the structural and conformational details of the target. This study focuses on, how the structural dynamics and conformational changes of two CK1 isoforms are synchronized in carcinogenic pathway. The conformational dynamics in kinases is the responsible for their action as has been supported by the molecular docking experiments. PMID:26788877

  15. Elucidating Molecular Motion through Structural and Dynamic Filters of Energy-Minimized Conformer Ensembles

    PubMed Central

    2015-01-01

    Complex RNA structures are constructed from helical segments connected by flexible loops that move spontaneously and in response to binding of small molecule ligands and proteins. Understanding the conformational variability of RNA requires the characterization of the coupled time evolution of interconnected flexible domains. To elucidate the collective molecular motions and explore the conformational landscape of the HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized structures generated by the program “Fragment Assembly of RNA with Full-Atom Refinement (FARFAR)”. We apply structural filters in the form of experimental residual dipolar couplings (RDCs) to select a subset of discrete energy-minimized conformers and carry out principal component analyses (PCA) to corroborate the choice of the filtered subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule using two simulation protocols that we previously published. We match the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results introduce a protocol to construct viable dynamic trajectories for RNA molecules that accord well with experimental NMR data and support the notion that the motions of the helical portions of this small RNA can be described by a relatively small number of discrete conformations exchanging over time scales longer than 1 μs. PMID:24479561

  16. A Script for Automated 3-Dimentional Structure Generation and Conformer Search from 2- Dimentional Chemical Drawing

    PubMed Central

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists. PMID:24391363

  17. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    PubMed

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists. PMID:24391363

  18. A numerical study of hybrid optimization methods for the molecular conformation problems

    SciTech Connect

    Meza, J.C.; Martinez, M.L.

    1993-05-01

    An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules depends on the accurate determination of their three-dimensional structure or conformation. Under the assumption that molecules will settle into a configuration for which their energy is at a minimum, this design problem can be formulated as a global optimization problem. The solution of the molecular conformation problem can then be obtained, at least in principle, through any number of optimization algorithms. Unfortunately, it can easily be shown that there exist a large number of local minima for most molecules which makes this an extremely difficult problem for any standard optimization method. In this study, we present results for various optimization algorithms applied to a molecular conformation problem. We include results for genetic algorithms, simulated annealing, direct search methods, and several gradient methods. The major result of this study is that none of these standard methods can be used in isolation to efficiently generate minimum energy configurations. We propose instead several hybrid methods that combine properties of several local optimization algorithms. These hybrid methods have yielded better results on representative test problems than single methods.

  19. Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism

    PubMed Central

    Ping, Jie; Hao, Pei; Li, Yi-Xue; Wang, Jing-Fang

    2013-01-01

    Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK. PMID:23936827

  20. Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods.

    PubMed

    Gilbert, Kathleen M; Skawinski, William J; Misra, Milind; Paris, Kristina A; Naik, Neelam H; Buono, Ronald A; Deutsch, Howard M; Venanzi, Carol A

    2004-11-01

    Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte > MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the

  1. A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure.

    PubMed

    Jeong, Jay I; Lattman, Eaton E; Chirikjian, Gregory S

    2006-04-01

    This paper presents a methodology to obtain candidate conformations of multidomain proteins for use in molecular replacement. For each separate domain, the orientational relationship between the template and the target structure is obtained using standard molecular replacement. The orientational relationships of the domains are then used to calculate the relative rotation between the domains in the target conformation by using pose-estimation techniques from the field of robotics and computer vision. With the angle of relative rotation between the domains as a cost function, iterative normal-mode analysis is used to drive the template structure to a candidate conformation that matches the X-ray crystallographic data obtained for the target conformation. The selection of the correct intra-protein domain orientations from among the many spurious maxima in the rotation function (including orientations obtained from domains in symmetry mates rather than within the same copy of the protein) presents a challenge. This problem is resolved by checking R factors of each domain, measuring the absolute value of relative rotation between domains, and evaluating the cost value after each candidate conformation is driven to convergence with iterative NMA. As a validation, the proposed method is applied to three test proteins: ribose-binding protein, lactoferrin and calcium ATPase. In each test case, the orientation and translation of the final candidate conformation in the unit cell are generated correctly from the suggested procedure. The results show that the proposed method can yield viable candidate conformations for use in molecular replacement and can reveal the structural details and pose of the target conformation in the crystallographic unit cell. PMID:16552141

  2. Electronic structure and conformation of polymers from cluster molecular orbital and molecular mechanics calculations: Polyimide

    SciTech Connect

    Kafafi, S.A. ); LaFemina, J.P. ); Nauss, J.L. )

    1990-11-21

    Full geometry optimizations using molecular mechanics and the quantum chemical AM1 method have been carried out to determine the minimum energy conformation of pyromellitic dianhydride-oxydianiline polyimide (PMDA-ODA PI). The phenyl-imide twist angle for this compound was determined to be {approximately}30. These computations also provided a quantitative determination of the energy gap (7 eV), electron affinity ({minus}2 eV), and ionization potential (8.97 eV). Computations on the PMDA-ODA PI radical anion provided an estimate of the hopping barrier for an electron to hop from one chain to another (3.2 eV), the mechanism believed responsible for photoconduction. Moreover, the use of qualitative molecular orbital theory (QMOT) arguments provided an interpretation of these results in a simple molecular orbital framework.

  3. Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion

    SciTech Connect

    Martin-Garcia, Fernando; Mendieta-Moreno, Jesus Ignacio; Mendieta, Jesus

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer Initial conformational change of paramyxovirus F protein is caused only by mechanical forces. Black-Right-Pointing-Pointer HRA region undergoes a structural change from a beta + alpha conformation to an extended coil and then to an all-alpha conformation. Black-Right-Pointing-Pointer HRS domains of F protein form three single {alpha}-helices prior to generation of the coiled coil. -- Abstract: The fusion of paramyxovirus to the cell membrane is mediated by fusion protein (F protein) present in the virus envelope, which undergoes a dramatic conformational change during the process. Unlike hemagglutinin in orthomyxovirus, this change is not mediated by an alteration of environmental pH, and its cause remains unknown. Steered molecular dynamics analysis leads us to suggest that the conformational modification is mediated only by stretching mechanical forces once the transmembrane fusion peptide of the protein is anchored to the cell membrane. Such elongating forces will generate major secondary structure rearrangement in the heptad repeat A region of the F protein; from {beta}-sheet conformation to an elongated coil and then spontaneously to an {alpha}-helix. In addition, it is proposed that the heptad repeat A region adopts a final three-helix coiled coil and that this structure appears after the formation of individual helices in each monomer.

  4. Ligand induced conformational changes of the human serotonin transporter revealed by molecular dynamics simulations.

    PubMed

    Koldsø, Heidi; Autzen, Henriette Elisabeth; Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  5. Ligand Induced Conformational Changes of the Human Serotonin Transporter Revealed by Molecular Dynamics Simulations

    PubMed Central

    Grouleff, Julie; Schiøtt, Birgit

    2013-01-01

    The competitive inhibitor cocaine and the non-competitive inhibitor ibogaine induce different conformational states of the human serotonin transporter. It has been shown from accessibility experiments that cocaine mainly induces an outward-facing conformation, while the non-competitive inhibitor ibogaine, and its active metabolite noribogaine, have been proposed to induce an inward-facing conformation of the human serotonin transporter similar to what has been observed for the endogenous substrate, serotonin. The ligand induced conformational changes within the human serotonin transporter caused by these three different types of ligands, substrate, non-competitive and competitive inhibitors, are studied from multiple atomistic molecular dynamics simulations initiated from a homology model of the human serotonin transporter. The results reveal that diverse conformations of the human serotonin transporter are captured from the molecular dynamics simulations depending on the type of the ligand bound. The inward-facing conformation of the human serotonin transporter is reached with noribogaine bound, and this state resembles a previously identified inward-facing conformation of the human serotonin transporter obtained from molecular dynamics simulation with bound substrate, but also a recently published inward-facing conformation of a bacterial homolog, the leucine transporter from Aquifex Aoelicus. The differences observed in ligand induced behavior are found to originate from different interaction patterns between the ligands and the protein. Such atomic-level understanding of how an inhibitor can dictate the conformational response of a transporter by ligand binding may be of great importance for future drug design. PMID:23776432

  6. Influence of rotational energy barriers to the conformational search of protein loops in molecular dynamics and ranking the conformations.

    PubMed

    Tappura, K

    2001-08-15

    An adjustable-barrier dihedral angle potential was added as an extension to a novel, previously presented soft-core potential to study its contribution to the efficacy of the search of the conformational space in molecular dynamics. As opposed to the conventional soft-core potential functions, the leading principle in the design of the new soft-core potential, as well as of its extension, the soft-core and adjustable-barrier dihedral angle (SCADA) potential (referred as the SCADA potential), was to maintain the main equilibrium properties of the original force field. This qualifies the methods for a variety of a priori modeling problems without need for additional restraints typically required with the conventional soft-core potentials. In the present study, the different potential energy functions are applied to the problem of predicting loop conformations in proteins. Comparison of the performance of the soft-core and SCADA potential showed that the main hurdles for the efficient sampling of the conformational space of (loops in) proteins are related to the high-energy barriers caused by the Lennard-Jones and Coulombic energy terms, and not to the rotational barriers, although the conformational search can be further enhanced by lowering the rotational barriers of the dihedral angles. Finally, different evaluation methods were studied and a few promising criteria found to distinguish the near-native loop conformations from the wrong ones. PMID:11455590

  7. Molecular dynamics and neutron scattering study of the dependence of polyelectrolyte dendrimer conformation on counterion behavior

    SciTech Connect

    Chen, Wei-Ren; Do, Changwoo; Egami, T; Hong, Kunlun; Li, Xin; Liu, Emily; Liu, Yun; Porcar, L.; Smith, Gregory Scott; Smith, Sean C; Wu, Bin

    2012-01-01

    Atomistic molecular dynamics (MD) simulations and contrast variation small angle neutron scattering (SANS) technique have been used to investigate the generation-5 (G5) polyelectrolyte polyamidoamine (PAMAM) starburst dendrimer with respect to its conformational dependence on counterion behavior at different levels of molecular charge. Satisfactory agreement is seen between the simulated results, such as the excess intra-dendrimer scattering length density (SLD) distribution and hydration level, and their experimental counterparts. The conformational evolution of charged dendrimer appears to be highly dependent on the association behavior of counterion. We explore the nature of the distribution of counterions around charged amines and qualitatively account for its sensitivity to the counterion valency on the difference of excess free energy. Moreover, via extending the concept of electrical double layer for compact charged colloids, we define an effective radius of charged dendrimer based on the spatial distribution of counterions in its vicinity. Within the same framework, the correlation between the strength of intra-dendrimer electrostatic repulsion and counterion valency and dynamics is also addressed.

  8. Investigation on surface molecular conformations and pervaporation performance of the poly(vinyl alcohol) (PVA) membrane.

    PubMed

    Zhang, Wei; Zhang, Zhennan; Wang, Xinping

    2009-05-01

    A simple method of changing pre-treatment temperature in the course of film formation was used to tune the surface structures of PVA membranes. Surface structure and property of the resulting membranes were characterized by X-ray photoelectron spectroscopy (XPS), sum frequency generation (SFG) vibrational spectroscopy, and contact angle measurements. The results show that PVA have different molecular conformations at the membrane surface while those membranes were prepared at different pre-treatment temperature. At higher pre-treatment temperatures, polar acetoxyl residues and hydroxyl groups of the PVA chains oriented in a more orderly fashion, as induced by the faster evaporation of water. When the membranes were in air, CH(3) groups adjacent to the acetoxyl groups covered the surface in order to minimize the surface free energy, while backbones of the PVA were rarely observed. These surfaces exhibited a hydrophilic nature upon contact with water due to rapid surface reconstruction. Conversely, at lower pre-treatment temperatures, the backbone CH(2) groups dominated the surface, forming a less hydrophilic surface. When the PVA membranes were employed to separate ethanol/water mixtures, it was found that the PVA membranes with more hydrophilic surface exhibited higher water selectivity. Our investigation indicates that molecular conformations on the membrane surface have considerable influence on pervaporation performance. PMID:19249794

  9. Prediction of enantiomeric selectivity in chromatography. Application of conformation-dependent and conformation-independent descriptors of molecular chirality.

    PubMed

    Aires-de-Sousa, João; Gasteiger, Johann

    2002-03-01

    In order to process molecular chirality by computational methods and to obtain predictions for properties that are influenced by chirality, a fixed-length conformation-dependent chirality code is introduced. The code consists of a set of molecular descriptors representing the chirality of a 3D molecular structure. It includes information about molecular geometry and atomic properties, and can distinguish between enantiomers, even if chirality does not result from chiral centers. The new molecular transform was applied to two datasets of chiral compounds, each of them containing pairs of enantiomers that had been separated by chiral chromatography. The elution order within each pair of isomers was predicted by means of Kohonen neural networks (NN) using the chirality codes as input. A previously described conformation-independent chirality code was also applied and the results were compared. In both applications clustering of the two classes of enantiomers (first eluted and last eluted enantiomers) could be successfully achieved by NN and accurate predictions could be obtained for independent test sets. The chirality code described here has a potential for a broad range of applications from stereoselective reactions to analytical chemistry and to the study of biological activity of chiral compounds. PMID:11885960

  10. Molecular simulations for the conformational assessment of a porphyrin-fullerene dyad in different environments.

    PubMed

    Tappura, Kirsi; Cramariuc, Oana; Hukka, Terttu I; Rantala, Tapio T

    2005-09-01

    Conformational space of a porphyrin-fullerene dyad with the donor and acceptor connected by a relatively flexible linker is studied by molecular dynamics simulations in both non-polar and polar solvents, as well as in vacuum. The most probable conformations obtained from the vacuum MD simulations were optimized with semi-empirical (SE) and density functional theory (DFT) methods and the extent of the structural changes is assessed. The computational results indicate the co-existence of different conformers in both polar and nonpolar solvents showing agreement with experimental results. The most probable vacuum conformations at 300 K are similar to the ones at 0 K, while the structures most often observed in the solvents show less compact conformations. Optimization with SE and DFT calculations leads to structures, which represent relatively well the folded conformations in solvent, which validates the electronic structure calculations relevant to describing photoinduced electron-transfer in H2P-O34-C60. PMID:16240023

  11. Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study.

    PubMed

    Murugan, N Arul

    2005-09-01

    Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle. PMID:16164354

  12. Can chromatin conformation technologies bring light into human molecular pathology?

    PubMed

    Kubiak, Marta; Lewandowska, Marzena Anna

    2015-01-01

    Regulation of gene expression in eukaryotes involves many complex processes, in which chromatin structure plays an important role. In addition to the epigenetic effects, such as DNA methylation and phosphorylation or histone modifications, gene expression is also controlled by the spatial organization of chromatin. For example, distant regulatory elements (enhancers, insulators) may come into direct physical interaction with target genes or other regulatory elements located in genomic regions of up to several hundred kilobases in size. Such long-range interactions result in the formation of chromatin loops. In the last several years, there has been a rapid increase in our knowledge of the spatial organization of chromatin in the nucleus through the chromosome conformation capture (3C) technology. Here we review and compare the original 3C and 3C-based methods including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), hi-resolution chromosome confomation capture (HiC). In this article, we discuss different aspects of how the nuclear organization of chromatin is associated with gene expression regulation and how this knowledge is useful in translational medicine and clinical applications. We demonstrate that the knowledge of the chromatin 3D organization may help understand the mechanisms of gene expression regulation of genes involved in the development of human diseases, such as CFTR (responsible for cystic fibrosis) or IGFBP3 (associated with breast cancer pathogenesis). Additionally, 3C-derivative methods have been also useful in the diagnosis of some leukemia subtypes. PMID:26328275

  13. Vibrational modes and changing molecular conformation of perfluororubrene in thin films and solution

    NASA Astrophysics Data System (ADS)

    Anger, F.; Scholz, R.; Gerlach, A.; Schreiber, F.

    2015-06-01

    We investigate the vibrational properties of perfluororubrene (PF-RUB) in thin films on silicon wafers with a native oxide layer as well as on silicon wafers covered with a self-assembled monolayer and in dichloromethane solution. In comparison with computed Raman and IR spectra, we can assign the molecular modes and identify two molecular conformations with twisted and planar tetracene backbones of the molecule. Moreover, we employ Raman imaging techniques to study the morphology and distribution of the molecular conformation in PF-RUB thin films.

  14. Probing flexible conformations in molecular junctions by inelastic electron tunneling spectroscopy

    SciTech Connect

    Deng, Mingsen; Ye, Gui; Jiang, Jun; Cai, Shaohong; Sun, Guangyu

    2015-01-15

    The probe of flexible molecular conformation is crucial for the electric application of molecular systems. We have developed a theoretical procedure to analyze the couplings of molecular local vibrations with the electron transportation process, which enables us to evaluate the structural fingerprints of some vibrational modes in the inelastic electron tunneling spectroscopy (IETS). Based on a model molecule of Bis-(4-mercaptophenyl)-ether with a flexible center angle, we have revealed and validated a simple mathematical relationship between IETS signals and molecular angles. Our results might open a route to quantitatively measure key geometrical parameters of molecular junctions, which helps to achieve precise control of molecular devices.

  15. New mechanistic insight in the thermal helix inversion of second-generation molecular motors.

    PubMed

    Klok, Martin; Walko, Martin; Geertsema, Edzard M; Ruangsupapichat, Nopporn; Kistemaker, Jos C M; Meetsma, Auke; Feringa, Ben L

    2008-01-01

    The introduction of dibenzocyclohepten-5-ylidene as part of a unidirectional light-driven molecular motor allows a more complete picture of the pathway of thermal helix inversion to be developed. The most stable conformation is similar to that found in related motors in that it has, overall, an anti-folded structure with the substituent at the stereogenic centre adopting an axial orientation. Photochemical cis/trans isomerisation at -40 degrees C results in the formation of an isomer in a syn-folded conformation with the methyl group in an axial orientation. This contrasts with previous studies on related molecular rotary motors. The conformation of the higher energy intermediate typically observed for this class of compound is the anti-folded conformation, in which the methyl group is in an equatorial orientation. This conformation is available through an energetically uphill upper half ring inversion of the observed photochemical product. However, this pathway competes with a second process that leads to the more stable anti-folded conformation in which the methyl group is oriented axially. It has been shown that the conformations and pathways available for second-generation molecular motors can be described by using similar overall geometries. Differences in the metastable high-energy species are attributable to the relative energy and position on the reaction coordinate of the transition states. Kinetic studies on these new molecular motors thus provide important insights into the conformational dynamics of the rotation cycle. PMID:18979464

  16. Influence of Molecular Solvation on the Conformation of Star Polymers

    SciTech Connect

    Li, Xin; Porcar, L.; Sanchez-Diaz, Luis E; Do, Changwoo; Liu, Yun; Smith, Gregory Scott; Hong, Kunlun; Chen, Wei-Ren

    2014-01-01

    We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.

  17. Molecular structure and conformations of caramboxin, a natural neurotoxin from the star fruit: A computational study

    NASA Astrophysics Data System (ADS)

    Pichierri, Fabio

    2015-01-01

    Using density functional theory calculations we investigate the molecular structure and conformations of caramboxin, a neurotoxin recently isolated from the star fruit Averroha carambola. Among the seven conformers that exist within an energy window of ∼16.0 kcal/mol, two of them are the most favored ones with an energy difference of less than 2.0 kcal/mol. The computed chemical shifts of these two low-energy conformers are in good agreement with the experimental values determined in deuterated dimethylsulfoxide thus confirming the 2D chemical structure assigned to the neurotoxin. A topological analysis of the theoretical electronic charge density of four caramboxin conformers reveals the existence of intramolecular CH⋯O/N interactions which, in addition to the classical OH⋯O/N H-bonding interactions, contribute to decrease the conformational freedom of the neurotoxin.

  18. Cyclo-biphenalenyl biradicaloid molecular materials: conformation, rearrangement, magnetism, and thermochromism

    SciTech Connect

    Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent; Tian, Yong-Hui; Kertesz, Prof. Miklos

    2010-01-01

    Cyclo-biphenalenyl biradicaloid molecular materials with chair- and boat-conformations are studied by restricted and broken-symmetry DFT using the M06 family of meta-GGA functionals. The global minima of these molecular materials are magnetically silent due to the sigma-bond connecting the two phenalenyls, while the sigma-bond may undergo low-barrier sigmatropic rearrangements via pi-pi bonded paramagnetic intermediates. The validation of theory is performed for the chair-conformation by comparing the sigma-bonded structures and the rearrangement barriers with experimental data. The boat-conformation is then studied using the validated functional. The electronic spectra of both chair- and boat-conformations are calculated and their applications in thermochromism are discussed.

  19. A conformational study of N-tosyl oxazolidines using molecular mechanics and crystallography

    NASA Astrophysics Data System (ADS)

    Belvisi, Laura; Carugo, Oliviero; Poli, Giovanni

    1994-03-01

    The conformational behavior of (4 S,5 R)-4-methyl-5-phenyl-3- p-toluenesulfonyl oxazolidines has been investigated. This was accomplished by combining a comparative analysis of nine crystal structures with a molecular mechanics conformational search. The required parametrization of the sulfonamide group was achieved by the appropriate combination of ab initio derived parameters with specific geometric features extracted from the crystal structures.

  20. An NMR and molecular dynamics investigation of the avian prion hexarepeat conformational features in solution

    NASA Astrophysics Data System (ADS)

    Pietropaolo, Adriana; Raiola, Luca; Muccioli, Luca; Tiberio, Giustiniano; Zannoni, Claudio; Fattorusso, Roberto; Isernia, Carla; Mendola, Diego La; Pappalardo, Giuseppe; Rizzarelli, Enrico

    2007-07-01

    The prion protein is a copper binding glycoprotein that in mammals can misfold into a pathogenic isoform leading to prion diseases, as opposed, surprisingly, to avians. The avian prion N-terminal tandem repeat is richer in prolines than the mammal one, and understanding their effect on conformation is of great biological importance. Here we succeeded in investigating the conformations of a single avian hexarepeat by means of NMR and molecular dynamics techniques. We found a high flexibility and a strong conformational dependence on pH: local turns are present at acidic and neutral pH, while unordered regions dominate at basic conditions.

  1. Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene

    NASA Astrophysics Data System (ADS)

    Zhao, Daohui; Li, Libo; He, Daohang; Zhou, Jian

    2016-07-01

    The fragment of viral protein R (Vpr), Vpr13-33, plays an important role in regulating nuclear importing of HIV genes through channel formation in which it adopts a leucine-zipper-like alpha-helical conformation. A recent experimental study reported that helical Vpr13-33 would transform to β-sheet or random coil structures and aggregate on the surface of graphene or graphene oxide through hydrophobic interactions. Due to experimental limitations, however, there is still a considerable lack of understanding on the adsorption dynamics at the early stage of the conformational transition at water-graphene interface and the underlying driving force at molecular level. In this study, atomistic molecular dynamics simulations were used to explore the conformation transition phenomena. Vpr13-33 kept α-helical structure in solution, but changed to β-sheet structure when strongly adsorbed onto graphene. Preferential adsorption of Vpr13-33 on graphene is dominated by hydrophobic interactions. The cluster analysis identified the most significant populated conformation and the early stage of structure conversion from α-helical to β-sheet was found, but the full β-sheet propagation was not observed. Free energy landscape analysis further complemented the transformation analysis of peptide conformations. These findings are consistent with experimental results, and give a molecular level interpretation for the reduced cytotoxicity of Vpr13-33 to some extent upon graphene exposure. Meanwhile, this study provides some significant insights into the detailed mechanism of graphene-induced protein conformation transition.

  2. Molecular Clustering Interrelationships and Carbohydrate Conformation in Hull and Seeds Among Barley Cultivars

    SciTech Connect

    N Liu; P Yu

    2011-12-31

    The objective of this study was to use molecular spectral analyses with the diffuse reflectance Fourier transform infrared spectroscopy (DRIFT) bioanlytical technique to study carbohydrate conformation features, molecular clustering and interrelationships in hull and seed among six barley cultivars (AC Metcalfe, CDC Dolly, McLeod, CDC Helgason, CDC Trey, CDC Cowboy), which had different degradation kinetics in rumen. The molecular structure spectral analyses in both hull and seed involved the fingerprint regions of ca. 1536-1484 cm{sup -1} (attributed mainly to aromatic lignin semicircle ring stretch), ca. 1293-1212 cm{sup -1} (attributed mainly to cellulosic compounds in the hull), ca. 1269-1217 cm{sup -1} (attributed mainly to cellulosic compound in the seeds), and ca. 1180-800 cm{sup -1} (attributed mainly to total CHO C-O stretching vibrations) together with an agglomerative hierarchical cluster (AHCA) and principal component spectral analyses (PCA). The results showed that the DRIFT technique plus AHCA and PCA molecular analyses were able to reveal carbohydrate conformation features and identify carbohydrate molecular structure differences in both hull and seeds among the barley varieties. The carbohydrate molecular spectral analyses at the region of ca. 1185-800 cm{sup -1} together with the AHCA and PCA were able to show that the barley seed inherent structures exhibited distinguishable differences among the barley varieties. CDC Helgason had differences from AC Metcalfe, MeLeod, CDC Cowboy and CDC Dolly in carbohydrate conformation in the seed. Clear molecular cluster classes could be distinguished and identified in AHCA analysis and the separate ellipses could be grouped in PCA analysis. But CDC Helgason had no distinguished differences from CDC Trey in carbohydrate conformation. These carbohydrate conformation/structure difference could partially explain why the varieties were different in digestive behaviors in animals. The molecular spectroscopy

  3. Next-generation molecular diagnostics.

    PubMed

    Aldape, Kenneth; Pfister, Stefan M

    2016-01-01

    The classification of brain tumors is based on the time-honored tradition of histologic examination, coupled with clinicopathologic correlation, and is based on the fundamental importance of microscopic morphologic interpretation. Supplementation by immunohistochemical markers is of substantial value to distinguish related entities and to confirm morphologic impressions. The use of techniques such as fluorescent in situ hybridization (FISH) is also critical in specific situations. However, with these practices, it is clear that the use of state-of-the-art molecular techniques has great promise to add to classification to (1) reduce the subjectivity inherent in interobserver discordance, particularly with specific entities; and (2) elucidate the biologic diversity of entities that are not resolvable by routine methods. In this chapter, we discuss these possibilities, focusing on several tumor types affecting the central nervous system, including diffuse glioma and ependymoma. PMID:26948351

  4. Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins

    PubMed Central

    Petrone, Luigi; Kumar, Akshita; Sutanto, Clarinda N.; Patil, Navinkumar J.; Kannan, Srinivasaraghavan; Palaniappan, Alagappan; Amini, Shahrouz; Zappone, Bruno; Verma, Chandra; Miserez, Ali

    2015-01-01

    Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus' assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives. PMID:26508080

  5. Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins.

    PubMed

    Petrone, Luigi; Kumar, Akshita; Sutanto, Clarinda N; Patil, Navinkumar J; Kannan, Srinivasaraghavan; Palaniappan, Alagappan; Amini, Shahrouz; Zappone, Bruno; Verma, Chandra; Miserez, Ali

    2015-01-01

    Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus' assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives. PMID:26508080

  6. Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins

    NASA Astrophysics Data System (ADS)

    Petrone, Luigi; Kumar, Akshita; Sutanto, Clarinda N.; Patil, Navinkumar J.; Kannan, Srinivasaraghavan; Palaniappan, Alagappan; Amini, Shahrouz; Zappone, Bruno; Verma, Chandra; Miserez, Ali

    2015-10-01

    Interfacial water constitutes a formidable barrier to strong surface bonding, hampering the development of water-resistant synthetic adhesives. Notwithstanding this obstacle, the Asian green mussel Perna viridis attaches firmly to underwater surfaces via a proteinaceous secretion (byssus). Extending beyond the currently known design principles of mussel adhesion, here we elucidate the precise time-regulated secretion of P. viridis mussel adhesive proteins. The vanguard 3,4-dihydroxy-L-phenylalanine (Dopa)-rich protein Pvfp-5 acts as an adhesive primer, overcoming repulsive hydration forces by displacing surface-bound water and generating strong surface adhesion. Using homology modelling and molecular dynamics simulations, we find that all mussel adhesive proteins are largely unordered, with Pvfp-5 adopting a disordered structure and elongated conformation whereby all Dopa residues reside on the protein surface. Time-regulated secretion and structural disorder of mussel adhesive proteins appear essential for optimizing extended nonspecific surface interactions and byssus' assembly. Our findings reveal molecular-scale principles to help the development of wet-resistant adhesives.

  7. Fluctuation theory of molecular association and conformational equilibria

    PubMed Central

    Jiao, Yuanfang; Smith, Paul E.

    2011-01-01

    General expressions relating the effects of pressure, temperature, and composition on solute association and conformational equilibria using the fluctuation theory of solutions are provided. The expressions are exact and can be used to interpret experimental or computer simulation data for any multicomponent mixture involving molecules of any size and character at any composition. The relationships involve particle-particle, particle-energy, and energy-energy correlations within local regions in the vicinity of each species involved in the equilibrium. In particular, it is demonstrated that the results can be used to study peptide and protein association or aggregation, protein denaturation, and protein-ligand binding. Exactly how the relevant fluctuating properties may be obtained from experimental or computer simulation data are also outlined. It is shown that the enthalpy, heat capacity, and compressibility differences associated with the equilibrium process can, in principle, be obtained from a single simulation. Fluctuation based expressions for partial molar heat capacities, thermal expansions, and isothermal compressibilities are also provided. PMID:21744905

  8. Artificial accelerators of the molecular chaperone Hsp90 facilitate rate-limiting conformational transitions.

    PubMed

    Zierer, Bettina K; Weiwad, Matthias; Rübbelke, Martin; Freiburger, Lee; Fischer, Gunter; Lorenz, Oliver R; Sattler, Michael; Richter, Klaus; Buchner, Johannes

    2014-11-01

    The molecular chaperone Hsp90 undergoes an ATP-driven cycle of conformational changes in which large structural rearrangements precede ATP hydrolysis. Well-established small-molecule inhibitors of Hsp90 compete with ATP-binding. We wondered whether compounds exist that can accelerate the conformational cycle. In a FRET-based screen reporting on conformational rearrangements in Hsp90 we identified compounds. We elucidated their mode of action and showed that they can overcome the intrinsic inhibition in Hsp90 which prevents these rearrangements. The mode of action is similar to that of the co-chaperone Aha1 which accelerates the Hsp90 ATPase. However, while the two identified compounds influence conformational changes, they target different aspects of the structural transitions. Also, the binding site determined by NMR spectroscopy is distinct. This study demonstrates that small molecules are capable of triggering specific rate-limiting transitions in Hsp90 by mechanisms similar to those in protein cofactors. PMID:25244159

  9. Molecular dynamics simulations of poly (ethylene oxide) hydration and conformation in solutions

    NASA Astrophysics Data System (ADS)

    Dahal, Udaya; Dormidontova, Elena

    Polyethylene oxide (PEO) is one of the most actively used polymers, especially in biomedical applications due to its high hydrophilicity, biocompatibility and potency to inhibit protein adsorption. PEO solubility and conformation in water depends on its capability to form hydrogen bonds. Using atomistic molecular dynamics simulations we investigated the details of water packing around PEO chain and characterized the type and lifetime of hydrogen bonds in aqueous and mixed solvent solutions. The observed polymer chain conformation varies from an extended coil in pure water to collapsed globule in hexane and a helical-like conformation in pure isobutyric acid or isobutyric acid -water mixture in agreement with experimental observations. We'll discuss the implications of protic solvent arrangement and stability of hydrogen bonds on PEO chain conformation and mobility. This research is supported by NSF (DMR-1410928).

  10. Conformational analysis of environmental agents: use of X-ray crystallographic data to determine molecular reactivity.

    PubMed Central

    Cody, V

    1985-01-01

    This paper explores the use of crystallographic techniques as an aid in understanding the molecular reactivities of a number of agents that are of concern to pharmacologists and toxicologists. The selected examples demonstrate the role of structural data in the determination of absolute configuration, configurational flexibility and active-site topology for a reactive species. For example, the role of absolute stereochemistry in understanding synthetic pyrethroid structure-activity relationships is shown from analysis of their crystal structures; conformational flexibility among DDT analogues, and the importance of conformational and electronic properties in phenylalkanoic acid herbicides are shown from systematic analysis of their crystal structures; and interpretation of active-site stereochemistry is made by study of computer modeling of enzyme inhibitors in the active sites of related protein crystal structures. Thus, the observed patterns in conformational flexibility and their resultant effects on substrate pharmacological profile can be interpreted in understanding the molecular level events that influence biological reactivity. PMID:3905372

  11. Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation.

    PubMed

    Riniker, Sereina; Landrum, Gregory A

    2015-12-28

    Small organic molecules are often flexible, i.e., they can adopt a variety of low-energy conformations in solution that exist in equilibrium with each other. Two main search strategies are used to generate representative conformational ensembles for molecules: systematic and stochastic. In the first approach, each rotatable bond is sampled systematically in discrete intervals, limiting its use to molecules with a small number of rotatable bonds. Stochastic methods, on the other hand, sample the conformational space of a molecule randomly and can thus be applied to more flexible molecules. Different methods employ different degrees of experimental data for conformer generation. So-called knowledge-based methods use predefined libraries of torsional angles and ring conformations. In the distance geometry approach, on the other hand, a smaller amount of empirical information is used, i.e., ideal bond lengths, ideal bond angles, and a few ideal torsional angles. Distance geometry is a computationally fast method to generate conformers, but it has the downside that purely distance-based constraints tend to lead to distorted aromatic rings and sp(2) centers. To correct this, the resulting conformations are often minimized with a force field, adding computational complexity and run time. Here we present an alternative strategy that combines the distance geometry approach with experimental torsion-angle preferences obtained from small-molecule crystallographic data. The torsional angles are described by a previously developed set of hierarchically structured SMARTS patterns. The new approach is implemented in the open-source cheminformatics library RDKit, and its performance is assessed by comparing the diversity of the generated ensemble and the ability to reproduce crystal conformations taken from the crystal structures of small molecules and protein-ligand complexes. PMID:26575315

  12. Molecular mechanics work station for protein conformational studies

    SciTech Connect

    Fine, R.; Levinthal, C.; Schoenborn, B.; Dimmier, G.; Rankowitz, C.

    1984-01-01

    Interest in computational problems in Biology has intensified over the last few years, partly due to the development of techniques for the rapid cloning, sequencing, and mutagenesis of genes from organisims ranging from E. coli to Man. The central dogma of molecular biology; that DNA codes for mRNA which codes for protein, has been understood in a linear programming sense since the genetic code was cracked. But what is not understood at present is how a protein, once assembled as a long sequence of amino acids, folds back on itself to produce a three-dimensional structure which is unique to that protein and which dictates its chemical and biological activity. This folding process is purely physics, and involves the time evolution of a system of several thousand atoms which interact with each other and with atoms from the surrounding solvent. Molecular dynamics simulations on smaller molecules suggest that approaches which treat the protein as a classical ensemble of atoms interacting with each other via an empirical Hamiltonian can yield the kind of predictive results one would like when applied to proteins.

  13. Probing the Conformation of FhaC with Small-Angle Neutron Scattering and Molecular Modeling

    PubMed Central

    Gabel, Frank; Lensink, Marc F.; Clantin, Bernard; Jacob-Dubuisson, Françoise; Villeret, Vincent; Ebel, Christine

    2014-01-01

    Probing the solution structure of membrane proteins represents a formidable challenge, particularly when using small-angle scattering. Detergent molecules often present residual scattering contributions even at their match point in small-angle neutron scattering (SANS) measurements. Here, we studied the conformation of FhaC, the outer-membrane, β-barrel transporter of the Bordetella pertussis filamentous hemagglutinin adhesin. SANS measurements were performed on homogeneous solutions of FhaC solubilized in n-octyl-d17-βD-glucoside and on a variant devoid of the α helix H1, which critically obstructs the FhaC pore, in two solvent conditions corresponding to the match points of the protein and the detergent, respectively. Protein-bound detergent amounted to 142 ± 10 mol/mol as determined by analytical ultracentrifugation. By using molecular modeling and starting from three distinct conformations of FhaC and its variant embedded in lipid bilayers, we generated ensembles of protein-detergent arrangement models with 120–160 detergent molecules. The scattered curves were back-calculated for each model and compared with experimental data. Good fits were obtained for relatively compact, connected detergent belts, which occasionally displayed small detergent-free patches on the outer surface of the β barrel. The combination of SANS and modeling clearly enabled us to infer the solution structure of FhaC, with H1 inside the pore as in the crystal structure. We believe that our strategy of combining explicit atomic detergent modeling with SANS measurements has significant potential for structural studies of other detergent-solubilized membrane proteins. PMID:24988353

  14. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    PubMed

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. PMID:26766517

  15. Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics

    PubMed Central

    DePaul, Allison J.; Thompson, Erik J.; Patel, Sarav S.; Haldeman, Kristin; Sorin, Eric J.

    2010-01-01

    Conformational equilibrium within the ubiquitous GNRA tetraloop motif was simulated at the ensemble level, including 10 000 independent all-atom molecular dynamics trajectories totaling over 110 µs of simulation time. This robust sampling reveals a highly dynamic structure comprised of 15 conformational microstates. We assemble a Markov model that includes transitions ranging from the nanosecond to microsecond timescales and is dominated by six key loop conformations that contribute to fluctuations around the native state. Mining of the Protein Data Bank provides an abundance of structures in which GNRA tetraloops participate in tertiary contact formation. Most predominantly observed in the experimental data are interactions of the native loop structure within the minor groove of adjacent helical regions. Additionally, a second trend is observed in which the tetraloop assumes non-native conformations while participating in multiple tertiary contacts, in some cases involving multiple possible loop conformations. This tetraloop flexibility can act to counterbalance the energetic penalty associated with assuming non-native loop structures in forming tertiary contacts. The GNRA motif has thus evolved not only to readily participate in simple tertiary interactions involving native loop structure, but also to easily adapt tetraloop secondary conformation in order to participate in larger, more complex tertiary interactions. PMID:20223768

  16. Conformational diversity of bacterial FabH: implications for molecular recognition specificity.

    PubMed

    Mittal, Anuradha; Johnson, Michael E

    2015-02-01

    The molecular basis of variable substrate and inhibitor specificity of the highly conserved bacterial fatty acid synthase enzyme, FabH, across different bacterial species remains poorly understood. In the current work, we explored the conformational diversity of FabH enzymes to understand the determinants of diverse interaction specificity across Gram-positive and Gram-negative bacteria. Atomistic molecular dynamics simulations reveal that FabH from E. coli and E. faecalis exhibit distinct native state conformational ensembles and dynamic behaviors. Despite strikingly similar substrate binding pockets, hot spot assessment using computational solvent mapping identified quite different favorable binding interactions between the two homologs. Our data suggest that FabH utilizes protein dynamics and seemingly minor sequence and structural differences to modulate its molecular recognition and substrate specificity across bacterial species. These insights will potentially facilitate the rational design and development of antibacterial inhibitors against FabH enzymes. PMID:25437098

  17. Theoretical studies on the molecular structure, conformational preferences, topological and vibrational analysis of allicin

    NASA Astrophysics Data System (ADS)

    Durlak, Piotr; Berski, Sławomir; Latajka, Zdzisław

    2016-01-01

    The molecular structure, conformational preferences, topological and vibrational analysis of allicin has been investigated at two different approaches. Calculations have been carried out on static (DFT and MP2) levels with an assortment of Dunning's basis sets and dynamic CPMD simulations. In this both case within the isolated molecule approximation. The results point out that at least twenty different conformers coexist on the PES as confirmed by the flexible character of this molecule. The topological analysis of ELF showed very similar nature of the Ssbnd S and Ssbnd O bonds. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed.

  18. DFT molecular modeling and NMR conformational analysis of a new longipinenetriolone diester

    NASA Astrophysics Data System (ADS)

    Cerda-García-Rojas, Carlos M.; Guerra-Ramírez, Diana; Román-Marín, Luisa U.; Hernández-Hernández, Juan D.; Joseph-Nathan, Pedro

    2006-05-01

    The structure and conformational behavior of the new natural compound (4 R,5 S,7 S,8 R,9 S,10 R,11 R)-longipin-2-en-7,8,9-triol-1-one 7-angelate-9-isovalerate (1) isolated from Stevia eupatoria, were studied by molecular modeling and NMR spectroscopy. A Monte Carlo search followed by DFT calculations at the B3LYP/6-31G* level provided the theoretical conformations of the sesquiterpene framework, which were in full agreement with results derived from the 1H- 1H coupling constant analysis.

  19. Conformers, infrared spectrum, UV-induced photochemistry, and near-IR-induced generation of two rare conformers of matrix-isolated phenylglycine

    SciTech Connect

    Borba, Ana Fausto, Rui; Gómez-Zavaglia, Andrea

    2014-10-21

    The conformational space of α-phenylglycine (PG) have been investigated theoretically at both the DFT/B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) levels of approximation. Seventeen different minima were found on the investigated potential energy surfaces, which are characterized by different dominant intramolecular interactions: type I conformers are stabilized by hydrogen bonds of the type N–H···O=C, type II by a strong O–H···N hydrogen bond, type III by weak N–H···O–H hydrogen bonds, and type IV by a C=O···H–C contact. The calculations indicate also that entropic effects are relevant in determining the equilibrium populations of the conformers of PG in the gas phase, in particular in the case of conformers of type II, where the strong intramolecular O–H···N hydrogen bond considerably diminishes entropy by reducing the conformational mobility of the molecule. In consonance with the relative energies of the conformers and barriers for conformational interconversion, only 3 conformers of PG were observed for the compound isolated in cryogenic Ar, Xe, and N{sub 2} matrices: the conformational ground state (ICa), and forms ICc and IITa. All other significantly populated conformers existing in the gas phase prior to deposition convert either to conformer ICa or to conformer ICc during matrix deposition. The experimental observation of ICc had never been achieved hitherto. Narrowband near-IR irradiation of the first overtone of νOH vibrational mode of ICa and ICc in nitrogen matrices (at 6910 and 6930 cm{sup −1}, respectively) led to selective generation of two additional conformers of high-energy, ITc and ITa, respectively, which were also observed experimentally for the first time. In addition, these experiments also provided the key information for the detailed vibrational characterization of the 3 conformers initially present in the matrices. On the other hand, UV irradiation (λ = 255 nm) of PG isolated in a xenon matrix revealed that

  20. S-Shaped Conformation of the Quaterthiophene Molecular Backbone in Two-Dimensional Bisterpyridine-Derivative Self-Assembled Nanoarchitecture.

    PubMed

    Kervella, Yann; Shilova, Ekaterina; Latil, Sylvain; Jousselme, Bruno; Silly, Fabien

    2015-12-15

    The conformation and the two-dimensional self-assembly of 4'-(3',4″-dihexyloxy-5,2':5',2″:5″,2‴-quaterthien-2,5‴-diyl)-bis(2,2':6',2″-terpyridine) molecules are theoretically and experimentally investigated. This molecular building block forms a hydrogen-bonded chiral supramolecular nanoarchitecture on graphite at the solid/liquid interface. Scanning tunneling microscopy (STM) shows that the molecule adopts an S-shaped conformation in this structure. DFTB+ calculations reveal that this conformation is not the lowest-energy conformation. The molecular nanoarchitecture appears to be stabilized by hydrogen bonding as well as van der Waals interactions. I-, L-, and D-shaped molecular conformations are, however, locally observed at the domain boundary, but these conformations do not self-assemble into organized 2D structures. PMID:26624809

  1. CENCALC: a computational tool for conformational entropy calculations from molecular simulations.

    PubMed

    Suárez, Ernesto; Díaz, Natalia; Méndez, Jefferson; Suárez, Dimas

    2013-09-01

    We present the CENCALC software that has been designed to estimate the conformational entropy of single molecules from extended Molecular Dynamics (MD) simulations in the gas-phase or in solution. CENCALC uses both trajectory coordinates and topology information in order to characterize the conformational states of the molecule of interest by discretizing the time evolution of internal rotations. The implemented entropy methods are based on the mutual information expansion, which is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, triads, and so on. Particularly, the correlation-corrected multibody local approximation selects an optimum cutoff in order to retrieve the maximum amount of genuine correlation from a given MD trajectory. We illustrate these capabilities by carrying out conformational entropy calculations for a decapeptide molecule either in its unbound form or in complex with a metalloprotease enzyme. CENCALC is distributed under the GNU public license at http://sourceforge.net/projects/cencalc/. PMID:24046838

  2. Molecular modeling of the conformational dynamics of the cellular prion protein

    NASA Astrophysics Data System (ADS)

    Nguyen, Charles; Colling, Ian; Bartz, Jason; Soto, Patricia

    2014-03-01

    Prions are infectious agents responsible for transmissible spongiform encephalopathies (TSEs), a type of fatal neurodegenerative disease in mammals. Prions propagate biological information by conversion of the non-pathological version of the prion protein to the infectious conformation, PrPSc. A wealth of knowledge has shed light on the nature and mechanism of prion protein conversion. In spite of the significance of this problem, we are far from fully understanding the conformational dynamics of the cellular isoform. To remedy this situation we employ multiple biomolecular modeling techniques such as docking and molecular dynamics simulations to map the free energy landscape and determine what specific regions of the prion protein are most conductive to binding. The overall goal is to characterize the conformational dynamics of the cell form of the prion protein, PrPc, to gain insight into inhibition pathways against misfolding. NE EPSCoR FIRST Award to Patricia Soto.

  3. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges

    PubMed Central

    D'Abramo, Marco; Besker, Neva; Chillemi, Giovanni; Grottesi, Alessandro

    2014-01-01

    Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to the intrinsic sampling limitations, much efforts have been done to model in a realistic way the conformational changes occurring in protein kinases. In this review we will address the principal biological achievements and structural aspects in studying kinases conformational transitions and will focus on the main challenges related to computational approaches such as molecular modeling and MD simulations. PMID:24860596

  4. Effect of Na+ binding on the conformation, stability and molecular recognition properties of thrombin

    PubMed Central

    De Filippis, Vincenzo; De Dea, Elisa; Lucatello, Filippo; Frasson, Roberta

    2005-01-01

    In the present work, the effect of Na+ binding on the conformational, stability and molecular recognition properties of thrombin was investigated. The binding of Na+ reduces the CD signal in the far-UV region, while increasing the intensity of the near-UV CD and fluorescence spectra. These spectroscopic changes have been assigned to perturbations in the environment of aromatic residues at the level of the S2 and S3 sites, as a result of global rigidification of the thrombin molecule. Indeed, the Na+-bound form is more stable to urea denaturation than the Na+-free form by ∼2 kcal/mol (1 cal≡4.184 J). Notably, the effects of cation binding on thrombin conformation and stability are specific to Na+ and parallel the affinity order of univalent cations for the enzyme. The Na+-bound form is even more resistant to limited proteolysis by subtilisin, at the level of the 148-loop, which is suggestive of the more rigid conformation this segment assumes in the ‘fast’ form. Finally, we have used hirudin fragment 1–47 as a molecular probe of the conformation of thrombin recognition sites in the fast and ‘slow’ form. From the effects of amino acid substitutions on the affinity of fragment 1–47 for the enzyme allosteric forms, we concluded that the specificity sites of thrombin in the Na+-bound form are in a more open and permissible conformation, compared with the more closed structure they assume in the slow form. Taken together, our results indicate that the binding of Na+ to thrombin serves to stabilize the enzyme into a more open and rigid conformation. PMID:15971999

  5. Molecular mechanics approach for design and conformational studies of macrocyclic ligands

    NASA Astrophysics Data System (ADS)

    Rohini, Akbar, Rifat; Kanungo, B. K.

    2015-08-01

    Computational Chemistry has revolutionized way of viewing molecules at the quantum mechanical scale by allowing simulating various chemical scenarios that are not possible to study in a laboratory. The remarkable applications of computational chemistry have promoted to design and test of the effectiveness of various methods for searching the conformational space of highly flexible molecules. In this context, we conducted a series of optimization and conformational searches on macrocyclic based ligands, 9N3Me5Ox, (1,4,7-tris(5-methyl-8-hydroxyquinoline)-1,4,7-triazacyclononane) and 12N3Me5Ox, (1,5,9-tris(5-methyl-8-hydroxyquinoline)-1,5,9-triazacyclododecane) and studied their selectivity and coordination behavior with some lanthanide metal ions in molecular mechanics and semiempirical methods. The methods include both systematic and random conformational searches for dihedral angles, torsion angles and Cartesian coordinates. Structural studies were carried out by using geometry optimization, coordination scans and electronic properties were evaluated. The results clearly show that chair-boat conformational isomer of 9N3Me5Ox ligand is more stable due to lower eclipsing ethane interaction and form stronger adduct complexes with lanthanide metal ion. This is because of the fact that, in a central unit of 9N3 of the ligand form six endo type bonds out of nine. The rest of bonds have trans conformation. In contrast, for the adduct of 12N3Me5Ox, two C-C bonds have on eclipsed conformation, and others have synclinal and antiperiplanar confirmations. The distortion of the two eclipsed conformations may affect the yields and the stability of the complexes.

  6. Molecular mechanics approach for design and conformational studies of macrocyclic ligands

    SciTech Connect

    Rohini,; Akbar, Rifat; Kanungo, B. K.

    2015-08-28

    Computational Chemistry has revolutionized way of viewing molecules at the quantum mechanical scale by allowing simulating various chemical scenarios that are not possible to study in a laboratory. The remarkable applications of computational chemistry have promoted to design and test of the effectiveness of various methods for searching the conformational space of highly flexible molecules. In this context, we conducted a series of optimization and conformational searches on macrocyclic based ligands, 9N3Me5Ox, (1,4,7-tris(5-methyl-8-hydroxyquinoline)-1,4,7-triazacyclononane) and 12N3Me5Ox, (1,5,9-tris(5-methyl-8-hydroxyquinoline)-1,5,9-triazacyclododecane) and studied their selectivity and coordination behavior with some lanthanide metal ions in molecular mechanics and semiempirical methods. The methods include both systematic and random conformational searches for dihedral angles, torsion angles and Cartesian coordinates. Structural studies were carried out by using geometry optimization, coordination scans and electronic properties were evaluated. The results clearly show that chair-boat conformational isomer of 9N3Me5Ox ligand is more stable due to lower eclipsing ethane interaction and form stronger adduct complexes with lanthanide metal ion. This is because of the fact that, in a central unit of 9N3 of the ligand form six endo type bonds out of nine. The rest of bonds have trans conformation. In contrast, for the adduct of 12N3Me5Ox, two C-C bonds have on eclipsed conformation, and others have synclinal and antiperiplanar confirmations. The distortion of the two eclipsed conformations may affect the yields and the stability of the complexes.

  7. Molecular structure and conformational preferences of gaseous 1-iodo-1-silacyclohexane

    NASA Astrophysics Data System (ADS)

    Belyakov, A. V.; Baskakov, A. A.; Berger, R. J. F.; Mitzel, N. W.; Oberhammer, H.; Arnason, I.; Wallevik, S. Ò.

    2012-03-01

    The molecular structure of the axial and equatorial conformers of 1-iodo-1-silacyclohexane, CH2(CH2CH2)2SiH-I, as well as thermodynamic equilibrium between these species were investigated by means of gas-phase electron diffraction (GED) and quantum chemical calculations up to MP2(full)/SDB-AUG-CC-pVTZ level of theory (MP2). According to electron diffraction data, the vapor of this compound comprises a mixture of conformers with chair conformation and Cs symmetry differing in the axial and equatorial position of the Si-I bond (axial = 73(7) mol%/equatorial = 27(7) mol%) at T = 352 K. This corresponds to a free energy difference of A = -0.59(22) kcal mol-1. The observed gas-phase electron diffraction parameters are in good agreement with those obtained from theory. NBO analysis revealed that axial conformer of 1-iodo-1-silacyclohexane is an example for electrostatic stabilization of a conformer which is unfavorable in terms of steric and conjugation interaction.

  8. Ab initio molecular dynamics simulation study of dissociative electron attachment to dialanine conformers.

    PubMed

    Feng, Wen-Ling; Tian, Shan Xi

    2015-03-12

    Dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in the gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupies the virtual molecular orbital π*, which is followed by the different dissociation processes. The electron attachments to conformers 1 and 2 having the stronger N-H···N and O-H···O intramolecular hydrogen bonds do not lead to fragmentations, but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process and demonstrate a promising way toward understanding of the radiation damages of complicated biological system. PMID:25679256

  9. Conformational Changes in Acetylcholine Binding Protein Investigated by Temperature Accelerated Molecular Dynamics

    PubMed Central

    Mohammad Hosseini Naveh, Zeynab; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni

    2014-01-01

    Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit. PMID:24551117

  10. Conformation of the umifenovir cation in the molecular and crystal structures of four carboxylic acid salts

    NASA Astrophysics Data System (ADS)

    Orola, Liana; Sarcevica, Inese; Kons, Artis; Actins, Andris; Veidis, Mikelis V.

    2014-01-01

    The umifenovir salts of maleic, salicylic, glutaric, and gentisic acid as well as the chloroform solvate of the salicylate were prepared. Single crystals of the five compounds were obtained and their molecular and crystal structures determined by X-ray diffraction. In each structure the conformation of phenyl ring with respect to the indole group of the umifenovir moiety is different. The water solubility and melting points of the studied umifenovir salts have been determined.

  11. Improved ligand binding energies derived from molecular dynamics: replicate sampling enhances the search of conformational space.

    PubMed

    Adler, Marc; Beroza, Paul

    2013-08-26

    Does a single molecular trajectory provide an adequate sample conformational space? Our calculations indicate that for Molecular Mechanics--Poisson-Boltzmann Surface Area (MM-PBSA) measurement of protein ligand binding, a single molecular dynamics trajectory does not provide a representative sampling of phase space. For a single trajectory, the binding energy obtained by averaging over a number of molecular dynamics frames in an equilibrated system will converge after an adequate simulation time. A separate trajectory with nearly identical starting coordinates (1% randomly perturbed by 0.001 Å), however, can lead to a significantly different calculated binding energy. Thus, even though the calculated energy converges for a single molecular dynamics run, the variation across separate runs implies that a single run inadequately samples the system. The divergence in the trajectories is reflected in the individual energy components, such as the van der Waals and the electrostatics terms. These results indicate that the trajectories sample different conformations that are not in rapid exchange. Extending the length of the dynamics simulation does not resolve the energy differences observed between different trajectories. By averaging over multiple simulations, each with a nearly equivalent starting structure, we find the standard deviation in the calculated binding energy to be ∼1.3 kcal/mol. The work presented here indicates that combining MM-PBSA with multiple samples of the initial starting coordinates will produce more precise and accurate estimates of protein/ligand affinity. PMID:23845109

  12. Spreading of Polymer Films at the Molecular Scale: Conformation, Orientation, and Fractionation.

    NASA Astrophysics Data System (ADS)

    Barrett, Michael; Nese, Alper; Matyjaszewski, Krzysztof; Sheiko, Sergei

    2009-03-01

    Previously, we have reported that comb-like polymer macromolecules undergo a plug-flow with an insignificant contribution of molecular diffusion (Phys. Rev. Lett. 93, 206103, 2004). It was also suggested that the composition of the flowing polymer melt was the same both inside the fluid reservoir (drop) and in the precursor film. This work called into question the macroscopic picture of polymer spreading. Through molecular imaging by AFM, we observe that macromolecules spread at different velocities depending on their size. We show that flow causes the molecules to align perpendicular to the flow direction We have also identified specific molecular conformations, such as hairpins, that become more abundant in spreading films. Lastly, we demonstrate that chain entanglements hinder permeation of long macromolecules from the drop to precursor film. These findings shed light on the molecular mechanism of spreading of polymer melts on natural, i.e. heterogeneous, substrates.

  13. Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations.

    PubMed

    Khuntawee, Wasinee; Rungrotmongkol, Thanyada; Wolschann, Peter; Pongsawasdi, Piamsook; Kungwan, Nawee; Okumura, Hisashi; Hannongbua, Supot

    2016-05-01

    There is growing interest in large-ring cyclodextrins (LR-CDs) which are known to be good host molecules for larger ligands. The isolation of a defined size LR-CD is an essential prerequisite for studying their structural properties. Unfortunately the purification procedure of these substances turned out to be very laborious. Finally the problem could be circumvented by a theoretical consideration: the highly advantageous replica exchange molecular dynamics (REMD) simulation (particularly suitable for studies of conformational changes) offers an ideal approach for studying the conformational change of ɛ-cyclodextrin (CD10), a smaller representative of LR-CDs. Three carbohydrate force fields and three solvent models were tested. The conformational behavior of CD10 was analyzed in terms of the flip (turn) of the glucose subunits within the macrocyclic ring. In addition a ranking of conformations with various numbers of turns was preformed. Our findings might be also helpful in the temperature controlled synthesis of LR-CDs as well as other experimental conditions, in particular for the host-guest reaction. PMID:26877001

  14. Ab initio computational studies on molecular conformation of N-methyl-glyphosate

    NASA Astrophysics Data System (ADS)

    Kaliannan, P.; Naseer Ali, M. Mohamed; Venuvanalingam, P.

    Conformational analysis of N-methyl-glyphosate has been carried out using an ab initio molecular orbital (MO) method at the HF/3-21G* levels of theory and the results are compared with the results of a previously studied compound, namely glyphosate. The potential energy surface of the molecule obtained by varying the central torsion angles (Φ, Ψ) was investigated in detail. Fourteen conformers with 5 kcal mol-1 energy cut-off have been selected from the potential energy surface for geometry optimization to locate the true minimum on the conformational space. The minimum has been found to be at (-62°, 110°) for the central torsion angles. This conformation is stabilized by hydrogen bond interactions (O-H···O and C-H···O) and the interactions due to protons nearer to each other. This cationic field leads to the formation of a hydrophobic patch in this structure, as well as in the structures closer to the global minimum. This patch may destabilize the favourable interaction of N-methyl-glyphosate with the surrounding amino acid residues in the binding cavity as they form the cationic field throughout the glyphosate binding region.

  15. Major Ampullate Spider Silk with Indistinguishable Spidroin Dope Conformations Leads to Different Fiber Molecular Structures.

    PubMed

    Dionne, Justine; Lefèvre, Thierry; Auger, Michèle

    2016-01-01

    To plentifully benefit from its properties (mechanical, optical, biological) and its potential to manufacture green materials, the structure of spider silk has to be known accurately. To this aim, the major ampullate (MA) silk of Araneus diadematus (AD) and Nephila clavipes (NC) has been compared quantitatively in the liquid and fiber states using Raman spectromicroscopy. The data show that the spidroin conformations of the two dopes are indistinguishable despite their specific amino acid composition. This result suggests that GlyGlyX and GlyProGlyXX amino acid motifs (X = Leu, Glu, Tyr, Ser, etc.) are conformationally equivalent due to the chain flexibility in the aqueous environment. Species-related sequence specificity is expressed more extensively in the fiber: the β-sheet content is lower and width of the orientation distribution of the carbonyl groups is broader for AD (29% and 58°, respectively) as compared to NC (37% and 51°, respectively). β-Sheet content values are close to the proportion of polyalanine segments, suggesting that β-sheet formation is mainly dictated by the spidroin sequence. The extent of molecular alignment seems to be related to the presence of proline (Pro) that may decrease conformational flexibility and inhibit chain extension and alignment upon drawing. It appears that besides the presence of Pro, secondary structure and molecular orientation contribute to the different mechanical properties of MA threads. PMID:27548146

  16. Major Ampullate Spider Silk with Indistinguishable Spidroin Dope Conformations Leads to Different Fiber Molecular Structures

    PubMed Central

    Dionne, Justine; Lefèvre, Thierry; Auger, Michèle

    2016-01-01

    To plentifully benefit from its properties (mechanical, optical, biological) and its potential to manufacture green materials, the structure of spider silk has to be known accurately. To this aim, the major ampullate (MA) silk of Araneus diadematus (AD) and Nephila clavipes (NC) has been compared quantitatively in the liquid and fiber states using Raman spectromicroscopy. The data show that the spidroin conformations of the two dopes are indistinguishable despite their specific amino acid composition. This result suggests that GlyGlyX and GlyProGlyXX amino acid motifs (X = Leu, Glu, Tyr, Ser, etc.) are conformationally equivalent due to the chain flexibility in the aqueous environment. Species-related sequence specificity is expressed more extensively in the fiber: the β-sheet content is lower and width of the orientation distribution of the carbonyl groups is broader for AD (29% and 58°, respectively) as compared to NC (37% and 51°, respectively). β-Sheet content values are close to the proportion of polyalanine segments, suggesting that β-sheet formation is mainly dictated by the spidroin sequence. The extent of molecular alignment seems to be related to the presence of proline (Pro) that may decrease conformational flexibility and inhibit chain extension and alignment upon drawing. It appears that besides the presence of Pro, secondary structure and molecular orientation contribute to the different mechanical properties of MA threads. PMID:27548146

  17. Imatinib (Gleevec@) conformations observed in single crystals, protein-Imatinib co-crystals and molecular dynamics: Implications for drug selectivity

    NASA Astrophysics Data System (ADS)

    Golzarroshan, B.; Siddegowda, M. S.; Li, Hong qi; Yathirajan, H. S.; Narayana, B.; Rathore, R. S.

    2012-06-01

    Structure and dynamics of the Leukemia drug, Imatinib, were examined using X-ray crystallography and molecular dynamics studies. Comparison of conformations observed in single crystals with several reported co-crystals of protein-drug complexes suggests existence of two conserved conformations of Imatinib, extended and compact (or folded), corresponding to two binding modes of interaction with the receptor. Furthermore, these conformations are conserved throughout a dynamics simulation. The present study attempts to draw a parallel on conformations and binding patterns of interactions, obtained from small-molecule single-crystal and macromolecule co-crystal studies, and provides structural insights for understanding the high selectivity of this drug molecule.

  18. Development of a sensor to study the DNA conformation using molecular logic gates

    NASA Astrophysics Data System (ADS)

    Roy, Arpan Datta; Dey, Dibyendu; Saha, Jaba; Chakraborty, Santanu; Bhattacharjee, D.; Hussain, Syed Arshad

    2015-02-01

    This communication reports our investigations on the Fluorescence Resonance Energy Transfer (FRET) between two laser dyes Acriflavine and Rhodamine B in absence and presence of DNA at different pH. It has been observed that energy transfer efficiency is largely affected by the presence of DNA as well as the pH of the system. It is well known that with increase in pH, DNA conformation changes from double stranded to single stranded (denaturation) and finally form random coil. Based on our experimental results two different types of molecular logic gates namely, XOR and OR logic have been demonstrated which can be used to have an idea about DNA conformation in solution.

  19. Conformational features of an actuator containing calix[4]arene and thiophene: a molecular dynamics study.

    PubMed

    Zanuy, David; Casanovas, Jordi; Aleman, Carlos

    2006-05-25

    Molecular dynamics simulations have been performed for poly(calix[4]arene bis(bithiophene)) in dichloromethane solution. This material responds to its electronic structure variations with significant conformational changes, producing contraction-expansion movements. Simulations have been performed for the three states of this molecular actuator (reduced, oxidized-nondeprotonated, and oxidized-deprotonated), a specific force-field being developed for each case. Results, which are fully consistent with previous ab initio quantum mechanical calculations on an isolated actuating unit, have revealed important findings about the dynamics of the system. Analyses of the flexibility/rigidity of the molecular chain with the state, the interaction of the polymer with the solvent molecules and the influence of environmental factors (as the viscosity of solvent, the counterions and the thermal agitation) on the dynamics have provided important insights to the actuation mechanism. PMID:16706442

  20. Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin

    PubMed Central

    Aykut, Ayse Ozlem; Atilgan, Ali Rana; Atilgan, Canan

    2013-01-01

    We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca2+-CaM). We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca2+-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca2+-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca2+-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength. PMID:24339763

  1. Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter

    PubMed Central

    Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.

    2015-01-01

    Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis. PMID:25330967

  2. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    PubMed

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces. PMID:27433998

  3. Electron transport in asymmetric biphenyl molecular junctions: effects of conformation and molecule-electrode distance

    NASA Astrophysics Data System (ADS)

    Parashar, Sweta; Srivastava, Pankaj; Pattanaik, Manisha; Jain, Sandeep Kumar

    2014-09-01

    On the basis of ab-initio calculations, we predict the effect of conformation and molecule-electrode distance on transport properties of asymmetric molecular junctions for different electrode materials M (M = Au, Ag, Cu, and Pt). The asymmetry in these junctions is created by connecting one end of the biphenyl molecule to conjugated double thiol (model A) and single thiol (model B) groups, while the other end to Cu atom. A variety of phenomena viz. rectification, negative differential resistance (NDR), switching has been observed that can be controlled by tailoring the interface state properties through molecular conformation and molecule-electrode distance for various M. These properties are further analyzed by calculating transmission spectra, molecular orbitals, and orbital energy. It is found that Cu electrode shows significantly enhanced rectifying performance with change in torsion angles, as well as with increase in molecule-electrode distances than Au and Ag electrodes. Moreover, Pt electrode manifests distinctive multifunctional behavior combining switch, diode, and NDR. Thus, the Pt electrode is suggested to be a good potential candidate for a novel multifunctional electronic device. Our findings are compared with available experimental and theoretical results. Supplementary material in the form of one pdf file available from the Journal web page at http://http//dx.doi.org/10.1140/epjb/e2014-50133-2

  4. Molecular Neuroanatomy: A Generation of Progress

    PubMed Central

    Pollock, Jonathan D.; Wu, Da-Yu; Satterlee, John

    2014-01-01

    The neuroscience research landscape has changed dramatically over the past decade. An impressive array of neuroscience tools and technologies have been generated, including brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity and function, cost effective genome sequencing, new technologies enabling genome manipulation, new imaging methods and new tools for mapping neuronal circuits. However, despite these technological advances, several significant scientific challenges must be overcome in the coming decade to enable a better understanding of brain function and to develop next generation cell type-targeted therapeutics to treat brain disorders. For example, we do not have an inventory of the different types of cells that exist in the brain, nor do we know how to molecularly phenotype them. We also lack robust technologies to map connections between cells. This review will provide an overview of some of the tools and technologies neuroscientists are currently using to move the field of molecular neuroanatomy forward and also discuss emerging technologies that may enable neuroscientists to address these critical scientific challenges over the coming decade. PMID:24388609

  5. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization and Orientation

    SciTech Connect

    Wang, Hongfei; Velarde, Luis; Gan, Wei; Fu, Li

    2015-04-01

    Sum-frequency generation vibrational spectroscopy (SFG) can provide detailed information and understanding of molecular vibrational spectroscopy, orientational and conformational structure, and interactions of molecular surfaces and interfaces, through quantitative measurement and analysis. In this review, we present the current status and discuss the main developments on the measurement of intrinsic SFG spectral lineshape, formulations for polarization measurement and orientation analysis of the SFG-VS spectra. The main focus is to present a coherent formulation and discuss the main concepts or issues that can help to make SFG-VS a quantitative analytical and research tool in revealing the chemistry and physics of complex molecular surface and interface.

  6. Nonadditivity in Conformational Entropy upon Molecular Rigidification Reveals a Universal Mechanism Affecting Folding Cooperativity

    PubMed Central

    Vorov, Oleg K.; Livesay, Dennis R.; Jacobs, Donald J.

    2011-01-01

    Previously, we employed a Maxwell counting distance constraint model (McDCM) to describe α-helix formation in polypeptides. Unlike classical helix-coil transition theories, the folding mechanism derives from nonadditivity in conformational entropy caused by rigidification of molecular structure as intramolecular cross-linking interactions form along the backbone. For example, when a hydrogen bond forms within a flexible region, both energy and conformational entropy decrease. However, no conformational entropy is lost when the region is already rigid because atomic motions are not constrained further. Unlike classical zipper models, the same mechanism also describes a coil-to-β-hairpin transition. Special topological features of the helix and hairpin structures allow the McDCM to be solved exactly. Taking full advantage of the fact that Maxwell constraint counting is a mean field approximation applied to the distribution of cross-linking interactions, we present an exact transfer matrix method that does not require any special topological feature. Upon application of the model to proteins, cooperativity within the folding transition is yet again appropriately described. Notwithstanding other contributing factors such as the hydrophobic effect, this simple model identifies a universal mechanism for cooperativity within polypeptide and protein-folding transitions, and it elucidates scaling laws describing hydrogen-bond patterns observed in secondary structure. In particular, the native state should have roughly twice as many constraints as there are degrees of freedom in the coil state to ensure high fidelity in two-state folding cooperativity, which is empirically observed. PMID:21320459

  7. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics

    PubMed Central

    2016-01-01

    We compare the performance of five magnesium (Mg2+) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg2+ to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA–Mg2+ interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg2+ free RNA to Mg2+ associated RNA structure in unrestrained molecular dynamics simulations. PMID:27294370

  8. Divalent Ion Dependent Conformational Changes in an RNA Stem-Loop Observed by Molecular Dynamics.

    PubMed

    Bergonzo, Christina; Hall, Kathleen B; Cheatham, Thomas E

    2016-07-12

    We compare the performance of five magnesium (Mg(2+)) ion models in simulations of an RNA stem loop which has an experimentally determined divalent ion dependent conformational shift. We show that despite their differences in parametrization and resulting van der Waals terms, including differences in the functional form of the nonbonded potential, when the RNA adopts its folded conformation, all models behave similarly across ten independent microsecond length simulations with each ion model. However, when the entire structure ensemble is accounted for, chelation of Mg(2+) to RNA is seen in three of the five models, most egregiously and likely artifactual in simulations using a 12-6-4 model for the Lennard-Jones potential. Despite the simple nature of the fixed point-charge and van der Waals sphere models employed, and with the exception of the likely oversampled directed chelation of the 12-6-4 potential models, RNA-Mg(2+) interactions via first shell water molecules are surprisingly well described by modern parameters, allowing us to observe the spontaneous conformational shift from Mg(2+) free RNA to Mg(2+) associated RNA structure in unrestrained molecular dynamics simulations. PMID:27294370

  9. Biological hydroperoxides and singlet molecular oxygen generation.

    PubMed

    Miyamoto, Sayuri; Ronsein, Graziella E; Prado, Fernanda M; Uemi, Miriam; Corrêa, Thais C; Toma, Izaura N; Bertolucci, Agda; Oliveira, Mauricio C B; Motta, Flávia D; Medeiros, Marisa H G; Mascio, Paolo Di

    2007-01-01

    The decomposition of lipid hydroperoxides (LOOH) into peroxyl radicals is a potential source of singlet molecular oxygen ((1)O(2)) in biological systems. Recently, we have clearly demonstrated the generation of (1)O(2) in the reaction of lipid hydroperoxides with biologically important oxidants such as metal ions, peroxynitrite and hypochlorous acid. The approach used to unequivocally demonstrate the generation of (1)O(2) in these reactions was the use of an isotopic labeled hydroperoxide, the (18)O-labeled linoleic acid hydroperoxide, the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O(2) light emission. Using this approach we have observed the formation of (18)O-labeled (1)O(2) by chemical trapping of (1)O(2) with anthracene derivatives and detection of the corresponding labeled endoperoxide by HPLC-MS/MS. The generation of (1)O(2) was also demonstrated by direct spectral characterization of (1)O(2) monomol light emission in the near-infrared region (lambda = 1270 nm). In summary, our studies demonstrated that LOOH can originate (1)O(2). The experimental evidences indicate that (1)O(2) is generated at a yield close to 10% by the Russell mechanism, where a linear tetraoxide intermediate is formed in the combination of two peroxyl radicals. In addition to LOOH, other biological hydroperoxides, including hydroperoxides formed in proteins and nucleic acids, may also participate in reactions leading to the generation (1)O(2). This hypothesis is currently being investigated in our laboratory. PMID:17505972

  10. Molecular Dynamics Simulations Elucidate Conformational Dynamics Responsible for the Cyclization Reaction in TEAS.

    PubMed

    Zhang, Fan; Chen, Nanhao; Wu, Ruibo

    2016-05-23

    The Mg-dependent 5-epi-aristolochene synthase from Nicotiana tabacum (called TEAS) could catalyze the linear farnesyl pyrophosphate (FPP) substrate to form bicyclic hydrocarbon 5-epi-aristolochene. The cyclization reaction mechanism of TEAS was proposed based on static crystal structures and quantum chemistry calculations in a few previous studies, but substrate FPP binding kinetics and protein conformational dynamics responsible for the enzymatic catalysis are still unclear. Herein, by elaborative and extensive molecular dynamics simulations, the loop conformation change and several crucial residues promoting the cyclization reaction in TEAS are elucidated. It is found that the unusual noncatalytic NH2-terminal domain is essential to stabilize Helix-K and the adjoining J-K loop of the catalytic COOH-terminal domain. It is also illuminated that the induce-fit J-K/A-C loop dynamics is triggered by Y527 and the optimum substrate binding mode in a "U-shape" conformation. The U-shaped ligand binding pose is maintained well with the cooperative interaction of the three Mg(2+)-containing coordination shell and conserved residue W273. Furthermore, the conserved Arg residue pair R264/R266 and aromatic residue pair Y527/W273, whose spatial orientations are also crucial to promote the closure of the active site to a hydrophobic pocket, as well as to form π-stacking interactions with the ligand, would facilitate the carbocation migration and electrophilic attack involving the catalytic reaction. Our investigation more convincingly proves the greater roles of the protein local conformational dynamics than do hints from the static crystal structure observations. Thus, these findings can act as a guide to new protein engineering strategies on diversifying the sesquiterpene products for drug discovery. PMID:27082764

  11. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    DOE PAGESBeta

    Wang, Xu; Le, Anh -Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-03-30

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. Lastly, amore » simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.« less

  12. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    NASA Astrophysics Data System (ADS)

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-03-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method.

  13. Retrieving transient conformational molecular structure information from inner-shell photoionization of laser-aligned molecules

    PubMed Central

    Wang, Xu; Le, Anh-Thu; Yu, Chao; Lucchese, R. R.; Lin, C. D.

    2016-01-01

    We discuss a scheme to retrieve transient conformational molecular structure information using photoelectron angular distributions (PADs) that have averaged over partial alignments of isolated molecules. The photoelectron is pulled out from a localized inner-shell molecular orbital by an X-ray photon. We show that a transient change in the atomic positions from their equilibrium will lead to a sensitive change in the alignment-averaged PADs, which can be measured and used to retrieve the former. Exploiting the experimental convenience of changing the photon polarization direction, we show that it is advantageous to use PADs obtained from multiple photon polarization directions. A simple single-scattering model is proposed and benchmarked to describe the photoionization process and to do the retrieval using a multiple-parameter fitting method. PMID:27025410

  14. Subfemtosecond Pulse Generation by Molecular Modulation

    NASA Astrophysics Data System (ADS)

    Sokolov, Alexei V.

    2002-05-01

    We describe a new source of coherent radiation, with spectrum extending over many octaves of optical bandwidth [1]. We demonstrate collinear generation of mutually-coherent spectral sidebands, ranging in wavelength from 2.95 μm in infrared to 195 nm in ultraviolet, with energy above 1 mJ per 10 ns pulse for each of the nine central sidebands. The essence of our technique is the adiabatic preparation of a macroscopic molecular ensemble in a single vibrational superposition-state [2]. When this is achieved, coherent molecular motion modulates laser light and produces a wide FM-like spectrum, which allows sub-cycle subfemtosecond pulse compression [3-5]. We use this source in two experiments: (I) We demonstrate generation and detection of amplitude and frequency modulated light with a 90 THz modulation frequency [6]. (II) We demonstrate coherent control of multiphoton ionization on a few-femtosecond time scale, under conditions where photoionization requires eleven photons of the lowest frequency and five photons of the highest frequency of the spectrum. Furthermore, we use the pulse-shape dependent ionization as a tool for characterization of our single-cycle waveform [7]. This is a first step toward studying subfemtosecond atomic and molecular dynamics. Future possibilities include studies of multiphoton phenomena as functions of molecular coordinates, and as functions of optical sub-cycle phase. REFERENCES: [1] A. V. Sokolov, D. R. Walker, D. D. Yavuz, G. Y. Yin, and S. E. Harris, Phys. Rev. Lett. 85, 562 (2000). [2] S. E. Harris and A. V. Sokolov, Phys. Rev. A 55, R4019 (1997). [3] S. E. Harris and A. V. Sokolov, Phys. Rev. Lett. 81, 2894 (1998). [4] A. V. Sokolov, D. D. Yavuz, and S. E. Harris, Opt. Lett. 24, 557-559 (1999). [5] A. V. Sokolov, Opt. Lett. 24, 1248 (1999). [6] A. V. Sokolov, D. D. Yavuz, D. R. Walker, G. Y. Yin, and S. E. Harris, Phys. Rev. A 63, 051801 (2001). [7] A. V. Sokolov, D. R. Walker, D. D. Yavuz, G. Y. Yin, and S. E. Harris, Phys. Rev

  15. Generation and characterization of novel conformation-specific monoclonal antibodies for α-synuclein pathology.

    PubMed

    Vaikath, Nishant N; Majbour, Nour K; Paleologou, Katerina E; Ardah, Mustafa T; van Dam, Esther; van de Berg, Wilma D J; Forrest, Shelley L; Parkkinen, Laura; Gai, Wei-Ping; Hattori, Nobutaka; Takanashi, Masashi; Lee, Seung-Jae; Mann, David M A; Imai, Yuzuru; Halliday, Glenda M; Li, Jia-Yi; El-Agnaf, Omar M A

    2015-07-01

    α-Synuclein (α-syn), a small protein that has the intrinsic propensity to aggregate, is implicated in several neurodegenerative diseases including Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA), which are collectively known as synucleinopathies. Genetic, pathological, biochemical, and animal modeling studies provided compelling evidence that α-syn aggregation plays a key role in the pathogenesis of PD and related synucleinopathies. It is therefore of utmost importance to develop reliable tools that can detect the aggregated forms of α-syn. We describe here the generation and characterization of six novel conformation-specific monoclonal antibodies that recognize specifically α-syn aggregates but not the soluble, monomeric form of the protein. The antibodies described herein did not recognize monomers or fibrils generated from other amyloidogenic proteins including β-syn, γ-syn, β-amyloid, tau protein, islet amyloid polypeptide and ABri. Interestingly, the antibodies did not react to overlapping linear peptides spanning the entire sequence of α-syn, confirming further that they only detect α-syn aggregates. In immunohistochemical studies, the new conformation-specific monoclonal antibodies showed underappreciated small micro-aggregates and very thin neurites in PD and DLB cases that were not observed with generic pan antibodies that recognize linear epitope. Furthermore, employing one of our conformation-specific antibodies in a sandwich based ELISA, we observed an increase in levels of α-syn oligomers in brain lysates from DLB compared to Alzheimer's disease and control samples. Therefore, the conformation-specific antibodies portrayed herein represent useful tools for research, biomarkers development, diagnosis and even immunotherapy for PD and related pathologies. PMID:25937088

  16. Isolation of Ion-Driven Conformations in Diphenylacetylene Molecular Switches Using Cryogenic Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Wolk, Arron B.; Garand, Etienne; Jones, Ian M.; Kamrath, Michael Z.; Hamilton, Rew; Johnson, Mark A.

    2012-06-01

    We report the infrared predissociation spectra of a family of ionic diphenylacetylene molecular switch complexes. The electrosprayed complexes were trapped and cooled in a cryogenic (10K) quadrupole ion trap and tagged with molecular deuterium. The infrared spectra of the vibrationally cold species reveal sharp transitions over a wide energy range (800 - 3800 cm-1), facilitating comparison to harmonic spectra. The evolution of the band pattern upon derivatization of the complexes exposes the signatures of the amide, urea, and carbonyl functionalities, enabling unambiguous identification of the non-covalent interactions that control the secondary structure of the molecule. Complexation with the tetramethylammonium cation reveals a conformation analogous to that of the neutral molecule, while halide ion attachment induces a conformational change similar to that observed earlier in solution. In several cases, both the donor and acceptor groups involved in the multidentate H-bonds are observed, providing a microscopic mechanical picture of the interactions at play. I. Jones, and A. Hamilton, Angew. Chem. Intl. Edit. 50, 4597 (2011).

  17. A Conformational Analysis Study on the Melanocortin 4 Receptor Using Multiple Molecular Dynamics Simulations.

    PubMed

    Shahlaei, Mohsen; Mousavi, Atefeh

    2015-09-01

    Taking into account the uncertainties involved in 3D model of biomolecule developed by homology modeling (HM), it is important to opportunely validate the initial structure before employing for different purposes such as drug design. Extended simulation times and the necessity of correct representation of interactions within the protein and the nearby molecules impose significant limitations on molecular dynamics (MD)-based refinement of structures developed by HM. Consequently, there is a pressing requirement for more efficient methods for HM and subsequent validation of developed structure. Multiple MD simulation runs are well suited for producing ensembles of structures. In this context, a computational investigation was presented to study the structure of melanocortin 4 receptor (MC4R) using molecular dynamics (MD) simulations in explicit phospholipids bilayer. Several MD runs with different initial velocities were employed to sample conformations in the neighborhood of the native structure of receptor, collecting trajectories spanning 0.21 ms. The coherence between the results, different structural analysis, and the convergence of parameters derived by principal component analysis (PCA) shows that an accurate description of the MC4R conformational space around the native state was achieved by multiple MD trajectories. PMID:25487745

  18. Earle K. Plyler Prize for Molecular Spectroscopy and Dynamics Lecture: 2D IR Spectroscopy of Peptide Conformation

    NASA Astrophysics Data System (ADS)

    Tokmakoff, Andrei

    2012-02-01

    Descriptions of protein and peptide conformation are colored by the methods we use to study them. Protein x-ray and NMR structures often lead to impressions of rigid or well-defined conformations, even though these are dynamic molecules. The conformational fluctuations and disorder of proteins and peptides is more difficult to quantify. This presentation will describe an approach toward characterizing and quantifying structural heterogeneity and disorder in peptides using 2D IR spectroscopy. Using amide I vibrational spectroscopy, isotope labeling strategies, and computational modeling based on molecular dynamics simulations and Markov state models allows us to characterize distinct peptide conformers and conformational variation. The examples illustrated include the beta-hairpin tripzip2 and elastin-like peptides.

  19. Analysis and elimination of a bias in targeted molecular dynamics simulations of conformational transitions: application to calmodulin.

    PubMed

    Ovchinnikov, Victor; Karplus, Martin

    2012-07-26

    The popular targeted molecular dynamics (TMD) method for generating transition paths in complex biomolecular systems is revisited. In a typical TMD transition path, the large-scale changes occur early and the small-scale changes tend to occur later. As a result, the order of events in the computed paths depends on the direction in which the simulations are performed. To identify the origin of this bias, and to propose a method in which the bias is absent, variants of TMD in the restraint formulation are introduced and applied to the complex open ↔ closed transition in the protein calmodulin. Due to the global best-fit rotation that is typically part of the TMD method, the simulated system is guided implicitly along the lowest-frequency normal modes, until the large spatial scales associated with these modes are near the target conformation. The remaining portion of the transition is described progressively by higher-frequency modes, which correspond to smaller-scale rearrangements. A straightforward modification of TMD that avoids the global best-fit rotation is the locally restrained TMD (LRTMD) method, in which the biasing potential is constructed from a number of TMD potentials, each acting on a small connected portion of the protein sequence. With a uniform distribution of these elements, transition paths that lack the length-scale bias are obtained. Trajectories generated by steered MD in dihedral angle space (DSMD), a method that avoids best-fit rotations altogether, also lack the length-scale bias. To examine the importance of the paths generated by TMD, LRTMD, and DSMD in the actual transition, we use the finite-temperature string method to compute the free energy profile associated with a transition tube around a path generated by each algorithm. The free energy barriers associated with the paths are comparable, suggesting that transitions can occur along each route with similar probabilities. This result indicates that a broad ensemble of paths needs to

  20. Sampling small-scale and large-scale conformational changes in proteins and molecular complexes

    NASA Astrophysics Data System (ADS)

    Yun, Mi-Ran; Mousseau, N.; Derreumaux, P.

    2007-03-01

    Sampling of small-scale and large-scale motions is important in various computational tasks, such as protein-protein docking and ligand binding. Here, we report further development and applications of the activation-relaxation technique for internal coordinate space trajectories (ARTIST). This method generates conformational moves of any complexity and size by identifying and crossing well-defined saddle points connecting energy minima. Simulations on two all-atom proteins and three protein complexes containing between 70 and 300 amino acids indicate that ARTIST opens the door to the full treatment of all degrees of freedom in dense systems such as protein-protein complexes.

  1. Quantum/molecular mechanics study of firefly bioluminescence on luciferase oxidative conformation

    NASA Astrophysics Data System (ADS)

    Pinto da Silva, Luís; Esteves da Silva, Joaquim C. G.

    2014-07-01

    This is the first report of a computational study of the color tuning mechanism of firefly bioluminescence, using the oxidative conformation of luciferase. The results of these calculations demonstrated that the electrostatic field generated by luciferase is fundamental both for the emission shift and efficiency. Further calculations indicated that a shift in emission is achieved by modulating the energy, at different degrees, of the emissive and ground states. These differences in energy modulation will then lead to changes in the energy gap between the states.

  2. Two-loop conformal generators for leading-twist operators in QCD

    NASA Astrophysics Data System (ADS)

    Braun, V. M.; Manashov, A. N.; Moch, S.; Strohmaier, M.

    2016-03-01

    QCD evolution equations in minimal subtraction schemes have a hidden symmetry: one can construct three operators that commute with the evolution kernel and form an SL(2) algebra, i.e. they satisfy (exactly) the SL(2) commutation relations. In this paper we find explicit expressions for these operators to two-loop accuracy going over to QCD in non-integer d = 4 - 2ɛ space-time dimensions at the intermediate stage. In this way conformal symmetry of QCD is restored on quantum level at the specially chosen (critical) value of the coupling, and at the same time the theory is regularized allowing one to use the standard renormalization procedure for the relevant Feynman diagrams. Quantum corrections to conformal generators in d = 4 - 2ɛ effectively correspond to the conformal symmetry breaking in the physical theory in four dimensions and the SL(2) commutation relations lead to nontrivial constraints on the renormalization group equations for composite operators. This approach is valid to all orders in perturbation theory and the result includes automatically all terms that can be identified as due to a nonvanishing QCD β-function (in the physical theory in four dimensions). Our result can be used to derive three-loop evolution equations for flavor-nonsinglet quark-antiquark operators including mixing with the operators containing total derivatives. These equations govern, e.g., the scale dependence of generalized hadron parton distributions and light-cone meson distribution amplitudes.

  3. Folding simulations of gramicidin A into the β-helix conformations: Simulated annealing molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Mori, Takaharu; Okamoto, Yuko

    2009-10-01

    Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the β6.3-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed β4.4-helix as the lowest-potential-energy structure, and left-handed β4.4-helix, right-handed and left-handed β6.3-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite β-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed β6.3-helix and β4.4-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these β-helix structures. The results suggested that β6.3-helix is more stable than β4.4-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the β6.3-helix conformation.

  4. Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study.

    PubMed

    Mori, Takaharu; Okamoto, Yuko

    2009-10-28

    Gramicidin A is a linear hydrophobic 15-residue peptide which consists of alternating D- and L-amino acids and forms a unique tertiary structure, called the beta(6.3)-helix, to act as a cation-selective ion channel in the natural conditions. In order to investigate the intrinsic ability of the gramicidin A monomer to form secondary structures, we performed the folding simulation of gramicidin A using a simulated annealing molecular dynamics (MD) method in vacuum mimicking the low-dielectric, homogeneous membrane environment. The initial conformation was a fully extended one. From the 200 different MD runs, we obtained a right-handed beta(4.4)-helix as the lowest-potential-energy structure, and left-handed beta(4.4)-helix, right-handed and left-handed beta(6.3)-helix as local-minimum energy states. These results are in accord with those of the experiments of gramicidin A in homogeneous organic solvent. Our simulations showed a slight right-hand sense in the lower-energy conformations and a quite beta-sheet-forming tendency throughout almost the entire sequence. In order to examine the stability of the obtained right-handed beta(6.3)-helix and beta(4.4)-helix structures in more realistic membrane environment, we have also performed all-atom MD simulations in explicit water, ion, and lipid molecules, starting from these beta-helix structures. The results suggested that beta(6.3)-helix is more stable than beta(4.4)-helix in the inhomogeneous, explicit membrane environment, where the pore water and the hydrogen bonds between Trp side-chains and lipid-head groups have a role to further stabilize the beta(6.3)-helix conformation. PMID:19894978

  5. Combinatorial selection of molecular conformations and supramolecular synthons in quercetin cocrystal landscapes: a route to ternary solids

    PubMed Central

    Dubey, Ritesh; Desiraju, Gautam R.

    2015-01-01

    The crystallization of 28 binary and ternary cocrystals of quercetin with dibasic coformers is analyzed in terms of a combinatorial selection from a solution of preferred molecular conformations and supramolecular synthons. The crystal structures are characterized by distinctive O—H⋯N and O—H⋯O based synthons and are classified as nonporous, porous and helical. Variability in molecular conformation and synthon structure led to an increase in the energetic and structural space around the crystallization event. This space is the crystal structure landscape of the compound and is explored by fine-tuning the experimental conditions of crystallization. In the landscape context, we develop a strategy for the isolation of ternary cocrystals with the use of auxiliary template molecules to reduce the molecular and supramolecular ‘confusion’ that is inherent in a molecule like quercetin. The absence of concomitant polymorphism in this study highlights the selectivity in conformation and synthon choice from the virtual combinatorial library in solution. PMID:26175900

  6. Molecular conformation-controlled vesicle/micelle transition of cationic trimeric surfactants in aqueous solution.

    PubMed

    Wu, Chunxian; Hou, Yanbo; Deng, Manli; Huang, Xu; Yu, Defeng; Xiang, Junfeng; Liu, Yu; Li, Zhibo; Wang, Yilin

    2010-06-01

    Two star-like trimeric cationic surfactants with amide groups in spacers, tri(dodecyldimethylammonioacetoxy)diethyltriamine trichloride (DTAD) and tri(dodecyldimethylammonioacetoxy)tris(2-aminoethyl)amine trichloride (DDAD), have been synthesized, and the aggregation behavior of the surfactants in aqueous solution has been investigated by surface tension, electrical conductivity, isothermal titration microcalorimetry, dynamic light scattering, cryogenic transmission electron microscopy, and NMR techniques. Typically, both the surfactants form vesicles just above critical aggregation concentration (CAC), and then the vesicles transfer to micelles gradually with an increase of the surfactant concentration. It is approved that the conformation of the surfactant molecules changes in this transition process. Just above the CAC, the hydrophobic chains of the surfactant molecules pack more loosely because of the rigid spacer and intramolecular electrostatic repulsion in the three-charged headgroup. With the increase of the surfactant concentration, hydrophobic interaction becomes strong enough to pack the hydrophobic tails tightly and turn the molecular conformation into a pyramid-like shape, thus leading to the vesicle to micelle transition. PMID:20426428

  7. A molecular modeling approach to understand the structure and conformation relationship of (GlcpA)Xylan.

    PubMed

    Guo, Qingbin; Kang, Ji; Wu, Yan; Cui, Steve W; Hu, Xinzhong; Yada, Rickey Y

    2015-12-10

    The structure and conformation relationships of a heteropolysaccharide (GlcpA)Xylan in terms of various molecular weights, Xylp/GlcpA ratio and the distribution of GlcpA along xylan chain were investigated using computer modeling. The adiabatic contour maps of xylobiose, XylpXylp(GlcpA) and (GlcpA)XylpXylp(GlcpA) indicated that the insertion of the side group (GlcpA) influenced the accessible conformational space of xylobiose molecule. RIS-Metropolis Monte Carlo method indicated that insertion of GlcpA side chain induced a lowering effect of the calculated chain extension at low GlcpA:Xylp ratio (GlcpA:Xylp = 1:3). The chain, however, became extended when the ratio of GlcpA:Xylp above 2/3. It was also shown that the spatial extension of the polymer chains was dependent on the distribution of side chain: the random distribution demonstrated the most flexible structure compared to block and alternative distribution. The present studies provide a unique insight into the dependence of both side chain ratio and distribution on the stiffness and flexibility of various (GlcpA)Xylan molecules. PMID:26428114

  8. Conformationally Constrained Peptidomimetic Inhibitors of Signal Transducer and Activator of Transcription 3: Evaluation and Molecular Modeling

    PubMed Central

    Mandal, Pijus K.; Limbrick, Donald; Coleman, David R.; Dyer, Garrett A.; Ren, Zhiyong; Birtwistle, J. Sanderson; Xiong, Chiyi; Chen, Xiaomin; Briggs, James M.; McMurray, John S.

    2009-01-01

    Signal transducer and activator of transcription 3 (Stat3) is involved in aberrant growth and survival signals in malignant tumor cells and is a validated target for anti-cancer drug design. We are targeting its SH2 domain to prevent docking to cytokine and growth factor receptors and subsequent signaling. The amino acids of our lead phosphopeptide, Ac-pTyr-Leu-Pro-Gln-Thr-Val-NH2, were replaced with conformationally constrained mimics. Structure-affinity studies led to the peptidomimetic, pCinn-Haic-Gln-NHBn (21) which had an IC50 of 162 nM (fluorescence polarization), as compared to 290 nM for the lead phosphopeptide (pCinn = 4-phosphoryloxycinnamate, Haic = (2S,5S)-5-amino-1,2,4,5,6,7-hexahydro-4-oxo-azepino[3,2,1-hi]indole-2-carboxylic acid). pCinn-Haic-Gln-OH was docked to the SH2 domain (AUTODOCK) and the two highest populated clusters were subjected to molecular dynamics simulations. Both converged to a common peptide conformation. The complex exhibits unique hydrogen bonding between Haic and Gln and Stat3 as well as hydrophobic interactions between the protein and pCinn and Haic. PMID:19334714

  9. Long-range conformational transition of a photoswitchable allosteric protein: molecular dynamics simulation study.

    PubMed

    Buchenberg, Sebastian; Knecht, Volker; Walser, Reto; Hamm, Peter; Stock, Gerhard

    2014-11-26

    A local perturbation of a protein may lead to functional changes at some distal site. An example is the PDZ2 domain of human tyrosine phosphatase 1E, which shows an allosteric transition upon binding to a peptide ligand. Recently Buchli et al. presented a time-resolved study of this transition by covalently linking an azobenzene photoswitch across the binding groove and using a femtosecond laser pulse that triggers the cis-trans photoisomerization of azobenzene. To aid the interpretation of these experiments, in this work seven microsecond runs of all-atom molecular dynamics simulations each for the wild-type PDZ2 in the ligand-bound and -free state, as well as the photoswitchable protein (PDZ2S) in the cis and trans states of the photoswitch, in explicit water were conducted. First the theoretical model is validated by recalculating the available NMR data from the simulations. By comparing the results for PDZ2 and PDZ2S, it is analyzed to what extent the photoswitch indeed mimics the free-bound transition. A detailed description of the conformational rearrangement following the cis-trans photoisomerization of PDZ2S reveals a series of photoinduced structural changes that propagate from the anchor residues of the photoswitch via intermediate secondary structure segments to the C-terminus of PDZ2S. The changes of the conformational distribution of the C-terminal region is considered as the distal response of the isolated allosteric protein. PMID:25365469

  10. Molecular identification of Amazonian stingless bees using polymerase chain reaction single-strand conformation polymorphism.

    PubMed

    Souza, M T; Carvalho-Zilse, G A

    2014-01-01

    In countries containing a mega diversity of wildlife, such as Brazil, identifying and characterizing biological diversity is a continuous process for the scientific community, even in face of technological and scientific advances. This activity demands initiatives for the taxonomic identification of highly diverse groups, such as stingless bees, including molecular analysis strategies. This type of bee is distributed in all of the Brazilian states, with the highest species diversity being found in the State of Amazônia. However, the estimated number of species diverges among taxonomists. These bees are considered the main pollinators in the Amazon rainforest, in which they obtain food and shelter; however, their persistence is constantly threatened by deforestation pressure. Hence, it is important to classify the number and abundance of bee specie, to measure their decline and implement meaningful, priority conservation strategies. This study aims to maximize the implementation of more direct, economic and successful techniques for the taxonomic identification of stingless bees. Specifically, the genes 16S rRNA and COI from mitochondrial DNA were used as molecular markers to differentiate 9 species of Amazonian stingless bees based on DNA polymorphism, using the polymerase chain reaction-single-strand conformation polymorphism technique. We registered different, exclusive SSCP haplotypes for both genes in all species analyzed. These results demonstrate that SSCP is a simple and cost-effective technique that is applicable to the molecular identification of stingless bee species. PMID:25117306

  11. Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin

    NASA Astrophysics Data System (ADS)

    Elber, R.; Karplus, M.

    1987-01-01

    A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima in the neighborhood of the native structure (for example, approximately 2000 minima were sampled in a 300-picosecond trajectory). This is expected to have important consequences for the interpretation of the activity of transport proteins and enzymes. Different minima correspond to changes in the relative orientation of the helices coupled with side-chain rearrangements that preserve the close packing of the protein interior. The conformational space sampled by the simulation is similar to that found in the evolutionary development of the globins. Glasslike behavior is expected at low temperatures. The minima obtained from the trajectory do not satisfy certain criteria for ultrametricity.

  12. Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site

    PubMed Central

    Stafford, Kate A.; Palmer III, Arthur G.

    2014-01-01

    Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially of the E. coli homolog, the interaction of the highly negatively charged active site with catalytically required magnesium ions remains poorly understood. In this work, we describe molecular dynamics simulations of the E. coli homolog in complex with magnesium ions, as well as simulations of other homologs in their apo states. Collectively, these results suggest that the active site is highly rigid in the apo state of all homologs studied and is conformationally preorganized to favor the binding of a magnesium ion. Notably, representatives of bacterial, eukaryotic, and retroviral RNases H all exhibit similar active-site rigidity, suggesting that this dynamic feature is only subtly modulated by amino acid sequence and is primarily imposed by the distinctive RNase H protein fold. PMID:25075292

  13. Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics

    SciTech Connect

    Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M.

    2012-03-16

    Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The {alpha}{beta} TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.

  14. Effects of molecular conformation on the spectroscopic properties of 4,4‧-disubstituted benzylideneanilines

    NASA Astrophysics Data System (ADS)

    Fang, Zhengjun; Wu, Feng; Yi, Bing; Cao, Chenzhong; Xie, Xin

    2016-01-01

    The relationship between the molecular conformation and spectroscopic properties of unsymmetrical 4,4‧-disubstituted benzylideneanilines, was explored by the combination of experiment and reference data. Crystal structure information and spectroscopic behaviors of the seventeen samples p-X-C6H4CHdbnd NC6H4-p-Y (X = NMe2, OMe, Me, Cl, CN, or NO2, Ydbnd NMe2, OMe, Me, Cl, CN, or NO2) were provided for this study. Among these seventeen compounds, nine ones were synthesized firstly, and five crystal structures were determined and analyzed. It was observed that the twist angle of the aniline ring with respect to the rest of the molecule (τ) is systematically controlled by the substituent at the aromatic ring. The correlation results show that the UV maximum absorption in wavenumbers (υmax) is dependent on the substituent at the aromatic ring and the dihedral angle τ of the titled molecules, and a sine function of τ (sin(τ)) is suitable to modify the substituent effects on the υmax. However, the dihedral angle τ has a limited effect on the values of 13C NMR chemical shifts δC(Cdbnd N). The results indicate that the dihedral angle τ has an significant effect on UV spectra of Schiff bases with different parent structure although there is something different about the parameter metrics. While it has a relatively limited effect on the values of δC(Cdbnd N) in both unsymmetrical and unsymmetrical Schiff bases. This study provides an sufficient evidence of the molecular conformation on spectroscopic properties of Schiff bases.

  15. A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers

    NASA Astrophysics Data System (ADS)

    Moradi, Mahmoud; Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

    2010-09-01

    Folded polyproline peptides can exist as either left-(PPII) or right-handed (PPI) helices, depending on their environment. In this work, we have characterized the conformations and the free energy landscapes of Ace-(Pro)n-Nme, n =2,3,…,9, and 13 peptides both in vacuo and in an implicit solvent environment. In order to enhance the sampling provided by regular molecular dynamics simulations, we have used the recently developed adaptively biased molecular dynamics method—which provides an accurate description of the free energy landscapes in terms of a set of relevant collective variables—combined with Hamiltonian and temperature replica exchange molecular dynamics methods. The collective variables, which are chosen so as to reflect the stable structures and the "slow modes" of the polyproline system, were based primarily on properties of length and of the cis/trans isomerization associated with the prolyl bonds. Results indicate that the space of peptide structures is characterized not just by pure PPII and PPI structures, but rather by a broad distribution of stable minima with similar free energies. These results are in agreement with recent experimental work. In addition, we have used steered molecular dynamics methods in order to quantitatively estimate the free energy difference of PPI and PPII for peptides of the length n =2,…,5 in vacuo and implicit water and qualitatively investigate transition pathways and mechanisms for the PPII to PPI transitions. A zipper-like mechanism, starting from either the center of the peptide or the amidated end, appear to be the most likely mechanisms for the PPII→PPI transition for the longer peptides.

  16. Molecular conformation of the full-length tumor suppressor NF2/Merlin—a small angle neutron scattering study

    PubMed Central

    Khajeh, Jahan Ali; Ju, Jeong Ho; Atchiba, Moussoubaou; Allaire, Marc; Stanley, Christopher; Heller, William T.; Callaway, David J.E.; Bu, Zimei

    2014-01-01

    Summary The tumor suppressor protein Merlin inhibits cell proliferation upon establishing cell-cell contacts. Because Merlin has high sequence similarity to the Ezrin-Radixin-Moesin (ERM) family of proteins, the structural model of ERM protein autoinhibition and cycling between closed/resting and open/active conformational states is often employed to explain Merlin function. However, recent biochemical studies suggest alternative molecular models of Merlin function. Here, we have determined the low resolution molecular structure and binding activity of Merlin and a Merlin(S518D) mutant that mimics the inactivating phosphorylation at S518 using small angle neutron scattering (SANS) and binding experiments. SANS shows that in solution both Merlin and Merlin(S518D) adopt a closed conformation, but binding experiments indicate that a significant fraction of either Merlin or Merlin(S518D) is capable of binding to the target protein NHERF1. Upon binding to the phosphatidylinositol 4,5-bisphosphate lipid, the wild-type Merlin adopts a more open conformation than in solution, but Merlin(S518D) remains in a closed conformation. This study supports a rheostat model of Merlin in NHERF1 binding, and contributes to resolve a controversy about the molecular conformation and binding activity of Merlin. PMID:24882693

  17. a Combined Molecular Dynamics and NMR Spectroscopic Protocol for the Conformational Analysis of Oligosaccharides.

    NASA Astrophysics Data System (ADS)

    Varma, Vikram

    A combined experimental and theoretical protocol for the conformational analysis of oligosaccharides is presented. Three disaccharides, methyl alpha - scD-mannopyranosyl-(1 to 3)-alpha- scD-mannopyranoside, methyl beta- scD-galactopyranosyl-(1 to 4)-beta- scD-glucopyranoside, and propyl beta- scD-2-acetamido -2-deoxy glucopyranosyl-(1 to 3)- alpha- scL-rhamnopyranoside, are used to evaluate a protocol for conformational analysis that makes use of molecular dynamics calculations with the CHARMM force field. Dynamics trajectories computed in vacuo and in water are used to calculate time-averaged NMR parameters such as spin-lattice relaxation times (T_1 ), Nuclear Overhauser Enhancements (NOE), and heteronuclear spin-spin coupling constants (^3J _{rm CH}). The calculated NMR parameters are then compared to experimental values and used to evaluate the computational procedure. The energetically accessible conformations are effectively sampled by the simulations. The method has been extended to the conformational analysis of higher-order oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus Group A, and the Shigella flexneri Y O-antigen. The Streptococcus Group A cell-wall polysaccharide is comprised of a backbone of rhamnopyranosyl units connected by alternating alpha- scL-(1 to 3) and alpha- scL -(1 to 2) linkages, to which are attached N-acetyl-beta- scD-glucosamine ( beta- scD-GlcpNAc) residues at the 3 positions of the rhamnose backbone.rm A&rm B^'qquad A^'& rm Bqquad Acr[{-alpha}{-}L{-}Rha {it p}{-}(1to2){-alpha }{-}L{-}Rha{it p} {-}(1to3){-alpha}{ -}L{-}Rha{it p}-(1to2) -alpha-L-Rha{it p}{-}(1 to3){-alpha}{-}L{- }Rha{it p}{-}cr&uparrow(1 to3)&uparrow(1to3)crbeta {-}D{-}&rm Glc{it p }NAcqquadbeta{-}D{-}& rm Glc{it p}NAccr&rm C ^'&rm C] A branched trisaccharide (A^' -(C)B), a tetrasaccharide (A^' -(C)B-A), a pentasaccharide (C^' -B^'-A ^'-(C)B), and two hexasaccharides (C^'-B^ '-A^' -(C)B-A) and (A-(C^')B ^'-A^' -(C)B), have been chosen

  18. Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90

    PubMed Central

    Boczek, Edgar E.; Reefschläger, Lasse G.; Dehling, Marco; Struller, Tobias J.; Häusler, Elisabeth; Seidl, Andreas; Kaila, Ville R. I.; Buchner, Johannes

    2015-01-01

    Hsp90 is a molecular chaperone involved in the activation of numerous client proteins, including many kinases. The most stringent kinase client is the oncogenic kinase v-Src. To elucidate how Hsp90 chaperones kinases, we reconstituted v-Src kinase chaperoning in vitro and show that its activation is ATP-dependent, with the cochaperone Cdc37 increasing the efficiency. Consistent with in vivo results, we find that Hsp90 does not influence the almost identical c-Src kinase. To explain these findings, we designed Src kinase chimeras that gradually transform c-Src into v-Src and show that their Hsp90 dependence correlates with compactness and folding cooperativity. Molecular dynamics simulations and hydrogen/deuterium exchange of Hsp90-dependent Src kinase variants further reveal increased transitions between inactive and active states and exposure of specific kinase regions. Thus, Hsp90 shifts an ensemble of conformations of v-Src toward high activity states that would otherwise be metastable and poorly populated. PMID:26056257

  19. Mechanism of Mcl-1 Conformational Regulation Upon Small Molecule Binding Revealed by Molecular Dynamic Simulation.

    PubMed

    Wang, Anhui; Song, Ting; Wang, Ziqian; Liu, Yubo; Fan, Yudan; Zhang, Yahui; Zhang, Zhichao

    2016-04-01

    Inhibition of interactions between Mcl-1 and proapoptotic proteins is considered to be a therapeutic strategy to induce apoptosis in cancer cells. Here, we adopted molecular dynamics simulation with molecular mechanics-Poisson Boltzmann/surface area method (MM-PB/SA) to study the inhibition mechanism of three Mcl-1 inhibitors, compounds 1, 2 and 3. Analysis of energy components shows that the better binding free energy of compound 3 than compounds 1 and 2 is attributable to the van der Waals energy (ΔEvdw ) and non-polar solvation energy (ΔGnp ) upon binding. In addition to the excellent agreement with previous experimentally determined affinities, our simulation results further show a bend of helix 4 on Mcl-1 upon compound 3 binding, which is driven by hydrophobic interaction with residue Val(253) , leading to a narrowed BH3-binding groove to impede Puma(BH) (3) binding. The computational result is consistent with our competitive isothermal titration calorimetry (ITC) assays, which shows that the competitive ability of compound 3 toward Mcl-1/Puma(BH) (3) complex is improved beyond its direct binding affinity toward Mcl-1 itself, and compound 3 exhibits much more efficiency to compete with Puma(BH) (3) than compound 2. Our study provides a new strategy to improve inhibitory activity on Mcl-1 based on the conformational dynamic change. PMID:26518611

  20. Computer simulations of cyclic and acyclic cholinergic agonists: conformational search and molecular dynamics simulations.

    PubMed Central

    McGroddy, K A; Brady, J W; Oswald, R E

    1994-01-01

    Molecular dynamics simulations have been performed on aqueous solutions of two chemically similar nicotinic cholinergic agonists in order to compare their structural and dynamical differences. The cyclic 1,1-dimethyl-4-acetylpiperazinium iodide (HPIP) molecule was previously shown to be a strong agonist for nicotinic acetylcholine receptors (McGroddy et al., 1993), while the acyclic N,N,N,N'-tetramethyl-N'-acetylethylenediamine iodide (HTED) derivative is much less potent. These differences were expected to arise from differences in the solution structures and internal dynamics of the two molecules. HPIP was originally thought to be relatively rigid; however, molecular dynamics simulations suggest that the acetyl portion of the molecule undergoes significant ring dynamics on a psec timescale. The less constrained HTED molecule is relatively rigid, with only one transition observed about any of the major dihedrals in four 100 psec simulations, each started from a different conformation. The average structures obtained from the simulations are very similar to the starting minimized structure in each case, except for the HTED simulation where a single rotation about the N-C-C-N(+) backbone occurred. In each case, HTED had three to five more water molecules in its primary solvation shell than HPIP, indicating that differences in the energetics of desolvation before binding may partially explain the increased potency of HPIP as compared to HTED. Images FIGURE 1 FIGURE 2 PMID:8161685

  1. Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

    PubMed Central

    Lovera, Silvia; Morando, Maria; Pucheta-Martinez, Encarna; Martinez-Torrecuadrada, Jorge L.; Saladino, Giorgio; Gervasio, Francesco L.

    2015-01-01

    Due to its inhibition of the Abl kinase domain in the BCR-ABL fusion protein, imatinib is strikingly effective in the initial stage of chronic myeloid leukemia with more than 90% of the patients showing complete remission. However, as in the case of most targeted anti-cancer therapies, the emergence of drug resistance is a serious concern. Several drug-resistant mutations affecting the catalytic domain of Abl and other tyrosine kinases are now known. But, despite their importance and the adverse effect that they have on the prognosis of the cancer patients harboring them, the molecular mechanism of these mutations is still debated. Here by using long molecular dynamics simulations and large-scale free energy calculations complemented by in vitro mutagenesis and microcalorimetry experiments, we model the effect of several widespread drug-resistant mutations of Abl. By comparing the conformational free energy landscape of the mutants with those of the wild-type tyrosine kinases we clarify their mode of action. It involves significant and complex changes in the inactive-to-active dynamics and entropy/enthalpy balance of two functional elements: the activation-loop and the conserved DFG motif. What is more the T315I gatekeeper mutant has a significant impact on the binding mechanism itself and on the binding kinetics. PMID:26606374

  2. Biophysical exploration of protein-flavonol recognition: effects of molecular properties and conformational flexibility.

    PubMed

    Ding, Fei; Peng, Wei; Peng, Yu-Kui

    2016-04-28

    The current work explores the biomolecular recognition of a series of flavonols by a protein and then uncovers the influences of the structural features of flavonols and the protein's own characteristics, e.g. the dynamics and flexibility, on the bioavailability of flavonols by using the pivotal biomacromolecule hemoglobin as a model. The experimental results revealed that flavonol may lead to a notable decrease in the steady-state fluorescence intensity of the β-37 Trp residue, and in the meantime the R-T transition of the protein transpired. Such noncovalent recognition forms the ground-state adduct, with an association intensity of 3.991 × 10(4) M(-1) in the reaction process, which has already been authenticated by the detailed analysis of time-resolved fluorescence and UV/vis absorption spectra. Furthermore, flavonol can form hydrogen bonds and π-conjugation effects with several amino acid residues on the polypeptide chain, for example, Trp-37, Arg-40, Asp-99 and Asn-102, and this event would induce self-regulation of the compact, regular conformation of the protein to a certain extent, which explicitly corroborates the results of circular dichroism. According to the study of molecular docking and structure-activity relationships, we could see that the recognition capacities of the protein-flavonols are inversely interrelated with the C log P values of the flavonol molecules. Moreover, the properties of the substituents in the structural B-ring unit of flavonols, i.e. polarity, position and number, will also prominently affect the degree of affinity and bioavailability of the protein-flavonol complexes. The analytical results of molecular dynamics (MD) simulation testified that the discussions of the structure-activity relationships are entirely logical, and the conformations of the amino acid residues forming noncovalent interactions tend to be stable in the MD simulation, as further elucidated from the dynamics data. Plainly, molecular recognition of

  3. Distance Geometry Protocol to Generate Conformations of Natural Products to Structurally Interpret Ion Mobility-Mass Spectrometry Collision Cross Sections

    PubMed Central

    2015-01-01

    Ion mobility-mass spectrometry (IM-MS) allows the separation of ionized molecules based on their charge-to-surface area (IM) and mass-to-charge ratio (MS), respectively. The IM drift time data that is obtained is used to calculate the ion-neutral collision cross section (CCS) of the ionized molecule with the neutral drift gas, which is directly related to the ion conformation and hence molecular size and shape. Studying the conformational landscape of these ionized molecules computationally provides interpretation to delineate the potential structures that these CCS values could represent, or conversely, structural motifs not consistent with the IM data. A challenge in the IM-MS community is the ability to rapidly compute conformations to interpret natural product data, a class of molecules exhibiting a broad range of biological activity. The diversity of biological activity is, in part, related to the unique structural characteristics often observed for natural products. Contemporary approaches to structurally interpret IM-MS data for peptides and proteins typically utilize molecular dynamics (MD) simulations to sample conformational space. However, MD calculations are computationally expensive, they require a force field that accurately describes the molecule of interest, and there is no simple metric that indicates when sufficient conformational sampling has been achieved. Distance geometry is a computationally inexpensive approach that creates conformations based on sampling different pairwise distances between the atoms within the molecule and therefore does not require a force field. Progressively larger distance bounds can be used in distance geometry calculations, providing in principle a strategy to assess when all plausible conformations have been sampled. Our results suggest that distance geometry is a computationally efficient and potentially superior strategy for conformational analysis of natural products to interpret gas-phase CCS data. PMID:25360896

  4. Exploring the structure and conformational landscape of human leptin. A molecular dynamics approach.

    PubMed

    Chimal-Vega, Brenda; Paniagua-Castro, Norma; Carrillo Vazquez, Jonathan; Rosas-Trigueros, Jorge L; Zamorano-Carrillo, Absalom; Benítez-Cardoza, Claudia G

    2015-11-21

    Leptin is a hormone that regulates energy homeostasis, inflammation, hematopoiesis and immune response, among other functions (Houseknecht et al., 1998; Zhang et al., 1995; Paz-Filho et al., 2010). To obtain its crystallographic structure, it was necessary to substitute a tryptophan for a glutamic acid at position 100, thus creating a mutant leptin that has been reported to have biological activity comparable to the activity of the wild type but that crystallizes more readily. Here, we report a comparative study of the conformational space of WT and W100E leptin using molecular dynamics simulations performed at 300, 400, and 500 K. We detected differences between the interactions of the two proteins with local and distal effects, resulting in changes in the conformation, accessible surface area, compactness, electrostatic potential and dynamic behavior. Additionally, the series of unfolding events that occur when leptin is subjected to high temperature differs for the two constructs. We observed that both proteins are mostly unstructured after 20 ns of MD simulation at 500 K. However, WT leptin maintains a significant amount of secondary structure in helix α2, while the most stable region of W100E leptin is helix α3. Furthermore, we found that the region between residues 25 and 42 might adopt interconverting secondary structures ranging from α-helices and random coils to β-strand structures. Thus, this region can be considered an intrinsically disordered region. This atomistic description supports our understanding of leptin signaling and consequently might facilitate the use of leptin in treatments for the pathophysiologies in which it is implicated. PMID:26342543

  5. Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors

    SciTech Connect

    McTigue, Michele; Murray, Brion William; Chen, Jeffrey H.; Deng, Ya-Li; Solowiej, James; Kania, Robert S.

    2012-09-17

    We performed analyses of compounds in clinical development which have shown that ligand efficient-molecules with privileged physical properties and low dose are less likely to fail in the various stages of clinical testing, have fewer postapproval withdrawals, and are less likely to receive black box safety warnings. However, detailed side-by-side examination of molecular interactions and properties within single drug classes are lacking. As a class, VEGF receptor tyrosine kinase inhibitors (VEGFR TKIs) have changed the landscape of how cancer is treated, particularly in clear cell renal cell carcinoma, which is molecularly linked to the VEGF signaling axis. Despite the clear role of the molecular target, member molecules of this validated drug class exhibit distinct clinical efficacy and safety profiles in comparable renal cell carcinoma clinical studies. The first head-to-head randomized phase III comparative study between active VEGFR TKIs has confirmed significant differences in clinical performance [Rini BI, et al. (2011) Lancet 378:193–1939]. To elucidate how fundamental drug potency–efficiency is achieved and impacts differentiation within the VEGFR TKI class, we determined potencies, time dependence, selectivities, and X-ray structures of the drug–kinase complexes using a VEGFR2 TK construct inclusive of the important juxtamembrane domain. Collectively, the studies elucidate unique drug–kinase interactions that are dependent on distinct juxtamembrane domain conformations, resulting in significant potency and ligand efficiency differences. Finally, the identified structural trends are consistent with in vitro measurements, which translate well to clinical performance, underscoring a principle that may be broadly applicable to prospective drug design for optimal in vivo performance.

  6. Conformation-dependent Molecular Orientation Deduced from First-principles Modeling of Oligo(ethylene glycol)-terminated and Amide Group Containing Alkanethiolates Self-assembled on Gold

    NASA Astrophysics Data System (ADS)

    Malysheva, L.; Onipko, A.; Valiokas, R.; Liedberg, B.

    2005-09-01

    We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations — all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.

  7. Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions.

    PubMed

    Gao, Kaifu; He, Hongqing; Yang, Minghui; Yan, Honggao

    2015-11-10

    6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions. PMID:26492157

  8. Conformational stability of digestion-resistant peptides of peanut conglutins reveals the molecular basis of their allergenicity

    PubMed Central

    Apostolovic, Danijela; Stanic-Vucinic, Dragana; de Jongh, Harmen H. J.; de Jong, Govardus A. H.; Mihailovic, Jelena; Radosavljevic, Jelena; Radibratovic, Milica; Nordlee, Julie A.; Baumert, Joseph L.; Milcic, Milos; Taylor, Steve L.; Garrido Clua, Nuria; Cirkovic Velickovic, Tanja; Koppelman, Stef J.

    2016-01-01

    Conglutins represent the major peanut allergens and are renowned for their resistance to gastro-intestinal digestion. Our aim was to characterize the digestion-resistant peptides (DRPs) of conglutins by biochemical and biophysical methods followed by a molecular dynamics simulation in order to better understand the molecular basis of food protein allergenicity. We have mapped proteolysis sites at the N- and C-termini and at a limited internal segment, while other potential proteolysis sites remained unaffected. Molecular dynamics simulation showed that proteolysis only occurred in the vibrant regions of the proteins. DRPs appeared to be conformationally stable as intact conglutins. Also, the overall secondary structure and IgE-binding potency of DRPs was comparable to that of intact conglutins. The stability of conglutins toward gastro-intestinal digestion, combined with the conformational stability of the resulting DRPs provide conditions for optimal exposure to the intestinal immune system, providing an explanation for the extraordinary allergenicity of peanut conglutins. PMID:27377129

  9. Conformational stability of digestion-resistant peptides of peanut conglutins reveals the molecular basis of their allergenicity.

    PubMed

    Apostolovic, Danijela; Stanic-Vucinic, Dragana; de Jongh, Harmen H J; de Jong, Govardus A H; Mihailovic, Jelena; Radosavljevic, Jelena; Radibratovic, Milica; Nordlee, Julie A; Baumert, Joseph L; Milcic, Milos; Taylor, Steve L; Garrido Clua, Nuria; Cirkovic Velickovic, Tanja; Koppelman, Stef J

    2016-01-01

    Conglutins represent the major peanut allergens and are renowned for their resistance to gastro-intestinal digestion. Our aim was to characterize the digestion-resistant peptides (DRPs) of conglutins by biochemical and biophysical methods followed by a molecular dynamics simulation in order to better understand the molecular basis of food protein allergenicity. We have mapped proteolysis sites at the N- and C-termini and at a limited internal segment, while other potential proteolysis sites remained unaffected. Molecular dynamics simulation showed that proteolysis only occurred in the vibrant regions of the proteins. DRPs appeared to be conformationally stable as intact conglutins. Also, the overall secondary structure and IgE-binding potency of DRPs was comparable to that of intact conglutins. The stability of conglutins toward gastro-intestinal digestion, combined with the conformational stability of the resulting DRPs provide conditions for optimal exposure to the intestinal immune system, providing an explanation for the extraordinary allergenicity of peanut conglutins. PMID:27377129

  10. On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A.

    PubMed

    Chopade, Prashant D; Sarma, Bipul; Santiso, Erik E; Simpson, Jeffrey; Fry, John C; Yurttas, Nese; Biermann, Kari L; Chen, Jie; Trout, Bernhardt L; Myerson, Allan S

    2015-12-28

    The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described. PMID:26723665

  11. On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

    SciTech Connect

    Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S.; Simpson, Jeffrey; Fry, John C.; Biermann, Kari L.; Yurttas, Nese

    2015-12-28

    The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

  12. On the connection between nonmonotonic taste behavior and molecular conformation in solution: The case of rebaudioside-A

    NASA Astrophysics Data System (ADS)

    Chopade, Prashant D.; Sarma, Bipul; Santiso, Erik E.; Simpson, Jeffrey; Fry, John C.; Yurttas, Nese; Biermann, Kari L.; Chen, Jie; Trout, Bernhardt L.; Myerson, Allan S.

    2015-12-01

    The diterpene steviol glycoside, rebaudioside A, is a natural high potency non-caloric sweetener extracted from the leaves of Stevia rebaudiana. This compound shows a parabolic change in sweet taste intensity with temperature which contrasts with the general finding for other synthetic or natural sweeteners whose sweet taste increases with temperature. The nonmonotonic taste behavior was determined by sensory analysis using large taste panels. The conformational landscape of rebaudioside A was established at a range of temperatures by means of nuclear magnetic resonance and molecular dynamics simulation. The relationship between various conformations and the observed sweetness of rebaudioside A is described.

  13. Formation of smooth, conformal molecular layers on ZnO surfaces via photochemical grafting.

    PubMed

    Ruther, Rose E; Franking, Ryan; Huhn, Alex M; Gomez-Zayas, Jaritza; Hamers, Robert J

    2011-09-01

    We have investigated the photochemical grafting of organic alkenes to atomically flat ZnO(10 ̅10) single crystals and ZnO nanorods as a way to produce functional molecule-semiconductor interfaces. Atomic force microscopy shows that photochemical grafting produces highly conformal, smooth molecular layers with no detectable changes in the underlying structure of the ZnO terraces or steps. X-ray photoelectron spectroscopy measurements show that grafting of a methyl ester-terminated alkene terminates near one monolayer, while alkenes bearing a trifluoroacetamide-protected amine form very smooth multilayers. Even with multilayers, it is possible to deprotect the amines and to link a second molecule to the surface with excellent efficiency and without significant loss of molecules from the surface. This demonstrates that the use of photochemical grafting, even in the case of multilayer formation, enables multistep chemical processes to be conducted on the ZnO surface. Photoresponse measurements demonstrate that functionalization of the surface does not affect the ability to induce field effects in the underlying ZnO, thereby suggesting that this approach to functionalization may be useful for applications in sensing and in hybrid organic-inorganic transistors and related devices. PMID:21777005

  14. Charge-dependent conformations and dynamics of pamam dendrimers revealed by neutron scattering and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Wu, Bin

    Neutron scattering and fully atomistic molecular dynamics (MD) are employed to investigate the structural and dynamical properties of polyamidoamine (PAMAM) dendrimers with ethylenediamine (EDA) core under various charge conditions. Regarding to the conformational characteristics, we focus on scrutinizing density profile evolution of PAMAM dendrimers as the molecular charge of dendrimer increases from neutral state to highly charged condition. It should be noted that within the context of small angle neutron scattering (SANS), the dendrimers are composed of hydrocarbon component (dry part) and the penetrating water molecules. Though there have been SANS experiments that studied the charge-dependent structural change of PAMAM dendrimers, their results were limited to the collective behavior of the aforementioned two parts. This study is devoted to deepen the understanding towards the structural responsiveness of intra-molecular polymeric and hydration parts separately through advanced contrast variation SANS data analysis scheme available recently and unravel the governing principles through coupling with MD simulations. Two kinds of acids, namely hydrochloric and sulfuric acids, are utilized to tune the pH condition and hence the molecular charge. As far as the dynamical properties, we target at understanding the underlying mechanism that leads to segmental dynamic enhancement observed from quasielstic neutron scattering (QENS) experiment previously. PAMAM dendrimers have a wealth of potential applications, such as drug delivery agency, energy harvesting medium, and light emitting diodes. More importantly, it is regarded as an ideal system to test many theoretical predictions since dendrimers conjugate both colloid-like globular shape and polymer-like flexible chains. This Ph.D. research addresses two main challenges in studying PAMAM dendrimers. Even though neutron scattering is an ideal tool to study this PAMAM dendrimer solution due to its matching temporal and

  15. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  16. Conformational Analysis of a Dermatan Sulfate-Derived Tetrasaccharide by NMR, Molecular Modeling, and Residual Dipolar Couplings

    PubMed Central

    Silipo, Alba; Zhang, Zhenqing; Cañada, F. Javier; Molinaro, Antonio

    2014-01-01

    The solution conformation behavior of a dermatan-derived tetrasaccharide—ΔHexA-(1→3)-GalNAc4S-β-(1→4)-IdoA-α-(1→3)-red-GalNAc4S (S is a sulfate group)—has been explored by means of NMR spectroscopy, especially by NOE-based conformational analysis. The tetrasaccharide was present as four species, two of which are chemically different in the anomeric orientation of the reducing 2-deoxy-2-acetamido-galactose (red-GalNAc) residue, while the other two are the result of different conformations of the iduronic acid (IdoA) unit. The two α–-interconverting anomers were present in a 0.6:1 ratio. Ring conformations have been defined by analysis of 3JH,H coupling constants and interresidual NOE contacts. Both 2-deoxy-2-acetamido-galactose (GalNAc) residues were found in the 4C1 chair conformation, the unsaturated uronic acid (Δ-Hex A) adopts a strongly predominant half-chair 1H2 conformation, while the IdoA residue exists either in the 1C4 chair or in the 2S0 skewed boat geometries, in a 4:1 ratio. There is a moderate flexibility of Φ and Ψ torsions as suggested by nuclear Overhauser effects (NOEs), molecular modeling (MM), and molecular dynamics (MD) studies. This was further investigated by residual dipolar couplings (RDCs). One-bond C–H RDCs (1DC,H) and long-range H–H (3DH,H) RDCs were measured for the tetrasaccharide in a phage solution and interpreted in combination with restrained MD simulation. The RDC-derived data substantially confirmed the validity of the conformer distribution resulting from the NOE-derived simulations, but allowed an improved definition of the conformational behavior of the oligosaccharides in solution. In summary, the data show a moderate flexibility of the four tetrasaccharide species at the central glycosidic linkage. Differences in the shapes of species with the IdoA in skew and in chair conformations and in the distribution of the sulfate groups have also been highlighted. PMID:18072186

  17. Exploring the conformational and binding properties of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 through docking and molecular dynamics simulations.

    PubMed

    Zacarías-Lara, Oscar J; Correa-Basurto, José; Bello, Martiniano

    2016-07-01

    B-cell lymphoma (Bcl-2) is commonly associated with the progression and preservation of cancer and certain lymphomas; therefore, it is considered as a biological target against cancer. Nevertheless, evidence of all its structural binding sites has been hidden because of the lack of a complete Bcl-2 model, given the presence of a flexible loop domain (FLD), which is responsible for its complex behavior. FLD region has been implicated in phosphorylation, homotrimerization, and heterodimerization associated with Bcl-2 antiapoptotic function. In this contribution, homology modeling, molecular dynamics (MD) simulations in the microsecond (µs) time-scale and docking calculations were combined to explore the conformational complexity of unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 systems. Conformational ensembles generated through MD simulations allowed for identifying the most populated unphosphorylated/phosphorylated monomeric conformations, which were used as starting models to obtain trimeric complexes through protein-protein docking calculations, also submitted to µs MD simulations. Principal component analysis showed that FLD represents the main contributor to total Bcl-2 mobility, and is affected by phosphorylation and oligomerization. Subsequently, based on the most representative unphosphorylated/phosphorylated monomeric and trimeric Bcl-2 conformations, docking studies were initiated to identify the ligand binding site of several known Bcl-2 inhibitors to explain their influence in homo-complex formation and phosphorylation. Docking studies showed that the different conformational states experienced by FLD, such as phosphorylation and oligomerization, play an essential role in the ability to make homo and hetero-complexes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 393-413, 2016. PMID:27016043

  18. Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering

    PubMed Central

    2015-01-01

    The epidermal growth factor receptor (EGFR) is aberrantly activated in various cancer cells and an important target for cancer treatment. Deep understanding of EGFR conformational changes between the active and inactive states is of pharmaceutical interest. Here we present a strategy combining multiply targeted molecular dynamics simulations, unbiased molecular dynamics simulations, and Bayesian clustering to investigate transition pathways during the activation/inactivation process of EGFR kinase domain. Two distinct pathways between the active and inactive forms are designed, explored, and compared. Based on Bayesian clustering and rough two-dimensional free energy surfaces, the energy-favorable pathway is recognized, though DFG-flip happens in both pathways. In addition, another pathway with different intermediate states appears in our simulations. Comparison of distinct pathways also indicates that disruption of the Lys745-Glu762 interaction is critically important in DFG-flip while movement of the A-loop significantly facilitates the conformational change. Our simulations yield new insights into EGFR conformational transitions. Moreover, our results verify that this approach is valid and efficient in sampling of protein conformational changes and comparison of distinct pathways. PMID:25136273

  19. Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study.

    PubMed

    Czub, Jacek; Neumann, Anna; Borowski, Edward; Baginski, Maciej

    2009-04-01

    Amphotericin B (AmB) is an effective but very toxic antifungal antibiotic. In our laboratory a series of AmB derivatives of improved selectivity of action was synthesized and tested. To understand molecular basis of this improvement, comparative conformational studies of amphotericin B and its two more selective derivatives were carried out in an aqueous solution and in a lipid membrane. These molecular simulation studies revealed that within a membrane environment the conformational behavior of the derivatives differs significantly from the one observed for the parent molecule. Possible reasons for such a difference are analyzed. Furthermore, we hypothesize that the observed conformational transition within the polar head of AmB derivatives may lead to destabilization of antibiotic-induced transmembrane channels. Consequently, the selective toxicity of the derivatives should increase as ergosterol-rich liquid-ordered domains are more rigid and conformationally ordered than their cholesterol-containing counterparts, and as such may better support less stable channel structure. PMID:19185412

  20. Molecular mechanisms for generating transmembrane proton gradients

    PubMed Central

    Gunner, M.R.; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun

    2013-01-01

    Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side. PMID:23507617

  1. Molecular mechanisms for generating transmembrane proton gradients.

    PubMed

    Gunner, M R; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun

    2013-01-01

    Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side. PMID:23507617

  2. Cluster analysis of molecular simulation trajectories for systems where both conformation and orientation of the sampled states are important.

    PubMed

    Abramyan, Tigran M; Snyder, James A; Thyparambil, Aby A; Stuart, Steven J; Latour, Robert A

    2016-08-01

    Clustering methods have been widely used to group together similar conformational states from molecular simulations of biomolecules in solution. For applications such as the interaction of a protein with a surface, the orientation of the protein relative to the surface is also an important clustering parameter because of its potential effect on adsorbed-state bioactivity. This study presents cluster analysis methods that are specifically designed for systems where both molecular orientation and conformation are important, and the methods are demonstrated using test cases of adsorbed proteins for validation. Additionally, because cluster analysis can be a very subjective process, an objective procedure for identifying both the optimal number of clusters and the best clustering algorithm to be applied to analyze a given dataset is presented. The method is demonstrated for several agglomerative hierarchical clustering algorithms used in conjunction with three cluster validation techniques. © 2016 Wiley Periodicals, Inc. PMID:27292100

  3. DETECTION OF MOLECULAR MONOLAYERS BY OPTICAL. SECOND HARMONIC GENERATION

    SciTech Connect

    Chen, C. K.; Heinz, T. F.; Ricard, D.; Shen, Y. R.

    1980-12-01

    Second harmonic generation is shown to be sensitive enough to detect molecular monolayers adsorbed on a silver surface. Adsorption of AgCl and pyridine on silver during and after an electrolytic cycle can be easily observed,

  4. On the use of Schwarz-Christoffel conformal mappings to the grid generation for global ocean models

    NASA Astrophysics Data System (ADS)

    Xu, S.; Wang, B.; Liu, J.

    2015-02-01

    In this article we propose two conformal mapping based grid generation algorithms for global ocean general circulation models (OGCMs). Contrary to conventional, analytical forms based dipolar or tripolar grids, the new algorithms are based on Schwarz-Christoffel (SC) conformal mapping with prescribed boundary information. While dealing with the basic grid design problem of pole relocation, these new algorithms also address more advanced issues such as smoothed scaling factor, or the new requirements on OGCM grids arisen from the recent trend of high-resolution and multi-scale modeling. The proposed grid generation algorithm could potentially achieve the alignment of grid lines to coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the generated grids are still orthogonal curvilinear, they can be readily utilized in existing Bryan-Cox-Semtner type ocean models. The proposed methodology can also be applied to the grid generation task for regional ocean modeling where complex land-ocean distribution is present.

  5. A New Efficient Method for Generating Conformations of Unfolded Proteins with Diverse Main-Chain Dihedral-Angle Distributions.

    PubMed

    Seki, Yasutaka; Shimbo, Yudai; Nonaka, Takamasa; Soda, Kunitsugu

    2011-07-12

    A new method for generating polypeptide-chain conformations has been developed for studying structural characteristics of unfolded proteins. It enables us to generate a large number of conformations very rapidly by avoiding atomic collisions efficiently with the use of main-chain dihedral-angle distributions derived from a crystal-structure database of proteins. In addition, combining main-chain dihedral-angle distributions for the amino acid residues incorporated in different secondary structures, we can obtain diverse conformational ensembles with different structural features. Structural characteristics of proteins denatured in high-concentration denaturant solution were analyzed by comparing predictions from this method with results from solution X-ray scattering (SXS) measurement. Analysis of the dependence of the mean square radius (Rsq) of protein on the number of residues and the shape of its Kratky profile has confirmed that the highly denaturing solvent serves as a good solvent in accordance with previous reports. It was also found that, in order for a conformational ensemble to reproduce experimental data, the percentage in which main-chain dihedral angles are found in the α region must be in the range of 20-40%. It agrees with studies on the (3)JHNα coupling constant using the multidimensional NMR method. These results confirm that our method for generating diverse conformations of polypeptide chains is very useful to the conformational analysis of unfolded protein, because it enables us to analyze comprehensively both of the local structural features obtained from NMR and the global ones obtained from SXS. PMID:26606484

  6. Molecular structure and conformational composition of 1,1-dichlorobutane: a gas-phase electron diffraction and ab initio investigation

    NASA Astrophysics Data System (ADS)

    Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar

    1997-09-01

    Gas-phase electron diffraction data obtained at 23°C, together with results from ab initio molecular orbital calculations ( {HF}/{6-31 G(d)}). were used to determine the structure and conformational composition of 1,1-dichlorobutane. Of the five distinguishable conformers (AA, G + A, AG +, G + G + and G + G -), the G + A conformer was found to be the low-energy form, and the investigation also indicated that certain amounts of the AA and G + G - conformers might be present. The symbols describing the conformers refer to torsion about the C 1C 2 and C 2C 3 bonds, anti (A) with H 5C 1C 2C 3 and C 1C 2C 3C 4 torsion angles of 180° and gauche (G + or G -) with torsion angles of + 60° or 300° (-60°) respectively. The results for the principal distances ( rg) and angles (∠ α) from the combined electron diffraction/ab initio study for the G + A conformer, with estimated 2σ uncertainties, were as follows: r( C1 C2) = 1.521(4) Å, r( C2 C3) = 1.539(4) Å, r( C3 C4) = 1.546(4) Å, r( C Cl6) = 1.782(3) Å, r( CCl7) = 1.782(3) Å, = 1.106(6) Å, ∠C 1C 2C 3 = 114.4(13)°, ∠C 2C 3C 4 = 112.5(13)°, ∠CCCl 6 = 110.4(7)°, ∠CCCl 7 = 111.9(7)°, <∠CCH> = 108.9(47)°. Only average values for r(CC), r(CCl), r(CH), ∠CCC, ∠CCX and ∠CCH were determined in the least-square refinements; the differences between the values for these parameters in the same conformer and between the different conformers were kept constant at the values obtained from the ab initio molecular orbital calculations.

  7. Theoretical studies of a molecular beam generator

    NASA Technical Reports Server (NTRS)

    Heinbockel, John H.

    1993-01-01

    The following is a proposed baseline model that is being developed for the simulation of hydrodynamic generator, which can be converted at a later date to magnetohydrodynamic MHD thruster by adding the necessary electric and magnetic fields. The following development will include the electric and magnetic terms, however, the initial computer program will not include these terms. The analysis that follows is a one species, single temperature model constructed over a domain that is defined by an enclosed region.

  8. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

    PubMed Central

    Sinko, William; de Oliveira, César; Williams, Sarah; Van Wynsberghe, Adam; Durrant, Jacob D; Cao, Rong; Oldfield, Eric; McCammon, J Andrew

    2011-01-01

    Undecaprenyl pyrophosphate synthase is a cis-prenyltransferase enzyme, which is required for cell wall biosynthesis in bacteria. Undecaprenyl pyrophosphate synthase is an attractive target for antimicrobial therapy. We performed long molecular dynamics simulations and docking studies on undecaprenyl pyrophosphate synthase to investigate its dynamic behavior and the influence of protein flexibility on the design of undecaprenyl pyrophosphate synthase inhibitors. We also describe the first X-ray crystallographic structure of Escherichia coli apo-undecaprenyl pyrophosphate synthase. The molecular dynamics simulations indicate that undecaprenyl pyrophosphate synthase is a highly flexible protein, with mobile binding pockets in the active site. By carrying out docking studies with experimentally validated undecaprenyl pyrophosphate synthase inhibitors using high- and low-populated conformational states extracted from the molecular dynamics simulations, we show that structurally dissimilar compounds can bind preferentially to different and rarely sampled conformational states. By performing structural analyses on the newly obtained apo-undecaprenyl pyrophosphate synthase and other crystal structures previously published, we show that the changes observed during the molecular dynamics simulation are very similar to those seen in the crystal structures obtained in the presence or absence of ligands. We believe that this is the first time that a rare ‘expanded pocket’ state, key to drug design and verified by crystallography, has been extracted from a molecular dynamics simulation. PMID:21294851

  9. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target

    SciTech Connect

    Sinko, William; de Oliveira, César; Williams, Sarah; Van Wynsberghe, Adam; Durrant, Jacob D.; Cao, Rong; Oldfield, Eric; McCammon, J. Andrew

    2012-04-30

    Undecaprenyl pyrophosphate synthase is a cis-prenyltransferase enzyme, which is required for cell wall biosynthesis in bacteria. Undecaprenyl pyrophosphate synthase is an attractive target for antimicrobial therapy. We performed long molecular dynamics simulations and docking studies on undecaprenyl pyrophosphate synthase to investigate its dynamic behavior and the influence of protein flexibility on the design of undecaprenyl pyrophosphate synthase inhibitors. We also describe the first X-ray crystallographic structure of Escherichia coli apo-undecaprenyl pyrophosphate synthase. The molecular dynamics simulations indicate that undecaprenyl pyrophosphate synthase is a highly flexible protein, with mobile binding pockets in the active site. By carrying out docking studies with experimentally validated undecaprenyl pyrophosphate synthase inhibitors using high- and low-populated conformational states extracted from the molecular dynamics simulations, we show that structurally dissimilar compounds can bind preferentially to different and rarely sampled conformational states. By performing structural analyses on the newly obtained apo-undecaprenyl pyrophosphate synthase and other crystal structures previously published, we show that the changes observed during the molecular dynamics simulation are very similar to those seen in the crystal structures obtained in the presence or absence of ligands. We believe that this is the first time that a rare 'expanded pocket' state, key to drug design and verified by crystallography, has been extracted from a molecular dynamics simulation.

  10. Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer

    PubMed Central

    Morra, Giulia; Verkhivker, Gennady; Colombo, Giorgio

    2009-01-01

    Hsp90 is a molecular chaperone essential for protein folding and activation in normal homeostasis and stress response. ATP binding and hydrolysis facilitate Hsp90 conformational changes required for client activation. Hsp90 plays an important role in disease states, particularly in cancer, where chaperoning of the mutated and overexpressed oncoproteins is important for function. Recent studies have illuminated mechanisms related to the chaperone function. However, an atomic resolution view of Hsp90 conformational dynamics, determined by the presence of different binding partners, is critical to define communication pathways between remote residues in different domains intimately affecting the chaperone cycle. Here, we present a computational analysis of signal propagation and long-range communication pathways in Hsp90. We carried out molecular dynamics simulations of the full-length Hsp90 dimer, combined with essential dynamics, correlation analysis, and a signal propagation model. All-atom MD simulations with timescales of 70 ns have been performed for complexes with the natural substrates ATP and ADP and for the unliganded dimer. We elucidate the mechanisms of signal propagation and determine “hot spots” involved in interdomain communication pathways from the nucleotide-binding site to the C-terminal domain interface. A comprehensive computational analysis of the Hsp90 communication pathways and dynamics at atomic resolution has revealed the role of the nucleotide in effecting conformational changes, elucidating the mechanisms of signal propagation. Functionally important residues and secondary structure elements emerge as effective mediators of communication between the nucleotide-binding site and the C-terminal interface. Furthermore, we show that specific interdomain signal propagation pathways may be activated as a function of the ligand. Our results support a “conformational selection model” of the Hsp90 mechanism, whereby the protein may exist in a

  11. Electronic transport in biphenyl single-molecule junctions with carbon nanotubes electrodes: The role of molecular conformation and chirality

    SciTech Connect

    Brito Silva, C. A. Jr.; Granhen, E. R.; Silva, S. J. S. da; Leal, J. F. P.; Del Nero, J.; Pinheiro, F. A.

    2010-08-15

    We investigate, by means of ab initio calculations, electronic transport in molecular junctions composed of a biphenyl molecule attached to metallic carbon nanotubes. We find that the conductance is proportional to cos{sup 2} {theta}, with {theta} the angle between phenyl rings, when the Fermi level of the contacts lies within the frontier molecular orbitals energy gap. This result, which agrees with experiments in biphenyl junctions with nonorganic contacts, suggests that the cos{sup 2} {theta} law has a more general applicability, irrespective of the nature of the electrodes. We calculate the geometrical degree of chirality of the junction, which only depends on the atomic positions, and demonstrate that it is not only proportional to cos{sup 2} {theta} but also is strongly correlated with the current through the system. These results indicate that molecular conformation plays the preponderant role in determining transport properties of biphenyl-carbon nanotubes molecular junctions.

  12. A molecular dynamics description of the conformational flexibility of the L-iduronate ring in glycosaminoglycans.

    PubMed

    Angulo, Jesús; Nieto, Pedro M; Martín-Lomas, Manuel

    2003-07-01

    For a synthetic hexasaccharide model it is shown that the conformational flexibility of the L-iduronate ring in glycosaminoglycans can be adequately described by using the PME methodology together with simulation protocols suitable for highly charged systems. PMID:12868729

  13. Observation of conformers with laser electronic spectroscopy in supersonic molecular beams

    NASA Astrophysics Data System (ADS)

    Philis, John G.; Kosmidis, Constantine E.; Tsekeris, Pericles

    1998-07-01

    We discuss the ability and effectiveness of electronic spectroscopy to reveal rotational isomerism by presenting some examples of the S1 implied by S0 electronic spectra of non-rigid molecules. One or two photon electronic spectra have multiple features when the molecule has more than one conformational preference. Torsional bands showing up in the spectrum complicate the assignment of conformers. Hole burning experiments give definite conclusions on the existence of rotational isomerism and an example from the literature is given.

  14. Molecular structure and pronounced conformational flexibility of doxorubicin in free and conjugated state within a drug-peptide compound.

    PubMed

    Tsoneva, Yana; Jonker, Hendrik R A; Wagner, Manfred; Tadjer, Alia; Lelle, Marco; Peneva, Kalina; Ivanova, Anela

    2015-02-19

    The search for targeted drug delivery systems requires the design of drug-carrier complexes, which could both reach the malignant cells and preserve the therapeutic substance activity. A promising strategy aimed at enhancing the uptake and reducing the systemic toxicity is to bind covalently the drug to a cell-penetrating peptide. To understand the structure-activity relationship in such preparations, the chemotherapeutic drug doxorubicin was investigated by unrestrained molecular dynamics simulations, supported by NMR, which yielded its molecular geometry in aqueous environment. Furthermore, the structure and dynamics of a conjugate of the drug with a cell-penetrating peptide was obtained from molecular dynamics simulations in aqueous solution. The geometries of the unbound compounds were characterized at different temperatures, as well as the extent to which they change after covalent binding and whether/how they influence each other in the drug-peptide conjugate. The main structural fragments that affect the conformational ensemble of every molecule were found. The results show that the transitions between different substructures of the three compounds require a modest amount of energy. At increased temperature, either more conformations become populated as a result of the thermal fluctuations or the relative shares of the various conformers equalize at the nanosecond scale. These frequent structural interconversions suggest expressed conformational freedom of the molecules. Conjugation into the drug-peptide compound partially immobilizes the molecules of the parent compounds. Nevertheless, flexibility still exists, as well as an effective intra- and intermolecular hydrogen bonding that stabilizes the structures. We observe compact packing of the drug within the peptide that is also based on stacking interactions. All this outlines the drug-peptide conjugate as a prospective building block of a more complex drug-carrier system. PMID:25603129

  15. Molecular Dynamics Investigations of the Local Structural Characteristics of DNA Oligonucleotides: Studies of Helical Axis Deformations, Conformational Sequence Dependence and Modified Nucleoside Perturbations.

    NASA Astrophysics Data System (ADS)

    Louise-May, Shirley

    The present DNA studies investigate the local structure of DNA oligonucleotides in order to characterize helical axis deformations, sequence dependent fine structure and modified nucleoside perturbations of selected oligonucleotide sequences. The molecular dynamics method is used to generate an ensemble of energetically feasible DNA conformations which can then be analyzed for dynamical conformational properties, some of which can be compared to experimentally derived values. A theory and graphical presentation for the analysis of helical deformations of DNA based on the configurational statistics of polymers, called "Persistence Analysis", was designed. The results of the analysis on prototype forms, static crystal structures and two solvated MD simulations of the sequence d(CGCGAATTCGCG) indicate that all of the expected features of bending can be sensitively and systematically identified by this approach. Comparison of the relative performance of three molecular dynamics potential functions commonly used for dynamical modeling of biological macromolecules; CHARMm, AMBER and GROMOS was investigated via in vacuo MD simulations on the dodecamer sequence d(CGCGAATTCGCG)_2 with respect to the conformational properties of each dynamical model and their ability to support A and B families of DNA. Vacuum molecular dynamics simulations using the CHARMm force field carried out on simple homo- and heteropolymers of DNA led to the conclusion that sequence dependent fine structure appears to be well defined for adenine-thymine rich sequences both at the base pair and base step level whereas much of the the fine structure found in cytosine -guanine rich sequences appears to be context dependent. The local conformational properties of the homopolymer poly (dA) -poly (dT) revealed one dynamical model which was found in general agreement with fiber models currently available. Investigation of the relative structural static and dynamical effect of the misincorporation of

  16. Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

    PubMed Central

    El-Turk, Farah; Fauvet, Bruno; Ashrafi, Amer; Ouertatani-Sakouhi, Hajer; Cho, Min-Kyu; Neri, Marilisa; Cascella, Michele; Rothlisberger, Ursula; Pojer, Florence; Zweckstetter, Markus; Lashuel, Hilal

    2012-01-01

    Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer formation, is essential for its keto-enol tautomerase activity and probably mediates several of its interactions and biological activities, including its binding to its receptor CD74 and activation of certain signaling pathways. Therefore, understanding the molecular factors governing the oligomerization of MIF and the role of quaternary structure in modulating its structural stability and multifunctional properties is crucial for understanding the function of MIF in health and disease. Herein, we describe highly conserved intersubunit interactions involving the hydrophobic packing of the side chain of Leu46 onto the β-strand β3 of one monomer within a hydrophobic pocket from the adjacent monomer constituted by residues Arg11, Val14, Phe18, Leu19, Val39, His40, Val41, Val42, and Pro43. To elucidate the structural significance of these intersubunit interactions and their relative contribution to MIF’s trimerization, structural stability and catalytic activity, we generated three point mutations where Leu46 was replaced by glycine (L46G), alanine (L46A) and phenylalanine (L46F), and their structural properties, stability, oligomerization state, and catalytic activity were characterized using a battery of biophysical methods and X-ray crystallography. Our findings provide new insights into the role of the Leu46 hydrophobic pocket in stabilizing the conformational state of MIF in solution. Disrupting the Leu46 hydrophobic interaction perturbs the secondary and tertiary structure of the protein but has no effect on its oligomerization state. PMID:23028743

  17. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy

    PubMed Central

    Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H.

    2016-01-01

    Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

  18. (13)CHD2-CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins.

    PubMed

    Rennella, Enrico; Huang, Rui; Velyvis, Algirdas; Kay, Lewis E

    2015-10-01

    An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of (13)CHD2 methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble. Experiments on a number of different protein systems, including a 360 kDa half-proteasome, establish that the sensitivity of this (13)CHD2 (13)C-CEST technique can be upwards of a factor of 5 times higher than for a previously published (13)CH3 (13)C-CEST approach (Bouvignies and Kay in J Biomol NMR 53:303-310, 2012), suggesting that the methodology will be powerful for studies of conformational exchange in high molecular weight proteins. PMID:26271302

  19. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy.

    PubMed

    Voltz, Karine; Léonard, Jérémie; Touceda, Patricia Tourón; Conyard, Jamie; Chaker, Ziyad; Dejaegere, Annick; Godet, Julien; Mély, Yves; Haacke, Stefan; Stote, Roland H

    2016-04-20

    Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies. PMID:26896800

  20. Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase

    PubMed Central

    Sündermann, Axel; Oostenbrink, Chris

    2013-01-01

    Cytochrome P450 reductase (CYPOR) undergoes a large conformational change to allow for an electron transfer to a redox partner to take place. After an internal electron transfer over its cofactors, it opens up to facilitate the interaction and electron transfer with a cytochrome P450. The open conformation appears difficult to crystallize. Therefore, a model of a human CYPOR in the open conformation was constructed to be able to investigate the stability and conformational change of this protein by means of molecular dynamics simulations. Since the role of the protein is to provide electrons to a redox partner, the interactions with cytochrome P450 2D6 (2D6) were investigated and a possible complex structure is suggested. Additionally, electron pathway calculations with a newly written program were performed to investigate which amino acids relay the electrons from the FMN cofactor of CYPOR to the HEME of 2D6. Several possible interacting amino acids in the complex, as well as a possible electron transfer pathway were identified and open the way for further investigation by site directed mutagenesis studies. PMID:23832577

  1. Molecular mechanism for generation of antibody memory

    PubMed Central

    Shivarov, Velizar; Shinkura, Reiko; Doi, Tomomitsu; Begum, Nasim A.; Nagaoka, Hitoshi; Okazaki, Il-Mi; Ito, Satomi; Nonaka, Taichiro; Kinoshita, Kazuo; Honjo, Tasuku

    2008-01-01

    Activation-induced cytidine deaminase (AID) is the essential enzyme inducing the DNA cleavage required for both somatic hypermutation and class switch recombination (CSR) of the immunoglobulin gene. We originally proposed the RNA-editing model for the mechanism of DNA cleavage by AID. We obtained evidence that fulfils three requirements for CSR by this model, namely (i) AID shuttling between nucleus and cytoplasm, (ii) de novo protein synthesis for CSR, and (iii) AID–RNA complex formation. The alternative hypothesis, designated as the DNA-deamination model, assumes that the in vitro DNA deamination activity of AID is representative of its physiological function in vivo. Furthermore, the resulting dU was removed by uracil DNA glycosylase (UNG) to generate a basic site, followed by phosphodiester bond cleavage by AP endonuclease. We critically examined each of these provisional steps. We identified a cluster of mutants (H48A, L49A, R50A and N51A) that had particularly higher CSR activities than expected from their DNA deamination activities. The most striking was the N51A mutant that had no ability to deaminate DNA in vitro but retained approximately 50 per cent of the wild-type level of CSR activity. We also provide further evidence that UNG plays a non-canonical role in CSR, namely in the repair step of the DNA breaks. Taking these results together, we favour the RNA-editing model for the function of AID in CSR. PMID:19022739

  2. Molecular modeling, mutational analysis and conformational switching in IL27: An in silico structural insight towards AIDS research.

    PubMed

    Banerjee, Arundhati; Ray, Sujay

    2016-01-15

    The advancement in proteomics and bioinformatics provokes to discern the molecular-level probe for HIV inhibitor; human interleukin-27 (IL27). Documentation documents that tyrosine residues in IL27 play a pivotal role for interacting with HIV, causing apoptosis of the HIV+ cells. Primarily, 3D structure of human wild-type (WT) IL27 was built through manifold molecular modeling techniques after the satisfaction of stereo-chemical properties. Its essential tyrosine residues were identified. Two mutant models for IL27 were prepared following the similar protocol by first substituting the tyrosine residues with glycine (MT_G) and then with alanine (MT_A) in the WT protein. Molecular dynamics (MD) simulation was performed to obtain a stable conformation. Conformational alterations in WT, MT_G and MT_A (before and after MD simulation) disclosed that MT_A was the steadiest one with the best secondary structure conformation supported by statistical significances. Though huge RMSD variations were observed on superimposing the MT structures on WT individually, the MTs were examined to share similar SCOP/CATH fold with TM-score=0.8, indicating that they retained their functionality even after mutation. Electrostatic surface potential again unveiled MT_A to be the most stable one. MT_A was thereby revealed to be the potent peptide inhibitor for HIV. This probe presents a pathway to investigate and compare the bio-molecular interaction of WT IL27 and MT_A IL27 (strongest model) with HIV in the future. This is the first report regarding the structural biology of IL27 accompanied by alteration at its genetic level and delving into the unknown residue-level and functional biochemistry for bringing about an annihilation towards AIDS. PMID:26432006

  3. Conformational analysis of vitamin D 3 derivatives by molecular mechanics . Part II. 1α,25-dihydroxyvitamin D 3 and analogues

    NASA Astrophysics Data System (ADS)

    Mosquera, Ricardo A.; Rios, Miguel A.; Tovar, Clara A.; Maestro, Miguel

    1989-10-01

    The conformational analysis of vitamin D 3 derivatives, including the biologically active form 1α,25-dihydroxyvitamin D 3 (III) and several synthetic analogues: b-deoxy-1α,25-dihydroxyvitamin D 3 (IV), 3-deoxy-3α-methyl-1α,25-dihydroxyvitamin D 3 (V), 3-deoxy-3β-methyl-1α,25-dihydroxyvitamin D 3 (VI), and 3-deoxy-3,3-dimethyl-1α,25-dihydroxyvitamin D 3 (VII), has been carried out employing Allinger's molecular mechanics method. The results obtained for conformational equilibrium populations are found to be in good agreement with those provided by NMR studies. Comparison of the active form of vitamin D 3 (1α,25-dihydroxyvitamin D 3) with the other species reveals no important geometrical differences.

  4. Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges.

    PubMed

    Jani, Vinod; Sonavane, Uddhavesh; Joshi, Rajendra

    2016-07-01

    Protein folding is a multi-micro second time scale event and involves many conformational transitions. Crucial conformational transitions responsible for biological functions of biomolecules are difficult to capture using current state-of-the-art molecular dynamics (MD) simulations. Protein folding, being a stochastic process, witnesses these transitions as rare events. Many new methodologies have been proposed for observing these rare events. In this work, a temperature-aided cascade MD is proposed as a technique for studying the conformational transitions. Folding studies for Engrailed homeodomain and Immunoglobulin domain B of protein A have been carried out. Using this methodology, the unfolded structures with RMSD of 20 Å were folded to a structure with RMSD of 2 Å. Three sets of cascade MD runs were carried out using implicit solvation, explicit solvation, and charge updation scheme. In the charge updation scheme, charges based on the conformation obtained are calculated and are updated in the topology file. In all the simulations, the structure of 2 Å was reached within a few nanoseconds using these methods. Umbrella sampling has been performed using snapshots from the temperature-aided cascade MD simulation trajectory to build an entire conformational transition pathway. The advantage of the method is that the possible pathways for a particular reaction can be explored within a short duration of simulation time and the disadvantage is that the knowledge of the start and end state is required. The charge updation scheme adds the polarization effects in the force fields. This improves the electrostatic interaction among the atoms, which may help the protein to fold faster. PMID:26872480

  5. Molecular Crowding Affects the Conformational Fluctuations, Peroxidase Activity, and Folding Landscape of Yeast Cytochrome c.

    PubMed

    Paul, Simanta Sarani; Sil, Pallabi; Chakraborty, Ritobrita; Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2016-04-26

    To understand how a protein folds and behaves inside living cells, the effects of synthetic crowding media on protein folding, function, stability, and association have been studied in detail. Because the effect of excluded volume is more prominent in an extended state than in the native protein, a majority of these studies have been conducted in the unfolded state of different model proteins. Here, we have used fluorescence correlation spectroscopy (FCS) and other biophysical methods to investigate the effect of crowding agents Ficoll70 and Dextran70 on the nativelike state of cytochrome c from yeast. Yeast cytochrome c (y-cytc) contains a substantial expanded state in its native folded condition, which is present in equilibrium with a compact conformer in aqueous buffer. We have found that the crowding medium affects the native state equilibrium between compact and expanded states, shifting its population toward the compact conformer. As a result, the peroxidase activity of y-cytc decreases. Urea-induced protein stability measurements show that the compaction destabilizes the protein due to charge repulsions between similar charged clusters. Interestingly, the time constant of conformational fluctuations between the compact and expanded conformers has been found to increase in the crowded milieu, suggesting a crucial role of the solution microviscosity. PMID:27050502

  6. Emission behaviors of unsymmetrical 1,3-diaryl-β-diketones: A model perfectly disclosing the effect of molecular conformation on luminescence of organic solids

    PubMed Central

    Cheng, Xiao; Li, Feng; Han, Shenghua; Zhang, Yufei; Jiao, Chuanjun; Wei, Jinbei; Ye, Kaiqi; Wang, Yue; Zhang, Hongyu

    2015-01-01

    A series of unsymmetrical 1,3-diaryl-β-diketones 1–6 displaying molecular conformation-dependent fluorescence quantum yields have been synthesized. Crystals with planar molecular conformation such as 1, 2, 3 and 4 are highly fluorescent (φf: 39–53%), and the one holding slightly twisted conformation (5) is moderately luminescent (φf = 17%), while crystal 6 possessing heavily bent structure is completely nonluminous (φf ~ 0). The distinct fluorescence efficiencies are ascribed to their different molecular conformations, since all the crystals hold the same crystal system, space group and crystal packing structures. Additionally, the fluorescent crystals 1–5 display low threshold amplified spontaneous emission (ASE) with small full widths at half-maximum (FWHM: 3–7 nm), indicating their potential as candidates for organic crystal lasing devices. PMID:25771808

  7. New generation of breast cancer clinical trials implementing molecular profiling

    PubMed Central

    Zardavas, Dimitrios; Piccart-Gebhart, Martine

    2016-01-01

    The implementation of molecular profiling technologies in oncology deepens our knowledge for the molecular landscapes of cancer diagnoses, identifying aberrations that could be linked with specific therapeutic vulnerabilities. In particular, there is an increasing list of molecularly targeted anticancer agents undergoing clinical development that aim to block specific molecular aberrations. This leads to a paradigm shift, with an increasing list of specific aberrations dictating the treatment of patients with cancer. This paradigm shift impacts the field of clinical trials, since the classical approach of having clinico-pathological disease characteristics dictating the patients' enrolment in oncology trials shifts towards the implementation of molecular profiling as pre-screening step. In order to facilitate the successful clinical development of these new anticancer drugs within specific molecular niches of cancer diagnoses, there have been developed new, innovative trial designs that could be classified as follows: i) longitudinal cohort studies that implement (or not) "nested" downstream trials, 2) studies that assess the clinical utility of molecular profiling, 3) "master" protocol trials, iv) "basket" trials, v) trials following an adaptive design. In the present article, we review these innovative study designs, providing representative examples from each category and we discuss the challenges that still need to be addressed in this era of new generation oncology trials implementing molecular profiling. Emphasis is put on the field of breast cancer clinical trials. PMID:27458530

  8. Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide.

    PubMed

    Zeng, Songwei; Zhou, Guoquan; Guo, Jianzhong; Zhou, Feng; Chen, Junlang

    2016-01-01

    Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO. PMID:27097898

  9. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions.

    PubMed

    Wang, Qing; Xue, Tuo; Song, Chunnian; Wang, Yan; Chen, Guangju

    2016-01-01

    Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes. PMID:27171075

  10. Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide

    PubMed Central

    Zeng, Songwei; Zhou, Guoquan; Guo, Jianzhong; Zhou, Feng; Chen, Junlang

    2016-01-01

    Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO. PMID:27097898

  11. Study on the Application of the Combination of TMD Simulation and Umbrella Sampling in PMF Calculation for Molecular Conformational Transitions

    PubMed Central

    Wang, Qing; Xue, Tuo; Song, Chunnian; Wang, Yan; Chen, Guangju

    2016-01-01

    Free energy calculations of the potential of mean force (PMF) based on the combination of targeted molecular dynamics (TMD) simulations and umbrella samplings as a function of physical coordinates have been applied to explore the detailed pathways and the corresponding free energy profiles for the conformational transition processes of the butane molecule and the 35-residue villin headpiece subdomain (HP35). The accurate PMF profiles for describing the dihedral rotation of butane under both coordinates of dihedral rotation and root mean square deviation (RMSD) variation were obtained based on the different umbrella samplings from the same TMD simulations. The initial structures for the umbrella samplings can be conveniently selected from the TMD trajectories. For the application of this computational method in the unfolding process of the HP35 protein, the PMF calculation along with the coordinate of the radius of gyration (Rg) presents the gradual increase of free energies by about 1 kcal/mol with the energy fluctuations. The feature of conformational transition for the unfolding process of the HP35 protein shows that the spherical structure extends and the middle α-helix unfolds firstly, followed by the unfolding of other α-helices. The computational method for the PMF calculations based on the combination of TMD simulations and umbrella samplings provided a valuable strategy in investigating detailed conformational transition pathways for other allosteric processes. PMID:27171075

  12. A 99 percent purity molecular sieve oxygen generator

    NASA Technical Reports Server (NTRS)

    Miller, G. W.

    1991-01-01

    Molecular sieve oxygen generating systems (MSOGS) have become the accepted method for the production of breathable oxygen on military aircraft. These systems separate oxygen for aircraft engine bleed air by application of pressure swing adsorption (PSA) technology. Oxygen is concentrated by preferential adsorption in nitrogen in a zeolite molecular sieve. However, the inability of current zeolite molecular sieves to discriminate between oxygen and argon results in an oxygen purity limitations of 93-95 percent (both oxygen and argon concentrate). The goal was to develop a new PSA process capable of exceeding the present oxygen purity limitations. A novel molecular sieve oxygen concentrator was developed which is capable of generating oxygen concentrations of up to 99.7 percent directly from air. The process is comprised of four absorbent beds, two containing a zeolite molecular sieve and two containing a carbon molecular sieve. This new process may find use in aircraft and medical breathing systems, and industrial air separation systems. The commercial potential of the process is currently being evaluated.

  13. Vibrational spectra and molecular conformation of taurine and its related compounds

    NASA Astrophysics Data System (ADS)

    Ohno, Keiichi; Mandai, Yoshitaka; Matsuura, Hiroatsu

    1992-04-01

    IR and Raman spectra have been measured for taurine (2-aminoethanesulfonic acid) and its sodium salt in the solid state and Raman spectra for aqueous solutions of taurine with different pH values. Normal coordinate treatment has been carried out. The analysis of the spectra has indicated that, in the solid state, the molecule of taurine takes the gauche form while that of the sodium salt takes the trans form, and that the trans and gauche forms coexist in both acidic and basic aqueous solutions. The CS stretching bands for the gauche and trans forms were observed at 742 cm -1 and 803 cm -1 respectively. These bands were applied to a conformational analysis of other compounds containing a taurine skeleton; sodium taurocholate takes the gauche conformation about the bond axis NCCS.

  14. Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.

    PubMed

    Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H

    2010-09-14

    A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4,  6,  8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude

  15. Molecular tubes for lipid sensing: tube conformations control analyte selectivity and fluorescent response.

    PubMed

    Avetta, Christopher T; Shorthill, Berkeley J; Ren, Chun; Glass, Timothy E

    2012-01-20

    Two fluorescent sensors for lipids have been prepared and tested for detection of a number of hydrophobic compounds of varying shape and size. The data suggest that the two sensors have a different mode of fluorescent response. Yet, the two sensors are only different in the bridging group--one having a flexible amide and one having a rigid allyl bridge. The fluorescence data are explained based on a difference in conformation of the two sensors in aqueous solution. PMID:22263717

  16. Molecular docking study of conformational polymorph: building block of crystal chemistry.

    PubMed

    Dubey, Rashmi; Tewari, Ashish Kumar; Singh, Ved Prakash; Singh, Praveen; Dangi, Jawahar Singh; Puerta, Carmen; Valerga, Pedro; Kant, Rajni

    2013-01-01

    Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl)-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b) seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2) receptor than the standard (Nimesulide). PMID:24250264

  17. The molecular mechanism of heme loss from oxidized soluble guanylate cyclase induced by conformational change.

    PubMed

    Pan, Jie; Zhang, Xiaoxue; Yuan, Hong; Xu, Qiming; Zhang, Huijuan; Zhou, Yajun; Huang, Zhong-Xian; Tan, Xiangshi

    2016-05-01

    Heme oxidation and loss of soluble guanylate cyclase (sGC) is thought to be an important contributor to the development of cardiovascular diseases. Nevertheless, it remains unknown why the heme loses readily in oxidized sGC. In the current study, the conformational change of sGC upon heme oxidation by ODQ was studied based on the fluorescence resonance energy transfer (FRET) between the heme and a fluorophore fluorescein arsenical helix binder (FlAsH-EDT2) labeled at different domains of sGC β1. This study provides an opportunity to monitor the domain movement of sGC relative to the heme. The results indicated that heme oxidation by ODQ in truncated sCC induced the heme-associated αF helix moving away from the heme, the Per/Arnt/Sim domain (PAS) domain moving closer to the heme, but led the helical domain going further from the heme. We proposed that the synergistic effect of these conformational changes of the discrete region upon heme oxidation forces the heme pocket open, and subsequent heme loss readily. Furthermore, the kinetic studies suggested that the heme oxidation was a fast process and the conformational change was a relatively slow process. The kinetics of heme loss from oxidized sGC was monitored by a new method based on the heme group de-quenching the fluorescence of FlAsH-EDT2. PMID:26876536

  18. Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein

    PubMed Central

    Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

    2015-01-01

    Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation. PMID:26492886

  19. Two forms of loops generate the chromatin conformation of the immunoglobulin heavy chain gene locus

    PubMed Central

    Guo, Changying; Gerasimova, Tatiana; Hao, Haiping; Ivanova, Irina; Chakraborty, Tirtha; Selimyan, Roza; Oltz, Eugene M.; Sen, Ranjan

    2013-01-01

    SUMMARY The immunoglobulin heavy chain (IgH) gene locus undergoes radial re-positioning within the nucleus and locus contraction in preparation for gene recombination. We demonstrate that IgH locus conformation involves two levels of chromosomal compaction. At the first level the locus folds into several multi-looped domains. One such domain at the 3′ end of the locus requires an enhancer, Eμ; two other domains at the 5′ end are Eμ-independent. At the second level, these domains are brought into spatial proximity by Eμ-dependent interactions with specific sites within the VH region. Eμ is also required for radial re-positioning of IgH alleles indicating its essential role in large scale chromosomal movements in developing lymphocytes. Our observations provide a comprehensive view of the conformation of IgH alleles in pro-B cells and the mechanisms by which it is established. PMID:21982154

  20. Molecular and environmental factors governing non-covalent bonding interactions and conformations of phosphorous functionalized γ-cyclodextrin hydrate systems.

    PubMed

    Ivanova, Bojidarka; Spiteller, Michael

    2016-06-01

    Recent strategies in molecular drugs-design shift efforts to nanomedicine. Large supra-molecular inclusion systems are implemented as therapeutics. The sophistication of design is based on major advances of cyclodextrins (CDs) as host molecules. They are friendly towards biological environment. CDs have good (bio)compatibility as well. CDs can form host-guest macromolecular systems incorporating small molecules with suitable shapes due to non-covalent interactions. Innovative strategies yield to polymeric nano-particles; micelles; linear polymers and/or CDs-functionalized dendrimeric nanostructures; nanofibers as well as hydrogels. Attractive are phosphorous containing (bio)matrerials, having high selectivity toward biological active molecules. The non-covalent interactions in aquatic CD-systems contribute to stability of host-guest systems under physiological conditions, determining conformational preferences of host-CD macromolecule and guest small molecular template. In this paper we have reported complementation application of mass spectrometric (MS) and quantum chemical analysis of phosphorous chemically substituted γ-cyclodextrin hydrates γ-CDPO/nH2O (n ∊ [0-14]), studying neutral and polynegatively charged molecules as an effort to describe realistic a representative scale of physiological conditions. The binding affinity and molecular conformations are discussed. The 250 neutral and charged systems (γ-CDPOHm/nH2O, n ∊ [10][0,14], m ∊ [0,15], γ-CDPOH-8/nH2O.8Na(+), and γ-CDPOH-16/nH2O.16Na(+)) in four main domains of non-covalent hydrogen bonding interactions are studied. PMID:26944657

  1. Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA

    SciTech Connect

    Chen, Guo; Mcmahon, Benjamin H; Tung, Chang - Shung

    2008-01-01

    Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from the full-length inactive structure of PrrA we introduced a local disturbance by phosphorylating the conserved aspartic acid residue, Asp-58, in the regulatory domain. A Go-model-type algorithm packaged with AMBER force fields was then applied to simulate the dynamics upon phosphorylation. The MD simulation shows that the phosphorylation of Asp-58 facilitates PrrA, whose inactive state has a compact conformation with a closed interdomain interface, to open up with its interdomain separation being increased by an average of about 1.5 {angstrom} for a simulation of 20 ns. The trans-activation loop, which is completely buried within the interdomain interface in the inactive PrrA, is found to become more exposed with the phosphorylated structure as well. These results provide more structural details of how the phosphorylation of a local aspartate activates PrrA to undergo a global conformational rearrangement toward its extended active state. This work also indicates that MD simulations can serve as a fast tool to unravel the regulation mechanisms of all RRs, which is especially valuable when the structures of full-length active RRs are currently unavailable.

  2. Modular hyperthermostable bacterial endo-β-1,4-mannanase: molecular shape, flexibility and temperature-dependent conformational changes.

    PubMed

    da Silva, Viviam M; Colussi, Francieli; de Oliveira Neto, Mario; Braz, Antonio S K; Squina, Fabio M; Oliveira, Cristiano L P; Garcia, Wanius

    2014-01-01

    Endo-β-1,4-mannanase from Thermotoga petrophila (TpMan) is a hyperthermostable enzyme that catalyzes the hydrolysis of β-1,4-mannoside linkages in various mannan-containing polysaccharides. A recent study reported that TpMan is composed of a GH5 catalytic domain joined by a linker to a carbohydrate-binding domain. However, at this moment, there is no three-dimensional structure determined for TpMan. Little is known about the conformation of the TpMan as well as the role of the length and flexibility of the linker on the spatial arrangement of the constitutive domains. In this study, we report the first structural characterization of the entire TpMan by small-angle X-ray scattering combined with the three-dimensional structures of the individual domains in order to shed light on the low-resolution model, overall dimensions, and flexibility of this modular enzyme at different temperatures. The results are consistent with a linker with a compact structure and that occupies a small volume with respect to its large number of amino acids. Furthermore, at 20°C the results are consistent with a model where TpMan is a molecule composed of three distinct domains and that presents some level of molecular flexibility in solution. Even though the full enzyme has some degree of molecular flexibility, there might be a preferable conformation, which could be described by the rigid-body modeling procedure. Finally, the results indicate that TpMan undergoes a temperature-driven transition between conformational states without a significant disruption of its secondary structure. Our results suggest that the linker can optimize the geometry between the other two domains with respect to the substrate at high temperatures. These studies should provide a useful basis for future biophysical studies of entire TpMan. PMID:24671161

  3. Modular Hyperthermostable Bacterial Endo-β-1,4-Mannanase: Molecular Shape, Flexibility and Temperature-Dependent Conformational Changes

    PubMed Central

    de Oliveira Neto, Mario; Braz, Antonio S. K.; Squina, Fabio M.; Oliveira, Cristiano L. P.; Garcia, Wanius

    2014-01-01

    Endo-β-1,4-mannanase from Thermotoga petrophila (TpMan) is a hyperthermostable enzyme that catalyzes the hydrolysis of β-1,4-mannoside linkages in various mannan-containing polysaccharides. A recent study reported that TpMan is composed of a GH5 catalytic domain joined by a linker to a carbohydrate-binding domain. However, at this moment, there is no three-dimensional structure determined for TpMan. Little is known about the conformation of the TpMan as well as the role of the length and flexibility of the linker on the spatial arrangement of the constitutive domains. In this study, we report the first structural characterization of the entire TpMan by small-angle X-ray scattering combined with the three-dimensional structures of the individual domains in order to shed light on the low-resolution model, overall dimensions, and flexibility of this modular enzyme at different temperatures. The results are consistent with a linker with a compact structure and that occupies a small volume with respect to its large number of amino acids. Furthermore, at 20°C the results are consistent with a model where TpMan is a molecule composed of three distinct domains and that presents some level of molecular flexibility in solution. Even though the full enzyme has some degree of molecular flexibility, there might be a preferable conformation, which could be described by the rigid-body modeling procedure. Finally, the results indicate that TpMan undergoes a temperature-driven transition between conformational states without a significant disruption of its secondary structure. Our results suggest that the linker can optimize the geometry between the other two domains with respect to the substrate at high temperatures. These studies should provide a useful basis for future biophysical studies of entire TpMan. PMID:24671161

  4. The effect of poly(trimethylene carbonate) molecular weight on macrophage behavior and enzyme adsorption and conformation.

    PubMed

    Vyner, Moira C; Li, Anne; Amsden, Brian G

    2014-11-01

    Poly(trimethylene carbonate) (PTMC) with molecular weights greater than 100 kg/mol is known to degrade readily in vivo while PTMC of less than 70 kg/mol is resistant to degradation. The reason for the molecular weight dependent degradation rate of PTMC is unclear, and may be due to differences in macrophage behavior or enzyme adsorption or activity. Macrophage number and production of reactive oxygen species (ROS) and esterase were measured when cultured on 60 and 100 kg/mol PTMC. Cholesterol esterase and lipase were adsorbed to 60 and 100 kg/mol PTMC and mass and viscoelastic properties of the adsorbed enzyme layers were measured. No significant differences were observed in macrophage number or production of degradative species. Significant differences were measured in mass, shear modulus and viscosity of the adsorbed cholesterol esterase layer, suggesting that the cholesterol esterase is adsorbing in a different conformation on the 60 and 100 kg/mol PTMC. Despite similar bulk moduli, the surface modulus of 60 kg/mol PTMC was significantly lower than 100 kg/mol. It is proposed that the difference in surface stiffness and polymer chain flexibility affect the arrangement of water bound to and freed from the polymer chains during adsorption, thus affecting enzymatic adsorption, conformation, and activity. PMID:25109440

  5. Conformational transitions of single polymer adsorption in poor solvent: Wetting transition due to molecular confinement induced line tension.

    PubMed

    Wei, Hsien-Hung; Li, Yen-Ching

    2016-07-01

    We report a theory capable of describing conformational transitions for single polymer adsorption in a poor solvent. We show that an additional molecular confinement effect near the contact line can act exactly like line tension, playing a critical role in the behavior of an absorbed polymer chain. Using this theory, distinct conformational states: desorbed globule (DG), surface attached cap (SAC), and adsorbed lens (AL), can be vividly revealed, resembling the drying-wetting transition of a nanodroplet. But the transitions between these states can behave rather differently from those in the usual wetting transitions. The DG-SAC transition is discrete, occurring at the adsorption threshold when the globule size at the desorbed state is equal to the adsorption blob. The SAC-AL transition is smooth for finite chain lengths, but can change to discontinuous in the infinite chain limit, characterized by the different end-to-end exponent 3/8 and the unique crossover exponent 1/4. Distinctive critical exponents near this transition are also determined, indicating that it is an additional universality class of phase transitions. This work also sheds light on nanodrop spreading, wherein the important role played by line tension might simply be a manifestation of the local molecular confinement near the contact line. PMID:27575170

  6. Conformational transitions of single polymer adsorption in poor solvent: Wetting transition due to molecular confinement induced line tension

    NASA Astrophysics Data System (ADS)

    Wei, Hsien-Hung; Li, Yen-Ching

    2016-07-01

    We report a theory capable of describing conformational transitions for single polymer adsorption in a poor solvent. We show that an additional molecular confinement effect near the contact line can act exactly like line tension, playing a critical role in the behavior of an absorbed polymer chain. Using this theory, distinct conformational states: desorbed globule (DG), surface attached cap (SAC), and adsorbed lens (AL), can be vividly revealed, resembling the drying-wetting transition of a nanodroplet. But the transitions between these states can behave rather differently from those in the usual wetting transitions. The DG-SAC transition is discrete, occurring at the adsorption threshold when the globule size at the desorbed state is equal to the adsorption blob. The SAC-AL transition is smooth for finite chain lengths, but can change to discontinuous in the infinite chain limit, characterized by the different end-to-end exponent 3/8 and the unique crossover exponent 1/4. Distinctive critical exponents near this transition are also determined, indicating that it is an additional universality class of phase transitions. This work also sheds light on nanodrop spreading, wherein the important role played by line tension might simply be a manifestation of the local molecular confinement near the contact line.

  7. Generation of monoclonal antibodies specific of the postfusion conformation of the Pneumovirinae fusion (F) protein.

    PubMed

    Rodríguez, Laura; Olmedillas, Eduardo; Mas, Vicente; Vázquez, Mónica; Cano, Olga; Terrón, María C; Luque, Daniel; Palomo, Concepción; Melero, José A

    2015-11-01

    Paramyxovirus entry into cells requires fusion of the viral and cell membranes mediated by one of the major virus glycoproteins, the fusion (F) glycoprotein which transits from a metastable pre-fusion conformation to a highly stable post-fusion structure during the membrane fusion process. F protein refolding involves large conformational changes of the protein trimer. One of these changes results in assembly of two heptad repeat sequences (HRA and HRB) from each protomer into a six-helix bundle (6HB) motif. To assist in distinguishing pre- and post-fusion conformations of the Pneumovirinae F proteins, and as extension of previous work (Palomo et al., 2014), a general strategy was designed to obtain polyclonal and particularly monoclonal antibodies specific of the 6HB motif of the Pneumovirinae fusion protein. The antibodies reported here should assist in the characterization of the structural changes that the F protein of human metapneumovirus or respiratory syncytial virus experiences during the process of membrane fusion. PMID:26275682

  8. MoFlow: visualizing conformational changes in molecules as molecular flow improves understanding

    PubMed Central

    2015-01-01

    Background Current visualizations of molecular motion use a Timeline-analogous representation that conveys "first the molecule was shaped like this, then like this...". This scheme is orthogonal to the Pathline-like human understanding of motion "this part of the molecule moved from here to here along this path". We present MoFlow, a system for visualizing molecular motion using a Pathline-analogous representation. Results The MoFlow system produces high-quality renderings of molecular motion as atom pathlines, as well as interactive WebGL visualizations, and 3D printable models. In a preliminary user study, MoFlow representations are shown to be superior to canonical representations for conveying molecular motion. Conclusions Pathline-based representations of molecular motion are more easily understood than timeline representations. Pathline representations provide other advantages because they represent motion directly, rather than representing structure with inferred motion. PMID:26361501

  9. Pseudo generators for under-resolved molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bittracher, A.; Hartmann, C.; Junge, O.; Koltai, P.

    2015-09-01

    Many features of a molecule which are of physical interest (e.g. molecular conformations, reaction rates) are described in terms of its dynamics in configuration space. This article deals with the projection of molecular dynamics in phase space onto configuration space. Specifically, we study the situation that the phase space dynamics is governed by a stochastic Langevin equation and study its relation with the configurational Smoluchowski equation in the three different scaling regimes: Firstly, the Smoluchowski equations in non-Cartesian geometries are derived from the overdamped limit of the Langevin equation. Secondly, transfer operator methods are used to describe the metastable behaviour of the system at hand, and an explicit small-time asymptotics is derived on which the Smoluchowski equation turns out to govern the dynamics of the position coordinate (without any assumptions on the damping). By using an adequate reduction technique, these considerations are then extended to one-dimensional reaction coordinates. Thirdly, we sketch three different approaches to approximate the metastable dynamics based on time-local information only.

  10. High-resolution microwave and infrared molecular-beam studies of the conformers of 1,1,2,2-tetrafluoroethane

    SciTech Connect

    Stone, S.C.; Philips, L.A.; Fraser, G.T.; Lovas, F.J.

    1996-12-31

    High-resolution microwave and infrared molecular-beam spectra have been measured for 1,1,2,2-tetrafluorethane (HFC134). For the higher-energy, polar, C{sub 1}-symmetry, gauche conformer, microwave spectra have been recorded for the normal and mono-{sup 13}C isotopomers and analyzed to determine a C-C bond length of 1.512(4) {Angstrom} and a CCF angle of 109.7(3){degrees}. A tunable microwave-sideband CO{sub 2} laser and electric-resonance optothermal spectrometer have been used to measure the infrared spectrum of the {nu}{sub 6}, C-C stretch of the gauche conformer near 906 cm{sup -1}. Microwave-infrared double resonance and precise ground-state combination-differences provided by the microwave measurements guide the assignment of the spectrum. A b- and c-type spectrum is observed and fit to a Watson asymmetric-top Hamiltonian to within the experimental uncertainty of 0.3 MHz. The high quality of the fit and the similarity of the centrifugal distortion constants to the ground-state values indicate that the band is effectively unperturbed. A number of strong unassigned lines are present in the spectrum. These transitions do not display any microwave-infrared double resonance effect. The attribution of these transitions to the nonpolar anti conformer is ruled out since the transition intensities are sensitive to the field strength of the inhomogeneous electric field used to focus the molecules. Pulsed slit-jet diode-laser spectra have been recorded for the {nu}{sub 16}, anti conformer near 1127 cm{sup -1}. An a- and c-type hybrid band is observed consistent with previous low-resolution assignments of this vibration to a B. mode. A total of 522 non-blended transitions were assigned and fit to determine ground- and excited-state constants. The ground-state constants of A = 5134.952(65), B = 3148.277(27), and C = 2067.106(43) MHz are the first experimental determination of rotational constants for this conformer.

  11. GRID3C: Computer program for generation of C type multilevel, three dimensional and boundary conforming periodic grids

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1982-01-01

    A fast computer program, GRID3C, was developed for accurately generating periodic, boundary conforming, three dimensional, consecutively refined computational grids applicable to realistic axial turbomachinery geometries. The method is based on using two functions to generate two dimensional grids on a number of coaxial axisymmetric surfaces positioned between the centerbody and the outer radial boundary. These boundary fitted grids are of the C type and are characterized by quasi-orthogonality and geometric periodicity. The built in nonorthogonal coordinate stretchings and shearings cause the grid clustering in the regions of interest. The stretching parameters are part of the input to GRID3C. In its present version GRID3C can generate and store a maximum of four consecutively refined three dimensional grids. The output grid coordinates can be calculated either in the Cartesian or in the cylindrical coordinate system.

  12. Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.

    PubMed

    Stavrakoudis, Athanassios

    2010-09-01

    Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes. PMID:20412039

  13. Molecular mechanics (MM3) study of the conformations of methyl esters and N, N-dimethylamides of diastereoisomeric 4-cyano-3,4-diphenyl-butanoic acids

    NASA Astrophysics Data System (ADS)

    Ivanov, P. M.

    2000-10-01

    Molecular mechanics (MM3 force field) was used to examine an unexpected observation by NMR for a preference of conformations with synclinal protons around the C(3)-C(4) bond in methyl esters and dimethylamides of diastereoisomeric 4-cyano-3,4-diphenyl-butanoic acids. After the reoptimization of three torsional parameters, related to structural units containing a cyano group, we obtained a good correlation between the MM3 computed populations of the conformations and the estimates from vicinal coupling constants. The electrostatic interactions have the decisive contribution for lowering the energies of the preferred conformations.

  14. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    PubMed

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID:26963288

  15. Molecular docking sites designed for the generation of highly crystalline covalent organic frameworks

    NASA Astrophysics Data System (ADS)

    Ascherl, Laura; Sick, Torben; Margraf, Johannes T.; Lapidus, Saul H.; Calik, Mona; Hettstedt, Christina; Karaghiosoff, Konstantin; Döblinger, Markus; Clark, Timothy; Chapman, Karena W.; Auras, Florian; Bein, Thomas

    2016-04-01

    Covalent organic frameworks (COFs) formed by connecting multidentate organic building blocks through covalent bonds provide a platform for designing multifunctional porous materials with atomic precision. As they are promising materials for applications in optoelectronics, they would benefit from a maximum degree of long-range order within the framework, which has remained a major challenge. We have developed a synthetic concept to allow consecutive COF sheets to lock in position during crystal growth, and thus minimize the occurrence of stacking faults and dislocations. Hereby, the three-dimensional conformation of propeller-shaped molecular building units was used to generate well-defined periodic docking sites, which guided the attachment of successive building blocks that, in turn, promoted long-range order during COF formation. This approach enables us to achieve a very high crystallinity for a series of COFs that comprise tri- and tetradentate central building blocks. We expect this strategy to be transferable to a broad range of customized COFs.

  16. Influence of sodium alginate pretreated by ultrasound on papain properties: Activity, structure, conformation and molecular weight and distribution.

    PubMed

    Feng, Liping; Cao, Yanping; Xu, Duoxia; You, Sasa; Han, Fu

    2016-09-01

    The aim of the study was to investigate the impact of sodium alginate (ALG) pretreated by ultrasound on the enzyme activity, structure, conformation and molecular weight and distribution of papain. ALG solutions were pretreated with ultrasound at varying power (0.05, 0.15, 0.25, 0.35, 0.45W/cm(2)), 135kHz, 50°C for 20min. The maximum relative activity of papain increased by 10.53% when mixed with ALG pretreated by ultrasound at 0.25W/cm(2), compared with the untreated ALG. The influence of ultrasound pretreated ALG on the conformation and secondary structure of papain were assessed by fluorescence spectroscopy and circular dichroism spectroscopy. The fluorescence spectra revealed that ultrasound pretreated ALG increased the number of tryptophan on papain surface, especially at 0.25W/cm(2). It indicated that ultrasound pretreatment induced molecular unfolding, causing the exposure of more hydrophobic groups and regions from inside to the outside of the papain molecules. Furthermore, ultrasound pretreated ALG resulted in minor changes in the secondary structure of the papain. The content of α-helix was slightly increased after ultrasound pretreatment and no significant change was observed at different ultrasound powers. ALG pretreated by ultrasound enhanced the stability of the secondary structure of papain, especially at 0.25W/cm(2). The free sulfhydryl (SH) content of papain was slightly increased and then decreased with the increase of ultrasonic power. The maximum content of free SH was observed at 0.25W/cm(2), under which the content of the free SH increased by 6.36% compared with the untreated ALG. Dynamic light scattering showed that the effect of ultrasound treatment was mainly the homogenization of the ALG particles in the mixed dispersion. The gel permeation chromatography coupled with the multi-angle laser light scattering photometer analysis showed that the molecular weight (Mw) of papain/ALG was decreased and then increased with the ultrasonic

  17. Molecular conformation and orientational order in nCB liquid crystals

    NASA Astrophysics Data System (ADS)

    Kobinata, Shunsuke; Kobayashi, Takamichi; Yoshida, Hiroshi; Chandani, A. D. L.; Maeda, Shiro

    1986-08-01

    A resonance Raman probe method for determining the second and fourth orientational order parameters ( P¯2 and P¯4) in liquid crystals is described. The method was applied to a series of nematic nCB near the nematic—isotropic transition temperature, using all trans β-carotene as a resonant probe. Both P¯2 and P¯4, thus obtained show a distinct even—odd effect, that is, zigzag change of the parameter value against the length of alkyl end chain. The origin of the even—odd effect was investigated by the mean field theory, taking the conformation variety of end chain into account following the method of Marcelja. On the basis of calculation, the function of the alkyl chain in the formation of the liquid crystalline state is discussed.

  18. Molecular conformational analysis, vibrational spectra, NBO, NLO analysis and molecular docking study of bis[(E)-anthranyl-9-acrylic]anhydride based on density functional theory calculations.

    PubMed

    Mary, Y Sheena; Panicker, C Yohannan; Thiemann, Thies; Al-Azani, Mariam; Al-Saadi, Abdulaziz A; Van Alsenoy, C; Raju, K; War, Javeed Ahmad; Srivastava, S K

    2015-12-01

    FT-IR and FT-Raman spectra of bis[(E)-anthranyl-9-acrylic]anhydride were recorded and analyzed. The conformational behavior is also investigated. The vibrational wave numbers were calculated using density functional theory (DFT) quantum chemical calculations. The data obtained from wave number calculations are used to assign vibrational bands obtained in Infrared and Raman spectra. Potential energy distribution was done using GAR2PED program. The geometrical parameters are compared with related structures. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using Natural Bonding Orbital (NBO) analysis. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) analysis are used to determine the charge transfer within the molecule. Molecular Electrostatic Potential (MEP) was performed by the DFT method. The calculated first hyperpolarizability of the title compound is comparable with the reported values of similar derivatives and is 4.23 times that of the standard nonlinear optical (NLO) material urea and the title compound and its derivatives are an attractive object for future studies of nonlinear optical properties. To evaluate the in silico antitumor activity of the title compound molecular docking studies were carried out against protein Bcl-xL. The (1)H-NMR spectrum is also reported. PMID:26143327

  19. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

    NASA Astrophysics Data System (ADS)

    De Simone, Alfonso; Derreumaux, Philippe

    2010-04-01

    The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

  20. Effect of graphene oxide on the conformational transitions of amyloid beta peptide: A molecular dynamics simulation study.

    PubMed

    Baweja, Lokesh; Balamurugan, Kanagasabai; Subramanian, Venkatesan; Dhawan, Alok

    2015-09-01

    The interactions between nanomaterials (NMs) and amyloid proteins are central to the nanotechnology-based diagnostics and therapy in neurodegenerative disorders such as Alzheimer's and Parkinson's. Graphene oxide (GO) and its derivatives have shown to modulate the aggregation pattern of disease causing amyloid beta (Aβ) peptide. However, the mechanism is still not well understood. Using molecular dynamics simulations, the effect of graphene oxide (GO) and reduced graphene oxide (rGO) having carbon:oxygen ratio of 4:1 and 10:1, respectively, on the conformational transitions (alpha-helix to beta-sheet) and the dynamics of the peptide was investigated. GO and rGO decreased the beta-strand propensity of amino acid residues in Aβ. The peptide displayed different modes of adsorption on GO and rGO. The adsorption on GO was dominated by electrostatic interactions, whereas on rGO, both van der Waals and electrostatic interactions contributed in the adsorption of the peptide. Our study revealed that the slight increase in the hydrophobic patches on rGO made it more effective inhibitor of conformational transitions in the peptide. Alpha helix-beta sheet transition in Aβ peptide could be one of the plausible mechanism by which graphene oxide may inhibit amyloid fibrillation. PMID:26275931

  1. Molecular Dynamics Simulation on the Conformational Transition of the Mad2 Protein from the Open to the Closed State

    PubMed Central

    Li, Chaoqun; Zhu, Yanyan; Wang, Yan; Chen, Guangju

    2014-01-01

    The Mad2 protein, with two distinct conformations of open- and closed-states, is a key player in the spindle checkpoint. The closed Mad2 state is more active than the open one. We carried out conventional and targeted molecular dynamics simulations for the two stable Mad2 states and their conformational transition to address the dynamical transition mechanism from the open to the closed state. The intermediate structure in the transition process shows exposure of the β6 strand and an increase of space around the binding sites of β6 strand due to the unfolding of the β7/8 sheet and movement of the β6/4/5 sheet close to the αC helix. Therefore, Mad2 binding to the Cdc20 protein in the spindle checkpoint is made possible. The interconversion between these two states might facilitate the functional activity of the Mad2 protein. Motion correlation analysis revealed the allosteric network between the β1 strand and β7/8 sheet via communication of the β5-αC loop and the β6/4/5 sheet in this transition process. PMID:24690997

  2. Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction

    PubMed Central

    Torres, Rhonda A.; Bruice, Thomas C.

    1998-01-01

    We have performed molecular dynamics (MD) calculations by using one of the recently solved crystal structures of a hammerhead ribozyme. By rotating the α, β, γ, δ, ɛ, and ζ torsion angles of the phosphate linkage of residue 17, the nucleobase at the cleavage site was slightly rotated out of the active site toward the solution. Unconstrained MD simulations exceeding 1 ns were performed on this starting structure solvated in water with explicit counter ions and two Mg2+ ions at the active site. Our results reveal that near attack conformations consistently were formed in the simulation. These near attack conformations are characterized by assumption of the 2′-hydroxyl to a near in-line position for attack on the -O-(PO2−)-O- phosphorous. Also during the time course of the MD study, one Mg2+ moved immediately to associate with a pro-R phosphate oxygen in the conserved core region, and the second Mg2+ remained associated with the pro-R oxygen on the phosphate linkage undergoing hydrolysis. These results are in accord with a one-metal ion mechanism of catalysis and give insight into the possible roles of many of the conserved residues in the ribozyme. PMID:9736692

  3. A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins.

    PubMed

    Poveda, L A; Ferro, V R; García de la Vega, J M; González-Jonte, R H

    2001-02-01

    Nonplanar saddled (sad) ruffled (ruf) and domed (dom) conformations of the Mg-porphyrin (MgP) macrocycle in several degrees of deformation have been computed. These symmetrical distortion modes were induced in unsubstituted macrocycle using molecular definitions for calculations which permits us to achieve a systematical variation of the nonplanarity varying only a convenient geometrical parameter of the molecule. Series of nonplanar macrocycles like those synthesized in previous works employing peripheral substitutions are obtained. The procedure here used to induce deformations gives the possibility of investigating the modulator role of the out-of-plane distortions on the geometry and electronic properties of the porphyrin avoiding additional influences due to the substituents or the surrounding protein scaffolding. PMID:11272704

  4. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    NASA Astrophysics Data System (ADS)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  5. Order and conformation of biphenyl in cyanobiphenyl liquid crystals: a combined atomistic molecular dynamics and 1H NMR study.

    PubMed

    Pizzirusso, Antonio; Di Pietro, Maria Enrica; De Luca, Giuseppina; Celebre, Giorgio; Longeri, Marcello; Muccioli, Luca; Zannoni, Claudio

    2014-05-19

    The alignment of biphenyl (2P) in the liquid-crystal phases of 4-n-pentyl-4'-cyanobiphenyl (5CB) and 4-n-octyl-4'-cyanobiphenyl (8CB) is investigated by using a combination of predictive atomistic molecular dynamics (MD) simulations and (1)H liquid-crystal nuclear magnetic resonance (LXNMR) residual dipolar coupling measurements. A detailed comparison and validation of the MD results with LXNMR is provided, showing a good agreement between the simulated and experimental dipolar couplings at the same reduced temperature. MD is then used to examine the location of 2P in the smectic phase, which is unavailable to LXNMR, and 2P is found to be rather uniformly distributed. The combination of MD and NMR spectroscopy provides detailed information about the order, interconnection between orientation and conformation, local positional order, and interactions with the liquid-crystalline solvent. PMID:24692106

  6. The Dynamic Conformational Cycle of the Group I Chaperonin C-Termini Revealed via Molecular Dynamics Simulation

    PubMed Central

    Dalton, Kevin M.; Frydman, Judith; Pande, Vijay S.

    2015-01-01

    Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins. PMID:25822285

  7. The dynamic conformational cycle of the group I chaperonin C-termini revealed via molecular dynamics simulation.

    PubMed

    Dalton, Kevin M; Frydman, Judith; Pande, Vijay S

    2015-01-01

    Chaperonins are large ring shaped oligomers that facilitate protein folding by encapsulation within a central cavity. All chaperonins possess flexible C-termini which protrude from the equatorial domain of each subunit into the central cavity. Biochemical evidence suggests that the termini play an important role in the allosteric regulation of the ATPase cycle, in substrate folding and in complex assembly and stability. Despite the tremendous wealth of structural data available for numerous orthologous chaperonins, little structural information is available regarding the residues within the C-terminus. Herein, molecular dynamics simulations are presented which localize the termini throughout the nucleotide cycle of the group I chaperonin, GroE, from Escherichia coli. The simulation results predict that the termini undergo a heretofore unappreciated conformational cycle which is coupled to the nucleotide state of the enzyme. As such, these results have profound implications for the mechanism by which GroE utilizes nucleotide and folds client proteins. PMID:25822285

  8. Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Brzozowski, K.; Stawikowski, M.; Ślusarz, R.; Sikorska, E.; Lesner, A.; Łęgowska, A.; Rolka, K.

    2015-11-01

    Trypsin inhibitor SFTI-1 is the smallest and the most potent among BBI inhibitors. It is also an interesting object for SAR studies since it is cyclic 14 amino acid molecule which additionally contains disulfide bridge. We showed that elimination of head-to-tail cycliztion did not influence its activity. Moreover peptoid monomers of Nlys and Nphe introduced in the substrate specificity P1 position of monocyclic SFTI-1 preserved trypsin and chymotripsin inhibitory activity respectively and made P1-P1‧ bond proteolytically stable. These findings motivated us to perform conformational analysis of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy and molecular dynamics calculations. Obtained structure occurred to be in a good agreement with published structures for wild-type SFTI-1, its monocyclic analog with disulfide bridge only as well as one containing Nlys peptoid monomer in P1 position.

  9. Interfacial molecular interactions based on the conformation recognition between the insoluble antitumor drug AD-1 and DSPC.

    PubMed

    Yin, Tian; Cao, Xiuxiu; Liu, Xiaolin; Wang, Jian; Shi, Caihong; Su, Jia; Zhang, Yu; Gou, Jingxin; He, Haibing; Guo, Haiyan; Tang, Xing; Zhao, Yuqing

    2016-10-01

    In this study, molecular interactions between the anti-cancer agent 20(R)-25-methoxyl-dammarane-3β, 12β, 20-triol (AD-1) and phospholipid 1,2-Distearoyl-sn-glycero-3-phosphocholine (DSPC) were investigated using the Langmuir film balance technique. The characteristics of binary Langmuir monolayers consisting of DSPC and AD-1 were conducted on the basis of the surface pressure-area per molecule (π-A) isotherms. It was found that the drug was able to become efficiently inserted into preformed DSPC monolayers, indicating a preferential interaction between AD-1 and DSPC. For the examined lateral pressure at 20mN/m, the largest negative values of ΔGex were found for the AD-1/DSPC monolayer, which should be the most stable. Based on the calculated values of ΔGex, we found that the AD-1/DSPC systems exhibited the best mixed characteristics when the molar fraction of the AD-1 was 0.8; at that relative concentration, the AD-1 molecules can mix better and interact with the phospholipid molecules. In addition, the drug-DSPC binary supramolecular structure was also deposited on the mica plates as shown by atomic force microscopy (AFM). Finally, molecular docking calculations explained satisfactorily that, based on the conformations interactions (conformation recognition), even at an AD-1/DSPC molar ratio as high as 8:2, the interfacial stabilization of the AD-1/DSPC system was fairly strong due to hydrophobic interactions. A higher loading capacity of DSPC might be possible, as it is associated with a more flexible geometrical environment, which allows these supramolecular structures to accept larger increases in drug loading upon steric binding. PMID:27469574

  10. High-Resolution Microwave and Infrared Molecular Beam Studies of the Conformers of 1, 1, 2, 2-Tetrafluoroethane

    SciTech Connect

    Stone, Steven C.; Philips, Laura A.; Fraser, Gerry; Lovas, Fj; Xu, Li-Hong; Sharpe, Steven W.)

    1998-01-01

    High-resolution microwave and infrared molecular-beam spectra have been measure for 1,1,2,2-tetraflouroethane (HFC134). For the higher energy, polar, C2 symmetry, gauche conformer, microwave spectra have been recorded for the normal and mono-13C isotopomers and analyzed to determine a C-C bond length of 1.512(4)?, in good agreement with a recent ab initio value (MP2/6-31**) of 1.515?[S. Papasavva, K.H. Illinger, and J.E. Kenny, J. Phys. Chem 100 10100-10110(1996)]. A tunable microwave-sideband CO2 laser and electric-resonance optethermal spectrometer have been used to measure the infrared spectrum of the v6, C-C stretch of the gauche conformer near 906 cm-1. Microwave-infrared double resonance and precise ground state combination differences provided by the microwave measurements guide the assignment of the spectrum. The observation of a c-type spectrum definitively establishes that the upper state vibration is of A symmetry in the C2 point group. The spectrum is fit to a Watson asymmetric-top Hamiltonian to a standard deviation of 0.24 MHz. A weak perturbation shifts the line positions for transitions near J=Kc=20 by as much as 12 MHz. The identity of the perturber is unknown. Pulsed slit-jet diode-laser spectra have been recorded for the v16 vibration of the anti conformer near 1127 cm-1. An a- and c-type hybrid band is observed, consistent with a Bu symmetry mode. Previous low-resolution studies have attributed the 1127-cm-1 mode to either a Bu or an Au symmetry vibration. A total of 522 nonblended transitions were assigned and fit to determine ground and excited state constants. The ground state constants of A=52 5.952(65) MHz, B= 3148.277(27) MHz, and C= 2067.106(43) MHz are the first experimental determinations of the rotational constants for this conformer. Here, type A standard uncertainties are given in the parenthese.

  11. Molecular Breeding for Improved Second Generation Bioenergy Crops.

    PubMed

    Allwright, Mike R; Taylor, Gail

    2016-01-01

    There is increasing urgency to develop and deploy sustainable sources of energy to reduce our global dependency on finite, high-carbon fossil fuels. Lignocellulosic feedstocks, used in power and liquid fuel generation, are valuable sources of non-food plant biomass. They are cultivated with minimal inputs on marginal or degraded lands to prevent competition with arable agriculture and offer significant potential for sustainable intensification (the improvement of yield without the necessity for additional inputs) through advanced molecular breeding. This article explores progress made in next generation sequencing, advanced genotyping, association genetics, and genetic modification in second generation bioenergy production. Using poplar as an exemplar where most progress has been made, a suite of target traits is also identified giving insight into possible routes for crop improvement and deployment in the immediate future. PMID:26541073

  12. Structural and spectroscopic properties of the second generation phosphorus-viologen “molecular asterisk”

    NASA Astrophysics Data System (ADS)

    Furer, V. L.; Vandukov, A. E.; Katir, N.; Majoral, J. P.; El Kadib, A.; Caminade, A. M.; Bousmina, M.; Kovalenko, V. I.

    2013-11-01

    The FTIR and FT Raman spectra of the second generation phosphorus-viologen “molecular asterisk” G2 built from cyclotriphosphazene core with 12 viologen units and 6 terminal phosphonate groups have been recorded and analyzed. The experimental X-ray data of 1,1-bis(4-formylbenzyl)-4,4‧-bipyridinium bis(hexaflurophosphate) was used in molecular modeling studies. The optimization of isolated 1,1-bis(4-formylbenzyl)-4,4‧-bipyridinium (BFBP) molecule without counter ions PF6- does not lead to significant changes of dihedral angles, thus the molecular conformation does not depend on interactions with the counter ions. The structural optimization and normal mode analysis were performed for G2 on the basis of the density functional theory (DFT). The calculated geometrical parameters and harmonic vibrational frequencies are predicted in a good agreement with the experimental data. It was found that G2 has a kind of “egg timer” structure with planar Osbnd C6H4sbnd CHdbnd Nsbnd N(CH3)sbnd fragments and slightly non-planar cyclotriphosphazene core. The experimental IR and Raman spectra of G2 were interpreted by means of potential energy distribution.

  13. Small Molecules Detected by Second-Harmonic Generation Modulate the Conformation of Monomeric α-Synuclein and Reduce Its Aggregation in Cells*

    PubMed Central

    Moree, Ben; Yin, Guowei; Lázaro, Diana F.; Munari, Francesca; Strohäker, Timo; Giller, Karin; Becker, Stefan; Outeiro, Tiago F.; Zweckstetter, Markus; Salafsky, Joshua

    2015-01-01

    Proteins are structurally dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. Here we applied a second-harmonic generation-based technique for studying protein conformation in solution and in real time to the intrinsically disordered, Parkinson disease related protein α-synuclein. From a fragment library, we identified small molecule modulators that bind to monomeric α-synuclein in vitro and significantly reduce α-synuclein aggregation in a neuronal cell culture model. Our results indicate that the conformation of α-synuclein is linked to the aggregation of protein in cells. They also provide support for a therapeutic strategy of targeting specific conformations of the protein to suppress or control its aggregation. PMID:26396193

  14. Structures of the NLRP14 pyrin domain reveal a conformational switch mechanism regulating its molecular interactions

    SciTech Connect

    Eibl, Clarissa; Hessenberger, Manuel; Wenger, Julia; Brandstetter, Hans

    2014-07-01

    Pyrin domains (PYDs) recruit downstream effector molecules in NLR signalling. A specific charge-relay system suggests a the formation of a signalling complex involving a PYD dimer. The cytosolic tripartite NLR receptors serve as important signalling platforms in innate immunity. While the C-terminal domains act as sensor and activation modules, the N-terminal death-like domain, e.g. the CARD or pyrin domain, is thought to recruit downstream effector molecules by homotypic interactions. Such homotypic complexes have been determined for all members of the death-domain superfamily except for pyrin domains. Here, crystal structures of human NLRP14 pyrin-domain variants are reported. The wild-type protein as well as the clinical D86V mutant reveal an unexpected rearrangement of the C-terminal helix α6, resulting in an extended α5/6 stem-helix. This reordering mediates a novel symmetric pyrin-domain dimerization mode. The conformational switching is controlled by a charge-relay system with a drastic impact on protein stability. How the identified charge relay allows classification of NLRP receptors with respect to distinct recruitment mechanisms is discussed.

  15. Co-conformational Exchange Triggered by Molecular Recognition in a Di(acylamino)pyridine-Based Molecular Shuttle Containing Two Pyridine Rings at the Macrocycle.

    PubMed

    Martinez-Cuezva, Alberto; Carro-Guillen, Fernando; Pastor, Aurelia; Marin-Luna, Marta; Orenes, Raul-Angel; Alajarin, Mateo; Berna, Jose

    2016-06-17

    We describe the incorporation of endo-pyridine units into the tetralactam ring of di(acylamino)pyridine-based rotaxanes. This macrocycle strongly associates with the linear interlocked component as confirmed by X-ray diffraction studies of rotaxane 2 b. Dynamic NMR studies of 2 b in solution revealed a rotational energy barrier that was higher than that of the related rotaxane 2 a, which lacks of pyridine rings in the macrocycle. The macrocycle distribution of the molecular shuttle 4 b, containing two endo-pyridine rings, shows that the major co-conformer is that with the cyclic component sitting over the di(acylamino)pyridine station. DFT calculations also support the marked preference of the ring for occupying the heterocyclic binding site. The association of N-hexylthymine with the di(acylamino)pyridine binding site of 4 b led to the formation of a rare 'S'-shaped co-conformer in which the tetralactam ring interacts simultaneously with both stations of the thread. PMID:26698891

  16. The role of conformational selection in the molecular recognition of the wild type and mutants XPA67-80 peptides by ERCC1.

    PubMed

    Fadda, Elisa

    2015-07-01

    Molecular recognition is a fundamental step in the coordination of biomolecular pathways. Understanding how recognition and binding occur between highly flexible protein domains is a complex task. The conformational selection theory provides an elegant rationalization of the recognition mechanism, especially valid in cases when unstructured protein regions are involved. The recognition of a poorly structured peptide, namely XPA67-80 , by its target receptor ERCC1, falls in this challenging study category. The microsecond molecular dynamics (MD) simulations, discussed in this work, show that the conformational propensity of the wild type XPA67-80 peptide in solution supports conformational selection as the key mechanism driving its molecular recognition by ERCC1. Moreover, all the mutations of the XPA67-80 peptide studied here cause a significant increase of its conformational disorder, relative to the wild type. Comparison to experimental data suggests that the loss of the recognized structural motifs at the microscopic time scale can contribute to the critical decrease in binding observed for one of the mutants, further substantiating the key role of conformational selection in recognition. Ultimately, because of the high sequence identity and analogy in binding, it is conceivable that the conclusions of this study on the XPA67-80 peptide also apply to the ERCC1-binding domain of the XPA protein. PMID:25973722

  17. Deleting the Redundant TSH Receptor C-Peptide Region Permits Generation of the Conformationally Intact Extracellular Domain by Insect Cells.

    PubMed

    Chen, Chun-Rong; Salazar, Larry M; McLachlan, Sandra M; Rapoport, Basil

    2015-07-01

    The TSH receptor (TSHR) extracellular domain (ECD) comprises a N-terminal leucine-rich repeat domain and an hinge region (HR), the latter contributing to ligand binding and critical for receptor activation. The crystal structure of the leucine-rich repeat domain component has been solved, but previous attempts to generate conformationally intact complete ECD or the isolated HR component for structural analysis have failed. The TSHR HR contains a C-peptide segment that is removed during spontaneous TSHR intramolecular cleavage into disulfide linked A- and B-subunits. We hypothesized that deletion of the redundant C-peptide would overcome the obstacle to generating conformationally intact TSHR ECD protein. Indeed, lacking the C-peptide region, the TSHR ECD (termed ECD-D1) and the isolated HR (termed HR-D1) were secreted into medium of insect cells infected with baculoviruses coding for these modified proteins. The identities of TSHR ECD-D1 and HR-D1 were confirmed by ELISA and immunoblotting using TSHR-specific monoclonal antibodies. The TSHR-ECD-D1 in conditioned medium was folded correctly, as demonstrated by its ability to inhibit radiolabeled TSH binding to the TSH holoreceptor. The TSHR ECD-D1 purification was accomplished in a single step using a TSHR monoclonal antibody affinity column, whereas the HR-D1 required a multistep protocol with a low yield. In conclusion, we report a novel approach to generate the TSHR ECD, as well as the isolated HR in insect cells, the former in sufficient amounts for structural studies. However, such studies will require previous complexing of the ECD with a ligand such as TSH or a thyroid-stimulating antibody. PMID:25860033

  18. Conformationally Constrained Penta(hetero)cyclic Molecular Architectures via Photoassisted Diversity-Oriented Synthesis

    PubMed Central

    Umstead, Weston J.; Mukhina, Olga A.

    2015-01-01

    Intramolecular cycloadditions of photogenerated azaxylylenes provide access to unprecedented polyheterocyclic scaffolds, suitable for subsequent postphotochemical modifications to further grow molecular complexity. Here we explore approaches to rapid “assembly” of novel photoprecursors with nitrogen/oxygen-rich tethers capable of producing potential pharmacophores and also compatible with subsequent 1,3-dipolar cycloadditions to furnish pentacyclic heterocycles with new structural cores, minimal number of rotatable bonds, and a high content of sp3 hybridized carbons. The modular “assembly” of the photoprecursors and potential variety of postphotochemical modifications of primary photoproducts provide framework for combinatorial implementation of this synthetic strategy. PMID:26257575

  19. Viscoelasticity Enhancement of Surfactant Solutions Depends on Molecular Conformation: Influence of Surfactant Headgroup Structure and Its Counterion.

    PubMed

    Lutz-Bueno, Viviane; Pasquino, Rossana; Liebi, Marianne; Kohlbrecher, Joachim; Fischer, Peter

    2016-05-01

    During the anisotropic growth from globular to wormlike micelles, the basic interactions among distinct parts of the surfactant monomer, its counterion, and additives are fundamental to tune molecular self-assembly. We investigate the addition of sodium salicylate (NaSal) to hexadecyltrimethylammonium chloride and bromide (CTAC and CTAB), 1-hexadecylpyridinium chloride and bromide (CPyCl and CPyBr), and benzyldimethylhexadecylammonium chloride (BDMC), which have the same hydrophobic tail. Their potential to enhance viscoelasticity by anisotropic micellar growth upon salt addition was compared in terms of (i) the influence of the headgroup structure, and (ii) the influence of surfactant counterion type. Employing proton nuclear magnetic resonance ((1)H NMR), we focused on the molecular conformation of surfactant monomers in the core and polar shell regions of the micelles and their interactions with increasing concentration of NaSal. The viscoelastic response was investigated by rotational and oscillatory rheology. We show that micellar growth rates can be tuned by varying the flexibility and size of the surfactant headgroup as well as the dissociation degree of the surfactant counterion, which directly influences the strength of headgroup-counterion pairing. As a consequence, the morphological transitions depend directly on charge neutralization by electrostatic screening. For example, the amount of salt necessary to start the rodlike-to-wormlike micelle growth depends directly on the number of dissociated counterions in the polar shell. PMID:27081871

  20. Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel

    PubMed Central

    Ulmschneider, Martin B.; Bagnéris, Claire; McCusker, Emily C.; DeCaen, Paul G.; Delling, Markus; Clapham, David E.; Ulmschneider, Jakob P.; Wallace, B. A.

    2013-01-01

    The crystal structure of the open conformation of a bacterial voltage-gated sodium channel pore from Magnetococcus sp. (NaVMs) has provided the basis for a molecular dynamics study defining the channel’s full ion translocation pathway and conductance process, selectivity, electrophysiological characteristics, and ion-binding sites. Microsecond molecular dynamics simulations permitted a complete time-course characterization of the protein in a membrane system, capturing the plethora of conductance events and revealing a complex mixture of single and multi-ion phenomena with decoupled rapid bidirectional water transport. The simulations suggest specific localization sites for the sodium ions, which correspond with experimentally determined electron density found in the selectivity filter of the crystal structure. These studies have also allowed us to identify the ion conductance mechanism and its relation to water movement for the NavMs channel pore and to make realistic predictions of its conductance properties. The calculated single-channel conductance and selectivity ratio correspond closely with the electrophysiology measurements of the NavMs channel expressed in HEK 293 cells. The ion translocation process seen in this voltage-gated sodium channel is clearly different from that exhibited by members of the closely related family of voltage-gated potassium channels and also differs considerably from existing proposals for the conductance process in sodium channels. These studies simulate sodium channel conductance based on an experimentally determined structure of a sodium channel pore that has a completely open transmembrane pathway and activation gate. PMID:23542377

  1. Thermally induced irreversible conformational changes in collagen probed by optical second harmonic generation and laser-induced fluorescence.

    PubMed

    Theodossiou, T; Rapti, G S; Hovhannisyan, V; Georgiou, E; Politopoulos, K; Yova, D

    2002-01-01

    Irreversible thermal conformational changes induced to collagen have been studied by optical methods. More specifically, second harmonic generation (SHG) from incident nanosecond Ng:YAG 1064 nm radiation and laser-induced fluorescence by 337 nm, pulsed nanosecond nitrogen laser excitation, at 405, 410 and 415 nm emission wavelengths were registered at eight temperatures (40 degrees, 50 degrees, 55 degrees, 60 degrees, 65 degrees, 70 degrees, 75 degrees and 80 degrees C) and normalised with respect to the corresponding values at the ambient temperature of 30 degrees C. The heating protocol used in this work, was selected to monitor only permanent changes reflecting in the optical properties of the samples under investigation. In this context, the SHG, directly related to the collagen fibril population in triple helix conformation, indicated on irreversible phase transition around 64 degrees C. On the other hand fluorescence related to the destruction of cross-linked chromophores in collagen, some of which are related to the triple helix tertiary structure, also indicated a permanent phase transition around 63 degrees C. These results are in agreement with previous results from studies with differential scanning calorimetry. However SHG and fluorescence, being non-invasive optical methods are expected to have a significant impact in the fields of laser ablative surgery and laser tissue welding. PMID:11845366

  2. On the use of Schwarz-Christoffel conformal mappings to the grid generation for global ocean models

    NASA Astrophysics Data System (ADS)

    Xu, S.; Wang, B.; Liu, J.

    2015-10-01

    In this article we propose two grid generation methods for global ocean general circulation models. Contrary to conventional dipolar or tripolar grids, the proposed methods are based on Schwarz-Christoffel conformal mappings that map areas with user-prescribed, irregular boundaries to those with regular boundaries (i.e., disks, slits, etc.). The first method aims at improving existing dipolar grids. Compared with existing grids, the sample grid achieves a better trade-off between the enlargement of the latitudinal-longitudinal portion and the overall smooth grid cell size transition. The second method addresses more modern and advanced grid design requirements arising from high-resolution and multi-scale ocean modeling. The generated grids could potentially achieve the alignment of grid lines to the large-scale coastlines, enhanced spatial resolution in coastal regions, and easier computational load balance. Since the grids are orthogonal curvilinear, they can be easily utilized by the majority of ocean general circulation models that are based on finite difference and require grid orthogonality. The proposed grid generation algorithms can also be applied to the grid generation for regional ocean modeling where complex land-sea distribution is present.

  3. Generation and reception of ultrasonic guided waves in composite plates using conformable piezoelectric transmitters and optical-fiber detectors.

    PubMed

    Gachagan, A; Hayward, G; McNab, A; Reynolds, P; Pierce, S G; Philp, W R; Culshaw, B

    1999-01-01

    A condition monitoring nondestructive evaluation (NDE) system, combining the generation of ultrasonic Lamb waves in thin composite plates and their subsequent detection using an embedded optical fiber system is described. The acoustic source is of low profile with respect to the composite plate thickness, surface conformable, and able to efficiently launch a known Lamb wave mode, at operating frequencies between 100 and 500 kHz, over typical propagation distances of 100 to 500 mm. It incorporates both piezocomposite technology and interdigital design techniques to generate the fundamental symmetrical Lamb wave mode in both metallic and carbon-fiber composite plates. Linear systems and finite element modeling techniques have been used to evaluate the operation of the transducer structure, and this is supplemented by experimental verification of the simulated data. An optical fiber, either bonded to the surface or embedded across the length of the composite plate samples, is used to detect the propagating ultrasonic Lamb waves. Single mode silica fiber has been used in conjunction with a portable 633 nm Mach-Zehnder interferometer for signal demodulation and subsequent data acquisition. This hybrid system is shown to generate and detect the fundamental symmetrical Lamb wave (s(0)) in both carbon-fiber and glass-fiber reinforced composite plates. Importantly, the system signal-to-noise ratio (SNR) associated with the acoustic source compares favorably with s(0) Lamb wave generation using a conventional transducer and angled perspex wedge arrangement. PMID:18238400

  4. An examination of polymorphic stability and molecular conformational flexibility as a function of crystal size associated with the nucleation and growth of benzophenone.

    PubMed

    Hammond, Robert B; Pencheva, Klimentina; Roberts, Kevin J

    2007-01-01

    The polymorphic behaviour of the aromatic ketone, benzophenone, which is a conformationally flexible molecule and forms crystal structures dominated by van der Waals intermolecular interactions, is examined. Crystallization of this material from the undercooled molten state yields the two known polymorphic forms, i.e. the stable alpha-form and the metastable beta-form. The relative, energetic stabilities are examined using both crystal lattice and molecular conformational modelling techniques. Examination of nano-sized faceted molecular clusters of these forms, with cluster sizes ranging from 3 to 100 molecules, reveals that at very small cluster size (< 5 molecules) the relative energetic stability of clusters representative for the two forms become very similar, indicating that for high melting undercooling (i.e. small critical cluster size for nucleation) crystallization of the metastable beta-phase becomes more likely. Detailed analysis of the variation in molecular conformations within the simulated molecular clusters reveals more disordered three-dimensional structures at small compared to larger cluster sizes. The conformational disorder was found to be higher for the metastable beta-form. This observation, together with the lower stability of clusters for this form is indicative of the difficulty in achieving crystallization of the metastable beta-form from the melt, which requires a considerable undercooling. PMID:17955805

  5. Molecular conformation changes of PET films under high-energy Ar ion bombardment

    NASA Astrophysics Data System (ADS)

    Liu, Changlong; Jin, Yunfan; Zhu, Zhiyong; Sun, Youmei; Hou, Mingdong; Wang, Zhiguang; Wang, Yanbin; Zhang, Chonghong; Chen, Xiaoxi; Liu, Jie; Li, Baoquan

    2000-06-01

    Investigation of the surface modification in molecular structure of semicrystalline polyethylene terephthalate (PET) films induced by Ar ion bombardment is presented. The PET samples are analysed by using Fourier transform infrared spectroscopy (FTIR), X-ray diffractometer (XRD), and X-ray photoelectron spectroscopy (XPS). A significant loss of crystallinity is observed, which is related to the configuration transformation of ethylene glycol residue from the trans into the gauche. Chain scissions are observed at the para position of di-substituted benzene rings, -CO bonds and C-O bonds. The C-O bonds are destroyed more selectively than -CO bonds. The benzene ring structures show only small change under irradiation and do not participate in degradation process. Extra CC bonds and alkyne end groups are created above a critical dose of 4.0 MGy. The results are briefly discussed.

  6. Heteroligand molecular "stirrups" using conformationally flexible ditopic pyridyl-pyrazolyl ligands.

    PubMed

    Lu, Jinzhen; Turner, David R; Harding, Lindsay P; Batten, Stuart R

    2009-08-17

    Heteroligand molecular "stirrups" form by the self-assembly of flexible ditopic ligands in combination with 4,4'-bipyridine and [(dppp)Pd)](2+). Crystallographic analysis shows that the ligands, bis[3-(4-pyridyl)pyrazolyl]-m-xylene (mXy(4py3pz)) and bis[4-(4-pyridyl)pyrazolyl]-p-xylene (pXy(4py4pz)) form complexes of the type [{(dppp)Pd}(2)(4,4'-bipy)(L)].4OTf (1.4OTf and 2.4OTf, respectively) in the solid state, with remarkably similar structures considering the differences in substitution patterns between the two ligands. The self-assembly of both 1(4+) and 2(4+) is assisted by face-to-face pi interactions on the exterior of the macrocycle between the phenyl rings of the dppp ligands and the pyridyl groups of the ditopic ligands. PMID:19594137

  7. Effects of osmolytes on the helical conformation of model peptide: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Mehrnejad, Faramarz; Ghahremanpour, Mohammad Mehdi; Khadem-Maaref, Mahmoud; Doustdar, Farahnoosh

    2011-01-01

    Co-solvents such as glycerol and sorbitol are small organic molecules solvated in the cellular solutions that can have profound effects on the protein structures. Here, the molecular dynamics simulations and comparative structural analysis of magainin, as a peptide model, in pure water, 2,2,2-trifluoroethanol/water, glycerol/water, and sorbitol/water are reported. Our results show that the peptide NMR structure is largely maintained its native structure in osmolytes-water mixtures. The simulation data indicates that the stabilizing effect of glycerol and sorbitol is induced by preferential accumulation of glycerol and sorbitol molecules around the nonpolar and aromatic residues. Thus, the presence of glycerol and sorbitol molecules decreases the interactions of water molecules with the hydrophobic residues of the peptide, and the alpha helical structure is stabilized.

  8. Molecular conformations of triton X 114 in the presence of a small amount of water

    NASA Astrophysics Data System (ADS)

    Zheliaskova, A.; Blinc, R.; Zupancic, I.; Sepe, A.; Derzhanski, A.

    1989-04-01

    The viscosity of the binary system Triton X 114-water and the self-diffusion of the detergent molecules of Triton X 114 have been determined experimentally in the region of small water concentrations (0-10 wt% of water). The temperature was varied from 10 to 50°C in steps of 5°C. The self-diffusion was measured by means of the NMR method. The viscosity of the samples was determined by an efflux viscosimeter. A deviation of the experimentally obtained temperature trend of the viscosity and of the molecular mobility from the theoretical expected exponential dependence was found. This may be due to the building of dimers from the detergent molecules, whose number increases in the low temperature interval.

  9. Conformational and Molecular Structures of α,β-Unsaturated Acrylonitrile Derivatives: Photophysical Properties and Their Frontier Orbitals.

    PubMed

    Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique

    2016-01-01

    We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported. PMID:27043499

  10. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach

    PubMed Central

    Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P.

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions. PMID:26908260

  11. Molecular Characterization of Transgenic Events Using Next Generation Sequencing Approach.

    PubMed

    Guttikonda, Satish K; Marri, Pradeep; Mammadov, Jafar; Ye, Liang; Soe, Khaing; Richey, Kimberly; Cruse, James; Zhuang, Meibao; Gao, Zhifang; Evans, Clive; Rounsley, Steve; Kumpatla, Siva P

    2016-01-01

    Demand for the commercial use of genetically modified (GM) crops has been increasing in light of the projected growth of world population to nine billion by 2050. A prerequisite of paramount importance for regulatory submissions is the rigorous safety assessment of GM crops. One of the components of safety assessment is molecular characterization at DNA level which helps to determine the copy number, integrity and stability of a transgene; characterize the integration site within a host genome; and confirm the absence of vector DNA. Historically, molecular characterization has been carried out using Southern blot analysis coupled with Sanger sequencing. While this is a robust approach to characterize the transgenic crops, it is both time- and resource-consuming. The emergence of next-generation sequencing (NGS) technologies has provided highly sensitive and cost- and labor-effective alternative for molecular characterization compared to traditional Southern blot analysis. Herein, we have demonstrated the successful application of both whole genome sequencing and target capture sequencing approaches for the characterization of single and stacked transgenic events and compared the results and inferences with traditional method with respect to key criteria required for regulatory submissions. PMID:26908260

  12. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins.

    PubMed

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7-15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4-3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its "parents" up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5-2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  13. Ligand Docking to Intermediate and Close-To-Bound Conformers Generated by an Elastic Network Model Based Algorithm for Highly Flexible Proteins

    PubMed Central

    Kurkcuoglu, Zeynep; Doruker, Pemra

    2016-01-01

    Incorporating receptor flexibility in small ligand-protein docking still poses a challenge for proteins undergoing large conformational changes. In the absence of bound structures, sampling conformers that are accessible by apo state may facilitate docking and drug design studies. For this aim, we developed an unbiased conformational search algorithm, by integrating global modes from elastic network model, clustering and energy minimization with implicit solvation. Our dataset consists of five diverse proteins with apo to complex RMSDs 4.7–15 Å. Applying this iterative algorithm on apo structures, conformers close to the bound-state (RMSD 1.4–3.8 Å), as well as the intermediate states were generated. Dockings to a sequence of conformers consisting of a closed structure and its “parents” up to the apo were performed to compare binding poses on different states of the receptor. For two periplasmic binding proteins and biotin carboxylase that exhibit hinge-type closure of two dynamics domains, the best pose was obtained for the conformer closest to the bound structure (ligand RMSDs 1.5–2 Å). In contrast, the best pose for adenylate kinase corresponded to an intermediate state with partially closed LID domain and open NMP domain, in line with recent studies (ligand RMSD 2.9 Å). The docking of a helical peptide to calmodulin was the most challenging case due to the complexity of its 15 Å transition, for which a two-stage procedure was necessary. The technique was first applied on the extended calmodulin to generate intermediate conformers; then peptide docking and a second generation stage on the complex were performed, which in turn yielded a final peptide RMSD of 2.9 Å. Our algorithm is effective in producing conformational states based on the apo state. This study underlines the importance of such intermediate states for ligand docking to proteins undergoing large transitions. PMID:27348230

  14. A Rigid Bicyclic Platform for the Generation of Conformationally Locked Neuraminidase Inhibitors

    PubMed Central

    2012-01-01

    Rapid mutation of the influenza virus through genetic mixing raises the prospect of new strains that are both highly transmissible and highly lethal, and which have the ability to evade both immunization strategies (through mutation of hemagglutinin) and current therapies (through mutation of neuraminidase). Inspired by a need for next-generation therapeutics, a synthetic strategy for a new class of rigid, bicyclic inhibitors of influenza neuraminidase is reported. PMID:23181823

  15. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    PubMed

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. PMID:25311860

  16. Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation

    PubMed Central

    Das, Amit; Chakrabarti, J.; Ghosh, Mahua

    2013-01-01

    We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically. PMID:23528087

  17. Conformational Ensemble of hIAPP Dimer: Insight into the Molecular Mechanism by which a Green Tea Extract inhibits hIAPP Aggregation.

    PubMed

    Mo, Yuxiang; Lei, Jiangtao; Sun, Yunxiang; Zhang, Qingwen; Wei, Guanghong

    2016-01-01

    Small oligomers formed early along human islet amyloid polypeptide (hIAPP) aggregation is responsible for the cell death in Type II diabetes. The epigallocatechin gallate (EGCG), a green tea extract, was found to inhibit hIAPP fibrillation. However, the inhibition mechanism and the conformational distribution of the smallest hIAPP oligomer - dimer are mostly unknown. Herein, we performed extensive replica exchange molecular dynamic simulations on hIAPP dimer with and without EGCG molecules. Extended hIAPP dimer conformations, with a collision cross section value similar to that observed by ion mobility-mass spectrometry, were observed in our simulations. Notably, these dimers adopt a three-stranded antiparallel β-sheet and contain the previously reported β-hairpin amyloidogenic precursor. We find that EGCG binding strongly blocks both the inter-peptide hydrophobic and aromatic-stacking interactions responsible for inter-peptide β-sheet formation and intra-peptide interaction crucial for β-hairpin formation, thus abolishes the three-stranded β-sheet structures and leads to the formation of coil-rich conformations. Hydrophobic, aromatic-stacking, cation-π and hydrogen-bonding interactions jointly contribute to the EGCG-induced conformational shift. This study provides, on atomic level, the conformational ensemble of hIAPP dimer and the molecular mechanism by which EGCG inhibits hIAPP aggregation. PMID:27620620

  18. Conformational effects, molecular orbitals, and reaction activities of bis(phthalocyaninato) lanthanum double-deckers: density functional theory calculations.

    PubMed

    Qi, Dongdong; Zhang, Lijuan; Wan, Liang; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

    2011-08-01

    The conformational effects on the frontier molecular orbital energy and stability for reduced, neutral, and oxidized bis(phthalocyaninato) lanthanum double-deckers have been revealed on the basis of density functional theory calculations. Calculation results indicate that the frontier orbital coupling degree changes along with the molecular conformation of the double-decker compound, first decreasing along with the increase of rotation angle β from 0 to 20° and then increasing along with the increase of rotation angle β from 20 to 45°. In addition, the stability for the three forms of double-decker changes in the same order, but first increasing and then decreasing along with the change of the rotation angle β in the range of 0 to 45° with a rotation energy barrier of (31.3 ± 3.1) kJ mol(-1) at 20°. This reveals that the rotation of the two phthalocyanine rings for the reduced, neutral, and oxidized bis(phthalocyaninato) lanthanum double-deckers are able to occur at room temperature. Nevertheless, the superior coordination reaction activity of the neutral bis(phthalocyaninato) lanthanum double-decker complex over their reduced form in forming sandwich-type tris(phthalocyaninato) lanthanum triple-decker compounds has also been clearly clarified on the basis of comparative calculations on the Fukui function of [La(Pc)(2)] and [La(Pc)(2)](-) using the DFT method. Fukui function analysis reveals the reaction center of the 18-electron-π-conjugated core in the bis(phthalocyaninato) lanthanum double-decker molecule against both electrophilic and radical attack. Nevertheless, the larger global chemical softness (S) for the neutral [La(Pc)(2)] than the reduced form [La(Pc)(2)](-) indicates the higher reaction activity of the former form over the latter one. This explains well the experimental findings that only the neutral instead of the reduced form of bis(tetrapyrrole) rare earth double-decker complexes, containing at least one phthalocyanine ligand, could be

  19. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    NASA Astrophysics Data System (ADS)

    Kamberaj, Hiqmet

    2015-09-01

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  20. The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates

    PubMed Central

    Kondo, Jiro; Westhof, Eric

    2008-01-01

    The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting ‘off’ state and an active decoding ‘on’ state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or bacteria have been solved. The resting ‘off’ state of the mitochondrial wild-type A site is surprisingly different from that of the bacterial A site. The mitochondrial A1555G mutant has two types of the ‘off’ states; one is similar to the mitochondrial wild-type ‘off’ state and the other is similar to the bacterial ‘off’ state. Our present results indicate that the dynamics of the A site in bacteria and mitochondria are different, a property probably related to the small number of tRNAs used for decoding in mitochondria. Based on these structures, we propose a hypothesis for the molecular mechanism of non-syndromic hearing loss due to the mitochondrial A1555G mutation. PMID:18346970

  1. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    SciTech Connect

    Kamberaj, Hiqmet

    2015-09-28

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  2. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    DOE PAGESBeta

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less

  3. Probing the ATP-induced conformational flexibility of the PcrA helicase protein using molecular dynamics simulation.

    PubMed

    Mhashal, Anil R; Choudhury, Chandan Kumar; Roy, Sudip

    2016-03-01

    Helicases are enzymes that unwind double-stranded DNA (dsDNA) into its single-stranded components. It is important to understand the binding and unbinding of ATP from the active sites of helicases, as this knowledge can be used to elucidate the functionality of helicases during the unwinding of dsDNA. In this work, we investigated the unbinding of ATP and its effect on the active-site residues of the helicase PcrA using molecular dynamic simulations. To mimic the unbinding process of ATP from the active site of the helicase, we simulated the application of an external force that pulls ATP from the active site and computed the free-energy change during this process. We estimated an energy cost of ~85 kJ/mol for the transformation of the helicase from the ATP-bound state (1QHH) to the ATP-free state (1PJR). Unbinding led to conformational changes in the residues of the protein at the active site. Some of the residues at the ATP-binding site were significantly reoriented when the ATP was pulled. We observed a clear competition between reorientation of the residues and energy stabilization by hydrogen bonds between the ATP and active-site residues. We also checked the flexibility of the PcrA protein using a principal component analysis of domain motion. We found that the ATP-free state of the helicase is more flexible than the ATP-bound state. PMID:26860503

  4. Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal.

    PubMed

    Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki; Liao, Jingling; Kawamura, Takashi; Tsuda, Chiemi; Takeda, Azusa; Yamamoto, Masaki; Kumasaka, Takashi; Kataoka, Tohru; Shima, Fumi

    2016-01-01

    Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PMID:27180801

  5. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    PubMed Central

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-01-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions. PMID:25453071

  6. Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal

    PubMed Central

    Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki; Liao, Jingling; Kawamura, Takashi; Tsuda, Chiemi; Takeda, Azusa; Yamamoto, Masaki; Kumasaka, Takashi; Kataoka, Tohru; Shima, Fumi

    2016-01-01

    Ras•GTP adopts two interconverting conformational states, state 1 and state 2, corresponding to inactive and active forms, respectively. However, analysis of the mechanism for state transition was hampered by the lack of the structural information on wild-type Ras state 1 despite its fundamental nature conserved in the Ras superfamily. Here we solve two new crystal structures of wild-type H-Ras, corresponding to state 1 and state 2. The state 2 structure seems to represent an intermediate of state transition and, intriguingly, the state 1 crystal is successfully derived from this state 2 crystal by regulating the surrounding humidity. Structural comparison enables us to infer the molecular mechanism for state transition, during which a wide range of hydrogen-bonding networks across Switch I, Switch II and the α3-helix interdependently undergo gross rearrangements, where fluctuation of Tyr32, translocation of Gln61, loss of the functional water molecules and positional shift of GTP play major roles. The NMR-based hydrogen/deuterium exchange experiments also support this transition mechanism. Moreover, the unveiled structural features together with the results of the biochemical study provide a new insight into the physiological role of state 1 as a stable pool of Ras•GTP in the GDP/GTP cycle of Ras. PMID:27180801

  7. Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

    SciTech Connect

    Wall, Michael E.; Van Benschoten, Andrew H.; Sauter, Nicholas K.; Adams, Paul D.; Fraser, James S.; Terwilliger, Thomas C.

    2014-12-01

    X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.

  8. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters.

    PubMed

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M; Lin, Jung-Hsin

    2009-07-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design. PMID:19433508

  9. SLITHER: a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating through channels in membrane transporters

    PubMed Central

    Lee, Po-Hsien; Kuo, Kuei-Ling; Chu, Pei-Ying; Liu, Eric M.; Lin, Jung-Hsin

    2009-01-01

    Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design. PMID:19433508

  10. Resistively Heated SiC Nozzle for Generating Molecular Beams

    NASA Technical Reports Server (NTRS)

    Cagiano, Steven; Abell, Robert; Patrick, Edward; Bendt, Miri; Gundersen, Cynthia

    2007-01-01

    An improved nozzle has been developed to replace nozzles used previously in an apparatus that generates a substantially unidirectional beam of molecules passing through a vacuum at speeds of several kilometers per second. The basic principle of operation of the apparatus is the same for both the previous and the present nozzle designs. The main working part of the nozzle is essentially a cylinder that is closed except that there is an inlet for a pressurized gas and, at one end, the cylinder is closed by a disk that contains a narrow central hole that serves as an outlet. The cylinder is heated to increase the thermal speeds of the gas molecules into the desired high-speed range. Heated, pressurized gas escapes through the outlet into a portion of the vacuum chamber that is separated, by a wall, from the rest of the vacuum chamber. In this portion of the vacuum chamber, the gas undergoes a free jet expansion. Most of the expanded gas is evacuated and thus does not become part of the molecular beam. A small fraction of the expanded beam passes through a narrow central orifice in the wall and thereby becomes a needle- thin molecular beam in the portion of the vacuum on the downstream side of the wall.

  11. The generation of meaningful information in molecular systems.

    PubMed

    Wills, Peter R

    2016-03-13

    The physico-chemical processes occurring inside cells are under the computational control of genetic (DNA) and epigenetic (internal structural) programming. The origin and evolution of genetic information (nucleic acid sequences) is reasonably well understood, but scant attention has been paid to the origin and evolution of the molecular biological interpreters that give phenotypic meaning to the sequence information that is quite faithfully replicated during cellular reproduction. The near universality and age of the mapping from nucleotide triplets to amino acids embedded in the functionality of the protein synthetic machinery speaks to the early development of a system of coding which is still extant in every living organism. We take the origin of genetic coding as a paradigm of the emergence of computation in natural systems, focusing on the requirement that the molecular components of an interpreter be synthesized autocatalytically. Within this context, it is seen that interpreters of increasing complexity are generated by series of transitions through stepped dynamic instabilities (non-equilibrium phase transitions). The early phylogeny of the amino acyl-tRNA synthetase enzymes is discussed in such terms, leading to the conclusion that the observed optimality of the genetic code is a natural outcome of the processes of self-organization that produced it. PMID:26857673

  12. Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: A molecular dynamics simulation study

    SciTech Connect

    Sieker, Florian; Straatsma, TP; Springer, Sebastian; Zacharias, Martin W

    2008-08-01

    Efficiency of peptide loading to MHC class I molecules in the endoplasmatic reticulum depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Molecular dynamics (MD) simulations on induced peptide termini dissociation from the α1/α2 peptide binding domains have been performed to characterize free energy changes and associated structural changes in the two alleles. A smooth free energy change along the distance dissociation coordinate was obtained for N terminus dissociation. A different shape and magnitude of the calculated free energy change and was obtained for induced peptide C terminus dissociation in case of the tapasin independent allele B*4405 compared to B*4402. Structural changes during C terminus dissociation occurred mainly in the first segment of the α2-1 helix that flanks the peptide C-terminus binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a stable shift towards an altered open F-pocket structure deviating significantly from the bound form was observed. In contrast, B*4405 showed only a transient opening of the F-pocket followed by relaxation towards a structure close to the bound form upon C terminus dissociation. The greater tendency for peptide-receptive conformation in the absence of peptide combined with a more long-range character of the interactions with the peptide C terminus facilitates peptide binding to B*4405 and could be responsible for the tapasin independence of this allele. A possible role of tapasin in case of HLA-B*4402 and other tapasin-dependent alleles could be the stabilization of a peptide receptive class I

  13. Exploring the correlation between molecular conformation and optoelectronic properties of conjugated polymers : side-chain versus main-chain electron acceptors

    NASA Astrophysics Data System (ADS)

    Huang, Yu-Chen; Huang, Ching-I.

    2013-03-01

    Polythiophene derivatives have been shown among the most promising materials for solar cell application because of their high charge mobility and light absorption. In the mostly studied, a recombination process often occurs, which is mainly due to the fact that the mobility of hole is much lower than that of electron. Hence, research about conjugated polymers containing donor-accepter pairs (such as PT-TPD) becomes quite popular because these materials have narrow band-gaps. Interestingly, these experimental studies have indicated a much more complex correlation between the optoelectronic properties and molecular conformation for polymers with acceptor units on either main or side chain. However, the effects associated with the molecular packing on the resultant chain conformation behavior and thereafter the optoelectronic properties have not been systematically discussed. In order to clarify the effects of the molecular conformation as well as the optoelectronic properties, we employ molecular dynamics and quantum mechanical methods to examine PBTTPD molecules with acceptor unit (TPD) on either main or side chain Computation resources from the National Center for High-Performance Computing of Taiwan and Computer and Information Networking Center of National Taiwan University.

  14. Multi-drug resistance profile of PR20 HIV-1 protease is attributed to distorted conformational and drug binding landscape: molecular dynamics insights.

    PubMed

    Chetty, Sarentha; Bhakat, Soumendranath; Martin, Alberto J M; Soliman, Mahmoud E S

    2016-01-01

    The PR20 HIV-1 protease, a variant with 20 mutations, exhibits high levels of multi-drug resistance; however, to date, there has been no report detailing the impact of these 20 mutations on the conformational and drug binding landscape at a molecular level. In this report, we demonstrate the first account of a comprehensive study designed to elaborate on the impact of these mutations on the dynamic features as well as drug binding and resistance profile, using extensive molecular dynamics analyses. Comparative MD simulations for the wild-type and PR20 HIV proteases, starting from bound and unbound conformations in each case, were performed. Results showed that the apo conformation of the PR20 variant of the HIV protease displayed a tendency to remain in the open conformation for a longer period of time when compared to the wild type. This led to a phenomena in which the inhibitor seated at the active site of PR20 tends to diffuse away from the binding site leading to a significant change in inhibitor-protein association. Calculating the per-residue fluctuation (RMSF) and radius of gyration, further validated these findings. MM/GBSA showed that the occurrence of 20 mutations led to a drop in the calculated binding free energies (ΔGbind) by ~25.17 kcal/mol and ~5 kcal/mol for p2-NC, a natural peptide substrate, and darunavir, respectively, when compared to wild type. Furthermore, the residue interaction network showed a diminished inter-residue hydrogen bond network and changes in inter-residue connections as a result of these mutations. The increased conformational flexibility in PR20 as a result of loss of intra- and inter-molecular hydrogen bond interactions and other prominent binding forces led to a loss of protease grip on ligand. It is interesting to note that the difference in conformational flexibility between PR20 and WT conformations was much higher in the case of substrate-bound conformation as compared to DRV. Thus, developing analogues of DRV by

  15. Singlet molecular oxygen generated in dark biological process.

    PubMed

    Di Mascio, Paolo; Medeiros, Marisa H G

    2014-10-01

    Ultraweak chemiluminescence arising from biomolecules oxidation has been attributed to the radiative deactivation of singlet molecular oxygen [(1)O2] and electronically excited triplet carbonyl products involving dioxetane intermediates. As examples, we will discuss the generation of (1)O2 from lipid hydroperoxides, which involves a cyclic mechanism from a linear tetraoxide intermediate. The generation of (1)O2 in aqueous solution via energy transfer from the excited triplet acetone arising from the thermodecomposition of dioxetane a chemical source, and horseradish peroxidase-catalyzed oxidation of 2-methylpropanal, as an enzymatic source, will also be discussed. The approach used to unequivocally demonstrate the generation of (1)O2 in these reactions is the use of (18)O-labeled hydroperoxide / triplet dioxygen ((18)[(3)O2]), the detection of labeled compounds by HPLC coupled to tandem mass spectrometry (HPLC-MS/MS) and the direct spectroscopic detection and characterization of (1)O2 light emission. Characteristic light emission at 1,270nm, corresponding to the singlet delta state monomolecular decay was observed. Using(18)[(3)O2], we observed the formation of (18)O-labeled (1)O2 ((18)[(1)O2]) by the chemical trapping of (18)[(1)O2]with the anthracene-9,10-diyldiethane-2,1-diyl disulfate disodium salt (EAS) and detected the corresponding (18)O-labeled EAS endoperoxide usingHPLC-MS/MS. The combined use of the thermolysis of a water-soluble naphthalene endoperoxide as a generator of (18)O labeled (1)O2 and the sensitivity of HPLC-MS/MS allowed the study of (1)O2reactivity toward biomolecules. Photoemission properties and chemical trapping clearly demonstrate that the production of hydroperoxide and excited carbonyls generates (18)[(1)O2], and points to the involvement of (1)O2 in physiological and pathophysiological mechanism. Supported by FAPESP (2012/12663-1), CAPES, INCT Redoxoma (FAPESP/CNPq/CAPES; 573530/2008-4), NAP Redoxoma (PRPUSP; 2011.1.9352.1.8), CEPID

  16. Backbone conformational flexibility of the lipid modified membrane anchor of the human N-Ras protein investigated by solid-state NMR and molecular dynamics simulation.

    PubMed

    Vogel, Alexander; Reuther, Guido; Roark, Matthew B; Tan, Kui-Thong; Waldmann, Herbert; Feller, Scott E; Huster, Daniel

    2010-02-01

    The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data. PMID:19819220

  17. Structure and conformational dynamics of the domain 5 RNA hairpin of a bacterial group II intron revealed by solution nuclear magnetic resonance and molecular dynamics simulations.

    PubMed

    Pechlaner, Maria; Sigel, Roland K O; van Gunsteren, Wilfred F; Dolenc, Jožica

    2013-10-01

    Nuclear magnetic resonance (NMR) nuclear Overhauser enhancement (NOE) data obtained for a 35-nucleotide RNA segment of a bacterial group II intron indicate a helical hairpin structure in which three parts, a terminal pentaloop, a bulge, and a G-A mismatch, display no Watson-Crick base pairing. The 668 NOE upper distance bounds for atom pairs are insufficient to uniquely determine the conformation of these segments. Therefore, molecular dynamics simulations including time-averaged distance restraints have been used to obtain a conformational ensemble compatible with the observed NMR data. The ensemble shows alternating hydrogen bonding patterns for the mentioned segments. In particular, in the pentaloop and in the bulge, the hydrogen bonding networks correspond to distinct conformational clusters that could not be captured by using conventional single-structure refinement techniques. This implies that, to obtain a realistic picture of the conformational ensemble of such flexible biomolecules, it is necessary to properly account for the conformational variability in the structure refinement of RNA fragments. PMID:24001362

  18. Helical shifts generate two distinct conformers in the atomic resolution structure of the CheA phosphotransferase domain from Thermotoga maritima.

    PubMed

    Quezada, Cindy M; Gradinaru, Cristian; Simon, Melvin I; Bilwes, Alexandrine M; Crane, Brian R

    2004-08-27

    phosphotransferase activity hydrogen bonds directly to His45 N(delta1). E67 generates a negative electrostatic surface surrounding the reactive His that is conserved by most CheA kinases, but absent in related phosphotransferase proteins. The P1 conformations that we observe are likely relevant to other helical or coiled-coil proteins and may be important for generating switches in signaling processes. PMID:15321722

  19. Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

    NASA Astrophysics Data System (ADS)

    Saravanan, R. R.; Seshadri, S.; Gunasekaran, S.; Mendoza-Meroño, R.; Garcia-Granda, S.

    2015-03-01

    Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

  20. Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide.

    PubMed

    Saravanan, R R; Seshadri, S; Gunasekaran, S; Mendoza-Meroño, R; Garcia-Granda, S

    2015-03-15

    Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values. PMID:25574651

  1. Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel

    PubMed Central

    Bjelkmar, Pär; Niemelä, Perttu S.; Vattulainen, Ilpo; Lindahl, Erik

    2009-01-01

    Structure and dynamics of voltage-gated ion channels, in particular the motion of the S4 helix, is a highly interesting and hotly debated topic in current membrane protein research. It has critical implications for insertion and stabilization of membrane proteins as well as for finding how transitions occur in membrane proteins—not to mention numerous applications in drug design. Here, we present a full 1 µs atomic-detail molecular dynamics simulation of an integral Kv1.2 ion channel, comprising 120,000 atoms. By applying 0.052 V/nm of hyperpolarization, we observe structural rearrangements, including up to 120° rotation of the S4 segment, changes in hydrogen-bonding patterns, but only low amounts of translation. A smaller rotation (∼35°) of the extracellular end of all S4 segments is present also in a reference 0.5 µs simulation without applied field, which indicates that the crystal structure might be slightly different from the natural state of the voltage sensor. The conformation change upon hyperpolarization is closely coupled to an increase in 310 helix contents in S4, starting from the intracellular side. This could support a model for transition from the crystal structure where the hyperpolarization destabilizes S4–lipid hydrogen bonds, which leads to the helix rotating to keep the arginine side chains away from the hydrophobic phase, and the driving force for final relaxation by downward translation is partly entropic, which would explain the slow process. The coordinates of the transmembrane part of the simulated channel actually stay closer to the recently determined higher-resolution Kv1.2 chimera channel than the starting structure for the entire second half of the simulation (0.5–1 µs). Together with lipids binding in matching positions and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations. PMID:19229308

  2. Systematic Comparison of Molecular Conformations of H+,K+-ATPase Reveals an Important Contribution of the A-M2 Linker for the Luminal Gating*

    PubMed Central

    Abe, Kazuhiro; Tani, Kazutoshi; Fujiyoshi, Yoshinori

    2014-01-01

    Gastric H+,K+-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K+-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H+,K+-ATPase is consistent with that observed in sarcoplasmic reticulum Ca2+-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general. PMID:25231997

  3. Systematic comparison of molecular conformations of H+,K+-ATPase reveals an important contribution of the A-M2 linker for the luminal gating.

    PubMed

    Abe, Kazuhiro; Tani, Kazutoshi; Fujiyoshi, Yoshinori

    2014-10-31

    Gastric H(+),K(+)-ATPase, an ATP-driven proton pump responsible for gastric acidification, is a molecular target for anti-ulcer drugs. Here we show its cryo-electron microscopy (EM) structure in an E2P analog state, bound to magnesium fluoride (MgF), and its K(+)-competitive antagonist SCH28080, determined at 7 Å resolution by electron crystallography of two-dimensional crystals. Systematic comparison with other E2P-related cryo-EM structures revealed that the molecular conformation in the (SCH)E2·MgF state is remarkably distinguishable. Although the azimuthal position of the A domain of the (SCH)E2·MgF state is similar to that in the E2·AlF (aluminum fluoride) state, in which the transmembrane luminal gate is closed, the arrangement of transmembrane helices in the (SCH)E2·MgF state shows a luminal-open conformation imposed on by bound SCH28080 at its luminal cavity, based on observations of the structure in the SCH28080-bound E2·BeF (beryllium fluoride) state. The molecular conformation of the (SCH)E2·MgF state thus represents a mixed overall structure in which its cytoplasmic and luminal half appear to be independently modulated by a phosphate analog and an antagonist bound to the respective parts of the enzyme. Comparison of the molecular conformations revealed that the linker region connecting the A domain and the transmembrane helix 2 (A-M2 linker) mediates the regulation of luminal gating. The mechanistic rationale underlying luminal gating observed in H(+),K(+)-ATPase is consistent with that observed in sarcoplasmic reticulum Ca(2+)-ATPase and other P-type ATPases and is most likely conserved for the P-type ATPase family in general. PMID:25231997

  4. Conformal Collineations in String Cosmology

    NASA Astrophysics Data System (ADS)

    Baysal, Hüsnü; Camci, U.ğur; Tarhan, İsmail; Yilmaz, İhsan; Yavuz, İlhami; Dolgov, A.

    In this paper, we study the consequences of the existence of conformal collineations (CC) for string cloud in the context of general relativity. Especially, we interest in special conformal collineation (SCC), generated by a special affine conformal collineation (SACC) in the string cloud. Some results on the restrictions imposed by a conformal collineation symmetry in the string cloud are obtained.

  5. New Molecular Ferroelectrics Accompanied by Ultrahigh Second-Harmonic Generation.

    PubMed

    Liu, Chuang; Gao, Kaige; Cui, Zepeng; Gao, Linsong; Fu, Da-Wei; Cai, Hong-Ling; Wu, X S

    2016-05-19

    Second-harmonic generation (SHG) is one of the outstanding properties for practical applications. However, the great majority of molecular ferroelectric materials have very low nonlinear optical coefficients, attenuating their attractive performance. Here we synthesized (4-amino-2-bromopyridinium)(4-amino-2-bromopyridine)tetrafluoroborate (1), whose second-order nonlinear optical coefficient reaches up to 2.56 pm V(-1), 2.67 times of that of KDP, and (4-amino-2-bromopyridinium)tetrafluoroborate (2), possessing a more incredible large second-order nonlinear optical coefficient as high as 10.24 pm V(-1), 10.67 times that of KDP. The compound 1 undergoes two reversible phase transitions at around T1 = 244.1 K and T2 = 154.6 K, caused by dramatic changes of the protonated cations and order-disorder of anions, which was disclosed by differential scanning calorimetry, heat capacity, dielectric anomalies, SHG, and single-crystal X-ray diffraction analysis. The pyroelectric measurements reveal that compound 1 is a Rochelle salt type ferroelectric, which has a large spontaneous polarization of about 3 μC/cm(2). PMID:27111056

  6. Molecular farming on rescue of pharma industry for next generations.

    PubMed

    Moustafa, Khaled; Makhzoum, Abdullah; Trémouillaux-Guiller, Jocelyne

    2016-10-01

    Recombinant proteins expressed in plants have been emerged as a novel branch of the biopharmaceutical industry, offering practical and safety advantages over traditional approaches. Cultivable in various platforms (i.e. open field, greenhouses or bioreactors), plants hold great potential to produce different types of therapeutic proteins with reduced risks of contamination with human and animal pathogens. To maximize the yield and quality of plant-made pharmaceuticals, crucial factors should be taken into account, including host plants, expression cassettes, subcellular localization, post-translational modifications, and protein extraction and purification methods. DNA technology and genetic transformation methods have also contributed to great parts with substantial improvements. To play their proper function and stability, proteins require multiple post-translational modifications such as glycosylation. Intensive glycoengineering research has been performed to reduce the immunogenicity of recombinant proteins produced in plants. Important strategies have also been developed to minimize the proteolysis effects and enhance protein accumulation. With growing human population and new epidemic threats, the need for new medications will be paramount so that the traditional pharmaceutical industry will not be alone to answer medication demands for upcoming generations. Here, we review several aspects of plant molecular pharming and outline some important challenges that hamper these ambitious biotechnological developments. PMID:26042351

  7. Laser spectroscopy probes of biomolecular conformation: Valley-to-valley searches for molecular-scale mountain passes

    NASA Astrophysics Data System (ADS)

    Zwier, Timothy

    2006-03-01

    This talk will describe recent studies of the spectroscopy and conformational isomerization dynamics of isolated gas-phase biomolecules with several flexible coordinates. These studies employ conformation-specific excitation and detection, taking advantage of the unique infrared and ultraviolet signatures of the individual conformations when cooled in a supersonic expansion. The examples given will include recent studies of the bichromophore 3-(4-hydroxyphenyl)-N-benzyl-propionamide (HNBPA) and of the `double-chain' molecule O-(acetamidoethyl)-N-acetyltyramine (OANAT). In collaboration with Jasper Clarkson, Esteban Baquero, Virgil Shubert, Tracy LeGreve and William James, Dept. of Chemistry, Purdue University.

  8. Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Gamage, I. H.; Jonker, A.; Zhang, X.; Yu, P.

    2014-01-01

    The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm-1 (carbonyl Cdbnd O ester, mainly related to lipid structure conformation), ca. 1725-1482 cm-1 (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm-1 (mainly associated with structural carbohydrate) and ca. 1180-800 cm-1 (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock sources

  9. Non-destructive analysis of the conformational differences among feedstock sources and their corresponding co-products from bioethanol production with molecular spectroscopy.

    PubMed

    Gamage, I H; Jonker, A; Zhang, X; Yu, P

    2014-01-24

    The objective of this study was to determine the possibility of using molecular spectroscopy with multivariate technique as a fast method to detect the source effects among original feedstock sources of wheat and their corresponding co-products, wheat DDGS, from bioethanol production. Different sources of the bioethanol feedstock and their corresponding bioethanol co-products, three samples per source, were collected from the same newly-built bioethanol plant with current bioethanol processing technology. Multivariate molecular spectral analyses were carried out using agglomerative hierarchical cluster analysis (AHCA) and principal component analysis (PCA). The molecular spectral data of different feedstock sources and their corresponding co-products were compared at four different regions of ca. 1800-1725 cm(-1) (carbonyl CO ester, mainly related to lipid structure conformation), ca. 1725-1482 cm(-1) (amide I and amide II region mainly related to protein structure conformation), ca. 1482-1180 cm(-1) (mainly associated with structural carbohydrate) and ca. 1180-800 cm(-1) (mainly related to carbohydrates) in complex plant-based system. The results showed that the molecular spectroscopy with multivariate technique could reveal the structural differences among the bioethanol feedstock sources and among their corresponding co-products. The AHCA and PCA analyses were able to distinguish the molecular structure differences associated with chemical functional groups among the different sources of the feedstock and their corresponding co-products. The molecular spectral differences indicated the differences in functional, biomolecular and biopolymer groups which were confirmed by wet chemical analysis. These biomolecular and biopolymer structural differences were associated with chemical and nutrient profiles and nutrient utilization and availability. Molecular spectral analyses had the potential to identify molecular structure difference among bioethanol feedstock

  10. High-Resolution Microwave and Infrared Molecular-Beam Studies of the Conformers of 1,1,2,2-Tetrafluoroethane

    NASA Astrophysics Data System (ADS)

    Stone, Stephen C.; Philips, Laura A.; Fraser, G. T.; Lovas, F. J.; Xu, Li-Hong; Sharpe, S. W.

    1998-11-01

    High-resolution microwave and infrared molecular-beam spectra have been measured for 1,1,2,2-tetrafluoroethane (HFC134). For the higher energy, polar,C2symmetry,gaucheconformer, microwave spectra have been recorded for the normal and mono-13C isotopomers and analyzed to determine a C-C bond length of 1.512(4) Å, in good agreement with a recentab initiovalue (MP2/6-31G**) of 1.515 Å [S. Papasavva, K. H. Illinger, and J. E. Kenny,J. Phys. Chem.100, 10100-10110 (1996)]. A tunable microwave-sideband CO2laser and electric-resonance optothermal spectrometer have been used to measure the infrared spectrum of the ν6, C-C stretch of thegaucheconformer near 906 cm-1. Microwave-infrared double resonance and precise ground state combination differences provided by the microwave measurements guide the assignment of the spectrum. The observation of ac-type spectrum definitively establishes that the upper state vibration is ofAsymmetry in theC2point group. The spectrum is fit to a Watson asymmetric-top Hamiltonian to a standard deviation of 0.24 MHz. A weak perturbation shifts the line positions for transitions nearJ = Kc= 20 by as much as 12 MHz. The identity of the perturber is unknown. Pulsed slit-jet diode-laser spectra have been recorded for the ν16vibration of theanticonformer near 1127 cm-1. Ana- andc-type hybrid band is observed, consistent with aBusymmetry mode. Previous low-resolution studies have attributed the 1127-cm-1mode to either aBuor anAusymmetry vibration. A total of 522 nonblended transitions were assigned and fit to determine ground and excited state constants. The ground state constants ofA= 5134.952(65) MHz,B= 3148.277(27) MHz, andC= 2067.106(43) MHz are the first experimental determinations of the rotational constants for this conformer. Here, typeAstandard uncertainties are given in the parentheses.

  11. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2

    PubMed Central

    Pisani, Pasquale; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  12. Molecular Dynamics Simulations and Classical Multidimensional Scaling Unveil New Metastable States in the Conformational Landscape of CDK2.

    PubMed

    Pisani, Pasquale; Caporuscio, Fabiana; Carlino, Luca; Rastelli, Giulio

    2016-01-01

    Protein kinases are key regulatory nodes in cellular networks and their function has been shown to be intimately coupled with their structural flexibility. However, understanding the key structural mechanisms of large conformational transitions remains a difficult task. CDK2 is a crucial regulator of cell cycle. Its activity is finely tuned by Cyclin E/A and the catalytic segment phosphorylation, whereas its deregulation occurs in many types of cancer. ATP competitive inhibitors have failed to be approved for clinical use due to toxicity issues raised by a lack of selectivity. However, in the last few years type III allosteric inhibitors have emerged as an alternative strategy to selectively modulate CDK2 activity. In this study we have investigated the conformational variability of CDK2. A low dimensional conformational landscape of CDK2 was modeled using classical multidimensional scaling on a set of 255 crystal structures. Microsecond-scale plain and accelerated MD simulations were used to populate this landscape by using an out-of-sample extension of multidimensional scaling. CDK2 was simulated in the apo-form and in complex with the allosteric inhibitor 8-anilino-1-napthalenesulfonic acid (ANS). The apo-CDK2 landscape analysis showed a conformational equilibrium between an Src-like inactive conformation and an active-like form. These two states are separated by different metastable states that share hybrid structural features with both forms of the kinase. In contrast, the CDK2/ANS complex landscape is compatible with a conformational selection picture where the binding of ANS in proximity of the αC helix causes a population shift toward the inactive conformation. Interestingly, the new metastable states could enlarge the pool of candidate structures for the development of selective allosteric CDK2 inhibitors. The method here presented should not be limited to the CDK2 case but could be used to systematically unmask similar mechanisms throughout the human

  13. Structural, conformational, and theoretical binding studies of antitumor antibiotic porfiromycin (N-methylmitomycin C), a covalent binder of DNA, by X-ray, NMR, and molecular mechanics.

    PubMed

    Arora, S K; Cox, M B; Arjunan, P

    1990-11-01

    X-ray, NMR, and molecular mechanics studies on antitumor antibiotic porfiromycin (C16H20N4O5), a covalent binder of DNA, have been carried out to study the structure, conformation, and theoretical interactions with DNA. The crystal structure was solved by direct methods and refined to an R value of 0.052. The configurations at C(9), C(9a), C(1), and C(2) are S, R, S, and S, except for the orientation of the aziridine ring and (carbamoyloxy)methyl side chain. The five-membered ring attached to the aziridine ring adopts an envelope conformation. The solution conformation is similar to that observed in the solid state except for the (carbamoyloxy)methyl side chain. Monovalent and cross-linked models of the drug bound to DNA have been energetically refined by using molecular mechanics. The results indicate that, in the case of monocovalent binding, the drug clearly prefers a d(CpG) sequence rather than a d(GpC) sequence. In the case of the cross-linked model there is no clear-cut preference of d(CpG) over d(GpC), indicating that the binding preference of the drug may be kinetic rather than thermodynamic. PMID:2231597

  14. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka

    2016-01-01

    The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.

  15. Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

    NASA Astrophysics Data System (ADS)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

  16. Charge carrier generation in photosensitive amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Barabash, Y.; Kharkyanen, V.; Zabolotny, M.; Zabolotnaya, T.

    2006-05-01

    Thermalization process in photosensitive amorphous molecular semiconductors are theoretically considered from standpoint of their parameters, namely: thermalization time, thermalization length. The heat electron formed in consequence of absorption of the light quantum by semiconductor molecules loses his surplus energy in the time of inelastic interaction with neighbouring atoms. The results of theoretical predictions are confirmed by the experimental ones obtained for a number of molecular semiconductors (anthracene, pentacene, PVC, PEPC).

  17. Molecular dynamic simulations of environment and sequence dependent DNA conformations: the development of the BMS nucleic acid force field and comparison with experimental results.

    PubMed

    Langley, D R

    1998-12-01

    Molecular dynamic (MD) simulations using the BMS nucleic acid force field produce environment and sequence dependent DNA conformations that closely mimic experimentally derived structures. The parameters were initially developed to reproduce the potential energy surface, as defined by quantum mechanics, for a set of small molecules that can be used as the building blocks for nucleic acid macromolecules (dimethyl phosphate, cyclopentane, tetrahydrofuran, etc.). Then the dihedral parameters were fine tuned using a series of condensed phase MD simulations of DNA and RNA (in zero added salt, 4M NaCl, and 75% ethanol solutions). In the tuning process the free energy surface for each dihedral was derived from the MD ensemble and fitted to the conformational distributions and populations observed in 87 A- and B-DNA x-ray and 17 B-DNA NMR structures. Over 41 nanoseconds of MD simulations are presented which demonstrate that the force field is capable of producing stable trajectories, in the correct environments, of A-DNA, double stranded A-form RNA, B-DNA, Z-DNA, and a netropsin-DNA complex that closely reproduce the experimentally determined and/or canonical DNA conformations. Frequently the MD averaged structure is closer to the experimentally determined structure than to the canonical DNA conformation. MD simulations of A- to B- and B- to A-DNA transitions are also shown. A-DNA simulations in a low salt environment cleanly convert into the B-DNA conformation and converge into the RMS space sampled by a low salt simulation of the same sequence starting from B-DNA. In MD simulations using the BMS force field the B-form of d(GGGCCC)2 in a 75% ethanol solution converts into the A-form. Using the same methodology, parameters, and conditions the A-form of d(AAATTT)2 correctly converts into the B-DNA conformation. These studies demonstrate that the force field is capable of reproducing both environment and sequence dependent DNA structures. The 41 nanoseconds (nsec) of MD

  18. Efficient molecular surface generation using level-set methods.

    PubMed

    Can, Tolga; Chen, Chao-I; Wang, Yuan-Fang

    2006-12-01

    Molecules interact through their surface residues. Calculation of the molecular surface of a protein structure is thus an important step for a detailed functional analysis. One of the main considerations in comparing existing methods for molecular surface computations is their speed. Most of the methods that produce satisfying results for small molecules fail to do so for large complexes. In this article, we present a level-set-based approach to compute and visualize a molecular surface at a desired resolution. The emerging level-set methods have been used for computing evolving boundaries in several application areas from fluid mechanics to computer vision. Our method provides a uniform framework for computing solvent-accessible, solvent-excluded surfaces and interior cavities. The computation is carried out very efficiently even for very large molecular complexes with tens of thousands of atoms. We compared our method to some of the most widely used molecular visualization tools (Swiss-PDBViewer, PyMol, and Chimera) and our results show that we can calculate and display a molecular surface 1.5-3.14 times faster on average than all three of the compared programs. Furthermore, we demonstrate that our method is able to detect all of the interior inaccessible cavities that can accommodate one or more water molecules. PMID:16621636

  19. Molecular typing of isolates of the fish pathogen, Flavobacterium columnare, by single-strand conformation polymorphism analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flavobacterium columnare intraspecies diversity was revealed by analyzing the 16S rRNA gene and the 16S-23S internal spacer region (ISR). Standard restriction fragment length polymorphism (RFLP) of these sequences was compared with single strand conformation polymorphism (SSCP). Diversity indexes sh...

  20. Conformational kinetics reveals affinities of protein conformational states

    PubMed Central

    Daniels, Kyle G.; Suo, Yang; Oas, Terrence G.

    2015-01-01

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein’s affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states. PMID:26162682

  1. Conformation analysis and molecular mobility of ethylene and tetrafluoroethylene copolymer using solid-state 19F MAS and 1H --> 19F CP/MAS NMR spectroscopy.

    PubMed

    Aimi, Keitaro; Ando, Shinji

    2004-07-01

    The changes in the conformation and molecular mobility accompanied by a phase transition in the crystalline domain were analyzed for ethylene (E) and tetrafluoroethylene (TFE) copolymer, ETFE, using variable-temperature (VT) solid-state 19F magic angle spinning (MAS) and 1H --> 19F cross-polarization (CP)/MAS NMR spectroscopy. The shifts of the signals for fluorines in TFE units to higher frequency and the continuing decrease and increase in the T1rho(F) values suggest that conformational exchange motions exist in the crystalline domain between 42 and 145 degrees C. Quantum chemical calculations of magnetic shielding constants showed that the high-frequency shift of TFE units should be induced by trans to gauche conformational changes at the CH2-CF2 linkage in the E-TFE unit. Although the 19F signals of the crystalline domain are substantially overlapped with those of the amorphous domain at ambient probe temperature (68 degrees C), they were successfully distinguished by using the dipolar filter and spin-lock pulse sequences at 145 degrees C. The dipolar coupling constants for the crystalline domain, which can be estimated by fitting the dipolar oscillation behaviors in the 1H --> 19F CP curve, showed a significant decrease with increasing temperature from 42 to 145 degrees C. This is due to the averaging of 1H-19F dipolar interactions originating from the molecular motion in the crystalline domain. The increase in molecular mobility in the crystalline domain was clearly shown by VT T1rho(F) and 1H --> 19F CP measurements in the phase transition temperature range. PMID:15181627

  2. Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries.

    PubMed

    Hansen, Halvor S; Hünenberger, Philippe H

    2010-09-14

    A new method, ball-and-stick local elevation umbrella sampling (B&S-LEUS), is proposed to enhance the sampling in computer simulations of (bio)molecular systems. It enables the calculation of conformational free-energy differences between states (or alchemical free-energy differences between molecules), even in situations where the definition of these states relies on a conformational subspace involving more than a few degrees of freedom. The B&S-LEUS method consists of the following steps: (A) choice of a reduced conformational subspace; (B) representation of the relevant states by means of spheres ("balls"), each associated with a biasing potential involving a one-dimensional radial memory-based term and a radial confinement term; (C) definition of a set of lines ("sticks") connecting these spheres, each associated with a biasing potential involving a one-dimensional longitudinal memory-based term and a transverse confinement term; (D) unification of the biasing potentials corresponding to the union of all of the spheres and lines (active subspace) into a single biasing potential according to the enveloping distribution sampling (EDS) scheme; (E) build-up of the memory using the local elevation (LE) procedure, leading to a biasing potential enabling a nearly uniform sampling (radially within the spheres, longitudinally within the lines) of the active subspace; (F) generation of a biased ensemble of configurations using this preoptimized biasing potential, following an umbrella sampling (US) approach; and (G) calculation of the relative free energies of the states via reweighting and state assignment. The main characteristics of this approach are: (i) a low internal dimensionality, that is, the memory only involves one-dimensional grids (acceptable memory requirements); (ii) a minimal irrelevant volume, that is, the conformational volume opened to sampling includes a minimal fraction of irrelevant regions in terms of the free energy of the physical system or of

  3. Molecular alignment allows low-order harmonic generation by circular light in a gas

    NASA Astrophysics Data System (ADS)

    Houzet, J.; Hertz, E.; Billard, F.; Lavorel, B.; Faucher, O.

    2013-08-01

    We experimentally investigate odd-order harmonic generation in molecular gases produced by circularly polarized laser fields. While forbidden in isotropic medium, this effect is allowed by symmetry breaking resulting from nonadiabatic laser-induced molecular alignment. The demonstration is provided by generating the third harmonic in CO2 molecules. Attractive properties and challenging potential applications are discussed in the context of higher-order harmonic generation.

  4. The molecular structure, equilibrium conformation and barrier to internal rotation in decachloroferrocene, Fe(η-C₅Cl₅)₂, determined by gas electron diffraction.

    PubMed

    Phillips, Leo; Cooper, Mervyn K; Haaland, Arne; Samdal, Svein; Giricheva, Nina I; Girichev, Georgiy V

    2010-05-21

    The molecular structure of decachloroferrocene has been determined by gas electron diffraction supported by quantum chemical calculations. The equilibrium conformation has staggered ligand rings and D(5d) symmetry. The barrier to internal rotation is, however, only 0.8(2) kJ mol⁻¹. This barrier is so low that even at room temperature the vast majority of molecules in the gas phase would have sufficient thermal energy to undergo virtually non-hindered internal rotation. While the eclipsed equilibrium conformation of unsubstituted ferrocene is determined by attractive dispersion interaction between the two cyclopentadienyl ligands, the staggered equilibrium conformation of Fe(η-C₅Cl₅)₂ is due to steric repulsion between Cl atoms at different rings. The ligands are non-planar: the C-Cl bonds are bent 3.7(3)° out of the plane of the C₅ ring away from the metal atom. The Fe-C, C-C and C-Cl bond distances (r(a)) are: 205.0(4) pm, 143.4(3) pm and 170.2(4) pm respectively. PMID:20372696

  5. The Periplasmic Bacterial Molecular Chaperone SurA Adapts Its Structure to Bind Peptides in Different Conformations to Assert a Sequence Preference for Aromatic Residues

    SciTech Connect

    Xu, X.; Wang, S.; Hu, Y.-X.; McKay, D.B.

    2009-06-04

    The periplasmic molecular chaperone protein SurA facilitates correct folding and maturation of outer membrane proteins in Gram-negative bacteria. It preferentially binds peptides that have a high fraction of aromatic amino acids. Phage display selections, isothermal titration calorimetry and crystallographic structure determination have been used to elucidate the basis of the binding specificity. The peptide recognition is imparted by the first peptidyl-prolyl isomerase (PPIase) domain of SurA. Crystal structures of complexes between peptides of sequence WEYIPNV and NFTLKFWDIFRK with the first PPIase domain of the Escherichia coli SurA protein at 1.3 A resolution, and of a complex between the dodecapeptide and a SurA fragment lacking the second PPIase domain at 3.4 A resolution, have been solved. SurA binds as a monomer to the heptapeptide in an extended conformation. It binds as a dimer to the dodecapeptide in an alpha-helical conformation, predicated on a substantial structural rearrangement of the SurA protein. In both cases, side-chains of aromatic residues of the peptides contribute a large fraction of the binding interactions. SurA therefore asserts a recognition preference for aromatic amino acids in a variety of sequence configurations by adopting alternative tertiary and quaternary structures to bind peptides in different conformations.

  6. Application of time series analysis on molecular dynamics simulations of proteins: A study of different conformational spaces by principal component analysis

    NASA Astrophysics Data System (ADS)

    Alakent, Burak; Doruker, Pemra; Camurdan, Mehmet C.

    2004-09-01

    Time series analysis is applied on the collective coordinates obtained from principal component analysis of independent molecular dynamics simulations of α-amylase inhibitor tendamistat and immunity protein of colicin E7 based on the Cα coordinates history. Even though the principal component directions obtained for each run are considerably different, the dynamics information obtained from these runs are surprisingly similar in terms of time series models and parameters. There are two main differences in the dynamics of the two proteins: the higher density of low frequencies and the larger step sizes for the interminima motions of colicin E7 than those of α-amylase inhibitor, which may be attributed to the higher number of residues of colicin E7 and/or the structural differences of the two proteins. The cumulative density function of the low frequencies in each run conforms to the expectations from the normal mode analysis. When different runs of α-amylase inhibitor are projected on the same set of eigenvectors, it is found that principal components obtained from a certain conformational region of a protein has a moderate explanation power in other conformational regions and the local minima are similar to a certain extent, while the height of the energy barriers in between the minima significantly change. As a final remark, time series analysis tools are further exploited in this study with the motive of explaining the equilibrium fluctuations of proteins.

  7. ARP/wARP and molecular replacement: the next generation

    PubMed Central

    Cohen, Serge X.; Ben Jelloul, Marouane; Long, Fei; Vagin, Alexei; Knipscheer, Puck; Lebbink, Joyce; Sixma, Titia K.; Lamzin, Victor S.; Murshudov, Garib N.; Perrakis, Anastassis

    2008-01-01

    Automatic iterative model (re-)building, as implemented in ARP/wARP and its new control system flex-wARP, is particularly well suited to follow structure solution by molecular replacement. More than 100 molecular-replacement solutions automatically solved by the BALBES software were submitted to three standard protocols in flex-wARP and the results were compared with final models from the PDB. Standard metrics were gathered in a systematic way and enabled the drawing of statistical conclusions on the advantages of each protocol. Based on this analysis, an empirical estimator was proposed that predicts how good the final model produced by flex-wARP is likely to be based on the experimental data and the quality of the molecular-replacement solution. To introduce the differences between the three flex-wARP protocols (keeping the complete search model, converting it to atomic coordinates but ignoring atom identities or using the electron-density map calculated from the molecular-replacement solution), two examples are also discussed in detail, focusing on the evolution of the models during iterative rebuilding. This highlights the diversity of paths that the flex-wARP control system can employ to reach a nearly complete and accurate model while actually starting from the same initial information. PMID:18094467

  8. Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.

    PubMed

    Rodrigues, João P G L M; Melquiond, Adrien S J; Bonvin, Alexandre M J J

    2016-01-01

    Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These improvements are also benefitting scientific education. Molecular simulations, their underlying theory, and their applications are particularly difficult to grasp for undergraduate students. Having hands-on experience with the methods contributes to a better understanding and solidification of the concepts taught during the lectures. To this end, we have created a computer practical class, which has been running for the past five years, composed of several sessions where students characterize the conformational landscape of small peptides using molecular dynamics simulations in order to gain insights on their binding to protein receptors. In this report, we detail the ingredients and recipe necessary to establish and carry out this practical, as well as some of the questions posed to the students and their expected results. Further, we cite some examples of the students' written reports, provide statistics, and share their feedbacks on the structure and execution of the sessions. These sessions were implemented alongside a theoretical molecular modelling course but have also been used successfully as a standalone tutorial during specialized workshops. The availability of the material on our web page also facilitates this integration and dissemination and lends strength to the thesis of open-source science and education. PMID:26751257

  9. Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles.

    PubMed

    Gillet, Jean-Numa

    2015-01-01

    Cell milking is a 100% renewable green energy for CO2 by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D1 before the irreversible folding transition time and the much smaller D2 thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D2=4.7 × 10(-7)cm(2)/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D2 value that is significantly below the critical threshold of 10(-6)cm(2)/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking. PMID:24735062

  10. Conformational Analysis, Molecular Structure and Solid State Simulation of the Antiviral Drug Acyclovir (Zovirax) Using Density Functional Theory Methods

    PubMed Central

    Alvarez-Ros, Margarita Clara; Palafox, Mauricio Alcolea

    2014-01-01

    The five tautomers of the drug acyclovir (ACV) were determined and optimised at the MP2 and B3LYP quantum chemical levels of theory. The stability of the tautomers was correlated with different parameters. On the most stable tautomer N1 was carried out a comprehensive conformational analysis, and the whole conformational parameters (R, β, Φ, φ1, φ2, φ3, φ4, φ5) were studied as well as the NBO Natural atomic charges. The calculations were carried out with full relaxation of all geometrical parameters. The search located at least 78 stable structures within 8.5 kcal/mol electronic energy range of the global minimum, and classified in two groups according to the positive or negative value of the torsional angle φ1. In the nitrogen atoms and in the O2' and O5' oxygen atoms of the most stable conformer appear a higher reactivity than in the natural nucleoside deoxyguanosine. The solid state was simulated through a dimer and tetramer forms and the structural parameters were compared with the X-ray crystal data available. Several general conclusions were emphasized. PMID:24915059

  11. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    PubMed

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences. PMID:25301518

  12. Molecular basis for multiple sulfatase deficiency and mechanism for formylglycine generation of the human formylglycine-generating enzyme.

    PubMed

    Dierks, Thomas; Dickmanns, Achim; Preusser-Kunze, Andrea; Schmidt, Bernhard; Mariappan, Malaiyalam; von Figura, Kurt; Ficner, Ralf; Rudolph, Markus Georg

    2005-05-20

    Sulfatases are enzymes essential for degradation and remodeling of sulfate esters. Formylglycine (FGly), the key catalytic residue in the active site, is unique to sulfatases. In higher eukaryotes, FGly is generated from a cysteine precursor by the FGly-generating enzyme (FGE). Inactivity of FGE results in multiple sulfatase deficiency (MSD), a fatal autosomal recessive syndrome. Based on the crystal structure, we report that FGE is a single-domain monomer with a surprising paucity of secondary structure and adopts a unique fold. The effect of all 18 missense mutations found in MSD patients is explained by the FGE structure, providing a molecular basis of MSD. The catalytic mechanism of FGly generation was elucidated by six high-resolution structures of FGE in different redox environments. The structures allow formulation of a novel oxygenase mechanism whereby FGE utilizes molecular oxygen to generate FGly via a cysteine sulfenic acid intermediate. PMID:15907468

  13. Molecular nitrogen in natural gas accumulations: Generation from sedimentary organic matter at high temperatures

    SciTech Connect

    Littke, R.; Krooss, B.; Frielingsdorf, J.; Idiz, E.

    1995-03-01

    The occurrence of natural gas accumulations with high percentages (up to 100%) of molecular nitrogen in various hydrocarbon provinces represents a largely unresolved problem and a serious exploration risk. In this context, a geochemical and basin modeling study was performed to evaluate the potential of sedimentary organic matter to generate molecular nitrogen. The masses of nitrogen present in coals - if converted into molecular nitrogen - are sufficient to fill commercial gas reservoirs. A calculation for gas accumulations in northern Germany, where percentages of molecular nitrogen range from less than 5 to greater than 90%, reveals that the molecular nitrogen generated in underlying coal-bearing strata is sufficient to account for the nitrogen gas even in the largest fields. In addition, much of the total nitrogen in clay-rich rock types, such as shales and mudstones, is fixed in sedimentary organic matter and may add to the nitrogen generation capacity of the coals.

  14. Molecular cobalt pentapyridine catalysts for generating hydrogen from water

    DOEpatents

    Long, Jeffrey R; Chang, Christopher J; Sun, Yujie

    2013-11-05

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition including the moiety of the general formula. [(PY5Me.sub.2)CoL].sup.2+, where L can be H.sub.2O, OH.sup.-, a halide, alcohol, ether, amine, and the like. In embodiments of the invention, water, such as tap water or sea water can be subject to low electric potentials, with the result being, among other things, the generation of hydrogen.

  15. Snowballing radical generation leads to ultrahigh molecular weight polymers.

    PubMed

    Laurino, Paola; Hernandez, Hugo F; Bräuer, Judith; Krüger, Kathleen; Grützmacher, Hansjörg; Tauer, Klaus; Seeberger, Peter H

    2012-10-26

    Styrene is the classical monomer obeying zero-one kinetics in radical emulsion polymerization. Accordingly, particles that are less than 100 nm in diameter contain either one or no growing radical(s). We describe a unique photoinitiated polymerization reaction accelerated by snowballing radical generation in a continuous flow reactor. Even in comparison to classical emulsion polymerization, these unprecedented snowballing reactions are rapid and high-yielding, with each particle simultaneously containing more than one growing radical. This is a consequence of photoinitiator incorporation into the nascent polymer backbone and repeated radical generation upon photo-irradiation. PMID:22837041

  16. Constrained nucleoside analogues - Crystal and molecular structure of 6,5‧-O-anhydrouridines fixed in the anti conformation

    NASA Astrophysics Data System (ADS)

    Gajda, Roman; Bagiński, Maciej; Tomczyk, Ewelina; Mieczkowski, Adam; Woźniak, Krzysztof

    2015-10-01

    A series of analogues of anhydrouridine have been synthesized and their crystal structures established using X-ray diffraction. For all cases, the ribose ring has O(4‧)-exo, C(4‧)-endo pucker and the pyrimidine base is in the anti conformation. Investigated compounds crystallize in different crystal systems (monoclinic, orthorhombic), have different space group symmetry (P21, P212121) and exhibit different intermolecular interactions (halogen and hydrogen bonds) among molecules in their crystal lattices. Moreover, in the case of the 5-benzyl-6,5‧-O-anhydrouridine a significant positional disorder is present with the phenyl rings existing in two orientations.

  17. Oligoyne Molecular Junctions for Efficient Room Temperature Thermoelectric Power Generation.

    PubMed

    Sadeghi, Hatef; Sangtarash, Sara; Lambert, Colin J

    2015-11-11

    Understanding phonon transport at a molecular scale is fundamental to the development of high-performance thermoelectric materials for the conversion of waste heat into electricity. We have studied phonon and electron transport in alkane and oligoyne chains of various lengths and find that, due to the more rigid nature of the latter, the phonon thermal conductances of oligoynes are counterintuitively lower than that of the corresponding alkanes. The thermal conductance of oligoynes decreases monotonically with increasing length, whereas the thermal conductance of alkanes initially increases with length and then decreases. This difference in behavior arises from phonon filtering by the gold electrodes and disappears when higher-Debye-frequency electrodes are used. Consequently a molecule that better transmits higher-frequency phonon modes, combined with a low-Debye-frequency electrode that filters high-energy phonons is a viable strategy for suppressing phonon transmission through the molecular junctions. The low thermal conductance of oligoynes, combined with their higher thermopower and higher electrical conductance lead to a maximum thermoelectric figure of merit of ZT = 1.4, which is several orders of magnitude higher than that of alkanes. PMID:26458053

  18. Fast generation of three-dimensional computational boundary-conforming periodic grids of C-type. [for turbine blades and propellers

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1982-01-01

    A fast computer program, GRID3C, was developed to generate multilevel three dimensional, C type, periodic, boundary conforming grids for the calculation of realistic turbomachinery and propeller flow fields. The technique is based on two analytic functions that conformally map a cascade of semi-infinite slits to a cascade of doubly infinite strips on different Riemann sheets. Up to four consecutively refined three dimensional grids are automatically generated and permanently stored on four different computer tapes. Grid nonorthogonality is introduced by a separate coordinate shearing and stretching performed in each of three coordinate directions. The grids are easily clustered closer to the blade surface, the trailing and leading edges and the hub or shroud regions by changing appropriate input parameters. Hub and duct (or outer free boundary) have different axisymmetric shapes. A vortex sheet of arbitrary thickness emanating smoothly from the blade trailing edge is generated automatically by GRID3C. Blade cross sectional shape, chord length, twist angle, sweep angle, and dihedral angle can vary in an arbitrary smooth fashion in the spanwise direction.

  19. Smooth, seamless, and structured grid generation with flexibility in resolution distribution on a sphere based on conformal mapping and the spring dynamics method

    NASA Astrophysics Data System (ADS)

    Iga, Shin-ichi

    2015-09-01

    A generation method for smooth, seamless, and structured triangular grids on a sphere with flexibility in resolution distribution is proposed. This method is applicable to many fields that deal with a sphere on which the required resolution is not uniform. The grids were generated using the spring dynamics method, and adjustments were made using analytical functions. The mesh topology determined its resolution distribution, derived from a combination of conformal mapping factors: polar stereographic projection (PSP), Lambert conformal conic projection (LCCP), and Mercator projection (MP). Their combination generated, for example, a tropically fine grid that had a nearly constant high-resolution belt around the equator, with a gradual decrease in resolution distribution outside of the belt. This grid can be applied to boundary-less simulations of tropical meteorology. The other example involves a regionally fine grid with a nearly constant high-resolution circular region and a gradually decreasing resolution distribution outside of the region. This is applicable to regional atmospheric simulations without grid nesting. The proposed grids are compatible with computer architecture because they possess a structured form. Each triangle of the proposed grids was highly regular, implying a high local isotropy in resolution. Finally, the proposed grids were examined by advection and shallow water simulations.

  20. Conformational Changes in the GM-CSF Receptor Suggest a Molecular Mechanism for Affinity Conversion and Receptor Signaling.

    PubMed

    Broughton, Sophie E; Hercus, Timothy R; Nero, Tracy L; Dottore, Mara; McClure, Barbara J; Dhagat, Urmi; Taing, Houng; Gorman, Michael A; King-Scott, Jack; Lopez, Angel F; Parker, Michael W

    2016-08-01

    The GM-CSF, IL-3, and IL-5 receptors constitute the βc family, playing important roles in inflammation, autoimmunity, and cancer. Typical of heterodimeric type I cytokine receptors, signaling requires recruitment of the shared subunit to the initial cytokine:α subunit binary complex through an affinity conversion mechanism. This critical process is poorly understood due to the paucity of crystal structures of both binary and ternary receptor complexes for the same cytokine. We have now solved the structure of the binary GM-CSF:GMRα complex at 2.8-Å resolution and compared it with the structure of the ternary complex, revealing distinct conformational changes. Guided by these differences we performed mutational and functional studies that, importantly, show GMRα interactions playing a major role in receptor signaling while βc interactions control high-affinity binding. These results support the notion that conformational changes underlie the mechanism of GM-CSF receptor activation and also suggest how related type I cytokine receptors signal. PMID:27396825

  1. Probing the Sequence of Conformationally-Induced Polarity Changes in the Molecular Chaperonin GroEL with Fluorescence Spectroscopy

    PubMed Central

    Kim, So Yeon; Semyonov, Alexander N.; Twieg, Robert J.; Horwich, Arthur L.; Frydman, Judith; Moerner, W. E.

    2006-01-01

    Hydrophobic interactions play a major role in binding non-native substrate proteins in the central cavity of the bacterial chaperonin GroEL. The sequence of local conformational changes by which GroEL and its cofactor GroES assist protein folding can be explored using the polarity-sensitive fluorescence probe Nile Red. A specific single-cysteine mutant of GroEL (Cys261), whose cysteine is located inside the central cavity at the apical region of the protein, was covalently labeled with synthetically prepared Nile Red maleimide (NR). Bulk fluorescence spectra of Cys261-NR were measured to examine the effects of binding of the stringent substrate, malate dehydrogenase (MDH), GroES, and nucleotide on the local environment of the probe. After binding denatured substrate, the fluorescence intensity increased by 32±7%, suggesting enhanced hydrophobicity at the position of the label. On the other hand, in the presence of ATP, the fluorescence intensity decreased by 13±3%, implying increased local polarity. In order to explore the sequence of local polarity changes, substrate, GroES, and various nucleotides were added in different orders; the resulting changes in emission intensity provide insight into the sequence of conformational changes occurring during GroEL-mediated protein folding. PMID:16375456

  2. Observation and modeling of conformational molecular structures driving the self-assembly of tri-adamantyl benzene on Ag(111).

    PubMed

    Calmettes, Bastien; Estrampes, Nicolas; Coudret, Christophe; Roussel, Thomas J; Faraudo, Jordi; Coratger, Roland

    2016-07-27

    The self-organization of tri-adamantyl (TAB) benzene molecules has been investigated using low temperature scanning tunneling microscopy (LT-STM). The molecular structures have also been studied using molecular modeling. In particular, these calculations have been performed on large areas (1000 nm(2)) from the atomic structure of the molecular building block, combining molecular dynamics (MD) and Monte-Carlo (MC) approaches. These investigations show that the structure of the molecule and its flexibility allow for the formation of different networks as a function of surface coverage. The calculations demonstrate that the stability of the largest structures is obtained through the increase of the interfacial energy induced by the rotation of the adamantyl groups, a behavior whose consequences explain the subtle contrasts observed in the experimental STM images. PMID:26667964

  3. Sum-frequency generation from molecular monolayers using 14 {mu}m radiation from the FELIX free-electron laser

    SciTech Connect

    Van der Ham, E.W.M.; Vrehen, Q.H.F.; Eliel, E.R.

    1995-12-31

    Sum-frequency generation (SFG) has developed into a widely applied tool for study of surfaces and interfaces where molecules are present. It combines the surface specificity of a second-order nonlinear optical technique with the power of a spectroscopic method, and it can be used under widely varying experimental conditions ranging from UHV to electrochemical cells. The important characteristic of SFG is that it allows one to study the average spatial orientation of a molecular bond in a monolayer of molecules at an interface. Until recently SFG measurements were confined to the frequency interval Y {mu} > 1700 cm{sup -1} because of a lack of suitable laser sources at wave-lengths {lambda} > 6 {mu}m. So for most molecules only a few vibrational modes and thus intramolecular bonds can be studied. We have developed a universal sum-frequency spectrometer around the FELIX free-electron law that covers the complete molecular fingerprint since we can generate any IR wavelength between 2.75 and 110 f{mu} at the FELIX facility. We have used this setup for a series of exploratory SFG experiments in a frequency range that was hitherto unexplored in the study of molecular monolayers. We have studied thiol monolayers chemisorbed on a variety of noble metals (Au, Ag, Pt) where we focussed on the C-S stretch vibration at {nu} = 702 cm{sup -1} ({lambda} = 14.3 {mu}m). We have found spectroscopic features revealing the presence of both the trane and gauche conformers of the adsorbed molecules. The present measurements open a whole new wavelength range for nonlinear optical studies of interfaces.

  4. Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies.

    PubMed

    De Capua, Antonia; Goodman, Murray; Amino, Yusuke; Saviano, Michele; Benedetti, Ettore

    2006-02-01

    We report here the synthesis and the conformation analysis by 1H NMR spectroscopy and computer simulations of six potent sweet molecules, N-[3-(3-hydroxy-4-methoxyphenyl)-3-methylbutyl]-alpha-L-aspartyl-S-tert-butyl-L-cysteine 1-methylester (1; 70 000 times more potent than sucrose), N-[3-(3-hydroxy-4-methoxyphenyl)-3-methylbutyl]-alpha-L-aspartyl-beta-cyclohexyl-L-alanine 1-methylester (2; 50 000 times more potent than sucrose), N-[3-(3-hydroxy-4-methoxyphenyl)-3-methylbutyl]-alpha-L-aspartyl-4-cyan-L-phenylalanine 1-methylester (3; 2 000 times more potent than sucrose), N-[3,3-dimethylbutyl]-alpha-L-aspartyl-(1R,2S,4S)-1-methyl-2-hydroxy-4-phenylhexylamide (4; 5500 times more potent than sucrose), N-[3-(3-hydroxy-4-methoxyphenyl)propyl]-alpha-L-aspartyl-(1R,2S,4S)-1-methyl-2-hydroxy-4-phenylhexylamide (5; 15 000 times more potent than sucrose), and N-[3-(3-hydroxy-4-methoxyphenyl)-3-methylbutyl]-alpha-L-aspartyl-(1R,2S,4S)-1-methyl-2-hydroxy-4-phenylhexylamide (6; 15 000 times more potent than sucrose). The "L-shaped" structure, which we believe to be responsible for sweet taste, is accessible to all six molecules in solution. This structure is characterized by a zwitterionic ring formed by the AH- and B-containing moieties located along the +y axis and by the hydrophobic group X pointing into the +x axis. Extended conformations with the AH- and B-containing moieties along the +y axis and the hydrophobic group X pointing into the -y axis were observed for all six sweeteners. For compound 5, the crystal-state conformation was also determined by an X-ray diffraction study. The result indicates that compound 5 adopts an L-shaped structure even in the crystalline state. The extraordinary potency of the N-arylalkylated or N-alkylated compounds 1-6, as compared with that of the unsubstituted aspartame-based sweet taste ligands, can be explained by the effect of a second hydrophobic binding domain in addition to interactions arising from the L-shaped structure. In our

  5. Molecular metal-Oxo catalysts for generating hydrogen from water

    SciTech Connect

    Long, Jeffrey R; Chang, Christopher J; Karunadasa, Hemamala I

    2015-02-24

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition having the general formula [(PY5W.sub.2)MO].sup.2+, wherein PY5W.sub.2 is (NC.sub.5XYZ)(NC.sub.5H.sub.4).sub.4C.sub.2W.sub.2, M is a transition metal, and W, X, Y, and Z can be H, R, a halide, CF.sub.3, or SiR.sub.3, where R can be an alkyl or aryl group. The two accompanying counter anions, in one embodiment, can be selected from the following Cl.sup.-, I.sup.-, PF.sub.6.sup.-, and CF.sub.3SO.sub.3.sup.-. In embodiments of the invention, water, such as tap water containing electrolyte or straight sea water can be subject to an electric potential of between 1.0 V and 1.4 V relative to the standard hydrogen electrode, which at pH 7 corresponds to an overpotential of 0.6 to 1.0 V, with the result being, among other things, the generation of hydrogen with an optimal turnover frequency of ca. 1.5 million mol H.sub.2/mol catalyst per h.

  6. Molecular Dynamics Simulations of the Fluctuating Conformational Dynamics of the Intrinsically Disordered Proteins α-Synuclein and τ

    NASA Astrophysics Data System (ADS)

    Smith, W.; Schreck, Carl; Nath, Abhinav; Rhoades, Elizabeth; O'Hern, Corey

    2013-03-01

    Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop united-atom and coarse-grained Langevin dynamics simulations for the IDPs α-synuclein and τ that include geometric,attractive hydrophobic, and screened electrostatic interactions and are calibrated to the inter-residue separations measured in recent smFRET experiments. We find that these IDPs have conformational statistics that are intermediate between random walk and collapsed globule behavior and demonstrate close resemblance to the known experimental data, with both electrostatics and hydrophobicity strongly influencing the dynamics. We investigate the propensity of α-synuclein to aggregate and form oligomers, and present preliminary results for the aggregation of τ and interactions between these IDPs and small molecules such as heparin and spermine which are known to induce aggregation.

  7. PMG: online generation of high-quality molecular pictures and storyboarded animations.

    PubMed

    Autin, Ludovic; Tufféry, Pierre

    2007-07-01

    The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html. PMID:17478496

  8. Conformational sampling techniques.

    PubMed

    Hatfield, Marcus P D; Lovas, Sándor

    2014-01-01

    The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed. The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed. PMID:23947647

  9. Molecular dynamics investigations of the α-helix to β-barrel conformational transformation in the RfaH transcription factor.

    PubMed

    Gc, Jeevan B; Bhandari, Yuba R; Gerstman, Bernard S; Chapagain, Prem P

    2014-05-15

    The C-terminal domain (CTD) of the transcription antiterminator RfaH folds to an α-helix bundle when it interacts with its N-terminal domain (NTD) but it undergoes an all-α to all-β conformational transformation when it does not interact with the NTD. The RfaH-CTD in the all-α topology is involved in regulating transcription whereas in the all-β topology it is involved in stimulating translation by recruiting a ribosome to an mRNA. Because the conformational transformation in RfaH-CTD gives it a different function, it is labeled as a transformer protein, a class that may eventually include many other functional proteins. The structure and function of RfaH is of interest for its own sake, as well as for the value it may serve as a model system for investigating structural transformations in general. We used replica exchange molecular dynamics simulations with implicit solvent to investigate the α-helix to β-structure transformation of RfaH-CTD, followed by structural relaxation with detailed all atom simulations for the best replica. The importance of interfacial interactions between the two domains of RfaH is highlighted by the compromised structural integrity of the helical form of the CTD in the absence NTD. Calculations of free-energy landscape and transfer entropy elucidate the details of the RfaH-CTD transformation process. PMID:24758259

  10. Force and motion generation of molecular motors: A generic description

    NASA Astrophysics Data System (ADS)

    Jülicher, Frank

    We review the properties of biological motor proteins which move along linear filaments that are polar and periodic. The physics of the operation of such motors can be described by simple stochastic models which are coupled to a chemical reaction. We analyze the essential features of force and motion generation and discuss the general properties of single motors in the framework of two-state models. Systems which contain large numbers of motors such as muscles and flagella motivate the study of many interacting motors within the framework of simple models. In this case, collective effects can lead to new types of behaviors such as dynamic instabilities of the steady states and oscillatory motion.

  11. Molecular characterization of the human Calpha-formylglycine-generating enzyme.

    PubMed

    Preusser-Kunze, Andrea; Mariappan, Malaiyalam; Schmidt, Bernhard; Gande, Santosh Lakshmi; Mutenda, Kudzai; Wenzel, Dirk; von Figura, Kurt; Dierks, Thomas

    2005-04-15

    Calpha-formylglycine (FGly) is the catalytic residue in the active site of sulfatases. In eukaryotes, it is generated in the endoplasmic reticulum by post-translational modification of a conserved cysteine residue. The FGly-generating enzyme (FGE), performing this modification, is an endoplasmic reticulum-resident enzyme that upon overexpression is secreted. Recombinant FGE was purified from cells and secretions to homogeneity. Intracellular FGE contains a high mannose type N-glycan, which is processed to the complex type in secreted FGE. Secreted FGE shows partial N-terminal trimming up to residue 73 without loosing catalytic activity. FGE is a calcium-binding protein containing an N-terminal (residues 86-168) and a C-terminal (residues 178-374) protease-resistant domain. The latter is stabilized by three disulfide bridges arranged in a clamp-like manner, which links the third to the eighth, the fourth to the seventh, and the fifth to the sixth cysteine residue. The innermost cysteine pair is partially reduced. The first two cysteine residues are located in the sequence preceding the N-terminal protease-resistant domain. They can form intramolecular or intermolecular disulfide bonds, the latter stabilizing homodimers. The C-terminal domain comprises the substrate binding site, as evidenced by yeast two-hybrid interaction assays and photocross-linking of a substrate peptide to proline 182. Peptides derived from all known human sulfatases served as substrates for purified FGE indicating that FGE is sufficient to modify all sulfatases of the same species. PMID:15657036

  12. The conformational flexibility of nucleic acid bases paired in gas phase: A Car-Parrinello molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Xiao, Shiyan; Liang, Haojun

    2012-05-01

    The flexibilities of pyrimidine and imidazole rings in the paired nucleobases are investigated using Car-Parrinello molecular dynamics simulation in gas phase. The pairing influence on the stiffness of rings is analyzed based on the molecular structure of the nucleobases and constraints caused by pairing. We prove that the flexibilities of pyrimidine rings in isolated state have subtle correlation with the degree of aromaticity of the rings. The pairings in nucleic base pairs cause the rings to be more rigid for G, T, and U but more flexible for A and the same for C.

  13. Steered molecular dynamics simulations of a bacterial type IV pilus reveal characteristics of an experimentally-observed, force-induced conformational transition

    NASA Astrophysics Data System (ADS)

    Baker, Joseph; Biais, Nicolas; Tama, Florence

    2011-10-01

    Type IV pili (T4P) are long, filamentous structures that emanate from the cellular surface of many infectious bacteria. They are built from a 158 amino acid long subunit called pilin. T4P can grow to many micrometers in length, and can withstand large tension forces. During the infection process, pili attach themselves to host cells, and therefore naturally find themselves under tension. We investigated the response of a T4 pilus to a pulling force using the method of steered molecular dynamics (SMD) simulation. Our simulations expose to the external environment an amino acid sequence initially hidden in the native filament, in agreement with experimental data. Therefore, our simulations might be probing the initial stage of the transition to a force-induced conformation of the T4 pilus. Additional exposed amino acid sequences that might be useful targets for drugs designed to mitigate bacterial infection were also predicted.

  14. GRID3O: Computer program for fast generation of multilevel, three-dimensional boundary-conforming O-type computational grids

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1981-01-01

    A fast algorithm was developed for accurately generating boundary-conforming, three-dimensional, consecutively refined computational grids applicable to arbitrary wing-body and axial turbomachinery geometries. The method is based on using an analytic function to generate two-dimensional grids on a number of coaxial axisymmetric surfaces positioned between the centerbody and the outer radial boundary. These grids are of the O-type and are characterized by quasi-orthogonality, geometric periodicity, and an adequate resolution throughout the flow field. Because the built-in nonorthogonal coordinate stretching and shearing cause the grid lines leaving the blade or wing trailing edge to end at downstream infinity, the numerical treatment of the three-dimensional trailing vortex sheets is simplified.

  15. Molecular modeling and conformational analysis of native and refolded viral genome-linked protein of cardamom mosaic virus.

    PubMed

    Jebasingh, T; Jose, M; Yadunandam, A Kasin; Backiyarani, S; Srividhya, K V; Krishnaswamy, S; Usha, R

    2011-10-01

    The viral genome-linked protein (VPg) of Potyviruses is covalently attached to the 5' end of the genomic RNA. Towards biophysical characterization, the VPg coding region of Cardamom mosaic virus (CdMV) was amplified from the cDNA and expressed in E. coli. Most of the expressed VPg aggregated as inclusion bodies that were solubilized with urea and refolded with L-arginine hydrochloride. The various forms of CdMV VPg (native, denatured and refolded) were purified and the conformational variations between these forms were observed with fluorescence spectroscopy. Native and refolded CdMV VPg showed unordered secondary structure in the circular dichroism (CD) spectrum. The model of CdMV VPg was built based on the crystal structure of phosphotriesterase (from Pseudomonas diminuta), which had the maximum sequence homology with VPg to identify the arrangement of conserved amino acids in the protein to study the functional diversity of VPg. This is the first report on the VPg of CdMV, which is classified as a new member of the Macluravirus genus of the Potyviridae family. PMID:22165292

  16. Fluorinated Polyhedral Oligomeric Silsesquioxane Based Giant Molecular Shape Amphiphiles: Hierarchical Self-Assembly with Unusual Chain Conformation

    NASA Astrophysics Data System (ADS)

    Dong, Xue-Hui; Bo NI Collaboration; Ziran Chen Collaboration; Yiwen Li Collaboration; Wen-Bin Zhang Collaboration; Stephen Z. D. Cheng Collaboration

    2014-03-01

    The fluorous phase has thus been considered as the third phase that repels both oil and water due to its ultra-low surface energy. Incorporation of fluorinated component into hydrophilic/hydrophobic polymers is anticipated to bring novel self-assembly behaviors in the bulk, solution and thin film states, which are not only academically intriguing but also technological relevant. Among them, fluorous molecular clusters are of particular interest. A topologic isomer pair of giant molecular shape amphiphiles can be constructed by tethering molecular nanoparticle at different location of block polymers. In this study, a fluorinated polyhedral oligomeric silsesquioxane (FPOSS) was precisely fixed onto polystyreneblockpoly(ethylene oxide) (PS- b-PEO) at chain end (FPOSS-PS- b-PEO), or junction point [PS-(FPOSS)-PEO]. The interplay between nanoparticle and block polymers results in hierarchical structures with three types of order. The incommensuration of cross-sectional area between FPOSS and block polymer stretches polymer chains, which found to enhance the immiscibility between PEO and PS block.

  17. Spatially Resolving Ordered and Disordered Conformers and Photocurrent Generation in Intercalated Conjugated Polymer/Fullerene Blend Solar Cells

    PubMed Central

    2015-01-01

    Resonance Raman spectroscopy was used to identify ordered and disordered conformers of poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT) blended with the electron acceptor [6,6]-phenyl C61 butyric acid methyl ester (PCBM) in bulk heterojunction (BHJ) solar cells where PCBM intercalates into PBTTT side groups. We show that the PBTTT thiophene ring symmetric C=C stretching mode consists of contributions from ordered (ℏωC=C = 1489 cm–1, fwhm ∼ 15 cm–1) and disordered (ℏωC=C = 1500 cm–1, fwhm ∼ 25 cm–1) components and their relative amounts are sensitive to PCBM loading, annealing and excitation energy. The 1500 cm–1 PBTTT component originates from twisted thiophene rings and disordered side groups due to PCBM intercalation in a mixed kinetic phase and thermal annealing promotes ordering of PBTTT chains from the formation of bimolecular PBTTT/PCBM crystals. Density functional theory (DFT) Raman simulations of PBTTT monomers support these assignments. Resonance Raman images of annealed PBTTT/PCBM model solar cells confirm that ordered PBTTT chains are most concentrated in PCBM-rich bimolecular crystals and corresponding intensity modulated photocurrent spectroscopy (IMPS) and imaging measurements show increased nongeminate charge recombination at the boundaries of ordered/disordered regions. PMID:25678742

  18. Application of next generation sequencing to molecular diagnosis of inherited diseases.

    PubMed

    Zhang, Wei; Cui, Hong; Wong, Lee-Jun C

    2014-01-01

    Recent development of high throughput, massively parallel sequencing (MPS or next generation sequencing, NGS) technology has revolutionized the molecular diagnosis of human genetic disease. The ability to generate enormous amount of sequence data in a short time at an affordable cost makes this approach ideal for a wide range of applications from sequencing a group of candidate genes, all coding regions (known as exome sequencing) to the entire human genome. The technology brings about an unprecedented application to the identification of the molecular basis of hard-to-diagnose genetic disorders. This chapter reviews the up-to-date published application of next generation sequencing in clinical molecular diagnostic laboratories. We also emphasize the various target gene enrichment methods and their advantages and shortcomings. Obstacles to compliance with regulatory authorities like CLIA/CAP in clinical settings are also briefly discussed. PMID:22576358

  19. A conformational analysis of mouse Nalp3 domain structures by molecular dynamics simulations, and binding site analysis.

    PubMed

    Sahoo, Bikash R; Maharana, Jitendra; Bhoi, Gopal K; Lenka, Santosh K; Patra, Mahesh C; Dikhit, Manas R; Dubey, Praveen K; Pradhan, Sukanta K; Behera, Bijay K

    2014-05-01

    Scrutinizing various nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) genes in higher eukaryotes is very important for understanding the intriguing mechanism of the host defense against pathogens. The nucleotide-binding domain (NACHT), leucine-rich repeat (LRR), and pyrin domains (PYD)-containing protein 3 (Nalp3), is an intracellular innate immune receptor and is associated with several immune system related disorders. Despite Nalp3's protective role during a pathogenic invasion, the molecular features and structural organization of this crucial protein is poorly understood. Using comparative modeling and molecular dynamics simulations, we have studied the structural architecture of Nalp3 domains, and characterized the dynamic and energetic parameters of adenosine triphosphate (ATP) binding in NACHT, and pathogen-derived ligands muramyl dipeptide (MDP) and imidazoquinoline with LRR domains. The results suggested that walker A, B and extended walker B motifs were the key ATP binding regions in NACHT that mediate self-oligomerization. The analysis of the binding sites of MDP and imidazoquinoline revealed LRR 7-9 to be the most energetically favored site for imidazoquinoline interaction. However, the binding free energy calculations using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method indicated that MDP is incompatible for activating the Nalp3 molecule in its monomeric form, and suggest its complex interaction with NOD2 or other NLRs accounts for MDP recognition. The high binding affinity of ATP with NACHT was correlated to the experimental data for human NLRs. Our binding site prediction for imidazoquinoline in LRR warrants further investigation via in vivo models. This is the first study that provides ligand recognition in mouse Nalp3 and its spatial structural arrangements. PMID:24595807

  20. Conformational study on an insect neuropeptide of the AKH/RPCH-family by combined 1H NMR spectroscopy and molecular mechanics.

    PubMed

    Zubrzycki, I Z; Gäde, G

    1994-01-14

    Peptides of the AKH/RPCH family are mainly involved in influencing energy metabolism in insects, i.e., regulating carbohydrate and/or lipid breakdown in the fat body. We have studied the solution conformation of a member of this family, the peptide Emp-AKH from praying mantis. It has been characterized by use of two dimensional nuclear magnetic resonance spectroscopy and molecular modelling. The proton spectrum of the Emp-AKH peptide was assigned by sequential assignment procedure. Proton-proton distances were derived from the volumes of cross-peaks in two dimensional nuclear Overhauser enhancement spectra. The three dimensional structure was built using Evans & Sutherland molecular modelling station. Our data indicate that the Emp-AKH peptide has adopted a beta-sheet structure for amino acids 1 to 5 and a beta-turn for amino acids at positions 5 to 8. The type of turn appears to be a Non-specific beta-turn. PMID:8292025

  1. High molecular weight first generation PMR polyimides for 343 C applications

    NASA Technical Reports Server (NTRS)

    Malarik, Diane C.; Vannucci, Raymond D.

    1991-01-01

    The effect of molecular weight on 343 C thermo-oxidative stability (TOS), mechanical properties, and processability, of the first generation PMR polyimides was studied. Graphite fiber reinforced PMR-15, PMR-30, PMR-50, and PMR-75 composites (corresponding to formulated molecular weights of 1500, 3000, 5000, and 7500, respectively) were fabricated using a simulated autoclave process. The data reveals that while alternate autoclave cure schedules are required for the high molecular weight resins, low void laminates can be fabricated which have significantly improved TOS over PMR-15, with only a small sacrifice in mechanical properties.

  2. High molecular weight first generation PMR polyimides for 343 C applications

    NASA Technical Reports Server (NTRS)

    Malarik, D. C.; Vannucci, R. D.

    1992-01-01

    The effect of molecular weight on 343 C thermo-oxidative stability (TOS), mechanical properties, and processability, of the first generation PMR polyimides was studied. Graphite fiber reinforced PMR-15, PMR-30, PMR-50, and PMR-75 composites (corresponding to formulated molecular weights of 1500, 3000, 5000, and 7500, respectively) were fabricated using a simulated autoclave process. The data reveal that while alternate autoclave cure schedules are required for the high molecular weight resins, low void laminates can be fabricated which have significantly improved TDS over PMR-15, with only a small sacrifice in mechanical properties.

  3. Functional conformations of the L11–ribosomal RNA complex revealed by correlative analysis of cryo-EM and molecular dynamics simulations

    PubMed Central

    Li, Wen; Sengupta, Jayati; Rath, Bimal K.; Frank, Joachim

    2006-01-01

    The interaction between the GTPase-associated center (GAC) and the aminoacyl-tRNA·EF-Tu·GTP ternary complex is of crucial importance in the dynamic process of decoding and tRNA accommodation. The GAC includes protein L11 and helices 43–44 of 23S rRNA (referred to as L11–rRNA complex). In this study, a method of fitting based on a systematic comparison between cryo-electron microscopy (cryo-EM) density maps and structures obtained by molecular dynamics simulations has been developed. This method has led to the finding of atomic models of the GAC that fit the EM maps with much improved cross-correlation coefficients compared with the fitting of the X-ray structure. Two types of conformations of the L11–rRNA complex, produced by the simulations, match the cryo-EM maps representing the states either bound or unbound to the aa-tRNA·EF-Tu·GTP ternary complex. In the bound state, the N-terminal domain of L11 is extended from its position in the crystal structure, and the base of nucleotide A1067 in the 23S ribosomal RNA is flipped out. This position of the base allows the RNA to reach the elbow region of the aminoacyl-tRNA when the latter is bound in the A/T site. In the unbound state, the N-terminal domain of L11 is rotated only slightly, and A1067 of the RNA is flipped back into the less-solvent-exposed position, as in the crystal structure. By matching our experimental cryo-EM maps with much improved cross-correlation coefficients compared to the crystal structure, these two conformations prove to be strong candidates of the two functional states. PMID:16682558

  4. Intramolecular fixation of t-butyl groups in thiolactim ethers influencing molecular conformation and the packing behavior

    NASA Astrophysics Data System (ADS)

    Hübscher, Jörg; Gruber, Thomas; Seichter, Wilhelm; Kortus, Jens; Weber, Edwin

    2015-07-01

    Derived from the result of a previous crystallographic study regarding an ethynylene bridged bispyrimidine, the presence of two intramolecular C-H⋯N hydrogen bonding contacts being responsible for a fixation of the terminal t-butylthio units to the azine nitrogens was noticed. Acting as stimulus, a series of different pyridine and pyridazine derivatives also featuring this unusual functionality has been synthesized and structurally studied. In order to support the investigations concerning this particular bonding pattern performed via X-ray structure analysis, calculations based on the density functional theory were carried out. It was found that the formation of the intramolecular hydrogen bonding motif has not only impact on the molecular stability but in some cases also predictably influences the reactivity and the packing behavior of the different heterocycles.

  5. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    SciTech Connect

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.

  6. A wrench in the works of human acetylcholinesterase: Soman induced conformational changes revealed by molecular dynamics simulations

    DOE PAGESBeta

    Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean -Luc; Emigh, Aiyana; Lightstone, Felice C.; Salsbury , Jr, Freddie

    2015-04-13

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone andmore » sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.« less

  7. A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations

    PubMed Central

    Fattebert, Jean-Luc; Emigh, Aiyana

    2015-01-01

    Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures. PMID:25874456

  8. The Interplay Between Conformation and Absolute Configuration in Chiral Electron Dynamics of Small Diols.

    PubMed

    Daly, Steven; Tia, Maurice; Garcia, Gustavo A; Nahon, Laurent; Powis, Ivan

    2016-09-01

    A competition between chiral characteristics alternatively attributable to either conformation or to absolute configuration is identified. Circular dichroism associated with photoexcitation of the outer orbital of configurational enantiomers of 1,3- and 2,3-butanediols has been examined with a focus on the large changes in electron chiral asymmetry produced by different molecular conformations. Experimental gas-phase measurements offer support for the theoretical modeling of this chiroptical effect. A surprising prediction is that a conformationally produced pseudo-enantiomerism in 1,3-butanediol generates a chiral response in the frontier electron dynamics that outweighs the influence of the permanent configurational handedness established at the asymmetrically substituted carbon. Induced conformation, and specifically induced conformational chirality, may thus be a dominating factor in chiral molecular recognition in such systems. PMID:27445202

  9. Understanding the Differences in Molecular Conformation of Carbohydrate and Protein in Endosperm Tissues of Grains with Different Biodegradation Kinetics Using Advanced Synchrotron Technology

    SciTech Connect

    Yu, P.; Block, H; Doiron, K

    2009-01-01

    Conventional 'wet' chemical analyses rely heavily on the use of harsh chemicals and derivatization, thereby altering native seed structures leaving them unable to detect any original inherent structures within an intact tissue sample. A synchrotron is a giant particle accelerator that turns electrons into light (million times brighter than sunlight) which can be used to study the structure of materials at the molecular level. Synchrotron radiation-based Fourier transform IR microspectroscopy (SR-FTIRM) has been developed as a rapid, direct, non-destructive and bioanalytical technique. This technique, taking advantage of the brightness of synchrotron light and a small effective source size, is capable of exploring the molecular chemistry within the microstructures of a biological tissue without the destruction of inherent structures at ultraspatial resolutions within cellular dimensions. This is in contrast to traditional 'wet' chemical methods, which, during processing for analysis, often result in the destruction of the intrinsic structures of feeds. To date there has been very little application of this technique to the study of plant seed tissue in relation to nutrient utilization. The objective of this study was to use novel synchrotron radiation-based technology (SR-FTIRM) to identify the differences in the molecular chemistry and conformation of carbohydrate and protein in various plant seed endosperms within intact tissues at cellular and subcellular level from grains with different biodegradation kinetics. Barley grain (cv. Harrington) with a high rate (31.3%/h) and extent (78%), corn grain (cv. Pioneer) with a low rate (9.6%/h) and extent of (57%), and wheat grain (cv. AC Barrie) with an intermediate rate (23%/h) and extent (72%) of ruminal DM degradation were selected for evaluation. SR-FTIRM evaluations were performed at the National Synchrotron Light Source at the Brookhaven National Laboratory (Brookhaven, NY). These results suggest that SR-FTIRM plus

  10. Receptor Activity-modifying Proteins 2 and 3 Generate Adrenomedullin Receptor Subtypes with Distinct Molecular Properties.

    PubMed

    Watkins, Harriet A; Chakravarthy, Madhuri; Abhayawardana, Rekhati S; Gingell, Joseph J; Garelja, Michael; Pardamwar, Meenakshi; McElhinney, James M W R; Lathbridge, Alex; Constantine, Arran; Harris, Paul W R; Yuen, Tsz-Ying; Brimble, Margaret A; Barwell, James; Poyner, David R; Woolley, Michael J; Conner, Alex C; Pioszak, Augen A; Reynolds, Christopher A; Hay, Debbie L

    2016-05-27

    Adrenomedullin (AM) is a peptide hormone with numerous effects in the vascular systems. AM signals through the AM1 and AM2 receptors formed by the obligate heterodimerization of a G protein-coupled receptor, the calcitonin receptor-like receptor (CLR), and receptor activity-modifying proteins 2 and 3 (RAMP2 and RAMP3), respectively. These different CLR-RAMP interactions yield discrete receptor pharmacology and physiological effects. The effective design of therapeutics that target the individual AM receptors is dependent on understanding the molecular details of the effects of RAMPs on CLR. To understand the role of RAMP2 and -3 on the activation and conformation of the CLR subunit of AM receptors, we mutated 68 individual amino acids in the juxtamembrane region of CLR, a key region for activation of AM receptors, and determined the effects on cAMP signaling. Sixteen CLR mutations had differential effects between the AM1 and AM2 receptors. Accompanying this, independent molecular modeling of the full-length AM-bound AM1 and AM2 receptors predicted differences in the binding pocket and differences in the electrostatic potential of the two AM receptors. Druggability analysis indicated unique features that could be used to develop selective small molecule ligands for each receptor. The interaction of RAMP2 or RAMP3 with CLR induces conformational variation in the juxtamembrane region, yielding distinct binding pockets, probably via an allosteric mechanism. These subtype-specific differences have implications for the design of therapeutics aimed at specific AM receptors and for understanding the mechanisms by which accessory proteins affect G protein-coupled receptor function. PMID:27013657

  11. Receptor Activity-modifying Proteins 2 and 3 Generate Adrenomedullin Receptor Subtypes with Distinct Molecular Properties*

    PubMed Central

    Watkins, Harriet A.; Chakravarthy, Madhuri; Abhayawardana, Rekhati S.; Gingell, Joseph J.; Garelja, Michael; Pardamwar, Meenakshi; McElhinney, James M. W. R.; Lathbridge, Alex; Constantine, Arran; Harris, Paul W. R.; Yuen, Tsz-Ying; Brimble, Margaret A.; Barwell, James; Poyner, David R.; Woolley, Michael J.; Conner, Alex C.; Pioszak, Augen A.; Reynolds, Christopher A.

    2016-01-01

    Adrenomedullin (AM) is a peptide hormone with numerous effects in the vascular systems. AM signals through the AM1 and AM2 receptors formed by the obligate heterodimerization of a G protein-coupled receptor, the calcitonin receptor-like receptor (CLR), and receptor activity-modifying proteins 2 and 3 (RAMP2 and RAMP3), respectively. These different CLR-RAMP interactions yield discrete receptor pharmacology and physiological effects. The effective design of therapeutics that target the individual AM receptors is dependent on understanding the molecular details of the effects of RAMPs on CLR. To understand the role of RAMP2 and -3 on the activation and conformation of the CLR subunit of AM receptors, we mutated 68 individual amino acids in the juxtamembrane region of CLR, a key region for activation of AM receptors, and determined the effects on cAMP signaling. Sixteen CLR mutations had differential effects between the AM1 and AM2 receptors. Accompanying this, independent molecular modeling of the full-length AM-bound AM1 and AM2 receptors predicted differences in the binding pocket and differences in the electrostatic potential of the two AM receptors. Druggability analysis indicated unique features that could be used to develop selective small molecule ligands for each receptor. The interaction of RAMP2 or RAMP3 with CLR induces conformational variation in the juxtamembrane region, yielding distinct binding pockets, probably via an allosteric mechanism. These subtype-specific differences have implications for the design of therapeutics aimed at specific AM receptors and for understanding the mechanisms by which accessory proteins affect G protein-coupled receptor function. PMID:27013657

  12. Molecular sieve generation of aviator's oxygen: Performance of a prototype system under simulated flight conditions.

    PubMed

    Miller, R L; Ikels, K G; Lamb, M J; Boscola, E J; Ferguson, R H

    1980-07-01

    The molecular sieve method of generating an enriched-oxygen breathing gas is one of several candidate onboard oxygen generation (OBOG) systems under joint Army-Navy-Air Force development for application in tactical aircraft. The performance of a nominal two-man-capacity molecular sieve oxygen generation system was characterized under simulated flight conditions. Data are given on the composition of the molecular sieve-generated breathing gas (oxygen, nitrogen, carbon dioxide, and argon) as a function of inlet air pressure, altitude, breathing gas flow rate, and ambient temperature. The maximum oxygen concentration observed was 95%, with the balance argon. At low demand flow rates and certain conditions of pressure and altitude, the argon enrichment factor exceeded that of oxygen giving a maximum argon concentration of 6.6% with the balance oxygen. The structural integrity of the unit was verified by vibration and centrifuge testing. The performance of the molecular sieve unit is discussed in the context of aircraft operating envelopes using both diluter-demand and 100% delivery subsystems. PMID:6774707

  13. Procedures for the Generation of Mature Chlamydomonas reinhardtii Zygotes for Molecular and Biochemical Analyses 1

    PubMed Central

    Wegener, Dorothee; Treier, Ulrike; Beck, Christoph F.

    1989-01-01

    Zygotes represent an important stage in the sexual cycle of the unicellular green alga Chlamydomonas reinhardtii. To study zygote germination at a molecular level, a protocol was elaborated for the generation of zygotes in large quantities and a method was developed for the extraction from zygotes of RNA that could be translated in vitro. Images Figure 1 Figure 3 PMID:16666800

  14. Molecular structures and conformations of 1-benzenesulphonyl-2-oxo-5-alkoxypyrrolidines with anti-amnesic activity. X-ray, 1H-NMR and quantum mechanical (PM3) studies

    NASA Astrophysics Data System (ADS)

    Amato, Maria E.; Bandoli, Giuliano; Dolmella, Alessandro; Grassi, Antonio; Pappalardo, Giuseppe C.; Toja, Emilio

    1991-04-01

    The crystal and molecular structures of the nootropic agents RU-47001 ((±) 1-(4-nitrobenzenesulphonyl)-2-oxo-5-ethoxypyrrolidine) and RU-47064 ((±) 1-(4-nitrobenzenesulphonyl)-2-oxo-5-isopropyloxypyrrolidine) have been determined by X-ray analysis and their solution conformation has been investigated using 1H NMR spectroscopy. The conformations of these molecules together with those of their analogues RU-35929 ((±) 1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine), RU-47010 ((±) 1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine) and RU-35965 ((±) 1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine) have been deduced from semi-quantitative PM3 type theoretical calculations. The main feature of all compounds consists of a common envelope conformation with C (4) at the flap of the pyrrolidinone ring in the solid, that in solution changes into the analogous, but opposite, possible puckered conformational isomer. The 5-alkoxy groups were found rather flexible in solution. Theoretical preferred conformations about NS and SC bonds were in acceptable agreement with those of the solid state. The calculated torsional energetics suggested that 1- 5 do not undergo conformational interconversion.

  15. A Molecular Dynamics Investigation of Mycobacterium tuberculosis Prenyl Synthases: Conformational Flexibility, and Implications for Computer-Aided Drug Discovery

    PubMed Central

    Kim, M. Olivia; Feng, Xinxin; Feixas, Ferran; Zhu, Wei; Lindert, Steffen; Bogue, Shannon; Sinko, William; de Oliveira, César; Rao, Guodong; Oldfield, Eric; McCammon, J. Andrew

    2014-01-01

    With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS) are involved in bacterial cell wall biosynthesis while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 µM inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC50 ~0.5-20 µM inhibitor (depending on substrate) of cis-DPPS, a ~660 nM inhibitor of Rv3378c as well as a 4.8 µM inhibitor of cis-FPPS, opening up the possibility of multi-target inhibition involving both cell wall biosynthesis as well as virulence factor formation. PMID:25352216

  16. Conformational alterations induced by novel green 16-E2-16 gemini surfactant in xanthine oxidase: Biophysical insights from tensiometry, spectroscopy, microscopy and molecular modeling.

    PubMed

    Akram, Mohd; Bhat, Imtiyaz Ahmad; Bhat, Waseem Feeroze; Kabir-ud-Din

    2015-11-01

    Herein we report the interaction of a biodegradable gemini surfactant, ethane-1,2-diyl bis(N,N-dimethyl-N-hexadecylammoniumacetoxy) dichloride (16-E2-16) with bovine milk xanthine oxidase (XO), employing tensiometry, fluorescence spectroscopy, UV spectroscopy, far-UV circular dichroism spectroscopy (CD), Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and computational molecular modeling. Surface tension results depict substantial changes in the micellar as well as interfacial parameters (CMC, ΠCMC, γCMC, Γmax, Amin, ΔGmic° and ΔGads°) of 16-E2-16 gemini surfactant upon XO combination, deciphering the interaction of XO with the gemini surfactant. Fluorescence measurements reveal that 16-E2-16 gemini surfactant causes quenching in the xanthine oxidase (XO) fluorescence spectra via static procedure and the values of various evaluated binding parameters (KSV, Kb, kq, ΔGb° and n) describe that 16-E2-16 effectively binds to XO. Three dimensional fluorescence, 8-anilino-1-naphthalene sulfonic acid (ANS) binding, F1F3 ratio, UV, CD, FTIR, SEM and TEM results delineate changes in the secondary structure of xanthine oxidase. Molecular docking results provide complement to the steady-state fluorescence findings and support the view that quenching occurs due to non-polar environment experienced by aromatic residues of the enzyme. The results of this study can help scientists to tune the conformation of an enzyme (XO) with biocompatible amphiphilic microstructures, which will help to unfold further understanding in the treatment modes of various diseases like gout, hyperuricemia, liver and brain necrosis. PMID:26057098

  17. Continuous and Pulsed THz generation with molecular gas lasers and photoconductive antennas gated by femtosecond pulses

    NASA Astrophysics Data System (ADS)

    Cruz, Flavio C.; Nogueira, T.; Costa, Leverson F. L.; Jarschel, Paulo F.; Frateschi, Newton C.; Viscovini, Ronaldo C.; Vieira, Bruno R. B.; Guevara, Victor M. B.; Pereira, Daniel

    2008-04-01

    We report THz generation based on two systems: 1) continuous-wave (cw) laser generation in molecular gas lasers, and 2) short pulse generation in photoconductive antennas, gated by femtosecond near-infrared Ti:sapphire lasers. With the first system, we have generated tens of monochromatic cw laser lines over the last years, extending roughly from 40 microns to several hundred microns. This is done by optical pumping of gas lasers based on polar molecules such as methanol and its isotopes. In the second system, under development, pulsed THz radiation is generated by a photoconductive antenna built in a semi-insulating GaAs substrate excited by femtosecond pulses from a near-infrared (800 nm) Ti:sapphire laser.

  18. Relationships among 3 Kochia species based on PCR-generated molecular sequences and molecular cytogenetics.

    PubMed

    Lee, B S; Kim, M Y; Wang, R R-C; Waldron, B L

    2005-12-01

    Forage kochia (Kochia prostrata ssp. virescens 'Immigrant' is native to the arid and semiarid regions of central Eurasia. It was introduced into the United States in 1966 as PI 314929 and released as a perennial forage shrub in 1984. Kochia americana is a perennial native to the United States, whereas Kochia scorparia is an introduced annual species that became a weed. To assess both the breeding potential and the possibility of genetic contamination, relationships among the 3 Kochia species were analyzed using random amplified polymorphic DNA (RAPD) markers, sequence tagged site (STS) marker sequences of the chloroplast NADH dehydrogenase gene (ndhF), genomic in situ hybridization (GISH), and multicolor fluorescence in situ hybridization (MC-FISH). Seventy decamer random primers yielded 458 polymorphic bands from 9 plants of K. americana, 20 plants of K. prostrata, and 7 plants of K. scoparia. Fifty-four and 55 species-specific RAPD markers were identified for K. americana and K. prostrata, whereas 80 RAPD markers were specific to K. scoparia. Based on the presence or absence of informative RAPD markers, the 3 species always grouped into 3 distinct clusters in a NTSYSpc2.01b-generated dendrogram. The same relationships were found among the 3 Kochia species based on ndhF DNA sequence divergence. Using a set of 7 STS markers that can identify each Kochia species, we did not find a single interspecific hybrid from artificial hybridizations among the 3 Kochia species. In GISH studies, chromosomes of 1 species fluoresced in green only when they were probed by genomic DNA of the same species. Cross-hybridization by genomic DNA of another species was not observed. In FISH studies using pTa71 (for 18S-5.8S-26S rDNAs) and pScT7 (for 5S rDNA) as probes, there were 1, 1 and 3 pTa71 sites and 2, 1, and 1 pScT7 sites in each haplome of K. prostrata, K. americana, and K. scoparia, respectively. It is concluded that these 3 Kochia species are so genomically distinct that gene

  19. Molecular mechanism for cyclic generation of somites: Lessons from mice and zebrafish.

    PubMed

    Yabe, Taijiro; Takada, Shinji

    2016-01-01

    The somite is the most prominent metameric structure observed during vertebrate embryogenesis, and its metamerism preserves the characteristic structures of the vertebrae and muscles in the adult body. During vertebrate somitogenesis, sequential formation of epithelialized cell boundaries generates the somites. According to the "clock and wavefront model," the periodical and sequential generation of somites is achieved by the integration of spatiotemporal information provided by the segmentation clock and wavefront. In the anterior region of the presomitic mesoderm, which is the somite precursor, the orchestration between the segmentation clock and the wavefront achieves morphogenesis of somites through multiple processes such as determination of somite boundary position, generation of morophological boundary, and establishment of the rostrocaudal polarity within a somite. Recently, numerous studies using various model animals including mouse, zebrafish, and chick have gradually revealed the molecular aspect of the "clock and wavefront" model and the molecular mechanism connecting the segmentation clock and the wavefront to the multiple processes of somite morphogenesis. In this review, we first summarize the current knowledge about the molecular mechanisms underlying the clock and the wavefront and then describe those of the three processes of somite morphogenesis. Especially, we will discuss the conservation and diversification in the molecular network of the somitigenesis among vertebrates, focusing on two typical model animals used for genetic analyses, i.e., the mouse and zebrafish. In this review, we described molecular mechanism for the generation of somites based on the spatiotemporal information provided by "segmentation clock" and "wavefront" focusing on the evidences obtained from mouse and zebrafish. PMID:26676827

  20. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. PMID:27038223

  1. The Relationship between Self-Assembly and Conformal Mappings

    NASA Astrophysics Data System (ADS)

    Duque, Carlos; Santangelo, Christian

    The isotropic growth of a thin sheet has been used as a way to generate programmed shapes through controlled buckling. We discuss how conformal mappings, which are transformations that locally preserve angles, provide a way to quantify the area growth needed to produce a particular shape. A discrete version of the conformal map can be constructed from circle packings, which are maps between packings of circles whose contact network is preserved. This provides a link to the self-assembly of particles on curved surfaces. We performed simulations of attractive particles on a curved surface using molecular dynamics. The resulting particle configurations were used to generate the corresponding discrete conformal map, allowing us to quantify the degree of area distortion required to produce a particular shape by finding particle configurations that minimize the area distortion.

  2. Hybrid Quantum/Classical Molecular Dynamics Simulations of the Proton Transfer Reactions Catalyzed by Ketosteroid Isomerase: Analysis of Hydrogen Bonding, Conformational Motions, and Electrostatics

    PubMed Central

    Chakravorty, Dhruva K.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2009-01-01

    Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ~8, and dynamical barrier recrossings decrease the rates by a factor of 3–4. For both proton transfer reactions, the donor-acceptor distance decreases substantially at the transition state. The carboxylate group of the Asp38 side chain, which serves as the proton acceptor and donor in the first and second steps, respectively, rotates significantly between the two proton transfer reactions. The hydrogen bonding interactions within the active site are consistent with the hydrogen bonding of both Asp99 and Tyr14 to the substrate. The simulations suggest that a hydrogen bond between Asp99 and the substrate is present from the beginning of the first proton transfer step, whereas the hydrogen bond between Tyr14 and the substrate is virtually absent in the first part of this step but forms nearly concurrently with the formation of the transition state. Both hydrogen bonds are present throughout the second proton transfer step until partial dissociation of the product. The hydrogen bond between Tyr14 and Tyr55 is present throughout both proton transfer steps. The active site residues are more mobile during the first step than during the second step. The van der Waals interaction energy between the substrate and the enzyme remains virtually constant along the reaction pathway, but the electrostatic interaction energy is significantly stronger for the dienolate intermediate than for the reactant and product. Mobile loop regions distal to the active site exhibit significant structural rearrangements and, in some cases, qualitative changes in the electrostatic potential during the catalytic reaction. These results suggest that

  3. Understanding the differences in molecular conformation of carbohydrate and protein in endosperm tissues of grains with different biodegradation kinetics using advanced synchrotron technology

    NASA Astrophysics Data System (ADS)

    Yu, P.; Block, H. C.; Doiron, K.

    2009-01-01

    Conventional "wet" chemical analyses rely heavily on the use of harsh chemicals and derivatization, thereby altering native seed structures leaving them unable to detect any original inherent structures within an intact tissue sample. A synchrotron is a giant particle accelerator that turns electrons into light (million times brighter than sunlight) which can be used to study the structure of materials at the molecular level. Synchrotron radiation-based Fourier transform IR microspectroscopy (SR-FTIRM) has been developed as a rapid, direct, non-destructive and bioanalytical technique. This technique, taking advantage of the brightness of synchrotron light and a small effective source size, is capable of exploring the molecular chemistry within the microstructures of a biological tissue without the destruction of inherent structures at ultraspatial resolutions within cellular dimensions. This is in contrast to traditional 'wet' chemical methods, which, during processing for analysis, often result in the destruction of the intrinsic structures of feeds. To date there has been very little application of this technique to the study of plant seed tissue in relation to nutrient utilization. The objective of this study was to use novel synchrotron radiation-based technology (SR-FTIRM) to identify the differences in the molecular chemistry and conformation of carbohydrate and protein in various plant seed endosperms within intact tissues at cellular and subcellular level from grains with different biodegradation kinetics. Barley grain (cv. Harrington) with a high rate (31.3%/h) and extent (78%), corn grain (cv. Pioneer) with a low rate (9.6%/h) and extent of (57%), and wheat grain (cv. AC Barrie) with an intermediate rate (23%/h) and extent (72%) of ruminal DM degradation were selected for evaluation. SR-FTIRM evaluations were performed at the National Synchrotron Light Source at the Brookhaven National Laboratory (Brookhaven, NY). The molecular structure spectral analysis

  4. Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

    NASA Astrophysics Data System (ADS)

    Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

    2014-03-01

    A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

  5. Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies

    PubMed Central

    Chakraborty, Kausik; Durani, Venuka; Miranda, Edward Roshan; Citron, Michael; Liang, Xiaoping; Schleif, William; Joyce, Joseph G.; Varadarajan, Raghavan

    2006-01-01

    gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding cell-tropism of the virus. 447-52D is a monoclonal antibody that recognizes the conserved tip of the V3 loop in a β-turn conformation. This antibody has previously been shown to neutralize diverse strains of the virus. In an attempt to generate an immunogen competent to generate 447-52D-like antibodies, the known epitope of 447-52D was inserted at three different surface loop locations in the small, stable protein Escherichia coli Trx (thioredoxin). At one of the three locations (between residues 74 and 75), the insertion was tolerated, the resulting protein was stable and soluble, and bound 447-52D with an affinity similar to that of intact gp120. Upon immunization, the V3 peptide-inserted Trx scaffold was able to generate anti-V3 antibodies that could compete out 447-52D binding to gp120. Epitope mapping studies demonstrated that these anti-V3 antibodies recognized the same epitope as 447-52D. Although the 447-52D-type antibodies were estimated to be present at concentrations of 50–400 μg/ml of serum, these were not able to effect neutralization of strains like JRFL and BAL but could neutralize the sensitive MN strain. The data suggest that because of the low accessibility of the V3 loop on primary isolates such as JRFL, it will be difficult to elicit a V3-specific, 447-52D-like antibody response to effectively neutralize such isolates. PMID:16827663

  6. Generation of Neutralizing Monoclonal Antibodies against a Conformational Epitope of Human Adenovirus Type 7 (HAdv-7) Incorporated in Capsid Encoded in a HAdv-3-Based Vector

    PubMed Central

    Li, Xiao; Zhou, Zhichao; Li, Chenyang; Zhou, Rong

    2014-01-01

    The generation of monoclonal antibodies (MAbs) by epitope-based immunization is difficult because the immunogenicity of simple peptides is poor and T cells must be potently stimulated and immunological memory elicited. A strategy in which antigen is incorporated into the adenoviral capsid protein has been used previously to develop antibody responses against several vaccine targets and may offer a solution to this problem. In this study, we used a similar strategy to develop HAdv-7-neutralizing MAbs using rAdMHE3 virions into which hexon hypervariable region 5 (HVR5) of adenovirus type 7 (HAdv-7) was incorporated. The epitope mutant rAdMHE3 was generated by replacing HVR5 of Ad3EGFP, a recombinant HAdv-3-based vector expressing enhanced green fluorescence protein, with HVR5 of HAdv-7. We immunized BALB/c mice with rAdMHE3 virions and produced 22 different MAbs against them, four of which showed neutralizing activity against HAdv-7 in vitro. Using an indirect enzyme-linked immunosorbent assay (ELISA) analysis and an antibody-binding-competition ELISA with Ad3EGFP, HAdv-7, and a series of chimeric adenoviral particles containing epitope mutants, we demonstrated that the four MAbs recognize the neutralization site within HVR5 of the HAdv-7 virion. Using an immunoblotting analysis and ELISA with HAdv-7, recombinant peptides, and a synthetic peptide, we also showed that the neutralizing epitope within HVR5 of the HAdv-7 virion is a conformational epitope. These findings suggest that it is feasible to use a strategy in which antigen is incorporated into the adenoviral capsid protein to generate neutralizing MAbs. This strategy may also be useful for developing therapeutic neutralizing MAbs and designing recombinant vector vaccines against HAdv-7, and in structural analysis of adenoviruses. PMID:25054273

  7. Conformation-controlled binding kinetics of antibodies

    NASA Astrophysics Data System (ADS)

    Galanti, Marta; Fanelli, Duccio; Piazza, Francesco

    2016-01-01

    Antibodies are large, extremely flexible molecules, whose internal dynamics is certainly key to their astounding ability to bind antigens of all sizes, from small hormones to giant viruses. In this paper, we build a shape-based coarse-grained model of IgG molecules and show that it can be used to generate 3D conformations in agreement with single-molecule Cryo-Electron Tomography data. Furthermore, we elaborate a theoretical model that can be solved exactly to compute the binding rate constant of a small antigen to an IgG in a prescribed 3D conformation. Our model shows that the antigen binding process is tightly related to the internal dynamics of the IgG. Our findings pave the way for further investigation of the subtle connection between the dynamics and the function of large, flexible multi-valent molecular machines.

  8. Conformation-controlled binding kinetics of antibodies.

    PubMed

    Galanti, Marta; Fanelli, Duccio; Piazza, Francesco

    2016-01-01

    Antibodies are large, extremely flexible molecules, whose internal dynamics is certainly key to their astounding ability to bind antigens of all sizes, from small hormones to giant viruses. In this paper, we build a shape-based coarse-grained model of IgG molecules and show that it can be used to generate 3D conformations in agreement with single-molecule Cryo-Electron Tomography data. Furthermore, we elaborate a theoretical model that can be solved exactly to compute the binding rate constant of a small antigen to an IgG in a prescribed 3D conformation. Our model shows that the antigen binding process is tightly related to the internal dynamics of the IgG. Our findings pave the way for further investigation of the subtle connection between the dynamics and the function of large, flexible multi-valent molecular machines. PMID:26755272

  9. Conformation-controlled binding kinetics of antibodies

    PubMed Central

    Galanti, Marta; Fanelli, Duccio; Piazza, Francesco

    2016-01-01

    Antibodies are large, extremely flexible molecules, whose internal dynamics is certainly key to their astounding ability to bind antigens of all sizes, from small hormones to giant viruses. In this paper, we build a shape-based coarse-grained model of IgG molecules and show that it can be used to generate 3D conformations in agreement with single-molecule Cryo-Electron Tomography data. Furthermore, we elaborate a theoretical model that can be solved exactly to compute the binding rate constant of a small antigen to an IgG in a prescribed 3D conformation. Our model shows that the antigen binding process is tightly related to the internal dynamics of the IgG. Our findings pave the way for further investigation of the subtle connection between the dynamics and the function of large, flexible multi-valent molecular machines. PMID:26755272

  10. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution

    PubMed Central

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H. A.; Vogel, Martin

    2016-01-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  11. Functional second harmonic generation microscopy probes molecular dynamics with high temporal resolution.

    PubMed

    Förderer, Moritz; Georgiev, Tihomir; Mosqueira, Matias; Fink, Rainer H A; Vogel, Martin

    2016-02-01

    Second harmonic generation (SHG) microscopy is a powerful tool for label free ex vivo or in vivo imaging, widely used to investigate structure and organization of endogenous SHG emitting proteins such as myosin or collagen. Polarization resolved SHG microscopy renders supplementary information and is used to probe different molecular states. This development towards functional SHG microscopy is calling for new methods for high speed functional imaging of dynamic processes. In this work we present two approaches with linear polarized light and demonstrate high speed line scan measurements of the molecular dynamics of the motor protein myosin with a time resolution of 1 ms in mammalian muscle cells. Such a high speed functional SHG microscopy has high potential to deliver new insights into structural and temporal molecular dynamics under ex vivo or in vivo conditions. PMID:26977360

  12. Molecular Order of Arterial Collagen Using Circular Polarization Second-Harmonic Generation Imaging.

    PubMed

    Turcotte, Raphaël; Mattson, Jeffrey M; Wu, Juwell W; Zhang, Yanhang; Lin, Charles P

    2016-02-01

    Second-harmonic generation (SHG) originates from the interaction between upconverted fields from individual scatterers. This renders SHG microscopy highly sensitive to molecular distribution. Here, we aim to take advantage of the difference in SHG between aligned and partially aligned molecules to probe the degree of molecular order during biomechanical testing, independently of the absolute orientation of the scattering molecules. Toward this goal, we implemented a circular polarization SHG imaging approach and used it to quantify the intensity change associated with collagen fibers straightening in the arterial wall during mechanical stretching. We were able to observe the delayed alignment of collagen fibers during mechanical loading, thus demonstrating a simple method to characterize molecular distribution using intensity information alone. PMID:26806883

  13. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Bandrauk, André D.

    2011-08-01

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe2+ molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0×1014 W/cm2, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schrödinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe2+, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  14. Generation of circularly polarized attosecond pulses by intense ultrashort laser pulses from extended asymmetric molecular ions

    SciTech Connect

    Yuan, Kai-Jun; Bandrauk, Andre D.

    2011-08-15

    We present a method for generation of single circularly polarized attosecond pulses in extended asymmetric HHe{sup 2+} molecular ions. By employing an intense ultrashort circularly polarized laser pulse with intensity 4.0x10{sup 14} W/cm{sup 2}, wavelength 400 nm, and duration 10 optical cycles, molecular high-order-harmonic generation (MHOHG) spectra with multiple plateaus exhibit characters of circular polarization. Using a classical laser-induced collision model, double collisions of continuum electrons first with neighboring ions and then second with parent ions are presented at a particular internuclear distance and confirmed from numerical solutions of a time-dependent Schroedinger equation. We analyze the MHOHG spectra with a Gabor time window and find that, due to the asymmetry of HHe{sup 2+}, a single collision trajectory of continuum electrons with ions can produce circularly polarized harmonics, leading to single circularly polarized attosecond pulses for specific internuclear distances.

  15. Measurement of molecular rotational temperature in a supersonic gas jet with high-order harmonic generation.

    PubMed

    Yoshii, Kazumichi; Miyaji, Godai; Miyazaki, Kenzo

    2009-06-01

    We apply high-order harmonic generation to sensitive measurements of the molecular rotational temperature in a thin supersonic gas beam. The method uses nonresonant pump and probe femtosecond laser pulses to generate harmonic radiation from coherently rotating molecules. The rotational temperature of molecules can be derived accurately with high spatial and temporal resolutions from the Fourier spectrum of time-dependent signals. The validity of this method was tested for an expanding flow of an N(2) beam with a rapid temperature decrease. The results show the versatile applicability of this method. PMID:19488137

  16. Theory of second-harmonic generation of molecular systems: The steady-state case

    SciTech Connect

    Lin, S.H.; Alden, R.G. ); Villaeys, A.A.; Pflumio, V. )

    1993-10-01

    In this paper, a general formalism for treating both steady-state and time-resolved second-harmonic generation for molecular systems is presented. Here, only the steady-state case will be reported. The adiabatic approximation is introduced. Four important cases, resonance-resonance, resonance--off-resonance, off-resonance--resonance, and off-resonance--off-resonance transitions, have been considered. Finally, numerical calculations of rhodamine 6G are performed to demonstrate the applications of theoretical results.

  17. A carbon-13 NMR spin-lattice relaxation study of the molecular conformation of the nootropic drug 2-oxopyrrolidin-1-ylacetamide

    NASA Astrophysics Data System (ADS)

    Baldo, M.; Grassi, A.; Guidoni, L.; Nicolini, M.; Pappalardo, G. C.; Viti, V.

    The spin-lattice relaxation times ( T1) of carbon-13 resonances of the drug 2-oxopyrrolidin- 1-ylacetamide ( 2OPYAC) were determined in CDCl 3 + DMSO and H 2O solutions to investigate the internal conformational flexibility. The measured T1s for the hydrogen-bearing carbon atoms of the 2-pyrrolidone ring fragment were diagnostic of a rigid conformation with respect to the acetamide linked moiety. The model of anisotropic reorientation of a rigid body was used to analyse the measured relaxation data in terms of a single conformation. Owing to the small number of T1 data available the fitting procedure for each of the possible conformations failed. The structure corresponding to the rigid conformation was therefore considered to be the one that is strongly stabilized by internal hydrogen bonding as predicted on the basis of theoretical MO ab initio quantum chemical calculations.

  18. Influence of molecular opacities on the generation of cool star winds

    NASA Astrophysics Data System (ADS)

    Helling, Ch.; Woitke, P.; Winters, J. M.; Sedlmayr, E.

    The possible influence of radiation pressure on molecules on the generation of winds of cool late-type stars is investigated. Strong molecular absorption may levitate the outer atmosphere of the star and improve the conditions for dust formation, or it might even drive a considerable outflow of matter alone. Our investigations are performed in the framework of the time-dependent hydrodynamical models developed by Fleischer et al. In these models, the radiation pressure on molecules is described in the grey approximation, where the flux weighted opacity is replaced by a certain pre-tabulated mean opacity. We have computed new mean gas opacities on the basis of molecular line and continuum opacity data (Jorgensen et al.), and calculated hydrodynamical models by using Planck and Rosseland means, which should provide an upper and lower limit for the effects of molecular absorption, respectively. The response of the circumstellar shell to strong molecular absorption is found to be complex concerning both the hydrodynamical and thermodynamical structure and the properties of the wind. In models computed with Planck mean opacities, the gas density is usually found to be smaller such that the conditions for effective dust formation are worsened. However, a mainly molecular driven wind may occur for particular ranges of stellar parameters. A further interesting feature of these models is the occurrence of pressure inversions at small radial distances from the star. Such inversions already appear in the static initial model and are preserved in the dynamic calculations.

  19. The molecular structure, conformation, potential to internal rotation and force field of 2,2,2-trifluoroacetamide as studied by gas electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Gundersen, Snefrid; Samdal, Svein; Seip, Ragnhild; Shorokhov, Dmitry J.; Strand, Tor G.

    1998-04-01

    2,2,2-Trifluoroacetamide (TFA) has been studied by electron diffraction (ED), ab initio Hartree-Fock (HF), density functional theory (DFT), and MP2 calculations. The calculations give one conformation with one of the CF bonds anti to the CO bond and a planar NH 2 group, except for MP2/6-311 + + G∗∗, which predicts a slightly pyramidale NH 2 group. A molecular force field has been determined, and the fundamental frequencies have tentatively been assigned. The refined structural parameters were determined using constrained ED, i.e. ab initio results are included as constraints in the analysis. The structural parameters are: rg(N-H 4) = 1.040(4), rg(CO) = 1.211(2), rg(C-N) = 1.362(4), rg = 1.562(1), rg(C-F 7) = 1.347(1), ∠ αOCN = 126.5(2), ∠ αCCN = 116.3(4), ∠ αCCF 7 = 111.9(1), and ∠ αCNH 4 = 118.5(11). Bond distances are in Å and bond angles in degrees. Uncertainties are one standard deviation from least squares refinement using a diagonal weight matrix and inclusion of the uncertainty in the electron wavelength. The structural parameters have been compared with related amides. The Fourier coefficients V3 and V6 in the potential to internal rotation of the CF 3 group, V(α) = 1/2∗V 3∗(1 - cos(3∗α)) + 1/2∗V 6∗(1 - cos(6∗α)) , are determined to be 2.7(4) and - 0.7(3) kJ/mol, respectively. The syn barrier is experimentally determined to be 2.6(4) kJ/mol, which is in good agreeent with theoretical calculations.

  20. Conformation Distributions in Adsorbed Proteins.

    NASA Astrophysics Data System (ADS)

    Meuse, Curtis W.; Hubbard, Joseph B.; Vrettos, John S.; Smith, Jackson R.; Cicerone, Marcus T.

    2007-03-01

    While the structural basis of protein function is well understood in the biopharmaceutical and biotechnology industries, few methods for the characterization and comparison of protein conformation distributions are available. New methods capable of measuring the stability of protein conformations and the integrity of protein-protein, protein-ligand and protein-surface interactions both in solution and on surfaces are needed to help the development of protein-based products. We are developing infrared spectroscopy methods for the characterization and comparison of molecular conformation distributions in monolayers and in solutions. We have extracted an order parameter describing the orientational and conformational variations of protein functional groups around the average molecular values from a single polarized spectrum. We will discuss the development of these methods and compare them to amide hydrogen/deuterium exchange methods for albumin in solution and on different polymer surfaces to show that our order parameter is related to protein stability.

  1. Effects of conformational distributions on sigma profiles in COSMO theories.

    PubMed

    Wang, Shu; Stubbs, John M; Siepmann, J Ilja; Sandler, Stanley I

    2005-12-15

    The charge density or sigma profile of a solute molecule is an essential component in COSMO (conductor-like screen model) based solvation theories, and its generation depends on the molecular conformation used. The usual procedure is to determine the conformation of an isolated molecule, and assume that this is unchanged when the molecule is placed in solution. In this paper, the conformations of 1-hexanol and 2-methoxy-ethanol in both the liquid and vapor phases obtained from Gibbs ensemble simulation and from an isolated-molecule quantum DFT optimization are used to determine the effect of realistic conformation differences on COSMO-based properties predictions. In particular, the vapor pressure at the normal boiling temperature and the binary mixture VLE (vapor-liquid equilibrium) predictions obtained using different conformations are investigated. The results show that the sigma profile for 1-hexanol varies only slightly using the different conformations, while the sigma profile of 2-methoxy-ethanol shows a significant difference between the liquid and vapor phases. Consequently, the vapor pressure predictions for 1-hexanol are similar regardless of the manner in which the conformation population was obtained, while there is a larger difference for 2-methoxy-ethanol depending on whether the liquid or vapor conformations from simulation or the DFT-optimized structure is used. These differences in predictions are seen to be largely due to differences in the ideal solvation energy term. In mixture VLE calculations involving 1-hexanol, we again see that there is little difference in the phase equilibrium predictions among the different conformations, while for the mixture with 2-methoxy-ethanol, the differences in the sigma profiles lead to a more noticeable, though not significant, difference in the phase equilibrium predictions. PMID:16331913

  2. Magnetoresistance effect of heat generation in a single-molecular spin-valve

    NASA Astrophysics Data System (ADS)

    Jiang, Feng; Yan, Yonghong; Wang, Shikuan; Yan, Yijing

    2016-02-01

    Based on non-equilibrium Green's functions' theory and small polaron transformation's technology, we study the heat generation by current through a single-molecular spin-valve. Numerical results indicate that the variation of spin polarization degree can change heat generation effectively, the spin-valve effect happens not only in electrical current but also in heat generation when Coulomb repulsion in quantum dot is smaller than phonon frequency and interestingly, when Coulomb repulsion is larger than phonon frequency, the inverse spin-valve effect appears by sweeping gate voltage and is enlarged with bias increasing. The inverse spin-valve effect will induce the unique heat magnetoresistance effect, which can be modulated from heat-resistance to heat-gain by gate voltage easily.

  3. Free Energy-Based Conformational Search Algorithm Using the Movable Type Sampling Method.

    PubMed

    Pan, Li-Li; Zheng, Zheng; Wang, Ting; Merz, Kenneth M

    2015-12-01

    In this article, we extend the movable type (MT) sampling method to molecular conformational searches (MT-CS) on the free energy surface of the molecule in question. Differing from traditional systematic and stochastic searching algorithms, this method uses Boltzmann energy information to facilitate the selection of the best conformations. The generated ensembles provided good coverage of the available conformational space including available crystal structures. Furthermore, our approach directly provides the solvation free energies and the relative gas and aqueous phase free energies for all generated conformers. The method is validated by a thorough analysis of thrombin ligands as well as against structures extracted from both the Protein Data Bank (PDB) and the Cambridge Structural Database (CSD). An in-depth comparison between OMEGA and MT-CS is presented to illustrate the differences between the two conformational searching strategies, i.e., energy-based versus free energy-based searching. These studies demonstrate that our MT-based ligand conformational search algorithm is a powerful approach to delineate the conformational ensembles of molecular species on free energy surfaces. PMID:26605406

  4. Automated Site-Directed Drug Design: The Formation of Molecular Templates in Primary Structure Generation

    NASA Astrophysics Data System (ADS)

    Lewis, R. A.; Dean, P. M.

    1989-03-01

    In this paper the spacer skeleton concept is used to produce molecular graphs of putative ligands for binding sites. The skeletons are transformed into molecular templates within the constraints of the accessible surface of the ligand-binding site. A distance-matrix method is used to compare ligand points with vertices of the spacer skeleton through a permutation of all possible correspondences. A tolerance parameter is used to screen for poor matches. As a result. a small number of matched vertices and ligand points are produced. These are fitted into the site by a constrained optimization routine using an analytical function. Ligand points fall within the site and are optimally positioned adjacent to the corresponding site points, other vertices of the spacer skeleton lying beneath the accessible surface of the site are clipped off. A molecular template is thereby formed with its vertices linked to the ligand points. The final step is to verify that the bonding integrity of the skeleton remains. The computational methods outlined in this paper have been tested at two binding sites the pteridine binding site in dihydrofolate reductase and the amidinophenylpyruvate site of trypsin. Molecular graphs for both sites were generated automatically, they showed strong similarity to those of the natural ligands.

  5. Molecular hydrogen physisorption on boron-nitride nanotubes probed by second harmonic generation

    NASA Astrophysics Data System (ADS)

    Salazar-Aparicio, R. V.; Vázquez-Nava, R. A.; Arzate, N.; Mendoza, B. S.

    2014-10-01

    We present ab initio calculations to investigate second harmonic generation (SHG) response of single wall zigzag pristine boron-nitride nanotubes (BNNTs) and BNNTs modified by the molecular hydrogen adsorption. Calculations have been performed using density functional theory (DFT) within the local-density approximation (LDA) together with the GW Green function method to determine the band gap. A length gauge approach has been used to calculate the nonlinear optical response with the scissors correction to obtain the nonlinear susceptibility χzzz(-2ω ;ω,ω) of the zigzag BNNTs. We have found that, contrary to reports in the literature, the (5,0) and (9,0) BNNTs have a nonvanishing SHG response. We have also found that SHG intensity decreases with the increase of the molecular hydrogen coverage.

  6. Orbital symmetry and interference effects in molecular high-order harmonic generation

    SciTech Connect

    Lagmago Kamta, G.; Bandrauk, A. D.

    2009-10-15

    We investigate harmonic generation from H{sub 2}{sup +} molecules driven by intense few-cycle laser pulses whose linearly polarization axis makes an arbitrary angle {chi} with respect to the molecular axis. The H{sub 2}{sup +} molecule is considered initially in various orbitals with nodal planes. It is found that a strong enhancement of high-order harmonics (HOHs) occurs when the laser polarization axis overlaps with major axes of electron distribution in the active orbital, while broad suppression of HOHs occurs when the laser polarization axis is parallel to a nodal plane of the active molecular orbital. We show that this harmonic suppression is enhanced by destructive interferences when the nodal and the laser polarization axes are parallel to the internuclear axis, which leads to a shortening of the harmonic cutoff. It follows that the orientation dependence of HOHs intensities mimics the electronic density in active orbitals through the angular dependence of ionization and recombination processes.

  7. Challenges of bringing next generation sequencing technologies to clinical molecular diagnostic laboratories.

    PubMed

    Wong, Lee-Jun C

    2013-04-01

    Molecular diagnosis of complex dual genome mitochondrial disorders is a challenge. It requires the identification of deleterious mutations in one of the ~1,500 nuclear genes and the mitochondrial genome. If the molecular defect is in the mitochondrial genome, quantification of degree of mutation load (heteroplasmy) in affected tissues is important. Due to the extreme clinical and genetic heterogeneity, conventional sequence analysis of the candidate genes one-by-one is impractical, if not impossible. The newly developed massively parallel next generation sequencing (NGS) technique, that allows simultaneous sequence analysis of multiple target genes, when appropriately validated with deep coverage and proper quality controls, can be used as an effective comprehensive diagnostic approach in CLIA certified clinical laboratories. PMID:23269496

  8. The molecular chaperone Brichos breaks the catalytic cycle that generates toxic Aβ oligomers

    PubMed Central

    Kurudenkandy, Firoz Roshan; Biverstal, Henrik; Dolfe, Lisa; Dunning, Christopher; Yang, Xiaoting; Frohm, Birgitta; Vendruscolo, Michele; Johansson, Jan; Dobson, Christopher M.; Fisahn, André; Knowles, Tuomas P. J.; Linse, Sara

    2015-01-01

    Alzheimer’s disease is an increasingly prevalent neurodegenerative disorder whose pathogenesis has been associated with aggregation of the amyloid-β peptide (Aβ42). Recent studies have revealed that once Aβ42 fibrils are generated, their surfaces strongly catalyse the formation of neurotoxic oligomers. Here we show that a molecular chaperone, a Brichos domain, can specifically inhibit this catalytic cycle and limit Aβ42 toxicity. We demonstrate in vitro that Brichos achieves this inhibition by binding to the surfaces of fibrils, thereby redirecting the aggregation reaction to a pathway that involves minimal formation of toxic oligomeric intermediates. We verify that this mechanism occurs in living brain tissue by means of cytotoxicity and electrophysiology experiments. These results reveal that molecular chaperones can help maintain protein homeostasis by selectively suppressing critical microscopic steps within the complex reaction pathways responsible for the toxic effects of protein misfolding and aggregation. PMID:25686087

  9. Spectral modulation of third-harmonic generation by molecular alignment and preformed plasma

    NASA Astrophysics Data System (ADS)

    Li, Min; Li, An-Yuan; He, Bo-Qu; Yuan, Shuai; Zeng, He-Ping

    2016-08-01

    We demonstrate spectral modulation of third-harmonic generation from molecular alignment effects. The third harmonic spectrum is broadened or narrowed under different influences of cross-phase modulations originating from various molecular alignment revivals. Furthermore, the spectrum and spatial distribution of the generated third harmonic pulse change dramatically in the presence of a preformed plasma. Under the influence of a preformed plasma, a narrower third harmonic spectrum is observed, and the conical third-harmonic pulse increases while the axial part decreases. The investigation provides an effective method to modulate the spectral characteristic and spatial distribution of third-harmonic generation from intense femtosecond filament. Project supported by the National Key Scientific Instrument Project, China (Grant No. 2012YQ150092), the National Basic Research Program of China (Grant No. 2011CB808105), the National Natural Science Foundation of China (Grant No. 11434005), China Postdoctoral Science Foundation (Grant No. 2014M560348), the National Natural Science Foundation of China (Grant No. 11504237), and the Shanghai Municipal Science and Technology Commission, China (Grant No. 14JC1401600).

  10. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

    SciTech Connect

    Laowanapiban, Poramaet; Kapustina, Maryna; Vonrhein, Clemens; Delarue, Marc; Koehl, Patrice; Carter Jr., Charles W.

    2009-03-05

    Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.

  11. The molecular structures, conformations and force fields of bis(chloroimino)butanedinitrile as studied by gas-phase electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Thomassen, H.; Gundersen, S.; Samdal, S.

    2009-06-01

    Quantum chemical calculations using levels up to MP2(Full)/aug-cc-pVTZ have been applied. B3LYP calculations using the 6-31G* basis set reveal that there are four conformations of bis(chloroimino)butanedinitrile. The planar anti-ZZ conformer with C2h symmetry is the most stable conformer. The non-planar EE conformer with C2 symmetry, the non-planar EZ conformer with C1 symmetry and the non-planar ZZ conformer with C2 symmetry are 16.8, 22.7, 27.2 kJ/mol, respectively, less stable than the planar anti-ZZ conformer according toB3LYP/6-31G* calculations. Calculated frequencies for the planar anti-ZZ conformer have been compared with observed frequencies, and some reassignments have been proposed. Several models have been used in the gas-phase electron diffraction analysis. The most reliable results are expected to be obtained using a dynamic model where the large amplitude motion is simulated by a harmonic angular motion using a Gaussian distribution about the central C sbnd C bond. Only the planar anti-ZZ conformer was used in the final refinements due to the high energy difference to the other conformers. The most important bond distances ( ra, Ångstrom) and bond angles (∠ α, degrees) are [GED/MP2(Full)/aug-cc-pVTZ]: rC 1sbnd C 2 = [1.509(15), 1.460], rC 2 = N 3 = [1.295(6), 1.292], rN 3sbnd Cl 5 = [1.706(5), 1.696], rC 2sbnd C 7 = [1.434(11), 1.421], rC 7tbnd N 9 = [1.165(4), 1.170], ∠C 1sbnd C 2dbnd N 3 = [114.5(11), 115.6], ∠C 2dbnd N 3sbnd Cl 5 = [115.0(4), 115.0], ∠C 1sbnd C 2sbnd C 7 = [118.8(8), 118.5], ∠C 2sbnd C 7tbnd N 9 = [178.2(15), 177.4]. The dihedral angle N 3C 2C 7N 9 is 0°, i.e. the cyano groups are bended towards the Cl atom. Error estimates from electron diffraction are given as: σr = 2.5[σ lsq2 + (0.001r) 2] ½ for bond distances and σ∠ = 2.5σ lsq for bond angles.

  12. Computational mutagenesis reveals the role of active-site tyrosine in stabilising a boat conformation for the substrate: QM/MM molecular dynamics studies of wild-type and mutant xylanases.

    PubMed

    Soliman, Mahmoud E S; Ruggiero, Giuseppe D; Pernía, J Javier Ruiz; Greig, Ian R; Williams, Ian H

    2009-02-01

    Molecular dynamics simulations have been performed for non-covalent complexes of phenyl beta-xylobioside with the retaining endo-beta-1,4-xylanase from B. circulans (BCX) and its Tyr69Phe mutant using a hybrid QM/MM methodology. A trajectory initiated for the wild-type enzyme-substrate complex with the proximal xylose ring bound at the -1 subsite (adjacent to the scissile glycosidic bond) in the (4)C(1) chair conformation shows spontaneous transformation to the (2,5)B boat conformation, and potential of mean force calculations indicate that the boat is approximately 30 kJ mol(-1) lower in free energy than the chair. Analogous simulations for the mutant lacking one oxygen atom confirm the key role of Tyr69 in stabilizing the boat in preference to the (4)C(1) chair conformation, with a relative free energy difference of about 20 kJ mol(-1), by donating a hydrogen bond to the endocyclic oxygen of the proximal xylose ring. QM/MM MD simulations for phenyl beta-xyloside in water, with and without a propionate/propionic acid pair to mimic the catalytic glutamate/glutamic acid pair of the enzyme, show the (4)C(1) chair to be stable, although a hydrogen bond between the OH group at C2 of xylose and the propionate moiety seems to provide some stabilization for the (2,5)B conformation. PMID:19156310

  13. Role of ionization in orientation dependence of molecular high-order harmonic generation

    NASA Astrophysics Data System (ADS)

    Chen, Y. J.; Hu, Bambi

    2009-12-01

    We investigate the orientation dependence of high-order harmonic generation (HHG) from O2 and CO2 molecules using the strong-field approximation (SFA). Our simulations reveal the important modulation of the ionization to the HHG orientation dependence, especially at larger orientation angles. By virtue of a simplified model arising from the SFA, we show that this modulation can be read from the harmonic order where the HHG spectra at different orientation angles intersect. These results give suggestions on probing the molecular structure and dynamics using HHG.

  14. 3D molecular models of whole HIV-1 virions generated with cellPACK

    PubMed Central

    Goodsell, David S.; Autin, Ludovic; Forli, Stefano; Sanner, Michel F.; Olson, Arthur J.

    2014-01-01

    As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology. PMID:25253262

  15. Chlorite dismutases – a heme enzyme family for use in bioremediation and generation of molecular oxygen

    PubMed Central

    Hofbauer, Stefan; Schaffner, Irene; Furtmüller, Paul G; Obinger, Christian

    2014-01-01

    Chlorite is a serious environmental concern, as rising concentrations of this harmful anthropogenic compound have been detected in groundwater, drinking water, and soil. Chlorite dismutases (Clds) are therefore important molecules in bioremediation as Clds catalyze the degradation of chlorite to chloride and molecular oxygen. Clds are heme b-containing oxidoreductases present in numerous bacterial and archaeal phyla. This review presents the phylogeny of functional Clds and Cld-like proteins, and demonstrates the close relationship of this novel enzyme family to the recently discovered dye-decolorizing peroxidases. The available X-ray structures, biophysical and enzymatic properties, as well as a proposed reaction mechanism, are presented and critically discussed. Open questions about structure-function relationships are addressed, including the nature of the catalytically relevant redox and reaction intermediates and the mechanism of inactivation of Clds during turnover. Based on analysis of currently available data, chlorite dismutase from “Candidatus Nitrospira defluvii” is suggested as a model Cld for future application in biotechnology and bioremediation. Additionally, Clds can be used in various applications as local generators of molecular oxygen, a reactivity already exploited by microbes that must perform aerobic metabolic pathways in the absence of molecular oxygen. For biotechnologists in the field of chemical engineering and bioremediation, this review provides the biochemical and biophysical background of the Cld enzyme family as well as critically assesses Cld's technological potential. PMID:24519858

  16. Molecular, electronic structure and conformational flexibility of the 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives

    NASA Astrophysics Data System (ADS)

    Shishkin, Oleg V.; Antonov, Dmitry M.

    1996-11-01

    Molecular and electronic structures of 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives have been studied using the semiempirical quantum-chemical method AM1. The equilibrium geometry of all molecules is planar. These results were confirmed by X-ray structural investigations of the 1-oxo- and 1-imino derivatives of 2,5-dimethyl-3-(2,2,2-trichloroethyl)-4,5-dihydrofuro[2,3-d]pyrimidine. However, the dihydropyrimidine ring in all compounds possesses a degree of conformational flexibility. The transition from a planar equilibrium conformation to a distorted sofa with the CNCC torsion angle ± 20° causes an increase of energy less than 1.5 kcal mol -1. The factors that determine this property of the dihydroheterocycle (bending strain, non-aromaticity, conjugation, 1,2-allylic strain) have been considered.

  17. Involvement of the glucose moiety in the molecular recognition of methyl beta-lactoside by ricin: synthesis, conformational analysis, and binding studies of different derivatives at the C-3 region.

    PubMed

    Fernández, P; Jiménez-Barbero, J; Martín-Lomas, M; Solís, D; Díaz-Mauriño, T

    1994-04-01

    Syntheses of the 3-aminodeoxy (4), 3-deoxy-3-methyl (5), and 3-epi (6) derivatives of methyl beta-lactoside (1) have been achieved from 1 in a straightforward way, and their solution conformations in water and dimethyl sulfoxide analysed through molecular mechanics and dynamics calculations and nuclear magnetic resonance data. The overall shape of all the compounds studied is fairly similar and may be described by conformers included in a low energy region with phi = 15 +/- 45 degrees and psi = -25 +/- 30 degrees, that is ca. 5% of the total potential energy surface for the glycosidic linkages of the disaccharides. The binding of the different compounds to ricin, the galactose-specific toxin from Ricinus communis, has been investigated. The results confirm the involvement of the C-3 region in a nonpolar interaction with the protein at the periphery of the combining site. PMID:8187100

  18. Towards conformal loop quantum gravity

    NASA Astrophysics Data System (ADS)

    H-T Wang, Charles

    2006-03-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity.

  19. Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy.

    PubMed

    Winden, Kellen D; Bragin, Anatol; Engel, Jerome; Geschwind, Dan H

    2015-06-01

    The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs. PMID:25818007

  20. Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy

    PubMed Central

    Winden, Kellen D.; Bragin, Anatol; Engel, Jerome; Geschwind, Dan H.

    2016-01-01

    The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs. PMID:25818007

  1. Effect of Side Chains on Molecular Conformation of Anthracene-Ethynylene-Phenylene-Vinylene Oligomers: A Comparative Density Functional Study With and Without Dispersion Interaction.

    PubMed

    Dong, Chuanding; Hoppe, Harald; Beenken, Wichard J D

    2016-06-01

    Using density functional calculations with and without dispersion interaction, we studied the effects of linear octyl and branched 2-ethylhexyl side chains on the oligomer conformation of the conjugated copolymer poly(p-anthracene-ethynylene)-alt-poly(p-phenylene-vinylene). With dispersion included, the branched side chains can cause significant bending of the oligomer backbone, while without dispersion they induce mainly torsional disorder. The oligomers with mainly linear side chains keep good planarity when optimized with and without dispersion. Despite their dramatically different conformations, the calculated absorption spectra of the oligomers with various side chain combinations are very similar, indicating that the conformation of the copolymer is not the main reason for the experimentally observed different spectra of ordered and disordered phases. PMID:27163652

  2. MM3(96) CONFORMATIONAL ANALYSIS OF D-GLUCARAMIDE AND X-RAY CRYSTAL STRUCTURES OF THREE D-GLUCARIC ACID DERIVATIVES - MODELS FOR SYNTHETIC POLY(ALKYLENE D-GLUCARAMIDES)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An exhaustive conformational analysis of D-glucaramide was carried out using MM3(96) [MM3(96). Molecular Mechanics Software used with permission from N.L. Allinger; University of Georgia]. Nine torsion angles were each driven in increments of 120 degrees, generating 19,683 starting conformations. ...

  3. Molecular Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the Whole Exome

    PubMed Central

    Bonnefond, Amélie; Durand, Emmanuelle; Sand, Olivier; De Graeve, Franck; Gallina, Sophie; Busiah, Kanetee; Lobbens, Stéphane; Simon, Albane; Bellanné-Chantelot, Christine; Létourneau, Louis; Scharfmann, Raphael; Delplanque, Jérôme; Sladek, Robert; Polak, Michel; Vaxillaire, Martine; Froguel, Philippe

    2010-01-01

    Background Accurate molecular diagnosis of monogenic non-autoimmune neonatal diabetes mellitus (NDM) is critical for patient care, as patients carrying a mutation in KCNJ11 or ABCC8 can be treated by oral sulfonylurea drugs instead of insulin therapy. This diagnosis is currently based on Sanger sequencing of at least 42 PCR fragments from the KCNJ11, ABCC8, and INS genes. Here, we assessed the feasibility of using the next-generation whole exome sequencing (WES) for the NDM molecular diagnosis. Methodology/Principal Findings We carried out WES for a patient presenting with permanent NDM, for whom mutations in KCNJ11, ABCC8 and INS and abnormalities in chromosome 6q24 had been previously excluded. A solution hybridization selection was performed to generate WES in 76 bp paired-end reads, by using two channels of the sequencing instrument. WES quality was assessed using a high-resolution oligonucleotide whole-genome genotyping array. From our WES with high-quality reads, we identified a novel non-synonymous mutation in ABCC8 (c.1455G>C/p.Q485H), despite a previous negative sequencing of this gene. This mutation, confirmed by Sanger sequencing, was not present in 348 controls and in the patient's mother, father and young brother, all of whom are normoglycemic. Conclusions/Significance WES identified a novel de novo ABCC8 mutation in a NDM patient. Compared to the current Sanger protocol, WES is a comprehensive, cost-efficient and rapid method to identify mutations in NDM patients. We suggest WES as a near future tool of choice for further molecular diagnosis of NDM cases, negative for chr6q24, KCNJ11 and INS abnormalities. PMID:21049026

  4. Next-generation biobanking of metastases to enable multidimensional molecular profiling in personalized medicine.

    PubMed

    Diaz, Zuanel; Aguilar-Mahecha, Adriana; Paquet, Eric R; Basik, Mark; Orain, Michèle; Camlioglu, Errol; Constantin, André; Benlimame, Naciba; Bachvarov, Dimcho; Jannot, Guillaume; Simard, Martin J; Chabot, Benoit; Gologan, Adrian; Klinck, Roscoe; Gagnon-Kugler, Thérèse; Lespérance, Bernard; Samson, Benoit; Kavan, Petr; Alcindor, Thierry; Dalfen, Richard; Lan, Cathy; Chabot, Catherine; Buchanan, Marguerite; Przybytkowski, Ewa; Qureshi, Samia; Rousseau, Caroline; Spatz, Alan; Têtu, Bernard; Batist, Gerald

    2013-11-01

    Great advances in analytical technology coupled with accelerated new drug development and growing understanding of biological challenges, such as tumor heterogeneity, have required a change in the focus for biobanking. Most current banks contain samples of primary tumors, but linking molecular signatures to therapeutic questions requires serial biopsies in the setting of metastatic disease, next-generation of biobanking. Furthermore, an integration of multidimensional analysis of various molecular components, that is, RNA, DNA, methylome, microRNAome and post-translational modifications of the proteome, is necessary for a comprehensive view of a tumor's biology. While data using such biopsies are now regularly presented, the preanalytical variables in tissue procurement and processing in multicenter studies are seldom detailed and therefore are difficult to duplicate or standardize across sites and across studies. In the context of a biopsy-driven clinical trial, we generated a detailed protocol that includes morphological evaluation and isolation of high-quality nucleic acids from small needle core biopsies obtained from liver metastases. The protocol supports stable shipping of samples to a central laboratory, where biopsies are subsequently embedded in support media. Designated pathologists must evaluate all biopsies for tumor content and macrodissection can be performed if necessary to meet our criteria of >60% neoplastic cells and <20% necrosis for genomic isolation. We validated our protocol in 40 patients who participated in a biopsy-driven study of therapeutic resistance in metastatic colorectal cancer. To ensure that our protocol was compatible with multiplex discovery platforms and that no component of the processing interfered with downstream enzymatic reactions, we performed array comparative genomic hybridization, methylation profiling, microRNA profiling, splicing variant analysis and gene expression profiling using genomic material isolated from

  5. Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism

    PubMed Central

    Guo, Hong; Cui, Qiang; Lipscomb, William N.; Karplus, Martin

    2001-01-01

    Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer. PMID:11481470

  6. Intense attosecond pulse generated from a molecular harmonic plateau of H2+ in mid-infrared laser fields

    NASA Astrophysics Data System (ADS)

    Yu, Chao; He, Haixiang; Wang, Yunhui; Shi, Qi; Zhang, Yadong; Lu, Ruifeng

    2014-03-01

    High-order harmonic generation from the molecular ion H2+ exposed to intense laser fields is investigated by the time-dependent quantum wave packet method. Molecular and atomic plateaus of harmonic spectra are effectively distinguished at large internuclear distances, where the harmonic efficiency of the molecular plateau is several orders of magnitude higher than that of the latter. We report on a physical model of the origin of the molecular supercontinua and reveal that the creation of this plateau directly results from the interference of the intramolecular electronic wave packet localized in two potential wells following the laser field. This is our first effort in utilizing the efficient molecular plateau to generate intense isolated attosecond pulses by controlling the dynamics of the nucleus and electrons with a mid-infrared laser. Further, we show that the harmonic plateau is enhanced at the macroscopic level by solving the Maxwell wave equation coupled with the Schrödinger equation.

  7. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model

    PubMed Central

    Kwasniewska, Alexandra C.; Lise, Stefano; Parolin Schnekenberg, Ricardo; Becker, Esther B. E.; Bera, Katarzyna D.; Shanks, Morag E.; Gregory, Lorna; Buck, David; Zameel Cader, M.; Talbot, Kevin; de Silva, Rajith; Fletcher, Nicholas; Hastings, Rob; Jayawant, Sandeep; Morrison, Patrick J.; Worth, Paul; Taylor, Malcolm; Tolmie, John; O’Regan, Mary; Valentine, Ruth; Packham, Emily; Evans, Julie; Seller, Anneke; Ragoussis, Jiannis

    2013-01-01

    Many neurological conditions are caused by immensely heterogeneous gene mutations. The diagnostic process is often long and complex with most patients undergoing multiple invasive and costly investigations without ever reaching a conclusive molecular diagnosis. The advent of massively parallel, next-generation sequencing promises to revolutionize genetic testing and shorten the ‘diagnostic odyssey’ for many of these patients. We performed a pilot study using heterogeneous ataxias as a model neurogenetic disorder to assess the introduction of next-generation sequencing into clinical practice. We captured 58 known human ataxia genes followed by Illumina Next-Generation Sequencing in 50 highly heterogeneous patients with ataxia who had been extensively investigated and were refractory to diagnosis. All cases had been tested for spinocerebellar ataxia 1–3, 6, 7 and Friedrich’s ataxia and had multiple other biochemical, genetic and invasive tests. In those cases where we identified the genetic mutation, we determined the time to diagnosis. Pathogenicity was assessed using a bioinformatics pipeline and novel variants were validated using functional experiments. The overall detection rate in our heterogeneous cohort was 18% and varied from 8.3% in those with an adult onset progressive disorder to 40% in those with a childhood or adolescent onset progressive disorder. The highest detection rate was in those with an adolescent onset and a family history (75%). The majority of cases with detectable mutations had a childhood onset but most are now adults, reflecting the long delay in diagnosis. The delays were primarily related to lack of easily available clinical testing, but other factors included the presence of atypical phenotypes and the use of indirect testing. In the cases where we made an eventual diagnosis, the delay was 3–35 years (mean 18.1 years). Alignment and coverage metrics indicated that the capture and sequencing was highly efficient and the

  8. Integration of molecular and enzymatic catalysts on graphene for biomimetic generation of antithrombotic species

    NASA Astrophysics Data System (ADS)

    Xue, Teng; Peng, Bo; Xue, Min; Zhong, Xing; Chiu, Chin-Yi; Yang, Si; Qu, Yongquan; Ruan, Lingyan; Jiang, Shan; Dubin, Sergey; Kaner, Richard B.; Zink, Jeffrey I.; Meyerhoff, Mark E.; Duan, Xiangfeng; Huang, Yu

    2014-02-01

    The integration of multiple synergistic catalytic systems can enable the creation of biocompatible enzymatic mimics for cascading reactions under physiologically relevant conditions. Here we report the design of a graphene-haemin-glucose oxidase conjugate as a tandem catalyst, in which graphene functions as a unique support to integrate molecular catalyst haemin and enzymatic catalyst glucose oxidase for biomimetic generation of antithrombotic species. Monomeric haemin can be conjugated with graphene through π-π interactions to function as an effective catalyst for the oxidation of endogenous L-arginine by hydrogen peroxide. Furthermore, glucose oxidase can be covalently linked onto graphene for local generation of hydrogen peroxide through the oxidation of blood glucose. Thus, the integrated graphene-haemin-glucose oxidase catalysts can readily enable the continuous generation of nitroxyl, an antithrombotic species, from physiologically abundant glucose and L-arginine. Finally, we demonstrate that the conjugates can be embedded within polyurethane to create a long-lasting antithrombotic coating for blood-contacting biomedical devices.

  9. Exploring the conformational energy landscape of glassy disaccharides by cross polarization magic angle spinning 13C nuclear magnetic resonance and numerical simulations. II. Enhanced molecular flexibility in amorphous trehalose

    NASA Astrophysics Data System (ADS)

    Lefort, Ronan; Bordat, Patrice; Cesaro, Attilio; Descamps, Marc

    2007-01-01

    This paper uses chemical shift surfaces to simulate experimental C13 cross polarization magic angle spinning spectra for amorphous solid state disaccharides, paying particular attention to the glycosidic linkage atoms in trehalose, sucrose, and lactose. The combination of molecular mechanics with density functional theory/gauge invariant atomic orbital ab initio methods provides reliable structural information on the conformational distribution in the glass. The results are interpreted in terms of an enhanced flexibility that trehalose possesses in the amorphous solid state, at least on the time scale of C13 nuclear magnetic resonance measurements. Implications of these findings for the fragility of trehalose glass and bioprotectant action are discussed.

  10. Conformations and Conformational Processes of Hexahydrobenzazocines by NMR and DFT Studies.

    PubMed

    Musielak, Bogdan; Holak, Tad A; Rys, Barbara

    2015-09-18

    Conformational processes that occur in hexahydrobenzazocines have been studied with the (1)H and (13)C dynamic nuclear magnetic resonance (DNMR) spectroscopy. The coalescence effects are assigned to two different conformational processes: the ring-inversion of the ground-state conformations and the interconversion between two different conformers. The barriers for these processes are in the range of 42-52 and 42-43 kJ mol(-1), respectively. Molecular modeling on the density functional theory (DFT) level and the gauge invariant atomic orbitals (GIAO)-DFT calculations of isotropic shieldings and coupling constants for the set of low-energy conformations were compared with the experimental NMR data. The ground-state of all compounds in solution is the boat-chair (BC) conformation. The BC form adopts two different conformations because the nitrogen atom can be in the boat or chair parts of the BC structure. These two conformers are engaged in the interconversion process. PMID:26317238

  11. Understanding oscillatory phenomena in molecular hydrogen generation via sodium borohydride hydrolysis.

    PubMed

    Budroni, M A; Biosa, E; Garroni, S; Mulas, G R C; Marchettini, N; Culeddu, N; Rustici, M

    2013-11-14

    The hydrolysis of borohydride salts represents one of the most promising processes for the generation of high purity molecular hydrogen under mild conditions. In this work we show that the sodium borohydride hydrolysis exhibits a fingerprinting periodic oscillatory transient in the hydrogen flow over a wide range of experimental conditions. We disproved the possibility that flow oscillations are driven by supersaturation phenomena of gaseous bubbles in the reactive mixture or by a nonlinear thermal feedback according to a thermokinetic model. Our experimental results indicate that the NaBH4 hydrolysis is a spontaneous inorganic oscillator, in which the hydrogen flow oscillations are coupled to an "oscillophor" in the reactive solution. The discovery of this original oscillator paves the way for a new class of chemical oscillators, with fundamental implications not only for testing the general theory on oscillations, but also with a view to chemical control of borohydride systems used as a source of hydrogen based green fuel. PMID:24084866

  12. Molecular molybdenum persulfide and related catalysts for generating hydrogen from water

    DOEpatents

    Long, Jeffrey R.; Chang, Christopher J.; Karunadasa, Hemamala I.; Majda, Marcin

    2016-04-19

    New metal persulfido compositions of matter are described. In one embodiment the metal is molybdenum and the metal persulfido complex mimics the structure and function of the triangular active edge site fragments of MoS.sub.2, a material that is the current industry standard for petroleum hydro desulfurization, as well as a promising low-cost alternative to platinum for electrocatalytic hydrogen production. This molecular [(PY5W.sub.2)MoS.sub.2].sup.x+ containing catalyst is capable of generating hydrogen from acidic-buffered water or even seawater at very low overpotentials at a turnover frequency rate in excess of 500 moles H.sub.2 per mole catalyst per second, with a turnover number (over a 20 hour period) of at least 19,000,000 moles H.sub.2 per mole of catalyst.

  13. Multiple exciton generation in quantum dots versus singlet fission in molecular chromophores for solar photon conversion.

    PubMed

    Beard, Matthew C; Johnson, Justin C; Luther, Joseph M; Nozik, Arthur J

    2015-06-28

    Both multiple exciton generation (MEG) in semiconductor nanocrystals and singlet fission (SF) in molecular chromophores have the potential to greatly increase the power conversion efficiency of solar cells for the production of solar electricity (photovoltaics) and solar fuels (artificial photosynthesis) when used in solar photoconverters. MEG creates two or more excitons per absorbed photon, and SF produces two triplet states from a single singlet state. In both cases, multiple charge carriers from a single absorbed photon can be extracted from the cell and used to create higher power conversion efficiencies for a photovoltaic cell or a cell that produces solar fuels, like hydrogen from water splitting or reduced carbon fuels from carbon dioxide and water (analogous to biological photosynthesis). The similarities and differences in the mechanisms and photoconversion cell architectures between MEG and SF are discussed. PMID:25987579

  14. Probing Nuclear Motion by Frequency Modulation of Molecular High-Order Harmonic Generation

    NASA Astrophysics Data System (ADS)

    Bian, Xue-Bin; Bandrauk, André D.

    2014-11-01

    Molecular high-order harmonic generation (MHOHG) in a non-Born-Oppenheimer treatment of H2 + , D2 + , is investigated by numerical simulations of the corresponding time-dependent Schrödinger equations in full dimensions. As opposed to previous studies on amplitude modulation of intracycle dynamics in MHOHG, we demonstrate redshifts as frequency modulation (FM) of intercycle dynamics in MHOHG. The FM is induced by nuclear motion using intense laser pulses. Compared to fixed-nuclei approximations, the intensity of MHOHG is much higher due to the dependence of enhanced ionization on the internuclear distance. The width and symmetry of the spectrum of each harmonic in MHOHG encode rich information on the dissociation process of molecules at the rising and falling parts of the laser pulses, which can be used to retrieve the nuclear dynamics. Isotope effects are studied to confirm the FM mechanism.

  15. Probing nuclear motion by frequency modulation of molecular high-order harmonic generation.

    PubMed

    Bian, Xue-Bin; Bandrauk, André D

    2014-11-01

    Molecular high-order harmonic generation (MHOHG) in a non-Born-Oppenheimer treatment of H(2)(+), D(2)(+), is investigated by numerical simulations of the corresponding time-dependent Schrödinger equations in full dimensions. As opposed to previous studies on amplitude modulation of intracycle dynamics in MHOHG, we demonstrate redshifts as frequency modulation (FM) of intercycle dynamics in MHOHG. The FM is induced by nuclear motion using intense laser pulses. Compared to fixed-nuclei approximations, the intensity of MHOHG is much higher due to the dependence of enhanced ionization on the internuclear distance. The width and symmetry of the spectrum of each harmonic in MHOHG encode rich information on the dissociation process of molecules at the rising and falling parts of the laser pulses, which can be used to retrieve the nuclear dynamics. Isotope effects are studied to confirm the FM mechanism. PMID:25415907

  16. Toward a simple molecular understanding of sum frequency generation at air-water interfaces

    SciTech Connect

    Noah-Vanhoucke, Joyce; Smith, Jared D.; Geissler, Phillip L.

    2009-01-13

    Second-order vibrational spectroscopies successfully isolate signals from interfaces, but they report on intermolecular structure in a complicated and indirect way. Here we adapt a perspective on vibrational response developed for bulk spectroscopies to explore the microscopic fluctuations to which sum frequency generation (SFG), a popular surface-specific measurement, is most sensitive. We focus exclusively on inhomogeneous broadening of spectral susceptibilities for OH stretching of HOD as a dilute solute in D{sub 2}O. Exploiting a simple connection between vibrational frequency shifts and an electric field variable, we identify several functions of molecular orientation whose averages govern SFG. The frequency-dependence of these quantities is well captured by a pair of averages, involving alignment of OH and OD bonds with the surface normal at corresponding values of the electric field. The approximate form we obtain for SFG susceptibility highlights a dramatic sensitivity to the way a simulated liquid slab is partitioned for calculating second-order response.

  17. BIO2010 and beyond: What undergraduate physics does the next generation of molecular biology researchers need?

    NASA Astrophysics Data System (ADS)

    Howard, Jonathon

    2004-03-01

    What fundamental skills in mathematics, chemistry, physics, computer science and engineering are required at the undergraduate level to prepare the next generation of biology majors who will become research scientists? To address this question, Bruce Alberts, President of the National Academy of Sciences, established BIO2010, a committee of the National Research Council (USA), chaired by Lubert Stryer. The report of the committee was published in 2003 as BIO2010: Transforming Undergraduate Education for Future Research Biologists (National Academies Press, Washington DC, www.national-academies.com). I will summarize the recommendations of the Physics and Engineering Panel that was chaired by John Hopfield and give my own views of what physics is essential for researchers in cell and molecular biology.

  18. Molecular dynamics study of two-dimensional sum frequency generation spectra at vapor/water interface

    SciTech Connect

    Ishiyama, Tatsuya; Morita, Akihiro; Tahara, Tahei

    2015-06-07

    Two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) spectra at vapor/water interface were studied by molecular dynamics (MD) simulation with a classical flexible and nonpolarizable model. The present model well describes the spectral diffusion of 2D infrared spectrum of bulk water as well as 2D HD-VSFG at the interface. The effect of isotopic dilution on the 2D HD-VSFG was elucidated by comparing the normal (H{sub 2}O) water and HOD water. We further performed decomposition analysis of 2D HD-VSFG into the hydrogen-bonding and the dangling (or free) OH vibrations, and thereby disentangled the different spectral responses and spectral diffusion in the 2D HD-VSFG. The present MD simulation demonstrated the role of anharmonic coupling between these modes on the cross peak in the 2D HD-VSFG spectrum.

  19. Preparation and evaluation a new generation of low molecular weight heparin.

    PubMed

    Zhao, Dan; Sang, Qing; Cui, Huifei

    2016-04-01

    Enoxaparin is widely used in clinic, but it has some disadvantages. For example, its anticoagulant activity is weaker compared with heparin and it can not be effectively neutralizad by protamine sulfate (PS) in case of bleeding. Therefore, in this work, a new generation of low molecular weight heparin (NG-LMWH) was prepared.The NG-LMWH was prepared with the method of alkaline β-elimination followed by gel chromatography. Estimating the molecular weight of the NG-LMWH by GPC-HPLC, it has a remarkably low polydispersity index and narrow molecular weight distribution. The polydispersity index of NG-LMWH was 1.052, which was lower than heparin (1.5) and enoxaparin (1.279). Anti-FXa and anti-FIIa potency of NG-LMWH was much higher than that of Enoxaparin, and close to that of heparin, which was determined by chromogenic substrate method. To test the degree of anti-FXa or anti-FIIa potency neutralized by PS, equivalent anti-FXa or anti-FIIa activity doses of different anticoagulant in plasma were titrated with increasing amounts of PS in plasma. The results indicate that NG-LMWH was more efficiently neutralized by PS than enoxaparin.The efficacy of anti-thrombus of NG-LMWH was superior to enoxaparin and the effect was dose dependent, which was evaluated with rat carotid artery thrombosis and inferior vena cava thrombosis model. The results of pharmacokinetics in New Zealand rabbits showed that the pharmacokinetic characteristics of NG-LMWH were similar to enoxaparin. The NG-LMWH prepared in this work has both advantages of heparin and enoxaparin with more effective and safer anticoagulation than enoxaparin. PMID:27044828

  20. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes

    PubMed Central

    Stefan, Christopher P.; Koehler, Jeffrey W.; Minogue, Timothy D.

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300–1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

  1. Structural analysis and investigation of molecular properties of Cefpodoxime acid, a third generation antibiotic

    NASA Astrophysics Data System (ADS)

    Suganthi, S.; Balu, P.; Sathyanarayanamoorthi, V.; Kannappan, V.; Kamil, M. G. Mohamed; Kumar, R.

    2016-03-01

    Extensive quantum mechanical studies are carried out on Cefpodoxime acid (CA), a new generation drug by Hartree-Fock (HF) and B3LYP methods to understand the structural and spectral characteristics of the molecule. The most stable geometry of the molecule was optimized and the bond parameters were reported. The spectroscopic properties of this pharmaceutically important compound were investigated by FT-IR, FT-Raman, UV and 1H NMR techniques. The scaled vibrational frequencies of CA in the ground state are calculated by HF and B3LYP methods with 6-311++G (d, p) basis set and compared with the observed FT-IR and FT-Raman spectra. The vibrational spectral analysis indicates the presence of two intra molecular hydrogen bonds in the molecule which is supported by theoretical study. 1H NMR chemical shifts (δ) were calculated for the CA molecule and compared with the experimental values. The theoretical electronic absorption spectral data in water and ethanol solvents were computed by TD-DFT method. UV-Vis absorption spectra of CA are recorded in these two solvents and compared with theoretical spectra. The spectral data and natural bond orbital (NBO) analysis confirm the occurrence of intra molecular interactions in CA. The electronic distribution, in conjunction with electrophilicity index of CA was used to establish the active site and type of interaction between CA and beta lactamases. Mulliken population analysis on atomic charges is also carried out and thermodynamic properties of the title compound are calculated.

  2. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature.

    PubMed

    Greytak, Sarah R; Engel, Kelly B; Bass, B Paige; Moore, Helen M

    2015-04-15

    Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens. PMID:25836717

  3. Targeted next-generation sequencing for the detection of ciprofloxacin resistance markers using molecular inversion probes.

    PubMed

    Stefan, Christopher P; Koehler, Jeffrey W; Minogue, Timothy D

    2016-01-01

    Antibiotic resistance (AR) is an epidemic of increasing magnitude requiring rapid identification and profiling for appropriate and timely therapeutic measures and containment strategies. In this context, ciprofloxacin is part of the first-line of countermeasures against numerous high consequence bacteria. Significant resistance can occur via single nucleotide polymorphisms (SNP) and deletions within ciprofloxacin targeted genes. Ideally, use of ciprofloxacin would be prefaced with AR determination to avoid overuse or misuse of the antibiotic. Here, we describe the development and evaluation of a panel of 44 single-stranded molecular inversion probes (MIPs) coupled to next-generation sequencing (NGS) for the detection of genetic variants known to confer ciprofloxacin resistance in Bacillus anthracis, Yersinia pestis, and Francisella tularensis. Sequencing results demonstrate MIPs capture and amplify targeted regions of interest at significant levels of coverage. Depending on the genetic variant, limits of detection (LOD) for high-throughput pooled sequencing ranged from approximately 300-1800 input genome copies. LODs increased 10-fold in the presence of contaminating human genome DNA. In addition, we show that MIPs can be used as an enrichment step with high resolution melt (HRM) real-time PCR which is a sensitive assay with a rapid time-to-answer. Overall, this technology is a multiplexable upfront enrichment applicable with multiple downstream molecular assays for the detection of targeted genetic regions. PMID:27174456

  4. DNA shuffling: induced molecular breeding to produce new generation long-lasting vaccines.

    PubMed

    Marshall, Sergio H

    2002-11-01

    The paradigm for classic vaccines has been to mimic natural infection, and their success relies mostly on the induction of neutralizing antibodies followed by long-lasting immunity. The outcome of aggressive chronic infections such as HIV and HCV, the reappearance of fastidious diseases such as tuberculosis and the progression of cancer growth suggest that natural immune responses are definitely insufficient in many cases. A new paradigm is needed to design and develop a new high-efficiency generation of vaccines ideally able to surpass the capabilities of natural immune responses. In vitro evolution is a new, important laboratory method to evolve molecules with desired properties, which appears as an appealing alternative to achieve this goal. In its battle against disease, the vertebrate immune system triggers a series of well-known molecular events in order to produce protective neutralizing antibodies. This natural in vivo response shares remarkable similarities with the in vitro technique known as molecular breeding or "DNA shuffling." This method exploits the recombination between genes to dramatically accelerate the rate at which genes can be evolved under selection pressure in the laboratory, producing optimized high-efficiency mutant proteins. Since new generation vaccines are aimed to overcome natural selection and environmental pressures to fully inactivate rapidly developing pathogen variants, they could be engineered, developed and selected through the application of directed DNA shuffling procedures. This review highlights the potential of the procedure in the complex context of natural immune responses and the equilibrium and interaction existing in nature between hosts and pathogens. PMID:14550030

  5. Augmented generation of protein fragments during wakefulness as the molecular cause of sleep: a hypothesis

    PubMed Central

    Varshavsky, Alexander

    2012-01-01

    Despite extensive understanding of sleep regulation, the molecular-level cause and function of sleep are unknown. I suggest that they originate in individual neurons and stem from increased production of protein fragments during wakefulness. These fragments are transient parts of protein complexes in which the fragments were generated. Neuronal Ca2+ fluxes are higher during wakefulness than during sleep. Subunits of transmembrane channels and other proteins are cleaved by Ca2+-activated calpains and by other nonprocessive proteases, including caspases and secretases. In the proposed concept, termed the fragment generation (FG) hypothesis, sleep is a state during which the production of fragments is decreased (owing to lower Ca2+ transients) while fragment-destroying pathways are upregulated. These changes facilitate the elimination of fragments and the remodeling of protein complexes in which the fragments resided. The FG hypothesis posits that a proteolytic cleavage, which produces two fragments, can have both deleterious effects and fitness-increasing functions. This (previously not considered) dichotomy can explain both the conservation of cleavage sites in proteins and the evolutionary persistence of sleep, because sleep would counteract deleterious aspects of protein fragments. The FG hypothesis leads to new explanations of sleep phenomena, including a longer sleep after sleep deprivation. Studies in the 1970s showed that ethanol-induced sleep in mice can be strikingly prolonged by intracerebroventricular injections of either Ca2+ alone or Ca2+ and its ionophore (Erickson et al., Science 1978;199:1219–1221; Harris, Pharmacol Biochem Behav 1979;10:527–534; Erickson et al., Pharmacol Biochem Behav 1980;12:651–656). These results, which were never interpreted in connection to protein fragments or the function of sleep, may be accounted for by the FG hypothesis about molecular causation of sleep. PMID:22930402

  6. Force Generation by Molecular-Motor-Powered Microtubule Bundles; Implications for Neuronal Polarization and Growth

    PubMed Central

    Jakobs, Maximilian; Franze, Kristian; Zemel, Assaf

    2015-01-01

    The heavily cross-linked microtubule (MT) bundles found in neuronal processes play a central role in the initiation, growth and maturation of axons and dendrites; however, a quantitative understanding of their mechanical function is still lacking. We here developed computer simulations to investigate the dynamics of force generation in 1D bundles of MTs that are cross-linked and powered by molecular motors. The motion of filaments and the forces they exert are investigated as a function of the motor type (unipolar or bipolar), MT density and length, applied load, and motor connectivity. We demonstrate that only unipolar motors (e.g., kinesin-1) can provide the driving force for bundle expansion, while bipolar motors (e.g., kinesin-5) oppose it. The force generation capacity of the bundles is shown to depend sharply on the fraction of unipolar motors due to a percolation transition that must occur in the bundle. Scaling laws between bundle length, force, MT length and motor fraction are presented. In addition, we investigate the dynamics of growth in the presence of a constant influx of MTs. Beyond a short equilibration period, the bundles grow linearly in time. In this growth regime, the bundle extends as one mass forward with most filaments sliding with the growth velocity. The growth velocity is shown to be dictated by the inward flux of MTs, to inversely scale with the load and to be independent of the free velocity of the motors. These findings provide important molecular-level insights into the mechanical function of the MT cytoskeleton in normal axon growth and regeneration after injury. PMID:26617489

  7. Attitudinal Conformity and Anonymity

    ERIC Educational Resources Information Center

    Tyson, Herbert; Kaplowitz, Stan

    1977-01-01

    Tested college students for conformity when conditions contributing to conformity were absent. Found that social pressures (responding in public, being surveyed by fellow group members) are necessary to produce conformity. (RL)

  8. Protein Conformational Switches: From Nature to Design

    PubMed Central

    Ha, Jeung-Hoi

    2012-01-01

    Protein conformational switches alter their shape upon receiving an input signal, such as ligand binding, chemical modification, or change in environment. The apparent simplicity of this transformation—which can be carried out by a molecule as small as a thousand atoms or so—belies its critical importance to the life of the cell as well as its capacity for engineering by humans. In the realm of molecular switches, proteins are unique because they are capable of performing a variety of biological functions. Switchable proteins are therefore of high interest to the fields of biology, bio-technology, and medicine. These molecules are beginning to be exploited as the core machinery behind a new generation of biosensors, functionally regulated enzymes, and “smart” biomaterials that react to their surroundings. As inspirations for these designs, researchers continue to analyze existing examples of allosteric proteins. Recent years have also witnessed the development of new methodologies for introducing conformational change into proteins that previously had none. Herein we review examples of both natural and engineered protein switches in the context of four basic modes of conformational change: rigid-body domain movement, limited structural rearrangement, global fold switching, and folding–unfolding. Our purpose is to highlight examples that can potentially serve as platforms for the design of custom switches. Accordingly, we focus on inducible conformational changes that are substantial enough to produce a functional response (e.g., in a second protein to which it is fused), yet are relatively simple, structurally well-characterized, and amenable to protein engineering efforts. PMID:22688954

  9. Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

    NASA Astrophysics Data System (ADS)

    Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

    1981-09-01

    Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

  10. Protein Allostery and Conformational Dynamics.

    PubMed

    Guo, Jingjing; Zhou, Huan-Xiang

    2016-06-01

    The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond-nanosecond local and microsecond-millisecond conformational exchange dynamics, are presented. PMID:26876046

  11. Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure.

    PubMed

    Chandran, Thyageshwar; Sharma, Alok; Vijayan, M

    2015-12-01

    The structures of nine independent crystals of bitter gourd seed lectin (BGSL), a non-toxic homologue of type II RIPs, and its sugar complexes have been determined. The four-chain, two-fold symmetric, protein is made up of two identical two-chain modules, each consisting of a catalytic chain and a lectin chain, connected by a disulphide bridge. The lectin chain is made up of two domains. Each domain carries a carbohydrate binding site in type II RIPs of known structure. BGSL has a sugar binding site only on one domain, thus impairing its interaction at the cell surface. The adenine binding site in the catalytic chain is defective. Thus, defects in sugar binding as well as adenine binding appear to contribute to the non-toxicity of the lectin. The plasticity of the molecule is mainly caused by the presence of two possible well defined conformations of a surface loop in the lectin chain. One of them is chosen in the sugar complexes, in a case of conformational selection, as the chosen conformation facilitates an additional interaction with the sugar, involving an arginyl residue in the loop. The N-glycosylation of the lectin involves a plant-specific glycan while that in toxic type II RIPs of known structure involves a glycan which is animal as well as plant specific. PMID:26648038

  12. Molecular dynamics of 17α- and 21-hydroxy progesterone studied by NMR. Relation between molecule conformation and height of the barrier for methyl group reorientations in steroid compounds

    NASA Astrophysics Data System (ADS)

    Szyczewski, A.; Hołderna-Natkaniec, K.

    2005-01-01

    For the two steroid compounds 17αOH-progesterone and 21OH-progesterone, the activation energies of reorientations of the methyl groups have been determined. Their values together with results of the quantum chemical calculations permitted establishment of the sequence of the onset of the methyl group reorientations about the three-fold symmetry axis of the C-C bond. On the basis of the asymmetry parameters, the conformations of the hitherto studied pregnane derivatives and testosterone have been determined. It has been found that the conformation of ring A has dominant effect on the activation energies of the reorientation of C(19)H 3. The reorientation of the methyl group C(18)H 3 significantly depends on the conformation of the side chain 17β (torsional angle C(13)-C(17)-C(20)-O(20)) and the distance between C18 and O20. The study has proved that the 1H NMR method in combination with the quantum chemistry calculations and inelastic incoherent neutron scattering (IINS) are effective for prediction of the sequence of the methyl group reorientations about the three-fold symmetry axis.

  13. FT-IR, FT-Raman spectra, density functional computations of the vibrational spectra and molecular conformational analysis of 2,5-di-tert-butyl-hydroquinone

    NASA Astrophysics Data System (ADS)

    Subramanian, N.; Sundaraganesan, N.; Dereli, Ö.; Türkkan, E.

    2011-12-01

    The purpose of finding conformer among six different possible conformers of 2,5-di-tert-butyl-hydroquinone (DTBHQ), its equilibrium geometry and harmonic wavenumbers were calculated by the B3LYP/6-31G(d,p) method. The infrared and Raman spectra of DTBHQ were recorded in the region 400-4000 cm -1 and 50-3500 cm -1, respectively. In addition, the IR spectra in CCl 4 at various concentrations of DTBHQ are also recorded. The computed vibrational wavenumbers were compared with the IR and Raman experimental data. Computational calculations at B3LYP level with two different basis sets 6-31G(d,p) and 6-311++G(d,p) are also employed in the study of the possible conformer of DTBHQ. The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA 4 program. The general agreement between the observed and calculated frequencies was established.

  14. The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n-butane conformation and SN2 reaction: RCl+Cl -

    NASA Astrophysics Data System (ADS)

    Humbel, Stéphane; Sieber, Stefan; Morokuma, Keiji

    1996-08-01

    A new theoretical method, called IMOMO (integrated MO (molecular orbital)+MO), for integration of two different levels of MO approximation is presented. Only the active or more difficult part of a molecule is treated at a higher level of approximation and the rest of the molecule at a lower level of approximation. The integrated total energy and energy derivatives are defined from three different calculations, and the structure of transition state as well as the equilibrium structure can be optimized using the integrated energy. Any combination of any molecular orbital approximations (ab initio, density functional to semi-empirical) can be used. Test calculations in the IMOMO method have been performed and compared with normal MO calculations for the conformation energy of ethane and n-butane and the SN2 reaction of ethyl, propyl, isobutyl, and neopentyl chloride with Cl-. The results indicate that these methods have a tremendous potential for theoretical study of larger molecules, in particular for transition states.

  15. Molecular characterization and comparison of shale oils generated by different pyrolysis methods

    USGS Publications Warehouse

    Birdwell, Justin E.; Jin, Jang Mi; Kim, Sunghwan

    2012-01-01

    Shale oils generated using different laboratory pyrolysis methods have been studied using standard oil characterization methods as well as Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with electrospray ionization (ESI) and atmospheric photoionization (APPI) to assess differences in molecular composition. The pyrolysis oils were generated from samples of the Mahogany zone oil shale of the Eocene Green River Formation collected from outcrops in the Piceance Basin, Colorado, using three pyrolysis systems under conditions relevant to surface and in situ retorting approaches. Significant variations were observed in the shale oils, particularly the degree of conjugation of the constituent molecules and the distribution of nitrogen-containing compound classes. Comparison of FT-ICR MS results to other oil characteristics, such as specific gravity; saturate, aromatic, resin, asphaltene (SARA) distribution; and carbon number distribution determined by gas chromatography, indicated correspondence between higher average double bond equivalence (DBE) values and increasing asphaltene content. The results show that, based on the shale oil DBE distributions, highly conjugated species are enriched in samples produced under low pressure, high temperature conditions, and under high pressure, moderate temperature conditions in the presence of water. We also report, for the first time in any petroleum-like substance, the presence of N4 class compounds based on FT-ICR MS data. Using double bond equivalence and carbon number distributions, structures for the N4 class and other nitrogen-containing compounds are proposed.

  16. High-order-harmonic generation in molecular sequential double ionization by intense circularly polarized laser pulses

    NASA Astrophysics Data System (ADS)

    Yuan, Kai-Jun; Lu, Huizhong; Bandrauk, André D.

    2015-08-01

    We present effects of electron energy transfer by electron collisions on high-order-harmonic generation (HHG) in molecular sequential double ionization by intense circularly polarized laser pulses. Results from numerical solutions of time-dependent Schrödinger equations for extended (large internuclear distance) H2 where electrons are entangled and hence delocalized by exchange show that HHG with cutoff energy up to Ip+24 Up can be obtained, where Ip is the molecule ionization potential and Up=I0/4 ω02 (in atomic units) is the ponderomotive energy for pulse intensity I0 and frequency ω0. A time-frequency analysis is employed to identify electron collisions for the generation of harmonics. Extended HHG arises from electron energy exchange, which agrees well with the prediction of a classical two electron collision model. Results for nonsymmetric HHe+ where initially electrons are localized on He are also compared and confirm the role of initial electron delocalization via entanglement for obtaining extended HHG plateaus.

  17. Generation of transmissible hepatitis C virions from a molecular clone in chimpanzees.

    PubMed

    Hong, Z; Beaudet-Miller, M; Lanford, R E; Guerra, B; Wright-Minogue, J; Skelton, A; Baroudy, B M; Reyes, G R; Lau, J Y

    1999-03-30

    Multiple alignments of hepatitis C virus (HCV) polyproteins from six different genotypes identified a total of 22 nonconsensus mutations in a clone derived from the Hutchinson (H77) isolate. These mutations, collectively, may have contributed to the failure in generating a "functionally correct" or "infectious" clone in earlier attempts. A consensus clone was constructed after systematic repair of these mutations, which yielded infectious virions in a chimpanzee after direct intrahepatic inoculation of in vitro transcribed RNAs. This RNA-infected chimpanzee has developed hepatitis and remained HCV positive for more than 11 months. To further verify this RNA-derived infectivity, a second naive chimpanzee was injected intravenously with serum collected from the first chimpanzee. Infectivity analysis of the second chimpanzee demonstrated that the HCV infection was successfully transmitted, which validated unequivocally the infectivity of our repaired molecular clone. Amino acid sequence comparisons revealed that our repaired infectious clone had 4 mismatches with the isogenic clone reported by Kolykhalov et al. (1997, Science 277, 570-574) and 8 mismatches with that reported by Yanagi et al. (1997, Proc. Natl. Acad. Sci. USA 94, 8738-8743). At the RNA level, more mismatches (43 and 67, respectively) were identified; most of them were synonymous substitutions. Further comparisons with 16 isolates from different genotypes demonstrated that our repaired clone shares greater consensus than the reported isogenic clones. This approach of generating infectious HCV RNA validates the importance of amino acid sequence consensus in relation to the biology of HCV. PMID:10087224

  18. Generation of a neutralization-resistant CCR5 tropic simian/human immunodeficiency virus (SHIV-MK38) molecular clone, a derivative of SHIV-89.6.

    PubMed

    Ishida, Yuki; Yoneda, Mai; Otsuki, Hiroyuki; Watanabe, Yuji; Kato, Fumihiro; Matsuura, Kanako; Kikukawa, Minako; Matsushita, Shuzo; Hishiki, Takayuki; Igarashi, Tatsuhiko; Miura, Tomoyuki

    2016-05-01

    Previously, we reported that a new genetically diverse CCR5 (R5) tropic simian/human immunodeficiency virus (SHIV-MK38) adapted to rhesus monkeys became more neutralization resistant to SHIV-infected plasma than did the parental SHIV-KS661 clone. Here, to clarify the significance of the neutralization-resistant phenotype of SHIV in a macaque model, we initially investigated the precise neutralization phenotype of the SHIVs, including SHIV-MK38 molecular clones, using SHIV-MK38-infected plasma, a pooled plasma of human immunodeficiency virus (HIV)-infected individuals, soluble CD4 and anti-HIV-1 neutralizing mAbs, the epitopes of which were known. The results show that SHIV-KS661 had tier 1 neutralization sensitivity, but monkey-adapted R5 tropic SHIV-MK38 acquired neutralization resistance similar to that of tier 2 or 3 as a clone virus. Sequence analysis of the env gene suggested that the neutralization-resistant phenotype of SHIV-MK38 was acquired by conformational changes in Env associated with the net charge and potential N-linked glycosylation sites. To examine the relationship between neutralization phenotype and stably persistent infection in monkeys, we performed in vivo rectal inoculation experiments using a SHIV-MK38 molecular clone. The results showed that one of three rhesus monkeys exhibited durable infection with a plasma viral load of 105 copies ml- 1 despite the high antibody responses that occurred in the host. Whilst further improvements are required in the development of a challenge virus, it will be useful to generate a neutralization-resistant R5 tropic molecular clone of the SHIV-89.6 lineage commonly used for vaccine development - a result that can be used to explore the foundation of AIDS pathogenesis. PMID:26850058

  19. Reactive molecular dynamics of network polymers: Generation, characterization and mechanical properties

    NASA Astrophysics Data System (ADS)

    Shankar, Chandrashekar

    The goal of this research was to gain a fundamental understanding of the properties of networks created by the ring opening metathesis polymerization (ROMP) of dicyclopentadiene (DCPD) used in self-healing materials. To this end we used molecular simulation methods to generate realistic structures of DCPD networks, characterize their structures, and determine their mechanical properties. Density functional theory (DFT) calculations, complemented by structural information derived from molecular dynamics simulations were used to reconstruct experimental Raman spectra and differential scanning calorimetry (DSC) data. We performed coarse-grained simulations comparing networks generated via the ROMP reaction process and compared them to those generated via a RANDOM process, which led to the fundamental realization that the polymer topology has a unique influence on the network properties. We carried out fully atomistic simulations of DCPD using a novel algorithm for recreating ROMP reactions of DCPD molecules. Mechanical properties derived from these atomistic networks are in excellent agreement with those obtained from coarse-grained simulations in which interactions between nodes are subject to angular constraints. This comparison provides self-consistent validation of our simulation results and helps to identify the level of detail necessary for the coarse-grained interaction model. Simulations suggest networks can classified into three stages: fluid-like, rubber-like or glass-like delineated by two thresholds in degree of reaction alpha: The onset of finite magnitudes for the Young's modulus, alphaY, and the departure of the Poisson ration from 0.5, alphaP. In each stage the polymer exhibits a different predominant mechanical response to deformation. At low alpha < alphaY it flows. At alpha Y < alpha < alphaP the response is entropic with no change in internal energy. At alpha > alphaP the response is enthalpic change in internal energy. We developed graph theory

  20. Identification of Distinct Conformations of the Angiotensin-II Type 1 Receptor Associated with the Gq/11 Protein Pathway and the β-Arrestin Pathway Using Molecular Dynamics Simulations*

    PubMed Central

    Cabana, Jérôme; Holleran, Brian; Leduc, Richard; Escher, Emanuel; Guillemette, Gaétan; Lavigne, Pierre

    2015-01-01

    Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. The angiotensin-II type 1 (AT1) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the Gq/11 protein and β-arrestins. It is believed that the activation of those two pathways can be associated with distinct conformations of the AT1 receptor. To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore the conformational landscape sampled by the WT-AT1 receptor, the N111G-AT1 receptor (constitutively active and biased for the Gq/11 pathway), and the D74N-AT1 receptor (biased for the β-arrestin1 and -2 pathways) in their apo-forms and in complex with AngII. The molecular dynamics simulations of the AngII-WT-AT1, N111G-AT1, and AngII-N111G-AT1 receptors revealed specific structural rearrangements compared with the initial and ground state of the receptor. Simulations of the D74N-AT1 receptor revealed that the mutation stabilizes the receptor in the initial ground state. The presence of AngII further stabilized the ground state of the D74N-AT1 receptor. The biased agonist [Sar1,Ile8]AngII also showed a preference for the ground state of the WT-AT1 receptor compared with AngII. These results suggest that activation of the Gq/11 pathway is associated with a specific conformational transition stabilized by the agonist, whereas the activation of the β-arrestin pathway is linked to the stabilization of the ground state of the receptor. PMID:25934394

  1. Tumor-Specific Proteolytic Processing of Cyclin E Generates Hyperactive Lower-Molecular-Weight Forms

    PubMed Central

    Porter, Donald C.; Zhang, Ning; Danes, Christopher; McGahren, Mollianne J.; Harwell, Richard M.; Faruki, Shamsa; Keyomarsi, Khandan

    2001-01-01

    Cyclin E is a G1 cyclin essential for S-phase entry and has a profound role in oncogenesis. Previously this laboratory found that cyclin E is overexpressed and present in lower-molecular-weight (LMW) isoforms in breast cancer cells and tumor tissues compared to normal cells and tissues. Such alteration of cyclin E is linked to poor patient outcome. Here we report that the LMW forms of cyclin E are hyperactive biochemically and they can more readily induce G1-to-S progression in transfected normal cells than the full-length form of the protein can. Through biochemical and mutational analyses we have identified two proteolytically sensitive sites in the amino terminus of human cyclin E that are cleaved to generate the LMW isoforms found in tumor cells. Not only are the LMW forms of cyclin E functional, as they phosphorylate substrates such as histone H1 and GST-Rb, but also their activities are higher than the full-length cyclin E. These nuclear localized LMW forms of cyclin E are also biologically functional, as their overexpression in normal cells increases the ability of these cells to enter S and G2/M. Lastly, we show that cyclin E is selectively cleaved in vitro by the elastase class of serine proteases to generate LMW forms similar to those observed in tumor cells. These studies suggest that the defective entry into and exit from S phase by tumor cells is in part due to the proteolytic processing of cyclin E, which generates hyperactive LMW isoforms whose activities have been modified from that of the full-length protein. PMID:11509668

  2. Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A Series of Hands-On Collaborative Practical Sessions for Undergraduate Students

    ERIC Educational Resources Information Center

    Rodrigues, João P. G. L. M.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.

    2016-01-01

    Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These…

  3. Molecular-Level Simulations of Shock Generation and Propagation in Soda-Lime Glass

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Bell, W. C.; Pandurangan, B.; Cheeseman, B. A.; Fountzoulas, C.; Patel, P.

    2012-08-01

    A non-equilibrium molecular dynamics method is employed to study the mechanical response of soda-lime glass (a material commonly used in transparent armor applications) when subjected to the loading conditions associated with the generation and propagation of planar shock waves. Specific attention is given to the identification and characterization of various (inelastic-deformation and energy-dissipation) molecular-level phenomena and processes taking place at, or in the vicinity of, the shock front. The results obtained revealed that the shock loading causes a 2-4% (shock strength-dependent) density increase. In addition, an increase in the average coordination number of the silicon atoms is observed along with the creation of smaller Si-O rings. These processes are associated with substantial energy absorption and dissipation and are believed to greatly influence the blast/ballistic impact mitigation potential of soda-lime glass. The present work was also aimed at the determination of the shock Hugoniot (i.e., a set of axial stress vs. density/specific-volume vs. internal energy vs. particle velocity vs. temperature) material states obtained in soda-lime glass after the passage of a shock wave of a given strength (as quantified by the shock speed). The availability of a shock Hugoniot is critical for construction of a high deformation-rate, large-strain, high pressure material model which can be used within a continuum-level computational analysis to capture the response of a soda-lime glass based laminated transparent armor structure (e.g., a military vehicle windshield, door window, etc.) to blast/ballistic impact loading.

  4. Feasibility of a workflow for the molecular characterization of single cells by next generation sequencing

    PubMed Central

    Salvianti, Francesca; Rotunno, Giada; Galardi, Francesca; De Luca, Francesca; Pestrin, Marta; Vannucchi, Alessandro Maria; Di Leo, Angelo; Pazzagli, Mario; Pinzani, Pamela

    2015-01-01

    The purpose of the study was to explore the feasibility of a protocol for the isolation and molecular characterization of single circulating tumor cells (CTCs) from cancer patients using a single-cell next generation sequencing (NGS) approach. To reach this goal we used as a model an artificial sample obtained by spiking a breast cancer cell line (MDA-MB-231) into the blood of a healthy donor. Tumor cells were enriched and enumerated by CellSearch® and subsequently isolated by DEPArray™ to obtain single or pooled pure samples to be submitted to the analysis of the mutational status of multiple genes involved in cancer. Upon whole genome amplification, samples were analysed by NGS on the Ion Torrent PGM™ system (Life Technologies) using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies), designed to investigate genomic “hot spot” regions of 50 oncogenes and tumor suppressor genes. We successfully sequenced five single cells, a pool of 5 cells and DNA from a cellular pellet of the same cell line with a mean depth of the sequencing reaction ranging from 1581 to 3479 reads. We found 27 sequence variants in 18 genes, 15 of which already reported in the COSMIC or dbSNP databases. We confirmed the presence of two somatic mutations, in the BRAF and TP53 gene, which had been already reported for this cells line, but also found new mutations and single nucleotide polymorphisms. Three variants were common to all the analysed samples, while 18 were present only in a single cell suggesting a high heterogeneity within the same cell line. This paper presents an optimized workflow for the molecular characterization of multiple genes in single cells by NGS. The described pipeline can be easily transferred to the study of single CTCs from oncologic patients. PMID:27077040

  5. Feasibility of a workflow for the molecular characterization of single cells by next generation sequencing.

    PubMed

    Salvianti, Francesca; Rotunno, Giada; Galardi, Francesca; De Luca, Francesca; Pestrin, Marta; Vannucchi, Alessandro Maria; Di Leo, Angelo; Pazzagli, Mario; Pinzani, Pamela

    2015-09-01

    The purpose of the study was to explore the feasibility of a protocol for the isolation and molecular characterization of single circulating tumor cells (CTCs) from cancer patients using a single-cell next generation sequencing (NGS) approach. To reach this goal we used as a model an artificial sample obtained by spiking a breast cancer cell line (MDA-MB-231) into the blood of a healthy donor. Tumor cells were enriched and enumerated by CellSearch(®) and subsequently isolated by DEPArray™ to obtain single or pooled pure samples to be submitted to the analysis of the mutational status of multiple genes involved in cancer. Upon whole genome amplification, samples were analysed by NGS on the Ion Torrent PGM™ system (Life Technologies) using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies), designed to investigate genomic "hot spot" regions of 50 oncogenes and tumor suppressor genes. We successfully sequenced five single cells, a pool of 5 cells and DNA from a cellular pellet of the same cell line with a mean depth of the sequencing reaction ranging from 1581 to 3479 reads. We found 27 sequence variants in 18 genes, 15 of which already reported in the COSMIC or dbSNP databases. We confirmed the presence of two somatic mutations, in the BRAF and TP53 gene, which had been already reported for this cells line, but also found new mutations and single nucleotide polymorphisms. Three variants were common to all the analysed samples, while 18 were present only in a single cell suggesting a high heterogeneity within the same cell line. This paper presents an optimized workflow for the molecular characterization of multiple genes in single cells by NGS. The described pipeline can be easily transferred to the study of single CTCs from oncologic patients. PMID:27077040

  6. Assessing the utility of whole genome amplified DNA for next-generation molecular ecology.

    PubMed

    Blair, Christopher; Campbell, C Ryan; Yoder, Anne D

    2015-09-01

    DNA quantity can be a hindrance in ecological and evolutionary research programmes due to a range of factors including endangered status of target organisms, available tissue type, and the impact of field conditions on preservation methods. A potential solution to low-quantity DNA lies in whole genome amplification (WGA) techniques that can substantially increase DNA yield. To date, few studies have rigorously examined sequence bias that might result from WGA and next-generation sequencing of nonmodel taxa. To address this knowledge deficit, we use multiple displacement amplification (MDA) and double-digest RAD sequencing on the grey mouse lemur (Microcebus murinus) to quantify bias in genome coverage and SNP calls when compared to raw genomic DNA (gDNA). We focus our efforts in providing baseline estimates of potential bias by following manufacturer's recommendations for starting DNA quantities (>100 ng). Our results are strongly suggestive that MDA enrichment does not introduce systematic bias to genome characterization. SNP calling between samples when genotyping both de-novo and with a reference genome are highly congruent (>98%) when specifying a minimum threshold of 20X stack depth to call genotypes. Relative genome coverage is also similar between MDA and gDNA, and allelic dropout is not observed. SNP concordance varies based on coverage threshold, with 95% concordance reached at ~12X coverage genotyping de-novo and ~7X coverage genotyping with the reference genome. These results suggest that MDA may be a suitable solution for next-generation molecular ecological studies when DNA quantity would otherwise be a limiting factor. PMID:25619406

  7. Molecular interaction forces generated during protein adsorption to well-defined polymer brush surfaces.

    PubMed

    Sakata, Sho; Inoue, Yuuki; Ishihara, Kazuhiko

    2015-03-17

    The molecular interaction forces generated during the adsorption of proteins to surfaces were examined by the force-versus-distance (f-d) curve measurements of atomic force microscopy using probes modified with appropriate molecules. Various substrates with polymer brush layers bearing zwitterionic, cationic, anionic, and hydrophobic groups were systematically prepared by surface-initiated atom transfer radical polymerization. Surface interaction forces on these substrates were analyzed by the f-d curve measurements using probes with the same polymer brush layer as the substrate. Repulsive forces, which decreased depending on the ionic strength, were generated between cationic or anionic polyelectrolyte brush layers; these were considered to be electrostatic interaction forces. A strong adhesive force was detected between hydrophobic polymer brush layers during retraction; this corresponded to the hydrophobic interaction between two hydrophobic polymer layers. In contrast, no significant interaction forces were detected between zwitterionic polymer brush layers. Direct interaction forces between proteins and polymer brush layers were then quantitatively evaluated by the f-d curve measurements using protein-immobilized probes consisting of negatively charged albumin and positively charged lysozyme under physiological conditions. In addition, the amount of protein adsorbed on the polymer brush layer was quantified by surface plasmon resonance measurements. Relatively large amounts of protein adsorbed to the polyelectrolyte brush layers with opposite charges. It was considered that the detachment of the protein after contact with the polymer brush layer hardly occurred due to salt formation at the interface. Both proteins adsorbed significantly on the hydrophobic polymer brush layer, which was due to hydrophobic interactions at the interface. In contrast, the zwitterionic polymer brush layer exhibited no significant interaction force with proteins and suppressed

  8. Conformational stability, molecular structure, vibrational, electronic, 1H and 13C spectral analysis of 3-pyridinemethanol using ab-initio/DFT method

    NASA Astrophysics Data System (ADS)

    Sivaranjani, T.; Periandy, S.; Xavier, S.

    2016-03-01

    The FT-IR and FT-Raman spectra of 3-pyridinemethanol (3PYRM) have been recorded in the regions 4000-400 and 4000-100 cm-1 respectively. The vibrational analysis of 3PYRM was carried out using wavenumbers computed by HF and DFT (B3LYP) methods with 6-311++G (d, p) basis set, along with experimental values. The conformational analyses were performed and the energies of the different possible conformers were determined. The total electron density and MESP surfaces of the molecules were constructed using B3LYP/6-311++G (d, p) method to display nucleophilic and electrophilic region globally. The HOMO and LUMO energies were measured and different reactivity descriptors are discussed the active sites of the molecule. Natural Bond Orbital Analysis is discussed and possible transition are correlated with the electronic transitions. Milliken's net charges and the atomic natural charges are also predicted. The 13C and 1H NMR chemical shifts were computed at the B3LYP/6-311++G (2d, p) level by applying GIAO theory and compared with the experimental spectra recorded using the high resolution of 100 MHz and 400 MHz NMR spectrometer with electromagnetic field strength 9.1T, respectively. The temperature dependence of the thermodynamic properties; heat capacity, entropy and enthalpy for the title compounds were also determined by B3LYP/6-311++G (d, p) method.

  9. Similar molecular constitutions but different conformations and different supramolecular assemblies in two related fused tetracyclic benzo[b]pyrimido[5,4-f]azepine derivatives.

    PubMed

    Acosta Quintero, Lina M; Burgos, Isidro; Palma, Alirio; Cobo, Justo; Glidewell, Christopher

    2016-01-01

    A simple and effective two-step approach to tricyclic pyrimidine-fused benzazepines has been adapted to give the tetracyclic analogues. In (RS)-8-chloro-6-methyl-1,2,6,7-tetrahydropyrimido[5',4':6,7]azepino[3,2,1-hi]indole, C15H14ClN3, (I), the five-membered ring adopts an envelope conformation, as does the reduced pyridine ring in (RS)-9-chloro-7-methyl-2,3,7,8-tetrahydro-1H-pyrimido[5',4':6,7]azepino[3,2,1-ij]quinoline, C16H16ClN3, (II). However, the seven-membered rings in (I) and (II) adopt very different conformations, with the result that the methyl substituent occupies a quasi-axial site in (I) but a quasi-equatorial site in (II). The molecules of (I) are linked by C-H...N hydrogen bonds to form C(5) chains and inversion-related pairs of chains are linked by a π-π stacking interaction. A combination of a C-H...π hydrogen bond and two C-Cl...π interactions links the molecules of (II) into complex sheets. Comparisons are made with some similar fused heterocyclic compounds. PMID:26742827

  10. Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

    PubMed Central

    Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; Lim, Sze Chern; Lieber, Daniel S.; Tucker, Elena J.; Laskowski, Adrienne; Garone, Caterina; Liu, Shangtao; Jaffe, David B.; Christodoulou, John; Fletcher, Janice M.; Bruno, Damien L; Goldblatt, Jack; DiMauro, Salvatore; Thorburn, David R.; Mootha, Vamsi K.

    2012-01-01

    Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. While in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic utility, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease, who were refractory to traditional molecular diagnosis. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with over 100 causal genes identified to date. We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Since patients and controls harbored a comparable number of such heterozygous alleles, we could not prioritize dominant acting genes. However, patients showed a five-fold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23/42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. 13 patients (31%) had mutations in nuclear genes never linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by cDNA complementation and evidence from multiple patients, respectively. The results underscore the immediate potential and challenges of deploying NGS in clinical settings. PMID:22277967

  11. Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges

    PubMed Central

    Luthra, Rajyalakshmi; Chen, Hui; Roy-Chowdhuri, Sinchita; Singh, R. Rajesh

    2015-01-01

    The application of next-generation sequencing (NGS) to characterize cancer genomes has resulted in the discovery of numerous genetic markers. Consequently, the number of markers that warrant routine screening in molecular diagnostic laboratories, often from limited tumor material, has increased. This increased demand has been difficult to manage by traditional low- and/or medium-throughput sequencing platforms. Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA. However, implementation of NGS technologies, most of which are for research use only (RUO), in a diagnostic laboratory, needs extensive validation in order to establish Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP)-compliant performance characteristics. Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors. We discuss the criteria for selecting gene markers to include in the NGS panel and the deciding factors for selecting target capture approaches and sequencing platforms. We also discuss challenges in result reporting, storage and retrieval of the voluminous sequencing data and the future potential of clinical NGS. PMID:26473927

  12. Molecular probes for two-photon excited fluorescence and second harmonic generation imaging of biological membranes

    NASA Astrophysics Data System (ADS)

    Porres, Laurent; Mongin, Olivier; Bhatthula, Bharath K. G.; Blanchard-Desce, Mireille H.; Ventelon, Lionel; Moreaux, Laurent; Pons, T.; Mertz, Jerome

    2002-11-01

    Novel microscopies based on nonlinear optical (NLO) phenomena are attracting increasing interest in the biology community owing to their potentialities in the area of real-time, non-damaging imaging of biological systems. In particular, second-harmonic generation (SHG) and two-photon excited fluorescence (TPEF) are NLO phenomena that scale with excitation intensity squared, and thus give rise to an intrinsic 3-dimensional resolution when used in microscopic imaging. In this perspective, we have implemented a molecular engineering approach toward NLO-probes specifically designed for SHG and/or TPEF imaging of cellular membranes. We have designed nanoscale rod-like fluorophores showing very large TPEF cross-sections in the visible red, outperforming standard fluorophores such as fluorescein by up to two orders of magnitude. Bolaamphiphilic derivatives combining high TPEF cross-sections and affinity for cellular membranes were prepared. Their incorporation into model or cell membranes can be monitored by TPEF microscopy. Amphiphilic push-pull chromophores showing both high TPA and SHG cross-sections in the near-IR region were designed as NLO-probes for imaging of biological membranes by simultaneous SHG and TPEF microscopy. These NLO-phores offer intriguing potentialities for imaging of fundamental biological processes such as adhesion, fusion or for reporting of membrane electrical potentials.

  13. A Theory of Dynamic Imaging of Coherent Molecular Rotations by High Harmonic Generation

    NASA Astrophysics Data System (ADS)

    Faisal, F. H. M.; Abdurrouf, A.

    A dynamic theory of mapping coherent molecular motions from high harmonic generation signals is presented. Application to mapping of coherent rotational motions of linear molecules is made. Results of concrete calculations for N2, O2 and CO2 are analyzed both in time and frequency domains. A "magic angle" for the polarization geometry is predicted at which the HHG signals for all pump-probe delay times become equal for linear molecules of σg orbital symmetry. In contrast only a "crossing neighborhood" near the magic angle is predicted for molecules with orbitals of π symmetry. They are expected to help in identifying the orbital symmetry in the inverse problem of orbital reconstruction from experimental data. Comparison with available experimental data show remarkable agreement with all the salient properties of dynamic HHG signals of linear diatomic molecules, N2 and O2, and some simple organic molecules. Additional results for the triatomic molecule CO2 are discussed that might help to test the theory further.

  14. MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing.

    PubMed

    Hempelmann, Jennifer A; Scroggins, Sheena M; Pritchard, Colin C; Salipante, Stephen J

    2015-11-01

    Molecular analysis of colon cancers currently requires multiphasic testing that uses various assays with different performance characteristics, adding cost and time to patient care. We have developed a single, next-generation sequencing assay to simultaneously evaluate colorectal cancers for mutations in relevant cancer genes (KRAS, NRAS, and BRAF) and for tumor microsatellite instability (MSI). In a sample set of 61 cases, the assay demonstrated overall sensitivity of 100% and specificity of 100% for identifying cancer-associated mutations, with a practical limit of detection at 2% mutant allele fraction. MSIplus was 97% sensitive (34 of 35 MSI-positive cases) and 100% specific (42 of 42 MSI-negative cases) for ascertaining MSI phenotype in a cohort of 78 tumor specimens. These performance characteristics were slightly better than for conventional multiplex PCR MSI testing (97% sensitivity and 95% specificity), which is based on comparison of microsatellite loci amplified from tumor and matched normal material, applied to the same specimen cohort. Because the assay uses an amplicon sequencing approach, it is rapid and appropriate for specimens with limited available material or fragmented DNA. This integrated testing strategy offers several advantages over existing methods, including a lack of need for matched normal material, sensitive and unbiased detection of variants in target genes, and an automated analysis pipeline enabling principled and reproducible identification of cancer-associated mutations and MSI status simultaneously. PMID:26322950

  15. Next-generation sequencing-based molecular diagnosis of neonatal hypotonia in Chinese Population

    PubMed Central

    Wang, Yan; Peng, Wei; Guo, Hong-Yan; Li, Hui; Tian, Jie; Shi, Yu-Jing; Yang, Xiao; Yang, Yao; Zhang, Wan-Qiao; Liu, Xin; Liu, Guan-Nan; Deng, Tao; Sun, Yi-Min; Xing, Wan-li; Cheng, Jing; Feng, Zhi-Chun

    2016-01-01

    Neonatal hypotonia is extremely challenging to diagnose because numerous disorders present similar clinical manifestations. Two panels for diagnosing neonatal hypotonia were developed, which enriches 35 genes corresponding to 61 neonatal hypotonia-related disorders. A cohort of 214 neonates with hypotonia was recruited from 2012 to 2014 in China for this study. Of these subjects, twenty-eight neonates with hypotonia were eliminated according to exclusion criteria and 97 were confirmed using traditional detection methods. The clinical diagnoses of the remaining 89 neonates with hypotonia were approached by targeted next-generation sequencing (NGS). Among the 89 tested neonates, 25 potentially pathogenic variants in nine genes (RYR1, MECP2, MUT, CDKL5, MPZ, PMM2, MTM1, LAMA2 and DMPK) were identified in 22 patients. Six of these pathogenic variants were novel. Of the 186 neonates with hypotonia, we identified the genetic causes for 117 neonates by the traditional detection methods and targeted NGS, achieving a high solving rate of 62.9%. In addition, we found seven neonates with RETT syndrome carrying five mutations, thus expanding the mutation profiles in Chinese neonates with hypotonia. Our study highlights the utility of comprehensive molecular genetic testing, which provides the advantage of speed and diagnostic specificity without invasive procedures. PMID:27353517

  16. Sum-frequency generation of acetate adsorption on Au and Pt surfaces: Molecular structure effects

    NASA Astrophysics Data System (ADS)

    Braunschweig, Björn; Mukherjee, Prabuddha; Kutz, Robert B.; Wieckowski, Andrzej; Dlott, Dana D.

    2010-12-01

    The reversible adsorption of acetate on polycrystalline Au and Pt surfaces was investigated with broadband sum-frequency generation (SFG) and cyclic voltammetry. Specifically adsorbed acetate as well as coadsorbed sulfuric acid anions are observed for the first time with SFG and give rise to dramatically different SFG intensities on Au and Pt surfaces. While similar coverages of acetate adlayers on Au and Pt surfaces are well established by previous studies, an identification of the interfacial molecular structure has been elusive. However, we have applied the high sensitivity of SFG for interfacial polar ordering to identify different acetate structures at Au and Pt surfaces in contact with HClO4 and H2SO4 electrolytes. Acetate competes with the formation of surface oxides and shifts the oxidation threshold of both Au and Pt electrodes anodically. Effects of the supporting electrolyte on the formation of acetate adlayers are revealed by comparing SFG spectra in HClO4 and H2SO4 solutions: Sulfuric acid anions modify the potential-dependent acetate adsorption, compete with adsorbed acetate on Au and coadsorb with acetate on Pt surfaces.

  17. Probing ice-nucleation processes on the molecular level using second harmonic generation spectroscopy

    NASA Astrophysics Data System (ADS)

    Abdelmonem, A.; Lützenkirchen, J.; Leisner, T.

    2015-08-01

    We present and characterize a novel setup to apply second harmonic generation (SHG) spectroscopy in total internal reflection geometry (TIR) to heterogeneous freezing research. It allows to monitor the evolution of water structuring at solid surfaces at low temperatures prior to heterogeneous ice nucleation. Apart from the possibility of investigating temperature dependence, a major novelty in our setup is the ability of measuring sheet-like samples in TIR geometry in a direct way. As a main experimental result, we find that our method can discriminate between good and poor ice nucleating surfaces. While at the sapphire basal plane, which is known to be a poor ice nucleator, no structural rearrangement of the water molecules is found prior to freezing, the basal plane surface of mica, an analogue to ice active mineral dust surfaces, exhibits a strong change in the nonlinear optical properties at temperatures well above the freezing transition. This is interpreted as a pre-activation, i.e. an increase in the local ordering of the interfacial water which is expected to facilitate the crystallization of ice at the surface. The results are in line with recent predictions by molecular dynamics simulations on a similar system.

  18. Fruit plant germplasm characterisation using molecular markers generated in RAPD and ISSR-PCR.

    PubMed

    Korbin, Małgorzata; Kuras, Anita; Zurawicz, Edward

    2002-01-01

    The genotypes of the strawberry (Fragaria x ananassa), apple (Malus domestica) and Ribes species (R. nigrum, R. rubrum and R. glossularia), maintained in our Institute's collection and used in breeding programs, were screened for DNA markers. Twenty primers for RAPD (among 60 tested) and seven for ISSR (among 10 tested) were chosen as creating polymorphic DNA bands differentiating the investigated genotypes. Based on those identity markers, the genetic distance between genotypes was determined, and their relatedness was estimated. In many cases, both RAPD- and ISSR-based genetic similarity confirmed relatedness connected with biological origin and with the place where the cultivar was developed. However, some diversity connected with the technique used for molecular marker generation was observed. Generally, the similarity values based on ISSR data were higher than those based on RAPD. Parallel study using two data sets seems to enable a reduction in the number of potential mistakes connected with each method's, technical limitations and ensures more precise relatedness determination. PMID:12378239

  19. Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges.

    PubMed

    Luthra, Rajyalakshmi; Chen, Hui; Roy-Chowdhuri, Sinchita; Singh, R Rajesh

    2015-01-01

    The application of next-generation sequencing (NGS) to characterize cancer genomes has resulted in the discovery of numerous genetic markers. Consequently, the number of markers that warrant routine screening in molecular diagnostic laboratories, often from limited tumor material, has increased. This increased demand has been difficult to manage by traditional low- and/or medium-throughput sequencing platforms. Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA. However, implementation of NGS technologies, most of which are for research use only (RUO), in a diagnostic laboratory, needs extensive validation in order to establish Clinical Laboratory Improvement Amendments (CLIA) and College of American Pathologists (CAP)-compliant performance characteristics. Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors. We discuss the criteria for selecting gene markers to include in the NGS panel and the deciding factors for selecting target capture approaches and sequencing platforms. We also discuss challenges in result reporting, storage and retrieval of the voluminous sequencing data and the future potential of clinical NGS. PMID:26473927

  20. Molecular Self-Probing Spectroscopy with High Harmonic Generation at Long Wavelengths

    NASA Astrophysics Data System (ADS)

    Camper, A.; Schoun, S. B.; Agostini, P.; Salieres, Pascal; Caillat, J.; Lucchese, R. R.; Dimauro, L.

    2015-05-01

    We used laser driven sub-femtosecond electronic wave packet (EWP) recollision to generate high-order harmonics (HHG) of a 1.3 μm laser pulse in aligned molecules. We performed a tomographic investigation of N2 [ItataniNature2004, HaesslerNatPhys2010, VozziNatPhys2011, DivekiNJP2012] by characterizing the HHG yield and spectral phase of the attosecond emission for different recollision angles of EWP with respect to the main axis of the angular distribution of the molecules. Thanks to the high degree of alignment and to the fine spectral sampling, our XUV quantum phase measurements [SchounPRL2014] reveal subtle features in the recombination dipole moment of N2. We interpret the latter within the Quantitative Rescattering Theory [LePRA2009] and emphasize the effect of the EWP scattering on the ion Coulombic potential and of the shape resonance in the X channel of N2 on HHG [LucchesePRA1982]. Compared to previous results at 800 nm, our experiment is deeper into the tunneling regime and only one ionization channel is enough to explain what we observed. Our results shine a new light on imaging molecular orbitals using laser-driven photo-recombination processes.

  1. Molecular mechanism and functional significance of acid generation in the Drosophila midgut

    PubMed Central

    Overend, Gayle; Luo, Yuan; Henderson, Louise; Douglas, Angela E.; Davies, Shireen A.; Dow, Julian A. T.

    2016-01-01

    The gut of Drosophila melanogaster includes a proximal acidic region (~pH 2), however the genome lacks the H+/K+ ATPase characteristic of the mammalian gastric parietal cell, and the molecular mechanisms of acid generation are poorly understood. Here, we show that maintenance of the low pH of the acidic region is dependent on H+ V-ATPase, together with carbonic anhydrase and five further transporters or channels that mediate K+, Cl− and HCO3− transport. Abrogation of the low pH did not influence larval survival under standard laboratory conditions, but was deleterious for insects subjected to high Na+ or K+ load. Insects with elevated pH in the acidic region displayed increased susceptibility to Pseudomonas pathogens and increased abundance of key members of the gut microbiota (Acetobacter and Lactobacillus), suggesting that the acidic region has bacteriostatic or bacteriocidal activity. Conversely, the pH of the acidic region was significantly reduced in germ-free Drosophila, indicative of a role of the gut bacteria in shaping the pH conditions of the gut. These results demonstrate that the acidic gut region protects the insect and gut microbiome from pathological disruption, and shed light on the mechanisms by which low pH can be maintained in the absence of H+, K+ ATPase. PMID:27250760

  2. Molecular mechanism and functional significance of acid generation in the Drosophila midgut.

    PubMed

    Overend, Gayle; Luo, Yuan; Henderson, Louise; Douglas, Angela E; Davies, Shireen A; Dow, Julian A T

    2016-01-01

    The gut of Drosophila melanogaster includes a proximal acidic region (~pH 2), however the genome lacks the H(+)/K(+) ATPase characteristic of the mammalian gastric parietal cell, and the molecular mechanisms of acid generation are poorly understood. Here, we show that maintenance of the low pH of the acidic region is dependent on H(+) V-ATPase, together with carbonic anhydrase and five further transporters or channels that mediate K(+), Cl(-) and HCO3(-) transport. Abrogation of the low pH did not influence larval survival under standard laboratory conditions, but was deleterious for insects subjected to high Na(+) or K(+) load. Insects with elevated pH in the acidic region displayed increased susceptibility to Pseudomonas pathogens and increased abundance of key members of the gut microbiota (Acetobacter and Lactobacillus), suggesting that the acidic region has bacteriostatic or bacteriocidal activity. Conversely, the pH of the acidic region was significantly reduced in germ-free Drosophila, indicative of a role of the gut bacteria in shaping the pH conditions of the gut. These results demonstrate that the acidic gut region protects the insect and gut microbiome from pathological disruption, and shed light on the mechanisms by which low pH can be maintained in the absence of H(+), K(+) ATPase. PMID:27250760

  3. Next-generation sequencing-based molecular diagnosis of neonatal hypotonia in Chinese Population.

    PubMed

    Wang, Yan; Peng, Wei; Guo, Hong-Yan; Li, Hui; Tian, Jie; Shi, Yu-Jing; Yang, Xiao; Yang, Yao; Zhang, Wan-Qiao; Liu, Xin; Liu, Guan-Nan; Deng, Tao; Sun, Yi-Min; Xing, Wan-Li; Cheng, Jing; Feng, Zhi-Chun

    2016-01-01

    Neonatal hypotonia is extremely challenging to diagnose because numerous disorders present similar clinical manifestations. Two panels for diagnosing neonatal hypotonia were developed, which enriches 35 genes corresponding to 61 neonatal hypotonia-related disorders. A cohort of 214 neonates with hypotonia was recruited from 2012 to 2014 in China for this study. Of these subjects, twenty-eight neonates with hypotonia were eliminated according to exclusion criteria and 97 were confirmed using traditional detection methods. The clinical diagnoses of the remaining 89 neonates with hypotonia were approached by targeted next-generation sequencing (NGS). Among the 89 tested neonates, 25 potentially pathogenic variants in nine genes (RYR1, MECP2, MUT, CDKL5, MPZ, PMM2, MTM1, LAMA2 and DMPK) were identified in 22 patients. Six of these pathogenic variants were novel. Of the 186 neonates with hypotonia, we identified the genetic causes for 117 neonates by the traditional detection methods and targeted NGS, achieving a high solving rate of 62.9%. In addition, we found seven neonates with RETT syndrome carrying five mutations, thus expanding the mutation profiles in Chinese neonates with hypotonia. Our study highlights the utility of comprehensive molecular genetic testing, which provides the advantage of speed and diagnostic specificity without invasive procedures. PMID:27353517

  4. Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases

    PubMed Central

    2015-01-01

    Members of the same protease family show different substrate specificity, even if they share identical folds, depending on the physiological processes they are part of. Here, we investigate the key factors for subpocket and global specificity of factor Xa, elastase, and granzyme B which despite all being serine proteases and sharing the chymotrypsin-fold show distinct substrate specificity profiles. We determined subpocket interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket interaction potentials determined for static X-ray structures turned out to be insufficient to explain serine protease specificity for all subpockets. Therefore, we generated conformational ensembles using molecular dynamics simulations. We identified representative binding site conformations using distance-based hierarchical agglomerative clustering and determined subpocket interaction potentials for each representative conformation of the binding site. Considering the differences in subpocket interaction potentials for these representative conformations as well as their abundance allowed us to quantitatively explain subpocket specificity for the nonprime side for all three example proteases on a molecular level. The methods to identify key regions determining subpocket specificity introduced in this study are directly applicable to other serine proteases, and the results provide starting points for new strategies in rational drug design. PMID:26709959

  5. Small molecular probes for G-protein-coupled C5a receptors: conformationally constrained antagonists derived from the C terminus of the human plasma protein C5a.

    PubMed

    Wong, A K; Finch, A M; Pierens, G K; Craik, D J; Taylor, S M; Fairlie, D P

    1998-08-27

    Activation of the human complement system of plasma proteins in response to infection or injury produces a 4-helix bundle glycoprotein (74 amino acids) known as C5a. C5a binds to G-protein-coupled receptors on cell surfaces triggering receptor-ligand internalization, signal transduction, and powerful inflammatory responses. Since excessive levels of C5a are associated with autoimmune and chronic inflammatory disorders, inhibitors of receptor activation may have therapeutic potential. We now report solution structures and receptor-binding and antagonist activities for some of the first small molecule antagonists of C5a derived from its hexapeptide C terminus. The antagonist NMe-Phe-Lys-Pro-D-Cha-Trp-D-Arg-CO2H (1) surprisingly shows an unusually well-defined solution structure as determined by 1H NMR spectroscopy. This is one of the smallest acyclic peptides found to possess a defined solution conformation, which can be explained by the constraining role of intramolecular hydrogen bonding. NOE and coupling constant data, slow deuterium exchange, and a low dependence on temperature for the chemical shift of the D-Cha-NH strongly indicate an inverse gamma turn stabilized by a D-Cha-NH. OC-Lys hydrogen bond. Smaller conformational populations are associated with a hydrogen bond between Trp-NH.OC-Lys, defining a type II beta turn distorted by the inverse gamma turn incorporated within it. An excellent correlation between receptor-affinity and antagonist activity is indicated for a limited set of synthetic peptides. Conversion of the C-terminal carboxylate of 1 to an amide decreases antagonist potency 5-fold, but potency is increased up to 10-fold over 1 if the amide bond is made between the C-terminal carboxylate and a Lys/Orn side chain to form a cyclic analogue. The solution structure of cycle 6 also shows gamma and beta turns; however, the latter occurs in a different position, and there are clear conformational changes in 6 vs 1 that result in enhanced activity

  6. The molecular matching problem

    NASA Technical Reports Server (NTRS)

    Kincaid, Rex K.

    1993-01-01

    Molecular chemistry contains many difficult optimization problems that have begun to attract the attention of optimizers in the Operations Research community. Problems including protein folding, molecular conformation, molecular similarity, and molecular matching have been addressed. Minimum energy conformations for simple molecular structures such as water clusters, Lennard-Jones microclusters, and short polypeptides have dominated the literature to date. However, a variety of interesting problems exist and we focus here on a molecular structure matching (MSM) problem.

  7. Studies of molecular monolayers at air-liquid interfaces by second harmonic generation: question of orientational phase transition

    SciTech Connect

    Rasing, T.; Shen, Y.R.; Kim, M.W.; Grubb, S.; Bock, J.

    1985-06-01

    Insoluble molecular monolayers at gas-liquid interfaces provide an insight to the understanding of surfactants, wetting, microemulsions and membrane structures and offer a possibility to study the rich world of 2-dimensional phase transitions. In the interpretation of the observed properties of these systems various assumptions about the molecular orientation are often made, but so far few clear experimental data exist. In this paper we will show how optical second harmonic generation (SHG) can be used to measure the molecular orientation of monolayers of surfactant molecules at water-air interfaces. By simultaneously measuring the surface pressure versus surface molecular area we can show for the first time that the observed liquid condensed-liquid expanded transition is an orientational phase transition. 7 refs., 4 figs.

  8. Conformation of one- and two-chain high molecular weight urokinase analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism

    SciTech Connect

    Mangel, W.F.; Lin, B.H.; Ramakrishnan, V. )

    1991-05-25

    The structures of one- and two-chain high molecular weight human urokinase were analyzed by small-angle neutron scattering and vacuum ultraviolet circular dichroism. Both one- and two-chain high molecular weight urokinases exhibited a radius of gyration of 31 A and a maximum dimension of 90 A. Neither parameter was affected by the presence of lysine sufficient to saturate all the lysine-binding sites in human plasminogen. These physical parameters are consistent with the sedimentation coefficient of high molecular weight urokinase and indicate that both proteins are highly asymmetric. Neither protein contained much alpha-helix or parallel beta-sheet. Most of the secondary structure was in the form of antiparallel beta-sheet and beta-turns, very similar to the secondary structure of plasminogen. The macroscopic kinetic constants, Km and kcat, for the hydrolysis of (pyroGlu-Gly-Arg-NH)2-rhodamine by two-chain high molecular weight urokinase and low molecular weight urokinase which lacks the epidermal growth factor and kringle domains were similar. These structural and kinetic data are consistent with the domains in both forms of urokinase being independent structural and functional units.

  9. Synthesis, Structure, and Molecular Recognition of S6 - and (SO2 )6 -Corona[6](het)arenes: Control of Macrocyclic Conformation and Properties by the Oxidation State of the Bridging Heteroatoms.

    PubMed

    Guo, Qing-Hui; Zhao, Liang; Wang, Mei-Xiang

    2016-05-10

    We report herein the synthesis, structure, and molecular recognition of S6 - and (SO2 )6 -corona[6](het)arenes, and demonstrate a unique and efficient strategy of regulating macrocyclic conformation and properties by adjusting the oxidation state of the heteroatom linkages. The one-pot nucleophilic aromatic substitution reaction of 1,4-benzenedithiol derivatives, biphenyl-4,4'-dithiol and 9,9-dipropyl-9H-fluorene-2,7-dithiol with 3,6-dichlorotetrazine afforded S6 -corona[3]arene[3]tetrazines. These compounds underwent inverse-electron-demand Diels-Alder reaction with enamines and norbornadiene to produce S6 -corona[3]arene[3]pyridazines. Facile oxidation of sulfide linkages yielded (SO2 )6 -corona[3]arene[3]pyridazines. All corona[6](het)arenes adopted generally hexagonal macrocyclic ring structures; however, their electronic properties and conformation could be fine-tuned by altering the oxidation state of the sulfur linkages. Whereas (SO2 )6 -corona[3]arene[3]pyridazines were electron-deficient, S6 -corona[3]arene[3]pyridazines acted as electron-rich macrocyclic hosts that recognized various organic cations in both aqueous and organic solutions. PMID:27062180

  10. Accurate Determination of Conformational Transitions in Oligomeric Membrane Proteins

    PubMed Central

    Sanz-Hernández, Máximo; Vostrikov, Vitaly V.; Veglia, Gianluigi; De Simone, Alfonso

    2016-01-01

    The structural dynamics governing collective motions in oligomeric membrane proteins play key roles in vital biomolecular processes at cellular membranes. In this study, we present a structural refinement approach that combines solid-state NMR experiments and molecular simulations to accurately describe concerted conformational transitions identifying the overall structural, dynamical, and topological states of oligomeric membrane proteins. The accuracy of the structural ensembles generated with this method is shown to reach the statistical error limit, and is further demonstrated by correctly reproducing orthogonal NMR data. We demonstrate the accuracy of this approach by characterising the pentameric state of phospholamban, a key player in the regulation of calcium uptake in the sarcoplasmic reticulum, and by probing its dynamical activation upon phosphorylation. Our results underline the importance of using an ensemble approach to characterise the conformational transitions that are often responsible for the biological function of oligomeric membrane protein states. PMID:26975211

  11. Fake conformal symmetry in conformal cosmological models

    NASA Astrophysics Data System (ADS)

    Jackiw, R.; Pi, So-Young

    2015-03-01

    We examine the local conformal invariance (Weyl invariance) in tensor-scalar theories used in recently proposed conformal cosmological models. We show that the Noether currents associated with Weyl invariance in these theories vanish. We assert that the corresponding Weyl symmetry does not have any dynamical role.

  12. Shock propagation and the generation of magnetohydrodynamic wave fields in inhomogeneous molecular clouds

    NASA Technical Reports Server (NTRS)

    Miesch, Mark S.; Zweibel, Ellen G.

    1994-01-01

    We develop a simple one-dimensional model for the interaction of a steady, thin, planar shock wave with a nonrigid cloud which may be in motion relative to the surrounding medium, and we apply the model to shocks impinging on, and propagating through, molecular clouds. Both 'adiabatic' (gamma = 5/3) and radiative (gamma = 1) shocks are considered and we allow for the presence of a uniform magnetic field directed either parallel or perpendicular to the shock normal. The former field orientation is equivalent to the hydrodynamic case, and the latter involves only fast MHD shocks. We focus on the manner in which such shocks can generate internal kinetic motions in the cloud on a range of size and density scales through the direct acceleration of cores and clumps by shocks transmitted into them and through the generation of an MHD wavefield via the reflection of the incident shock at clump boundaries. We find that stronger incident Mach numbers and smaller density contrasts lead to more efficient cloud acceleration, as do isothermal intercloud shocks and small intercloud magnetic field strengths. The acceleration efficiency is insensitive to the adiabatic index and the magnetic field strength in the cloud itself. For typical parameter choices, the direct acceleration of clouds and clumps by strong shocks is found to be substantial and could at least in part account for their observed velocity dispersions. If the shocks are moderately weak, the final velocity of the cloud is linearly related to its initial velocity, with higher acceleration giving shallower slopes (i.e., final velocity distributions which are less sensitive to the initial distribution). Compared to the kinetic energy of the postshock cloud, the energy given to the wavefield at each encounter is small, and the heating of the interclump medium by the dissipation of this wavefield is found to be insufficient to balance the cooling rate in the cloud as a whole (although it may be important in particular

  13. Squamousness: Next-generation sequencing reveals shared molecular features across squamous tumor types

    PubMed Central

    Schwaederle, Maria; Elkin, Sheryl K; Tomson, Brett N; Carter, Jennifer Levin; Kurzrock, Razelle

    2015-01-01

    In order to gain a better understanding of the underlying biology of squamous cell carcinoma (SCC), we tested the hypothesis that SCC originating from different organs may possess common molecular alterations. SCC samples (N = 361) were examined using clinical-grade targeted next-generation sequencing (NGS). The most frequent SCC tumor types were head and neck, lung, cutaneous, gastrointestinal and gynecologic cancers. The most common gene alterations were TP53 (64.5% of patients), PIK3CA (28.5%), CDKN2A (24.4%), SOX2 (17.7%), and CCND1 (15.8%). By comparing NGS results of our SCC cohort to a non-SCC cohort (N = 277), we found that CDKN2A, SOX2, NOTCH1, TP53, PIK3CA, CCND1, and FBXW7 were significantly more frequently altered, unlike KRAS, which was less frequently altered in SCC specimens (all P < 0.05; multivariable analysis). Therefore, we identified “squamousness” gene signatures (TP53, PIK3CA, CCND1, CDKN2A, SOX2, NOTCH 1, and FBXW7 aberrations, and absence of KRAS alterations) that were significantly more frequent in SCC versus non-SCC histologies. A multivariable co-alteration analysis established 2 SCC subgroups: (i) patients in whom TP53 and cyclin pathway (CDKN2A and CCND1) alterations strongly correlated but in whom PIK3CA aberrations were less frequent; and (ii) patients with PIK3CA alterations in whom TP53 mutations were less frequent (all P ≤ 0 .001, multivariable analysis). In conclusion, we identified a set of 8 genes altered with significantly different frequencies when SCC and non-SCC were compared, suggesting the existence of patterns for “squamousness.” Targeting the PI3K-AKT-mTOR and/or cyclin pathway components in SCC may be warranted. PMID:26030731

  14. Next-generation sequencing for molecular diagnosis of autosomal recessive polycystic kidney disease.

    PubMed

    Edrees, Burhan M; Athar, Mohammad; Al-Allaf, Faisal A; Taher, Mohiuddin M; Khan, Wajahatullah; Bouazzaoui, Abdellatif; Al-Harbi, Naffaa; Safar, Ramzia; Al-Edressi, Howaida; Alansary, Khawala; Anazi, Abulkareem; Altayeb, Naji; Ahmed, Muawia A; Abduljaleel, Zainularifeen

    2016-10-10

    Autosomal recessive polycystic kidney disease (ARPKD) a rare genetic disorder, described by formation of cysts in the kidney. A targeted customized sequencing of genes implicated in ARPKD phenotype was performed to identify candidate variants using the Ion torrent PGM next-generation sequencing. The results identified likely pathogenic disease causing variants during the validation process. Four potential pathogenic variants [c.4870C>T, p.(Arg1624Trp)], [c.5725C>T, p.(Arg1909Trp)], c.1736C>T, p.(Thr579Met)] and [(c.10628T>G), p.(Leu3543Trp)] were observed in PKHD1 gene among 12 out of 18 samples. The rest of the patient samples also showed few variants in ADPKD (Autosomal Dominant Polycystic Kidney Disease) disease causing genes PKD1 and PKD2 i.e. [c.12433G>A, p.(Val4145Ile)] and [c.1445T>G, p.(Phe482Cys)], respectively. All causative variants were validated by capillary sequencing, confirming the presence of a novel homozygous variants [c.10628T>G, p.(Leu3543Trp)] found in exon 61 of a male proband. All potentially deleterious variants identified in PKHD1, PKD1, and PKD2 gene, also exhibited pathologically or clinically significance based on the computational predictions involved in predicting the impact of non-synonymous SNPs (nsSNPs) on protein function such as Sorting Intolerant From Tolerant (SIFT) and Polymorphism Phenotyping (PolyPhen2). SIFT classified 50% of our nsSNPs as "deleterious", while PolyPhen2 identified 45% of our nsSNPs as "Probably damaged" and the results from both programs were largely complementary. Taken together, these results suggest that the NGS strategies provide a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in targeted genes sequence analysis. PMID:27401137

  15. DFT and NMR parameterized conformation of valeranone.

    PubMed

    Torres-Valencia, J Martín; Meléndez-Rodríguez, Myriam; Alvarez-García, Rocío; Cerda-García-Rojas, Carlos M; Joseph-Nathan, Pedro

    2004-10-01

    A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing density functional theory (DFT) calculations at the B3LYP/6-31G* level and a Boltzmann analysis of the total energies, generated accurate molecular models which describe the conformational behavior of the antispasmodic bicyclic sesquiterpene valeranone (1). The theoretical H-C-C-H dihedral angles gave the corresponding 1H, 1H vicinal coupling constants using a generalized Karplus-type equation. In turn, the 3J(H,H) values were used as initial input data for the spectral simulation of 1, which after iteration provided an excellent correlation with the experimental 1H NMR spectrum. The calculated 3J(H,H) values closely predicted the experimental values, excepting the coupling constant between the axial hydrogen alpha to the carbonyl group and the equatorial hydrogen beta to the carbonyl group (J(2beta, 3beta)). The difference is explained in terms of the electron density distribution found in the highest occupied molecular orbital (HOMO) of 1. The simulated spectrum, together with 2D NMR experiments, allowed the total assignment of the 1H and 13C NMR spectra of 1. PMID:15366065

  16. Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.

    PubMed

    Xie, Bin-Bin; Bian, Fei; Chen, Xiu-Lan; He, Hai-Lun; Guo, Jun; Gao, Xiang; Zeng, Yin-Xin; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2009-04-01

    Increased conformational flexibility is the prevailing explanation for the high catalytic efficiency of cold-adapted enzymes at low temperatures. However, less is known about the structural determinants of flexibility. We reported two novel cold-adapted zinc metalloproteases in the thermolysin family, vibriolysin MCP-02 from a deep sea bacterium and vibriolysin E495 from an Arctic sea ice bacterium, and compared them with their mesophilic homolog, pseudolysin from a terrestrial bacterium. Their catalytic efficiencies, k(cat)/K(m) (10-40 degrees C), followed the order pseudolysin < MCP-02 < E495 with a ratio of approximately 1:2:4. MCP-02 and E495 have the same optimal temperature (T(opt), 57 degrees C, 5 degrees C lower than pseudolysin) and apparent melting temperature (T(m) = 64 degrees C, approximately 10 degrees C lower than pseudolysin). Structural analysis showed that the slightly lower stabilities resulted from a decrease in the number of salt bridges. Fluorescence quenching experiments and molecular dynamics simulations showed that the flexibilities of the proteins were pseudolysin < MCP-02 < E495, suggesting that optimization of flexibility is a strategy for cold adaptation. Molecular dynamics results showed that the ordinal increase in flexibility from pseudolysin to MCP-02 and E495, especially the increase from MCP-02 to E495, mainly resulted from the decrease of hydrogen-bond stability in the dynamic structure, which was due to the increase in asparagine, serine, and threonine residues. Finally, a model for the cold adaptation of MCP-02 and E495 was proposed. This is the first report of the optimization of hydrogen-bonding dynamics as a strategy for cold adaptation and provides new insights into the structural basis underlying conformational flexibility. PMID:19181663

  17. Theoretical models for the conformations and the protonation of triacetonamine.

    PubMed

    Navajas, C C; Montero, L A; La Serna, B

    1990-12-01

    In this paper we propose theoretical models for the conformations of triacetonamine and protonated triacetonamine (Vincubine, an anticancer chemotherapeutic agent) developed by quantum and molecular mechanics techniques. We discuss the theoretical factors which are involved in the stabilization of the conformations calculated by the MNDO, MM2 and COPEANE methods and show the relative percent abundance of each molecular shape. Graphic representations of the conformers are depicted. PMID:1965442

  18. Finding a Potential Dipeptidyl Peptidase-4 (DPP-4) Inhibitor for Type-2 Diabetes Treatment Based on Molecular Docking, Pharmacophore Generation, and Molecular Dynamics Simulation.

    PubMed

    Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J P; Chen, Yu-Ching

    2016-01-01

    Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes. PMID:27304951

  19. Finding a Potential Dipeptidyl Peptidase-4 (DPP-4) Inhibitor for Type-2 Diabetes Treatment Based on Molecular Docking, Pharmacophore Generation, and Molecular Dynamics Simulation

    PubMed Central

    Meduru, Harika; Wang, Yeng-Tseng; Tsai, Jeffrey J. P.; Chen, Yu-Ching

    2016-01-01

    Dipeptidyl peptidase-4 (DPP-4) is the vital enzyme that is responsible for inactivating intestinal peptides glucagon like peptide-1 (GLP-1) and Gastric inhibitory polypeptide (GIP), which stimulates a decline in blood glucose levels. The aim of this study was to explore the inhibition activity of small molecule inhibitors to DPP-4 following a computational strategy based on docking studies and molecular dynamics simulations. The thorough docking protocol we applied allowed us to derive good correlation parameters between the predicted binding affinities (pKi) of the DPP-4 inhibitors and the experimental activity values (pIC50). Based on molecular docking receptor-ligand interactions, pharmacophore generation was carried out in order to identify the binding modes of structurally diverse compounds in the receptor active site. Consideration of the permanence and flexibility of DPP-4 inhibitor complexes by means of molecular dynamics (MD) simulation specified that the inhibitors maintained the binding mode observed in the docking study. The present study helps generate new information for further structural optimization and can influence the development of new DPP-4 inhibitors discoveries in the treatment of type-2 diabetes. PMID:27304951

  20. Capturing Chromosome Conformation

    NASA Astrophysics Data System (ADS)

    Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

    2002-02-01

    We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

  1. Use of 1–4 interaction scaling factors to control the conformational equilibrium between α-helix and β-strand

    SciTech Connect

    Pang, Yuan-Ping

    2015-02-06

    Highlights: • 1–4 interaction scaling factors are used to adjust conformational energy. • This article reports the effects of these factors on protein conformations. • Reducing these factors changes a helix to a strand in molecular dynamics simulation. • Increasing these factors causes the reverse conformational change. • These factors control the conformational equilibrium between helix and strand. - Abstract: 1–4 interaction scaling factors are used in AMBER forcefields to reduce the exaggeration of short-range repulsion caused by the 6–12 Lennard-Jones potential and a nonpolarizable charge model and to obtain better agreements of small-molecule conformational energies with experimental data. However, the effects of these scaling factors on protein secondary structure conformations have not been investigated until now. This article reports the finding that the 1–4 interactions among the protein backbone atoms separated by three consecutive covalent bonds are more repulsive in the α-helix conformation than in two β-strand conformations. Therefore, the 1–4 interaction scaling factors of protein backbone torsions ϕ and ψ control the conformational equilibrium between α-helix and β-strand. Molecular dynamics simulations confirm that reducing the ϕ and ψ scaling factors readily converts the α-helix conformation of AcO-(AAQAA){sub 3}-NH{sub 2} to a β-strand conformation, and the reverse occurs when these scaling factors are increased. These results suggest that the ϕ and ψ scaling factors can be used to generate the α-helix or β-strand conformation in situ and to control the propensities of a forcefield for adopting secondary structure elements.

  2. Conformational analysis of 2-substituted piperazines.

    PubMed

    Kallel, E Adam; Vangel, Colin; Elbaum, Daniel

    2016-07-01

    The unusual activity differences of carbon linked versus oxygen linked 2-substituted piperazines as α7 nicotinic acetylcholine receptor agonists led to a conformational study of several examples. The conformational preferences of which are absent from the literature. We report the first study and explanation of the conformational preference of 2-substiturted piperazines and show an example of how this preference controls binding in a pharmaceutically relevant case. In all cases the axial conformation for these 1-acyl and 1 aryl 2-substituted piperazines was found to be preferred. For the ether linked compounds, the axial conformation was found to be further stabilized by an intramolecular hydrogen bond. The axial orientation also places the basic and pyridyl nitrogens into a special orientation that closely mimics nicotine. Molecular modeling studies confirm that the R enantiomers of the compounds can bind to the α7 nicotinic acetylcholine receptor with the basic and pyridyl nitrogens colocalized with their counterparts in Epibatidine. PMID:27212066

  3. Dolastatin 11 conformations, analogues and pharmacophore.

    PubMed

    Ali, Md Ahad; Bates, Robert B; Crane, Zackary D; Dicus, Christopher W; Gramme, Michelle R; Hamel, Ernest; Marcischak, Jacob; Martinez, David S; McClure, Kelly J; Nakkiew, Pichaya; Pettit, George R; Stessman, Chad C; Sufi, Bilal A; Yarick, Gayle V

    2005-07-01

    Twenty analogues of the natural antitumor agent dolastatin 11, including majusculamide C, were synthesized and tested for cytotoxicity against human cancer cells and stimulation of actin polymerization. Only analogues containing the 30-membered ring were active. Molecular modeling and NMR evidence showed the low-energy conformations. The amide bonds are all trans except for the one between the Tyr and Val units, which is cis. Since an analogue restricted to negative 2-3-4-5 angles stimulated actin polymerization but was inactive in cells, the binding conformation (most likely the lowest-energy conformation in water) has a negative 2-3-4-5 angle, whereas a conformation with a positive 2-3-4-5 angle (most likely the lowest energy conformation in chloroform) goes through cell walls. The highly active R alcohol from borohydride reduction of dolastatin 11 is a candidate for conversion to prodrugs. PMID:15878670

  4. Linkage-specific conformational ensembles of non-canonical polyubiquitin chains.

    PubMed

    Castañeda, Carlos A; Chaturvedi, Apurva; Camara, Christina M; Curtis, Joseph E; Krueger, Susan; Fushman, David

    2016-02-17

    Polyubiquitination is a critical protein post-translational modification involved in a variety of processes in eukaryotic cells. The molecular basis for selective recognition of the polyubiquitin signals by cellular receptors is determined by the conformations polyubiquitin chains adopt; this has been demonstrated for K48- and K63-linked chains. Recent studies of the so-called non-canonical chains (linked via K6, K11, K27, K29, or K33) suggest they play important regulatory roles in growth, development, and immune system pathways, but biophysical studies are needed to elucidate the physical/structural basis of their interactions with receptors. A first step towards this goal is characterization of the conformations these chains adopt in solution. We assembled diubiquitins (Ub2) comprised of every lysine linkage. Using solution NMR measurements, small-angle neutron scattering (SANS), and in silico ensemble generation, we determined population-weighted conformational ensembles that shed light on the structure and dynamics of the non-canonical polyubiquitin chains. We found that polyubiquitin is conformationally heterogeneous, and each chain type exhibits unique conformational ensembles. For example, K6-Ub2 and K11-Ub2 (at physiological salt concentration) are in dynamic equilibrium between at least two conformers, where one exhibits a unique Ub/Ub interface, distinct from that observed in K48-Ub2 but similar to crystal structures of these chains. Conformers for K29-Ub2 and K33-Ub2 resemble recent crystal structures in the ligand-bound state. Remarkably, a number of diubiquitins adopt conformers similar to K48-Ub2 or K63-Ub2, suggesting potential overlap of biological function among different lysine linkages. These studies highlight the potential power of determining function from elucidation of conformational states. PMID:26422168

  5. Molecular profile of liquid biopsies: next generation biomarkers to improve lung cancer treatment

    PubMed Central

    Bianchi, Fabrizio

    2015-01-01

    Molecular profiling of liquid biopsies is now emerging as pivotal for cancer biomarker discovery. The low-invasive nature of the approach used for collecting biospecimens (i.e. blood, urine, saliva, etc.) may allow a widespread application of novel molecular diagnostics based on liquid biopsies. This is relevant, for example, in cancer screening programmes where it is essential to reduce costs and the complexity of screening tests in order to increase study compliance and effectiveness. Here, I discuss recent advances in biomarkers for the early cancer detection and prediction of chemotherapy response based on the molecular profiling of liquid biopsies. PMID:26635902

  6. Elucidation of molecular structures at buried polymer interfaces and biological interfaces using sum frequency generation vibrational spectroscopy

    PubMed Central

    Zhang, Chi; Myers, John; Chen, Zhan

    2013-01-01

    Sum frequency generation (SFG) vibrational spectroscopy has been developed into an important technique to study surfaces and interfaces. It can probe buried interfaces in situ and provide molecular level structural information such as the presence of various chemical moieties, quantitative molecular functional group orientation, and time dependent kinetics or dynamics at such interfaces. This paper focuses on these three most important advantages of SFG and reviews some of the recent progress in SFG studies on interfaces related to polymer materials and biomolecules. The results discussed here demonstrate that SFG can provide important molecular structural information of buried interfaces in situ and in real time, which is difficult to obtain by other surface sensitive analytical techniques. PMID:23710244

  7. Binding, Conformational Transition and Dimerization of Amyloid-β Peptide on GM1-Containing Ternary Membrane: Insights from Molecular Dynamics Simulation

    PubMed Central

    Manna, Moutusi; Mukhopadhyay, Chaitali

    2013-01-01

    Interactions of amyloid-β (Aβ) with neuronal membrane are associated with the progression of Alzheimer’s disease (AD). Ganglioside GM1 has been shown to promote the structural conversion of Aβ and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs) to investigate the behavior of Aβ monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for Aβ-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a β-hairpin motif was formed at the C-terminus of the GM1-bound Aβ-monomer; that didn’t appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium) within the simulation time span. For Aβ-dimers, the β-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of Aβ to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D23-K28 salt-bridge and a turn at V24GSN27 region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide ato