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Sample records for investigating molecular interactions

  1. Spectroscopic investigations, molecular interactions, and molecular docking studies on the potential inhibitor "thiophene-2-carboxylicacid"

    NASA Astrophysics Data System (ADS)

    Karthick, T.; Balachandran, V.; Perumal, S.

    2015-04-01

    Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.

  2. A quantum mechanical/molecular mechanical approach to the investigation of particle-molecule interactions

    NASA Astrophysics Data System (ADS)

    Sloth, Marianne; Bilde, Merete; Mikkelsen, Kurt V.

    2003-06-01

    A quantum mechanical/molecular mechanical aerosol model is developed to describe the interaction between gas phase molecules and atmospheric particles. The model enables the calculation of interaction energies and time-dependent properties. We use the model to investigate how a succinic acid molecule interacts with an aqueous particle. We show how the interaction energies and linear response properties (excitation energies, transition moments, and polarizabilities) depend on the distance between aerosol particle and molecule and on their relative orientation. The results are compared with those obtained previously using a dielectric continuum model [Sloth et al., J. Phys. Chem. (submitted)].

  3. Investigation on the binding interaction between silybin and pepsin by spectral and molecular docking.

    PubMed

    Zeng, Hua-jin; You, Jing; Liang, Hui-li; Qi, Tingting; Yang, Ran; Qu, Ling-bo

    2014-06-01

    In this study, the binding mode of silybin with pepsin was investigated by spectroscopic and molecular docking methods. Silybin can interact with pepsin to form a silybin-pepsin complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that silybin could spontaneously bind with pepsin mainly through hydrophobic interaction with one binding site. Molecular docking results revealed that silybin bound into the pepsin cavity site. Synchronous fluorescence and three-dimensional fluorescence results provide data concerning conformational and some micro-environmental changes of pepsin. Furthermore, in order to reveal whether the binding process can inhibit the activity of pepsin in vivo, the effect of silybin on pepsin activity in rat was investigated. The present study provides direct evidence at a molecular level to show that exposure to silybin could induce changes in the enzyme pepsin structure and function.

  4. An investigation of molecular dynamics simulation and molecular docking: interaction of citrus flavonoids and bovine β-lactoglobulin in focus.

    PubMed

    Sahihi, M; Ghayeb, Y

    2014-08-01

    Citrus flavonoids are natural compounds with important health benefits. The study of their interaction with a transport protein, such as bovine β-lactoglobulin (BLG), at the atomic level could be a valuable factor to control their transport to biological sites. In the present study, molecular docking and molecular dynamics simulation methods were used to investigate the interaction of hesperetin, naringenin, nobiletin and tangeretin as citrus flavonoids and BLG as transport protein. The molecular docking results revealed that these flavonoids bind in the internal cavity of BLG and the BLG affinity for binding the flavonoids follows naringenin>hesperetin>tangeretin>nobiletin. The docking results also indicated that the BLG-flavonoid complexes are stabilized through hydrophobic interactions, hydrogen bond interactions and π-π stacking interactions. The analysis of molecular dynamics (MD) simulation trajectories showed that the root mean square deviation (RMSD) of various systems reaches equilibrium and fluctuates around the mean value at various times. Time evolution of the radius of gyration, total solvent accessible surface of the protein and the second structure of protein showed as well that BLG and BLG-flavonoid complexes were stable around 2500ps, and there was not any conformational change as for BLG-flavonoid complexes. Further, the profiles of atomic fluctuations indicated the rigidity of the ligand binding site during the simulation.

  5. Interaction of sulfanilamide and sulfamethoxazole with bovine serum albumin and adenine: Spectroscopic and molecular docking investigations

    NASA Astrophysics Data System (ADS)

    Rajendiran, N.; Thulasidhasan, J.

    2015-06-01

    Interaction between sulfanilamide (SAM) and sulfamethoxazole (SMO) with BSA and DNA base (adenine) was investigated by UV-visible, fluorescence, cyclic voltammetry and molecular docking studies. Stern-Volmer fluorescence quenching constant (Ka) suggests SMO is more quenched with BSA/adenine than that of SAM. The distance r between donor (BSA/adenine) and acceptor (SAM and SMO) was obtained according to fluorescence resonance energy transfer (FRET). The results showed that hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the SAM and SMO with BSA/adenine binding interaction. During the interaction, sulfa drugs could insert into the hydrophobic pocket, where the non-radioactive energy transfer from BSA/adenine to sulfa drugs occurred with high possibility. Cyclic voltammetry results suggested that when the drug concentration is increased, the anodic electrode potential deceased. The docking method indicates aniline group is interacted with the BSA molecules.

  6. Interaction of sulfanilamide and sulfamethoxazole with bovine serum albumin and adenine: spectroscopic and molecular docking investigations.

    PubMed

    Rajendiran, N; Thulasidhasan, J

    2015-06-05

    Interaction between sulfanilamide (SAM) and sulfamethoxazole (SMO) with BSA and DNA base (adenine) was investigated by UV-visible, fluorescence, cyclic voltammetry and molecular docking studies. Stern-Volmer fluorescence quenching constant (Ka) suggests SMO is more quenched with BSA/adenine than that of SAM. The distance r between donor (BSA/adenine) and acceptor (SAM and SMO) was obtained according to fluorescence resonance energy transfer (FRET). The results showed that hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the SAM and SMO with BSA/adenine binding interaction. During the interaction, sulfa drugs could insert into the hydrophobic pocket, where the non-radioactive energy transfer from BSA/adenine to sulfa drugs occurred with high possibility. Cyclic voltammetry results suggested that when the drug concentration is increased, the anodic electrode potential deceased. The docking method indicates aniline group is interacted with the BSA molecules.

  7. Spectroscopic and structural investigation of interaction product of 8-mercaptoquinoline with molecular iodine

    NASA Astrophysics Data System (ADS)

    Chernov'yants, Margarita S.; Starikova, Zoya A.; Karginova, Anastasia O.; Kolesnikova, Tatiana S.; Tereznikov, Alexander Yu.

    2013-11-01

    The behavior of 8-mercaptoquinoline, which is a potential antithyroid drug toward molecular iodine was investigated. The ability of 8-mercaptoquinoline to form the outer-sphere charge-transfer complex C9H7NS·I2 with iodine molecular in dilute chloroform solution has been studied by UV/vis spectroscopy (lg β = 3.14). The crystal structure of the new salt 8-(quinoline-8-yldisulfonyl)quinolinium triiodide - product of irreversible oxidation of 8-mercaptoquinoline was determined by X-ray diffraction. Intramolecular hydrogen bond of N-H⋯N type is presented in the organic cation. The triiodide ion is the nearly centrosymmetrical anion. The 8-(quinoline-8-yldisulfanyl)quinolinium cations form dimers through π-π-stacking interaction between quinolinium rings. The reduced intramolecular interactions are observed between iodine - sulfur atoms and iodine-hydrogen atoms with shortened contacts (less of sum of van-der-waals contacts).

  8. A nanostructural investigation of glassy gelatin oligomers: molecular organization and interactions with low molecular weight diluents

    NASA Astrophysics Data System (ADS)

    Roussenova, M.; Enrione, J.; Diaz-Calderon, P.; Taylor, A. J.; Ubbink, J.; Alam, M. A.

    2012-03-01

    The effects of low molecular weight diluents (namely water and glycerol) on the nanostructure and thermodynamic state of low water content gelatin matrices are explored systematically by combining positron annihilation lifetime spectroscopy (PALS) with calorimetric measurements. Bovine gelatin matrices with a variation in the glycerol content (0-10 wt.%) are equilibrated in a range of water activities (aw = 0.11-0.68, T = 298 K). Both water and glycerol reduce the glass transition temperature, Tg, and the temperature of dissociation of the ordered triple helical segments, Tm, while having no significant effect on the level of re-naturation of the gelatin matrices. Our PALS measurements show that over the concentration range studied, glycerol acts as a packing enhancer and in the glassy state it causes a nonlinear decrease in the average hole size, vh, of the gelatin matrices. Finally, we report complex changes in vh for the gelatin matrices as a function of the increasing level of hydration. At low water contents (Qw ˜ 0.01-0.10), water acts as a plasticizer, causing a systematic increase in vh. Conversely, for water contents higher than Qw ˜ 0.10, vh is found to decrease, as small clusters of water begin to form between the polypeptide chains.

  9. [Molecular interactions in dilute supercritical mixtures: Molecular dynamics investigation]. Final technical report, December 1, 1990--August 31, 1993

    SciTech Connect

    Debenedetti, P.G.

    1993-12-31

    Research was done in the following areas: computational and theoretical studies of molecular interactions in supercritical mixtures; supercooled liquids, network fluids, and glasses; and fast algorithms for simulating large systems on a vector processor.

  10. Investigation of the Interaction of Naringin Palmitate with Bovine Serum Albumin: Spectroscopic Analysis and Molecular Docking

    PubMed Central

    Zhang, Xia; Li, Lin; Xu, Zhenbo; Liang, Zhili; Su, Jianyu; Huang, Jianrong; Li, Bing

    2013-01-01

    Background Bovine serum albumin (BSA) contains high affinity binding sites for several endogenous and exogenous compounds and has been used to replace human serum albumin (HSA), as these two compounds share a similar structure. Naringin palmitate is a modified product of naringin that is produced by an acylation reaction with palmitic acid, which is considered to be an effective substance for enhancing naringin lipophilicity. In this study, the interaction of naringin palmitate with BSA was characterised by spectroscopic and molecular docking techniques. Methodology/Principal Findings The goal of this study was to investigate the interactions between naringin palmitate and BSA under physiological conditions, and differences in naringin and naringin palmitate affinities for BSA were further compared and analysed. The formation of naringin palmitate-BSA was revealed by fluorescence quenching, and the Stern-Volmer quenching constant (KSV) was found to decrease with increasing temperature, suggesting that a static quenching mechanism was involved. The changes in enthalpy (ΔH) and entropy (ΔS) for the interaction were detected at −4.11±0.18 kJ·mol−1 and −76.59±0.32 J·mol−1·K−1, respectively, which indicated that the naringin palmitate-BSA interaction occurred mainly through van der Waals forces and hydrogen bond formation. The negative free energy change (ΔG) values of naringin palmitate at different temperatures suggested a spontaneous interaction. Circular dichroism studies revealed that the α-helical content of BSA decreased after interacting with naringin palmitate. Displacement studies suggested that naringin palmitate was partially bound to site I (subdomain IIA) of the BSA, which was also substantiated by the molecular docking studies. Conclusions/Significance In conclusion, naringin palmitate was transported by BSA and was easily removed afterwards. As a consequence, an extension of naringin applications for use in food, cosmetic and medicinal

  11. Protein-Protein Interaction Investigated by Steered Molecular Dynamics: The TCR-pMHC Complex

    PubMed Central

    Cuendet, Michel A.; Michielin, Olivier

    2008-01-01

    We present a novel steered molecular dynamics scheme to induce the dissociation of large protein-protein complexes. We apply this scheme to study the interaction of a T cell receptor (TCR) with a major histocompatibility complex (MHC) presenting a peptide (p). Two TCR-pMHC complexes are considered, which only differ by the mutation of a single amino acid on the peptide; one is a strong agonist that produces T cell activation in vivo, while the other is an antagonist. We investigate the interaction mechanism from a large number of unbinding trajectories by analyzing van der Waals and electrostatic interactions and by computing energy changes in proteins and solvent. In addition, dissociation potentials of mean force are calculated with the Jarzynski identity, using an averaging method developed for our steering scheme. We analyze the convergence of the Jarzynski exponential average, which is hampered by the large amount of dissipative work involved and the complexity of the system. The resulting dissociation free energies largely underestimate experimental values, but the simulations are able to clearly differentiate between wild-type and mutated TCR-pMHC and give insights into the dissociation mechanism. PMID:18621828

  12. Molecular dynamics investigation of nanoscale substrate topography and its interaction with liquids

    NASA Astrophysics Data System (ADS)

    Cordeiro Rodrigues, Jhonatam

    Nanotechnology has been presenting successful applications in several areas. However, experimentation with nanoscale materials is costly and limited in analysis capability. This research investigates the use of molecular dynamics (MD) simulations to model and study nanomaterials and manufacturing processes. MD simulations are employed to reduce cost, optimize design, increase productivity and allow for the investigation of material interactions not yet observable through experimentation. This work investigates the interaction of water with substrates at the nanoscale. The effect of temperature, droplet impingement velocities and size, as well as substrate material, are investigated at the nanoscale. Several substrate topography designs were modeled to reveal their influence on the wettability of the substrate. Nanoscale gold and silicon substrates are more hydrophilic at higher temperatures than at room temperature. The reduction in droplet diameter increases its wettability. High impingement velocity of droplets does not influence final wettability of substrates but induces higher diffusion rates of droplets in a heated environment. Droplets deposited over a gradient of surface exposure presents spontaneous movement. The Leidenfrost effect was investigated at the nanoscale. Droplets of 4 and 10nm in diameter presented behaviors pertinent to the Leidenfrost effect at 373K, significantly lower than at micro scale and of potential impact to the field. Topographical features were manipulated using superhydrophobic coating resulting in micro whiskers. Nanoimprint lithography (NIL) was used to manufacture substrate topographies at the nanoscale. Water droplets were deposited on the substrates and their wettability was measured using droplet contact angles. Lower surface area exposure resulted in higher contact angles. The experimental relationships between surface topography and substrate wettability were used to validate the insights gained from MD simulations for

  13. Molecular dynamics investigation of the interaction of dislocations with carbides in BCC Fe

    NASA Astrophysics Data System (ADS)

    Granberg, F.; Terentyev, D.; Nordlund, K.

    2015-06-01

    Different types of carbides are present in many steels used as structural materials. To safely use steel in demanding environments, like nuclear power plants, it is important to know how defects will affect the mechanical properties of the material. In this study, the effect of carbide precipitates on the edge dislocation movement is investigated. Three different types of carbides were investigated by means of molecular dynamics, with a Tersoff-like bond order interatomic potential by Henriksson et al. The obstacles were 4 nm in diameter and were of Fe3C- (cementite-), Fe23C6- and Cr23C6-type. The critical unpinning stress was calculated for each type at different temperatures, to get the temperature-dependent obstacle strength. The results showed a decreasing critical stress with increasing temperature, consistent with previous studies. The critical unpinning stress was seen to be dependent on the type of carbide, but the differences were small. A difference was also observed between the obstacles with the same structure, but with different composition. This study shows the relation between the existing Cr23C6 carbide and the experimentally non-existing Fe23C6 carbide, which needs to be used as a model system for investigations with interatomic potentials not able to describe the interaction of Cr in the Fe-C-system. We found the difference to be a between 7% and 10% higher critical unpinning stress for the chromium carbide, than for the iron carbide of the same type.

  14. Investigation of the interaction between five alkaloids and human hemoglobin by fluorescence spectroscopy and molecular modeling.

    PubMed

    He, Wu; Dou, Huanjing; Li, Zhigang; Wang, Xiaogai; Wang, Lvjing; Wang, Ruiyong; Chang, Junbiao

    2014-04-05

    This work studied the interaction of human hemoglobin (HHb) with aminophylline, acefylline, caffeine, theophylline and diprophylline systematically by UV-vis absorption spectroscopy and fluorescence spectroscopy in combination with molecular modeling. Five alkaloids caused the fluorescence quenching of HHb by the formation of alkaloids-HHb complex. The binding constants and thermodynamic parameters were obtained. The hydrophobic and electrostatic interactions were the predominant intermolecular forces to stabilize these complexes. Results of thermodynamic analysis and molecular modeling showed that aminophylline was the strongest quencher and diprophylline was the weakest quencher.

  15. Investigating molecular interactions between beta-lactoglobulin and sugar beet pectin by multi-detection HPSEC

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular interaction between beta-lactoglobulin (beta-LG) and beta-sugar beet pectin (beta-SBP), both by direct mixing and by thermal treatment prior to mixing at pH 6.75 and low ionic strength (50 mM) was studied using High Performance Size Exclusion Chromatography (HPSEC). The analysis of the hy...

  16. Molecular investigation on the interaction of spermine with proteinase K by multispectroscopic techniques and molecular simulation studies.

    PubMed

    Hosseini-Koupaei, Mansoore; Shareghi, Behzad; Saboury, Ali Akbar; Davar, Fateme

    2017-01-01

    The alteration in structure, function and stability of proteinase K in the presence of spermine was investigated using spectroscopic methods and simulation techniques. The stability and enzyme activity of proteinase K-spermine complex were significantly enhanced as compared to that of the pure enzyme. The increase in the value of Vmax and the catalytic efficiency of Proteinase K in presence of spermine confirmed that the polyamine could bring the enzyme hyperactivation. UV-vis spectroscopy, intrinsic fluorescence and circular dichroism methods demonstrated that the binding of spermine changed the microenvironment and structure of proteinase K. The fluorescence studies, showing that spermine quenched the intensity of proteinase K with static mechanism. Thermodynamic parameters analysis suggested that hydrogen bond and van der Waals forces play a key role in complex stability which is in agreement with modeling studies. The CD spectra represented the secondary structure alteration of proteinase K with an increase in α-helicity and a decrease in β-sheet of proteinase K upon spermine conjugation. The molecular simulation results proposed that spermine could interact with proteinase K spontaneously at single binding site, which is in agreement with spectroscopic results. This agreement between experimental and theoretical results may be a worth method for protein-ligand complex studies.

  17. Solid-State Spectroscopic Investigation of Molecular Interactions between Clofazimine and Hypromellose Phthalate in Amorphous Solid Dispersions.

    PubMed

    Nie, Haichen; Su, Yongchao; Zhang, Mingtao; Song, Yang; Leone, Anthony; Taylor, Lynne S; Marsac, Patrick J; Li, Tonglei; Byrn, Stephen R

    2016-11-07

    It has been technically challenging to specify the detailed molecular interactions and binding motif between drugs and polymeric inhibitors in the solid state. To further investigate drug-polymer interactions from a molecular perspective, a solid dispersion of clofazimine (CLF) and hypromellose phthalate (HPMCP), with reported superior amorphous drug loading capacity and physical stability, was selected as a model system. The CLF-HPMCP interactions in solid dispersions were investigated by various solid state spectroscopic methods including ultraviolet-visible (UV-vis), infrared (IR), and solid-state NMR (ssNMR) spectroscopy. Significant spectral changes suggest that protonated CLF is ionically bonded to the carboxylate from the phthalyl substituents of HPMCP. In addition, multivariate analysis of spectra was applied to optimize the concentration of polymeric inhibitor used to formulate the amorphous solid dispersions. Most interestingly, proton transfer between CLF and carboxylic acid was experimentally investigated from 2D (1)H-(1)H homonuclear double quantum NMR spectra by utilizing the ultrafast magic-angle spinning (MAS) technique. The molecular interaction pattern and the critical bonding structure in CLF-HPMCP dispersions were further delineated by successfully correlating ssNMR findings with quantum chemistry calculations. These high-resolution investigations provide critical structural information on active pharmaceutical ingredient-polymer interaction, which can be useful for rational selection of appropriate polymeric carriers, which are effective crystallization inhibitors for amorphous drugs.

  18. Molecular interactions of organic molecules at the air/water interface investigated by sum frequency generation vibrational spectroscopy.

    PubMed

    Wang, Wenting; Ye, Shuji

    2017-02-08

    The molecular structure and dynamics of organic molecules at the aqueous interface have attracted a number of investigations owing to their importance and specific nature. However, there are relatively few studies on the direct characterization of the molecular interactions at the air/water interface because they are extremely difficult to measure in experiments. In this study, we use dibutyl ester molecules (R1CO2R2O2CR1) as a model of organic molecules, and investigate their molecular structure and interactions using sum frequency generation vibrational spectroscopy. We demonstrate that the molecular interactions can be estimated by measuring the intensity ratio of the symmetric stretching (ν1) and Fermi resonant bands (2ν2) of methyl groups. Here, dibutyl ester molecules are widely used as plasticizers in polymers to improve the properties of the plastics and polymers. It is found that the orientation angles of the tailed methyl groups at the air/water interface decrease from 34° to 19° when the chain length of R2 increases from 0 to 8. The total intermolecular interactions of the dibutyl ester molecules decrease as the chain length of R2 increases because the van der Waals interactions between the hydrocarbon chains increase, while the hydrogen bond interactions between the carbonyl group and water molecules decrease. Our study demonstrates the stability of ester-based plasticizers in polymers can be well predicted from the intensity ratio of the ν1 and 2ν2 bands of methyl group. Such an intensity ratio can be thus used as an effective vibrational optical ruler for characterizing molecular interactions between plasticizers and polymers.

  19. Molecular-dynamic investigation of the interaction of vacancies with symmetrical tilt grain boundaries in aluminum

    NASA Astrophysics Data System (ADS)

    Weckman, A. V.; Demyanov, B. F.; Dragunov, A. S.

    2015-06-01

    The molecular-dynamic method has been used to study the interaction of lattice vacancies with symmetrical grain boundaries (GBs) in aluminum. The fraction of trapped vacancies has been found to depend linearly on the distance to the GB plane. The average velocity of the vacancy migration toward the boundary decreases exponentially with an increase in the distance between the GB plane and vacancy. The radius of the region of trapping of a vacancy by the boundary is limited to two to three lattice parameters and grows with an increase in temperature. Four types of boundaries, which are characterized by different capability for the trapping of vacancies, have been determined.

  20. Investigation and correlation of drug polymer miscibility and molecular interactions by various approaches for the preparation of amorphous solid dispersions.

    PubMed

    Meng, Fan; Trivino, Anne; Prasad, Dev; Chauhan, Harsh

    2015-04-25

    Curcumin (CUR) was used as a poorly soluble drug whereas polyvinyl pyrrolidone K90 (PVP), Eudragit EPO (EPO), hydroxypropyl methylcellulose E5 (HPMC) and polyethylene glycol 8000 (PEG) were used as hydrophilic polymers. CUR polymer miscibility was evaluated by solubility parameter, melting point depression and glass transition temperature (Tg) measurements. Molecular interactions between CUR and polymers were determined by Fourier-transform infrared spectroscopy (FTIR) and Raman. Amorphous solid dispersions were prepared with CUR-polymer ratio of 70:30 (w/w) by solvent evaporation technique and were evaluated for dissolution enhancement using USP II method. Physical states of solid dispersions were characterized by X-ray diffraction (XRD) whereas thermal behaviors were investigated using modulated differential scanning calorimetry (MDSC). CUR-EPO system showed good miscibility through all the approaches, whereas immiscibility was found in other CUR-polymer systems. CUR-EPO and CUR-HPMC systems showed significant molecular interactions whereas CUR-PVP and CUR-PEG showed no molecular interactions. All solid dispersions showed significant dissolution enhancement with CUR-EPO showing highest dissolution rate during first 1h whereas CUR-HPMC was effective in maintaining high CUR concentrations for 6h. The study highlights the importance of investigating and correlating drug polymer miscibility and molecular interactions by various approaches for successful formulation of amorphous solid dispersions.

  1. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Wong, C. H.; Vijayaraghavan, V.

    2014-01-01

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  2. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

    PubMed Central

    Natarajan, Sathishkumar; Thamilarasan, Senthil Kumar; Park, Jong-In; Chung, Mi-Young; Nou, Ill-Sup

    2015-01-01

    Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea) was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER) webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin. PMID:26703735

  3. Investigation of Molecular Interactions between AFM-Tip and Thiol Films

    NASA Astrophysics Data System (ADS)

    Touhami, Ahmed; Moore, Justin; Lee, T. Randall

    Among various self-assembly processes, the formation of a self-assembled monolayer (SAM) is one of the most elegant ways for making an organic film with specific surface properties. Recently, much effort has been devoted in using AFM-based single-molecule force spectroscopy (SMFS) to understanding the formation of alkanethiol SAMs on gold surfaces. Investigating the factors that affect the AFM tip-SAMs interactions is necessary to clarify the controversial results of these studies. Here, we investigated the interactions between bare AFM-tips and several SAMs thiols-gold surfaces under controlled humidity conditions. Our results demonstrate that the Tip-SAM interactions can be used to precisely determine the length of the thiol chains, the adhesion force between thiols head groups and the AFM tip, and the strength of the thiol-gold contact. Our findings on the dynamics and the structure of the SAMs of alkanethiols on gold are useful for detail understanding of the thermodynamics, kinetics and mechanisms of SAM technology assembly. NSF.

  4. Investigation of interaction of antibacterial drug sulfamethoxazole with human serum albumin by molecular modeling and multi-spectroscopic method.

    PubMed

    Wang, Qin; Zhang, Sheng-Rui; Ji, Xiaohui

    2014-04-24

    Interaction of sulfamethoxazole (SMX) with human serum albumin (HSA) was investigated by molecular modeling and multi-spectroscopic methods under physiological conditions. The interaction mechanism was firstly predicted through molecular modeling that confirmed the interaction between SMX and HSA. The binding parameters and the thermodynamic parameters at different temperatures for the reaction had been calculated according to the Stern-Volmer, Hill, Scatchard and the Van't Hoff equations, respectively. One independent class of binding site existed during the interaction between HSA and SMX. The binding constants decreased with the increasing temperatures, which meant that the quenching mechanism was a static quenching. The thermodynamic parameters of the reaction, namely standard enthalpy ΔH(0) and entropy ΔS(0), had been calculated to be -16.40 kJ mol(-1) and 32.33 J mol(-1) K(-1), respectively, which suggested that the binding process was exothermic, enthalpy driven and spontaneous. SMX bound to HSA was mainly based on electrostatic interaction, but hydrophobic interactions and hydrogen bonds could not be excluded from the binding. The conformational changes of HSA in the presence of SMX were confirmed by the three-dimensional fluorescence spectroscopy, UV-vis absorption spectroscopy and circular dichroism (CD) spectroscopy. CD data suggested that the protein conformation was altered with the reduction of α-helices from 55.37% to 41.97% at molar ratio of SMX/HSA of 4:1.

  5. Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions.

    PubMed

    Heifetz, Alexander; Aldeghi, Matteo; Chudyk, Ewa I; Fedorov, Dmitri G; Bodkin, Mike J; Biggin, Philip C

    2016-04-15

    The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.

  6. Investigation the interaction of Daphnin with human serum albumin using optical spectroscopy and molecular modeling methods

    NASA Astrophysics Data System (ADS)

    Zhu, Jinhua; Wu, Liye; Zhang, Qingyou; Chen, Xingguo; Liu, Xiuhua

    2012-09-01

    The interaction between Daphnin with human serum albumin has been studied for the first time by spectroscopic methods including fluorescence quenching technology, circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy under simulative physiological conditions. The results of fluorescence titration revealed that Daphnin can quench the intrinsic fluorescence of HSA by static quenching and there is a single class of binding site on HSA. In addition, the studies of CD spectroscopy and FT-IR spectroscopy showed that the protein secondary structure changed with increases of α-helices at the drug to protein molar ratio of 2. Furthermore, the thermodynamic functions ΔH0 and ΔS0 for the reaction were calculated to be 11.626 kJ mol-1 and 118.843 J mol-1 K-1 according to Van't Hoff equation. The thermodynamic parameters (ΔH0 and ΔS0) and the molecular modeling study indicated that hydrophobic force played an important role to stabilize the Daphnin-HSA complex, and Daphnin could bind within the subdomain IIA of the HSA.

  7. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    PubMed

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  8. Investigating molecular interactions and surface morphology of wax-doped asphaltenes.

    PubMed

    Pahlavan, Farideh; Mousavi, Masoumeh; Hung, Albert; Fini, Ellie H

    2016-04-07

    The nature and origin of bee-like microstructures (bees) in asphalt binders and their impact on asphalt oxidation have been the subject of extensive discussions in recent years. While several studies refer to the bees as solely surface features, some others consider them to be bulk microcrystalline components that are formed due to co-precipitation of wax and asphaltene molecules. In this study, we use a rigorous theoretical and experimental approach to investigate the interplay of asphalt components (mainly asphaltene and wax) and their impact on bee formation. In the theoretical section, quantum-mechanical calculations using density functional theory (DFT) are used to evaluate the strength of interactions between asphaltene unit sheets in the presence and absence of a wax component, as well as the mutual interactions between asphaltene molecules (monomers and dimers) and paraffin wax. The results of this section reveal that paraffin waxes not only do not reinforce the interaction between the asphaltene unit sheets, they destabilize asphaltene assembly and dimerization. AIM (Atom in Molecules) analysis shows the destabilizing effect of wax on asphaltene assembly as a reduction in the number of cage and bond critical points between asphaltenes. This destabilization effect among interacting systems (asphaltene-asphaltene and wax-asphaltene) does not support the hypothesis that interaction between paraffin waxes and non-wax components, such as asphaltene, is responsible for their co-precipitation and bee formation. To further examine the effect of wax component on asphalt microstructure experimentally, we used atomic force microscopy (AFM) to study the surface morphology of an asphalt sample doped with 1% to 25% paraffin wax. In agreement with the conclusions drawn from the DFT approach, our experiments indicate that paraffin wax tends to crystallize separately and form lamellar paraffin wax crystal inclusions with 10 nm thickness. Moreover, the addition of 3% wax

  9. Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies

    PubMed Central

    Aghili, Zahra; Taheri, Saba; Zeinabad, Hojjat Alizadeh; Pishkar, Leila; Saboury, Ali Akbar; Rahimi, Arash; Falahati, Mojtaba

    2016-01-01

    Herein, the interaction of hen egg white lysozyme (HEWL) with iron nanoparticle (Fe NP) was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV) to HEWL (8.57±0.54 mV) can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV). In addition, dynamic light scattering (DLS) study revealed that addition of Fe NP (92.95±6.11 nm) to HEWL (2.68±0.37 nm) increases suspension potential of protein/nanoparticle system (51.17±3.19 nm). Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp) residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m)) of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD) experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein–ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL. PMID:27776180

  10. Investigation on the interactions of clenbuterol to bovine serum albumin and lysozyme by molecular fluorescence technique.

    PubMed

    Bi, Shuyun; Pang, Bo; Wang, Tianjiao; Zhao, Tingting; Yu, Wang

    2014-01-01

    Clenbuterol interacting with bovine serum albumin (BSA) or lysozyme (LYS) in physiological buffer (pH 7.4) was investigated by the fluorescence spectroscopy and UV-vis absorption spectroscopy. The results indicated that clenbuterol quenched the intrinsic fluorescence of BSA and LYS via a static quenching procedure. The binding constants of clenbuterol with BSA and LYS were 1.16×10(3) and 1.49×10(3) L mol(-1) at 291 K. The values of ΔH and ΔS implied that hydrophobic and electrostatic interaction played a major role in stabilizing the complex (clenbuterol-BSA or clenbuterol-LYS). In the presence of Fe2+, Fe3+, Cu2+, Mg2+, Ca2+, or Zn2+, the binding constants of clenbuterol to BSA or LYS had no significant differences. The distances between the donor (BSA or LYS) and acceptor (clenbuterol) were 2.61 and 2.19 nm for clenbuterol-BSA and clenbuterol-LYS respectively. Furthermore, synchronous fluorescence spectrometry was used to analyze the conformational changes of BSA and LYS.

  11. Spectroscopic investigations on the interaction between carbon nanotubes and catalase on molecular level.

    PubMed

    Guan, Jin; Dai, Jingping; Zhao, Xingchen; Liu, Chunhua; Gao, Canzhu; Liu, Rutao

    2014-05-01

    The interactions between well-dispersed multiwalled carbon nanotubes (MWCNTs) and catalase (CAT) were investigated. The activity of CAT was inhibited with the addition of MWCNTs. After deducting the inner filter effect, the fluorescence spectra revealed that the tryptophan (Trp) residues were exposed and the fluorescence intensities of CAT increased with the increase in the MWCNTs concentration. At the same time, the environment of the Trp residues became more hydrophobic. The results of UV-vis absorption spectroscopy and CD spectra indicated that the secondary structure of CAT had been changed, and the amino acid residues were located in a more hydrophobic environment. Meanwhile, the UV-vis spectra indicated that the conformation of the heme porphyrin rings was changed. The microenvironment of CAT activity sites may be interfered by MWCNTs. This research showed that MWCNTs could not only contribute to the conformational changes of protein but also change the enzyme function.

  12. Investigating the Interaction Pattern and Structural Elements of a Drug-Polymer Complex at the Molecular Level.

    PubMed

    Nie, Haichen; Mo, Huaping; Zhang, Mingtao; Song, Yang; Fang, Ke; Taylor, Lynne S; Li, Tonglei; Byrn, Stephen R

    2015-07-06

    Strong associations between drug and polymeric carriers are expected to contribute to higher drug loading capacities and better physical stability of amorphous solid dispersions. However, molecular details of the interaction patterns and underlying mechanisms are still unclear. In the present study, a series of amorphous solid dispersions of clofazimine (CLF), an antileprosy drug, were prepared with different polymers by applying the solvent evaporation method. When using hypromellose phthalate (HPMCP) as the carrier, the amorphous solid dispersion system exhibits not only superior drug loading capacity (63% w/w) but also color change due to strong drug-polymer association. In order to further explain these experimental observations, the interaction between CLF and HPMCP was investigated in a nonpolar volatile solvent system (chloroform) prior to forming the solid dispersion. We observed significant UV/vis and (1)H NMR spectral changes suggesting the protonation of CLF and formation of ion pairs between CLF and HPMCP in chloroform. Furthermore, nuclear Overhauser effect spectroscopy (NOESY) and diffusion order spectroscopy (DOSY) were employed to evaluate the strength of associations between drug and polymers, as well as the molecular mobility of CLF. Finally, by correlating the experimental values with quantum chemistry calculations, we demonstrate that the protonated CLF is binding to the carboxylate group of HPMCP as an ion pair and propose a possible structural model of the drug-polymer complex. Understanding the drug and carrier interaction patterns from a molecular perspective is critical for the rational design of new amorphous solid dispersions.

  13. Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

    PubMed

    Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

    2011-03-01

    The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

  14. Atomic & Molecular Interactions

    SciTech Connect

    2002-07-12

    The Gordon Research Conference (GRC) on Atomic & Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  15. Investigation of TNB/NNAP cocrystal synthesis, molecular interaction and formation process

    NASA Astrophysics Data System (ADS)

    Chen, Peng-Yuan; Zhang, Lin; Zhu, Shun-Guan; Cheng, Guang-Bin; Li, Ning-Rui

    2017-01-01

    A novel cocrystal of 1,3,5-trinitrobenzene (TNB) and 1-nitronaphthalene (NNAP) was synthesized by solution and mechanochemical method, respectively. The crystal structure was characterized by single crystal X-ray diffraction (SXRD). Then the intermolecular interaction was illustrated quantitatively by Hirshfeld surface analysis accordingly. Two other isostructural cocrystals, TNT (2,4,6-trinitrotoluene)/NNAP and TNP (2,4,6-trinitrophenol)/NNAP were also calculated for comparison. Among the three cocrystals, TNB/NNAP cocrystal has the largest proportion of π-π stacking interaction (12.7%). While TNP/NNAP cocrystal has a greater percentage of hydrogen bonding than the other two cocrystals, which is 43.2% of the total interactions. These results indicate electronic effect has an influence on the intermolecular interaction in the cocrystal. The IR spectra of the intermediate products provide more information about the formation process of hydrogen bonding and π-π stacking. We can tell from the differential scanning calorimetry (DSC) thermograms that a eutectic mixture was generated first after TNB and NNAP were physically mixed without grinding, and then turned into the cocrystal and finally transformed completely.

  16. Interaction of human chymase with ginkgolides, terpene trilactones of Ginkgo biloba investigated by molecular docking simulations.

    PubMed

    Dubey, Amit; Marabotti, Anna; Ramteke, Pramod W; Facchiano, Angelo

    2016-04-29

    The search for natural chymase inhibitors has a good potential to provide a novel therapeutic approach against the cardiovascular diseases and other heart ailments. We selected from literature 20 promising Ginkgo biloba compounds, and tested them for their potential ability to bind chymase enzyme using docking and a deep analysis of surface pocket features. Docking results indicated that the compounds may interact with the active site of human chymase, with favorable distinct interactions with important residues Lys40, His57, Lys192, Phe191, Val146, Ser218, Gly216, and Ser195. In particular, proanthocyanidin is the one with the best-predicted binding energy, with seven hydrogen bonds. Interestingly, all active G. biloba compounds have formed the hydrogen bond interactions with the positively charged Lys192 residue at the active site, involved in the mechanism of pH enhancement for the cleavage of angiotensin I site. Ginkgolic acid and proanthocyanidin have better predicted binding energy towards chymase than other serine proteases, i.e kallikrein, tryptase and elastase, suggesting specificity for chymase inhibition. Our study suggests these G. biloba compounds are a promising starting point for developing chymase inhibitors for the potential development of future drugs.

  17. Investigation of the interaction between quercetin and human serum albumin by multiple spectra, electrochemical impedance spectra and molecular modeling.

    PubMed

    Dai, Jie; Zou, Ting; Wang, Li; Zhang, Yezhong; Liu, Yi

    2014-12-01

    Quercetin (Qu), a flavonoid compound, exists widely in the human diet and exhibits a variety of pharmacological activities. This work is aimed at studying the effect of Qu on the bioactive protein, human serum albumin (HSA) under simulated biophysical conditions. Multiple spectroscopic methods (including fluorescence and circular dichroism), electrochemical impedance spectra (EIS) and molecular modeling were employed to investigate the interaction between Qu and HSA. The fluorescence quenching and EIS experimental results showed that the fluorescence quenching of HSA was caused by formation of a Qu-HSA complex in the ground state, which belonged to the static quenching mechanism. Based on the calculated thermodynamic parameters, it concluded that the interaction was a spontaneous process and hydrogen bonds combined with van der Waal's forces played a major role in stabilizing the Qu-HSA complex. Molecular modeling results demonstrated that several amino acids participated in the binding process and the formed Qu-HSA complex was stabilized by H-bonding network at site I in sub-domain IIA, which was further confirmed by the site marker competitive experiments. The evidence from circular dichroism (CD) indicated that the secondary structure and microenvironment of HSA were changed. Alterations in the conformation of HSA were observed with a reduction in the amount of α helix from 59.9% (free HSA) to 56% (Qu-HSA complex), indicating a slight unfolding of the protein polypeptides.

  18. Multi-spectroscopic and molecular modelling approach to investigate the interaction of riboflavin with human serum albumin.

    PubMed

    Alam, Md Maroof; Abul Qais, Faizan; Ahmad, Iqbal; Alam, Parvez; Hasan Khan, Rizwan; Naseem, Imrana

    2017-03-09

    Riboflavin (RF) plays an important role in various metabolic redox reactions in the form of flavin adenine dinucleotide and flavin mononucleotide. Human serum albumin (HSA) is an important protein involved in the transportation of drugs, hormones, fatty acid and other molecules which determine the biodistribution and physiological fate of these molecules. In this study, we have investigated the interaction of riboflavin RF with HSA under simulative physiological conditions using various biophysical, calorimetric and molecular docking techniques. Results demonstrate the formation of riboflavin-HSA complex with binding constant in the order of 10(4) M(-1). Fluorescence spectroscopy confirms intermediate strength having a static mode of quenching with stoichiometry of 1:1. Experimental results suggest that the binding site of riboflavin mainly resides in sub-domain IIA of HSA and that ligand interaction increases the α-helical content of HSA. These parameters were further verified by isothermal titration calorimetry ITC which confirms the thermodynamic parameters obtained by fluorescence spectroscopy. Molecular docking was employed to suggest a binding model. Based on thermodynamic, spectroscopic and computational observations it can be concluded that HSA-riboflavin complex is mainly stabilized by various non-covalent forces with binding energy of -7.2 kcal mol(-1).

  19. Molecular interaction investigation between three CdTe:Zn(2+) quantum dots and human serum albumin: A comparative study.

    PubMed

    Huang, Shan; Qiu, Hangna; Liu, Yi; Huang, Chusheng; Sheng, Jiarong; Su, Wei; Xiao, Qi

    2015-12-01

    Water-soluble Zn-doped CdTe quantum dots (CdTe:Zn(2+) QDs) have attracted great attention in biological and biomedical applications. In particular, for any potential in vivo application, the interaction of CdTe:Zn(2+) QDs with human serum albumin (HSA) is of greatest importance. As a step toward the elucidation of the fate of CdTe:Zn(2+) QDs introduced to organism, the molecular interactions between CdTe:Zn(2+) QDs with three different sizes and HSA were systematically investigated by spectroscopic techniques. Three CdTe:Zn(2+) QDs with maximum emission of 514 nm (green QDs, GQDs), 578 nm (yellow QDs, YQDs), and 640 nm (red QDs, RQDs) were tested. The binding of CdTe:Zn(2+) QDs with HSA was a result of the formation of HSA-QDs complex and electrostatic interactions played major roles in stabilizing the complex. The Stern-Volmer quenching constant, associative binding constant, and corresponding thermodynamic parameters were calculated. The site-specific probe competitive experiments revealed that the binding location of CdTe:Zn(2+) QDs with HSA was around site I. The microenvironmental and conformational changes of HSA induced by CdTe:Zn(2+) QDs were analyzed. These results suggested that the conformational change of HSA was dramatically at secondary structure level and the biological activity of HSA was weakened in the present of CdTe:Zn(2+) QDs with bigger size.

  20. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    NASA Astrophysics Data System (ADS)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  1. Does glimepiride alter the pharmacokinetics of sildenafil citrate in diabetic nephropathy animals: investigating mechanism of interaction by molecular modeling studies.

    PubMed

    Tripathi, Alok Shiomurti; Timiri, Ajay Kumar; Mazumder, Papiya Mitra; Chandewar, Anil

    2015-10-01

    The present study evaluates possible drug interactions between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ)-induced diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction based on molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg kg(-1), i.p.) and was confirmed by assessing blood and urine biochemical parameters 28 days after induction. Selected DN animals were used to explore the drug interaction between GLIM (0.5 mg kg(-1), p.o.) and SIL (2.5 mg kg(-1), p.o.) on the 29th and 70th day of the protocol. Possible drug interaction was assessed by evaluating the plasma drug concentration using HPLC-UV and changes in biochemical parameters in blood and urine were also determined. The mechanism of the interaction was postulated from the results of a molecular modeling study using the Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in blood and urine biochemical parameters in STZ-treated groups. The concentration of SIL increased significantly (P < 0.001) in rat plasma when co-administered with GLIM on the 70th day of the protocol. Molecular modeling revealed important interactions with rat serum albumin and CYP2C9. GLIM has a strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL, whereas for CYP2C9, GLIM forms a stronger hydrogen bond than SIL with polar contacts and hydrophobic interactions. The present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals, and the mechanism is supported by molecular modeling studies.

  2. Interactive molecular dynamics

    NASA Astrophysics Data System (ADS)

    Schroeder, Daniel V.

    2015-03-01

    Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

  3. Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods

    NASA Astrophysics Data System (ADS)

    Cui, Yanrui; Hao, Erjun; Hui, Guangquan; Guo, Wei; Cui, Fengling

    2013-06-01

    A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

  4. Investigations on the Interactions of 5-Fluorouracil with Herring Sperm DNA: Steady State/Time Resolved and Molecular Modeling Studies

    NASA Astrophysics Data System (ADS)

    Chinnathambi, Shanmugavel; Karthikeyan, Subramani; Velmurugan, Devadasan; Hanagata, Nobutaka; Aruna, Prakasarao; Ganesan, Singaravelu

    2015-04-01

    In the present study, the interaction of 5-Fluorouracil with herring sperm DNA is reported using spectroscopic and molecular modeling techniques. This binding study of 5-FU with hs-DNA is of paramount importance in understanding chemico-biological interactions for drug design, pharmacy and biochemistry without altering the original structure. The challenge of the study was to find the exact binding mode of the drug 5-Fluorouracil with hs-DNA. From the absorption studies, a hyperchromic effect was observed for the herring sperm DNA in the presence of 5-Fluorouracil and a binding constant of 6.153 × 103 M-1 for 5-Fluorouracil reveals the existence of weak interaction between the 5-Fluorouracil and herring sperm DNA. Ethidium bromide loaded herring sperm DNA showed a quenching in the fluorescence intensity after the addition of 5-Fluorouracil. The binding constants for 5-Fluorouracil stranded DNA and competitive bindings of 5-FU interacting with DNA-EB systems were examined by fluorescence spectra. The Stern-Volmer plots and fluorescence lifetime results confirm the static quenching nature of the drug-DNA complex. The binding constant Kb was 2.5 × 104 L mol-1 and the number of binding sites are 1.17. The 5-FU on DNA system was calculated using double logarithmic plot. From the Forster nonradiative energy transfer study it has been found that the distance of 5-FU from DNA was 4.24 nm. In addition to the spectroscopic results, the molecular modeling studies also revealed the major groove binding as well as the partial intercalation mode of binding between the 5-Fluorouracil and herring sperm DNA. The binding energy and major groove binding as -6.04 kcal mol-1 and -6.31 kcal mol-1 were calculated from the modeling studies. All the testimonies manifested that binding modes between 5-Fluorouracil and DNA were evidenced to be groove binding and in partial intercalative mode.

  5. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    PubMed Central

    Bai, Qifeng; Yao, Xiaojun

    2016-01-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1. PMID:26887338

  6. Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis

    NASA Astrophysics Data System (ADS)

    Bai, Qifeng; Yao, Xiaojun

    2016-02-01

    Metabotropic glutamate receptor 1 (mGlu1), which belongs to class C G protein-coupled receptors (GPCRs), can be coupled with G protein to transfer extracellular signal by dimerization and allosteric regulation. Unraveling the dimer packing and allosteric mechanism can be of great help for understanding specific regulatory mechanism and designing more potential negative allosteric modulator (NAM). Here, we report molecular dynamics simulation studies of the modulation mechanism of FITM on the wild type, T815M and Y805A mutants of mGlu1 through weak interaction analysis and free energy calculation. The weak interaction analysis demonstrates that van der Waals (vdW) and hydrogen bonding play an important role on the dimer packing between six cholesterol molecules and mGlu1 as well as the interaction between allosteric sites T815, Y805 and FITM in wild type, T815M and Y805A mutants of mGlu1. Besides, the results of free energy calculations indicate that secondary binding pocket is mainly formed by the residues Thr748, Cys746, Lys811 and Ser735 except for FITM-bound pocket in crystal structure. Our results can not only reveal the dimer packing and allosteric regulation mechanism, but also can supply useful information for the design of potential NAM of mGlu1.

  7. Electrostatic interactions in molecular materials

    NASA Astrophysics Data System (ADS)

    Painelli, Anna; Terenziani, Francesca

    2004-03-01

    Non-additive collective behavior appears in molecular materials as a result of intermolecular interactions. We present a model for interacting polar and polarizable molecules that applies to different supramolecular architectures of donor-π-acceptor molecules. We follow a bottom-up modeling strategy: the detailed analysis of spectroscopic data of solvated molecules leads to the definition of a simple two-state model for the molecular units. Classical electrostatic interactions are then introduced to model molecular clusters. The molecular properties are strickingly affected by supramolecular interactions, as demonstrated by spectroscopic studies. Brand new phenomena, like phase transitions and multielectron transfer, with no counterpart at the molecular level are observed as direct consequences of electrostatic intermolecular interactions.

  8. Investigations on the interactions between naphthalimide-based anti-tumor drugs and human serum albumin by spectroscopic and molecular modeling methods.

    PubMed

    Cheng, Huiyuan; Zou, Ting; Xu, Yongliang; Wang, Ying; Wu, Aibin; Dai, Jie; Zhang, Yezhong; Liu, Yi

    2016-02-01

    The interactions between the three kinds of naphthalimide-based anti-tumor drugs (NADA, NADB, NADC) and human serum albumin (HSA) under simulated physiological conditions were investigated by fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results of the fluorescence quenching spectroscopy showed that the quenching mechanisms for different drugs were static and their affinity was in a descending order of NADA > NADB > NADC. The relative thermodynamic parameters indicated that hydrophobic force was the predominant intermolecular force in the binding of NAD to HSA, while van der Waals interactions and hydrogen bonds could not be ignored. The results of site marker competitive experiment confirmed that the binding site of HSA primarily took place in site I. Furthermore, the molecular modeling study was consistent with these results. The study of circular dichroism spectra demonstrated that the presence of NADs decreased the α-helical content of HSA and induced the change of the secondary structure of HSA.

  9. Molecular docking of opiates and opioid peptides, a tool for the design of selective agonists and antagonists, and for the investigation of atypical ligand-receptor interactions.

    PubMed

    Gentilucci, L; Tolomelli, A; De Marco, R; Artali, R

    2012-01-01

    In the last years, molecular docking emerged as a powerful tool to investigate the interactions between opioid ligands and their receptors, thus driving the design and development of new selective agonists or antagonists of therapeutic interest. This review especially covers the most representative and recent comparative molecular docking analyses of structurally related compounds, as well as of agonists and antagonists within the active and inactive states of the receptors. The comparative analyses gave important information on the structural determinants responsible for the affinity and selectivity of the ligands, and defined the features responsible for the activation of the receptors. A special section is dedicated to the analyses of recently discovered, unusual agonists lacking of the tyramine pharmacophore, such as Salvinorin A, and the cyclopeptides which comprise the D-Trp-Phe pharmacophoric motif. For the atypical structure of these compounds, the docking proved to be essential to disclose how they interact with and activate the receptors.

  10. Investigation of the Interaction between 1,3-Diazaheterocyclic Compounds and the Fat Mass and Obesity-Associated Protein by Fluorescence Spectroscopy and Molecular Modeling.

    PubMed

    Zhang, Lijiao; Ren, Ting; Tian, Xianhai; Wang, Zechun; Yu, Wenquan; Wang, Ruiyong; Chang, Junbiao

    2017-01-01

    In this paper, The binding of twelve 1,3-diazaheterocyclic compounds (1a-1 l) to the fat mass and obesity-associated (FTO) protein was investigated by fluorescence, UV-vis absorption spectroscopy and molecular modeling. Results indicated that the intrinsic fluorescence of FTO is quenched by the nine compounds (1a-1i) with a static quenching procedure. No interaction was observed between FTO protein and compounds (1j-1 l). The thermodynamic parameters obtained from the fluorescence data showed that the hydrophobic force played a major role in stabilizing the complex. The results of synchronous and three-dimensional fluorescence spectra showed that the conformation of FTO was changed. In addition, the influence of molecular structure on the quenching effect has been investigated.

  11. An investigation of nonadiabatic interactions in Cl(2Pj) + D2 via crossed-molecular-beam scattering.

    PubMed

    Parsons, Bradley F; Chandler, David W

    2005-05-01

    We have determined limits on the cross section for both electronically nonadiabatic excitation and quenching in the Cl((2)P(j)) + D(2) system. Our experiment incorporates crossed-molecular-beam scattering with state-selective Cl((2)P(12,32)) detection and velocity-mapped ion imaging. By colliding atomic chlorine with D(2), we address the propensity for collisions that result in a change of the spin-orbit level of atomic chlorine either through electronically nonadiabatic spin-orbit excitation Cl((2)P(32)) + D(2)-->Cl(*)((2)P(12)) + D(2) or through electronically nonadiabatic spin-orbit quenching Cl(*)((2)P(12)) + D(2)-->Cl((2)P(32)) + D(2). In the first part of this report, we estimate an upper limit for the electronically nonadiabatic spin-orbit excitation cross section at a collision energy of 5.3 kcal/mol, which lies above the energy of the reaction barrier (4.9 kcal/mol). Our analysis and simulation of the experimental data determine an upper limit for the excitation cross section as sigma(NA)< or =0.012 A(2). In the second part of this paper we investigate the propensity for electronically nonadiabatic spin-orbit quenching of Cl(*) following a collision with D(2) or He. We perform these experiments at collision energies above and below the energy of the reaction barrier. By comparing the amount of scattered Cl(*) in our images to the amount of Cl(*) lost from the atomic beam we obtain the maximum cross section for electronically nonadiabatic quenching as sigma(NA)< or =15(-15) (+44) A(2) for a collision energy of 7.6 kcal/mol. Our experiments show the probability for electronically nonadiabatic quenching in Cl(*) + D(2) to be indistinguishable to that for the kinematically identical system of Cl(*) + He.

  12. Detection of molecular interactions

    DOEpatents

    Groves, John T [Berkeley, CA; Baksh, Michael M [Fremont, CA; Jaros, Michal [Brno, CH

    2012-02-14

    A method and assay are described for measuring the interaction between a ligand and an analyte. The assay can include a suspension of colloidal particles that are associated with a ligand of interest. The colloidal particles are maintained in the suspension at or near a phase transition state from a condensed phase to a dispersed phase. An analyte to be tested is then added to the suspension. If the analyte binds to the ligand, a phase change occurs to indicate that the binding was successful.

  13. Interaction of O and OH radicals with a simple model system for lipids in the skin barrier: a reactive molecular dynamics investigation for plasma medicine

    NASA Astrophysics Data System (ADS)

    Van der Paal, Jonas; Aernouts, Stefaan; van Duin, Adri C. T.; Neyts, Erik C.; Bogaerts, Annemie

    2013-10-01

    Plasma medicine has been claimed to provide a novel route to heal wounds and regenerate skin, although very little is currently known about the elementary processes taking place. We carried out a series of ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of O and OH radicals with lipids, more specifically with α-linolenic acid as a model for the free fatty acids present in the upper skin layer. Our calculations predict that the O and OH radicals most typically abstract a H atom from the fatty acids, which can lead to the formation of a conjugated double bond, but also to the incorporation of alcohol or aldehyde groups, thereby increasing the hydrophilic character of the fatty acids and changing the general lipid composition of the skin. Within the limitations of the investigated model, no formation of possibly toxic products was observed.

  14. Using Affinity Chromatography to Investigate Novel Protein-Protein Interactions in an Undergraduate Cell and Molecular Biology Lab Course

    ERIC Educational Resources Information Center

    Belanger, Kenneth D.

    2009-01-01

    Inquiry-driven lab exercises require students to think carefully about a question, carry out an investigation of that question, and critically analyze the results of their investigation. Here, we describe the implementation and assessment of an inquiry-based laboratory exercise in which students obtain and analyze novel data that contribute to our…

  15. Synthesis of F16 conjugated with 5-fluorouracil and biophysical investigation of its interaction with bovine serum albumin by a spectroscopic and molecular modeling approach.

    PubMed

    Xiang, Chen; Li, Dong-Wei; Qi, Zu-De; Jiang, Feng-Lei; Ge, Yu-Shu; Liu, Yi

    2013-01-01

    5-Fluorouracil (5-FU) has been widely used as a chemotherapy agent in the treatment of many types of solid tumors. Investigation of its antimetabolites led to the development of an entire class of fluorinated pyrimidines. However, the toxicity profile associated with 5-FU is significant and includes diarrhea, mucositis, hand-foot syndrome and myelosuppression. In aiming at reducing of the side effects of 5-FU, we have designed and synthesized delocalized lipophilic cations (DLCs) as a vehicle for the delivery of 5-FU. DLCs accumulate selectively in the mitochondria of cancer cells because of the high mitochondrial transmembrane potential (ΔΨm). Many DLCs exhibited anti-cancer efficacy and were explored as potential anti-cancer drugs based on their selective accumulation in the mitochondria of cancer cells. F16, the DLC we used as a vehicle, is a small molecule that selectively inhibits tumor cell growth and dissipates mitochondrial membrane potential. The binding of the conjugate F16-5-FU to bovine serum albumin (BSA) was investigated using spectroscopic and molecular modeling approaches. Fluorescence quenching constants were determined using the Stern-Volmer equation to provide a measure of the binding affinity between F16-5-FU and BSA. The activation energy of the interaction between F16-5-FU and BSA was calculated and the unusually high value was discussed in terms of the special structural block indicated by the molecular modeling approach. Molecular modeling showed that F16-5-FU binds to human serum albumin in site II, which is consistent with the results of site-competitive replacement experiments. It is suggested that hydrophobic and polar forces played important roles in the binding reaction, in accordance with the results of thermodynamic experiments.

  16. How to Predict Molecular Interactions between Species?

    PubMed Central

    Schulze, Sylvie; Schleicher, Jana; Guthke, Reinhard; Linde, Jörg

    2016-01-01

    Organisms constantly interact with other species through physical contact which leads to changes on the molecular level, for example the transcriptome. These changes can be monitored for all genes, with the help of high-throughput experiments such as RNA-seq or microarrays. The adaptation of the gene expression to environmental changes within cells is mediated through complex gene regulatory networks. Often, our knowledge of these networks is incomplete. Network inference predicts gene regulatory interactions based on transcriptome data. An emerging application of high-throughput transcriptome studies are dual transcriptomics experiments. Here, the transcriptome of two or more interacting species is measured simultaneously. Based on a dual RNA-seq data set of murine dendritic cells infected with the fungal pathogen Candida albicans, the software tool NetGenerator was applied to predict an inter-species gene regulatory network. To promote further investigations of molecular inter-species interactions, we recently discussed dual RNA-seq experiments for host-pathogen interactions and extended the applied tool NetGenerator (Schulze et al., 2015). The updated version of NetGenerator makes use of measurement variances in the algorithmic procedure and accepts gene expression time series data with missing values. Additionally, we tested multiple modeling scenarios regarding the stimuli functions of the gene regulatory network. Here, we summarize the work by Schulze et al. (2015) and put it into a broader context. We review various studies making use of the dual transcriptomics approach to investigate the molecular basis of interacting species. Besides the application to host-pathogen interactions, dual transcriptomics data are also utilized to study mutualistic and commensalistic interactions. Furthermore, we give a short introduction into additional approaches for the prediction of gene regulatory networks and discuss their application to dual transcriptomics data. We

  17. Terahertz Technology and Molecular Interactions

    DTIC Science & Technology

    2010-12-16

    fingerprint, as the concentration of the target gas is increased from zero at some concentration the identification statistics rapidly change from ran...REPORT THz Technology and Molecular Interactions 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The purpose of this project was to explore opportunities...development of compact solid state point sensors for chemical identification with ‘absolute’ specificity, (2) studies of the phenomenology that underlies

  18. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    PubMed

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  19. Molecular interactions between desmosomal cadherins.

    PubMed Central

    Syed, Shabih-e-Hassnain; Trinnaman, Brian; Martin, Stephen; Major, Sarah; Hutchinson, Jon; Magee, Anthony I

    2002-01-01

    Desmocollins (Dscs) and desmogleins (Dsgs) are cell-adhesion molecules involved in the formation of desmosome cell-cell junctions and share structural similarities to classical cadherins such as E-cadherin. In order to identify and provide quantitative information on the types of protein-protein interactions displayed by the type 2 isoforms and investigate the role of Ca(2+) in this process, we have developed an Escherichia coli expression system to generate recombinant proteins containing the first two extracellular domains, namely Dsg2(1-2) and Dsc2(1-2). Analytical ultracentrifugation, chemical cross-linking, CD, fluorescence and BIAcore have been used to provide the first direct evidence of Ca(2+) binding to desmosomal cadherins. These studies suggest that Dsc2(1-2) not only exhibits homophilic interactions in solution, but can also form heterophilic interactions with Dsg2(1-2). The latter, on the other hand, shows much weaker homophilic association. Our results further demonstrate that heterophilic interactions are Ca(2+)-dependent, whereas the Ca(2+)-dependence of homophilic association is less clear. Our data indicate that the functional properties of Dsc2(1-2) are more similar to those of classical cadherins, consistent with the observation that Dsc shares a higher level of sequence homology with classical cadherins than does Dsg. In addition to corroborating the conclusions of previously reported transfection studies which suggest the formation of lateral heterodimers and homodimers, our results also provide direct quantitative information on the strength of these interactions which are essential for understanding the adhesion mechanism. PMID:11853539

  20. Investigation of the Coupled Effects of Molecular Weight and Charge-Transfer Interactions on the Optical and Photochemical Properties of Dissolved Organic Matter.

    PubMed

    McKay, Garrett; Couch, Kylie D; Mezyk, Stephen P; Rosario-Ortiz, Fernando L

    2016-08-02

    We studied the formation of photochemically produced reactive intermediates (RI) from dissolved organic matter (DOM). Specifically, we focused on the effects of variable molecular weight and chemical reduction on the optical properties of DOM (absorbance and fluorescence) and the formation of singlet oxygen ((1)O2), DOM triplet excited states ((3)DOM*), and the hydroxyl radical ((•)OH). The data are largely evaluated in terms of a charge-transfer (CT) model, but deficiencies in the model to explain the data are pointed out when evident. A total of two sets of samples were studied that were subjected to different treatments; the first set included secondary-treated wastewaters and a wastewater-impacted stream, and the second was a DOM isolate. Treatments included size fractionation and chemical reduction using sodium borohydride. Taken as a whole, the results demonstrate that decreasing molecular weight and borohydride reduction work in opposition regarding quantum efficiencies for (1)O2 and (3)DOM* production but in concert for fluorescence and (•)OH production. The optical and photochemical data provide evidence for a limited role of CT interactions occurring in lower-molecular-weight DOM molecules. In addition, the data suggest that the observed optical and photochemical properties of DOM are a result of multiple populations of chromophores and that their relative contribution is changed by molecular-weight fractionation and borohydride reduction.

  1. Interaction of vitamin B1 with bovine serum albumin investigation using vitamin B1-selective electrode: potentiometric and molecular modeling study.

    PubMed

    Hosseinzadeh, Reza; Khorsandi, Khatereh

    2016-09-01

    Vitamin B1 or thiamin is one of the B vitamins. All B vitamins help the body to convert food (carbohydrates) into fuel (glucose), which produces energy. The B vitamins are necessary for healthy skin, eyes, hair, and liver. It also could help the nervous system function properly, and is necessary for brain functions. Drug interactions with protein can affect the distribution of the drug and eliminate the drug in living systems. In this study, the binding of thiamine hydrochloride (vitamin B1) to bovine serum albumin (BSA) was evaluated using a new proposed vitamin B1 (thiamine)-selective membrane electrode under various experimental conditions, such as pH, ionic strength, and protein concentration; in addition molecular modeling was applied as well. The binding isotherms plotted based on potentiometric data and analyzed using the Wyman binding potential concept. The apparent binding constant was determined and used for the calculation of intrinsic Gibbs free energy of binding. According to the electrochemical and molecular docking results, it can be concluded that the hydrophobic interactions and hydrogen binding are major interactions between BSA and vitamin B1.

  2. Investigation into the interaction of losartan with human serum albumin and glycated human serum albumin by spectroscopic and molecular dynamics simulation techniques: A comparison study.

    PubMed

    Moeinpour, Farid; Mohseni-Shahri, Fatemeh S; Malaekeh-Nikouei, Bizhan; Nassirli, Hooriyeh

    2016-09-25

    The interaction between losartan and human serum albumin (HSA), as well as its glycated form (gHSA) was studied by multiple spectroscopic techniques and molecular dynamics simulation under physiological conditions. The binding information, including the binding constants, effective quenching constant and number of binding sites showed that the binding partiality of losartan to HSA was higher than to gHSA. The findings of three-dimensional fluorescence spectra demonstrated that the binding of losartan to HSA and gHSA would alter the protein conformation. The distances between Trp residue and the binding sites of the drug were evaluated on the basis of the Förster theory, and it was indicated that non-radiative energy transfer from HSA and gHSA to the losartan happened with a high possibility. According to molecular dynamics simulation, the protein secondary and tertiary structure changes were compared in HSA and gHSA for clarifying the obtained results.

  3. Spin–orbit interaction mediated molecular dissociation

    SciTech Connect

    Kokkonen, E. Jänkälä, K.; Kettunen, J. A.; Heinäsmäki, S.; Karpenko, A.; Huttula, M.; Löytynoja, T.

    2014-05-14

    The effect of the spin–orbit interaction to photofragmentation is investigated in the mercury(II) bromide (HgBr{sub 2}) molecule. Changes in the fragmentation between the two spin–orbit components of Hg 5d photoionization, as well as within the molecular-field-splitted levels of these components are observed. Dissociation subsequent to photoionization is studied with synchrotron radiation and photoelectron-photoion coincidence spectroscopy. The experimental results are accompanied by relativistic ab initio analysis of the photoelectron spectrum.

  4. Molecular gas in interacting galaxies

    NASA Astrophysics Data System (ADS)

    Zhu, Ming

    2001-10-01

    A systematic study of the molecular gas properties in strongly interacting galaxies (SIGs) has been undertaken, which includes two parts: (1)a statistical study of a large, optically-selected, complete sample of SIGs; (2)a case study of the nearest colliding pair NGC 4038/9 (``the Antennae'') with multi-transition data of both 12CO and 13CO. Consisting of 126 galaxies in 92 systems, our complete sample of SIGs includes all the SIGs in the northern sky with optical magnitude BT < 14.5. CO data have been collected for 95 SIGs (59 of which were observed by us) as well as for comparison samples of 59 weakly interacting and 69 isolated spiral galaxies. The statistical analysis of the samples shows that the SIGs, especially the colliding and merging systems, have a higher CO luminosity than isolated spiral galaxies. However, there is no significant difference in the atomic gas contents between the samples. This indicates that the excess CO emission is not due to the conversion of atomic gas to molecular gas, but may be more plausibly accounted for by a lower CO-to- H2 conversion factor X. For the Antennae galaxies, we have obtained high quality, fully sampled, single dish maps at 12CO J = 1-0 and 32 transitions with an angular resolution of 15' (1.5 kpc), together with 12CO J = 2-1, 13CO J = 2-1 and 3-2 data at selected regions with similar resolutions. Our Nobeyama 45m map recovers twice as much 12CO J = 1-0 flux as was reported by Wilson et al. (2000). The 12CO J = 1-0, 2-1 and 3-2 emission all peak in an off-nucleus region adjacent to where the two disks overlap. The 12CO/13 CO J = 2-1 and 3-2 integrated intensity ratios are remarkably high in the overlap region. Detailed LVG modeling indicates that the 12 CO and 13CO emission come from different spatial components. The 12CO emission originates from a nonvirialized low density gas component with a large velocity gradient. Such a large velocity gradient can produce ``over luminous'' CO emission, and the derived X

  5. Molecular mechanisms of membrane interaction at implantation.

    PubMed

    Davidson, Lien M; Coward, Kevin

    2016-03-01

    Successful pregnancy is dependent upon the implantation of a competent embryo into a receptive endometrium. Despite major advancement in our understanding of reproductive medicine over the last few decades, implantation failure still occurs in both normal pregnancies and those created artificially by assisted reproductive technology (ART). Consequently, there is significant interest in elucidating the etiology of implantation failure. The complex multistep process of implantation begins when the developing embryo first makes contact with the plasma membrane of epithelial cells within the uterine environment. However, although this biological interaction marks the beginning of a fundamental developmental process, our knowledge of the intricate physiological and molecular processes involved remains sparse. In this synopsis, we aim to provide an overview of our current understanding of the morphological changes which occur to the plasma membrane of the uterine endothelium, and the molecular mechanisms that control communication between the early embryo and the endometrium during implantation. A multitude of molecular factors have been implicated in this complex process, including endometrial integrins, extracellular matrix molecules, adhesion molecules, growth factors, and ion channels. We also explore the development of in vitro models for embryo implantation to help researchers investigate mechanisms which may underlie implantation failure. Understanding the precise molecular pathways associated with implantation failure could help us to generate new prognostic/diagnostic biomarkers, and may identify novel therapeutic targets.

  6. Molecular Handshake: Recognition through Weak Noncovalent Interactions

    ERIC Educational Resources Information Center

    Murthy, Parvathi S.

    2006-01-01

    The weak noncovalent interactions between substances, the handshake in the form of electrostatic interactions, van der Waals' interactions or hydrogen bonding is universal to all living and nonliving matter. They significantly influence the molecular and bulk properties and behavior of matter. Their transient nature affects chemical reactions and…

  7. Theoretical studies of molecular interactions

    SciTech Connect

    Lester, W.A. Jr.

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  8. Theoretical Analysis of Dynamic Processes for Interacting Molecular Motors.

    PubMed

    Teimouri, Hamid; Kolomeisky, Anatoly B; Mehrabiani, Kareem

    2015-02-13

    Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by analyzing a new class of totally asymmetric exclusion processes where interactions are accounted for in a thermodynamically consistent fashion. It allows us to connect explicitly microscopic features of motor proteins with their collective dynamic properties. Theoretical analysis that combines various mean-field calculations and computer simulations suggests that dynamic properties of molecular motors strongly depend on interactions, and correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motors transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  9. Theoretical analysis of dynamic processes for interacting molecular motors

    NASA Astrophysics Data System (ADS)

    Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem

    2015-02-01

    Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.

  10. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    SciTech Connect

    Sebbari, Karim; Roques, Jerome; Simoni, Eric; Domain, Christophe

    2012-10-28

    The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  11. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    NASA Astrophysics Data System (ADS)

    Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric

    2012-10-01

    The behavior of the UO22+ uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d_{U{-O}_{adsorption}}= 2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  12. Understanding polycaroboxylate interactions with counterions: A molecular modeling approach

    SciTech Connect

    Fitzwater, S.; Freeman, M.B.

    1993-12-31

    Low molecular weight polycarboyxlates, such as poly(acrylic acid), have utility as dispersants in a variety of commercial applications including home laundry detergents, mineral processing and water treatment. In general, counterions (Ca, Mg, Fe, etc.) are unavoidable in these applications and often dictate the polymer composition and molecular weight necessary for successful performance. The authors have been investigating the interaction of polycarboxylates with counterions in order to better understand how that interaction impacts on the dispersant properties of a polymer. Using computer modeling, it can be seen how molecular geometry, molecular dynamics, and the shape/polarity of the molecular surface are affected by counterion binding and polymer composition. The authors can then combine information from the modeling with experimental information and literature concepts to provide a direction toward the synthesis of improved low molecular weight polycarboxylate dispersants.

  13. Interactive association between biopolymers and biofunctions in carinata seeds as energy feedstock and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation: current advanced molecular spectroscopic investigations.

    PubMed

    Yu, Peiqiang; Xin, Hangshu; Ban, Yajing; Zhang, Xuewei

    2014-05-07

    Recent advances in biofuel and bio-oil processing technology require huge supplies of energy feedstocks for processing. Very recently, new carinata seeds have been developed as energy feedstocks for biofuel and bio-oil production. The processing results in a large amount of coproducts, which are carinata meal. To date, there is no systematic study on interactive association between biopolymers and biofunctions in carinata seed as energy feedstocks for biofuel and bioethanol processing and their processing coproducts (carinata meal). Molecular spectroscopy with synchrotron and globar sources is a rapid and noninvasive analytical technique and is able to investigate molecular structure conformation in relation to biopolymer functions and bioavailability. However, to date, these techniques are seldom used in biofuel and bioethanol processing in other research laboratories. This paper aims to provide research progress and updates with molecular spectroscopy on the energy feedstock (carinata seed) and coproducts (carinata meal) from biofuel and bioethanol processing and show how to use these molecular techniques to study the interactive association between biopolymers and biofunctions in the energy feedstocks and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation.

  14. Modelling refractive index changes due to molecular interactions

    NASA Astrophysics Data System (ADS)

    Varma, Manoj

    2016-03-01

    There are a large number of sensing techniques which use optical changes to monitor interactions between molecules. In the absence of fluorophores or other labels, the basic signal transduction mechanism relies on refractive index changes arising from the interactions of the molecules involved. A quantitative model incorporating molecular transport, reaction kinetics and optical mixing is presented which reveals important insights concerning the optimal detection of molecular interactions optically. Although conceptually simple, a comprehensive model such as this has not been reported anywhere. Specifically, we investigate the pros and cons of detecting molecular interactions in free solution relative to detecting molecular interactions on surfaces using surface bound receptor molecules such as antibodies. The model reveals that the refractive index change produced in surface based sensors is 2-3 orders of magnitude higher than that from interactions in free solution. On the other hand, the model also reveals that it is indeed possible to distinguish specific molecular interactions from non-specific ones based on free-solution bulk refractometry without any washing step necessary in surface based sensors. However, the refractive index change for free solution interactions predicted by the model is smaller than 10-7 RIU, even for large proteins such as IgG in sufficiently high concentrations. This value is smaller than the typical 10-6 RIU detection limit of most state of the art optical sensing techniques therefore requiring techniques with substantially higher index sensitivity such as Back Scattering Interferometry.

  15. Analysis of molecular interactions in solid dosage forms; challenge to molecular pharmaceutics.

    PubMed

    Yamamoto, Keiji; Limwikrant, Waree; Moribe, Kunikazu

    2011-01-01

    The molecular states of active pharmaceutical ingredients (APIs) in pharmaceutical dosage forms strongly affect the properties and quality of a drug. Various important fundamental physicochemical studies were reviewed from the standpoint of molecular pharmaceutics. Mechanochemical effects were evaluated in mixtures of APIs and pharmaceutical additives. Amorphization, complex formation and nanoparticle formation are observed after grinding process depending on the combination of APIs and pharmaceutical additives. Sealed-heating method and mesoporous materials have been used to investigate drug molecular interactions in dosage forms. Molecular states have been investigated using powder X-ray diffraction, thermal analysis, IR, solid state fluorometry, and NMR.

  16. Microbial interactions: ecology in a molecular perspective.

    PubMed

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community.

  17. Predicting polymer nanofiber interactions via molecular simulations.

    PubMed

    Buell, Sezen; Rutledge, Gregory C; Vliet, Krystyn J Van

    2010-04-01

    Physical and functional properties of nonwoven textiles and other fiberlike materials depend strongly on the number and type of fiber-fiber interactions. For nanoscale polymeric fibers in particular, these interactions are governed by the surfaces of and contacts between fibers. We employ both molecular dynamics (MD) simulations at a temperature below the glass transition temperature T(g) of the polymer bulk, and molecular statics (MS), or energy minimization, to study the interfiber interactions between prototypical polymeric fibers of 4.6 nm diameter, comprising multiple macromolecular chains each of 100 carbon atoms per chain (C100). Our MD simulations show that fibers aligned parallel and within 9 nm of one another experience a significant force of attraction. These fibers tend toward coalescence on a very short time scale, even below T(g). In contrast, our MS calculations suggest an interfiber interaction that transitions from an attractive to a repulsive force at a separation distance of 6 nm. The results of either approach can be used to obtain a quantitative, closed-form relation describing fiber-fiber interaction energies U(s). However, the predicted form of interaction is quite different for the two approaches, and can be understood in terms of differences in the extent of molecular mobility within and between fibers for these different modeling perspectives. The results of these molecular-scale calculations of U(s) are used to interpret experimental observations for electrospun polymer nanofiber mats. These findings highlight the role of temperature and kinetically accessible molecular configurations in predicting interface-dominated interactions at polymer fiber surfaces, and prompt further experiments and simulations to confirm these effects in the properties of nonwoven mats comprising such nanoscale fibers.

  18. Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles.

    PubMed

    Ebrahimi, Malihe; Khayamian, Taghi; Hadadzadeh, Hassan; Sayed Tabatabaei, Badraldin Ebrahim; Jannesari, Zahra; Khaksar, Ghazale

    2015-01-01

    The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)3-3' (HTG21) was investigated using spectroscopic methods, molecular modeling, and polymerase chain reaction (PCR) assays. The spectroscopic methods of UV-vis, fluorescence, and circular dichroism showed that the metal complex can effectively induce and stabilize G-quadruplex structure in the G-rich 21-mer sequence. Also, the binding constant between the Fe(III) complex and G-quadruplex was measured by these methods and it was found to be 4.53(±0.30) × 10(5) M(-1)). The PCR stop assay indicated that the Fe(III) complex inhibits DNA amplification. The cell viability assay showed that the complex has significant antitumor activities against Hela cells. According to the UV-vis results, the interaction of the Fe(III) complex with duplex DNA is an order of magnitude lower than G-quadruplex. Furthermore, the release of the complex incorporated in bovine serum albumin nanoparticles was also investigated in physiological conditions. The release of the complex followed a bi-phasic release pattern with high and low releasing rates at the first and second phases, respectively. Also, in order to obtain the binding mode of the Fe(III) complex with G-quadruplex, molecular modeling was performed. The molecular docking results showed that the Fe(III) complex was docked to the end-stacked of the G-quadruplex with a π-π interaction, created between the meloxicam ligand and the guanine bases of the G-quadruplex.

  19. Molecular interactions investigated with DFT calculations of QTAIM and NBO analyses: An application to dimeric structures of rice α-amylase/subtilisin inhibitor

    NASA Astrophysics Data System (ADS)

    Astani, Elahe K.; Hadipour, Nasser L.; Chen, Chun-Jung

    2017-03-01

    Characterization of the dimer interactions at the dimeric interface of the crystal structure of rice α-amylase/subtilisin inhibitor (RASI) were performed using the quantum theory of atoms in molecules (QTAIM) and natural bonding orbital (NBO) analyses at the density-functional theory (DFT) level. The results revealed that Gly27 and Arg151 of chain A are the main residues involved in hydrogen bonds, dipole-dipole, and charge-dipole interactions with Gly64, Ala66, Ala67 and Arg81 of chain B at the dimeric interface. Calcium ion of chain A plays the significant role in the stability of the dimeric structure through a strong charge-charge interaction with Ala66.

  20. Interactive investigations into planetary interiors

    NASA Astrophysics Data System (ADS)

    Rose, I.

    2015-12-01

    Many processes in Earth science are difficult to observe or visualize due to the large timescales and lengthscales over which they operate. The dynamics of planetary mantles are particularly challenging as we cannot even look at the rocks involved. As a result, much teaching material on mantle dynamics relies on static images and cartoons, many of which are decades old. Recent improvements in computing power and technology (largely driven by game and web development) have allowed for advances in real-time physics simulations and visualizations, but these have been slow to affect Earth science education.Here I demonstrate a teaching tool for mantle convection and seismology which solves the equations for conservation of mass, momentum, and energy in real time, allowing users make changes to the simulation and immediately see the effects. The user can ask and answer questions about what happens when they add heat in one place, or take it away from another place, or increase the temperature at the base of the mantle. They can also pause the simulation, and while it is paused, create and visualize seismic waves traveling through the mantle. These allow for investigations into and discussions about plate tectonics, earthquakes, hot spot volcanism, and planetary cooling.The simulation is rendered to the screen using OpenGL, and is cross-platform. It can be run as a native application for maximum performance, but it can also be embedded in a web browser for easy deployment and portability.

  1. Teaching Noncovalent Interactions Using Protein Molecular Evolution

    ERIC Educational Resources Information Center

    Fornasari, Maria Silvina; Parisi, Gustavo; Echave, Julian

    2008-01-01

    Noncovalent interactions and physicochemical properties of amino acids are important topics in biochemistry courses. Here, we present a computational laboratory where the capacity of each of the 20 amino acids to maintain different noncovalent interactions are used to investigate the stabilizing forces in a set of proteins coming from organisms…

  2. Molecular interactions of graphene oxide with human blood plasma proteins

    NASA Astrophysics Data System (ADS)

    Kenry, Affa Affb Affc; Loh, Kian Ping; Lim, Chwee Teck

    2016-04-01

    We investigate the molecular interactions between graphene oxide (GO) and human blood plasma proteins. To gain an insight into the bio-physico-chemical activity of GO in biological and biomedical applications, we performed a series of biophysical assays to quantify the molecular interactions between GO with different lateral size distributions and the three essential human blood plasma proteins. We elucidate the various aspects of the GO-protein interactions, particularly, the adsorption, binding kinetics and equilibrium, and conformational stability, through determination of quantitative parameters, such as GO-protein association constants, binding cooperativity, and the binding-driven protein structural changes. We demonstrate that the molecular interactions between GO and plasma proteins are significantly dependent on the lateral size distribution and mean lateral sizes of the GO nanosheets and their subtle variations may markedly influence the GO-protein interactions. Consequently, we propose the existence of size-dependent molecular interactions between GO nanosheets and plasma proteins, and importantly, the presence of specific critical mean lateral sizes of GO nanosheets in achieving very high association and fluorescence quenching efficiency of the plasma proteins. We anticipate that this work will provide a basis for the design of graphene-based and other related nanomaterials for a plethora of biological and biomedical applications.

  3. Molecular Mediators Governing Iron-Copper Interactions

    PubMed Central

    Gulec, Sukru; Collins, James F.

    2015-01-01

    Given their similar physiochemical properties, it is a logical postulate that iron and copper metabolism are intertwined. Indeed, iron-copper interactions were first documented over a century ago, but the homeostatic effects of one on the other has not been elucidated at a molecular level to date. Recent experimental work has, however, begun to provide mechanistic insight into how copper influences iron metabolism. During iron deficiency, elevated copper levels are observed in the intestinal mucosa, liver, and blood. Copper accumulation and/or redistribution within enterocytes may influence iron transport, and high hepatic copper may enhance biosynthesis of a circulating ferroxidase, which potentiates iron release from stores. Moreover, emerging evidence has documented direct effects of copper on the expression and activity of the iron-regulatory hormone hepcidin. This review summarizes current experimental work in this field, with a focus on molecular aspects of iron-copper interplay and how these interactions relate to various disease states. PMID:24995690

  4. Green tea catechins in chemoprevention of cancer: a molecular docking investigation into their interaction with glutathione S-transferase (GST P1-1).

    PubMed

    Artali, Roberto; Beretta, Giangiacomo; Morazzoni, Paolo; Bombardelli, Ezio; Meneghetti, Fiorella

    2009-02-01

    The anti- and pro-oxidant effects of green tea catechins have been implicated in the alterations of cellular functions determining their chemoprotective and therapeutic potentials in toxicity and diseases. The glutathione S-transferases (GSTs; EC 2.5.1.18) family is a widely distributed phase-II detoxifying enzymes and the GST P1-1 isoenzyme has been shown to catalyze the conjugation of GSH with some alkylating anti-cancer agents, suggesting that over-expression of GST P1-1 would result in tumor cell resistance. Here we report the docking study of four green tea catechins and four alkylating anticancer drugs into the GST P1-1 model, as GSTs were found to be affected by tea catechins. The EGCG ligands exhibit higher docking potential with respect to the anticancer agents, with a ligand-receptor interaction pattern indicating an high conformational stability. Consequently, the competition mechanisms favourable for the green tea catechins could lead to enzyme(s) desensitisation with a reduction of the alkylating drugs metabolism. The results provide a useful theoretical contribution in understanding the biochemical mechanisms implicated in the chemotherapeutic use of green tea catechins in oxidative stress-related diseases.

  5. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  6. Interacting molecular motors: Efficiency and work fluctuations

    NASA Astrophysics Data System (ADS)

    Slanina, František

    2009-12-01

    We investigate the model of “reversible ratchet” with interacting particles, presented by us earlier [F. Slanina, EPL 84, 50009 (2008)]. We further clarify the effect of efficiency enhancement due to interaction and show that it is of energetic origin, rather than a consequence of reduced fluctuations. We also show complicated structures emerging in the interaction and density dependence of the current and response function. The fluctuation properties of the work and input energy indicate in detail the far-from-equilibrium nature of the dynamics.

  7. Molecular interactions of flavonoids to pepsin: Insights from spectroscopic and molecular docking studies.

    PubMed

    Zeng, Hua-Jin; Yang, Ran; Liang, Huili; Qu, Ling-Bo

    2015-01-01

    In the work described on this paper, the inhibitory effect of 10 flavonoids on pepsin and the interactions between them were investigated by a combination of spectroscopic and molecular docking methods. The results indicated that all flavonoids could bind with pepsin to form flavonoid-pepsin complexes. The binding parameters obtained from the data at different temperatures revealed that flavonoids could spontaneously interact with pepsin mainly through electrostatic forces and hydrophobic interactions with one binding site. According to synchronous and three-dimensional fluorescence spectra and molecular docking results, all flavonoids bound directly into the enzyme cavity site and the binding influenced the microenvironment and conformation of the pepsin activity site which resulted in the reduced enzyme activity. The present study provides direct evidence at a molecular level to understand the mechanism of digestion caused by flavonoids.

  8. Molecular interaction studies using microscale thermophoresis.

    PubMed

    Jerabek-Willemsen, Moran; Wienken, Chistoph J; Braun, Dieter; Baaske, Philipp; Duhr, Stefan

    2011-08-01

    Abstract The use of infrared laser sources for creation of localized temperature fields has opened new possibilities for basic research and drug discovery. A recently developed technology, Microscale Thermophoresis (MST), uses this temperature field to perform biomolecular interaction studies. Thermophoresis, the motion of molecules in temperature fields, is very sensitive to changes in size, charge, and solvation shell of a molecule and thus suited for bioanalytics. This review focuses on the theoretical background of MST and gives a detailed overview on various applications to demonstrate the broad applicability. Experiments range from the quantification of the affinity of low-molecular-weight binders using fluorescently labeled proteins, to interactions between macromolecules and multi-component complexes like receptor containing liposomes. Information regarding experiment and experimental setup is based on the Monolith NT.115 instrument (NanoTemper Technologies GmbH).

  9. 2010 Atomic & Molecular Interactions Gordon Research Conference

    SciTech Connect

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  10. A prototype molecular interactive collaborative environment (MICE).

    PubMed

    Bourne, P; Gribskov, M; Johnson, G; Moreland, J; Wavra, S; Weissig, H

    1998-01-01

    Illustrations of macromolecular structure in the scientific literature contain a high level of semantic content through which the authors convey, among other features, the biological function of that macromolecule. We refer to these illustrations as molecular scenes. Such scenes, if available electronically, are not readily accessible for further interactive interrogation. The basic PDB format does not retain features of the scene; formats like PostScript retain the scene but are not interactive; and the many formats used by individual graphics programs, while capable of reproducing the scene, are neither interchangeable nor can they be stored in a database and queried for features of the scene. MICE defines a Molecular Scene Description Language (MSDL) which allows scenes to be stored in a relational database (a molecular scene gallery) and queried. Scenes retrieved from the gallery are rendered in Virtual Reality Modeling Language (VRML) and currently displayed in WebView, a VRML browser modified to support the Virtual Reality Behavior System (VRBS) protocol. VRBS provides communication between multiple client browsers, each capable of manipulating the scene. This level of collaboration works well over standard Internet connections and holds promise for collaborative research at a distance and distance learning. Further, via VRBS, the VRML world can be used as a visual cue to trigger an application such as a remote MEME search. MICE is very much work in progress. Current work seeks to replace WebView with Netscape, Cosmoplayer, a standard VRML plug-in, and a Java-based console. The console consists of a generic kernel suitable for multiple collaborative applications and additional application-specific controls. Further details of the MICE project are available at http:/(/)mice.sdsc.edu.

  11. Molecular modelling of protein-protein/protein-solvent interactions

    NASA Astrophysics Data System (ADS)

    Luchko, Tyler

    The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule

  12. Molecular dynamics simulations on the interactions of low molecular weight natural organic acids with C60.

    PubMed

    Sun, Qian; Xie, Hong-Bin; Chen, Jingwen; Li, Xuehua; Wang, Zhuang; Sheng, Lianxi

    2013-07-01

    As an important part of dissolved organic matter (DOM), low molecular weight organic acids (LOAs) may play a key role in the process for DOM stabilizing carbon nanomaterials (e.g. C60) suspensions in aquatic environment. In addition, both LOAs and C60 have been detected in the troposphere and therefore have a chance to interact with each other in the gaseous phase. However, the mechanism for LOAs-C60 interactions and their environmental implications need further investigations. In this study, molecular dynamics (MD) simulation was employed to investigate the interactions between both neutral and ionic LOAs with C60 in vacuum and water. The results showed that the adsorptions of all LOAs on C60 in energy are favorable, and the aromatic acids have stronger interactions with C60 than the aliphatic acids in vacuum and water. The interaction energies (Eint) of the LOA anions with C60 were weaker than those of their corresponding neutral LOA molecules. The models were also developed to predict and interpret Eint based on the results from MD simulations. Dispersion, induction and hydrophobic interactions were found to be the dominating factor in Eint. These findings indicate that cost-efficient MD simulation can be employed as an important tool to predict the adsorption behavior of LOAs on carbon nanomaterials.

  13. Enlightening molecular mechanisms through study of protein interactions

    PubMed Central

    Rizo, Josep; Rosen, Michael K.; Gardner, Kevin H.

    2012-01-01

    The investigation of molecular mechanisms is a fascinating area of current biological research that unites efforts from scientists with very diverse expertise. This review provides a perspective on the characterization of protein interactions as a central aspect of this research. We discuss case studies on the neurotransmitter release machinery that illustrate a variety of principles and emphasize the power of combining nuclear magnetic resonance (NMR) spectroscopy with other biophysical techniques, particularly X-ray crystallography. These studies have shown that: (i) the soluble SNAP receptor (SNARE) proteins form a tight complex that brings the synaptic vesicle and plasma membranes together, which is key for membrane fusion; (ii) the SNARE syntaxin-1 adopts an autoinhibitory closed conformation; (iii) Munc18-1 plays crucial functions through interactions with closed syntaxin-1 and with the SNARE complex; (iv) Munc13s mediate the opening of syntaxin-1; (v) complexins play dual roles through distinct interactions with the SNARE complex; (vi) synaptotagmin-1 acts a Ca2+ sensor, interacting simultaneously with the membranes and the SNAREs; and (vii) a Munc13 homodimer to Munc13-RIM heterodimer switch modulates neurotransmitter release. Overall, this research underlines the complexities involved in elucidating molecular mechanisms and how these mechanisms can depend critically on an interplay between strong and weak protein interactions. PMID:22735643

  14. Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

    SciTech Connect

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J.; Killelea, Daniel R.

    2014-11-14

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas

  15. Molecular interactions with ice: molecular embedding, adsorption, detection, and release.

    PubMed

    Gibson, K D; Langlois, Grant G; Li, Wenxin; Killelea, Daniel R; Sibener, S J

    2014-11-14

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF4 molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF4 embedding probability is much less than for Xe. In addition, a larger molecule, SF6, did not embed at the same translational energies that both CF4 and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF4 > SF6. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF4. Tentatively, this order suggests that for Xe and CF4, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF6 molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas collection and release, and the chemical composition of

  16. Molecular Recognition and Specific Interactions for Biosensing Applications

    PubMed Central

    Kim, Dong Chung; Kang, Dae Joon

    2008-01-01

    Molecular recognition and specific interactions are reliable and versatile routes for site-specific and well-oriented immobilization of functional biomolecules on surfaces. The control of surface properties via the molecular recognition and specific interactions at the nanoscale is a key element for the nanofabrication of biosensors with high sensitivity and specificity. This review intends to provide a comprehensive understanding of the molecular recognition- and specific interaction-mediated biosensor fabrication routes that leads to biosensors with well-ordered and controlled structures on both nanopatterned surfaces and nanomaterials. Herein self-assembly of the biomolecules via the molecular recognition and specific interactions on nanoscaled surfaces as well as nanofabrication techniques of the biomolecules for biosensor architecture are discussed. We also describe the detection of molecular recognition- and specific interaction-mediated molecular binding as well as advantages of nanoscale detection. PMID:27873889

  17. Molecular Basis of Laminin-Integrin Interactions.

    PubMed

    Yamada, Masashi; Sekiguchi, Kiyotoshi

    2015-01-01

    Laminins are composed of three polypeptide chains, designated as α, β, and γ. The C-terminal region of laminin heterotrimers, containing coiled-coil regions, short tails, and laminin globular (LG) domains, is necessary and sufficient for binding to integrins, which are the major laminin receptor class. Laminin recognition by integrins critically requires the α chain LG domains and a glutamic acid residue of the γ chain at the third position from the C-terminus. Furthermore, the C-terminal region of the β chain contains a short amino acid sequence that modulates laminin affinity for integrins. Thus, all three of the laminin chains act cooperatively to facilitate integrin binding. Mammals possess 5 α (α1-5), 3 β (β1-3), and 3 γ (γ1-3) chains, combinations of which give rise to 16 distinct laminin isoforms. Each isoform is expressed in a tissue-specific and developmental stage-specific manner, exerting its functions through binding of integrins. In this review, we detail the current knowledge surrounding the molecular basis and physiological relevance of specific interactions between laminins and integrins, and describe the mechanisms underlying laminin action through integrins.

  18. Investigation of migrant-polymer interaction in pharmaceutical packaging material using the linear interaction energy algorithm.

    PubMed

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2014-10-01

    The interaction between drug products and polymeric packaging materials is an important topic in the pharmaceutical industry and often associated with high costs because of the required elaborative interaction studies. Therefore, a theoretical prediction of such interactions would be beneficial. Often, material parameters such as the octanol water partition coefficient are used to predict the partitioning of migrant molecules between a solvent and a polymeric packaging material. Here, we present the investigation of the partitioning of various migrant molecules between polymers and solvents using molecular dynamics simulations for the calculation of interaction energies. Our results show that the use of a model for the interaction between the migrant and the polymer at atomistic detail can yield significantly better results when predicting the polymer solvent partitioning than a model based on the octanol water partition coefficient.

  19. Molecular Indicators of Soil Humification and Interaction with Heavy Metals

    SciTech Connect

    Fan, Teresa W.-M.; Higashi, Richard M.; Cassel, Teresa; Green, Peter; Lane, Andrew N.

    2003-03-26

    For stabilization of heavy metals at contaminated sites, interaction of soil organic matter (SOM) with heavy metal ions is critically important for long-term sustainability, a factor that is poorly understood at the molecular level. Using 13C- and 15N-labeled soil humates (HS), we investigated the turnover of five organic amendments (celluose, wheat straw, pine shavings, chitin and bone meal) in relation to heavy metal ion leaching in soil column experiments. The labeled molecular substructures in HS were examined by multinuclear 2-D NMR and pyrolysis GC-MS while the element profile in the leachates was analyzed by ICP-MS. Preliminary analysis revealed that peptidic and polysaccharidic structures were highly enriched, which suggests their microbial origin. Cd(II) leaching was significantly attenuated with humification of lignocellulosic materials. Correlation of 13C and 15N turnovers of HS substructures to metal leaching is underway.

  20. Hepatitis A virus: host interactions, molecular epidemiology and evolution.

    PubMed

    Vaughan, Gilberto; Goncalves Rossi, Livia Maria; Forbi, Joseph C; de Paula, Vanessa S; Purdy, Michael A; Xia, Guoliang; Khudyakov, Yury E

    2014-01-01

    Infection with hepatitis A virus (HAV) is the commonest viral cause of liver disease and presents an important public health problem worldwide. Several unique HAV properties and molecular mechanisms of its interaction with host were recently discovered and should aid in clarifying the pathogenesis of hepatitis A. Genetic characterization of HAV strains have resulted in the identification of different genotypes and subtypes, which exhibit a characteristic worldwide distribution. Shifts in HAV endemicity occurring in different parts of the world, introduction of genetically diverse strains from geographically distant regions, genotype displacement observed in some countries and population expansion detected in the last decades of the 20th century using phylogenetic analysis are important factors contributing to the complex dynamics of HAV infections worldwide. Strong selection pressures, some of which, like usage of deoptimized codons, are unique to HAV, limit genetic variability of the virus. Analysis of subgenomic regions has been proven useful for outbreak investigations. However, sharing short sequences among epidemiologically unrelated strains indicates that specific identification of HAV strains for molecular surveillance can be achieved only using whole-genome sequences. Here, we present up-to-date information on the HAV molecular epidemiology and evolution, and highlight the most relevant features of the HAV-host interactions.

  1. Molecular Contamination Investigation Facility (MCIF) Capabilities

    NASA Technical Reports Server (NTRS)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  2. Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

    DTIC Science & Technology

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John...encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

  3. VISUALIZATION OF MOLECULAR INTERACTIONS BY FLUORESCENCE COMPLEMENTATION

    PubMed Central

    Kerppola, Tom K.

    2008-01-01

    The visualization of protein complexes in living cells enables validation of protein interactions in their normal environment and determination of their subcellular localization. The bimolecular fluorescence complementation (BiFC) assay has been used to visualize interactions among multiple proteins in many cell types and organisms. This assay is based on the association between two fluorescent-protein fragments when they are brought together by an interaction between proteins fused to the fragments. Modified forms of this assay have been used to visualize the competition between alternative interaction partners and the covalent modification of proteins by ubiquitin family peptides. PMID:16625152

  4. Detailed Investigations of Interactions between Ionizing Radiation and Neutral Gases

    SciTech Connect

    Landers, Allen L

    2014-03-31

    We are investigating phenomena that stem from the many body dynamics associated with ionization of an atom or molecule by photon or charged particle. Our program is funded through the Department of Energy EPSCoR Laboratory Partnership Award in collaboration with Lawrence Berkeley National Laboratory. We are using variations on the well established COLTRIMS technique to measure ions and electrons ejected during these interactions. Photoionization measurements take place at the Advanced Light Source at LBNL as part of the ALS-COLTRIMS collaboration with the groups of Reinhard Dörner at Frankfurt and Ali Belkacem at LBNL. Additional experiments on charged particle impact are conducted locally at Auburn University where we are studying the dissociative molecular dynamics following interactions with either ions or electrons over a velocity range of 1 to 12 atomic units.

  5. Complex molecular assemblies at hand via interactive simulations.

    PubMed

    Delalande, Olivier; Férey, Nicolas; Grasseau, Gilles; Baaden, Marc

    2009-11-30

    Studying complex molecular assemblies interactively is becoming an increasingly appealing approach to molecular modeling. Here we focus on interactive molecular dynamics (IMD) as a textbook example for interactive simulation methods. Such simulations can be useful in exploring and generating hypotheses about the structural and mechanical aspects of biomolecular interactions. For the first time, we carry out low-resolution coarse-grain IMD simulations. Such simplified modeling methods currently appear to be more suitable for interactive experiments and represent a well-balanced compromise between an important gain in computational speed versus a moderate loss in modeling accuracy compared to higher resolution all-atom simulations. This is particularly useful for initial exploration and hypothesis development for rare molecular interaction events. We evaluate which applications are currently feasible using molecular assemblies from 1900 to over 300,000 particles. Three biochemical systems are discussed: the guanylate kinase (GK) enzyme, the outer membrane protease T and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors complex involved in membrane fusion. We induce large conformational changes, carry out interactive docking experiments, probe lipid-protein interactions and are able to sense the mechanical properties of a molecular model. Furthermore, such interactive simulations facilitate exploration of modeling parameters for method improvement. For the purpose of these simulations, we have developed a freely available software library called MDDriver. It uses the IMD protocol from NAMD and facilitates the implementation and application of interactive simulations. With MDDriver it becomes very easy to render any particle-based molecular simulation engine interactive. Here we use its implementation in the Gromacs software as an example.

  6. STALK : an interactive virtual molecular docking system.

    SciTech Connect

    Levine, D.; Facello, M.; Hallstrom, P.; Reeder, G.; Walenz, B.; Stevens, F.; Univ. of Illinois

    1997-04-01

    Several recent technologies-genetic algorithms, parallel and distributed computing, virtual reality, and high-speed networking-underlie a new approach to the computational study of how biomolecules interact or 'dock' together. With the Stalk system, a user in a virtual reality environment can interact with a genetic algorithm running on a parallel computer to help in the search for likely geometric configurations.

  7. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    NASA Technical Reports Server (NTRS)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  8. Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

    NASA Astrophysics Data System (ADS)

    Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

    2013-11-01

    Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

  9. Characteristics of Quasi-Molecular State Interaction

    SciTech Connect

    Devdariani, A.; Dalimier, E.; Kereselidze, T.; Noselidze, I.; Rebentrost, F.; Sauvan, P.

    2008-10-22

    The quasi-molecular dipole transition moments have been considered analytically within the framework of the two-state approximation with particular emphasis on their roots (zeros) on spectral manifestations of the roots in the adiabatic diabatic limits. The interrelation between the spectral features the non-adiabatic transitions found in [1] has been demonstrated for excited state charge exchange Al{sup +12}(n = 4)+C{sup +6}{yields}Al{sup +13}+C{sup +5}(n = 2)

  10. Use of potentiometric sensors to study (bio)molecular interactions.

    PubMed

    De Wael, K; Daems, D; Van Camp, G; Nagels, L J

    2012-06-05

    Potentiometric sensors were used to study molecular interactions in liquid environments with sensorgram methodology. This is demonstrated with a lipophilic rubber-based and a collagen-based hydrogel sensor coating. The investigated molecules were promazine and tartaric acid, respectively. The sensors were placed in a hydrodynamic wall-jet system for the recording of sensorgrams. Millivolt sensor responses were first converted to a signal, expressing the concentration of adsorbed organic ions. Using a linearization method, a pseudo-first order-kinetic model of adsorption was shown to fit the experimental results perfectly. K(assoc), k(on), and k(off) values were calculated. The technique can be used over 4 decades of concentration, and it is very sensitive to low-MW compounds as well as to multiply charged large biomolecules. This study is the first to demonstrate the application of potentiometric sensors as an alternative and complement to surface plasmon resonance methods.

  11. Molecular dynamics study on hydrocarbon interaction with plasma facing walls

    NASA Astrophysics Data System (ADS)

    Ohya, K.; Inai, K.; Kikuhara, Y.; Mohara, N.; Ito, A.; Nakamura, H.; Tanabe, T.

    2011-10-01

    A molecular dynamics (MD) simulation was undertaken to investigate hydrocarbon interactions with fusion related W and C surfaces. W-C mixed and hydrogenated amorphous C layers on the surface were prepared by collisions of C and H atoms at different impact energies on a W crystalline cell. The reflection coefficient for CH y and C 2H y and the distribution of the reflected species were calculated and we determined their dependence on energy and angle. The mixing of W with C reduces the reflection coefficient where C atoms dominate the distribution at energies of 30 eV or more, and this is similar to non-doped W. The amorphization of graphite strongly decreases the reflection coefficient where the emission of small hydrocarbons is suppressed but hydrogen uptake in the amorphous C increases it slightly. The amount of injected hydrogen per hydrocarbon impact on different material surfaces is discussed in relation to the fuel retention of plasma facing walls.

  12. DockingShop: A Tool for Interactive Molecular Docking

    SciTech Connect

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  13. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    NASA Astrophysics Data System (ADS)

    Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

    2015-02-01

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  14. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  15. Molecular Articulation in Response to Interactive Atomic Forces in Docker

    DTIC Science & Technology

    1996-12-01

    MOLECULAR ARTICULATION IN RESPONSE TO INTERACTIVE ATOMIC FORCES IN DOCKER THESIS Todd R. Kellett, Captain, USAF < AFIT/GCS/ENG/96D- 15 IDb~tzkac Unkg...ARTICULATION IN RESPONSE TO INTERACTIVE ATOMIC FORCES IN DOCKER THESIS Todd R. Kellett, Captain, USAF AFIT/GCS/ENG/96D- 15 Approved for public...INTERACTIVE ATOMIC FORCES IN DOCKER THESIS Presented to the Faculty of the Graduate School of Engineering of the Air Force Institute of Technology Air

  16. Molecular contamination study by interaction of a molecular beam with a platinum surface

    NASA Technical Reports Server (NTRS)

    Nuss, H. E.

    1976-01-01

    The capability of molecular beam scattering from a solid surface is analyzed for identification of molecular contamination of the surface. The design and setup of the molecular beam source and the measuring setup for the application of a phase sensitive measuring technique for the determination of the scattered beam intensity are described. The scattering distributions of helium and nitrogen molecular beams interacting with a platinum surface were measured for different amounts of contamination from diffusion pump oil for surface temperatures ranging from 30 to 400 C. The results indicate the scattering of molecular beams from a platinum surface is a very sensitive method for detecting surface contamination.

  17. Speeding up biomolecular interactions by molecular sledding

    SciTech Connect

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; Mangel, Walter F.; Herrmann, Andreas; van Oijen, Antoine M.

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.

  18. Speeding up biomolecular interactions by molecular sledding

    DOE PAGES

    Turkin, Alexander; Zhang, Lei; Marcozzi, Alessio; ...

    2015-10-07

    In numerous biological processes associations involve a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Moreover, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We also demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalize binding partners with the peptidemore » and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.« less

  19. Structural modifications of 4-aryl-4-oxo-2-aminylbutanamides and their acetyl- and butyrylcholinesterase inhibitory activity. Investigation of AChE-ligand interactions by docking calculations and molecular dynamics simulations.

    PubMed

    Vitorović-Todorović, Maja D; Koukoulitsa, Catherine; Juranić, Ivan O; Mandić, Ljuba M; Drakulić, Branko J

    2014-06-23

    Congeneric set of thirty-eight 4-aryl-4-oxo-2-(N-aryl/cycloalkyl)butanamides has been designed, synthesized and evaluated for acetyl- and butyrylcholinesterase inhibitory activity. Structural variations included cycloalkylamino group attached to C2 position of butanoyl moiety, and variation of amido moiety of molecules. Twelve compounds, mostly piperidino and imidazolo derivatives, inhibited AChE in low micromolar range, and were inactive toward BChE. Several N-methylpiperazino derivatives showed inhibition of BChE in low micromolar or submicromolar concentrations, and were inactive toward AChE. Therefore, the nature of the cycloalkylamino moiety governs the AChE/BChE selectivity profile of compounds. The most active AChE inhibitor showed mixed-type inhibition modality, indicating its binding to free enzyme and to enzyme-substrate complex. Thorough docking calculations of the seven most potent AChE inhibitors from the set, showed that the hydrogen bond can be formed between amide -NH- moiety of compounds and -OH group of Tyr 124. The 10 ns unconstrained molecular dynamic simulation of the AChE-compound 18 complex shows that this interaction is the most persistent. This is, probably, the major anchoring point for the binding.

  20. Developing a molecular roadmap of drug-food interactions.

    PubMed

    Jensen, Kasper; Ni, Yueqiong; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2015-02-01

    Recent research has demonstrated that consumption of food -especially fruits and vegetables- can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes. Despite the recognition of such drug-food associations as an important element for successful therapeutic interventions, a systematic approach for identifying, predicting and preventing potential interactions between food and marketed or novel drugs is not yet available. The overall objective of this work was to sketch a comprehensive picture of the interference of ∼ 4,000 dietary components present in ∼1800 plant-based foods with the pharmacokinetics and pharmacodynamics processes of medicine, with the purpose of elucidating the molecular mechanisms involved. By employing a systems chemical biology approach that integrates data from the scientific literature and online databases, we gained a global view of the associations between diet and dietary molecules with drug targets, metabolic enzymes, drug transporters and carriers currently deposited in DrugBank. Moreover, we identified disease areas and drug targets that are most prone to the negative effects of drug-food interactions, showcasing a platform for making recommendations in relation to foods that should be avoided under certain medications. Lastly, by investigating the correlation of gene expression signatures of foods and drugs we were able to generate a completely novel drug-diet interactome map.

  1. Developing a Molecular Roadmap of Drug-Food Interactions

    PubMed Central

    Jensen, Kasper; Ni, Yueqiong; Panagiotou, Gianni; Kouskoumvekaki, Irene

    2015-01-01

    Recent research has demonstrated that consumption of food -especially fruits and vegetables- can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes. Despite the recognition of such drug-food associations as an important element for successful therapeutic interventions, a systematic approach for identifying, predicting and preventing potential interactions between food and marketed or novel drugs is not yet available. The overall objective of this work was to sketch a comprehensive picture of the interference of ∼ 4,000 dietary components present in ∼1800 plant-based foods with the pharmacokinetics and pharmacodynamics processes of medicine, with the purpose of elucidating the molecular mechanisms involved. By employing a systems chemical biology approach that integrates data from the scientific literature and online databases, we gained a global view of the associations between diet and dietary molecules with drug targets, metabolic enzymes, drug transporters and carriers currently deposited in DrugBank. Moreover, we identified disease areas and drug targets that are most prone to the negative effects of drug-food interactions, showcasing a platform for making recommendations in relation to foods that should be avoided under certain medications. Lastly, by investigating the correlation of gene expression signatures of foods and drugs we were able to generate a completely novel drug-diet interactome map. PMID:25668218

  2. Plant-aphid interactions: molecular and ecological perspectives.

    PubMed

    Goggin, Fiona L

    2007-08-01

    Many aphids are major agricultural pests because of their unparalleled reproductive capacity and their ability to manipulate host plant physiology. Aphid population growth and its impact on plant fitness are strongly influenced by interactions with other organisms, including plant pathogens, endophytes, aphid endosymbionts, predators, parasitoids, ants, and other herbivores. Numerous molecular and genomic resources have recently been developed to identify sources of aphid resistance in plants, as well as potentially novel targets for control in aphids. Moreover, the same model systems that are used to explore direct molecular interactions between plants and aphids can be utilized to study the ecological context in which they occur.

  3. Theoretical investigation of gas-surface interactions

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1990-01-01

    A Dirac-Hartree-Fock code was developed for polyatomic molecules. The program uses integrals over symmetry-adapted real spherical harmonic Gaussian basis functions generated by a modification of the MOLECULE integrals program. A single Gaussian function is used for the nuclear charge distribution, to ensure proper boundary conditions at the nuclei. The Gaussian primitive functions are chosen to satisfy the kinetic balance condition. However, contracted functions which do not necessarily satisfy this condition may be used. The Fock matrix is constructed in the scalar basis and transformed to a jj-coupled 2-spinor basis before diagonalization. The program was tested against numerical results for atoms with a Gaussian nucleus and diatomic molecules with point nuclei. The energies converge on the numerical values as the basis set size is increased. Full use of molecular symmetry (restricted to D sub 2h and subgroups) is yet to be implemented.

  4. Investigation of the Composition and Formation Constant of Molecular Complexes

    PubMed Central

    Sahai, R.; Loper, G. L.; Lin, S. H.; Eyring, H.

    1974-01-01

    It has been the purpose of the present paper to investigate and explore the conditions under which the linear relation between Δ/CD0 and Δ in the Hanna-Ashbaugh-Foster-Fyfe equation for the evaluation of equilibrium constants holds, (CD0 is initial concentration of a donor and Δ is the observed chemical shift relative to the chemical shift of the acceptor) to obtain the equation representing the exact linear relation between Δ/CD0 and Δ, when the linear relation between Δ/CD0 and Δ holds, and to discuss how to use the Job method in nuclear magnetic resonance measurements to determine the stoichiometry of molecular complexes. We have found that the conventional belief that CD0 should always be chosen to be much greater than CA0 (initial concentration of acceptor) is not necessarily always true and the exact linear relation between Δ/CD0 and Δ is represented by the equation Δ/CD0 = K1Δ0/(1 + K1CA0) - K1Δ/(1 + K1CA0)2, where K1 is the formation constant of the complex. It is shown that in the Job method of nuclear magnetic resonance measurements one has to plot ΔCA0 against the mole fraction, and the mole fraction at the maximum should give us the composition of the complex. Theoretical results have been verified experimentally on the weak interaction between naphthalene and methyl iodide. PMID:16592155

  5. Investigation of synthetic molecular recognition for biosensing applications

    NASA Astrophysics Data System (ADS)

    Stratis-Cullum, Dimitra N.; McMasters, Sun; Sooter, Letha J.; Pellegrino, Paul M.

    2007-04-01

    A fundamental understanding of the factors which influence binding performance is critical to any technology or methodology relying on molecular recognition of a specific target species. For the Army, there is a growing need for a basic understanding of these interactions with traditional recognition elements (e.g., antibodies) in non-traditional environmental conditions, such as with new and emerging threats. There is a similar need for building a base of knowledge on non-traditional affinity ligands that are biomimetic or biosynthetic in nature. In this paper, specific research at the Army Research Laboratory towards the development, evaluation and use of synthetic affinity ligands for sensing applications is discussed. This includes the results of our investigations of aptamer-based affinity ligands targeting Campylobacter jejuni. Using capillary electrophoretic techniques, the relative binding affinities of the aptamer ligands towards the target pathogen as well as the degree of cross-reactivity with other food borne-pathogens (i.e., Escherichia coli O157:H7 and Salmonella typhimurium) were evaluated. Current progress towards the development of synthetic affinity ligands for sensing applications will also be discussed.

  6. Origin of molecular conformational stability: perspectives from molecular orbital interactions and density functional reactivity theory.

    PubMed

    Liu, Shubin; Schauer, Cynthia K

    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.

  7. 2004 Atomic and Molecular Interactions Gordon Research Conference

    SciTech Connect

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  8. Quantum Mechanical Molecular Interactions for Calculating the Excitation Energy in Molecular Environments: A First-Order Interacting Space Approach

    PubMed Central

    Hasegawa, Jun-ya; Yanai, Kazuma; Ishimura, Kazuya

    2015-01-01

    Intermolecular interactions regulate the molecular properties in proteins and solutions such as solvatochromic systems. Some of the interactions have to be described at an electronic-structure level. In this study, a commutator for calculating the excitation energy is used for deriving a first-order interacting space (FOIS) to describe the environmental response to solute excitation. The FOIS wave function for a solute-in-solvent cluster is solved by second-order perturbation theory. The contributions to the excitation energy are decomposed into each interaction and for each solvent. PMID:25393373

  9. VIBE: A virtual biomolecular environment for interactive molecular modeling

    SciTech Connect

    Cruz-Neira, C.; Langley, R.; Bash, P.A.

    1996-12-31

    Virtual reality tightly coupled to high performance computing and communications ushers in a new era for the study of molecular recognition and the rational design of pharmaceutical compounds. We have created a Virtual Biomolecular Environment (VIBE), which consists of (1) massively parallel computing to simulate the physical and chemical properties of a molecular system, (2) the Cave Automatic Virtual Environment (CAVE) for immersive display and interaction with the molecular system, and (3) a high-speed network interface to exchange data between the simulation and the CAVE. VIBE enables molecular scientists to have a visual, auditory, and haptic experience with a chemical system, while simultaneously manipulating its physical properties by steering, in real-time, a simulation executed on a supercomputer. We demonstrate the characteristics of VIBE using an HIV protease-cyclic urea inhibitor complex. 22 refs., 4 figs.

  10. Investigation of the ion beryllium surface interaction

    SciTech Connect

    Guseva, M.I.; Birukov, A.Yu.; Gureev, V.M.

    1995-09-01

    The self -sputtering yield of the Be was measured. The energy dependence of the Be self-sputtering yield agrees well with that calculated by W. Eckstein et. al. Below 770 K the self-sputtering yield is temperature independent; at T{sub irr}.> 870 K it increases sharply. Hot-pressed samples at 370 K were implanted with monoenergetic 5 keV hydrogen ions and with a stationary plasma (flux power {approximately} 5 MW/m{sup 2}). The investigation of hydrogen behavior in beryllium shows that at low doses hydrogen is solved, but at doses {ge} 5x10{sup 22} m{sup -2} the bubbles and channels are formed. It results in hydrogen profile shift to the surface and decrease of its concentration. The sputtering results in further concentration decrease at doses > 10{sup 25}m{sup -2}.

  11. Theoretical investigation of gas-surface interactions

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1994-01-01

    The goal of this project was to develop computational tools for the calculation of the electronic structure of molecules containing heavy atoms, and to use these tools in the study of catalytic processes, with the overall objective of gaining an understanding of the catalytic process which could be used to design more efficient catalysts. The main catalytic system of interest was the combustion of hydrogen on platinum surfaces. Under this project, a flexible Dirac-Hartree-Fock (DHF) program has been developed, a code to calculate DHF correlation energies at the second-order Moeller-Plesset perturbation (PP2) level is almost complete, and code to include correlation at the MCSCF and MCSCF/MP2 level is planned. The tools so far developed have been validated and used to calibrate some more approximate methods, and applied to investigate the importance of relativistic effects in the bonding of hydrogen to platinum.

  12. Electron-Phonon Interactions in C_28-derived Molecular Solids

    NASA Astrophysics Data System (ADS)

    Romero, Nichols A.; Kim, Jeongnim; Martin, Richard M.

    2004-03-01

    We have investigated molecular solids made from various small close-shell fullerenes to determine their structural and electronic properties in their pristine and doped forms. Binding energies, band structure, and electron-phonon coupling were calculated using the ab initio SIESTA [1] code. We find a C_28H4 solid that binds weakly and exhibits many of the salient features of solid C_60. The electron-phonon interaction potential is over twice as large as that of C_60. Our calculations show that endohedral doping of the C_28H4 solid produces an electronic structure similar to that of the alkal-doped fullerides which is suggestive of high superconducting transition temperatures T_c. In keeping with simple estimates of Tc carried out in the literature (e.g. [2]), one obtains T_c( Na@ C_28 H_4)≈ 6T_c( K_3 C_60)≈ 116K. *Supported by NSF DMR 99-76550 and DOE DEFG-96-ER45439. [1] J. Soler et. al, J. Phys.: Condens. Matter 14, 2745 (2002). [2] N. Breda et. al, Phys. Rev. B 62, 130 (2000).

  13. Molecular Interactions between a Novel Soybean Oil-Based Polymer and Doxorubicin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel soybean oil-based polymer, hydrolyzed polymers of epoxidized soybean oil (HPESO), was developed and investigated for drug delivery. This work was aimed at determining the molecular interactions between HPESO and doxorubicin (DOX), an anticancer drug. Powder X-ray diffraction, ATR-FTIR and ...

  14. Growth mechanism, electronic spectral investigation and molecular orbital studies of L-prolinium phosphate.

    PubMed

    Liu, Xiaojing; Sun, Xin; Xu, Xijin; Sun, Ping

    2015-01-01

    By using atomic force microscopy, birth and spread has proved to be the primary growth mechanism for L-prolinium phosphate (LPP). The phenomenon of newly formed islands expanding to the edge of the preceding terrace was observed. The optimized molecular structure and the molecular properties were calculated by density functional theory method. Natural bond orbital analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of LPP leading to high NLO activity. Molecular electrostatic potential, frontier molecular orbital analysis and thermodynamic properties were investigated to get a better insight of the molecular properties. Global and local reactivity descriptors were computed to predict the reactivity and reactive sites on the molecules. Non-linear optical (NLO) properties such as the total dipole moment (μ) and first order hyperopolarizability (β) were also calculated to predict NLO behavior.

  15. Theoretical investigation of gas-surface interactions

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.

    1992-01-01

    The investigation into the appearance of intruder states from the negative continuum when some of the two-electron integrals were omitted was completed. The work shows that, provided all integrals involving core contracted functions in an atomic general contraction are included, or that the core functions are radially localized, meaningful results are obtained and intruder states do not appear. In the area of program development, the Dirac-Hartree-Fock (DHF) program for closed-shell polyatomic molecules was extended to permit Kramers-restricted open-shell DHF calculations with one electron in an open shell or one hole in a closed shell, or state-averaged DHF calculations over several particle or hole doublet states. One application of the open-shell code was to the KO molecule. Another major area of program development is the transformation of integrals from the scalar basis in which they are generated to the 2-spinor basis employed in parts of the DHF program, and hence to supermatrix form. Particularly concerning the omission of small component integrals, and with increase in availability of disk space, it is now possible to consider transforming the integrals. The use of ordered integrals, either in the scalar basis or in the 2-spinor basis, would considerably speed up the construction of the Fock matrix, and even more so if supermatrices were constructed. A considerable amount of effort was spent on analyzing the integral ordering and tranformation for the DHF program. The work of assessing the reliability of the relativistic effective core potentials (RECPs) was continued with calculation of the group IV monoxides. The perturbation of the metal atom provided by oxygen is expected to be larger than that provided by hydrogen and thus provide a better test of the qualification of the RECPs. Calculations on some platinum hydrides were carried out at nonrelativistic (NR), perturbation theory (PT) and DHF levels. Reprints of four papers describing this work are

  16. Quantitation of Interacting Molecular Species and Measurement of Molecular Avidity by Single Radial (Immuno) Diffusion

    DTIC Science & Technology

    1989-09-01

    FIGURE LEGEND 1lL ;Ta ,j - ’V y ilii INTRODUCTION Mancini et al. (1965) developed a single radial immunodiffusion (SRID) method for the quantitation of...quantitation of antigens by single radial immunodiffusion . Immunochem, 2, 5. Mancini , G., Nash, D. R. and Heremans, J. F. (1970) Further studies on...FIELD GROUP SUB-GROUP Single radial immunodiffusion , Single radial diffusion, Molecular interaction, Molecular avidity, endotoxin ’-." 19 A63TRACT

  17. Hadronic molecular states from the Kbar{K}^{ast} interaction

    NASA Astrophysics Data System (ADS)

    Lü, Pei-Liang; He, Jun

    2016-12-01

    In this work, the Kbar{K}^{ast} interaction is studied in a quasipotential Bethe-Salpeter equation approach combined with the one-boson-exchange model. With the help of the hidden-gauge Lagrangian, the exchanges of pseudoscalar mesons (π and η) and vector mesons (ρ, ω and φ) are considered to describe the Kbar{K}^{ast} interaction. Besides the direct vector-meson exchange which can be related to the Weinberg-Tomozawa term, pseudoscalar-meson exchanges also play important roles in the mechanism of the Kbar{K}^{ast} interaction. The poles of scattering amplitude are searched to find the molecular states produced from the Kbar{K}^{ast} interaction. In the case of quantum number IG(J^{PC}) = 0+(1^{++}), a pole is found with a reasonable cutoff, which can be related to the f1(1285) in experiment. Another bound state with 0-(1^{+-}) is also produced from the Kbar{K}^{ast} interaction, which can be related to the h1(1380). In the isovector sector, the interaction is much weaker and a bound state with 1+(1+) relevant to the b1(1235) is produced but at a larger cutoff. Our results suggest that in the hadronic molecular state picture the f1(1285) and b1(1235) are the strange partners of the X(3872) and Zc(3900), respectively.

  18. Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

    NASA Astrophysics Data System (ADS)

    Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki

    2012-09-01

    Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.

  19. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  20. Molecular Interaction between Magainin 2 and Model Membranes in Situ

    PubMed Central

    Nguyen, Khoi; Le Clair, Stéphanie V.; Ye, Shuji; Chen, Zhan

    2009-01-01

    In this paper, we investigated the molecular interactions of Magainin 2 with model cell membranes using Sum Frequency Generation (SFG) vibrational spectroscopy and Attenuated Total Reflectance – Fourier Transform Infrared spectroscopy (ATR-FTIR). Symmetric 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-rac-(1-glycerol)] (POPG) and 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine (POPC) bilayers, which model the bacterial and mammalian cell membranes respectively, were used in the studies. It was observed by SFG that Magainin 2 orients relatively parallel to the POPG lipid bilayer surface at low solution concentrations, around 200 nM. When increasing the Magainin 2 concentration to 800 nM, both SFG and ATR-FTIR results indicate that Magainin 2 molecules insert into the POPG bilayer and adopt a transmembrane orientation with an angle of about 20 degrees from the POPG bilayer normal. For the POPC bilayer, even at a much higher peptide concentration of 2.0 µM, no ATR-FTIR signal was detected. For this concentration on POPC, SFG studies indicated that Magainin 2 molecules adopt an orientation nearly parallel to the bilayer surface, with an orientation angle of 75 degrees from the surface normal. This shows that SFG has a much better detection limit than ATR-FTIR and can therefore be applied to study interfacial molecules with much lower surface coverage. This Magainin 2 orientation study and further investigation of the lipid bilayer SFG signals support the proposed toroidal pore model for the antimicrobial activity of Magainin 2. PMID:19728722

  1. Molecular and Cellular Quantitative Microscopy: theoretical investigations, technological developments and applications to neurobiology

    NASA Astrophysics Data System (ADS)

    Esposito, Alessandro

    2006-05-01

    This PhD project aims at the development and evaluation of microscopy techniques for the quantitative detection of molecular interactions and cellular features. The primarily investigated techniques are Fαrster Resonance Energy Transfer imaging and Fluorescence Lifetime Imaging Microscopy. These techniques have the capability to quantitatively probe the biochemical environment of fluorophores. An automated microscope capable of unsupervised operation has been developed that enables the investigation of molecular and cellular properties at high throughput levels and the analysis of cellular heterogeneity. State-of-the-art Förster Resonance Energy Transfer imaging, Fluorescence Lifetime Imaging Microscopy, Confocal Laser Scanning Microscopy and the newly developed tools have been combined with cellular and molecular biology techniques for the investigation of protein-protein interactions, oligomerization and post-translational modifications of α-Synuclein and Tau, two proteins involved in Parkinson’s and Alzheimer’s disease, respectively. The high inter-disciplinarity of this project required the merging of the expertise of both the Molecular Biophysics Group at the Debye Institute - Utrecht University and the Cell Biophysics Group at the European Neuroscience Institute - Gαttingen University. This project was conducted also with the support and the collaboration of the Center for the Molecular Physiology of the Brain (Göttingen), particularly with the groups associated with the Molecular Quantitative Microscopy and Parkinson’s Disease and Aggregopathies areas. This work demonstrates that molecular and cellular quantitative microscopy can be used in combination with high-throughput screening as a powerful tool for the investigation of the molecular mechanisms of complex biological phenomena like those occurring in neurodegenerative diseases.

  2. Towards an integrated molecular model of plant-virus interactions.

    PubMed

    Elena, Santiago F; Rodrigo, Guillermo

    2012-12-01

    The application in recent years of network theory methods to the study of host-virus interactions is providing a new perspective to the way viruses manipulate the host to promote their own replication. An integrated molecular model of such pathosystems require three detailed maps describing, firstly, the interactions between viral elements, secondly, the interactions between host elements, and thirdly, the cross-interactions between viral and host elements. Here, we compile available information for Potyvirus infecting Arabidopsis thaliana. With an integrated model, it is possible to analyze the mode of virus action and how the perturbation of the virus targets propagates along the network. These studies suggest that viral pathogenicity results not only from the alteration of individual elements but it is a systemic property.

  3. Collective transport of weakly interacting molecular motors with Langmuir kinetics

    NASA Astrophysics Data System (ADS)

    Chandel, Sameep; Chaudhuri, Abhishek; Muhuri, Sudipto

    2015-04-01

    Filament-based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as kinesins weakly interact among themselves during transport and with the surrounding cellular environment. Motivated by these observations we study a driven lattice gas model for collective unidirectional transport of molecular motors on open filament. This model incorporates short-range next-nearest-neighbour (NNN) interactions between the motors and couples the transport process on filament with surrounding cellular environment through adsorption-desorption Langmuir kinetics (LK) of the motors. We analyse this model within the framework of a mean-field (MF) theory in the limit of weak interactions between the motors. We point to the mapping of this model with the non-conserved version of the Katz-Lebowitz-Spohn (KLS) model. The system exhibits rich phase behavior with a variety of inhomogeneous phases including localized shocks in the bulk of the filament. We obtain the steady-state density and current profiles, analyse their variation as a function of the strength of interaction and construct the non-equilibrium MF phase diagram. We compare these MF results with Monte Carlo simulations and find that the MF analysis shows reasonably good agreement with simulation results as long as the motors are weakly interacting. For sufficently strong NNN interaction between the motors, the mean-field results deviate significantly, and for very strong NNN interaction in the absence of LK, the current in the lattice is determined solely by the NNN interaction parameter and it becomes independent of entry and exit rates of motors at the filament boundaries.

  4. Molecular interactions between proteins and synthetic membrane polymer films

    SciTech Connect

    Pincet, F.; Perez, E.; Belfort, G.

    1995-04-01

    To help understand the effects of protein adsorption on membrane filtration performance, we have measured the molecular interactions between cellulose acetate films and two proteins with different properties (ribonuclease A and human serum albumin) with a surface force apparatus. Comparison of forces between two protein layers with those between a protein layer and a cellulose acetate (CA) film shows that, at high pH, both proteins retained their native conformation on interacting with the CA film while at the isoelectric point (pI) or below the tertiary structure of proteins was disturbed. These measurements provide the first molecular evidence that disruption of protein tertiary structure could be responsible for the reduced permeation flows observed during membrane filtration of protein solutions and suggest that operating at high pH values away from the pI of proteins will reduce such fouling. 60 refs., 9 figs., 5 tabs.

  5. Experimental investigation of interactions between proteins and carbon nanomaterials

    NASA Astrophysics Data System (ADS)

    Sengupta, Bishwambhar

    The global market for nanomaterials based products is forecasted to reach $1 trillion per annum per annum for 2015. Engineered nanomaterials (ENMs) exhibit unique physicochemical properties with potential to impact diverse aspects of society through applications in electronics, renewable energy, and medicine. While the research and proposed applications of ENMs continue to grow rapidly, the health and safety of ENMs still remains a major concern to the public as well as to policy makers and funding agencies. It is now widely accepted that focused efforts are needed for identifying the list of physicochemical descriptors of ENM before they can be evaluated for nanotoxicity and biological response. This task is surprisingly challenging, as many physicochemical properties of ENMs are closely inter related and cannot be varied independently (e.g. increasing the size of an ENM can introduce additional defects). For example, varying toxic response may ensue due to different methods of nanomaterial preparation, dissimilar impurities and defects. Furthermore, the inadvertent coating of proteins on ENM surface in any biological milieu results in the formation of the so-called "protein/bio-corona" which can in turn alter the fate of ENMs and their biological response. Carbon nanomaterials (CNMs) such as carbon nanotubes, graphene, and graphene oxide are widely used ENMs. It is now known that defects in CNMs play an important role not only in materials properties but also in the determination of how materials interact at the nano-bio interface. In this regard, this work investigates the influence of defect-induced hydrophilicity on the bio-corona formation using micro Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge transfer between them, inducing protein unfolding which enhances conformational entropy and

  6. Solution structures and molecular interactions of selective melanocortin receptor antagonists.

    PubMed

    Lee, Chul-Jin; Yun, Ji-Hye; Lim, Sung-Kil; Lee, Weontae

    2010-12-01

    The solution structures and inter-molecular interaction of the cyclic melanocortin antagonists SHU9119, JKC363, HS014, and HS024 with receptor molecules have been determined by NMR spectroscopy and molecular modeling. While SHU9119 is known as a nonselective antagonist, JKC363, HS014, and HS024 are selective for the melanocortin subtype-4 receptor (MC4R) involved in modulation of food intake. Data from NMR and molecular dynamics suggest that the conformation of the Trp9 sidechain in the three MC4R-selective antagonists is quite different from that of SHU9119. This result strongly supports the concept that the spatial orientation of the hydrophobic aromatic residue is more important for determining selectivity than the presence of a basic, "arginine-like" moiety responsible for biological activity. We propose that the conformation of hydrophobic residues of MCR antagonists is critical for receptor-specific selectivity.

  7. Molecular Analysis of AFP and HSA Interactions with PTEN Protein.

    PubMed

    Zhu, Mingyue; Lin, Bo; Zhou, Peng; Li, Mengsen

    2015-01-01

    Human cytoplasmic alpha-fetoprotein (AFP) has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA), but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP), and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog), demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN. In silicon substitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

  8. Rheological investigation of highly filled polymers: Effect of molecular weight

    NASA Astrophysics Data System (ADS)

    Hnatkova, Eva; Hausnerova, Berenika; Hales, Andrew; Jiranek, Lukas; Vera, Juan Miguel Alcon

    2015-04-01

    The paper deals with rheological properties of highly filled polymers used in powder injection molding. Within the experimental framework seven PIM feedstocks based on superalloy Inconel 718 powder were prepared. Each feedstock contains the fixed amount of powder loading and the same composition of binder system consisting of three components: polyethylene glycol (PEG) differing in molecular weight, poly (methyl methacrylate) (PMMA) and stearic acid (SA). The aim is to investigate the influence of PEG's molecular weight on the flow properties of feedstocks. Non-Newtonian indices, representing the shear rate sensitivity of the feedstocks, are obtained from a polynomial fit, and found to vary within measured shear rates range from 0.2 to 0.8. Temperature effect is considered via activation energies, showing decreasing trend with increasing of molecular weight of PEG (except of feedstock containing 1,500 g.mol-1 PEG).

  9. Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

    PubMed

    Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

    2016-11-08

    Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively (13)C-labeled choline with (29)Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like (1)H-(13)C CP-REDOR (rotational-echo double resonance), (1)H-(13)C HETCOR (heteronuclear correlation), and (1)H-(29)Si-(1)H double CP are employed to determine spatial parameters. The measurement of (29)Si-(13)C internuclear distances for selectively (13)C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

  10. [Molecular interactions of membrane proteins and erythrocyte deformability].

    PubMed

    Boivin, P

    1984-06-01

    The structural and functional properties of the erythrocytic membrane constitute one of the essential elements of the red cell deformability. They intervene not only in the flexibility of the membrane, but also in the surface/volume relation and, through transmembrane exchanges, in the internal viscosity of the red cells. These properties depend essentially on the molecular composition of the elements which constitute the membrane, and on their interactions. The shape of the red cell and the flexibility of its membrane depend, to a great extent, on the membrane skeleton, whose main components are spectrin, actin, and protein 4.1. The spectrin basic molecule is a heterodimer, but there occur interactions between dimers in vitro as well as in vivo, which lead to the formation of tetrameric and oligomeric structures of higher complexity. Disturbances of these interactions, such as have been observed in pathological cases, lead to an instability of the membrane, a loss of membrane fragments, and a decrease in the surface/volume relation, with, as a consequence, a reduced deformability. The stability of the membrane skeleton also depends on the interactions between spectrin and protein 4.1. These interactions occur through a binding site on the beta chain of spectrin apparently close to actin and calmodulin binding sites. Other interactions occur between the hydrophobic segment of spectrin and membrane lipids. The cytoskeleton is bound to the transmembrane proteins: by ankyrin to the internal segment of protein band 3, and by protein 4.1 to a glycoprotein named glycoconnectin. There seems to exist other, more direct, lower affinity bindings between the cytoskeleton on the one hand, and band 3 and glycophorin transmembrane proteins on the other hand, whose lateral mobilities are modified when the structure of the skeleton is perturbed. The membrane proteins, which are in contact with the cytosol, interact with the cytosolic proteins, in particular with certain enzymes

  11. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations.

    PubMed

    Mi, Ran; Tu, Bao; Bai, Xiao-Ting; Chen, Jun; Ouyang, Yu; Hu, Yan-Jun

    2015-12-01

    Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.

  12. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies

    PubMed Central

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala

    2017-01-01

    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo. PMID:28321247

  13. Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.

    2015-04-01

    An experimental and modeling study of a complex nanoclay-based polymeric scaffold system is presented here. A representative molecular model of polymeric nanocomposite scaffold system for bone tissue engineering applications was developed. Polymeric scaffolds were synthesized using organically modified montmorillonite clay (OMMT) with biomineralized hydroxyapatite and polycaprolactone (OMMT-HAP-PCL). The OMMT-HAP-PCL representative model was constructed and validated using transmission electron microscopy, x-ray diffraction and material density results. We observed strong molecular interactions between OMMT, hydroxyapatite (HAP) and polycaprolactone (PCL) in the OMMT-HAP-PCL system. Attractive and repulsive interactions between PCL and different constituents of OMMT and HAP indicate influence of OMMT-HAP on PCL. Polymeric scaffolds were found to have improved nanomechanical properties as compared to pristine PCL due to the introduction of OMMT-HAP. Stress-strain response for the representative OMMT-HAP-PCL model was evaluated using constant force steered molecular dynamics (SMD) simulations. Two distinct stress-strain responses observed in the system indicate a two-phase nanomechanical behavior of OMMT-HAP-PCL obtained at low and high applied stresses. The results obtained from the MD and SMD simulations provide quantitative understanding of molecular interactions between different constituents of OMMT, HAP and PCL and mechanical response in the OMMT-HAP-PCL system.

  14. Interaction between Cassiopeia A and nearby molecular clouds

    SciTech Connect

    Kilpatrick, C. D.; Bieging, J. H.; Rieke, G. H.

    2014-12-01

    We present spectroscopy of the supernova remnant Cassiopeia A (Cas A) observed at infrared wavelengths from 10 to 40 μm with the Spitzer Space Telescope and at millimeter wavelengths in {sup 12}CO and {sup 13}CO J =2-1 (230 and 220 GHz) with the Heinrich Hertz Submillimeter Telescope. The IR spectra demonstrate high-velocity features toward a molecular cloud coincident with a region of bright radio continuum emission along the northern shock front of Cas A. The millimeter observations indicate that CO emission is broadened by a factor of two in some clouds toward Cas A, particularly to the south and west. We believe that these features trace interactions between the Cas A shock front and nearby molecular clouds. In addition, some of the molecular clouds that exhibit broadening in CO lie 1'-2' away from the furthest extent of the supernova remnant shock front. We propose that this material may be accelerated by ejecta with velocity significantly larger than the observed free-expansion velocity of the Cas A shock front. These observations may trace cloud interactions with fast-moving outflows such as the bipolar outflow along the southwest to northeast axis of the Cas A supernova remnant, as well as fast-moving knots seen emerging in other directions.

  15. Investigation of the influence factors of polyethylene molecule encapsulated into carbon nanotubes by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Li, Qun; He, Guofang; Zhao, Rengao; Li, Yanfei

    2011-09-01

    In this work, the influence factors, namely chirality, temperature, radius and surface chemical modification, of the interaction energy for polyethylene (PE) molecule encapsulated into single-walled carbon nanotubes (SWNTs) had been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulation. The results showed that all these factors would influence the interaction energy between PE and SWNTs. The interaction energy between PE molecule and the armchair SWNTs is largest among eight kinds of chiral SWNTs. The interaction energy decreases with the increase of temperature or the SWNT radius. The methyl, phenyl, hydroxyl, carboxyl, -F, and amino groups, have been introduced onto the surface of the SWNTs by the simulation software and the influence of SWNT chemical modification has also been investigated. The interaction energy between PE and chemically modified SWNTs is larger than that between PE and pristine SWNTs, and increases with increasing the concentration of the modified groups monotonously. In addition, the group electronegativity and van der Waals force will affect the interaction energy between PE and chemically modified SWNTs greatly, which can be attributed to the electronic structures of the chemically modified groups. This study can provide some useful suggestions for the composite material design and drug transport.

  16. Unraveling Hydrophobic Interactions at the Molecular Scale Using Force Spectroscopy and Molecular Dynamics Simulations.

    PubMed

    Stock, Philipp; Monroe, Jacob I; Utzig, Thomas; Smith, David J; Shell, M Scott; Valtiner, Markus

    2017-03-28

    Interactions between hydrophobic moieties steer ubiquitous processes in aqueous media, including the self-organization of biologic matter. Recent decades have seen tremendous progress in understanding these for macroscopic hydrophobic interfaces. Yet, it is still a challenge to experimentally measure hydrophobic interactions (HIs) at the single-molecule scale and thus to compare with theory. Here, we present a combined experimental-simulation approach to directly measure and quantify the sequence dependence and additivity of HIs in peptide systems at the single-molecule scale. We combine dynamic single-molecule force spectroscopy on model peptides with fully atomistic, both equilibrium and nonequilibrium, molecular dynamics (MD) simulations of the same systems. Specifically, we mutate a flexible (GS)5 peptide scaffold with increasing numbers of hydrophobic leucine monomers and measure the peptides' desorption from hydrophobic self-assembled monolayer surfaces. Based on the analysis of nonequilibrium work-trajectories, we measure an interaction free energy that scales linearly with 3.0-3.4 kBT per leucine. In good agreement, simulations indicate a similar trend with 2.1 kBT per leucine, while also providing a detailed molecular view into HIs. This approach potentially provides a roadmap for directly extracting qualitative and quantitative single-molecule interactions at solid/liquid interfaces in a wide range of fields, including interactions at biointerfaces and adhesive interactions in industrial applications.

  17. Isothermal microcalorimetry to investigate non specific interactions in biophysical chemistry.

    PubMed

    Ball, Vincent; Maechling, Clarisse

    2009-07-28

    Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of "specific" host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these "non specific" interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur.

  18. Isothermal Microcalorimetry to Investigate Non Specific Interactions in Biophysical Chemistry

    PubMed Central

    Ball, Vincent; Maechling, Clarisse

    2009-01-01

    Isothermal titration microcalorimetry (ITC) is mostly used to investigate the thermodynamics of “specific” host-guest interactions in biology as well as in supramolecular chemistry. The aim of this review is to demonstrate that ITC can also provide useful information about non-specific interactions, like electrostatic or hydrophobic interactions. More attention will be given in the use of ITC to investigate polyelectrolyte-polyelectrolyte (in particular DNA-polycation), polyelectrolyte-protein as well as protein-lipid interactions. We will emphasize that in most cases these “non specific” interactions, as their definition will indicate, are favoured or even driven by an increase in the entropy of the system. The origin of this entropy increase will be discussed for some particular systems. We will also show that in many cases entropy-enthalpy compensation phenomena occur. PMID:20111693

  19. Ab initio investigation of benzene clusters: Molecular tailoring approach

    NASA Astrophysics Data System (ADS)

    Mahadevi, A. Subha; Rahalkar, Anuja P.; Gadre, Shridhar R.; Sastry, G. Narahari

    2010-10-01

    An exhaustive study on the clusters of benzene (Bz)n, n =2-8, at MP2/6-31++G∗∗ level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (˜0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n -1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.

  20. Molecular interaction of ctDNA and HSA with sulfadiazine sodium by multispectroscopic methods and molecular modeling.

    PubMed

    Geng, Shaoguang; Liu, Guosheng; Li, Wei; Cui, Fengling

    2013-01-01

    Interactions of sulfadiazine sodium (SD-Na) with calf thymus DNA (ctDNA) and human serum albumin (HSA) were studied using fluorescence spectroscopy, UV absorption spectroscopy and molecular modeling. The fluorescence experiments showed that the processes were static quenching. The results of UV spectra and molecular modeling of the interaction between SD-Na and ctDNA indicated that the binding mode might be groove binding. In addition, the interaction of SD-Na with HSA under simulative physiological conditions was also investigated. The binding constants (K) and the number of binding sites (n) at different temperatures (292, 302, 312 K) were 5.23 × 10(3) L/mol, 2.18; 4.50 × 10(3) L/mol, 2.35; and 4.08 × 10(3) L/mol, 2.47, respectively. Thermodynamic parameters including enthalpy change (ΔH) and entropy change (ΔS) were calculated, the results suggesting that hydrophobic force played a very important role in SD-Na binding to HSA, which was in good agreement with the molecular modeling study. Moreover, the effect of SD-Na on the conformation of HSA was analyzed using three-dimensional fluorescence spectra.

  1. Unravelling Protein-DNA Interactions at Molecular Level: A DFT and NCI Study.

    PubMed

    González, J; Baños, I; León, I; Contreras-García, J; Cocinero, E J; Lesarri, A; Fernández, J A; Millán, J

    2016-02-09

    Histone-DNA interactions were probed computationally at a molecular level, by characterizing the bimolecular clusters constituted by selected amino acid derivatives with polar (asparagine and glutamine), nonpolar (alanine, valine, and isoleucine), and charged (arginine) side chains and methylated pyrimidinic (1-methylcytosine and 1-methylthymine) and puric (9-methyladenine and 9-methylguanine) DNA bases. The computational approach combined different methodologies: a molecular mechanics (MMFFs forced field) conformational search and structural and vibrational density-functional calculations (M06-2X with double and triple-ζ Pople's basis sets). To dissect the interactions, intermolecular forces were analyzed with the Non-Covalent Interactions (NCI) analysis. The results for the 24 different clusters studied show a noticeable correlation between the calculated binding energies and the propensities for protein-DNA base interactions found in the literature. Such correlation holded even for the interaction of the selected amino acid derivatives with Watson and Crick pairs. Therefore, the balance between hydrogen bonds and van der Waals interactions (specially stacking) in the control of the final shape of the investigated amino acid-DNA base pairs seems to be well reproduced in dispersion-corrected DFT molecular models, reinforcing the idea that the specificity between the amino acids and the DNA bases play an important role in the regulation of DNA.

  2. Ab Initio Study of Molecular Interactions in Cellulose Iα

    SciTech Connect

    Devarajan, Ajitha; Markutsya, Serjiy; Lamm, Monica H.; Cheng, Xiaolin; Smith, Jeremy C.; Baluyut, John Y.; Kholod, Yana; Gordon, Mark S.; Windus, Theresa L.

    2013-08-12

    Biomass recalcitrance, the resistance of cellulosic biomass to degradation, is due in part to the stability of the hydrogen bond network and stacking forces between the polysaccharide chains in cellulose microfibers. The fragment molecular orbital (FMO) method at the correlated Møller–Plesset second order perturbation level of theory was used on a model of the crystalline cellulose Iα core with a total of 144 glucose units. These computations show that the intersheet chain interactions are stronger than the intrasheet chain interactions for the crystalline structure, while they are more similar to each other for a relaxed structure. An FMO chain pair interaction energy decomposition analysis for both the crystal and relaxed structures reveals an intricate interplay between electrostatic, dispersion, charge transfer, and exchange repulsion effects. The role of the primary alcohol groups in stabilizing the interchain hydrogen bond network in the inner sheet of the crystal and relaxed structures of cellulose Iα, where edge effects are absent, was analyzed. The maximum attractive intrasheet interaction is observed for the GT-TG residue pair with one intrasheet hydrogen bond, suggesting that the relative orientation of the residues is as important as the hydrogen bond network in strengthening the interaction between the residues.

  3. Molecular and cellular basis of cannabinoid and opioid interactions.

    PubMed

    Viganò, Daniela; Rubino, Tiziana; Parolaro, Daniela

    2005-06-01

    Cannabinoids and opioids have been shown to possess several similar pharmacological effects, including analgesia and stimulation of brain circuitry that are believed to underlie drug addiction and reward. In recent years, these phenomena have supported the possible existence of functional links in the mechanisms of action of both types of drugs. The present review addresses the recent advances in the study of biochemical and molecular mechanisms underlying opioid and cannabinoid interaction. Several hypothesis have been formulated to explain this cross-modulation including the release of opioid peptides by cannabinoids or endocannabinoids by opioids and interaction at the level of receptor and/or their signal transduction mechanisms. Moreover it is important to consider that the nature of cannabinoid and opioid interaction might differ in the brain circuits mediating reward and in those mediating other pharmacological properties, such as antinociception. While in vitro studies point to the presence of interaction at various steps along the signal transduction pathway, studies in intact animals are frequently contradictory pending on the used species and the adopted protocol. The presence of reciprocal alteration in receptor density and efficiency as well as the modification in opioid/cannabinoid endogenous systems often do not reflect the behavioral results. Further studies are needed since a better knowledge of the opioid-cannabinoid interaction may lead to exciting therapeutic possibilities.

  4. Electron-phonon interaction within classical molecular dynamics

    SciTech Connect

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-14

    Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.

  5. Electron-phonon interaction within classical molecular dynamics

    DOE PAGES

    Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

    2016-07-14

    Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

  6. Electron-phonon interaction within classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Tamm, A.; Samolyuk, G.; Correa, A. A.; Klintenberg, M.; Aabloo, A.; Caro, A.

    2016-07-01

    We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e -ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.

  7. Comparison between Free and Immobilized Ion Effects on Hydrophobic Interactions: A Molecular Dynamics Study.

    PubMed

    Huang, Kai; Gast, Sebastian; Ma, C Derek; Abbott, Nicholas L; Szlufarska, Izabela

    2015-10-15

    Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using β-peptide-inspired nanorods, we investigate the effects of both free ions (dissolved salts) and proximally immobilized ions on hydrophobic interactions. We find that the free ion effect is correlated with the water density fluctuation near a nonpolar molecular surface, showing that such fluctuation can be an indicator of hydrophobic interactions in the case of solution additives. In the case of immobilized ion, our results demonstrate that hydrophobic interactions can be switched on and off by choosing different spatial arrangements of proximal ions on a nanorod. For globally amphiphilic nanorods, we find that the magnitude of the interaction can be further tuned using proximal ions with varying ionic sizes. In general, univalent proximal anions are found to weaken hydrophobic interactions. This is in contrast to the effect of free ions, which according to our simulations strengthen hydrophobic interactions. In addition, immobilized anions of increasing ionic size do not follow the same ordering (Hofmeister-like ranking) as free ions when it comes to their impact on hydrophobic interactions. The immobilized ion effect is not simply correlated with the water density fluctuation near the nonpolar side of the amphiphilic nanorod. We propose a molecular picture that explains the contrasting effects of immobilized versus free ions.

  8. Investigation of Chiral Molecular Micelles by NMR Spectroscopy and Molecular Dynamics Simulation

    PubMed Central

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2013-01-01

    NMR spectroscopy and molecular dynamics (MD) simulation analyses of the chiral molecular micelles poly-(sodium undecyl-(L,L)-leucine-valine) (poly-SULV) and poly-(sodium undecyl-(L,L)- valine-leucine) (poly-(SUVL)) are reported. Both molecular micelles are used as chiral selectors in electrokinetic chromatography and each consists of covalently linked surfactant chains with chiral dipeptide headgroups. To provide experimental support for the structures from MD simulations, NOESY spectra were used to identify protons in close spatial proximity. Results from the NOESY analyses were then compared to radial distribution functions from MD simulations. In addition, the hydrodynamic radii of both molecular micelles were calculated from NMR-derived diffusion coefficients. Corresponding radii from the MD simulations were found to be in agreement with these experimental results. NMR diffusion experiments were also used to measure association constants for polar and non-polar binaphthyl analytes binding to both molecular micelles. Poly(SUVL) was found to bind the non-polar analyte enantiomers more strongly, while the more polar analyte enantiomers interacted more strongly with poly(SULV). MD simulations in tum showed that poly(SUL V) had a more open structure that gave greater access for water molecules to the dipeptide headgroup region. PMID:23991355

  9. Molecular interactions between amantadine and model cell membranes.

    PubMed

    Wu, Fu-Gen; Yang, Pei; Zhang, Chi; Li, Bolin; Han, Xiaofeng; Song, Minghu; Chen, Zhan

    2014-07-22

    Sum frequency generation (SFG) vibrational spectroscopy was applied to study molecular interactions between amantadine and substrate supported lipid bilayers serving as model cell membranes. Both isotopically asymmetric and symmetric lipid bilayers were used in the research. SFG results elucidated how the water-soluble drug, amantadine, influenced the packing state of each leaflet of a lipid bilayer and how the drugs affected the lipid flip-flop process. It is difficult to achieve such detailed molecular-level information using other analytical techniques. Especially, from the flip-flop rate change of isotopically asymmetric lipid bilayer induced by amantadine, important information on the drug-membrane interaction mechanism can be derived. The results show that amantadine can be associated with zwitterionic PC bilayers but has a negligible influence on the flip-flop behavior of PC molecules unless at high concentrations. Different effects of amantadine on the lipid bilayer were observed for the negatively charged DPPG bilayer; low concentration amantadine (e.g., 0.20 mM) in the subphase could immediately disturb the outer lipid leaflet and then the lipid associated amantadine molecules gradually reorganize to cause the outer leaflet to return to the original orderly packed state. Higher concentration amantadine (e.g., 5.0 mM) immediately disordered the packing state of the outer lipid leaflet. For both the high and low concentration cases, amantadine molecules only bind to the outer PG leaflet and cannot translocate to the inner layer. The presence of amantadine within the negatively charged lipid layers has certain implications for using liposomes as drug delivery carriers for amantadine. Besides, by using PC or PG bilayers with both leaflets deuterated, we were able to examine how amantadine is distributed and/or oriented within the lipid bilayer. The present work demonstrates that SFG results can provide an in-depth understanding of the molecular mechanisms of

  10. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

    PubMed Central

    Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

    2015-01-01

    The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA. PMID:26140374

  11. Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

    PubMed Central

    Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

    2013-01-01

    This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

  12. Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

    NASA Astrophysics Data System (ADS)

    Koishi, Takahiro; Yasuoka, Kenji; Ebisuzaki, Toshikazu; Yoo, S.; Zeng, X. C.

    2005-11-01

    We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.

  13. Transient Induced Molecular Electronic Spectroscopy (TIMES) for study of protein-ligand interactions

    PubMed Central

    Zhang, Tiantian; Ku, Ti-Hsuan; Han, Yuanyuan; Subramanian, Ramkumar; Niaz, Iftikhar Ahmad; Luo, Hua; Chang, Derrick; Huang, Jian-Jang; Lo, Yu-Hwa

    2016-01-01

    We present a method, Transient Induced Molecular Electronic Spectroscopy (TIMES), to detect protein-ligand interactions without any protein engineering or chemical modification. We developed a physics model for the TIMES signal and mathematically formulated the problem to attain physical insight of protein-ligand interactions without any disturbances by molecular probes, fluorescent labels, or immobilization of molecules. To demonstrate the functionality of this method, we have used the TIMES signals to find the dissociation constants for the affinity of reactions, the shear-stress dependent adsorption time of molecules on surface, and other interesting features of protein-ligand interaction in native conditions. As a unique tool, TIMES offers a simple and effective method to investigate fundamental protein chemistry and drug discoveries. PMID:27759045

  14. Shock induced phase transition of water: Molecular dynamics investigation

    SciTech Connect

    Neogi, Anupam; Mitra, Nilanjan

    2016-02-15

    Molecular dynamics simulations were carried out using numerous force potentials to investigate the shock induced phenomenon of pure bulk liquid water. Partial phase transition was observed at single shock velocity of 4.0 km/s without requirement of any external nucleators. Change in thermodynamic variables along with radial distribution function plots and spectral analysis revealed for the first time in the literature, within the context of molecular dynamic simulations, the thermodynamic pathway leading to formation of ice VII from liquid water on shock loading. The study also revealed information for the first time in the literature about the statistical time-frame after passage of shock in which ice VII formation can be observed and variations in degree of crystallinity of the sample over the entire simulation time of 100 ns.

  15. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html.

  16. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei

    2017-03-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems.

  17. Quantum mechanical calculation of nanomaterial-ligand interaction energies by molecular fractionation with conjugated caps method

    PubMed Central

    Zhang, Dawei

    2017-01-01

    Molecular fractionation with conjugate caps (MFCC) method is introduced for the efficient estimation of quantum mechanical (QM) interaction energies between nanomaterial (carbon nanotube, fullerene, and graphene surface) and ligand (charged and neutral). In the calculations, nanomaterials are partitioned into small fragments and conjugated caps that are properly capped, and the interaction energies can be obtained through the summation of QM calculations of the fragments from which the contribution of the conjugated caps is removed. All the calculations were performed by density functional theory (DFT) and dispersion contributions for the attractive interactions were investigated by dispersion corrected DFT method. The predicted interaction energies by MFCC at each computational level are found to give excellent agreement with full system (FS) calculations with the mean energy deviation just a fractional kcal/mol. The accurate determination of nanomaterial-ligand interaction energies by MFCC suggests that it is an effective method for performing QM calculations on nanomaterial-ligand systems. PMID:28300179

  18. Three-body interactions and solid-liquid phase equilibria: application of a molecular dynamics algorithm.

    PubMed

    Wang, Liping; Sadus, Richard J

    2006-09-01

    The effect of three-body interactions on the solid-liquid phase boundaries of argon, krypton, and xenon is investigated via a novel technique that combines both nonequilibrium and equilibrium molecular dynamics. The simulations involve the evaluation of two- and three-body forces using accurate two-body and three-body intermolecular potentials. The effect of three-body interactions is to substantially increase the coexistence pressure and to lower the densities of liquid and solid phases. Comparison with experiment indicates that three-body interactions are required to accurately determine the total pressure. In contrast to vapor-liquid phase equilibria, the relative contribution of three-body interactions to the freezing pressure exceeds the contribution of two-body interactions at all temperatures.

  19. A molecular dynamics study on slow ion interactions with the polycyclic aromatic hydrocarbon molecule anthracene

    SciTech Connect

    Postma, J.; Hoekstra, R.; Schlathölter, T.; Tielens, A. G. G. M.

    2014-03-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on analytical interaction potentials to model the interaction of low energy hydrogen and helium projectiles with isolated anthracene (C{sub 14}H{sub 10}) molecules. This approach allows for a very detailed investigation of the elastic interaction dynamics on an event by event basis. From the simulation data the threshold projectile kinetic energies above which direct C atom knock out sets in were determined. Anthracene differential energy transfer cross sections and total (dissociation) cross sections were computed for a wide range of projectile kinetic energies. The obtained results are interpreted in the context of PAH destruction in astrophysical environments.

  20. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

    PubMed Central

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  1. Predicting drug pharmacokinetic properties using molecular interaction fields and SIMCA

    NASA Astrophysics Data System (ADS)

    Wolohan, Philippa R. N.; Clark, Robert D.

    2003-01-01

    We have developed a method that combines molecular interaction fields with soft independent modeling of class analogy (SIMCA) Wold:1977 to predict pharmacokinetic drug properties. Several additional considerations to those made in traditional QSAR are required in order to develop a successful QSPR strategy that is capable of accommodating the many complex factors that contribute to key pharmacokinetic properties such as ADME (absorption, distribution, metabolism, and excretion) and toxicology. An accurate prediction of oral bioavailability, for example, requires that absorption and first-pass hepatic elimination both be taken into consideration. To accomplish this, general properties of molecules must be related to their solubility and ability to penetrate biological membranes, and specific features must be related to their particular metabolic and toxicological profiles. Here we describe a method, which is applicable to structurally diverse data sets while utilizing as much detailed structural information as possible. We address the issue of the molecular alignment of a structurally diverse set of compounds using idiotropic field orientation (IFO), a generalization of inertial field orientation Clark:1998. We have developed a second flavor of this method, which directly incorporates electrostatics into the molecular alignment. Both variations of IFO produce a characteristic orientation for each structure and the corresponding molecular fields can then be analyzed using SIMCA. Models are presented for human intestinal absorption, blood-brain barrier penetration and bioavailability to demonstrate ways in which this tool can be used early in the drug development process to identify leads likely to exhibit poor pharmacokinetic behavior in pre-clinical studies, and we have explored the influence of conformation and molecular field type on the statistical properties of the models obtained.

  2. Investigation of glassy state molecular motions in thermoset polymers

    NASA Astrophysics Data System (ADS)

    Tu, Jianwei

    This dissertation presents the investigation of the glassy state molecular motions in isomeric thermoset epoxies by means of solid-state deuterium (2H) NMR spectroscopy technique. The network structure of crosslinked epoxies was altered through monomer isomerism; specifically, diglycidyl ether of bisphenol A (DGEBA) was cured with isomeric amine curatives, i.e., the meta-substituted diaminodiphenylsulfone (33DDS) and para-substituted diaminodiphenylsulfone (44DDS). The use of structural isomerism provided a path way for altering macroscopic material properties while maintaining identical chemical composition within the crosslinked networks. The effects of structural isomerism on the glassy state molecular motions were studied using solid-state 2H NMR spectroscopy, which offers unrivaled power to monitor site-specific molecular motions. Three distinctive molecular groups on each isomeric network, i.e., the phenylene rings in the bisphenol A structure (BPA), the phenylene rings in the diaminodiphenylsulfone structure (DDS), and the hydroxypropoyl ether group (HPE) have been selectively deuterated for a comprehensive study of the structure-dynamics- property relationships in thermoset epoxies. Quadrupolar echo experiments and line shape simulations were employed as the main research approach to gain both qualitative and quantitative motional information of the epoxy networks in the glassy state. Quantitative information on the geometry and rate of the molecular motions allows the elucidation of the relationship between molecular motions and macro physical properties and the role of these motions in the mechanical relaxation. Specifically, it is revealed that both the BPA and HPE moieties in the isomeric networks have almost identical behaviors in the deep glassy state, which indicates that the molecular motions in the glassy state are localized, and the correlation length of the motions does not exceed the length of the DGEBA repeat unit. BPA ring motions contribute

  3. Gene × Environment Interactions: From Molecular Mechanisms to Behavior.

    PubMed

    Halldorsdottir, Thorhildur; Binder, Elisabeth B

    2017-01-03

    Gene-by-environment interactions (G×Es) can provide important biological insights into psychiatric disorders and may consequently have direct clinical implications. In this review, we begin with an overview of the major challenges G×E studies have faced (e.g., difficulties replicating findings and high false discovery rates). In light of these challenges, this review focuses on describing examples in which we might begin to understand G×Es on the molecular, cellular, circuit, and behavioral level and link this interaction to altered risk for the development of psychiatric disorders. We also describe recent studies that utilize a polygenic approach to examine G×Es. Finally, we discuss how gaining a deeper understanding of G×Es may translate into a therapeutic practice with more targeted treatments.

  4. Reversible Mechanical Switching of Magnetic Interactions in a Molecular Shuttle

    PubMed Central

    Bleve, Valentina; Schäfer, Christian; Franchi, Paola; Silvi, Serena; Mezzina, Elisabetta; Credi, Alberto; Lucarini, Marco

    2015-01-01

    Invited for this months cover are the groups of Professors Marco Lucarini and Alberto Credi at the University of Bologna. The cover picture shows coupled and uncoupled states of a [2]rotaxane incorporating stable nitroxide radical units in both the ring and dumbbell components. Interaction between nitroxide radicals could be switched between noncoupled (three-line electron paramagnetic resonance (EPR) spectrum) and coupled (five-line EPR spectrum) upon deprotonation of the rotaxane NH2+ centers that effects a quantitative displacement of a dibenzocrown macroring to a 4,4’-bipyridinium recognition site. The complete base- and acid-induced switching cycle of the EPR pattern was repeated several times without an appreciable loss of signal, highlighting the reversibility of the process. Hence, this molecular machine is capable of switching on/off magnetic interactions by chemically driven reversible mechanical effects. For more details, see the Communication on p. 18 ff. PMID:25870780

  5. Molecular dynamics modeling of a nanomaterials-water surface interaction

    NASA Astrophysics Data System (ADS)

    Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid

    2016-04-01

    In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.

  6. New insights on molecular interactions of organophosphorus pesticides with esterases.

    PubMed

    Mangas, Iris; Estevez, Jorge; Vilanova, Eugenio; França, Tanos Celmar Costa

    2017-02-01

    Organophosphorus compounds (OPs) are a large and diverse class of chemicals mainly used as pesticides and chemical weapons. People may be exposed to OPs in several occasions, which can produce several distinct neurotoxic effects depending on the dose, frequency of exposure, type of OP, and the host factors that influence susceptibility and sensitivity. These neurotoxic effects are mainly due to the interaction with enzyme targets involved in toxicological or detoxication pathways. In this work, the toxicological relevance of known OPs targets is reviewed. The main enzyme targets of OPs have been identified among the serine hydrolase protein family, some of them decades ago (e.g. AChE, BuChE, NTE and carboxylesterases), others more recently (e.g. lysophospholipase, arylformidase and KIA1363) and others which are not molecularly identified yet (e.g. phenylvalerate esterases). Members of this family are characterized by displaying serine hydrolase activity, containing a conserved serine hydrolase motif and having an alpha-beta hydrolase fold. Improvement in Xray-crystallography and in silico methods have generated new data of the interactions between OPs and esterases and have established new methods to study new inhibitors and reactivators of cholinesterases. Mass spectrometry for AChE, BChE and APH have characterized the active site serine adducts with OPs being useful to detect biomarkers of OPs exposure and inhibitory and postinhibitory reactions of esterases and OPs. The purpose of this review is focus specifically on the interaction of OP with esterases, mainly with type B-esterases, which are able to hydrolyze carboxylesters but inhibited by OPs by covalent phosphorylation on the serine or tyrosine residue in the active sites. Other related esterases in some cases with no-irreversible effect are also discussed. The understanding of the multiple molecular interactions is the basis we are proposing for a multi-target approach for understanding the

  7. Density functional theory based study of molecular interactions, recognition, engineering, and quantum transport in π molecular systems.

    PubMed

    Cho, Yeonchoo; Cho, Woo Jong; Youn, Il Seung; Lee, Geunsik; Singh, N Jiten; Kim, Kwang S

    2014-11-18

    CONSPECTUS: In chemical and biological systems, various interactions that govern the chemical and physical properties of molecules, assembling phenomena, and electronic transport properties compete and control the microscopic structure of materials. The well-controlled manipulation of each component can allow researchers to design receptors or sensors, new molecular architectures, structures with novel morphology, and functional molecules or devices. In this Account, we describe the structures and electronic and spintronic properties of π-molecular systems that are important for controlling the architecture of a variety of carbon-based systems. Although DFT is an important tool for describing molecular interactions, the inability of DFT to accurately represent dispersion interactions has made it difficult to properly describe π-interactions. However, the recently developed dispersion corrections for DFT have allowed us to include these dispersion interactions cost-effectively. We have investigated noncovalent interactions of various π-systems including aromatic-π, aliphatic-π, and non-π systems based on dispersion-corrected DFT (DFT-D). In addition, we have addressed the validity of DFT-D compared with the complete basis set (CBS) limit values of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] and Møller-Plesset second order perturbation theory (MP2). The DFT-D methods are still unable to predict the correct ordering in binding energies within the benzene dimer and the cyclohexane dimer. Nevertheless, the overall DFT-D predicted binding energies are in reasonable agreement with the CCSD(T) results. In most cases, results using the B97-D3 method closely reproduce the CCSD(T) results with the optimized energy-fitting parameters. On the other hand, vdW-DF2 and PBE0-TS methods estimate the dispersion energies from the calculated electron density. In these approximations, the interaction energies around the equilibrium

  8. Interaction of peptides with cell membranes: insights from molecular modeling

    NASA Astrophysics Data System (ADS)

    Li, Zhen-lu; Ding, Hong-ming; Ma, Yu-qiang

    2016-03-01

    The investigation of the interaction of peptides with cell membranes is the focus of active research. It can enhance the understanding of basic membrane functions such as membrane transport, fusion, and signaling processes, and it may shed light on potential applications of peptides in biomedicine. In this review, we will present current advances in computational studies on the interaction of different types of peptides with the cell membrane. Depending on the properties of the peptide, membrane, and external environment, the peptide-membrane interaction shows a variety of different forms. Here, on the basis of recent computational progress, we will discuss how different peptides could initiate membrane pores, translocate across the membrane, induce membrane endocytosis, produce membrane curvature, form fibrils on the membrane surface, as well as interact with functional membrane proteins. Finally, we will present a conclusion summarizing recent progress and providing some specific insights into future developments in this field.

  9. Studies on molecular interactions between nalidixic acid and liposomes.

    PubMed

    Budai, M; Szabó, Zs; Zimmer, A; Szögyi, M; Gróf, P

    2004-07-26

    The interaction between nalidixic acid sodium salt (NANa) and liposomes prepared from alpha-L-dipalmitoyl-phosphatidylcholine (DPPC) or from its binary mixture with dioleoyl-phosphatidylcholine (DOPC) was studied with differential scanning calorimetry (DSC) and electron paramagnetic resonance (EPR) spectroscopy. We evaluated the role of broadband ultraviolet-B (UV-B) irradiation on the molecular interactions between the lipids and the NANa, and determined the decay-kinetics of the incorporated spin labeled fatty-acid free radicals. Multilamellar and unilamellar vesicles were prepared by sonication and extrusion. The entrapment efficiencies were determined spectrophotometrically. The size-distribution of the liposomes and its change in time was checked by dynamic light scattering (DLS). Our results indicate that NANa mainly interacts with lipid head groups. However, its effect and presumably the formation of the free radicals, induced by broadband ultraviolet-B, is not localized only to the head group region of the lipid molecules. Depending on DOPC content, interaction between the NANa and the lipids modifies the phase-transition parameters of the liposome dispersions.

  10. A microcalorimetric study of molecular interactions between immunoglobulin G and hydrophobic charge-induction ligand.

    PubMed

    Yuan, Xiao-Ming; Lin, Dong-Qiang; Zhang, Qi-Lei; Gao, Dong; Yao, Shan-Jing

    2016-04-22

    Hydrophobic charge-induction chromatography (HCIC) with 4-mercaptoethyl-pyridine (MEP) as the ligand is a novel technology for antibody purification. In this study, isothermal titration calorimetry (ITC) was used to evaluate the molecular interactions between MEP ligand and immunoglobulin G (IgG). Three types of IgG molecules including human IgG (hIgG), bovine IgG (bIgG) and a monoclonal antibody (mAb) were investigated with human serum albumins (HSA) and bovine serum albumin (BSA) as the comparison. The thermodynamic parameters obtained from ITC were compared with the adsorption data. The results indicated that MEP binding to protein at neutral pH was entropy driven and induced by multimodal molecular interactions that was dominated by hydrophobic forces. The interactions between MEP and IgGs were stronger than that of albumins, which resulted in high binding affinity of IgGs. Moreover, the effects of pH and salt addition on MEP-hIgG binding were studied. The change of enthalpy increased obviously with the decrease of pH, which revealed that the electrostatic forces dominated the MEP-hIgG interactions at acidic condition and caused typical charge-induced elution of HCIC. Salt addition influenced both hydrophobic and electrostatic interactions. With the increase of salt concentration, the hydrophobic interactions decreased first and then increased, while the electrostatic interactions showed the opposite trend. This resulted in trade-off between the multimodal interactions, which caused the salt-tolerant property of MEP resin. In general, ITC studies revealed the molecular mechanism of three critical characteristics of HCIC, multimodal interactions, pH-dependent and salt-tolerant properties.

  11. Investigations of ice nanoparticles and aerosols in molecular beams

    NASA Astrophysics Data System (ADS)

    Farnik, Michal

    2015-03-01

    We have recently set up a versatile experiment which allows for different experiments with molecular clusters and nanoparticles in molecular beams. Here we concentrate on the experiments with ice nanoparticles (large water clusters (H2O)N, N ~ 102-103) doped with atmospherically relevant molecules, e.g., hydrogen halides, CFCs, nitric acid, NxOy, etc. Such species are relevant to ozone depletion and other atmospheric processes. We investigate (1) the UV-photochemistry using velocity map imaging techniques, and (2) the uptake cross section for the molecules on the ice nanoparticles from velocity measurements. In addition, we record (3) mass spectra of the particles implementing different ionization methods: electron ionization (EI) at variable electron energies, photoionization, and special method of electron photodetachment after Na-doping (NaPI). The unique combination of all these different methods performed with the same nanoparticles provides detailed molecular level information about the studied species and their (photo)physics and chemistry. In particular, an investigation of mixed water-nitric acid particles by means of EI and NaPI revealed the prominent role of the HNO3 molecule as the condensation nuclei. The uptake of atmospheric molecules by ice nanoparticles has been studied, and the pickup cross sections for some molecules exceed significantly the geometrical sizes of the ice nanoparticles. It has been argued that the large particles composed of several hundred water molecules which grow in the supersonic expansions tend to have highly irregular shapes -nanosnowflakes. Photodissociation of hydrogen halides on ice nanoparticles has been investigated, and shown to proceed via excitation of acidically dissociated ion pair and subsequent biradical generation and H3O dissociation. The photodissociation of CF2Cl2 molecules in clusters leads to efficient Cl-fragment caging caused by formation of halogen bond. Grant agency of the Czech Republic, Grant No.: 14

  12. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors.

    PubMed

    Xie, Huiding; Li, Yupeng; Yu, Fang; Xie, Xiaoguang; Qiu, Kaixiong; Fu, Jijun

    2015-11-16

    In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds) in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA), and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  13. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    PubMed Central

    Xie, Huiding; Li, Yupeng; Yu, Fang; Xie, Xiaoguang; Qiu, Kaixiong; Fu, Jijun

    2015-01-01

    In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD) simulation and binding free energy (ΔGbind) calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds) in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA), and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors. PMID:26580609

  14. Targeting molecular interactions essential for Plasmodium sexual reproduction

    PubMed Central

    Vega-Rodriguez, Joel; Perez-Barreto, Davinia; Ruiz-Reyes, Antonio; Jacobs-Lorena, Marcelo

    2015-01-01

    Summary Malaria remains one of the most devastating infectious diseases, killing up to a million people every year. Whereas much progress has been made in understanding the life cycle of the parasite in the human host and in the mosquito vector, significant gaps of knowledge remain. Fertilization of malaria parasites, a process that takes place in the lumen of the mosquito midgut, is poorly understood and the molecular interactions (receptor–ligand) required for Plasmodium fertilization remain elusive. By use of a phage display library, we identified FG1 (Female Gamete peptide 1), a peptide that binds specifically to the surface of female Plasmodium berghei gametes. Importantly, FG1 but not a scrambled version of the peptide, strongly reduces P. berghei oocyst formation by interfering with fertilization. In addition, FG1 also inhibits P. falciparum oocyst formation suggesting that the peptide binds to a molecule on the surface of the female gamete whose structure is conserved. Identification of the molecular interactions disrupted by the FG1 peptide may lead to the development of novel malaria transmission-blocking strategies. PMID:25944054

  15. Molecular Interactions in Particular Van der Waals Nanoclusters

    NASA Astrophysics Data System (ADS)

    Jungclas, Hartmut; Komarov, Viacheslav V.; Popova, Anna M.; Schmidt, Lothar

    2017-01-01

    A method is presented to analyse the interaction energies in a nanocluster, which is consisting of three neutral molecules bound by non-covalent long range Van der Waals forces. One of the molecules (M0) in the nanocluster has a permanent dipole moment, whereas the two other molecules (M1 and M2) are non-polar. Analytical expressions are obtained for the numerical calculation of the dispersion and induction energies of the molecules in the considered nanocluster. The repulsive forces at short intermolecular distances are taken into account by introduction of damping functions. Dispersion and induction energies are calculated for a nanocluster with a definite geometry, in which the polar molecule M0 is a linear hydrocarbon molecule C5H10 and M1 and M2 are pyrene molecules. The calculations are done for fixed distances between the two pyrene molecules. The results show that the induction energies in the considered three-molecular nanocluster are comparable with the dispersion energies. Furthermore, the sum of induction energies in the substructure (M0, M1) of the considered nanocluster is much higher than the sum of induction energies in a two-molecular nanocluster with similar molecules (M0, M1) because of the absence of an electrostatic field in the latter case. This effect can be explained by the essential intermolecular induction in the three-molecular nanocluster.

  16. A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida).

    PubMed

    Clamp, John C; Williams, Daniel

    2006-01-01

    The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.

  17. Optimizing molecular electrostatic interactions: Binding affinity and specificity

    NASA Astrophysics Data System (ADS)

    Kangas, Erik

    The design of molecules that bind tightly and specifically to designated target molecules is an important goal in many fields of molecular science. While the shape of the molecule to be designed is a relatively well defined problem with an intuitive answer, determination of the distribution of electrostatic charge that it should have in order to possess high affinity and/or specificity for a target is a subtle problem involving a tradeoff between an unfavorable electrostatic desolvation penalty incurred due to the removal of solvent from the interacting surfaces of the reactants, and the generally favorable intermolecular interactions made in the bound state. In this thesis, a theoretical formalism based on a continuum electrostatic approximation is developed in which charge distributions leading to optimal affinity and/or high specificity may be obtained. Methods for obtaining these charge distributions are developed in detail and analytical solutions are obtained in several special cases (where the molecules are shaped as infinite membranes, spheres, and spheroids). Their existence and non-uniqueness are also shown, and it is proven that the resulting optimized electrostatic binding free energies are favorable (negative) in many cases of physical interest. Affinity and specificity optimization is then applied to the chorismate mutase family of enzymes, including the catalytic antibody 1F7. It is shown that affinity optimization can be used to suggest better molecular inhibitors and that specificity optimization can be used to help elucidate molecular function and possibly aid in the creation of improved haptens. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

  18. Targeting chk2 kinase: molecular interaction maps and therapeutic rationale.

    PubMed

    Pommier, Yves; Sordet, Olivier; Rao, V Ashutosh; Zhang, Hongliang; Kohn, Kurt W

    2005-01-01

    Most anticancer drugs presently used clinically target genomic DNA. The selectivity of these anticancer drugs for tumor tissues is probably due to tumor-specific defects suppressing cell cycle checkpoints and DNA repair, and enhancing apoptotic response in the tumor. We will review the molecular interactions within the ATM-Chk2 pathway implicating the DNA damage sensor kinases (ATM, ATR and DNA-PK), the adaptor BRCT proteins (Nbs1, Brca1, 53BP1, MDC1) and the effector kinases (Chk2, Chk1, Plk3, JNK, p38). The molecular interaction map convention (MIM) will be used for presenting this molecular network (http://discover.nci.nih.gov/mim/). A characteristic of the ATM-Chk2 pathway is its redundancy. First, ATM and Chk2 phosphorylate common substrates including p53, E2F1, BRCA1, and Chk2 itself, which suggests that Chk2 (also known as CHECK2, Cds1 in fission yeast, and Dmchk2 or Dmnk or Loki in the fruit fly) acts as a relay for ATM and/or as a salvage pathway when ATM is inactivated. Secondly, redundancy is apparent for the substrates, which can be phosphorylated/activated at similar residues by Chk2, Chk1, and the polo kinases (Plk's). Functionally, Chk2 can activate both apoptosis (via p53, E2F1 and PML) and cell cycle checkpoint (via Cdc25A and Cdc25C, p53, and BRCA1). We will review the short list of published Chk2 inhibitors. We will also propose a novel paradigm for screening interfacial inhibitors of Chk2. Chk2 inhibitors might be used to enhance the tumor selectivity of DNA targeted agents in p53-deficient tumors, and for the treatment of tumors whose growth depends on enhanced Chk2 activity.

  19. Molecular structures and π π interactions of some flavonoids and biflavonoids

    NASA Astrophysics Data System (ADS)

    Jiang, Ren-Wang; Ye, Wen-Cai; Woo, Ka-Yan; Du, Jiang; Che, Chun-Tao; But, Paul Pui-Hay; Mak, Thomas C. W.

    2002-12-01

    The molecular structures of two flavones, wogonin ( 1) and mikanin ( 2), and two biflavonoids, cupressuflavone ( 3) and neochamaejasmin A ( 4), were determined by single-crystal X-ray analysis. The intermolecular π-π interactions in 1- 4 and the flavanones alpinetin ( 5) and naringenin ( 6) were investigated. Compounds 1- 4 feature offset face-to-face intermolecular π-π interactions with centroid-centroid distances ranging from 3.70 to 3.81 Å and displacement angles ranging from 2.7 to 9.9°.

  20. Intra-membrane molecular interactions of K+ channel proteins :

    SciTech Connect

    Moczydlowski, Edward G.

    2013-07-01

    Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

  1. Molecular recognition of malachite green by hemoglobin and their specific interactions: insights from in silico docking and molecular spectroscopy.

    PubMed

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

    2014-01-01

    Malachite green is an organic compound that can be widely used as a dyestuff for various materials; it has also emerged as a controversial agent in aquaculture. Since malachite green is proven to be carcinogenic and mutagenic, it may become a hazard to public health. For this reason, it is urgently required to analyze this controversial dye in more detail. In our current research, the interaction between malachite green and hemoglobin under physiological conditions was investigated by the methods of molecular modeling, fluorescence spectroscopy, circular dichroism (CD) as well as hydrophobic ANS displacement experiments. From the molecular docking, the central cavity of hemoglobin was assigned to possess high-affinity for malachite green, this result was corroborated by time-resolved fluorescence and hydrophobic ANS probe results. The recognition mechanism was found to be of static type, or rather the hemoglobin-malachite green complex formation occurred via noncovalent interactions such as π-π interactions, hydrogen bonds and hydrophobic interactions with an association constant of 10(4) M(-1). Moreover, the results also show that the spatial structure of the biopolymer was changed in the presence of malachite green with a decrease of the α-helix and increase of the β-sheet, turn and random coil suggesting protein damage, as derived from far-UV CD and three-dimensional fluorescence. Results of this work will help to further comprehend the molecular recognition of malachite green by the receptor protein and the possible toxicological profiles of other compounds, which are the metabolites and ramifications of malachite green.

  2. Predicting Molecular Crowding Effects in Ion-RNA Interactions.

    PubMed

    Yu, Tao; Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

    2016-09-01

    We develop a new statistical mechanical model to predict the molecular crowding effects in ion-RNA interactions. By considering discrete distributions of the crowders, the model can treat the main crowder-induced effects, such as the competition with ions for RNA binding, changes of electrostatic interaction due to crowder-induced changes in the dielectric environment, and changes in the nonpolar hydration state of the crowder-RNA system. To enhance the computational efficiency, we sample the crowder distribution using a hybrid approach: For crowders in the close vicinity of RNA surface, we sample their discrete distributions; for crowders in the bulk solvent away from the RNA surface, we use a continuous mean-field distribution for the crowders. Moreover, using the tightly bound ion (TBI) model, we account for ion fluctuation and correlation effects in the calculation for ion-RNA interactions. Applications of the model to a variety of simple RNA structures such as RNA helices show a crowder-induced increase in free energy and decrease in ion binding. Such crowding effects tend to contribute to the destabilization of RNA structure. Further analysis indicates that these effects are associated with the crowder-ion competition in RNA binding and the effective decrease in the dielectric constant. This simple ion effect model may serve as a useful framework for modeling more realistic crowders with larger, more complex RNA structures.

  3. Towards understanding of molecular interactions between rice and the brown planthopper.

    PubMed

    Cheng, Xiaoyan; Zhu, Lili; He, Guangcun

    2013-05-01

    The brown planthopper (BPH) is the most notorious pest of rice (Oryza sativa). Studies of rice-BPH interaction have contributed to development of new rice varieties, offering an effective means for long-lasting control of BPH. Here, we review the status of knowledge of the molecular basis of rice-BPH interaction, from the perspective of immunity. The BPH has complicated feeding behaviors on rice, which are mainly related to host resistance. Now, 24 resistance genes have been detected in rice, indicating gene-for-gene relationships with biotypes of the BPH. However, only one BPH resistance gene (Bph14) was identified and characterized using map-based cloning. Bph14 encodes an immune receptor of NB-LRR family, providing a means for studying the molecular mechanisms of rice resistance to BPH. Plant hormones (e.g. salicylic acid and jasmonate/ethylene), Ca(2+), mitogen-activated protein kinases (MAPKs), and OsRac1 play important roles in the immune response of rice to BPH. Signal transduction leads to modifying expression of defense-related genes and defense mechanisms against BPH, including sieve tube sealing, production of secondary metabolites, and induction of proteinase inhibitor. A model for the molecular interactions between rice and the BPH is proposed, although many details remain to be investigated that are valuable for molecular design of BPH-resistant rice varieties.

  4. Probing the molecular interaction of triazole fungicides with human serum albumin by multispectroscopic techniques and molecular modeling.

    PubMed

    Zhang, Jing; Zhuang, Shulin; Tong, Changlun; Liu, Weiping

    2013-07-31

    Triazole fungicides, one category of broad-spectrum fungicides, are widely applied in agriculture and medicine. The extensive use leads to many residues and casts potential detrimental effects on aquatic ecosystems and human health. After exposure of the human body, triazole fungicides may penetrate into the bloodstream and interact with plasma proteins. Whether they could have an impact on the structure and function of proteins is still poorly understood. By using multispectroscopic techniques and molecular modeling, the interaction of several typical triazole fungicides with human serum albumin (HSA), the major plasma protein, was investigated. The steady-state and time-resolved fluorescence spectra manifested that static type, due to complex formation, was the dominant mechanism for fluorescence quenching. Structurally related binding modes speculated by thermodynamic parameters agreed with the prediction of molecular modeling. For triadimefon, hydrogen bonding with Arg-218 and Arg-222 played an important role, whereas for imazalil, myclobutanil, and penconazole, the binding process was mainly contributed by hydrophobic and electrostatic interactions. Via alterations in three-dimensional fluorescence and circular dichroism spectral properties, it was concluded that triazoles could induce slight conformational and some microenvironmental changes of HSA. It is anticipated that these data can provide some information for possible toxicity risk of triazole fungicides to human health and be helpful in reinforcing the supervision of food safety.

  5. Virtual Manipulatives on the Interactive Whiteboard: A Preliminary Investigation

    ERIC Educational Resources Information Center

    Mildenhall, Paula; Swan, Paul; Northcote, Maria; Marshall, Linda

    2008-01-01

    As part of the project titled "Hands-On Heads-On: The Effective Use of Manipulatives Both Virtual and Physical" being undertaken at Edith Cowan University, there was an investigation into the use of virtual manipulatives and the interactive whiteboard (IWB). Virtual manipulatives may be defined as a virtual representation of a physical…

  6. Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study.

    PubMed

    Qais, Faizan Abul; Abdullah, K M; Alam, Md Maroof; Naseem, Imrana; Ahmad, Iqbal

    2017-04-01

    Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waal's forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted.

  7. Molecular self-assembly for biological investigations and nanoscale lithography

    NASA Astrophysics Data System (ADS)

    Cheunkar, Sarawut

    Small, diffusible molecules when recognized by their binding partners, such as proteins and antibodies, trigger enzymatic activity, cell communication, and immune response. Progress in analytical methods enabling detection, characterization, and visualization of biological dynamics at the molecular level will advance our exploration of complex biological systems. In this dissertation, analytical platforms were fabricated to capture membrane-associated receptors, which are essential proteins in cell signaling pathways. The neurotransmitter serotonin and its biological precursor were immobilized on gold substrates coated with self-assembled monolayers (SAMs) of oligo(ethylene glycol)alkanethiols and their reactive derivatives. The SAM-coated substrates present the biologically selective affinity of immobilized molecules to target native membrane-associated receptors. These substrates were also tested for biospecificity using antibodies. In addition, small-molecule-functionalized platforms, expressing neurotransmitter pharmacophores, were employed to examine kinetic interactions between G-protein-coupled receptors and their associated neurotransmitters. The binding interactions were monitored using a quartz crystal microbalance equipped with liquid-flow injection. The interaction kinetics of G-protein-coupled serotonin 1A receptor and 5-hydroxytyptophan-functionalized surfaces were studied in a real-time, label-free environment. Key binding parameters, such as equilibrium dissociation constants, binding rate constants, and dissociative half-life, were extracted. These parameters are critical for understanding and comparing biomolecular interactions in modern biomedical research. By integrating self-assembly, surface functionalization, and nanofabrication, small-molecule microarrays were created for high-throughput screening. A hybrid soft-lithography, called microcontact insertion printing, was used to pattern small molecules at the dilute scales necessary for highly

  8. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    NASA Astrophysics Data System (ADS)

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-12-01

    Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  9. Molecular View of Protein Crystal Growth: Molecular Interactions, Surface Reconstruction and Growth Mechanism

    NASA Technical Reports Server (NTRS)

    Nadarajah, Arunan; Li, Huayu; Konnert, John H.; Pusey, Marc L.

    2000-01-01

    Studies of the growth and molecular packing of tetragonal lysozyme crystals suggest that there is an underlying molecular growth mechanism, in addition to the classical one involving screw dislocation/2D) nucleation growth. These crystals are constructed by strongly bonded molecular chains forming helices about the 43 axes. The helices are connected to each other by weaker bonds. Crystal growth proceeds by the formation of these 4(sub 3) helices, which would explain some unexpected observations by earlier investigators, such as bimolecular growth steps on the (110) face. Another consequence of these molecular considerations is that only one of two possible packing arrangements could occur on the crystal faces and that their growth unit was at least a tetramer corresponding to the 4(sub 3) helix. Two new high resolution atomic force microscopy (AFM) techniques were developed to directly confirm these predictions on tetragonal lysozyme crystals. Most earlier investigations of protein crystal growth with AFM were in the low resolution mode which is adequate to investigate the classical growth mechanisms, but cannot resolve molecular features and mechanisms. Employing the first of the newly developed techniques, high resolution AFM images of the (110) face were compared with the theoretically constructed images for the two possible packing arrangements on this face. The prediction that the molecular packing arrangement of these faces corresponded to that for complete 4(sub 3) helices was confirmed in this manner. This investigation also showed the occurrence of surface reconstruction on protein crystals. The molecules on the surface of the (110) face were found to pack closer along the 4(sub 3) axes than those in the interior. The second new AFM technique was used to follow the growth process by measuring the dimensions of individual growth units on the (110) face. Linescans across a growth step, performed near the saturation limit of the crystals, allowed the growth

  10. Interactive display of molecular models using a microcomputer system

    NASA Technical Reports Server (NTRS)

    Egan, J. T.; Macelroy, R. D.

    1980-01-01

    A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

  11. Investigation of binding features: effects on the interaction between CYP2A6 and inhibitors.

    PubMed

    Ai, Chunzhi; Li, Yan; Wang, Yonghua; Li, Wei; Dong, Peipei; Ge, Guangbo; Yang, Ling

    2010-07-15

    A computational investigation has been carried out on CYP2A6 and its naphthalene inhibitors to explore the crucial molecular features contributing to binding specificity. The molecular bioactive orientations were obtained by docking (FlexX) these compounds into the active site of the enzyme. And the density functional theory method was further used to optimize the molecular structures with the subsequent analysis of molecular lipophilic potential (MLP) and molecular electrostatic potential (MEP). The minimal MLPs, minimal MEPs, and the band gap energies (the energy difference between the highest occupied molecular orbital and lowest unoccupied molecular orbital) showed high correlations with the inhibition activities (pIC(50)s), illustrating their significant roles in driving the inhibitor to adopt an appropriate bioactive conformation oriented in the active site of CYP2A6 enzyme. The differences in MLPs, MEPs, and the orbital energies have been identified as key features in determining the binding specificity of this series of compounds to CYP2A6 and the consequent inhibitory effects. In addition, the combinational use of the docking, MLP and MEP analysis is also demonstrated as a good attempt to gain an insight into the interaction between CYP2A6 and its inhibitors.

  12. Spectroscopy and molecular docking study on the interaction behavior between nobiletin and pepsin.

    PubMed

    Zeng, Hua-jin; Qi, Tingting; Yang, Ran; You, Jing; Qu, Ling-bo

    2014-07-01

    In this study, the binding mode of nobiletin (NOB) with pepsin was investigated by spectroscopic and molecular docking methods. NOB can interact with pepsin to form a NOB-pepsin complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that NOB could spontaneously bind with pepsin through hydrophobic and electrostatic forces with one binding site. Molecular docking results revealed that NOB bound into the pepsin cavity. Synchronous and three-dimensional fluorescence spectra results provide data concerning conformational and some micro-environmental changes of pepsin. Furthermore, the binding of NOB can inhibit pepsin activity in vitro. The present study provides direct evidence at a molecular level to show that NOB could induce changes in the enzyme pepsin structure and function.

  13. Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

    PubMed

    Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

    2014-12-01

    2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT.

  14. The molecular interactions of buspirone analogues with the serotonin transporter.

    PubMed

    Jarończyk, Małgorzata; Chilmonczyk, Zdzisław; Mazurek, Aleksander P; Nowak, Gabriel; Ravna, Aina W; Kristiansen, Kurt; Sylte, Ingebrigt

    2008-10-15

    A major problem with the selective serotonin reuptake inhibitors (SSRIs) is the delayed onset of action. A reason for that may be that the initial SSRI-induced increase in serotonin levels activates somatodendritic 5-HT(1A) autoreceptors, causing a decrease in serotonin release in major forebrain areas. It has been suggested that compounds combining inhibition of the serotonin transport protein with antagonistic effects on the 5-HT(1A) receptor will shorten the onset time. The anxiolytic drug buspirone is known as 5-HT(1A) partial agonist. In the present work, we are studying the inhibition of the serotonin transporter protein by a series of buspirone analogues by molecular modelling and by experimental affinity measurements. Models of the transporter protein were constructed using the crystal structure of the Escherichia coli major facilitator family transporter-LacY and the X-ray structure of the neurotransmitter symporter family (NSS) transporter-LeuT(Aa) as templates. The buspirone analogues were docked into both SERT models and the interactions with amino acids within the protein were analyzed. Two putative binding sites were identified on the LeuT(Aa) based model, one suggested to be a high-affinity site, and the other suggested to be a low-affinity binding site. Molecular dynamic simulations of the LacY based model in complex with ligands did not induce a helical architecture of the LacY based model into an arrangement more similar to that of the LeuT(Aa) based model.

  15. Thermal and molecular investigation of laser tissue welding

    SciTech Connect

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  16. Simulating social interactions for the experimental investigation of joint attention.

    PubMed

    Caruana, Nathan; McArthur, Genevieve; Woolgar, Alexandra; Brock, Jon

    2017-03-01

    Social interactions are, by their nature, dynamic and reciprocal - your behaviour affects my behaviour, which affects your behaviour in return. However, until recently, the field of social cognitive neuroscience has been dominated by paradigms in which participants passively observe social stimuli from a detached "third person" perspective. Here we consider the unique conceptual and methodological challenges involved in adopting a "second person" approach whereby social cognitive mechanisms and their neural correlates are investigated within social interactions (Schilbach et al., 2013). The key question for researchers is how to distil a complex, intentional interaction between two individuals into a tightly controlled and replicable experimental paradigm. We explore these issues within the context of recent investigations of joint attention - the ability to coordinate a common focus of attention with another person. We review pioneering neurophysiology and eye-tracking studies that have begun to address these issues; offer recommendations for the optimal design and implementation of interactive tasks, and discuss the broader implications of interactive approaches for social cognitive neuroscience.

  17. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  18. Quantum-chemical investigations of small molecular anions

    NASA Astrophysics Data System (ADS)

    Botschwina, P.; Seeger, S.; Mladenović, M.; Schulz, B.; Horn, M.; Schmatz, S.; Flügge, J.; Oswald, R.

    Dedicated to Dr Gerhard Herzberg on the occasion of his 90th birthday Recent large-scale ab initio calculations for small negative molecular ions are reviewed. Accurate equilibrium geometries are established for several species like NH2-, HCC-, NO2-, CH2N- C5- and C6-. Predictions are made for various spectroscopic properties like vibrational frequencies, rotational constants and infrared intensities. The effects of a shallow energy minimum in the T-shaped configuration on the rovibrational term energies of HCC - are investigated. The calculated vibrational structures of the photoelectron spectra of SiH3- and CH2N - are in very good agreement with the experiment. The present calculations support the assignment of an absorption observed at 608 nm in a neon matrix to the

  19. All-atom Molecular-level Computational Simulations of Planar Longitudinal Shockwave Interactions with Polyurea, Soda-lime Glass and Polyurea/Glass Interfaces

    DTIC Science & Technology

    2014-01-01

    All-atom molecular-level computational simulations of planar longitudinal shockwave interactions with polyurea, soda-lime glass and polyurea/glass...sandwich structures under dynamic-loading conditions involving propagation of planar longitudinal shockwaves . Design/methodology/approach – The problem...of shockwave generation, propagation and interaction with material boundaries is investigated using non-equilibrium molecular dynamics. The results

  20. Creep rupture of fiber bundles: A molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Linga, G.; Ballone, P.; Hansen, Alex

    2015-08-01

    The creep deformation and eventual breaking of polymeric samples under a constant tensile load F is investigated by molecular dynamics based on a particle representation of the fiber bundle model. The results of the virtual testing of fibrous samples consisting of 40 000 particles arranged on Nc=400 chains reproduce characteristic stages seen in the experimental investigations of creep in polymeric materials. A logarithmic plot of the bundle lifetime τ versus load F displays a marked curvature, ruling out a simple power-law dependence of τ on F . A power law τ ˜F-4 , however, is recovered at high load. We discuss the role of reversible bond breaking and formation on the eventual fate of the sample and simulate a different type of creep testing, imposing a constant stress rate on the sample up to its breaking point. Our simulations, relying on a coarse-grained representation of the polymer structure, introduce new features into the standard fiber bundle model, such as real-time dynamics, inertia, and entropy, and open the way to more detailed models, aiming at material science aspects of polymeric fibers, investigated within a sound statistical mechanics framework.

  1. An experimental investigation of the parallel blade-vortex interaction

    NASA Technical Reports Server (NTRS)

    Caradonna, F. X.; Laub, G. H.; Tung, C.

    1984-01-01

    A scheme for investigating the parallel blade vortex interaction (BVI) has been designed and tested. The scheme involves setting a vortex generator upstream of a nonlifting rotor so that the vortex interacts with the blade at the forward azimuth. The method has revealed two propagation mechanisms: a type C shock propagation from the leading edge induced by the vortex at high tip speeds, and a rapid but continuous pressure pulse associated with the proximity of the vortex to the leading edge. The latter is thought to be the more important source. The effects of Mach number and vortex proximity are discussed.

  2. Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions

    PubMed Central

    Scholes, Natalie S.; Weinzierl, Robert O. J.

    2016-01-01

    Transcriptional activation domains (ADs) are generally thought to be intrinsically unstructured, but capable of adopting limited secondary structure upon interaction with a coactivator surface. The indeterminate nature of this interface made it hitherto difficult to study structure/function relationships of such contacts. Here we used atomistic accelerated molecular dynamics (aMD) simulations to study the conformational changes of the GCN4 AD and variants thereof, either free in solution, or bound to the GAL11 coactivator surface. We show that the AD-coactivator interactions are highly dynamic while obeying distinct rules. The data provide insights into the constant and variable aspects of orientation of ADs relative to the coactivator, changes in secondary structure and energetic contributions stabilizing the various conformers at different time points. We also demonstrate that a prediction of α-helical propensity correlates directly with the experimentally measured transactivation potential of a large set of mutagenized ADs. The link between α-helical propensity and the stimulatory activity of ADs has fundamental practical and theoretical implications concerning the recruitment of ADs to coactivators. PMID:27175900

  3. Multitargeting by curcumin as revealed by molecular interaction studies.

    PubMed

    Gupta, Subash C; Prasad, Sahdeo; Kim, Ji Hye; Patchva, Sridevi; Webb, Lauren J; Priyadarsini, Indira K; Aggarwal, Bharat B

    2011-11-01

    Curcumin (diferuloylmethane), the active ingredient in turmeric (Curcuma longa), is a highly pleiotropic molecule with anti-inflammatory, anti-oxidant, chemopreventive, chemosensitization, and radiosensitization activities. The pleiotropic activities attributed to curcumin come from its complex molecular structure and chemistry, as well as its ability to influence multiple signaling molecules. Curcumin has been shown to bind by multiple forces directly to numerous signaling molecules, such as inflammatory molecules, cell survival proteins, protein kinases, protein reductases, histone acetyltransferase, histone deacetylase, glyoxalase I, xanthine oxidase, proteasome, HIV1 integrase, HIV1 protease, sarco (endo) plasmic reticulum Ca(2+) ATPase, DNA methyltransferases 1, FtsZ protofilaments, carrier proteins, and metal ions. Curcumin can also bind directly to DNA and RNA. Owing to its β-diketone moiety, curcumin undergoes keto-enol tautomerism that has been reported as a favorable state for direct binding. The functional groups on curcumin found suitable for interaction with other macromolecules include the α, β-unsaturated β-diketone moiety, carbonyl and enolic groups of the β-diketone moiety, methoxy and phenolic hydroxyl groups, and the phenyl rings. Various biophysical tools have been used to monitor direct interaction of curcumin with other proteins, including absorption, fluorescence, Fourier transform infrared (FTIR) and circular dichroism (CD) spectroscopy, surface plasmon resonance, competitive ligand binding, Forster type fluorescence resonance energy transfer (FRET), radiolabeling, site-directed mutagenesis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), immunoprecipitation, phage display biopanning, electron microscopy, 1-anilino-8-naphthalene-sulfonate (ANS) displacement, and co-localization. Molecular docking, the most commonly employed computational tool for calculating binding affinities and predicting

  4. Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

    NASA Astrophysics Data System (ADS)

    Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

    2013-07-01

    The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

  5. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    PubMed

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  6. Investigation of High-Temperature Slag/Copper/Spinel Interactions

    NASA Astrophysics Data System (ADS)

    De Wilde, Evelien; Bellemans, Inge; Campforts, Mieke; Guo, Muxing; Blanpain, Bart; Moelans, Nele; Verbeken, Kim

    2016-12-01

    An important cause for the mechanical entrainment of copper droplets in slags during primary and secondary copper production is their interaction with solid spinel particles, hindering the sedimentation of the copper droplets. In the present study, the interactions between the three phases involved (slag-Cu droplets-spinel solids) were investigated using an adapted sessile drop experiment, combined with detailed microstructural investigation of the interaction zone. An industrially relevant synthetic PbO-CaO-SiO2-Cu2O-Al2O3-FeO-ZnO slag system, a MgAl2O4 spinel particle, and pure copper were examined with electron microscopy after their brief interaction at 1523 K (1250 °C). Based on the experimental results, a mechanism depending on the interlinked dissolved Cu and oxygen contents within the slag is proposed to describe the origin of the phenomenon of sticking Cu alloy droplets. In addition, the oxygen potential gradient across the phases ( i.e., liquid Cu, slag, and spinel) appears to affect the Cu entrainment, as deduced from a microstructural analysis.

  7. Molecular interaction study of flavonoid derivative 3d with human serum albumin using multispectroscopic and molecular modeling approach.

    PubMed

    Wei, Juntong; Jin, Feng; Wu, Qin; Jiang, Yuyang; Gao, Dan; Liu, Hongxia

    2014-08-01

    Human serum albumin (HSA) has been developed as a model protein to study drug-protein interaction. In the present work, the interaction between our synthesized flavonoid derivative 3d (possessing potent antitumor activity against HepG2 cells) and HSA was investigated using fluorescence spectroscopy, circular dichroism spectroscopy, UV-vis spectroscopy and molecular modeling approach. Fluorescence spectroscopy showed that the fluorescence of HSA can be quenched remarkably by 3d under physiological condition with a slight shift of maximum fluorescence emission bands from 360nm to 363nm. Calculated results from Stern-Volmer equation and modified Stern-Volmer equation indicated that the fluorescence was quenched by static quenching processing with association constant 5.26±0.04×10(4)L mol(-1) at 298K. After comprehensive consideration of the free energy change ΔG, enthalpy change ΔH and entropy change ΔS, electrostatic interactions were confirmed as the main factor that participate in stabilizing the 3d-HSA complex. Both dichroism spectroscopy and UV-vis spectroscopy indicated conformational change of HSA after binding to 3d. Moreover, the structure of HSA was loosened and the percentage of α-helix decreased with increasing concentration of 3d. Molecular modeling results demonstrated that 3d could bind to HSA well into subdomain IIA, which is related to its capability of deposition and delivery. Three cation-π interactions and three hydrogen bonds occurred between 3d and amino acid residuals ARG218, ARG222 and LYS199. In conclusion, flavonoid derivative 3d can bind to HSA with noncovalent bond in a relatively stable way, so it can be delivered by HSA in a circulatory system.

  8. A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

    PubMed

    Li, Yating; Wei, Haoran; Liu, Rutao

    2014-03-01

    Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study.

  9. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    SciTech Connect

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of the substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  10. Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase

    DOE PAGES

    Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; ...

    2015-02-25

    A recombinant carboxylesterase, cloned from Pseudomonas putida and designated as rPPE, is capable of catalyzing the bioresolution of racemic 2-acetoxy-2-(2 -chlorophenyl)acetate (rac-AcO-CPA) with excellent (S)-enantioselectivity. Semi-rational design of the enzyme showed that the W187H variant could increase the activity by ~100-fold compared to the wild type (WT) enzyme. In this study, we performed all-atom molecular dynamics (MD) simulations of both apo-rPPE and rPPE in complex with (S)-AcO-CPA to gain insights into the origin of the increased catalysis in the W187H mutant. Moreover, our results show differential binding of (S)-AcO-CPA in the WT and W187H enzymes, especially the interactions of themore » substrate with the two active site residues Ser159 and His286. The replacement of Trp187 by His leads to considerable structural rearrangement in the active site of W187H. Unlike in the WT rPPE, the cap domain in the W187 mutant shows an open conformation in the simulations of both apo and substrate-bound enzymes. This open conformation exposes the catalytic triad to the solvent through a water accessible channel, which may facilitate the entry of the substrate and/or the exit of the product. Binding free energy calculations confirmed that the substrate binds more strongly in W187H than in WT. Based on these computational results, furthermore, we predicted that the mutations W187Y and D287G might also be able to increase the substrate binding, thus improve the enzyme s catalytic efficiency. Experimental binding and kinetic assays on W187Y and D287G show improved catalytic efficiency over WT, but not W187H. Contrary to our prediction, W187Y shows slightly decreased substrate binding coupled with a 100 fold increase in turn-over rate, while in D287G the substrate binding is 8 times stronger but with a slightly reduced turn-over rate. Finally, our work provides important molecular-level insights into the binding of the (S)-AcO-CPA substrate to carboxylesterase r

  11. Hadronic Scenarios for Gamma-Ray Emission from Three Supernova Remnants Interacting with Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Yu, Huan; Fang, Jun; Zhang, Li

    2014-04-01

    GeV γ-rays detected with the large area telescope on board the Fermi Gamma-ray space telescope in the direction of HB21, MSH 17-39 and G337.0-0.1 have been recently reported. The three supernova remnants (SNRs) show interactions with molecular clouds, and they are effective gamma-ray emitters as the relativistic protons accelerated by the SNR shocks inelastically colliding with the dense gas in the clouds. The origin of the observed γ-rays for the three remnants is investigated in the scenario of the diffusive shock acceleration. In the model, a part of the SNR shock transmits into the nearby molecular clouds, and the shock velocity is greatly reduced. As a result, a shock with a relatively low Alfvén Mach number is generated, and the spectra of the accelerated protons and the γ-ray photons produced via proton-proton interaction can be obtained. The results show that the observed γ-ray spectra for the three SNRs interacting with the molecular clouds can be reproduced. It can be concluded that the hadronic origin of the γ-rays for the three SNRs is approved, and the ability of SNR shocks to accelerate protons is also supported.

  12. Molecular interaction mechanism between 2-mercaptobenzimidazole and copper-zinc superoxide dismutase.

    PubMed

    Teng, Yue; Zou, Luyi; Huang, Ming; Chen, Yadong

    2014-01-01

    2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment is potentially harmful. In the present work, the toxic interaction of MBI with the important antioxidant enzyme copper-zinc superoxide dismutase (Cu/ZnSOD) was investigated using spectroscopic and molecular docking methods. MBI can interact with Cu/ZnSOD to form an MBI-Cu/ZnSOD complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that MBI could spontaneously bind with Cu/ZnSOD with one binding site through hydrogen bonds and van der Waals forces. MBI bound into the Cu/ZnSOD interface of two subdomains, which caused some microenvironmental and secondary structure changes of Cu/ZnSOD and further resulted in the inhibition of Cu/ZnSOD activity. This work provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme Cu/ZnSOD. The estimated methods in this work may be applied to probe molecular interactions of biomacromolecules and other pollutants and drugs.

  13. Molecular Interaction Mechanism between 2-Mercaptobenzimidazole and Copper-Zinc Superoxide Dismutase

    PubMed Central

    Teng, Yue; Zou, Luyi; Huang, Ming; Chen, Yadong

    2014-01-01

    2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment is potentially harmful. In the present work, the toxic interaction of MBI with the important antioxidant enzyme copper-zinc superoxide dismutase (Cu/ZnSOD) was investigated using spectroscopic and molecular docking methods. MBI can interact with Cu/ZnSOD to form an MBI-Cu/ZnSOD complex. The binding constant, number of binding sites and thermodynamic parameters were measured, which indicated that MBI could spontaneously bind with Cu/ZnSOD with one binding site through hydrogen bonds and van der Waals forces. MBI bound into the Cu/ZnSOD interface of two subdomains, which caused some microenvironmental and secondary structure changes of Cu/ZnSOD and further resulted in the inhibition of Cu/ZnSOD activity. This work provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme Cu/ZnSOD. The estimated methods in this work may be applied to probe molecular interactions of biomacromolecules and other pollutants and drugs. PMID:25157630

  14. Experimental and theoretical investigation on the interaction between cyclovirobuxine D and human serum albumin

    NASA Astrophysics Data System (ADS)

    Yue, Yuanyuan; Liu, Ren; Liu, Jianming; Dong, Qiao; Fan, Jing

    2014-07-01

    Cyclovirobuxine D is an active compound extracted from the plant Buxux microphylla, and widely available as medications; however, its abuse may casts potential detrimental effects on human health. By using multispectroscopic techniques and molecular modeling, the interaction of cyclovirobuxine D with human serum albumin was investigated. The fluorescence results manifested that static type was the operative mechanism for the interaction with human serum albumin. The structural investigation of the complexed HSA through CD, three-dimensional, FT-IR and synchronous fluorescence shown the polypeptide chain of HSA partially destabilizing. Docking studies revealed the molecule to be bound in the subdomain IIA. Finally, we investigated the distance between the bound ligand and Trp-214 of human serum albumin.

  15. Investigation on the interaction of the toxicant, gentian violet, with bovine hemoglobin.

    PubMed

    Liu, Yan; Lin, Jingjing; Chen, Mingmao; Song, Ling

    2013-08-01

    Gentian violet (GV) is a well-known triarylmethane dye that is used in aquacultural, industrial and medicinal fields. But concerns in growing number have been paid to its potential health problems to human beings and its hazardous effects to environment. Herein, the toxic interaction of GV with bovine hemoglobin (BHb) was investigated by a series of spectroscopic methods and molecular modeling method. The fluorescence emission profile exhibited a remarkable quenching upon addition of GV to the buffered aqueous solution of BHb and the analysis of results revealed the dominant role of static quenching mechanism in GV-BHb interaction. The negative ΔH and positive ΔS values demonstrated that the electrostatic interactions mainly stabilized this toxicantprotein complex. Synchronous fluorescence, UV-Vis absorption and CD spectroscopic studies proved that the conformational change of BHb was induced by GV's combination. Molecular modeling studies exhibited the binding mode of GV-BHb complex and the detailed information of related driving forces. During the (1)H nuclear magnetic resonance spectra ((1)H NMR) study, the chemical shift perturbation and spin-lattice relaxation times of different protons were further used to investigate the interaction of GV with BHb and the results indicated that GV bound orientationally to BHb.

  16. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    PubMed Central

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring. PMID:26750747

  17. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  18. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    PubMed

    Miller, Matthew J; Esser, Helen J; Loaiza, Jose R; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the dynamics of

  19. Molecular Ecological Insights into Neotropical Bird–Tick Interactions

    PubMed Central

    Esser, Helen J.; Loaiza, Jose R.; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds’ role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually–sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical–Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically–identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly–discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the

  20. Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

    PubMed

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2012-07-15

    The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems.

  1. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations.

    PubMed

    Zhang, Xuejin; Gong, Zhen; Li, Jian; Lu, Tao

    2015-10-26

    Intermolecular S···O interactions are very common and are important in biological systems, but until recently, the presence of these contacts in protein-ligand systems largely depended on serendipitous discovery instead of rational design. Here we provide insight into the phenomenon of intermolecular S···O contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the S···O interactions and to determine their energy dependence on their geometric parameters. Protein Data Bank mining is performed to systematically determine the occurrence and geometry of intermolecular S···O interactions, and several representative examples are discussed. Three typical cases are investigated using a combined quantum mechanics/molecular mechanics approach to demonstrate the potential of these interactions in improving binding affinities and physiochemical properties. Overall, our work elucidates the structures and energy features of intermolecular S···O interactions and addresses their use in molecular design.

  2. An experimental investigation of shock wave/vortex interaction

    NASA Astrophysics Data System (ADS)

    Cattafesta, Louis Nicholas, III

    Although shock wave/vortex interaction is a basic and important fluid dynamics problem, very little research has been conducted on this topic. Therefore, a detailed experimental study of the interaction between a supersonic streamwise turbulent vortex and a shock wave has been carried out at the Penn State Gas Dynamics Laboratory. A vortex is produced by replaceable swirl vanes located upstream of the throat of various converging-diverging nozzles. The supersonic vortex is then injected into either a coflowing supersonic stream or ambient air. The structure of the isolated vortex is investigated in a supersonic wind tunnel using miniature, fast-response, five-hole and total temperature probes and in a free jet using Laser Doppler Velocimetry. The cases tested have unit Reynolds numbers in excess of 25 million per meter, axial Mach numbers ranging from 2.5 to 4.0, and peak tangential Mach numbers from 0 (i.e. a pure jet) to about 0.7. The results show that the typical supersonic wake-like vortex consists of a non-isentropic, rotational core, where the reduced circulation distribution is self-similar, and an outer isentropic, irrotational region. The vortex core is also a region of significant turbulent fluctuations. Radial profiles of turbulent kinetic energy and axial-tangential Reynolds stress are presented. The interactions between the vortex and both oblique and normal shock waves are investigated using nonintrusive optical diagnostics (i.e. schlieren, Planar Laser Scattering, and Laser Doppler Velocimetry). Of the various types, two Mach 2.5 overexpanded-nozzle Mach-disc interactions are examined in detail. Below a certain vortex strength, a 'weak' interaction exists in which the normal shock is perturbed locally into an unsteady 'bubble' shock near the vortex axis, but vortex breakdown (i.e. a stagnation point) does not occur. For stronger vortices, a random unsteady 'strong' interaction results that causes vortex breakdown. The vortex core reforms downstream

  3. Investigation of the Molecular Response of Belugas to Stressors

    DTIC Science & Technology

    2014-09-30

    To apply molecular methods to describe and quantify changes in the expression of immunological “stress” markers in peripheral blood from captive and...wild belugas. 4. To apply molecular methods to describe and quantify the expression of immunological markers in skin. 5. To correlate the...molecular marker to be used in this study. Being a part of vertebrate innate immune system, Toll-like receptors are located at the direct interface

  4. Optoelectronic investigation of nanodiamond interactions with human blood

    NASA Astrophysics Data System (ADS)

    Ficek, M.; Wróbel, M. S.; Wasowicz, M.; Jedrzejewska-Szczerska, M.

    2016-03-01

    We present optoelectronic investigation of in vitro interactions of whole human blood with different nanodiamond biomarkers. Plasmo-chemical modifications of detonation nanodiamond particles gives the possibility for controlling their surface for biological applications. Optical investigations reveal the biological activity of nanodiamonds in blood dependent on its surface termination. We compare different types of nanodiamonds: commercial non-modified detonation nanodiamonds, and nanodiamonds modified by MW PACVD method with H2-termination, and chemically modified nanodiamond with O2-termination. The absorption spectra, and optical microscope investigations were conducted. The results indicate haemocompatibility of non-modified detonation nanodiamond as well as modified nanodiamonds, which enables their application for drug delivery, as well as sensing applications.

  5. Molecular Structures and Interactions in the Yeast Kinetochore

    PubMed Central

    Cho, U.-S.; Corbett, K.D.; Al-Bassam, J.; Bellizzi, J.J.; De Wulf, P.; Espelin, C.W.; Miranda, J.J.; Simons, K.; Wei, R.R.; Sorger, P.K.; Harrison, S.C.

    2011-01-01

    Kinetochores are the elaborate protein assemblies that attach chromosomes to spindle microtubules in mitosis and meiosis. The kinetochores of point-centromere yeast appear to represent an elementary module, which repeats a number of times in kinetochores assembled on regional centromeres. Structural analyses of the discrete protein subcomplexes that make up the budding-yeast kinetochore have begun to reveal principles of kinetochore architecture and to uncover molecular mechanisms underlying functions such as transmission of tension and establishment and maintenance of bipolar attachment. The centromeric DNA is probably wrapped into a compact organization, not only by a conserved, centromeric nucleosome, but also by interactions among various other DNA-bound kinetochore components. The rod-like, heterotetrameric Ndc80 complex, roughly 600 Å long, appears to extend from the DNA-proximal assembly to the plus end of a microtubule, to which one end of the complex is known to bind. Ongoing structural studies will clarify the roles of a number of other well-defined complexes. PMID:21467141

  6. Cellular and molecular interactions of phosphoinositides and peripheral proteins.

    PubMed

    Stahelin, Robert V; Scott, Jordan L; Frick, Cary T

    2014-09-01

    Anionic lipids act as signals for the recruitment of proteins containing cationic clusters to biological membranes. A family of anionic lipids known as the phosphoinositides (PIPs) are low in abundance, yet play a critical role in recruitment of peripheral proteins to the membrane interface. PIPs are mono-, bis-, or trisphosphorylated derivatives of phosphatidylinositol (PI) yielding seven species with different structure and anionic charge. The differential spatial distribution and temporal appearance of PIPs is key to their role in communicating information to target proteins. Selective recognition of PIPs came into play with the discovery that the substrate of protein kinase C termed pleckstrin possessed the first PIP binding region termed the pleckstrin homology (PH) domain. Since the discovery of the PH domain, more than ten PIP binding domains have been identified including PH, ENTH, FYVE, PX, and C2 domains. Representative examples of each of these domains have been thoroughly characterized to understand how they coordinate PIP headgroups in membranes, translocate to specific membrane docking sites in the cell, and function to regulate the activity of their full-length proteins. In addition, a number of novel mechanisms of PIP-mediated membrane association have emerged, such as coincidence detection-specificity for two distinct lipid headgroups. Other PIP-binding domains may also harbor selectivity for a membrane physical property such as charge or membrane curvature. This review summarizes the current understanding of the cellular distribution of PIPs and their molecular interaction with peripheral proteins.

  7. Elucidating nitric oxide synthase domain interactions by molecular dynamics.

    PubMed

    Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

    2016-02-01

    Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis.

  8. Mechanical properties of borophene films: a reactive molecular dynamics investigation

    NASA Astrophysics Data System (ADS)

    Quy Le, Minh; Mortazavi, Bohayra; Rabczuk, Timon

    2016-11-01

    The most recent experimental advances could provide ways for the fabrication of several atomic thick and planar forms of boron atoms. For the first time, we explore the mechanical properties of five types of boron films with various vacancy ratios ranging from 0.1-0.15, using molecular dynamics simulations with ReaxFF force field. It is found that the Young’s modulus and tensile strength decrease with increasing the temperature. We found that boron sheets exhibit an anisotropic mechanical response due to the different arrangement of atoms along the armchair and zigzag directions. At room temperature, 2D Young’s modulus and fracture stress of these five sheets appear in the range 63-136 N m-1 and 12-19 N m-1, respectively. In addition, the strains at tensile strength are in the ranges of 9%-14%, 11%-19%, and 10%-16% at 1, 300, and 600 K, respectively. This investigation not only reveals the remarkable stiffness of 2D boron, but establishes relations between the mechanical properties of the boron sheets to the loading direction, temperature and atomic structures.

  9. Novel molecular beacon DNA probes for protein-nucleic acid interaction studies

    NASA Astrophysics Data System (ADS)

    Li, Jianwei J.; Perlette, John; Fang, Xiaohong; Kelley, Shannon; Tan, Weihong

    2000-03-01

    We report a novel approach to study protein-nucleic acid interactions by using molecular beacons (MBs). Molecular beacons are hairpin-shaped DNA oligonucleotide probes labeled with a fluorophore and a quencher, and can report the presence of target DNA/RNA sequences. MBs can also report the existence of single-stranded DNA binding proteins (SSB) through non-sequence specific binding. The interaction between SSB and MB has resulted in significant fluorescence restoration of the MB. The fluorescence enhancement brought by SSB and by complementary DNA is very comparable. The molar ratio of the binding between SSB and the molecular beacon is 1:1 with a binding constant of 2 X 107 M-1. Using the MB-SSB binding, we are able to determine SSB at 2 X 10-10 M with a conventional spectrometer. We have also applied MB DNA probes for the analysis of an enzyme lactic dehydrogenase (LDH), and for the investigation of its binding properties with ssDNA. The biding process between MB and different isoenzymes of LDH has been studied. We also show that there are significant differences in MB binding affinity to different proteins, which will enable selective binding studies of a variety of proteins. This new approach is potentially useful for protein-DNA/RNA interaction studies that require high sensitivity, speed and convenience. The results also open the possibility of using easily obtainable, custom designed, modified DNA molecules for studies of drug interactions and targeting. Our results demonstrate that MB can be effectively used for sensitive protein quantitation and for efficient protein-DNA interaction studies. MB has the signal transduction mechanism built within the molecule, and can thus be used for quick protein assay development and for real-time measurements.

  10. Interactions of cephalexin with bovine serum albumin: displacement reaction and molecular docking

    PubMed Central

    Hamishehkar, Hamed; Hosseini, Soheila; Naseri, Abdolhossein; Safarnejad, Azam; Rasoulzadeh, Farzaneh

    2016-01-01

    Introduction: The drug-plasma protein interaction is a fundamental issue in guessing and checking the serious drug side effects related with other drugs. The purpose of this research was to study the interaction of cephalexin with bovine serum albumin (BSA) and displacement reaction using site probes. Methods: The interaction mechanism concerning cephalexin (CPL) with BSA was investigated using various spectroscopic methods and molecular modeling method. The binding sites number, n, apparent binding constant, K, and thermodynamic parameters, ΔG0, ΔH0, and ΔS0 were considered at different temperatures. To evaluate the experimental results, molecular docking modeling was calculated. Results: The distance, r=1.156 nm between BSA and CPL were found in accordance with the Forster theory of non-radiation energy transfer (FRET) indicating energy transfer occurs between BSA and CPL. According to the binding parameters and ΔG0= negative values and ΔS0= 28.275 j mol-1K-1, a static quenching process is effective in the CPL-BSA interaction spontaneously. ΔG0 for the CPL-BSA complex obtained from the docking simulation is -28.99 kj mol-1, which is close to experimental ΔG of binding, -21.349 kj mol-1 that indicates a good agreement between the results of docking methods and experimental data. Conclusion: The outcomes of spectroscopic methods revealed that the conformation of BSA changed during drug-BSA interaction. The results of FRET propose that CPL quenches the fluorescence of BSA by static quenching and FRET. The displacement study showed that phenylbutazon and ketoprofen displaced CPL, indicating that its binding site on albumin is site I and Gentamicin cannot be displaced from the binding site of CPL. All results of molecular docking method agreed with the results of experimental data. PMID:27853676

  11. Interaction of glutathione with bovine serum albumin: Spectroscopy and molecular docking.

    PubMed

    Jahanban-Esfahlan, Ali; Panahi-Azar, Vahid

    2016-07-01

    This study aims to investigate the interaction between glutathione and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence spectroscopies under simulated physiological conditions (pH 7.4) and molecular docking methods. The results of fluorescence spectroscopy indicated that the fluorescence intensity of BSA was decreased considerably upon the addition of glutathione through a static quenching mechanism. The fluorescence quenching obtained was related to the formation of BSA-glutathione complex. The values of KSV, Ka and Kb for the glutathione and BSA interaction were in the order of 10(5). The thermodynamic parameters including enthalpy change (ΔH), entropy change (ΔS) and also Gibb's free energy (ΔG) were determined using Van't Hoff equation. These values showed that hydrogen bonding and van der Waals forces were the main interactions in the binding of glutathione to BSA and the stabilization of the complex. Also, the interaction of glutathione and BSA was spontaneous. The effects of glutathione on the BSA conformation were determined using UV-vis spectroscopy. Moreover, glutathione was docked in BSA using ArgusLab as a molecular docking program. It was recognized that glutathione binds within the sub-domain IIA pocket in domain II of BSA.

  12. Molecular Epidemiology Investigation of Obesity and Lethal Prostate Cancer

    DTIC Science & Technology

    2015-09-01

    in the field of molecular epidemiology. During the award period the PI performed research incorporating tissue -level biomarker data into...Using whole transcriptome gene expression profiling data, she identified a chromatin gene signature that is enriched in the tumor tissue of overweight...prostate cancer, obesity, tissue biomarkers, gene expression, growth factor signaling, inflammation, angiogenesis, molecular epidemiology 16

  13. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  14. Phonon-magnon interactions in body centered cubic iron: A combined molecular and spin dynamics study

    SciTech Connect

    Perera, Dilina Landau, David P.; Nicholson, Don M.; Malcolm Stocks, G.; Eisenbach, Markus; Yin, Junqi; Brown, Gregory

    2014-05-07

    Combining an atomistic many-body potential with a classical spin Hamiltonian parameterized by first principles calculations, molecular-spin dynamics computer simulations were performed to investigate phonon-magnon interactions in body centered cubic iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, additional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.

  15. Phonon-magnon interactions in BCC iron: A combined molecular and spin dynamics study

    SciTech Connect

    Perera, Meewanage Dilina N; Landau, David P; Nicholson, Don M; Stocks, George Malcolm; Eisenbach, Markus; Yin, Junqi; Brown, Greg

    2014-01-01

    Combining an atomistic many-body potential with a classical spin Hamiltonian pa- rameterized by first principles calculations, molecular-spin dynamics computer sim- ulations were performed to investigate phonon-magnon interactions in BCC iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, addi- tional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.

  16. Molecular weight control in organochromium olefin polymerization catalysis by hemilabile ligand–metal interactions

    PubMed Central

    Mark, Stefan; Wadepohl, Hubert

    2016-01-01

    Summary A series of Cr(III) complexes based on quinoline-cyclopentadienyl ligands with additional hemilabile side arms were prepared and used as single-site catalyst precursors for ethylene polymerization. The additional donor functions interact with the metal centers only after activation with the co-catalyst. Evidence for this comes from DFT-calculations and from the differing behavior of the complexes in ethylene polymerization. All complexes investigated show very high catalytic activity and the additional side arm minimizes chain-transfer reactions, leading to increase of molecular weights of the resulting polymers. PMID:27559387

  17. High-resolution single-molecule recognition imaging of the molecular details of ricin-aptamer interaction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The molecular details of DNA aptamer-ricin interactions were investigated. The toxic protein ricin molecules were immobilized on Au(111) surface using N-hydroxysuccinimide (NHS) ester to specifically react with lysine residues located on the ricin B chains. A single ricin molecule was visualized in ...

  18. Molecular dynamics investigation of dislocation pinning by a nanovoid in copper

    SciTech Connect

    Hatano, Takahiro; Matsui, Hideki

    2005-09-01

    The interaction between an edge dislocation and a void in copper is investigated by means of a molecular dynamics simulation. The depinning stresses of the leading partial and of the trailing partial show qualitatively different behaviors. The depinning stress of the trailing partial increases logarithmically with the void radius, while that of the leading partial behaves in a different manner due to the interaction between two partials. The pinning angle, which characterizes the obstacle strength, approaches zero when the void radius exceeds 3 nm. No temperature dependence is found in the critical stress and the critical angle. This is attributed to an absence of climb motion. It is also found that the distance between the void center and a glide plane asymmetrically affects the pinning strength.

  19. Molecular interactions of alcohols with zeolite BEA and MOR frameworks.

    PubMed

    Stückenschneider, Kai; Merz, Juliane; Schembecker, Gerhard

    2013-12-01

    Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1-C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1-C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.

  20. Matrix metalloproteinase expression and molecular interaction network analysis in gastric cancer

    PubMed Central

    Xu, Jianting; E, Changyong; Yao, Yongfang; Ren, Shuangchun; Wang, Guoqing; Jin, Haofan

    2016-01-01

    Gastric cancer (GC) is one of the most common types of cancer of the digestive tract. Invasion of tumor cells into surrounding tissue and metastasis are among the most significant checkpoints in tumor progression. It is known that matrix metalloproteinases (MMPs) are involved in these processes; however, knowledge of their molecular interaction networks is still limited. Investigation of these networks could provide a more comprehensive picture of the function of MMPs in tumorigenesis. Furthermore, it could be used to develop new approaches to targeted anticancer therapy. In this study, we performed microarray analysis, and 1666 genes that were aberrantly expressed in GC tissues were identified (fold change >2, P<0.05). In addition, quantitative polymerase chain reaction analysis has confirmed that MMP1, MMP3, MMP7, MMP10, MMP11 and MMP12 expression is upregulated in GC. In addition, the MMP3 expression level was negatively correlated with GC differentiation (P<0.05). By integrating the microarray information and BioGRID and STRING databases, we constructed an MMP-related molecular interaction network and observed that 18 genes (including MMPs) were highly expressed in GC tissues. The most enriched of these 18 genes in the Gene Oncology (GO) and pathway analysis were in extracellular matrix disassembly (GO biological process) and extracellular matrix-receptor interaction (KEGG pathway), which are closely correlated with cancer invasion and metastasis. Collectively, our results suggest that the MMP-related interaction network has a role in GC progression, and therefore further studies are required in order to investigate these network interactions in tumorigenesis. PMID:27698806

  1. Ochratoxin A: Molecular Interactions, Mechanisms of Toxicity and Prevention at the Molecular Level.

    PubMed

    Kőszegi, Tamás; Poór, Miklós

    2016-04-15

    Ochratoxin A (OTA) is a widely-spread mycotoxin all over the world causing major health risks. The focus of the present review is on the molecular and cellular interactions of OTA. In order to get better insight into the mechanism of its toxicity and on the several attempts made for prevention or attenuation of its toxic action, a detailed description is given on chemistry and toxicokinetics of this mycotoxin. The mode of action of OTA is not clearly understood yet, and seems to be very complex. Inhibition of protein synthesis and energy production, induction of oxidative stress, DNA adduct formation, as well as apoptosis/necrosis and cell cycle arrest are possibly involved in its toxic action. Since OTA binds very strongly to human and animal albumin, a major emphasis is done regarding OTA-albumin interaction. Displacement of OTA from albumin by drugs and by natural flavonoids are discussed in detail, hypothesizing their potentially beneficial effect in order to prevent or attenuate the OTA-induced toxic consequences.

  2. Ochratoxin A: Molecular Interactions, Mechanisms of Toxicity and Prevention at the Molecular Level

    PubMed Central

    Kőszegi, Tamás; Poór, Miklós

    2016-01-01

    Ochratoxin A (OTA) is a widely-spread mycotoxin all over the world causing major health risks. The focus of the present review is on the molecular and cellular interactions of OTA. In order to get better insight into the mechanism of its toxicity and on the several attempts made for prevention or attenuation of its toxic action, a detailed description is given on chemistry and toxicokinetics of this mycotoxin. The mode of action of OTA is not clearly understood yet, and seems to be very complex. Inhibition of protein synthesis and energy production, induction of oxidative stress, DNA adduct formation, as well as apoptosis/necrosis and cell cycle arrest are possibly involved in its toxic action. Since OTA binds very strongly to human and animal albumin, a major emphasis is done regarding OTA-albumin interaction. Displacement of OTA from albumin by drugs and by natural flavonoids are discussed in detail, hypothesizing their potentially beneficial effect in order to prevent or attenuate the OTA-induced toxic consequences. PMID:27092524

  3. Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

    NASA Technical Reports Server (NTRS)

    Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

    1999-01-01

    A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

  4. Molecular weight recognition in the multiple-stranded helix of a synthetic polymer without specific monomer-monomer interaction.

    PubMed

    Kumaki, Jiro; Kawauchi, Takehiro; Ute, Koichi; Kitayama, Tatsuki; Yashima, Eiji

    2008-05-21

    Stereoregular isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) are known to form a multiple-stranded complementary helix, so-called stereocomplex (SC) through van der Waals interactions, which is a rare example of helical supramolecular structures formed by a commodity polymer. In this study, we prepared SCs by using uniform it- and st-PMMAs and those with a narrow molecular weight distribution having different molecular weights and investigated their structures in detail using high-resolution atomic force microscopy as a function of the molecular weight and molecular weight distribution of the component PMMAs. We found that complementary it- and st-PMMAs with the longer molecular length determine the total length of the SC, and molecules of the shorter component associate until they fill up or cover the longer component. These observations support a supramolecular triple-stranded helical structure of the SCs composed of a double-stranded helix of two intertwined it-PMMA chains included in a single helix of st-PMMA, and this triple-stranded helix model of the SCs appears to be applicable to the it- and st-PMMAs having a wide range of molecular weights we employed in this study. In homogeneous double-stranded helices of it-PMMA, it has been found that, in mixtures of two it-PMMAs with different molecular weights, chains of the same molecular weight selectively form a double-stranded it-PMMA helix, or recognize the molecular weights of each other ("molecular sorting"). We thus demonstrate that molecular weight recognition is possible, without any specific interaction between monomer units, through the formation of a topological multiple-stranded helical structure based upon van der Waals interaction.

  5. Investigations and advanced concepts on gyrotron interaction modeling and simulations

    SciTech Connect

    Avramidis, K. A.

    2015-12-15

    In gyrotron theory, the interaction between the electron beam and the high frequency electromagnetic field is commonly modeled using the slow variables approach. The slow variables are quantities that vary slowly in time in comparison to the electron cyclotron frequency. They represent the electron momentum and the high frequency field of the resonant TE modes in the gyrotron cavity. For their definition, some reference frequencies need to be introduced. These include the so-called averaging frequency, used to define the slow variable corresponding to the electron momentum, and the carrier frequencies, used to define the slow variables corresponding to the field envelopes of the modes. From the mathematical point of view, the choice of the reference frequencies is, to some extent, arbitrary. However, from the numerical point of view, there are arguments that point toward specific choices, in the sense that these choices are advantageous in terms of simulation speed and accuracy. In this paper, the typical monochromatic gyrotron operation is considered, and the numerical integration of the interaction equations is performed by the trajectory approach, since it is the fastest, and therefore it is the one that is most commonly used. The influence of the choice of the reference frequencies on the interaction simulations is studied using theoretical arguments, as well as numerical simulations. From these investigations, appropriate choices for the values of the reference frequencies are identified. In addition, novel, advanced concepts for the definitions of these frequencies are addressed, and their benefits are demonstrated numerically.

  6. Investigation of cellular responses upon interaction with silver nanoparticles

    PubMed Central

    Subbiah, Ramesh; Jeon, Seong Beom; Park, Kwideok; Ahn, Sang Jung; Yun, Kyusik

    2015-01-01

    In order for nanoparticles (NPs) to be applied in the biomedical field, a thorough investigation of their interactions with biological systems is required. Although this is a growing area of research, there is a paucity of comprehensive data in cell-based studies. To address this, we analyzed the physicomechanical responses of human alveolar epithelial cells (A549), mouse fibroblasts (NIH3T3), and human bone marrow stromal cells (HS-5), following their interaction with silver nanoparticles (AgNPs). When compared with kanamycin, AgNPs exhibited moderate antibacterial activity. Cell viability ranged from ≤80% at a high AgNPs dose (40 µg/mL) to >95% at a low dose (10 µg/mL). We also used atomic force microscopy-coupled force spectroscopy to evaluate the biophysical and biomechanical properties of cells. This revealed that AgNPs treatment increased the surface roughness (P<0.001) and stiffness (P<0.001) of cells. Certain cellular changes are likely due to interaction of the AgNPs with the cell surface. The degree to which cellular morphology was altered directly proportional to the level of AgNP-induced cytotoxicity. Together, these data suggest that atomic force microscopy can be used as a potential tool to develop a biomechanics-based biomarker for the evaluation of NP-dependent cytotoxicity and cytopathology. PMID:26346562

  7. Investigation of Ribosomes Using Molecular Dynamics Simulation Methods.

    PubMed

    Makarov, G I; Makarova, T M; Sumbatyan, N V; Bogdanov, A A

    2016-12-01

    The ribosome as a complex molecular machine undergoes significant conformational changes while synthesizing a protein molecule. Molecular dynamics simulations have been used as complementary approaches to X-ray crystallography and cryoelectron microscopy, as well as biochemical methods, to answer many questions that modern structural methods leave unsolved. In this review, we demonstrate that all-atom modeling of ribosome molecular dynamics is particularly useful in describing the process of tRNA translocation, atomic details of behavior of nascent peptides, antibiotics, and other small molecules in the ribosomal tunnel, and the putative mechanism of allosteric signal transmission to functional sites of the ribosome.

  8. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    SciTech Connect

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  9. Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

    NASA Astrophysics Data System (ADS)

    Heinz, Hendrik; Pramanik, Chandrani; Heinz, Ozge; Ding, Yifu; Mishra, Ratan K.; Marchon, Delphine; Flatt, Robert J.; Estrela-Lopis, Irina; Llop, Jordi; Moya, Sergio; Ziolo, Ronald F.

    2017-02-01

    Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning ;surface active agents;, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.

  10. Molecular modeling of polymer composite-analyte interactions in electronic nose sensors.

    PubMed

    Shevade, A V; Ryan, M A; Homer, M L; Manfreda, A M; Zhou, H; Manatt, K S

    2003-08-01

    We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL electronic nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereoisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings with no hydrogens. The Dreiding 2.21 force field is used for the polymer, solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4-vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic and organic compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites.

  11. Molecular modeling of polymer composite-analyte interactions in electronic nose sensors

    NASA Technical Reports Server (NTRS)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K. S.

    2003-01-01

    We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL electronic nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereoisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings with no hydrogens. The Dreiding 2.21 force field is used for the polymer, solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4-vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic and organic compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites. c2003 Elsevier Science B.V. All rights reserved.

  12. Analogue Investigations into Magma-Cryosphere Interactions on Mars

    NASA Astrophysics Data System (ADS)

    Tyson, S.; Wilson, L.; Lane, S. J.; Airey, M. W.; Gilbert, J. S.

    2011-12-01

    Many landforms and morphological features thought to have resulted from magma-cryosphere interactions have been identified on Mars. However, few experimental studies have been conducted to investigate the physical and thermal changes that should occur in the subsurface during these interactions. This project aims to begin to address this by conducting a series of laboratory analogue experiments. We introduce a heat source into a block of analogue cryosphere material (a carefully-prepared mixture of solid grains and ice) and record the thermal development within the block using thermocouples. We use these measurements to interpret the physical activity within the block, such as when and where phase changes occur, what sequence of shapes the developing melt region takes, and the extent of convection of any fluid phase H20. Blocks are also dissected after each run and documented photographically to record any physical movement of grains. Results will be used to constrain variables within a heat flow model that we are developing. This model will then be applied to the interpretation of landforms on Mars to help determine what set of processes could have realistically occurred during their formation. A second series of experiments will investigate surface morphological changes on the cryosphere analogue blocks. Resultant morphologies will be recorded and compared with existing martian landforms to again provide insight into formation processes.

  13. Theoretical investigation of interaction between the set of ligands and α7 nicotinic acetylcholine receptor

    NASA Astrophysics Data System (ADS)

    Glukhova, O. E.; Prytkova, T. R.; Shmygin, D. S.

    2016-03-01

    Nicotinic acetylcholine receptors (nAChRs) are neuron receptor proteins that provide a transmission of nerve impulse through the synapses. They are composed of a pentametric assembly of five homologous subunits (5 α7 subunits for α7nAChR, for example), oriented around the central pore. These receptors might be found in the chemical synapses of central and peripheral nervous system, and also in the neuromuscular synapses. Transmembrane domain of the one of such receptors constitutes ion channel. The conductive properties of ion channel strongly depend on the receptor conformation changes in the response of binding with some molecule, f.e. acetylcholine. Investigation of interaction between ligands and acetylcholine receptor is important for drug design. In this work we investigate theoretically the interaction between the set of different ligands (such as vanillin, thymoquinone, etc.) and the nicotinic acetylcholine receptor (primarily with subunit of the α7nAChR) by different methods and packages (AutodockVina, GROMACS, KVAZAR, HARLEM, VMD). We calculate interaction energy between different ligands in the subunit using molecular dynamics. On the base of obtained calculation results and using molecular docking we found an optimal location of different ligands in the subunit.

  14. Molecular sonography with targeted microbubbles: current investigations and potential applications.

    PubMed

    Hwang, Misun; Lyshchik, Andrej; Fleischer, Arthur C

    2010-06-01

    Sonography using targeted microbubbles affords a variety of diagnostic and potentially therapeutic clinical applications. It provides a whole new world of functional information at the cellular and molecular level. This information can then be used to diagnose and possibly prevent diseases at early stages as well as devise therapeutic strategies at the molecular level. It is also useful in monitoring tumor response to therapy and devising treatment timing and plans based on the molecular state of an individual's health. Moreover, targeted microbubble-enhanced sonography has several advantages over other imaging modalities, including widespread availability, low cost, fast acquisition times, and lack of radiation risk. These traits are likely to advance it as one of the imaging methods of choice in future clinical trials examining the impact of molecular imaging on treatment outcome. This review describes the fundamental concepts of targeted microbubble-enhanced sonography as well as its potential clinical applications.

  15. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    SciTech Connect

    Nash, Kenneth; Guelis, Artem; Lumetta, Gregg J.; Sinkov, Sergey

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  16. A novel method for the study of molecular interaction by using microscale thermophoresis.

    PubMed

    Mao, Yexuan; Yu, Lanlan; Yang, Ran; Qu, Ling-bo; Harrington, Perter de B

    2015-01-01

    The fundamental studies for the binding events of protein and its partner are crucial in drug development. In this study, a novel technology named microscale thermophoresis (MST) was applied in the investigation of molecular interaction between an organic dye fluorescein isothiocyanate (FITC) and bovine serum albumin (BSA), and the results were compared with those obtained from conventional fluorescence spectroscopy. The MST data demonstrated that with a short interaction time, FITC showed a high binding affinity for BSA by weak interaction instead of labeling the protein. By using competitive strategies in which warfarin and ibuprofen acted as the site markers of BSA, FITC was proven to mainly bind to the hydrophobic pocket of site II of BSA compared to site I of BSA. Except for the binding affinity, MST also provided additional information with respect to the aggregation of BSA and the binding of FITC to BSA aggregates, which is unobtainable by fluorescence spectroscopy. This work proves that MST as a new approach is powerful and reliable for investigation of protein-small molecule interaction.

  17. Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking.

    PubMed

    Tan, Xijuan; Wang, Zhuming; Chen, Donghua; Luo, Kai; Xiong, Xunyu; Song, Zhenghua

    2014-08-01

    The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI-CL model of lg[(I0-I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 10(3)-10(5) L mol(-1) and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT-pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT.

  18. Toxic interaction between acid yellow 23 and trypsin: spectroscopic methods coupled with molecular docking.

    PubMed

    Wang, Jing; Liu, Rutao; Qin, Pengfei

    2012-09-01

    Acid yellow 23 (AY23) is a pervasive azo dye used in many fields which is potentially harmful to the environment and human health. This paper studied the toxic effects of AY23 on trypsin by spectroscopic and molecular docking methods. The addition of AY23 effectively quenched the intrinsic fluorescence of trypsin via static quenching with association constants of K(290 K) = 3.67 × 10(5) L mol(-1) and K(310 K) = 1.83 × 10(5) L mol(-1). The calculated thermodynamic parameters conformed that AY23 binds to trypsin predominantly via electrostatic forces with one binding site. Conformational investigations indicated the skeletal structure of trypsin unfolded and the microenvironment of tryptophan changed with the addition of AY23. Molecular docking study showed that AY23 interacted with the His 57 and Lys 224 residue of trypsin and led to the inhibition of enzyme activity. This study offers a more comprehensive picture of AY23-trypsin interaction and indicates their interaction may perform toxic effects within the organism.

  19. Investigation of the inclusions of puerarin and daidzin with beta-cyclodextrin by molecular dynamics simulation.

    PubMed

    Zhang, Haiyang; Feng, Wei; Li, Cong; Tan, Tianwei

    2010-04-15

    Puerarin and daidzin, two major isoflavonoids of Radix puerariae , are widely adopted in traditional Chinese medicine. Foundational aspects related to separating the two compounds are essential to develop a more economical purification process. Inclusion models of the two compounds with beta-cyclodextrin (beta-CD) have been investigated by molecular dynamics simulation. Computational results reveal that both puerarin and daidzin can induce a conformational change of beta-CD, which is compressed in one direction and stretched in the other. The effect of solvent and media on the conformational change of beta-CD and the movement of guest molecules inside the cavity has been investigated. Furthermore, hydrogen bonding interactions have been analyzed, and the results have been utilized for the explanation of separating puerarin from daidzin.

  20. Demixing transition and molecular interactions in Poly(N-isopropyl acrylamide) solutions compared to its monomer

    NASA Astrophysics Data System (ADS)

    Futscher, Moritz; Philipp, Martine; Mueller-Buschbaum, Peter; Schulte, Alfons

    2015-03-01

    Temperature-sensitive hydrogels such as poly(N-isopropyl acrylamide) (PNIPAM) exhibit a coil to globule transition of the polymer chains with a lower critical solution temperature (LCST) near 305 K. The cooperative dehydration of bound water molecules upon heating plays a significant role. The hydrogen bonding with the the amide groups in the side chains has to be contrasted with the hydration interaction of the hydrophobic main chain hydro-carbons. Employing FTIR spectroscopy we probe molecular changes in the various chemical groups. PNIPAM and its monomer NIPAM are investigated at a concentration of 20% in aqueous solution. We observe a nearly discontinuous shift of the the peak frequencies and the intensities of vibrational bands (amides, CH) in PNIPAM, whereas in NIPAM there is a continuous linear shift with temperature. The results are discussed with respect to hydration changes in the amide group and cooperative interactions with bound water along the backbone chain.

  1. Molecular spectroscopic study on the interaction of tetracyclines with serum albumins

    NASA Astrophysics Data System (ADS)

    Bi, Shuyun; Song, Daqian; Tian, Yuan; Zhou, Xin; Liu, Zhongying; Zhang, Hanqi

    2005-02-01

    A molecular spectroscopic investigation of the interaction between tetracyclines antibiotics and human serum albumin or bovine serum albumin was reported. The influences of some metal ions on the interaction were also studied. When tetracyclines drugs were added into the solution containing serum albumins, the fluorescence intensity of serum albumins decreased with the increasing of the drugs concentrations, which is due to the formation of new non-fluorescence complexes of drug-serum albumin. The tetracyclines acted as quenchers and quenched the fluorescence of the serum albumins. The binding constants and the number of the binding sites of the reaction of tetracyclines and serum albumins were obtained. The main sorts of acting force between the drugs and serum albumins were found and the action distances and the energy transfer efficiencies between donor-acceptor were calculated based on the Föster energy transference.

  2. Identifying gene-environment interactions in schizophrenia: contemporary challenges for integrated, large-scale investigations.

    PubMed

    van Os, Jim; Rutten, Bart P; Myin-Germeys, Inez; Delespaul, Philippe; Viechtbauer, Wolfgang; van Zelst, Catherine; Bruggeman, Richard; Reininghaus, Ulrich; Morgan, Craig; Murray, Robin M; Di Forti, Marta; McGuire, Philip; Valmaggia, Lucia R; Kempton, Matthew J; Gayer-Anderson, Charlotte; Hubbard, Kathryn; Beards, Stephanie; Stilo, Simona A; Onyejiaka, Adanna; Bourque, Francois; Modinos, Gemma; Tognin, Stefania; Calem, Maria; O'Donovan, Michael C; Owen, Michael J; Holmans, Peter; Williams, Nigel; Craddock, Nicholas; Richards, Alexander; Humphreys, Isla; Meyer-Lindenberg, Andreas; Leweke, F Markus; Tost, Heike; Akdeniz, Ceren; Rohleder, Cathrin; Bumb, J Malte; Schwarz, Emanuel; Alptekin, Köksal; Üçok, Alp; Saka, Meram Can; Atbaşoğlu, E Cem; Gülöksüz, Sinan; Gumus-Akay, Guvem; Cihan, Burçin; Karadağ, Hasan; Soygür, Haldan; Cankurtaran, Eylem Şahin; Ulusoy, Semra; Akdede, Berna; Binbay, Tolga; Ayer, Ahmet; Noyan, Handan; Karadayı, Gülşah; Akturan, Elçin; Ulaş, Halis; Arango, Celso; Parellada, Mara; Bernardo, Miguel; Sanjuán, Julio; Bobes, Julio; Arrojo, Manuel; Santos, Jose Luis; Cuadrado, Pedro; Rodríguez Solano, José Juan; Carracedo, Angel; García Bernardo, Enrique; Roldán, Laura; López, Gonzalo; Cabrera, Bibiana; Cruz, Sabrina; Díaz Mesa, Eva Ma; Pouso, María; Jiménez, Estela; Sánchez, Teresa; Rapado, Marta; González, Emiliano; Martínez, Covadonga; Sánchez, Emilio; Olmeda, Ma Soledad; de Haan, Lieuwe; Velthorst, Eva; van der Gaag, Mark; Selten, Jean-Paul; van Dam, Daniella; van der Ven, Elsje; van der Meer, Floor; Messchaert, Elles; Kraan, Tamar; Burger, Nadine; Leboyer, Marion; Szoke, Andrei; Schürhoff, Franck; Llorca, Pierre-Michel; Jamain, Stéphane; Tortelli, Andrea; Frijda, Flora; Vilain, Jeanne; Galliot, Anne-Marie; Baudin, Grégoire; Ferchiou, Aziz; Richard, Jean-Romain; Bulzacka, Ewa; Charpeaud, Thomas; Tronche, Anne-Marie; De Hert, Marc; van Winkel, Ruud; Decoster, Jeroen; Derom, Catherine; Thiery, Evert; Stefanis, Nikos C; Sachs, Gabriele; Aschauer, Harald; Lasser, Iris; Winklbaur, Bernadette; Schlögelhofer, Monika; Riecher-Rössler, Anita; Borgwardt, Stefan; Walter, Anna; Harrisberger, Fabienne; Smieskova, Renata; Rapp, Charlotte; Ittig, Sarah; Soguel-dit-Piquard, Fabienne; Studerus, Erich; Klosterkötter, Joachim; Ruhrmann, Stephan; Paruch, Julia; Julkowski, Dominika; Hilboll, Desiree; Sham, Pak C; Cherny, Stacey S; Chen, Eric Y H; Campbell, Desmond D; Li, Miaoxin; Romeo-Casabona, Carlos María; Emaldi Cirión, Aitziber; Urruela Mora, Asier; Jones, Peter; Kirkbride, James; Cannon, Mary; Rujescu, Dan; Tarricone, Ilaria; Berardi, Domenico; Bonora, Elena; Seri, Marco; Marcacci, Thomas; Chiri, Luigi; Chierzi, Federico; Storbini, Viviana; Braca, Mauro; Minenna, Maria Gabriella; Donegani, Ivonne; Fioritti, Angelo; La Barbera, Daniele; La Cascia, Caterina Erika; Mulè, Alice; Sideli, Lucia; Sartorio, Rachele; Ferraro, Laura; Tripoli, Giada; Seminerio, Fabio; Marinaro, Anna Maria; McGorry, Patrick; Nelson, Barnaby; Amminger, G Paul; Pantelis, Christos; Menezes, Paulo R; Del-Ben, Cristina M; Gallo Tenan, Silvia H; Shuhama, Rosana; Ruggeri, Mirella; Tosato, Sarah; Lasalvia, Antonio; Bonetto, Chiara; Ira, Elisa; Nordentoft, Merete; Krebs, Marie-Odile; Barrantes-Vidal, Neus; Cristóbal, Paula; Kwapil, Thomas R; Brietzke, Elisa; Bressan, Rodrigo A; Gadelha, Ary; Maric, Nadja P; Andric, Sanja; Mihaljevic, Marina; Mirjanic, Tijana

    2014-07-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi-center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype.

  3. Identifying Gene-Environment Interactions in Schizophrenia: Contemporary Challenges for Integrated, Large-scale Investigations

    PubMed Central

    2014-01-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi–center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype. PMID:24860087

  4. Interaction of cyproheptadine hydrochloride with human serum albumin using spectroscopy and molecular modeling methods.

    PubMed

    Jiang, Hua; Chen, Rongrong; Wang, Hongcui; Pu, Hanlin

    2013-01-01

    The interaction between cyproheptadine hydrochloride (CYP) and human serum albumin (HSA) was investigated by fluorescence spectroscopy, UV-vis absorption spectroscopy, Fourier transform infrared spectroscopy (FT-IR) and molecular modeling at a physiological pH (7.40). Fluorescence of HSA was quenched remarkably by CYP and the quenching mechanism was considered as static quenching since it formed a complex. The association constants Ka and number of binding sites n were calculated at different temperatures. According to Förster's theory of non-radiation energy transfer, the distance r between donor (human serum albumin) and acceptor (cyproheptadine hydrochloride) was obtained. The effect of common ions on the binding constant was also investigated. The effect of CYP on the conformation of HSA was analyzed using FT-IR, synchronous fluorescence spectroscopy and 3D fluorescence spectra. The thermodynamic parameters ΔH and ΔS were calculated to be -14.37 kJ mol(-1) and 38.03 J mol(-1) K(-1), respectively, which suggested that hydrophobic forces played a major role in stabilizing the HSA-CYP complex. In addition, examination of molecular modeling indicated that CYP could bind to site I of HSA and that hydrophobic interaction was the major acting force, which was in agreement with binding mode studies.

  5. Molecular interaction of anti-diabetic drugs with Acetylcholinesterase and Sodium Glucose Co-Transporter 2.

    PubMed

    Shakil, Shazi

    2017-04-07

    Type 2 Diabetes Mellitus (T2DM) and Alzheimer's disease (AD) are the two disorders which are known to share pertinent pathological and therapeutic links. Sodium glucose co-transporter- (SGLT2) and Acetylcholinesterase (AChE) are established inhibition targets for T2DM and AD treatments, respectively. Reports suggest that anti-diabetic drugs could be used for AD treatment also. The present study used molecular docking by Autodock4.2 using our "Click-By-Click"-protocol, Ligplot1.4.3 and 'change in accessible surface area (ΔASA)-calculations' to investigate the binding of two investigational anti-diabetic drugs, Ertugliflozin and Sotagliflozin to an established target (SGLT2) and a research target (human brain AChE). Sotagliflozin appeared more promising for SGLT2 as well as AChE-inhibition with reference to ΔG and Ki values in comparison to Ertugliflozin. The ΔG and Ki values for 'Sotagliflozin:AChE-binding' were -7.16 kcal/mol and 5.6 μM, respectively while the same were found to be -8.47 kcal/mol and 0.62 μM, respectively for its interaction with SGLT2. Furthermore, 'Sotagliflozin:SGLT2-interaction' was subjected to (un)binding simulation analyses by 'Molecular-Motion-Algorithms'. This information is significant as the exact binding mode, interacting amino acid residues and simulation results for the said interaction have not been described yet. Also no X-ray crystal is available for the same. Finally, the results described herein indicate that Sotagliflozin could have an edge over Ertugliflozin for treatment of Type 2 diabetes. Future design of drugs based on Sotagliflozin scaffolds for treatment of Type 2 and/or Type 3 diabetes are highly recommended. As these drugs are still in late phases of clinical trials, the results described herein appear timely. This article is protected by copyright. All rights reserved.

  6. "Zwitterionic Proton Sponge" Hydrogen Bonding Investigations on the Basis of Car-Parrinello Molecular Dynamics.

    PubMed

    Jezierska, Aneta; Panek, Jarosław J

    2015-06-22

    1,8-Bis(dimethylamino)-4,5-dihydroxynaphthalene has been investigated on the basis of static DFT computations and Car-Parrinello molecular dynamics. The simulations were performed in the gas phase and in the solid state. The studied "zwitterionic proton sponge" possesses two, short intramolecular hydrogen bonds (O-H···O and N-H···N) classified as Low Barrier Hydrogen Bonds (LBHBs); therefore, the system studied is strongly anharmonic. In addition, the compound exists as a "zwitterion" in solution and in the solid state, thus the intramolecular hydrogen bonds belong to the class of charge-assisted interactions. The applied quantum-chemical methods enabled investigations of metric and spectroscopic parameters of the molecule. The time-evolution investigations of the H-bonding showed a strong delocalization of the bridge protons and their high mobility, reflected in the low barriers on the free energy surfaces. Frequent proton transfer phenomena were noticed. The power spectra of atomic velocity were computed to analyze the vibrational features associated with O-H and N-H stretching. A broad absorption was indicated for both hydrogen bridges. For the first time, Car-Parrinello molecular dynamics results are reported for the compound, and they indicate a broad, shallow but not barrierless, potential well for each of the bridge protons.

  7. Investigation of Cellular Interactions of Nanoparticles by Helium Ion Microscopy

    SciTech Connect

    Arey, Bruce W.; Shutthanandan, V.; Xie, Yumei; Tolic, Ana; Williams, Nolann G.; Orr, Galya

    2011-06-01

    The helium ion mircroscope (HIM) probes light elements (e.g. C, N, O, P) with high contrast due to the large variation in secondary electron yield, which minimizes the necessity of specimen staining. A defining characteristic of HIM is its remarkable capability to neutralize charge by the implementation of an electron flood gun, which eliminates the need for coating non-conductive specimens for imaging at high resolution. In addition, the small convergence angle in HeIM offers a large depth of field (~5x FE-SEM), enabling tall structures to be viewed in focus within a single image. Taking advantage of these capabilities, we investigate the interactions of engineered nanoparticles (NPs) at the surface of alveolar type II epithelial cells grown at the air-liquid interface (ALI). The increasing use of nanomaterials in a wide range of commercial applications has the potential to increase human exposure to these materials, but the impact of such exposure on human health is still unclear. One of the main routs of exposure is the respiratory tract, where alveolar epithelial cells present a vulnerable target at the interface with ambient air. Since the cellular interactions of NPs govern the cellular response and ultimately determine the impact on human health, our studies will help delineating relationships between particle properties and cellular interactions and response to better evaluate NP toxicity or biocompatibility. The Rutherford backscattered ion (RBI) is a helium ions imaging mode, which backscatters helium ions from every element except hydrogen, with a backscatter yield that depends on the atomic number of the target. Energy-sensitive backscatter analysis is being developed, which when combined with RBI image information, supports elemental identification at helium ion nanometer resolution. This capability will enable distinguishing NPs from cell surface structures with nanometer resolution.

  8. Investigation of cellular interactions of nanoparticles by helium ion microscopy

    NASA Astrophysics Data System (ADS)

    Arey, B. W.; Shutthanandan, V.; Xie, Y.; Tolic, A.; Williams, N.; Orr, G.

    2011-06-01

    The helium ion microscope (HIM) probes light elements (e.g. C, N, O, P) with high contrast due to the large variation in secondary electron yield, which minimizes the necessity of specimen staining. A defining characteristic of HIM is its remarkable capability to neutralize charge by the implementation of an electron flood gun, which eliminates the need for coating non-conductive specimens for imaging at high resolution. In addition, the small convergence angle in HeIM offers a large depth of field (~5× FE-SEM), enabling tall structures to be viewed in focus within a single image. Taking advantage of these capabilities, we investigate the interactions of engineered nanoparticles (NPs) at the surface of alveolar type II epithelial cells grown at the airliquid interface (ALI). The increasing use of nanomaterials in a wide range of commercial applications has the potential to increase human exposure to these materials, but the impact of such exposure on human health is still unclear. One of the main routs of exposure is the respiratory tract, where alveolar epithelial cells present a vulnerable target at the interface with ambient air. Since the cellular interactions of NPs govern the cellular response and ultimately determine the impact on human health, our studies will help delineating relationships between particle properties and cellular interactions and response to better evaluate NP toxicity or biocompatibility. The Rutherford backscattered ion (RBI) is a helium ions imaging mode, which backscatters helium ions from every element except hydrogen, with a backscatter yield that depends on the atomic number of the target. Energy-sensitive backscatter analysis is being developed, which when combined with RBI image information, supports elemental identification at helium ion nanometer resolution. This capability will enable distinguishing NPs from cell surface structures with nanometer resolution.

  9. Investigation on interaction of prulifloxacin with pepsin: A spectroscopic analysis

    NASA Astrophysics Data System (ADS)

    Huang, Yabei; Yan, Jie; Liu, Benzhi; Yu, Zhang; Gao, Xiaoyan; Tang, Yingcai; Zi, Yanqin

    2010-03-01

    The interaction between prulifloxacin, a kind of new oral taking antibiotic and pepsin, a kind of enzyme in the stomach has been investigated in vitro under a simulated physiological condition by different spectroscopic methods. The intrinsic fluorescence of pepsin was strongly quenched by prulifloxacin. This effect was rationalized in terms of a static quenching procedure. The binding parameters have been evaluated by fluorescence quenching methods. The negative value of Δ G0 reveals that the binding process is a spontaneous process. The binding distance R between donor (pepsin) and acceptor (prulifloxacin) was obtained according to the Förster's resonance energy transfer theory and found to be 0.95 nm. The results obtained herein will be of biological significance in pharmacology and clinical medicine.

  10. Investigation on interaction of prulifloxacin with pepsin: a spectroscopic analysis.

    PubMed

    Huang, Yabei; Yan, Jie; Liu, Benzhi; Yu, Zhang; Gao, Xiaoyan; Tang, Yingcai; Zi, Yanqin

    2010-03-01

    The interaction between prulifloxacin, a kind of new oral taking antibiotic and pepsin, a kind of enzyme in the stomach has been investigated in vitro under a simulated physiological condition by different spectroscopic methods. The intrinsic fluorescence of pepsin was strongly quenched by prulifloxacin. This effect was rationalized in terms of a static quenching procedure. The binding parameters have been evaluated by fluorescence quenching methods. The negative value of DeltaG(0) reveals that the binding process is a spontaneous process. The binding distance R between donor (pepsin) and acceptor (prulifloxacin) was obtained according to the Förster's resonance energy transfer theory and found to be 0.95 nm. The results obtained herein will be of biological significance in pharmacology and clinical medicine.

  11. Raman scattering investigation of VOCs in interaction with ice particles

    NASA Astrophysics Data System (ADS)

    Facq, Sébastien; Oancea, Adriana; Focsa, Cristian; Chazallon, Bertrand

    2010-05-01

    Cirrus clouds that form in the Earth's upper troposphere (UT) are known to play a significant role in the radiation budget and climate [1]. These clouds that cover about 35% of the Earth's surface [2] are mainly composed of small ice particles that can provide surfaces for trace gas interactions [3]. Volatile Organic Compounds (VOCs) are present in relative high abundance in the UT [4][5]. They promote substantial sources of free OH radicals that are responsible for driving photochemical cycles in the atmosphere. Their presence can both influence the oxidizing capacity and the ozone budget of the atmosphere. VOCs can interact with ice particles via different trapping processes (adsorption, diffusion, freezing, and co-deposition, i.e., incorporation of trace gases during growing ice conditions) which can result in the perturbation of the chemistry and photochemistry of the UT. Knowledge of the incorporation processes of VOCs in ice particles is important in order to understand and predict their impact on the ice particles structure and reactivity and more generally on the cirrus cloud formation. This proceeds via the in-situ characterization of the ice condensed phase in a pressure and temperature range of the UT. An important mechanism of UT cirrus cloud formation is the heterogeneous ice freezing process. In this study, we examine and characterize the interaction of a VOC, i.e., ethanol (EtOH) with ice particles during freezing. Vibrational spectra of water O-H and EtOH C-H spectral regions are analysed using confocal micro-Raman spectroscopy. Information at the molecular level on the surface structure can be derived from accompanying changes observed in band shapes and vibrational mode frequencies. Depending of the EtOH content, different crystalline phases have been identified and compared to hydrates previously reported for the EtOH-water system. Particular attention is paid on the effect of EtOH aqueous solutions cooling rate and droplet sizes on the phases

  12. Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation

    PubMed Central

    Cui, Fengchao; Yang, Kecheng; Li, Yunqi

    2015-01-01

    To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation. We found that catechins with different structures bound to a conservative pocket S1 of trypsin, which is comprised of residues 189–195, 214–220 and 225–228. In the trypsin-catechin complexes, Asp189 by forming strong hydrogen bonding, and Gln192, Trp215 and Gly216 through hydrophobic interactions, all significantly contribute to the binding of catechins. The number and the position of hydroxyl and aromatic groups, the structure of stereoisomers, and the orientation of catechins in the binding pocket S1 of trypsin all affect the binding affinity. The binding affinity is in the order of Epigallocatechin gallate (EGCG) > Epicatechin gallate (ECG) > Epicatechin (EC) > Epigallocatechin (EGC), and 2R-3R EGCG shows the strongest binding affinity out of other stereoisomers. Meanwhile, the synergic conformational changes of residues and catechins were also analyzed. These findings will be helpful in understanding the knowledge of interactions between catechins and trypsin and referable for the design of novel polyphenol based functional food and nutriceutical formulas. PMID:25938485

  13. 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.

  14. Investigation of the torsional barrier of EDOT using molecular mechanics and DFT methods.

    PubMed

    Durães, Jussara A; da Silva Filho, Demétrio A; Ceschin, Artemis M; Sales, Maria J A; Martins, João B L

    2014-08-01

    When heterocyclic monomers are polymerized by electrochemical or chemical methods, they form fully conjugated polymers which have a wide range of applications due to their outstanding electronic properties. Among this class of compounds, thiophene derivatives are widely used due to their chemical stability and synthesis flexibility. With the goal to investigate the torsion barrier of polymer chains, a few units of 3,4-ethylenedioxythiophene (EDOT) were chosen and submitted to molecular mechanics (MM), density functional theory (DFT) and coupled cluster CCSD(T) calculations. This study helps to understand the performance and transferability of force fields used in molecular mechanics and molecular dynamics simulations often used to describe structure-property relationships of those systems. Determination of inter-ring torsion angle was performed in a comparative study using both force field, DFT and CCSD(T) methods. A good agreement was noticed between MM and QC results and highlights the importance of the description of the interactions involving the oxygen atoms present in the structure of EDOT. These observations are related to the α,α-coupling that occurs between the monomer units and yields a linear polymer. DFT HOMO and LUMO orbitals were also presented. Finally, UV-vis spectra of EDOT units were obtained using several levels of theory by means of time-dependent DFT calculations (TD-DFT).

  15. Using solvents with different molecular sizes to investigate the structure of Antheraea pernyi silk.

    PubMed

    Wang, Yu; Porter, David; Shao, Zhengzhong

    2013-11-11

    The interaction between silk and polar solvents of different molecular size can be an important tool for understanding the structural features of natural silk; in particular, the disordered regions associated with the key property of mechanical toughness. In this work, we investigate the transitions induced in the tensile performance and structure of as-reeled Antheraea pernyi silks from different silkworms by a range of solvents that can only soften the protein chains in the amorphous regions. The results indicate that polar solvents with different molecular sizes affect the silk to different degrees, and silks with slightly different structures display significantly different tensile performance in the same solvent. The solvent molecular size is quantitatively correlated with the accessible volume in the amorphous regions before and after the yield point, which suggests that the volume accessible to the solvent molecules decreases as the solvent radius increases. Moreover, silks with more ordered structure (less free volume) in the amorphous regions are less sensitive to solvents than those with more disordered structures. However, silks with higher free volume have higher toughness due to the greater strain to failure.

  16. [Molecular genetic investigation of sugar beet (Beta vulgaris L.)].

    PubMed

    Butorina, A K; Kornienko, A V

    2011-10-01

    Molecular genetic studies of sugar beet (Beta vulgaris L.) are reviewed as a basis for the development of genomics of this species. The methods used to study structural and functional genomics are considered. The results and their application to increase the efficiency of sugar beet breeding are discussed.

  17. Fire safety in space - Investigating flame spread interaction over wires

    NASA Astrophysics Data System (ADS)

    Citerne, Jean-Marie; Dutilleul, Hugo; Kizawa, Koki; Nagachi, Masashi; Fujita, Osamu; Kikuchi, Masao; Jomaas, Grunde; Rouvreau, Sébastien; Torero, Jose L.; Legros, Guillaume

    2016-09-01

    A new rig for microgravity experiments was used for the study flame spread of parallel polyethylene-coated wires in concurrent and opposed airflow. The parabolic flight experiments were conducted at small length- and time scales, i.e. typically over 10 cm long samples for up to 20 s. For the first time, the influence of neighboring spread on the mass burning rate was assessed in microgravity. The observations are contrasted with the influence characterized in normal gravity. The experimental results are expected to deliver meaningful guidelines for future, planned experiments at a larger scale. Arising from the current results, the issue of the potential interaction among spreading flames also needs to be carefully investigated as this interaction plays a major role in realistic fire scenarios, and therefore on the design of the strategies that would allow the control of such a fire. Once buoyancy has been removed, the characteristic length and time scales of the different modes of heat and mass transfer are modified. For this reason, interaction among spreading flames may be revealed in microgravity, while it would not at normal gravity, or vice versa. Furthermore, the interaction may lead to an enhanced spread rate when mutual preheating dominates or, conversely, a reduced spread rate when oxidizer flow vitiation is predominant. In more general terms, the current study supports both the SAFFIRE and the FLARE projects, which are large projects with international scientific teams. First, material samples will be tested in a series of flight experiments (SAFFIRE 1-3) conducted in Cygnus vehicles after they have undocked from the ISS. These experiments will allow the study of ignition and possible flame spread in real spacecraft conditions, i.e. over real length scale samples within real time scales. Second, concomitant research conducted within the FLARE project is dedicated to the assessment of new standard tests for materials that a spacecraft can be composed of

  18. Role of the Strength of Drug-Polymer Interactions on the Molecular Mobility and Crystallization Inhibition in Ketoconazole Solid Dispersions.

    PubMed

    Mistry, Pinal; Mohapatra, Sarat; Gopinath, Tata; Vogt, Frederick G; Suryanarayanan, Raj

    2015-09-08

    The effects of specific drug-polymer interactions (ionic or hydrogen-bonding) on the molecular mobility of model amorphous solid dispersions (ASDs) were investigated. ASDs of ketoconazole (KTZ), a weakly basic drug, with each of poly(acrylic acid) (PAA), poly(2-hydroxyethyl methacrylate) (PHEMA), and polyvinylpyrrolidone (PVP) were prepared. Drug-polymer interactions in the ASDs were evaluated by infrared and solid-state NMR, the molecular mobility quantified by dielectric spectroscopy, and crystallization onset monitored by differential scanning calorimetry (DSC) and variable temperature X-ray diffractometry (VTXRD). KTZ likely exhibited ionic interactions with PAA, hydrogen-bonding with PHEMA, and weaker dipole-dipole interactions with PVP. On the basis of dielectric spectroscopy, the α-relaxation times of the ASDs followed the order: PAA > PHEMA > PVP. In addition, the presence of ionic interactions also translated to a dramatic and disproportionate decrease in mobility as a function of polymer concentration. On the basis of both DSC and VTXRD, an increase in strength of interaction translated to higher crystallization onset temperature and a decrease in extent of crystallization. Stronger drug-polymer interactions, by reducing the molecular mobility, can potentially delay the crystallization onset temperature as well as crystallization extent.

  19. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  20. Molecular Social Interactions: Drosophila melanogaster Seminal Fluid Proteins as a Case Study

    PubMed Central

    Sirot, Laura K.; LaFlamme, Brooke A.; Sitnik, Jessica L.; Rubinstein, C. Dustin; Avila, Frank W.; Chow, Clement Y.; Wolfner, Mariana F.

    2014-01-01

    Studies of social behavior generally focus on interactions between two or more individual animals. However, these interactions are not simply between whole animals, but also occur between molecules that were produced by the interacting individuals. Such “molecular social interactions” can both influence and be influenced by the organismal-level social interactions. We illustrate this by reviewing the roles played by seminal fluid proteins (Sfps) in molecular social interactions between males and females of the fruit fly Drosophila melanogaster. Sfps, which are produced by males and transferred to females during mating, are involved in inherently social interactions with female-derived molecules, and they influence social interactions between males and females and between a female’s past and potential future mates. Here, we explore four examples of molecular social interactions involving D. melanogaster Sfps: processes that influence mating, sperm storage, ovulation, and ejaculate transfer. We consider the molecular and organismal players involved in each interaction and the consequences of their interplay for the reproductive success of both sexes. We conclude with a discussion of the ways in which Sfps can both shape and be shaped by (in an evolutionary sense) the molecular social interactions in which they are involved. PMID:20109658

  1. Investigation of laser-tissue interaction in medicine by means of laser spectroscopic measurements

    NASA Astrophysics Data System (ADS)

    Lademann, Juergen; Weigmann, Hans-Juergen

    1995-01-01

    Toxic and carcinogenic substances were produced during laser application in medicine for the cutting and evaporation of tissue. The laser smoke presents a danger potential for the medical staff and the patients. The laser tissue interaction process was investigated by means of laser spectroscopic measurements which give the possibility of measuring metastable molecular states directly as a prerequisite to understand and to influence fundamental laser tissue interaction processes in order to reduce the amount of harmful chemicals. Highly excited atomic and molecular states and free radicals (CN, OH, C2, CH, CH2) have been detected applying spontaneous and laser induced fluorescence methods. It was found that the formation of harmful substances in the laser plumes can be reduced significantly by optimization of the surrounding gas atmosphere. A high content of oxygen or water in the interaction zone has been found, in agreement with the results of classical and analytical methods, as a suitable way to decrease pollutant emission. The experimental methods and the principal results are applicable not only in laser medicine but in laser material treatment generally.

  2. Investigation of soil-atmosphere interaction in pyroclastic soils

    NASA Astrophysics Data System (ADS)

    Rianna, Guido; Pagano, Luca; Urciuoli, Gianfranco

    2014-03-01

    This paper investigates the interaction between soil and atmosphere in pyroclastic soils with a view to understanding whether and to what extent the prediction of the hydraulic (and mechanical) behaviour of geotechnical problems (cuts, slope stabilities, embankments, foundation, retaining structures) regulated by rainfall-induced fluctuations of matric suction is influenced by evaporation phenomena. Evaporation fluxes are quantified and compared with other fluxes (precipitation, run-off, deep drainage) affecting soil water content and matric suction. This work is based on the data collected through a physical model over 2 years of experimental tests. The model consisted of a 1 m3 tank, filled in this case with pyroclastic soil and exposed to natural weather elements. The system was extensively monitored to record atmospheric and soil variables. The results provided by the experiments highlight the importance of the top-soil state in determining the intensities of infiltrating rainfall and actual evaporation. The results also bring to light the significance of evaporation which, during the dry season, largely prevails over infiltration, raising suction to very high values. Also during the wet season, evaporation gives rise to a non-negligible flux with respect to the infiltrated precipitation. The reliability of two pre-existing empirical models to estimate evaporation flux is also investigated and appraised within this paper.

  3. Molecular modeling and molecular dynamics simulation studies on the interactions of hydroxylated polychlorinated biphenyls with estrogen receptor-β.

    PubMed

    Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Shi, Wei; Qian, XiangPing; Zhu, YongLiang; Yu, HongXia

    2013-10-01

    Endocrine-disrupting chemicals have attracted great concern. As major metabolites of polychlorinated biphenyls (PCBs), hydroxylated polychlorinated biphenyls (HO-PCBs) may disrupt estrogen hormone status because of their structural similarity to estrogen endogenous compounds. However, interactions between HO-PCBs and estrogen receptors (ERs) are not fully understood. In the present work, a molecular modeling study combining molecular docking, molecular dynamics simulations, and binding free energy calculations was performed to characterize the interactions of three HO-PCBs (4'-HO-PCB50, 2'-HO-PCB65, and 4'-HO-PCB69) having much different estrogenic activities with ERβ. Docking results showed that binding between ligands and ERβ was stabilized by hydrogen bond and hydrophobic interactions. The binding free energies of three ligands with ERβ were calculated, and further binding free energy decomposition analysis indicated that the dominating driving force of the binding between the ligands and ERβ was the van der Waals interaction. Some key residues, such as Leu298, Phe356, Gly472, His475, and Leu476, played important roles in ligand-receptor interactions by forming hydrophobic and hydrogen bond interactions with ligands. The results may be beneficial to increase understanding of the interactions between HO-PCBs and ERβ.

  4. Investigation of the interaction of pepsin with ionic liquids by using fluorescence spectroscopy.

    PubMed

    Fan, Yunchang; Zhang, Sheli; Wang, Qiang; Li, Junhai; Fan, Haotian; Shan, Dongkai

    2013-06-01

    The molecular mechanism of the interaction between pepsin and two typical ionic liquids (ILs), 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) and 1-octyl-3-methylimidazolium chloride ([C8mim]Cl), was investigated with fluorescence spectroscopy, ultraviolet absorption, and circular dichroism spectroscopy at a pH value of 1.6. The results suggest that ILs could quench the intrinsic fluorescence of pepsin, probably via a dynamic quenching mechanism. The fluorescence quenching constants were determined by employing the classic Stern-Volmer equation. The constant values are very small, indicating that only a very weak interaction between ILs and pepsin exists. The Gibbs free-energy change, enthalpy change (ΔH), and entropy change (ΔS) during the interaction of pepsin and ILs were estimated. Positive values of ΔH and ΔS indicate that the interaction between ILs and pepsin is mainly driven by hydrophobic interaction. Synchronous and three-dimensional fluorescence spectra demonstrate that the addition of ILs (0-0.20 mol L(-1) for each IL) does not bring apparent changes to the microenvironments of tyrosine and tryptophan residues. Activity experiments show that the activity of pepsin is concentration dependent; higher concentrations of ILs (>0.22 mol L(-1) for [C8mim]Cl and >0.30 mol L(-1) for [C4mim]Cl) cause the remarkable reduction of enzyme activity. The presence of ILs also does not improve the thermal stability of pepsin.

  5. Phase equilibrium calculations of ternary liquid mixtures with binary interaction parameters and molecular size parameters determined from molecular dynamics.

    PubMed

    Oh, Suk Yung; Bae, Young Chan

    2010-07-15

    The method presented in this paper was developed to predict liquid-liquid equilibria in ternary liquid mixtures by using a combination of a thermodynamic model and molecular dynamics simulations. In general, common classical thermodynamic models have many parameters which are determined by fitting a model with experimental data. This proposed method, however, provides a simple procedure for calculating liquid-liquid equilibria utilizing binary interaction parameters and molecular size parameters determined from molecular dynamics simulations. This method was applied to mixtures containing water, hydrocarbons, alcohols, chlorides, ketones, acids, and other organic liquids over various temperature ranges. The predicted results agree well with the experimental data without the use of adjustable parameters.

  6. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps.

    PubMed

    Boninsegna, Lorenzo; Gobbo, Gianpaolo; Noé, Frank; Clementi, Cecilia

    2015-12-08

    Identification of the collective coordinates that describe rare events in complex molecular transitions such as protein folding has been a key challenge in the theoretical molecular sciences. In the Diffusion Map approach, one assumes that the molecular configurations sampled have been generated by a diffusion process, and one uses the eigenfunctions of the corresponding diffusion operator as reaction coordinates. While diffusion coordinates (DCs) appear to provide a good approximation to the true dynamical reaction coordinates, they are not parametrized using dynamical information. Thus, their approximation quality could not, as yet, be validated, nor could the diffusion map eigenvalues be used to compute relaxation rate constants of the system. Here we combine the Diffusion Map approach with the recently proposed Variational Approach for Conformation Dynamics (VAC). Diffusion Map coordinates are used as a basis set, and their optimal linear combination is sought using the VAC, which employs time-correlation information on the molecular dynamics (MD) trajectories. We have applied this approach to ultra-long MD simulations of the Fip35 WW domain and found that the first DCs are indeed a good approximation to the true reaction coordinates of the system, but they could be further improved using the VAC. Using the Diffusion Map basis, excellent approximations to the relaxation rates of the system are obtained. Finally, we evaluate the quality of different metric spaces and find that pairwise minimal root-mean-square deviation performs poorly, while operating in the recently introduced kinetic maps based on the time-lagged independent component analysis gives the best performance.

  7. Polymorphism and disorder in caffeine: Dielectric investigation of molecular mobilities

    NASA Astrophysics Data System (ADS)

    Descamps, M.; Decroix, A. A.

    2014-12-01

    Using dielectric relaxation data we have characterized the molecular mobilities of caffeine both in phase I (stable and metastable) and in phase II. In phase I effects of sublimation and phase transformation kinetics were carefully considered. In plane rotational motions were followed on a wide temperature range. A noticeable antiferroelectric short range order developing at the approach of the glass-like transition is characterized. Condition for occurrence of a critical-like behaviour is discussed. At high temperature the emergence of an additional ultra slow relaxation process is highlighted. Possible molecular mechanisms are proposed for both processes. In phase II the existence of a less intense relaxation process is confirmed. Close similarity with the main process developing in phase I hints at a common origin of the dipolar motions. Careful consideration of recent structure determinations leads to suggest that this process is associated to similar molecular in plane rotations but developing at the surface of crystalline samples. Lower cooperativity at the surface is reflected in the smaller activation entropy of the relaxation.

  8. Molecular interactions in 1-butanol + IL solutions by measuring and modeling activity coefficients.

    PubMed

    Nann, Alexander; Mündges, Jan; Held, Christoph; Verevkin, Sergey P; Sadowski, Gabriele

    2013-03-21

    Molecular interactions in 1-butanol + ionic liquid (IL) solutions have been investigated by measuring and modeling activity-coefficient data. The activity coefficients in binary solutions containing 1-butanol and an IL were determined experimentally: the ILs studied were 1-decyl-3-methyl-imidazolium tetracyanoborate ([Im10.1](+)[tcb](-)), 4-decyl-4-methyl-morpholinium tetracyanoborate ([Mo10.1](+)[tcb](-)), 1-decyl-3-methyl-imidazolium bis(trifluoromethylsulfonyl)imide ([Im10.1](+)[ntf2](-)), and 4-decyl-4-methyl-morpholinium bis(trifluoromethylsulfonyl)imide ([Mo10.1](+)[ntf2](-)). The methods used to determine the activity coefficients included vapor-pressure osmometry, headspace-gas chromatography, and gas-liquid chromatography. The results from all of these techniques were combined to obtain activity-coefficient data over the entire IL concentration range, and the ion-specific interactions of the ILs investigated were identified with 1-butanol. The highest (1-butanol)-IL interactions of the ILs considered in this work were found for [Im10.1](+)[tcb](-); thus, [Im10.1](+)[tcb](-) showed the highest affinity for 1-butanol in a binary mixture. The experimental data were modeled with the Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT). PC-SAFT was able to accurately describe the pure IL and (1-butanol)-IL data. Moreover, the model was shown to be predictive and extrapolative with respect to concentration and temperature.

  9. Radiative interactions in molecular gases under local and nonlocal thermodynamic equilibrium conditions

    NASA Technical Reports Server (NTRS)

    Tiwari, S. N.; Jha, M. K.

    1993-01-01

    Basic formulations, analyses, and numerical procedures are presented to investigate radiative heat interactions in diatomic and polyatomic gases under local and nonlocal thermodynamic equilibrium conditions. Essential governing equations are presented for both gray and nongray gases. Information is provided on absorption models, relaxation times, and transfer equations. Radiative flux equations are developed which are applicable under local and nonlocal thermodynamic equilibrium conditions. The problem is solved for fully developed laminar incompressible flows between two parallel plates under the boundary condition of a uniform surface heat flux. For specific applications, three diatomic and three polyatomic gases are considered. The results are obtained numerically by employing the method of variation of parameters. The results are compared under local and nonlocal thermodynamic equilibrium conditions at different temperature and pressure conditions. Both gray and nongray studies are conducted extensively for all molecular gases considered. The particular gases selected for this investigation are CO, NO, OH, CO2, H2O, and CH4. The temperature and pressure range considered are 300-2000 K and 0.1-10 atmosphere, respectively. In general, results demonstrate that the gray gas approximation overestimates the effect of radiative interaction for all conditions. The conditions of NLTE, however, result in underestimation of radiative interactions. The method developed for this study can be extended to solve complex problems of radiative heat transfer involving nonequilibrium phenomena.

  10. Molecular dynamics simulation of amorphous indomethacin-poly(vinylpyrrolidone) glasses: solubility and hydrogen bonding interactions.

    PubMed

    Xiang, Tian-Xiang; Anderson, Bradley D

    2013-03-01

    Amorphous drug dispersions are frequently employed to enhance solubility and dissolution of poorly water-soluble drugs and thereby increase their oral bioavailability. Because these systems are metastable, phase separation of the amorphous components and subsequent drug crystallization may occur during storage. Computational methods to determine the likelihood of these events would be very valuable, if their reliability could be validated. This study investigates amorphous systems of indomethacin (IMC) in poly(vinylpyrrolidone) (PVP) and their molecular interactions by means of molecular dynamics (MD) simulations. IMC and PVP molecules were constructed using X-ray diffraction data, and force-field parameters were assigned by analogy with similar groups in Amber-ff03. Five assemblies varying in PVP and IMC composition were equilibrated in their molten states then cooled at a rate of 0.03 K/ps to generate amorphous glasses. Prolonged aging dynamic runs (100 ns) at 298 K and 1 bar were then carried out, from which solubility parameters, the Flory-Huggins interaction parameter, and associated hydrogen bonding properties were obtained. Calculated glass transition temperature (T(g)) values were higher than experimental results because of the faster cooling rates in MD simulations. Molecular mobility as characterized by atomic fluctuations was substantially reduced below the T(g) with IMC-PVP systems exhibiting lower mobilities than that found in amorphous IMC, consistent with the antiplasticizing effect of PVP. The number of IMC-IMC hydrogen bonds (HBs) formed per IMC molecule was substantially lower in IMC-PVP mixtures, particularly the fractions of IMC molecules involved in two or three HBs with other IMC molecules that may be potential precursors for crystal growth. The loss of HBs between IMC molecules in the presence of PVP was largely compensated for by the formation of IMC-PVP HBs. The difference (6.5 MPa(1/2)) between the solubility parameters in amorphous IMC

  11. Carbon Dioxide - rock interaction: from molecular observations to theorised interactions in fluid-rock systems

    NASA Astrophysics Data System (ADS)

    Calcara, Massimo; Borgia, Andrea

    2013-04-01

    Current global warming theories have produced some benefits: among them, detailed studies on CO2 and its properties, possible applications and perspectives. Starting from its use as a "green solvent" (for instance in decaffeination process), to enhance system in oil recovery, to capture and storage enough amount of CO2 in geological horizon. So, a great debate is centred around this molecule. One More useful research in natural horizon studies is its theorised use in Enhanced Geothermal Systems with CO2 as the only working fluid. In any case, the CO2 characteristics should be deeply understood, before injecting a molecule prone to change easily its aggregation state at relatively shallow depth. CO2 Rock interaction becomes therefore a focal point in approaching research sectors linked in some manner to natural or induced presence of carbon dioxide in geological horizons. Possible chemical interactions between fluids and solids have always been a central topic in defining evolution of the system as a whole in terms of dissolutions, reactions, secondary mineral formation and, in case of whichever plant, scaling. Questions arise in case of presence of CO2 with host rocks. Chemical and molecular properties are strategic. CO2 Rock interactions are based on eventual solubility capability of pure liquid and supercritical CO2 seeking and eventually quantifying its polar and/or ionic solvent capabilities. Single molecule at STP condition is linear, with central carbon atom and oxygen atoms at opposite site on a straight line with a planar angle. It has a quadrupolar moment due to the electronegativity difference between carbon and oxygen. As soon as CO2 forms bond with water, it deforms even at atmospheric pressure, assuming an induced dipole moment with a value around 0.02 Debye. Hydrated CO2 forms a hydrophilic bond; it deforms with an angle of 178 degrees. Pure CO2 forms self aggregates. In the simplest case a dimer, with two molecules of CO2 exerting mutual attraction

  12. Study on the interactions of mapenterol with serum albumins using multi-spectroscopy and molecular docking.

    PubMed

    Bi, Shuyun; Zhao, Tingting; Wang, Yu; Zhou, Huifeng

    2016-03-01

    The interactions of mapenterol with bovine serum albumin (BSA) and human serum albumin (HSA) have been investigated systematically using fluorescence spectroscopy, absorption spectroscopy, circular dichroism (CD) and molecular docking techniques. Mapenterol has a strong ability to quench the intrinsic fluorescence of BSA and HSA through static quenching procedures. At 291 K, the binding constants, Ka, were 1.93 × 10(3) and 2.73 × 10(3) L/mol for mapenterol-BSA and mapenterol-HAS, respectively. Electrostatic forces and hydrophobic interactions played important roles in stabilizing the mapenterol-BSA/has complex. Using site marker competitive studies, mapenterol was found to bind at Sudlow site I on BSA/HSA. There was little effect of K(+), Ca(2+), Cu(2+), Zn(2+) and Fe(3+) on the binding. The conformation of BSA/HSA was changed by mapenterol, as seen from the synchronous fluorescence spectra. The CD spectra showed that the binding of mapenterol to BSA/HSA changed the secondary structure of BSA/HSA. Molecular docking further confirmed that mapenterol could bind to Sudlow site I of BSA/HSA. According to Förster non-radiative energy transfer theory (FRET), the distances r0 between the donor and acceptor were calculated as 3.18 and 2.75 nm for mapenterol-BSA and mapenterol-HAS, respectively.

  13. Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

    NASA Astrophysics Data System (ADS)

    Shahabadi, Nahid; Bagheri, Somayeh

    2015-02-01

    The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb = 2 × 103 M-1). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

  14. Effect of electron-vibration interactions on the thermoelectric efficiency of molecular junctions.

    PubMed

    Hsu, Bailey C; Chiang, Chi-Wei; Chen, Yu-Chang

    2012-07-11

    From first-principles approaches, we investigate the thermoelectric efficiency of a molecular junction where a benzene molecule is connected directly to the platinum electrodes. We calculate the thermoelectric figure of merit ZT in the presence of electron-vibration interactions with and without local heating under two scenarios: linear response and finite bias regimes. In the linear response regime, ZT saturates around the electrode temperature T(e) = 25 K in the elastic case, while in the inelastic case we observe a non-saturated and a much larger ZT beyond T(e) = 25 K attributed to the tail of the Fermi-Dirac distribution. In the finite bias regime, the inelastic effects reveal the signatures of the molecular vibrations in the low-temperature regime. The normal modes exhibiting structures in the inelastic profile are characterized by large components of atomic vibrations along the current density direction on top of each individual atom. In all cases, the inclusion of local heating leads to a higher wire temperature T(w) and thus magnifies further the influence of the electron-vibration interactions due to the increased number of local phonons.

  15. Molecular insights on TNKS1/TNKS2 and inhibitor-IWR1 interactions.

    PubMed

    Kirubakaran, Palani; Kothandan, Gugan; Cho, Seung J; Muthusamy, Karthikeyan

    2014-02-01

    Tankyrases (TNKS) belong to the poly(ADP-ribose)polymerase (PARP) protein super family and play a vital role in the Wnt/β-catenin signaling pathway. TNKS is a potential target for therapeutic intervention against various cancers, heritable diseases (e.g. cherubism) and implications in the replication of herpes simplex virus (HSV). The recent discovery of the structure of TNKS with an IWR1 inhibitor has provided insight into the binding modes which are specific for the TNKS protein which will aid in the development of drugs that are specific for the TNKS protein. The current study investigates molecular interactions between the induced pocket of TNKS1 and TNKS2 with an IWR1 compound using computational approaches. Molecular docking analysis of IWR1 at the induced pocket of TNKS1 and TNKS2 was performed. The resulting protein-ligand complexes were simulated for a timescale of 100 ns. Results revealed the stable binding of IWR1 at the induced pocket of TNKS1 and TNKS2 proteins. Apart from active site amino acids, π-π stack paring interactions were also crucial for the protein-ligand binding and stability of the complex. Further, energy-optimized pharmacophore mapping was performed and the resulting pharmacophore model contained a four (TNKS1-IWR1) and five (TNKS2-IWR1) featured sites. Based on the pharmacophore models, the best inhibitors were screened from the ZINC natural product compound database and these could be used as potential drugs against TNKS1 and TNKS2.

  16. From protein denaturant to protectant: Comparative molecular dynamics study of alcohol/protein interactions

    NASA Astrophysics Data System (ADS)

    Shao, Qiang; Fan, Yubo; Yang, Lijiang; Qin Gao, Yi

    2012-03-01

    It is well known that alcohols can have strong effects on protein structures. For example, monohydric methanol and ethanol normally denature, whereas polyhydric glycol and glycerol protect, protein structures. In a recent combined theoretical and NMR experimental study, we showed that molecular dynamics simulations can be effectively used to understand the molecular mechanism of methanol denaturing protein. In this study, we used molecular dynamics simulations to investigate how alcohols with varied hydrophobicity and different numbers of hydrophilic groups (hydroxyl groups) exert effects on the structure of the model polypeptide, BBA5. First, we showed that methanol and trifluoroethanol (TFE) but not glycol or glycerol disrupt hydrophobic interactions. The latter two alcohols instead protect the assembly of the α- and β-domains of the polypeptide. Second, all four alcohols were shown to generally increase the stability of secondary structures, as revealed by the increased number of backbone hydrogen bonds formed in alcohol/water solutions compared to that in pure water, although individual hydrogen bonds can be weakened by certain alcohols, such as TFE. The two monohydric alcohols, methanol and TFE, display apparently different sequence-dependence in affecting the backbone hydrogen bond stability: methanol tends to enhance the stability of backbone hydrogen bonds of which the carbonyl groups are from polar residues, whereas TFE tends to stabilize those involving non-polar residues. These results demonstrated that subtle differences in the solution environment could have distinct consequences on protein structures.

  17. Investigation of imprinting parameters and their recognition nature for quinine-molecularly imprinted polymers

    NASA Astrophysics Data System (ADS)

    He, Jian-feng; Zhu, Quan-hong; Deng, Qin-ying

    2007-08-01

    A series of molecularly imprinted polymers (MIPs) was prepared using quinine as the template molecules by bulk polymerization. The presence of monomer-template solution complexes in non-covalent MIPs systems has been verified by both fluorescence and UV-vis spectrometric detection. The influence of different synthetic conditions (porogen, functional monomer, cross-linkers, initiation methods, monomer-template ratio, etc.) on recognition properties of the polymers was investigated. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymer. The corresponding dissociation constants were estimated to be 45.00 μmol l -1 and 1.42 mmol l -1, respectively, by utilizing a multi-site recognition model. The binding characteristics of the imprinted polymers were explored in various solvents using equilibrium binding experiments. In the organic media, results suggested that polar interactions (hydrogen bonding, ionic interactions, etc.) between acidic monomer/polymer and template molecules were mainly responsible for the recognition, whereas in aqueous media, hydrophobic interactions had a remarkable non-specific contribution to the overall binding. The specificity of MIP was evaluated by rebinding the other structurally similar compounds. The results indicated that the imprinted polymers exhibited an excellent stereo-selectivity toward quinine.

  18. Preliminary investigations into surface molecularly imprinted nanoparticles for Helicobacter pylori eradication

    PubMed Central

    Han, Jiaying; Sun, Yinjing; Hou, Jiapeng; Wang, Yuyan; Liu, Yu; Xie, Cao; Lu, Weiyue; Pan, Jun

    2015-01-01

    This paper reports investigations into the preparation and characterization of surface molecularly imprinted nanoparticles (SMINs) designed to adhere to Helicobacter pylori (H. pylori). Imprinted nanoparticles were prepared by the inverse microemulsion polymerization method. A fraction of Lpp20, an outer membrane protein of H. pylori known as NQA, was chosen as template and modified with myristic acid to facilitate its localization on the surface of the nanoparticles. The interaction between these SMINs with the template NQA were evaluated using surface plasmon resonance (SPR), change in zeta potential and fluorescence polarization (FP). The results were highly consistent in demonstrating a preferential recognition of the template NQA for SMINs compared with the control nanoparticles. In vitro experiments also indicate that such SMINs are able to adhere to H. pylori and may be useful for H. pylori eradication. PMID:26713273

  19. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  20. Investigation of plasma particle interactions with variable particle sizes

    NASA Astrophysics Data System (ADS)

    Dropmann, Michael; Laufer, Rene; Herdrich, Georg; Matthews, Lorin; Hyde, Truell

    2015-11-01

    In dusty plasmas, the dust particles are subjected to many forces of different origins. Both the gas and plasma directly affect the dust particles through electric fields, neutral drag, ion drag and thermophoretic forces, while the particles themselves interact with one another through a screened coulomb potential, which can be influenced by flowing ions. Recently, micron sized particles have been used as probes to analyze the electric fields in the plasma directly. A proper analysis of the resulting data requires a full understanding of the manner in which these forces couple to the dust particles. In most cases each of the forces exhibit unique characteristics, many of which are partially dependent on the particle size. In this study, five different particle sizes are used to investigate the forces resident in the sheath above the lower electrode of a GEC RF reference cell. The particles are tracked using a high-speed camera, yielding two-dimensional force maps allowing the force on the particles to be described as a polynomial series. It will be shown that the data collected can be analyzed to reveal information about the origins of the various forces. Support from the NSF and the DOE (award numbers PHY-1262031 and PHY-1414523) is gratefully acknowledged.

  1. Investigating hard sphere interactions through spin echo scattering angle measurement

    NASA Astrophysics Data System (ADS)

    Washington, Adam

    Spin Echo Scattering Angle Measurement (SESAME) allows neutron scattering instruments to perform real space measurements on large micron scale samples by encoding the scattering angle into the neutron's spin state via Larmor precession. I have built a SESAME instrument at the Low Energy Neutron Source. I have also assisted in the construction of a modular SESAME instrument on the ASTERIX beamline at Los Alamos National lab. The ability to tune these instruments has been proved mathematically and optimized and automated experimentally. Practical limits of the SESAME technique with respect to polarization analyzers, neutron spectra, Larmor elements, and data analysis were investigated. The SESAME technique was used to examine the interaction of hard spheres under depletion. Poly(methyl methacrylate) spheres suspended in decalin had previously been studied as a hard sphere solution. The interparticle correlations between the spheres were found to match the Percus-Yevick closure, as had been previously seen in dynamical light scattering experiments. To expand beyond pure hard spheres, 900kDa polystyrene was added to the solution in concentrations of less than 1% by mass. The steric effects of the polystyrene were expected to produce a short-range, attractive, "sticky" potential. Experiment showed, however, that the "sticky" potential was not a stable state and that the spheres would eventually form long range aggregates.

  2. Investigating joint attention mechanisms through spoken human-robot interaction.

    PubMed

    Staudte, Maria; Crocker, Matthew W

    2011-08-01

    Referential gaze during situated language production and comprehension is tightly coupled with the unfolding speech stream (Griffin, 2001; Meyer, Sleiderink, & Levelt, 1998; Tanenhaus, Spivey-Knowlton, Eberhard, & Sedivy, 1995). In a shared environment, utterance comprehension may further be facilitated when the listener can exploit the speaker's focus of (visual) attention to anticipate, ground, and disambiguate spoken references. To investigate the dynamics of such gaze-following and its influence on utterance comprehension in a controlled manner, we use a human-robot interaction setting. Specifically, we hypothesize that referential gaze is interpreted as a cue to the speaker's referential intentions which facilitates or disrupts reference resolution. Moreover, the use of a dynamic and yet extremely controlled gaze cue enables us to shed light on the simultaneous and incremental integration of the unfolding speech and gaze movement. We report evidence from two eye-tracking experiments in which participants saw videos of a robot looking at and describing objects in a scene. The results reveal a quantified benefit-disruption spectrum of gaze on utterance comprehension and, further, show that gaze is used, even during the initial movement phase, to restrict the spatial domain of potential referents. These findings more broadly suggest that people treat artificial agents similar to human agents and, thus, validate such a setting for further explorations of joint attention mechanisms.

  3. Investigation of helicopter rotor blade/wake interactive impulsive noise

    NASA Technical Reports Server (NTRS)

    Miley, S. J.; Hall, G. F.; Vonlavante, E.

    1987-01-01

    An analysis of the Tip Aerodynamic/Aeroacoustic Test (TAAT) data was performed to identify possible aerodynamic sources of blade/vortex interaction (BVI) impulsive noise. The identification is based on correlation of measured blade pressure time histories with predicted blade/vortex intersections for the flight condition(s) where impulsive noise was detected. Due to the location of the recording microphones, only noise signatures associated with the advancing blade were available, and the analysis was accordingly restricted to the first and second azimuthal quadrants. The results show that the blade tip region is operating transonically in the azimuthal range where previous BVI experiments indicated the impulsive noise to be. No individual blade/vortex encounter is identifiable in the pressure data; however, there is indication of multiple intersections in the roll-up region which could be the origin of the noise. Discrete blade/vortex encounters are indicated in the second quadrant; however, if impulsive noise were produced here, the directivity pattern would be such that it was not recorded by the microphones. It is demonstrated that the TAAT data base is a valuable resource in the investigation of rotor aerodynamic/aeroacoustic behavior.

  4. A molecular-genetic approach to studying source-sink interactions in Arabidopsis thalian. Final report

    SciTech Connect

    Gibson, S. I.

    2000-06-01

    This is a final report describing the results of the research funded by the DOE Energy Biosciences Program grant entitled ''A Molecular-Genetic Approach to Studying Source-Sink Interactions in Arabidiopsis thaliana''.

  5. Molecular Diagnosis of Natural enemy-host Interactions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The cryptic behaviors, small size, and rapid movement and feeding actions of arthropod natural enemies dictate the need for alternative technologies for the study of trophic linkages to replace the traditional approaches of direct observation and laboratory experimentation. Many molecular approaches...

  6. Molecular dynamics simulation and NMR investigation of the association of the β-blockers atenolol and propranolol with a chiral molecular micelle

    NASA Astrophysics Data System (ADS)

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2015-08-01

    Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies.

  7. Investigation of molecular penetration depth variation with SMBI fluxes

    NASA Astrophysics Data System (ADS)

    Zhou, Yu-Lin; Wang, Zhan-Hui; Xu, Min; Wang, Qi; Nie, Lin; Feng, Hao; Sun, Wei-Guo

    2016-09-01

    We study the molecular penetration depth variation with the SMBI fluxes. The molecular transport process and the penetration depth during SMBI with various injection velocities and densities are simulated and compared. It is found that the penetration depth of molecules strongly depends on the radial convective transport of SMBI and it increases with the increase of the injection velocity. The penetration depth does not vary much once the SMBI injection density is larger than a critical value due to the dramatic increase of the dissociation rate on the fueling path. An effective way to improve the SMBI penetration depth has been predicted, which is SMBI with a large radial injection velocity and a lower molecule injection density than the critical density. Project supported by the National Natural Science Foundation of China (Grant Nos. 11375053, 11575055, 11405022, and 11405112), the Chinese National Fusion Project for ITER (Grant Nos. 2013GB107001 and 2013GB112005), the International S&T Cooperation Program of China (Grant No. 2015DFA61760), and the Funds of the Youth Innovation Team of Science and Technology in Sichuan Province of China (Grant No. 2014TD0023).

  8. Optical investigation of molecular structure of sophisticated materials for photonics

    NASA Astrophysics Data System (ADS)

    Gnyba, Marcin; Keraenen, Mikko

    2003-10-01

    Permanent development of photonics stimulates a searching for new materials, which have better optical, mechanical and electrical properties. One of the new classes of materials with large application and development potential are hybrid polymers, synthesized in sol-gel technology. Thanks to incorporation of organic components into an in organic network, a combination of advantages of both class of materials became available. Properties of hybrids may be formed in wide range. These materials can be used in photonics to produce planar waveguides, lenses, Bragg gratings and components for integrated optics. Moreover, dielectric layers, coatings and packaging are made from hybrids. Additionally, research to apply them in optical fiber sensors (including bio-sensors) and solid state lasers is underway. However, to obtain a high quality product, a strict control of its molecular structure must be ensured. This is a very difficult task, because of a sophisticated structure of hybrid polymers. To address these problems, optical, non-destructive measurement techniques such as Raman and infrared spectroscopy were used. They are compementary methods, so their simultaneous application, as it was shown in this paper, can significantly increase the amoung of information about molecular structure of materials and process of their synthesis.

  9. Revealing the molecular signatures of host-pathogen interactions

    PubMed Central

    2011-01-01

    Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary co-existence. PMID:22011345

  10. Inhibition of MMP-9 by green tea catechins and prediction of their interaction by molecular docking analysis.

    PubMed

    Sarkar, Jaganmay; Nandy, Suman Kumar; Chowdhury, Animesh; Chakraborti, Tapati; Chakraborti, Sajal

    2016-12-01

    Green tea polyphenolic catechins have been shown to prevent various types of diseases such as pulmonary hypertension (PAH), cancer and cardiac and neurological disorders. Matrix metalloproteinases (MMPs) play an important role in the development of PAH. The present study demonstrated that among the four green tea catechins (EGCG, ECG, EC and EGC), EGCG and ECG inhibit pro-/active MMP-9 activities in pulmonary artery smooth muscle cell culture supernatant. Based on the above, we investigated the interactions of pro-/active MMP-9 with the green tea catechins by computational methods. In silico molecular docking analysis revealed a strong interaction between pro-/active MMP-9 and EGCG/ECG, and galloyl group appears to be responsible for this enhanced interaction. The molecular docking studies corroborate our experimental observation that EGCG and ECG are mainly active in preventing both the proMMP-9 and MMP-9 activities.

  11. Hydrolysable ATP is a requirement for the correct interaction of molecular chaperonins cpn60 and cpn10.

    PubMed Central

    Walters, Chris; Errington, Neil; Rowe, Arther J; Harding, Stephen E

    2002-01-01

    Over recent years the binding ability of the molecular chaperone cpn60 (GroEL14) and its co-chaperone cpn10 (GroES7) has been reported to occur under an assortment of specific conditions from the use of non-hydrolysable ATP analogues (namely adenosine 5'-[gamma-thio]triphosphate) to requiring hydrolysable ATP for any interaction to occur. We have investigated this further using the molecular hydrodynamic methods (hydrodynamic bead modelling, sedimentation-velocity analytical ultracentrifugation and dynamic light-scattering), allowing the process to be followed under physiologically relevant dilute solution conditions, combined with absorption spectrophotometry to determine GroES7-GroEL14 interaction through the rate inhibition of the cpn60's ATPase activity by GroES7. The results found here indicate that the presence of hydrolysable ATP is required to facilitate correct GroES7 interaction with GroEL14 in solution. PMID:12049650

  12. Multi-spectroscopic and molecular modeling studies of bovine serum albumin interaction with sodium acetate food additive.

    PubMed

    Mohammadzadeh-Aghdash, Hossein; Ezzati Nazhad Dolatabadi, Jafar; Dehghan, Parvin; Panahi-Azar, Vahid; Barzegar, Abolfazl

    2017-08-01

    Sodium acetate (SA) has been used as a highly effective protectant in food industry and the possible effect of this additive on the binding to albumin should be taken into consideration. Therefore, for the first time, the mechanism of SA interaction with bovine serum albumin (BSA) has been investigated by multi-spectroscopic and molecular modeling methods under physiological conditions. Stern-Volmer fluorescence quenching analysis showed an increase in the fluorescence intensity of BSA upon increasing the amounts of SA. The high affinity of SA to BSA was demonstrated by a binding constant value (1.09×10(3) at 310°K). The thermodynamic parameters indicated that hydrophobic binding plays a main role in the binding of SA to Albumin. Furthermore, the results of UV-vis spectra confirmed the interaction of this additive to BSA. In addition, molecular modeling study demonstrated that A binding sites of BSA play the main role in the interaction with acetate.

  13. Molecular interactions between the olive and the fruit fly Bactrocera oleae

    PubMed Central

    2012-01-01

    Background The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. Results We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. Conclusions This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction. PMID:22694925

  14. Influence of molecular shape, conformability, net surface charge, and tissue interaction on transscleral macromolecular diffusion.

    PubMed

    Srikantha, Nishanthan; Mourad, Fatma; Suhling, Klaus; Elsaid, Naba; Levitt, James; Chung, Pei Hua; Somavarapu, Satyanarayana; Jackson, Timothy L

    2012-09-01

    The purpose of this study was to investigate the influence of molecular shape, conformability, net surface charge and tissue interaction on transscleral diffusion. Unfixed, porcine sclera was clamped in an Ussing chamber. Fluorophore-labelled neutral albumin, neutral dextran, or neutral ficoll were placed in one hemi-chamber and the rate of transscleral diffusion was measured over 24 h using a spectrophotometer. Experiments were repeated using dextrans and ficoll with positive or negative net surface charges. Fluorescence recovery after photobleaching (FRAP) was undertaken to compare transscleral diffusion with diffusion through a solution. All molecules were 70 kDa. With FRAP, the diffusion coefficient (D) of neutral molecules was highest for albumin, followed by ficoll, then dextran (p < 0.0001). Positive dextrans diffused fastest, followed by negative, then neutral dextrans (p = 0.0004). Neutral ficoll diffused the fastest, followed by positive then negative ficoll (p = 0.5865). For the neutral molecules, transscleral D was highest for albumin, followed by dextran, then ficoll (p < 0.0001). D was highest for negative ficoll, followed by neutral, then positive ficoll (p < 0.0001). By contrast, D was highest for positive dextran, followed by neutral, then negative dextran (p = 0.0021). In conclusion, diffusion in free solution does not predict transscleral diffusion and the molecular-tissue interaction is important. Molecular size, shape, and charge may all markedly influence transscleral diffusion, as may conformability to a lesser degree, but their effects may be diametrically opposed in different molecules, and their influence on diffusion is more complex than previously thought. Each variable cannot be considered in isolation, and the interplay of all these variables needs to be tested, when selecting or designing drugs for transscleral delivery.

  15. Challenges and novel approaches for investigating molecular mediation

    PubMed Central

    Richmond, R.C.; Hemani, G.; Tilling, K.; Davey Smith, G.; Relton, C.L.

    2016-01-01

    Understanding mediation is useful for identifying intermediates lying between an exposure and an outcome which, when intervened upon, will block (some or all of) the causal pathway between the exposure and outcome. Mediation approaches used in conventional epidemiology have been adapted to understanding the role of molecular intermediates in situations of high-dimensional omics data with varying degrees of success. In particular, the limitations of observational epidemiological study including confounding, reverse causation and measurement error can afflict conventional mediation approaches and may lead to incorrect conclusions regarding causal effects. Solutions to analysing mediation which overcome these problems include the use of instrumental variable methods such as Mendelian randomization, which may be applied to evaluate causality in increasingly complex networks of omics data. PMID:27439390

  16. [Mitochondrial diseases: molecular mechanisms, clinical presentations and diagnosis investigations].

    PubMed

    Auré, Karine; Jardel, Claude; Lombès, Anne

    2005-09-01

    Mitochondrial diseases are relatively common inherited metabolic diseases due to mitochondrial respiratory chain dysfunction. Their clinical presentation is extremely diverse, multisystemic or confined to a single tissue, sporadic or transmitted, by maternal or mendelian inheritance. The diagnosis of mitochondrial disorders is difficult. It is based upon several types of clues both clinical (family history, type of symptoms but also their association in syndromic presentation,...) and biological (alteration of the lactate metabolism, brain imaging, morphological alterations especially of muscle tissue). The diagnosis relies upon the demonstration of a defect of the respiratory chain activities and/or upon the identification of the underlying genetic alteration. Molecular diagnosis remains quite difficult and up to-date concerns essentially mitochondrial DNA mutations. On one hand, clinical and biological presentations as well as enzymatic defects lack specificity. On the other hand, candidate genes are very numerous and part of them are probably still unknown.

  17. A molecular dynamics investigation of surface reconstruction on magnetite (001)

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Wasserman, E.; Felmy, A. R.

    1999-07-01

    Molecular dynamics calculations using analytical potential functions with polarizable oxygen ions have been used to identify a novel mode of reconstruction on the half-occupied tetrahedral layer termination of the magnetite (Fe 3O 4) (001) surface. In the proposed reconstruction, the twofold coordinated iron ion in the top monolayer rotates downward to occupy a vacant half-octahedral site in the plane of the second-layer iron ions. At the same time, half of the tetrahedral iron ions in the third iron layer are pushed upward to occupy an adjacent octahedral vacancy at the level of the second-layer iron ions. The other half of the third-layer iron ions remain roughly in their original positions. The proposed reconstruction is consistent with recent low-energy electron diffraction and X-ray photoelectron spectroscopy results. It also provides a compelling interpretation for the arrangement of atoms suggested by high-resolution scanning-tunneling microscopy studies.

  18. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures

    PubMed Central

    Caetano, Fabiana A.; Dirk, Brennan S.; Tam, Joshua H. K.; Cavanagh, P. Craig; Goiko, Maria; Ferguson, Stephen S. G.; Pasternak, Stephen H.; Dikeakos, Jimmy D.; de Bruyn, John R.; Heit, Bryan

    2015-01-01

    Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. PMID:26657340

  19. Vitamin E-drug interactions: molecular basis and clinical relevance.

    PubMed

    Podszun, Maren; Frank, Jan

    2014-12-01

    Vitamin E (α-, β-, γ- and δ-tocopherol and -tocotrienol) is an essential factor in the human diet and regularly taken as a dietary supplement by many people, who act under the assumption that it may be good for their health and can do no harm. With the publication of meta-analyses reporting increased mortality in persons taking vitamin E supplements, the safety of the micronutrient was questioned and interactions with prescription drugs were suggested as one potentially underlying mechanism. Here, we review the evidence in the scientific literature for adverse vitamin E-drug interactions and discuss the potential of each of the eight vitamin E congeners to alter the activity of drugs. In summary, there is no evidence from animal models or randomised controlled human trials to suggest that the intake of tocopherols and tocotrienols at nutritionally relevant doses may cause adverse nutrient-drug interactions. Consumption of high-dose vitamin E supplements ( ≥  300 mg/d), however, may lead to interactions with the drugs aspirin, warfarin, tamoxifen and cyclosporine A that may alter their activities. For the majority of drugs, however, interactions with vitamin E, even at high doses, have not been observed and are thus unlikely.

  20. Molecular force spectroscopy of homophilic nectin-1 interactions

    SciTech Connect

    Vedula, Sri Ram Krishna; Lim, T.S.; Hui Shi; Kausalya, P. Jaya; Lane, E. Birgitte; Rajagopal, Gunaretnam; Hunziker, Walter; Lim, C.T.

    2007-11-03

    Nectins are Ca{sup 2+} independent cell adhesion molecules localizing at the cadherin based adherens junctions. In this study, we have used atomic force microscopy to study interaction of a chimera of extra cellular fragment of nectin-1 and Fc of human IgG (nef-1) with wild type L-fibroblasts that express endogenous nectin-1 to elucidate the biophysical characteristics of homophilic nectin-1 trans-interactions at the level of single molecule. Bond strength distribution revealed three distinct bound states (or configurations) of trans-interactions between paired nectins, where each bound state has a unique unstressed off-rate and reactive compliance. Kinetic analysis of force-dependent off-rate of the bound state involving trans-interacting V-V domains between paired nectin-1 (unstressed off-rate {approx}1.465 {+-} 0.779 s{sup -1}, reactive compliance {approx}0.143 {+-} 0.072 nm) was found to be closest to E-cadherin, indicating that V-V domain trans-interactions are probably necessary to initiate and promote adhesions of E-cadherin at adherens junctions (AJs)

  1. Molecular magnetic resonance imaging of brain–immune interactions

    PubMed Central

    Gauberti, Maxime; Montagne, Axel; Quenault, Aurélien; Vivien, Denis

    2014-01-01

    Although the blood–brain barrier (BBB) was thought to protect the brain from the effects of the immune system, immune cells can nevertheless migrate from the blood to the brain, either as a cause or as a consequence of central nervous system (CNS) diseases, thus contributing to their evolution and outcome. Accordingly, as the interface between the CNS and the peripheral immune system, the BBB is critical during neuroinflammatory processes. In particular, endothelial cells are involved in the brain response to systemic or local inflammatory stimuli by regulating the cellular movement between the circulation and the brain parenchyma. While neuropathological conditions differ in etiology and in the way in which the inflammatory response is mounted and resolved, cellular mechanisms of neuroinflammation are probably similar. Accordingly, neuroinflammation is a hallmark and a decisive player of many CNS diseases. Thus, molecular magnetic resonance imaging (MRI) of inflammatory processes is a central theme of research in several neurological disorders focusing on a set of molecules expressed by endothelial cells, such as adhesion molecules (VCAM-1, ICAM-1, P-selectin, E-selectin, …), which emerge as therapeutic targets and biomarkers for neurological diseases. In this review, we will present the most recent advances in the field of preclinical molecular MRI. Moreover, we will discuss the possible translation of molecular MRI to the clinical setting with a particular emphasis on myeloperoxidase imaging, autologous cell tracking, and targeted iron oxide particles (USPIO, MPIO). PMID:25505871

  2. The molecular mechanism for interaction of ceruloplasmin and myeloperoxidase

    NASA Astrophysics Data System (ADS)

    Bakhautdin, Bakytzhan; Bakhautdin, Esen Göksöy

    2016-04-01

    Ceruloplasmin (Cp) is a copper-containing ferroxidase with potent antioxidant activity. Cp is expressed by hepatocytes and activated macrophages and has been known as physiologic inhibitor of myeloperoxidase (MPO). Enzymatic activity of MPO produces anti-microbial agents and strong prooxidants such as hypochlorous acid and has a potential to damage host tissue at the sites of inflammation and infection. Thus Cp-MPO interaction and inhibition of MPO has previously been suggested as an important control mechanism of excessive MPO activity. Our aim in this study was to identify minimal Cp domain or peptide that interacts with MPO. We first confirmed Cp-MPO interaction by ELISA and surface plasmon resonance (SPR). SPR analysis of the interaction yielded 30 nM affinity between Cp and MPO. We then designed and synthesized 87 overlapping peptides spanning the entire amino acid sequence of Cp. Each of the peptides was tested whether it binds to MPO by direct binding ELISA. Two of the 87 peptides, P18 and P76 strongly interacted with MPO. Amino acid sequence analysis of identified peptides revealed high sequence and structural homology between them. Further structural analysis of Cp's crystal structure by PyMOL software unfolded that both peptides represent surface-exposed sites of Cp and face nearly the same direction. To confirm our finding we raised anti-P18 antisera in rabbit and demonstrated that this antisera disrupts Cp-MPO binding and rescues MPO activity. Collectively, our results confirm Cp-MPO interaction and identify two nearly identical sites on Cp that specifically bind MPO. We propose that inhibition of MPO by Cp requires two nearly identical sites on Cp to bind homodimeric MPO simultaneously and at an angle of at least 120 degrees, which, in turn, exerts tension on MPO and results in conformational change.

  3. Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

    PubMed Central

    Allnér, Olof; Nilsson, Lennart; Villa, Alessandra

    2013-01-01

    Riboswitches are mRNA-based molecules capable of controlling the expression of genes. They undergo conformational changes upon ligand binding, and as a result, they inhibit or promote the expression of the associated gene. The close connection between structural rearrangement and function makes a detailed knowledge of the molecular interactions an important step to understand the riboswitch mechanism and efficiency. We have performed all-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, one key tertiary element in the aptamer structure. We investigated the aptamer domain of the add A-riboswitch in complex with its cognate ligand and in the absence of the ligand. The opening of the hairpins was simulated using umbrella sampling using the distance between two loops as the reaction coordinate. A two-step process was observed in all the simulated systems. First, a general loss of stacking and hydrogen bond interactions is seen. The last interactions that break are the two base pairs G37-C61 and G38-C60, but the break does not affect the energy profile, indicating their pivotal role in the tertiary structure formation but not in the structure stabilization. The junction area is partially organized before the kissing loop formation and residue A24 anchors together the loop helices. Moreover, when the distance between the loops is increased, one of the hairpins showed more flexibility by changing its orientation in the structure, while the other conserved its coaxial arrangement with the rest of the structure. PMID:23716711

  4. Interaction between phillygenin and human serum albumin based on spectroscopic and molecular docking

    NASA Astrophysics Data System (ADS)

    Song, W.; Ao, M. Z.; Shi, Y.; Yuan, L. F.; Yuan, X. X.; Yu, L. J.

    2012-01-01

    In this paper, the interaction of human serum albumin (HSA) with phillygenin was investigated by fluorescence, circular dichroism (CD), UV-vis spectroscopic and molecular docking methods under physiological conditions. The Stern-Volmer analysis indicated that the fluorescence quenching of HSA by phillygenin resulted from static mechanism, and the binding constants were 1.71 × 10 5, 1.61 × 10 5 and 1.47 × 10 4 at 300, 305 and 310 K, respectively. The results of UV-vis spectra show that the secondary structure of the protein has been changed in the presence of phillygenin. The CD spectra showed that HSA conformation was altered by phillygenin with a major reduction of α-helix and an increase in β-sheet and random coil structures, indicating a partial protein unfolding. The distance between donor (HSA) and acceptor (phillygenin) was calculated to be 3.52 nm and the results of synchronous fluorescence spectra showed that binding of phillygenin to HSA can induce conformational changes in HSA. Molecular docking experiments found that phillygenin binds with HSA at IIIA domain of hydrophobic pocket with hydrogen bond interactions. The ionic bonds were formed with the O (4), O (5) and O (6) of phillygenin with nitrogen of ASN109, ARG186 and LEU115, respectively. The hydrogen bonds are formed between O (2) of phillygenin and SER419. In the presence of copper (II), iron (III) and alcohol, the apparent association constant KA and the number of binding sites of phillygenin on HSA were both decreased in the range of 88.84-91.97% and 16.09-18.85%, respectively. In view of the evidence presented, it is expected to enrich our knowledge of the interaction dynamics of phillygenin to the important plasma protein HSA, and it is also expected to provide important information of designs of new inspired drugs.

  5. Xanthan-alginate composite gel beads: molecular interaction and in vitro characterization.

    PubMed

    Pongjanyakul, Thaned; Puttipipatkhachorn, Satit

    2007-02-22

    Xanthan gum (XG), a trisaccharide branched polymer, was applied to reinforce calcium alginate beads in this study. Composite beads consisting of XG and sodium alginate (SA) were prepared using ionotropic gelation method. Diclofenac calcium-alginate (DCA) beads incorporated with different amounts of XG were produced as well. Molecular interaction between SA and XG in the composite beads and the XG-DCA beads was investigated using FTIR spectroscopy. Physical properties of the XG-DCA beads such as entrapment efficiency of diclofenac sodium (DS), thermal property, water uptake, swelling and DS release in various media were examined. XG could form intermolecular hydrogen bonding with SA in the composite beads with or without DS. Differential scanning calorimetric study indicated that XG did not affect thermal property of the DCA beads. The DS entrapment efficiency of the DCA beads increased with increasing amount of XG added. The XG-DCA beads showed higher water uptake and swelling in pH 6.8 phosphate buffer and distilled water than the DCA beads. A longer lag time and a higher DS release rate of the XG-DCA beads in pH 6.8 phosphate buffer were found. In contrast, the 0.3%XG-DCA beads could retard the drug release in distilled water because interaction between XG and SA gave higher tortuosity of the bead matrix. However, higher content of XG in the DCA beads increased the release rate of DS. This can be attributed to erosion of small aggregates of XG on the surface of the DCA beads. This finding suggested that XG could modulate physicochemical properties and drug release of the DCA beads, which based on the existence of molecular interaction between XG and SA.

  6. An Investigation into the Sex-Race-Ability Interaction.

    ERIC Educational Resources Information Center

    Strauch, Barry

    In a recent article Jensen proposed the existence of what was termed the sex x race x ability interaction in which the differences in mental ability between the black sexes were larger than the corresponding differences among whites. Three large sources of data that were analyzed failed to reveal the interaction. Since Jensen's own work suggested…

  7. An Interactive Graphics Program for Investigating Digital Signal Processing.

    ERIC Educational Resources Information Center

    Miller, Billy K.; And Others

    1983-01-01

    Describes development of an interactive computer graphics program for use in teaching digital signal processing. The program allows students to interactively configure digital systems on a monitor display and observe their system's performance by means of digital plots on the system's outputs. A sample program run is included. (JN)

  8. Protein Interaction Data Curation - The International Molecular Exchange Consortium (IMEx)

    PubMed Central

    Orchard, Sandra; Kerrien, Samuel; Abbani, Sara; Aranda, Bruno; Bhate, Jignesh; Bidwell, Shelby; Bridge, Alan; Briganti, Leonardo; Brinkman, Fiona S. L.; Cesareni, Gianni; Chatr-aryamontri, Andrew; Chautard, Emilie; Chen, Carol; Dumousseau, Marine; Goll, Johannes; Hancock, Robert E. W.; Hannick, Linda I.; Jurisica, Igor; Khadake, Jyoti; Lynn, David J.; Mahadevan, Usha; Perfetto, Livia; Raghunath, Arathi; Ricard-Blum, Sylvie; Roechert, Bernd; Salwinski, Lukasz; Stümpflen, Volker; Tyers, Mike; Uetz, Peter; Xenarios, Ioannis; Hermjakob, Henning

    2013-01-01

    The IMEx consortium is an international collaboration between major public interaction data providers to share curation effort and make a non-redundant set of protein interactions available in a single search interface on a common website (www.imexconsortium.org). Common curation rules have been developed and a central registry is used to manage the selection of articles to enter into the dataset. The advantages of such a service to the user, quality control measures adopted and data distribution practices are discussed. PMID:22453911

  9. Virus and host genomic, molecular, and cellular interactions during Marek's disease pathogenesis and oncogenesis

    PubMed Central

    McPherson, M. C.; Delany, M. E.

    2016-01-01

    Marek's Disease Virus (MDV) is a chicken alphaherpesvirus that causes paralysis, chronic wasting, blindness, and fatal lymphoma development in infected, susceptible host birds. This disease and its protective vaccines are highly relevant research targets, given their enormous impact within the poultry industry. Further, Marek's disease (MD) serves as a valuable model for the investigation of oncogenic viruses and herpesvirus patterns of viral latency and persistence—as pertinent to human health as to poultry health. The objectives of this article are to review MDV interactions with its host from a variety of genomic, molecular, and cellular perspectives. In particular, we focus on cytogenetic studies, which precisely assess the physical status of the MDV genome in the context of the chicken host genome. Combined, the cytogenetic and genomic research indicates that MDV-host genome interactions, specifically integration of the virus into the host telomeres, is a key feature of the virus life cycle, contributing to the viral achievement of latency, transformation, and reactivation of lytic replication. We present a model that outlines the variety of virus-host interactions, at the multiple levels, and with regard to the disease states. PMID:26755654

  10. Effect of substituent pattern and molecular weight of cellulose ethers on interactions with different bile salts.

    PubMed

    Torcello-Gómez, Amelia; Fernández Fraguas, Cristina; Ridout, Mike J; Woodward, Nicola C; Wilde, Peter J; Foster, Timothy J

    2015-03-01

    Some known mechanisms proposed for the reduction of blood cholesterol by dietary fibre are: binding with bile salts in the duodenum and prevention of lipid absorption, which can be partially related with the bile salt binding. In order to gain new insights into the mechanisms of the binding of dietary fibre to bile salts, the goal of this work is to study the main interactions between cellulose derivatives and two types of bile salts. Commercial cellulose ethers: methyl (MC), hydroxypropyl (HPC) and hydroxypropylmethyl cellulose (HPMC), have been chosen as dietary fibre due to their highly functional properties important in manufactured food products. Two types of bile salts: sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), have been chosen to understand the effect of the bile salt type. Interactions in the bulk have been investigated by means of differential scanning calorimetry (DSC) and linear mechanical spectroscopy. Results show that both bile salts have inhibitory effects on the thermal structuring of cellulose ethers and this depends on the number and type of substitution in the derivatised celluloses, and is not dependent upon molecular weight. Concerning the bile salt type, the more hydrophobic bile salt (NaTDC) has greater effect on these interactions, suggesting more efficient adsorption onto cellulose ethers. These findings may have implications in the digestion of cellulose-stabilised food matrices, providing a springboard to develop new healthy cellulose-based food products with improved functional properties.

  11. Balancing local order and long-ranged interactions in the molecular theory of liquid water.

    PubMed

    Shah, J K; Asthagiri, D; Pratt, L R; Paulaitis, M E

    2007-10-14

    A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish outside a finite spatial range, and therefore provides a precise analysis tool for investigating the effects of longer-ranged intermolecular interactions. We show how local order can be introduced through quasichemical theory. Long-ranged interactions are characterized generally by a conditional distribution of binding energies, and this formulation is interpreted as a regularization of the primitive statistical thermodynamic problem. These binding-energy distributions for liquid water are observed to be unimodal. The Gaussian approximation proposed is remarkably successful in predicting the Gibbs free energy and the molar entropy of liquid water, as judged by comparison with numerically exact results. The remaining discrepancies are subtle quantitative problems that do have significant consequences for the thermodynamic properties that distinguish water from many other liquids. The basic subtlety of liquid water is found then in the competition of several effects which must be quantitatively balanced for realistic results.

  12. Binding interaction of atorvastatin with bovine serum albumin: Spectroscopic methods and molecular docking.

    PubMed

    Wang, Qi; Huang, Chuan-ren; Jiang, Min; Zhu, Ying-yao; Wang, Jing; Chen, Jun; Shi, Jie-hua

    2016-03-05

    The interaction of atorvastatin with bovine serum albumin (BSA) was investigated using multi-spectroscopic methods and molecular docking technique for providing important insight into further elucidating the store and transport process of atorvastatin in the body and the mechanism of action and pharmacokinetics. The experimental results revealed that the fluorescence quenching mechanism of BSA induced atorvastatin was a combined dynamic and static quenching. The binding constant and number of binding site of atorvastatin with BSA under simulated physiological conditions (pH=7.4) were 1.41 × 10(5) M(-1) and about 1 at 310K, respectively. The values of the enthalpic change (ΔH(0)), entropic change (ΔS(0)) and Gibbs free energy (ΔG(0)) in the binding process of atorvastatin with BSA at 310K were negative, suggesting that the binding process of atorvastatin and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen bonding interaction. Moreover, atorvastatin was bound into the subdomain IIA (site I) of BSA, resulting in a slight change of the conformation of BSA.

  13. Binding interaction of atorvastatin with bovine serum albumin: Spectroscopic methods and molecular docking

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Huang, Chuan-ren; Jiang, Min; Zhu, Ying-yao; Wang, Jing; Chen, Jun; Shi, Jie-hua

    2016-03-01

    The interaction of atorvastatin with bovine serum albumin (BSA) was investigated using multi-spectroscopic methods and molecular docking technique for providing important insight into further elucidating the store and transport process of atorvastatin in the body and the mechanism of action and pharmacokinetics. The experimental results revealed that the fluorescence quenching mechanism of BSA induced atorvastatin was a combined dynamic and static quenching. The binding constant and number of binding site of atorvastatin with BSA under simulated physiological conditions (pH = 7.4) were 1.41 × 105 M- 1 and about 1 at 310 K, respectively. The values of the enthalpic change (ΔH0), entropic change (ΔS0) and Gibbs free energy (ΔG0) in the binding process of atorvastatin with BSA at 310 K were negative, suggesting that the binding process of atorvastatin and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen bonding interaction. Moreover, atorvastatin was bound into the subdomain IIA (site I) of BSA, resulting in a slight change of the conformation of BSA.

  14. Protein-Carbohydrate Interactions Studied by NMR: From Molecular Recognition to Drug Design

    PubMed Central

    Fernández-Alonso, María del Carmen; Díaz, Dolores; Berbis, Manuel Álvaro; Marcelo, Filipa; Cañada, Javier; Jiménez-Barbero, Jesús

    2012-01-01

    Diseases that result from infection are, in general, a consequence of specific interactions between a pathogenic organism and the cells. The study of host-pathogen interactions has provided insights for the design of drugs with therapeutic properties. One area that has proved to be promising for such studies is the constituted by carbohydrates which participate in biological processes of paramount importance. On the one hand, carbohydrates have shown to be information carriers with similar, if not higher, importance than traditionally considered carriers as amino acids and nucleic acids. On the other hand, the knowledge on molecular recognition of sugars by lectins and other carbohydrate-binding proteins has been employed for the development of new biomedical strategies. Biophysical techniques such as X-Ray crystallography and NMR spectroscopy lead currently the investigation on this field. In this review, a description of traditional and novel NMR methodologies employed in the study of sugar-protein interactions is briefly presented in combination with a palette of NMR-based studies related to biologically and/or pharmaceutically relevant applications. PMID:23305367

  15. Spectroscopy and Molecular Modeling Study on the Interaction Between Mycophenolate Mofetil and Pepsin.

    PubMed

    Ma, Xiaoli; Guo, Liuqi; Wang, Qing; He, Jiawei; Li, Hui

    2016-03-01

    Mycophenolate mofetil (MMF) is an immunosuppressant used in clinical practice to limit the rejection of transplanted organs. MMF is absorbed and metabolized by the gastrointestinal tract and converted to mycophenolic acid by esterases in the plasma, liver, and kidney. Mycophenolic acid is the resulting active metabolite. The interaction of MMF with pepsin may affect the transfer and distribution of MMF. Given this effect, the present study investigated the interaction behavior between pepsin with MMF using docking simulation and spectroscopy method at different temperatures. The results of spectroscopy revealed that MMF has strong ability to quench the fluorescence of pepsin. The results also show that the acting force for binding was composed of hydrophobic forces. The three-dimensional fluorescence spectra and synchronous spectroscopy employed to determine the conformation showed that the binding of MMF with pepsin could induce MMF conformation and microenvironment changes. Furthermore, the molecular interaction distance and energy-transfer efficiency between pepsin and MMF were determined based on the Förster non-radiative energy-transfer mechanism. Docking simulation showed that MMF entered the hydrophobic cavity of pepsin, and a hydrogen bond was formed between the oxygen atoms of the carbanyl group of MMF and hydrogen atoms of tyrosine 189 of pepsin.

  16. VCD spectroscopy as a novel probe for chirality transfer in molecular interactions.

    PubMed

    Sadlej, Joanna; Dobrowolski, Jan Cz; Rode, Joanna E

    2010-05-01

    Most of the research in contemporary physical chemistry is devoted to the development of methods that extend our understanding, interpretation, and capacity to predict structural properties and dynamic behavior of molecules. The optical and magnetic spectroscopies, as well as diffraction techniques, are the principal methods for studying properties of molecules, biomolecules, and biopolymers of which the vast majority are chiral. On the other hand, information on molecular configuration can be obtained mainly from optical spectroscopies because other well-established spectroscopic techniques used for structural investigations, such as crystallographic, ESR, and NMR methods, do not allow for registration of signals from an individual conformer owing to intrinsic slow response to structural changes. This is the reason why the optical spectroscopy methods, based on natural chiroptical phenomena, have become so important and their renaissance in the last decade is noticed. Vibrational circular dichroism (VCD) spectroscopy is one such chiroptical technique that sheds new light on many important phenomena studied intensively. We provide an overview of recent theoretical predictions and innovative VCD observations of chirality transfer (called by other authors "induced chirality") from a chiral molecule to an achiral one as a result of hydrogen bond interactions between them. In this tutorial review we search for answers as to whether we can obtain further information about intermolecular interactions using the VCD technique. In our opinion this technique has opened new horizons for both understanding and monitoring intermolecular interactions and it could be used as a relatively new and powerful physicochemical method.

  17. Guest:host interactions of lidocaine and prilocaine with natural cyclodextrins: Spectral and molecular modeling studies

    NASA Astrophysics Data System (ADS)

    Rajendiran, N.; Mohandoss, T.; Saravanan, J.

    2014-11-01

    Inclusion complex formation of two local anesthetics drugs (lidocaine (LC) and prilocaine (PC)) with α- and β-cyclodextrins (CDs) in aqueous solution were studied by absorption, fluorescence, time-resolved fluorescence and molecular modeling methods. The formation of inclusion complexes was confirmed by 1H NMR, FTIR, differential scanning calorimetry, SEM, TEM and X-ray diffractometry. Both drugs formed 1:1 inclusion complex and exhibit biexponential decay in water whereas triexponential decay in the CD solution. Nanosized self-aggregated particles of drug: CD complexes were found by TEM. Both experimental and theoretical studies revealed that the phenyl ring with the amide group of the drug is encapsulated in the hydrophobic CD nanocavity. Investigations of energetic and thermodynamic properties confirmed the stability of the inclusion complexes. van der Waals interactions are mainly responsible for enthalpy driven complex formation of LC and PC with CDs.

  18. Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

    PubMed Central

    Latour, Robert A.

    2009-01-01

    While the importance of protein adsorption to materials surfaces is widely recognized, little is understood at this time regarding how to design surfaces to control protein adsorption behavior. All-atom empirical force field molecular simulation methods have enormous potential to address this problem by providing an approach to directly investigate the adsorption behavior of peptides and proteins at the atomic level. As with any type of technology, however, these methods must be appropriately developed and applied if they are to provide realistic and useful results. Three issues that are particularly important for the accurate simulation of protein adsorption behavior are the selection of a valid force field to represent the atomic-level interactions involved, the accurate representation of solvation effects, and system sampling. In this article, each of these areas is addressed and future directions for continued development are presented. PMID:19809597

  19. Molecular Dynamics Investigations of the alpha-helix to Beta-barrel Conformational Transformation in RfaH

    NASA Astrophysics Data System (ADS)

    Gc, Jeevan; Bhandari, Yuba; Gerstman, Bernard; Chapagain, Prem

    2015-03-01

    We used combination of replica exchange molecular dynamics simulations with implicit solvent and detailed all-atom simulations with explicit solvent to investigate the α-helix to β-structure transformation of RfaH-CTD. While interacting with the N-terminal domain (NTD), the C-terminal domain (CTD) of RfaH folds to a α-helix bundle 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. Calculations of free-energy landscape and transfer entropy elucidate the details of the RfaH-CTD transformation process. 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. We also studied interdomain and intradomain interactions in RfaH using Steered Molecular Dynamics Simulations. We investigated the role of the interdomain salt-bridge interaction in the domain stability Potential mean force was calculated to obtain free energy profile using Jarzynski Equality.

  20. Challenges for automatically extracting molecular interactions from full-text articles

    PubMed Central

    McIntosh, Tara; Curran, James R

    2009-01-01

    Background The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction (IE) tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles. Results We manually annotated passages from full-text articles that describe interactions summarised in a Molecular Interaction Map (MIM). Our corpus tracks the process of identifying facts to form the MIM summaries and captures any factual dependencies that must be resolved to extract the fact completely. For example, a fact in the results section may require a synonym defined in the introduction. The passages are also annotated with negated and coreference expressions that must be resolved. We describe the guidelines for identifying relevant passages and possible dependencies. The corpus includes 2162 sentences from 78 full-text articles. Our corpus analysis demonstrates the necessity of full-text processing; identifies the article sections where interactions are most commonly stated; and quantifies the proportion of interaction statements requiring coherent dependencies. Further, it allows us to report on the relative importance of identifying synonyms and resolving negated expressions. We also experiment with an oracle sentence retrieval system using the corpus as a gold-standard evaluation set. Conclusion We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation set for full-text IR tasks

  1. Synthesis of novel anthraquinones: Molecular structure, molecular chemical reactivity descriptors and interactions with DNA as antibiotic and anti-cancer drugs

    NASA Astrophysics Data System (ADS)

    Al-Otaibi, Jamelah S.; EL Gogary, Tarek M.

    2017-02-01

    Anthraquinones are well-known anticancer drugs. Anthraquinones anticancer drugs carry out their cytotoxic activities through their interaction with DNA, and inhibition of topoisomerase II activity. Anthraquinones (AQ5 and AQ5H) were synthesized and studied with 1,5-DAAQ by computational and experimental tools. The purpose of this study is to shade more light on mechanism of interaction between anthraquinone DNA affinic agents and different types of DNA. This study will lead to gain of information useful for drug design and development. Molecular structures were optimized using DFT B3LYP/6-31 + G(d). Depending on intramolecular hydrogen bonding interactions four conformers of AQ5 were detected within the range of about 42 kcal/mol. Molecular reactivity of the anthraquinone compounds was explored using global and condensed descriptors (electrophilicity and Fukui functions). NMR and UV-VIS electronic absorption spectra of anthraquinones/DNA were investigated at the physiological pH. The interaction of the anthraquinones (AQ5 and AQ5H) were studied with different DNA namely, calf thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]). UV-VIS electronic absorption spectral data were employed to measure the affinity constants of drug/DNA binding using Scatchard analysis. NMR study confirms qualitatively the drug/DNA interaction in terms of peak shift and broadening.

  2. Dynamic Wetting on Graphene-Coated Surface: Molecular Dynamics Investigation

    NASA Astrophysics Data System (ADS)

    Hung, Shih-Wei; Shiomi, Junichiro

    2015-11-01

    Wettability of graphene-coated surface gained significant attention recently due to discussion on the ``transparency'' (whether the wetting characteristics follow that of graphene or the underlying surface) and practical applications of graphene. In terms of static contact angle, the wettability of graphene-coated surfaces have been widely studied by experiments, simulations, and theory in recent years. However, the studies of dynamic wetting on graphene-coated surfaces are limited. In the present study, molecular dynamics simulation was performed to study the dynamic wetting of water droplet on graphene-coated surfaces from a microscopic point of view. The results show that the degree of similarity between the spreading behavior on graphene-coated surface and that on pure graphene (or that on the underlying surface) depends on time, i.e. how nonequilibrium the interface dynamics is. We also found that this feature can be altered by introducing defects into graphene. The work is partially supported by Grant-in-Aid for JSPS Fellows 26-04364 and JST CREST.

  3. A First-principles Molecular Dynamics Investigation of Superionic Conductivity

    NASA Astrophysics Data System (ADS)

    Wood, Brandon; Marzari, Nicola

    2007-03-01

    Superionic materials---solids with liquid-like transport properties---have found widespread use in a variety of applications in fuel cells, switches, sensors, and batteries. However, reasons for fast-ion conduction in such materials, as well as the specific atomistic mechanisms involved, remain ill understood. Our work uses first-principles molecular dynamics to illuminate the mechanisms, pathways, and motivations for superionic conductivity in two materials representing different classes of ion conductors: α-AgI, an archetypal Type-I superionic; and CsHSO4, an anhydrous solid-state electrolyte candidate for hydrogen fuel cells. For α-AgI, we trace common pathways for silver ion conduction and discuss how a chemical signature in the electronic structure relates to enhanced silver ion mobility. We also characterize the dynamical lattice structure in the superionic phase and present the likely motivations for its existence. For CsHSO4, we isolate the dominant atomistic mechanisms involved in superprotonic conduction and discuss the effect of correlated diffusive events in enhancing proton transport. We also offer a detailed description of the dynamics of the hydrogen bond network topology in the course of proton diffusion and discuss the relevance of atomistic processes with competing timescales in facilitating proton transport.

  4. Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

    SciTech Connect

    Thomas, Robert E.; Overy, Catherine; Opalka, Daniel; Alavi, Ali; Knowles, Peter J.; Booth, George H.

    2015-08-07

    Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.

  5. Molecular analyses of nuclear-cytoplasmic interactions affecting plant growth and yield. Final technical report

    SciTech Connect

    Newton, K.J.

    1998-11-01

    Mitochondria have a central role in the production of cellular energy. The biogenesis and functioning of mitochondria depends on the expression of both mitochondrial and nuclear genes. One approach to investigating the role of nuclear-mitochondrial cooperation in plant growth and development is to identify combinations of nuclear and mitochondrial genomes that result in altered but sublethal phenotypes. Plants that have certain maize nuclear genotypes in combination with cytoplasmic genomes from more distantly-related teosintes can exhibit incompatible phenotypes, such as reduced plant growth and yield and cytoplasmic male sterility, as well as altered mitochondrial gene expression. The characterization of these nuclear-cytoplasmic interactions was the focus of this grant. The authors were investigating the effects of two maize nuclear genes, RcmI and Mct, on mitochondrial function and gene expression. Plants with the teosinte cytoplasms and homozygous for the recessive rcm allele are small (miniature) and-slow-growing and the kernels are reduced in size. The authors mapped this locus to molecular markers on chromosome 7 and attempted to clone this locus by transposon tagging. The effects of the nuclear-cytoplasmic interaction on mitochondrial function and mitochondrial protein profiles were also studied.

  6. Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Thomas, Robert E.; Opalka, Daniel; Overy, Catherine; Knowles, Peter J.; Alavi, Ali; Booth, George H.

    2015-08-01

    Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, "replica" ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation.

  7. Detecting differential patterns of interaction in molecular pathways

    PubMed Central

    Yajima, Masanao; Telesca, Donatello; Ji, Yuan; Müller, Peter

    2015-01-01

    We consider statistical inference for potentially heterogeneous patterns of association characterizing the expression of bio-molecular pathways across different biologic conditions. We discuss a modeling approach based on Gaussian-directed acyclic graphs and provide computational and methodological details needed for posterior inference. Our application finds motivation in reverse phase protein array data from a study on acute myeloid leukemia, where interest centers on contrasting refractory versus relapsed patients. We illustrate the proposed method through both synthetic and case study data. PMID:25519431

  8. Investigation of multilayer painting by means of molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Kadikova, I. F.; Grigorieva, I. A.

    2016-12-01

    The study of paintings' layer structure under microscope was implemented in the early XX century; since that time method of cross-section preparation as well as composition of embedded materials changed and capabilities of optical microscopy broadened. Nevertheless, until recently cross-sections were prepared only for analysis of paintings' layer-specific structure, morphological and technological features, tracks of restoration treatments. Examination of chemical composition required additional sampling as well as division of these samples layer by layer in order to determine pigments and binding media; these procedures didn't always lead to proper results. Micro-Raman and micro-FTIR spectroscopy allow carrying out investigation of painting cross-sections without any additional preliminary sampling; this is shown on example of investigation of a number of paintings.

  9. Interaction investigations of crustacean β-GBP recognition toward pathogenic microbial cell membrane and stimulate upon prophenoloxidase activation.

    PubMed

    Sivakamavalli, Jeyachandran; Selvaraj, Chandrabose; Singh, Sanjeev Kumar; Vaseeharan, Baskaralingam

    2014-04-01

    In invertebrates, crustaceans' immune system consists of pattern recognition receptors (PRRs) instead of immunoglobulin's, which involves in the microbial recognition and initiates the protein-ligand interaction between hosts and pathogens. In the present study, PRRs namely β-1,3 glucan binding protein (β-GBP) from mangrove crab Episesarma tetragonum and its interactions with the pathogens such as bacterial and fungal outer membrane proteins (OMP) were investigated through microbial aggregation and computational interaction studies. Molecular recognition and microbial aggregation results of Episesarma tetragonum β-GBP showed the specific binding affinity toward the fungal β-1,3 glucan molecule when compared to other bacterial ligands. Because of this microbial recognition, prophenoloxidase activity was enhanced and triggers the innate immunity inside the host animal. Our findings disclose the role of β-GBP in molecular recognition, host-pathogen interaction through microbial aggregation, and docking analysis. In vitro results were concurred with the in silico docking, and molecular dynamics simulation analysis. This study would be helpful to understand the molecular mechanism of β-GBP and update the current knowledge on the PRRs of crustaceans.

  10. Modeling of molecular photocells: Application to two-level photovoltaic system with electron-hole interaction.

    PubMed

    Nemati Aram, Tahereh; Anghel-Vasilescu, Petrutza; Asgari, Asghar; Ernzerhof, Matthias; Mayou, Didier

    2016-09-28

    We present a novel simple model to describe molecular photocells where the energy conversion process takes place by a single molecular donor-acceptor complex attached to electrodes. By applying quantum scattering theory, an open quantum system method, the coherent molecular photocell is described by a wave function. We analyze photon absorption, energy conversion, and quantum yield of a molecular photocell by considering the effects of electron-hole interaction and non-radiative recombination. We model the exciton creation, dissociation, and subsequent effects on quantum yield in the energy domain. We find that depending on the photocell structure, the electron-hole interaction can normally decrease or abnormally increase the cell efficiency. The proposed model helps to understand the mechanisms of molecular photocells, and it can be used to optimize their yield.

  11. Molecular dynamics investigation of mechanisms of femtosecond laser ablation

    NASA Astrophysics Data System (ADS)

    Cheng, Changrui

    Laser micro-machining has been widely applied for material processing in many industries. A phenomenon called "laser ablation" is usually involved in the laser micro-machining process. Laser ablation is the process of material removal after the irradiation of a laser beam onto the material. It is commonly characterized by small temporal and spatial scales, extremely high material temperature and pressure, and strong non-equilibrium thermodynamic state. In this work, molecular dynamics (MD) simulation is conducted to study the femtosecond laser ablation of metals (nickel and copper) and dielectrics (fused silica, or glass). The laser heating and the ablation processes are numerically modeled, and the computation is accelerated by parallel processing technique. Both the pair-wise Morse potential and the many-body EAM (Embedded-Atom Method) potential are employed for metals. In the simulation of fused silica, the BKS (van Beest, Kramer and van Santen) potential is used, and the generation of free electrons, the energy transport from laser beam to free electrons and energy coupling between electrons and the lattice are considered. The main goal of this work is to illustrate the detailed processes of femtosecond laser ablation and to study its mechanisms. From the MD results, it is found that the mechanism of femtosecond laser ablation is strongly dependent on the laser fluences. For metals, low fluence laser ablation is mainly through phase explosion (homogeneous gas bubble nucleation), while spinodal decomposition is responsible for high fluence ablation. Ablation mechanism is determined by whether or not the material (liquid) temperature exceeds the critical temperature. For fused silica, the generation and existence of free electrons are found to affect ablation significantly, especially at low fluence, where Coulomb explosion is found to play an important role in material separation.

  12. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  13. Modelling social interaction as perceptual crossing: an investigation into the dynamics of the interaction process

    NASA Astrophysics Data System (ADS)

    Froese, Tom; Di Paolo, Ezequiel A.

    2010-03-01

    This paper continues efforts to establish a mutually informative dialogue between psychology and evolutionary robotics in order to investigate the dynamics of social interaction. We replicate a recent simulation model of a minimalist experiment in perceptual crossing and confirm the results with significantly simpler artificial agents. A series of psycho-physical tests of their behaviour informs a hypothetical circuit model of their internal operation. However, a detailed study of the actual internal dynamics reveals this circuit model to be unfounded, thereby offering a tale of caution for those hypothesising about sub-personal processes in terms of behavioural observations. In particular, it is shown that the behaviour of the agents largely emerges out of the interaction process itself rather than being an individual achievement alone. We also extend the original simulation model in two novel directions in order to test further the extent to which perceptual crossing between agents can self-organise in a robust manner. These modelling results suggest new hypotheses that can become the basis for further psychological experiments.

  14. Molecular interactions between caffeine and catechins in green tea.

    PubMed

    Colon, Marta; Nerin, Cristina

    2014-07-16

    Migration of green tea components from an active packaging material containing green tea extract was performed in water and 3% acetic acid in water. The migration values for acid simulant were much higher than the values obtained in water. The influence of the acidic media in solutions of catechin standards and green tea extract was evaluated by liquid chromatography. Catechin, epicatechin, and caffeine from the green tea extract exhibited major variation in their concentrations values, with increases of 29.90, 20.75, and 15.95%, respectively, in acidic medium. The results suggested that catechins and caffeine form complexes through intermolecular interactions in neutral media and that these interactions are broken in acidic media. The continuous variation method was also performed to confirm the stoichiometry of the complexes between catechins and caffeine. Finally, a computer simulation was applied by Chem Pro 12.0, and the energies involved were calculated to confirm the experimental results obtained.

  15. Functional analysis of molecular interactions in synthetic auxin response circuits

    PubMed Central

    Lanctot, Amy; Hageman, Amber; Nemhauser, Jennifer L.

    2016-01-01

    Auxin-regulated transcription pivots on the interaction between the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) repressor proteins and the AUXIN RESPONSE FACTOR (ARF) transcription factors. Recent structural analyses of ARFs and Aux/IAAs have raised questions about the functional complexes driving auxin transcriptional responses. To parse the nature and significance of ARF–DNA and ARF–Aux/IAA interactions, we analyzed structure-guided variants of synthetic auxin response circuits in the budding yeast Saccharomyces cerevisiae. Our analysis revealed that promoter architecture could specify ARF activity and that ARF19 required dimerization at two distinct domains for full transcriptional activation. In addition, monomeric Aux/IAAs were able to repress ARF activity in both yeast and plants. This systematic, quantitative structure-function analysis identified a minimal complex—comprising a single Aux/IAA repressing a pair of dimerized ARFs—sufficient for auxin-induced transcription. PMID:27647902

  16. Spectroscopic Evidence for Room Temperature Interaction of Molecular Oxygen with Cobalt Porphyrin Linker Sites within a Metal-Organic Framework.

    PubMed

    Lahanas, Nicole; Kucheryavy, Pavel; Lockard, Jenny V

    2016-10-17

    Metalloporphyrin-based metal-organic frameworks offer a promising platform for developing solid-state porous materials with accessible, coordinatively unsaturated metal sites. Probing small-molecule interactions at the metalloporphyrin sites within these materials on a molecular level under ambient conditions is crucial for both understanding and ultimately harnessing this functionality for potential catalytic purposes. Co-PCN-222, a metal-organic framework based on cobalt(II) porphyrin linkers. is investigated using in situ UV-vis diffuse-reflectance and X-ray absorption spectroscopy. Spectroscopic evidence for the axial interaction of diatomic oxygen with the framework's open metalloporphyrin sites at room temperature is presented and discussed.

  17. Molecular architecture of the Dam1 complex–microtubule interaction

    PubMed Central

    Legal, Thibault; Zou, Juan; Sochaj, Alicja; Rappsilber, Juri

    2016-01-01

    Mitosis is a highly regulated process that allows the equal distribution of the genetic material to the daughter cells. Chromosome segregation requires the formation of a bipolar mitotic spindle and assembly of a multi-protein structure termed the kinetochore to mediate attachments between condensed chromosomes and spindle microtubules. In budding yeast, a single microtubule attaches to each kinetochore, necessitating robustness and processivity of this kinetochore–microtubule attachment. The yeast kinetochore-localized Dam1 complex forms a direct interaction with the spindle microtubule. In vitro, the Dam1 complex assembles as a ring around microtubules and couples microtubule depolymerization with cargo movement. However, the subunit organization within the Dam1 complex, its higher-order oligomerization and how it interacts with microtubules remain under debate. Here, we used chemical cross-linking and mass spectrometry to define the architecture and subunit organization of the Dam1 complex. This work reveals that both the C termini of Duo1 and Dam1 subunits interact with the microtubule and are critical for microtubule binding of the Dam1 complex, placing Duo1 and Dam1 on the inside of the ring structure. Integrating this information with available structural data, we provide a coherent model for how the Dam1 complex self-assembles around microtubules. PMID:26962051

  18. Interferons and viruses: an evolutionary arms race of molecular interactions

    PubMed Central

    Hoffmann, Hans-Heinrich; Schneider, William M.; Rice, Charles M.

    2015-01-01

    Over half a century has passed since interferons (IFNs) were discovered and shown to inhibit virus infection in cultured cells. Since then, researchers have steadily brought to light the molecular details of IFN signaling, catalogued their pleiotropic effects on cells, and harnessed their therapeutic potential for a variety of maladies. While advances have been plentiful, several fundamental questions have yet to be answered and much complexity remains to be unraveled. We explore the current knowledge surrounding four main questions: are type I IFN subtypes differentially produced in response to distinct pathogens? How are IFN subtypes distinguished by cells? What are the mechanisms and consequences of viral antagonism? Lastly, how can the IFN response be harnessed to improve vaccine efficacy? PMID:25704559

  19. Effect of molecular interactions on carbon nanotube friction

    NASA Astrophysics Data System (ADS)

    Heo, SeongJun; Sinnott, Susan B.

    2007-09-01

    The mechanical responses of carbon nanotubes (CNTs) under compressive and sliding forces are examined using classical molecular dynamics simulations. Several different types of nanotube systems are considered, including pristine single-walled tubes that are empty, filled with fullerenes to form nanopeapods, and filled with other nanotubes to form multiwalled tubes. In addition, the responses of systems where benzene molecules are introduced between and around the walls of single-walled nanotubes and peapods are considered. The results indicate that the filled CNT bundles can sustain higher compressive forces than the hollow CNT bundles. However, the filled CNT bundle has a similar friction coefficient to the hollow CNT bundles during sliding at low compressive pressures. The simulations further demonstrate the way in which the introduction of additive lubricants influences the friction coefficient of CNT bundles.

  20. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    NASA Astrophysics Data System (ADS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B.

    2015-04-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations.

  1. Theoretical investigation of the interaction of glycerol with aluminum and magnesium phthalocyanines.

    PubMed

    Silva, V H C; Camargo, L T F M; Napolitano, H B; Pérez, C N; Camargo, A J

    2010-09-01

    Glycerol is a byproduct produced in great quantity by biodiesel industries in transesterification reactions. Finding new applications for glycerol is a current concern of many research groups around the world. This work focuses on a theoretical investigation, at the B3LYP/6-31G* level of theory, into the possibility of using aluminum phthalocyanine (AlPc) and magnesium phthalocyanine (MgPc) in the modelling of catalysts to convert glycerol into alcohol, which has wider industrial applicability. According to our calculations there are strong interactions between the O-terminus of glycerol and the central metal atom of AlPc and MgPc. By applying the Fukui function, HSAB theory and analysis of the frontier molecular orbital, it was possible to explain the way in which glycerol interacts with AlPc and MgPc. As a result of these interactions, there is a considerable change in both electronic and geometric parameters of glycerol, which can be used in designing new strategies to convert glycerol into alcohol.

  2. Pasting investigation, SEM observation and the possible interaction study on rice starch-pullulan combination.

    PubMed

    Chen, Long; Ren, Fei; Yu, Xueping; Zhang, Zipei; Xu, Dejun; Tong, Qunyi

    2015-02-01

    The pasting properties of rice starch (RS) with high concentration (10%, w/w) were investigated in the presence or absence of pullulan (PUL) using a rapid visco-analyzer (RVA). Addition of pullulan resulted in the reduction of peak viscosity, trough viscosity, final viscosity, and setback value of RS. Furthermore, an interesting phenomenon, i.e. a small viscosity peak appeared in the RVA curves of RS-PUL mixtures, was observed. It indicated that addition of pullulan might suppress the gelatinization of starch granules by maintaining the integration of some granules. The scanning electron microscope (SEM) observation of samples suggested that starch granules could be wrapped by a thin membrane composed of pullulan and/or pullulan-amylose associations. The coating ability of pullulan and/or the possible molecular interactions between pullulan and amylose could be responsible for these results.

  3. Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4(+) Interactions.

    PubMed

    Khan, Hanif M; Grauffel, Cédric; Broer, Ria; MacKerell, Alexander D; Havenith, Remco W A; Reuter, Nathalie

    2016-11-08

    Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.

  4. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    ERIC Educational Resources Information Center

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  5. Interactions of helquats with chiral acidic aromatic analytes investigated by partial-filling affinity capillary electrophoresis.

    PubMed

    Růžička, Martin; Koval, Dušan; Vávra, Jan; Reyes-Gutiérrez, Paul E; Teplý, Filip; Kašička, Václav

    2016-10-07

    Noncovalent molecular interactions between helquats, a new class of dicationic helical extended diquats, and several chiral acidic aromatic drugs and catalysts have been investigated using partial-filling affinity capillary electrophoresis (PF-ACE). Helquats dissolved at 1mM concentration in the aqueous background electrolyte (40mM Tris, 20mM acetic acid, pH 8.1) were introduced as ligand zones of variable length (0-130mm) into the hydroxypropylcellulose coated fused silica capillary whereas 0.1mM solutions of negatively charged chiral drugs or catalysts (warfarin, ibuprofen, mandelic acid, etodolac, binaphthyl phosphate and 11 other acidic aromatic compounds) were applied as a short analyte zone at the injection capillary end. After application of electric field, analyte and ligand migrated against each other and in case of their interactions, migration time of the analyte was increasing with increasing length of the ligand zone. From the tested compounds, only isomers of those exhibiting helical chirality and/or possessing conjugated aromatic systems were enantioselectively separated through their differential interactions with helquats. Some compounds with conjugated aromatic groups interacted with helquats moderately strongly but non-enantiospecifically. Small compounds with single benzene ring exhibited no or very weak non-enantiospecific interactions. PF-ACE method allowed to determine binding constants of the analyte-helquat complexes from the changes of migration times of the analytes. Binding constants of the weakest complexes of the analytes with helquats were less than 50L/mol, whereas binding constants of the strongest complexes were in the range 1 000-1 400L/mol.

  6. Molecular Modeling of Interaction between Diabetic Drug and Antioxidant in Controlling Sucrose

    NASA Astrophysics Data System (ADS)

    Rakesh, Leela; Lee, Choon

    2009-09-01

    This article examined the possible protective effect of N-acetylcysteine (NAC) taurine, quercetin and Syringaldehyde dendritic antioxidants against the oxidative stress induced by diabetic or pre-diabetic patient case due to high sucrose intake by computer simulation. We also compared these results with the well-known diabetic drugs glizipid and Avandia. Towards this understanding we undertook a molecular level computer model in order to study the molecular interaction between high sugar content with antioxidant by varying ratios of sucrose molecules with and without the presence of diabetic drugs. From our study it shows that with the presence of various antioxidant combinations diabetics drugs could be much more beneficial to the patients in terms of its side effects such a heart attack. Many interesting results have been obtained by this study. The application of this driving force may be used to predict the feasibility and benefit in order to understand the high-sucrose diet-induced obesity, which certainly would bring new insights on obesity-related adverse control and may possibly suggest the impact of N-acetylcysteine and syringaldehyde in such cases. Hyperglycemia is an important predictor of cardiovascular mortality in patients with diabetes. We also investigated the hypothesis that diabetes or acute hyperglycemia attenuates the reduction of myocardial infarct size produced by activation of mitochondrial ATP-regulated potassium (KATP) channels. The results indicate that diabetes/hyperglycemia impairs activation of mitochondrial KATP channels.

  7. Molecular interaction and energy transfer between human serum albumin and bioactive component Aloe dihydrocoumarin

    NASA Astrophysics Data System (ADS)

    Zhang, Xiu-Feng; Xie, Ling; Liu, Yang; Xiang, Jun-Feng; Li, Lin; Tang, Ya-Lin

    2008-10-01

    Aloe dihydrocoumarin is an antioxidant and a candidate of immunomodulatory drug on the immune system and can balance physiological reactive oxygen species (ROS) levels which may be useful to maintain homeostasis. In order to explore the mechanism of drug action at a molecular level, the binding of Aloe dihydrocoumarin with human serum albumin (HSA) has been investigated by fluorescence, ultraviolet (UV), circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, fluorescence dynamics, and molecular dynamic docking for the first time. We observed a quenching of fluorescence of HSA in the presence of Aloe dihydrocoumarin and also analyzed the quenching results using the Stern-Volmer equation and obtained high affinity binding to HSA. A Förster type fluorescence resonance energy transfer mechanism is involved in this quenching of Trp fluorescence by Aloe dihydrocoumarin. From the CD and FT-IR results, it is apparent that the interaction of Aloe dihydrocoumarin with HSA causes a conformational change of the protein, with the loss of α-helix stability and the gain of β-sheet and β-turn content. Data obtained by fluorescence spectroscopy, fluorescence dynamics, CD, and FT-IR experiments along with the docking studies suggest that Aloe dihydrocoumarin binds to residues located in subdomain IIA of HSA.

  8. Predicting the molecular shape of polysaccharides from dynamic interactions with water.

    PubMed

    Almond, Andrew; Sheehan, John K

    2003-04-01

    How simple monosaccharides, once polymerized, become the basis for structural materials remains a mystery. A framework is developed to investigate the role of water in the emergence of dynamic structure in polysaccharides, using the important beta(1-->4) linkage as an example. This linkage is studied within decasaccharide fragments of cellulose, chitin, mannan, xylan, and hyaluronan, using molecular simulations in the presence of explicit water solvent. Although cellulose, mannan, chitin, and xylan are chemically similar, their intramolecular hydrogen-bond dynamics and interaction with water are predicted to differ. Cellulose, mannan, and chitin favor relatively static intramolecular hydrogen bonds, xylan prefers dynamic water bridges, and multiple water configurations are predicted at the beta(1-->4) linkages of hyaluronan. With such a variety of predicted dynamics, the hypothesis that the beta(1-->4) linkage is stabilized by intramolecular hydrogen bonds was rejected. Instead, it is proposed that favored molecular configurations are consistent with maximum rotamer and water degrees of freedom, explaining observations made previously by X-ray diffraction. Furthermore, polysaccharides predicted to be conformationally restricted in simulations (cellulose, chitin, and mannan) prefer the solid state in reality, even as oligosaccharides. Those predicted to be more flexible (xylan and hyaluronan) are known to be soluble, even as high polymers. Therefore an intriguing correlation between chemical composition, water organization, polymer properties, and biological function is proposed.

  9. Molecular aspects of the interaction of spermidine and α-chymotrypsin.

    PubMed

    Farhadian, Sadegh; Shareghi, Behzad; Saboury, Ali A; Babaheydari, Ali Kazemi; Raisi, Fatame; Heidari, Ehsan

    2016-11-01

    Polyamines such as spermidine are essential for survival. The purpose of the present study was to investigate how spermidine could influence the conformation, thermal stability and the activity of α-chymotrypsin. The influence of spermidine on the structure and stability of α-Chymotrypsin (α-Chy) explored using different spectroscopy method and molecular docking simulations. The stability and activity of α-Chy were increased in the presence of spermidine. Increasing of the α-Chy absorption in the presence of spermidine was as a result of the formation of a spermidine - α-Chy complex. The results of fluorescence spectroscopic measurements suggested that spermidine has a vigorous ability to quench the intrinsic fluorescence of α-Chy through the dynamic quenching procedure. Near and Far-UV CD studies also confirmed the transfer of aromatic residues to a more flexible environment. The absorption increasing of α-Chy in the presence of spermidine was as a result of the formation of spermidine - α-Chy complex. Molecular docking results also revealed the presence of one binding site with a negative value for the Gibbs free energy of the binding of spermidine to α-Chy. Further, the docking study revealed that van der Waals interactions and hydrogen bonds play a main role in stabilizing the complex.

  10. Spectroscopy, calorimetry and molecular simulation studies on the interaction of catalase with copper ion.

    PubMed

    Hao, Fang; Jing, Mingyang; Zhao, Xingchen; Liu, Rutao

    2015-02-01

    In this research, the binding mechanism of Cu(2+) to bovine liver catalase (BLC) was studied by fluorescence spectroscopy, ultraviolet-visible (UV-vis) absorption spectroscopy, circular dichroism (CD) spectroscopy, isothermal titration calorimetry (ITC) and molecular docking methods. The cellar experiment was firstly carried out to investigate the inhibition effect of catalase. During the fluorescence quenching study, after correcting the inner filter effect (IFE), the fluorescence of BLC was found to be quenched by Cu(2+). The quenching mechanism was determined by fluorescence lifetime measurement, and was confirmed to be the dynamic mode. The secondary structure content of BLC was changed by the addition of Cu(2+), as revealed by UV-vis absorption and CD spectra, which further induces the decrease in BLC activity. Molecular simulation study indicates that Cu(2+) is located between two β-sheets and two random coils of BLC near to the heme group, and interacts with His 74 and Ser 113 residues near a hydrophilic area. The decrease of α-helix and the binding of His 74 are considered to be the major reason for the inhibition of BLC activity caused by Cu(2+). The ITC results indicate that the binding stoichiometry of Cu(2+) to catalase is 11.4. Moreover, the binding of Cu(2+) to BLC destroyed H-bonds, which was confirmed by the CD result.

  11. Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation.

    PubMed

    Zhang, Yan-Jun; Ding, Jing-Na; Zhong, Hui; Han, Ju-Guang

    2017-02-16

    Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation. R312A/R322A double mutations results in a completely different binding site and orientation upon the structure analyses. The calculated binding free energy results reveal that R312A, R322A, and K339A single mutations decrease the binding free energies by 17.82, 13.18, and 13.68 kcal/mol, respectively. The binding energy decomposition indicates that the strong binding affinity of the key residues are mainly due to the contributions of electrostatic interactions in the gas phase, where come from the positively charged side chain and the negatively charged dsRNA backbone. R312A, R322A, and K339A single mutations have no significant effect on VP35 IID conformation, but the mutations influence the contributions of electrostatic interactions in the gas phase. The calculated results reveal that end-cap residues which mainly contribute VDW interactions can recognize and capture dsRNA blunt ends, and the central basic residues (R312, R322, and K339) which mainly contribute favorable electrostatic interactions with dsRNA backbone can fix dsRNA binding site and orientation. This article is protected by copyright. All rights reserved.

  12. Inhibition of pro-/active MMP-2 by green tea catechins and prediction of their interaction by molecular docking studies.

    PubMed

    Chowdhury, Animesh; Nandy, Suman Kumar; Sarkar, Jaganmay; Chakraborti, Tapati; Chakraborti, Sajal

    2017-03-01

    Matrix metalloproteinases (MMPs) play a crucial role in developing different types of lung diseases, e.g., pulmonary arterial hypertension (PAH). Green tea polyphenolic catechins such as EGCG and ECG have been shown to ameliorate various types of diseases including PAH. Our present study revealed that among the four green tea catechins (EGCG, ECG, EC, and EGC), EGCG and ECG inhibit pro-/active MMP-2 activities in pulmonary artery smooth muscle cell (PASMC) culture supernatant. Based on the above, we investigated the interactions of pro-/active MMP-2 with the green tea catechins by computational methods. In silico analysis revealed a strong interaction of pro-/active MMP-2 with EGCG/ECG, and galloyl group has been observed to be responsible for this interaction. The in silico analysis corroborated our experimental observation that EGCG and ECG are active in preventing both the proMMP-2 and MMP-2 activities. Importantly, these two catechins appeared to be better inhibitors for proMMP-2 in comparison to MMP-2 as revealed by gelatin zymogram and also by molecular docking studies. In many type of cells, activation of proMMP-2 occurs via an increase in the level of MT1-MMP (MMP-14). We, therefore, determined the interactions of MT1-MMP with the green tea catechins by molecular docking analysis. The study revealed a strong interaction of MT1-MMP with EGCG/ECG, and galloyl group has been observed to be responsible for the interaction.

  13. Experimental and theoretical investigation of a pyridine containing Schiff base: Hirshfeld analysis of crystal structure, interaction with biomolecules and cytotoxicity

    NASA Astrophysics Data System (ADS)

    Chithiraikumar, S.; Neelakantan, M. A.

    2016-03-01

    A pyridine containing Schiff base (E)-2-methoxy-6-(((pyridin-2-ylmethyl)imino)methyl) phenol (L) was isolated in single crystals. The molecular structure of L was studied by FT-IR, NMR, UV-Vis techniques, single crystal XRD analysis and computationally by DFT method. L prefers enol form in the solid state. Electronic spectrum of L was recorded in different organic solvents to investigate the dependence of tautomerism on solvent types. The polar solvents facilitate the proton transfer by decreasing the activation energy needed for transition state. Potential energy curve for the intramolecular proton transfer in the ground state is generated in gas and solution phases. The 3D Hirshfeld surfaces and the associated 2D fingerprint plots were investigated. The percentages of various interactions were analyzed by fingerprint plots of Hirshfeld surface. The interaction of L with CT DNA was investigated under physiological conditions using UV-Vis spectroscopy, fluorescence quenching and molecular docking methods. Molecular docking studies reveal that binding of L to the groove of B-DNA is through hydrogen bonding and hydrophobic interactions. The in vitro cytotoxicity of L was carried out in two different human tumor cell lines, MCF 7 and MIA-Pa-Ca-2 exhibits moderate activity.

  14. Cellular microbiology and molecular ecology of Legionella-amoeba interaction.

    PubMed

    Richards, Ashley M; Von Dwingelo, Juanita E; Price, Christopher T; Abu Kwaik, Yousef

    2013-05-15

    Legionella pneumophila is an aquatic organism that interacts with amoebae and ciliated protozoa as the natural hosts, and this interaction plays a central role in bacterial ecology and infectivity. Upon transmission to humans, L. pneumophila infect and replicate within alveolar macrophages causing pneumonia. Intracellular proliferation of L. pneumophila within the two evolutionarily distant hosts is facilitated by bacterial exploitation of evolutionarily conserved host processes that are targeted by bacterial protein effectors injected into the host cell by the Dot/Icm type VIB translocation system. Although cysteine is semi-essential for humans and essential for amoeba, it is a metabolically favorable source of carbon and energy generation by L. pneumophila. To counteract host limitation of cysteine, L. pneumophila utilizes the AnkB Dot/Icm-translocated F-box effector to promote host proteasomal degradation of polyubiquitinated proteins within amoebae and human cells. Evidence indicates ankB and other Dot/Icm-translocated effector genes have been acquired through inter-kingdom horizontal gene transfer.

  15. "Rules of Engagement" of Protein-Glycoconjugate Interactions: A Molecular View Achievable by using NMR Spectroscopy and Molecular Modeling.

    PubMed

    Marchetti, Roberta; Perez, Serge; Arda, Ana; Imberty, Anne; Jimenez-Barbero, Jesus; Silipo, Alba; Molinaro, Antonio

    2016-08-01

    Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectroscopic methods permitted us to deeply dissect the fine structural details of biologically relevant molecular recognition processes with high resolution. This Review focuses on the development and use of modern nuclear magnetic resonance (NMR) techniques to dissect binding events. These spectroscopic methods, complementing X-ray crystallography and molecular modeling methodologies, will be taken into account as indispensable tools to provide a complete picture of protein-glycoconjugate binding mechanisms related to biomedicine applications against infectious diseases.

  16. Molecular Investigations into the Mechanics of a Muscle Anchoring Complex

    PubMed Central

    Bodmer, Nicholas K.; Theisen, Kelly E.; Dima, Ruxandra I.

    2015-01-01

    The titin-telethonin complex, essential for anchoring filaments in the Z-disk of the sarcomere, is composed of immunoglobulin domains. Surprisingly, atomic force microscopy experiments showed that it resists forces much higher than the typical immunoglobulin domain and that the force distribution is unusually broad. To investigate the origin of this behavior, we developed a multiscale simulation approach, combining minimalist and atomistic models (SOP-AT). By following the mechanical response of the complex on experimental timescales, we found that the mechanical stability of titin-telethonin is modulated primarily by the strength of contacts between telethonin and the two titin chains, and secondarily by the timescales of conformational excursions inside telethonin and the pulled titin domains. Importantly, the conformational transitions executed by telethonin in simulations support its proposed role in mechanosensing. Our SOP-AT computational approach thus provides a powerful tool for the exploration of the link between conformational diversity and the broadness of the mechanical response, which can be applied to other multidomain complexes. PMID:25954889

  17. Direct evidence of the molecular interaction propagation in the phase transition of liquid crystals

    NASA Astrophysics Data System (ADS)

    Katayama, Kenji; Sato, Takahiro; Kuwahara, Shota

    2016-09-01

    The molecular interaction sometimes propagates in a collective manner, reaching for a long distance on the order of millimeters. Such interactions have been well known in the field of strongly-correlated electron systems in a beautiful crystal interleaved by donor and acceptor layers, induced by photo-stimulus. The other examples can be found in liquid crystals (LCs), which could be found in many places in nature such as bio-membrane. Different from crystals, LCs features "softness", which enables it to be a curved structure such as a cell. In LCs, even a small molecular change would trigger the overall structural change by the propagation of the molecular interaction. Here we will show, for the first time, how long and how fast the molecular interaction propagates in LCs. The patterned phase transition was induced in a LC, causing the phase transition propagation in a controlled way and the propagation was measured with an time-resolved optical technique, called the transient grating. A LC sample doped with azobenzene was put into a thermally controlled LC cell. A grating pattern of a pulse light with 355 nm was impinged to the LC cell, and the light was absorbed by the dyes, releasing heat or photomechanical motion. We could observe the fringe spacing dependence on the phase transition response, which indicates that phase transition was delayed as the fringe spacing due to the delay by the phase transition propagation. This is the first direct evidence of the molecular interaction propagation of the LC molecules.

  18. Potential dual molecular interaction of the Drosophila 7-pass transmembrane cadherin Flamingo in dendritic morphogenesis.

    PubMed

    Kimura, Hiroshi; Usui, Tadao; Tsubouchi, Asako; Uemura, Tadashi

    2006-03-15

    Seven-pass transmembrane cadherins (7-TM cadherins) play pleiotropic roles in epithelial planar cell polarity, shaping dendritic arbors and in axonal outgrowth. In contrast to their role in planar polarity, how 7-TM cadherins control dendritic and axonal outgrowth at the molecular level is largely unknown. Therefore, we performed extensive structure-function analysis of the Drosophila 7-TM cadherin Flamingo (Fmi) and investigated the activities of individual mutant forms mostly in dendritogenesis of dendritic arborization (da) neurons. One of the fmi-mutant phenotypes was overgrowth of branches in the early stage of dendrite development. In da neurons but not in their adjacent non-neuronal cells, expression of a truncated form (deltaN) that lacks the entire cadherin repeat sequence, rescues flies--at least partially--from this phenotype. Another phenotype is observed at a later stage, when dendritic terminals outgrowing from the contralateral sides meet and then avoid each other. In the fmi mutant, by contrast, those branches overlapped. Overexpression of the deltaN form on the wild-type background phenocopied the overlap phenotype in the mutant, and analysis in heterologous systems supported the possibility that this effect might be because the Fmi-Fmi homophilic interaction is inhibited by deltaN. We propose that a dual molecular function of Fmi play pivotal roles in dendrite morphogenesis. In the initial growing phase, Fmi might function as a receptor for a sofar-unidentified ligand and this hypothetical heterophilic interaction would be responsible for limiting branch elongation. At a later stage, homophilic Fmi-binding at dendro-dendritic interfaces would elicit avoidance between dendritic terminals.

  19. Molecular orbital studies of gas-phase interactions between complex molecules.

    PubMed

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

  20. Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

    NASA Astrophysics Data System (ADS)

    Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

    2017-01-01

    The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

  1. Influence of free surface nanorelief on the rear spallation threshold: Molecular-dynamics investigation

    NASA Astrophysics Data System (ADS)

    Mayer, Alexander E.; Ebel, Andrej A.

    2016-10-01

    By means of molecular dynamics simulation, we investigate the interaction of picosecond-duration compression pulses excited by a flat impactor with flat and nano-structured rear surfaces of copper and aluminum samples. It is shown that protrusions on the rear surface can increase the threshold value of the impact velocity, leading to spallation. As the shock wave reaches the perturbed rear surface, an unloading on the lateral surfaces of the protrusions begins; it leads to an intensive plastic deformation in the surface layer of metal. A part of the compression pulse energy is spent on the plastic deformation that restricts the rarefaction wave amplitude and suppresses the spall fracture. An increase in threshold velocity can be observed for all investigated thicknesses of the targets. The increase is substantial with respect to comparability between the protrusion height and the compression pulse width (the impactor thickness). Another condition is the ratio of the protrusion cross-section to the total surface area, which should be neither small nor large-approximately 0.3-0.4 for the best case. At high protrusion heights (higher than the compression pulse width), as well as at large protrusion cross sections, instability develops on the rear surface of the target and is accompanied by mass ejection. The instability violates the rear surface integrity and restricts the threshold velocity, although the loss of integrity in this case goes through mass ejection, not spallation.

  2. Molecular dynamics simulations of formamide interaction with hydrocyanic acid on a catalytic surface TiO2

    NASA Astrophysics Data System (ADS)

    Artoshina, O. V.; Vorob'eva, M. Yu.; Dushanov, E. B.; Kholmurodov, Kh. T.

    2014-06-01

    The behavior of water—formamide and hydrocyanic acid—formamide solutions on an anatase surface have been studied using molecular dynamics (MD) simulation method. The interaction activation energies have been estimated for the temperature range from 250 up to 400 K. The diffusion coefficients and structural radial distribution functions have been calculated for the formamide, water and hydrocyanic acid on an anatase surface. The calculated activation energies of the water—formamide—anatase and hydrocyanic acid—formamide—anatase systems were analyzed and compared. A comparative analysis of the systems under investigation was performed and a possible correlation between the obtained MD results and the molecular mechanism involving the formamide's interaction with dioxide titan adsorbing surface were discussed.

  3. Molecular interactions between green tea catechins and cheese fat studied by solid-state nuclear magnetic resonance spectroscopy.

    PubMed

    Rashidinejad, Ali; Birch, Edward J; Hindmarsh, Jason; Everett, David W

    2017-01-15

    Molecular integrations between green tea catechins and milk fat globules in a cheese matrix were investigated using solid-state magic angle spinning nuclear magnetic resonance spectroscopy. Full-fat cheeses were manufactured containing free catechin or free green tea extract (GTE), and liposomal encapsulated catechin or liposomal encapsulated GTE. Molecular mobility of the carbon species in the cheeses was measured by a wide-line separation technique. The (1)H evolution frequency profile of the (13)C peak at 16ppm obtained for the control cheese and cheeses containing encapsulated polyphenols (catechin or GTE) were similar, however, the spectrum was narrower for cheeses containing free polyphenols. Differences in spectral width indicates changes in the molecular mobility of --CH3- or -C-C-PO4- species through hydrophobic and/or cation-π associations between green tea catechins and cheese fat components. However, the similar spectral profile suggests that encapsulation protects cheese fat from interaction with catechins.

  4. Molecular interaction of pinic acid with sulfuric acid: exploring the thermodynamic landscape of cluster growth.

    PubMed

    Elm, Jonas; Kurtén, Theo; Bilde, Merete; Mikkelsen, Kurt V

    2014-09-11

    We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated from the corresponding ΔG values. The first two additions of sulfuric acid to pinic acid are found to be favorable with ΔG values of -9.06 and -10.41 kcal/mol. Addition of a third sulfuric acid molecule is less favorable and leads to a structural rearrangement forming a bridged sulfuric acid-pinic acid cluster. The involvement of more than one pinic acid molecule in a single cluster is observed to lead to the formation of favorable (pinic acid)2(H2SO4) and (pinic acid)2(H2SO4)2 clusters. The identified most favorable growth paths starting from a single pinic acid molecule lead to closed structures without the further possibility for attachment of either sulfuric acid or pinic acid. This suggests that pinic acid cannot be a key species in the first steps in nucleation, but the favorable interactions between sulfuric acid and pinic acid imply that pinic acid can contribute to the subsequent growth of an existing nucleus by condensation.

  5. A combined spectroscopic, molecular docking and molecular dynamic simulation study on the interaction of quercetin with β-casein nanoparticles.

    PubMed

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Parastar, Hadi

    2013-10-05

    The interaction of quercetin with β-casein nanoparticle micelle was studied at various temperatures in order to do a complete thermodynamic and molecular analysis on the binding process. The results of fluorescence studies showed the possibility of fluorescence energy transfer between excited tryptophan and quercetin. The determined values of critical transfers distance and the mean distance of ligand from Trp-143 residues in β-casein micelle represents a non-radiative energy transfer mechanism for quenching and the existence of a significant interaction between this flavonoid and β-casein nanoparticle. The equilibrium binding of quercetin with β-casein micelle at different temperatures was studied by using UV-Vis absorption spectroscopy. The chemometric analysis (principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods) on spectrophotometric data revealed the existence of two components in solution (quercetin and β-casein-quercetin complex) and resolved their pure concentration and spectral profiles. This information let us to calculate the equilibrium binding constant at various temperatures and the relevant thermodynamic parameters of interaction (enthalpy, entropy and Gibbs free energy) with low uncertainty. The negative values of entropy and enthalpy changes represent the predominate role of hydrogen binding and van der Waals interactions in the binding process. Docking calculations showed the probable binding site of quercetin is located in the hydrophobic core of β-casein where the quercetin molecule is lined by hydrophobic residues and make five hydrogen bonds and several van der Waals contacts with them. Moreover, molecular dynamic (MD) simulation results suggested that this flavonoid can interact with β-casein, without affecting the secondary structure of β-casein. Simulations, molecular docking and experimental data reciprocally supported each other.

  6. Numerical investigation of acoustic radiation from vortex-airfoil interaction

    NASA Astrophysics Data System (ADS)

    Legault, Anne; Ji, Minsuk; Wang, Meng

    2012-11-01

    Numerical simulations of vortices interacting with a NACA 0012 airfoil and a flat-plate airfoil at zero angle of attack are carried out to assess the applicability and accuracy of classical theories. Unsteady lift and sound are computed and compared with the predictions by theories of Sears and Amiet, which assume a thin-plate airfoil in an inviscid flow. A Navier-Stokes solver is used in the simulations, and therefore viscous effects are taken into consideration. For the thin-plate airfoil, the effect of viscosity is negligible. For a NACA 0012 airfoil, the viscous contribution to the unsteady lift and sound mainly comes from coherent vortex shedding in the wake of the airfoil and the interaction of the incoming vortices with the airfoil wake, which become stronger at higher Reynolds numbers for a 2-D laminar flow. When the flow is turbulent at chord Reynolds number of 4 . 8 ×105 , however, the viscous contribution becomes negligible as coherent vortex shedding is not present. Sound radiation from vortex-airfoil interaction at turbulent Reynolds numbers is computed numerically via Lighthill's theory and the result is compared with the predictions of Amiet and Curle. The effect of the airfoil thickness is also examined. Supported by ONR Grant N00014-09-1-1088.

  7. Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

    PubMed

    Li, Jiao; Zhu, Xiaoyan; Chen, Jake Yue

    2009-07-01

    The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for

  8. Resolving solvophobic interactions inferred from experimental solvation free energies and evaluated from molecular simulations

    NASA Astrophysics Data System (ADS)

    Barnett, J. Wesley; Bhutta, Amna; Bierbrier, Sarah C.; da Silva Moura, Natalia; Ashbaugh, Henry S.

    2017-01-01

    Ben-Naim estimated the solvent-mediated interaction between methanes based on experimental solvation free energy differences between chemically similar hydrocarbons. Interactions were predicted to be strongest in water, dominated by characteristic entropic gains. We use molecular simulations in combination with an empirical interpolation procedure that bridges interactions from outside methane's excluded volume down to overlap to test Ben-Naim's estimates. While Ben-Naim's approach captures many distinctive trends, the alchemical differences between methane and a methyl unit play a non-trivial role on the predicted association strength and the sign of enthalpic and entropic components of the interaction free energy in water and ethanol.

  9. Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic

    PubMed Central

    Chaudhari, Mangesh I.; Holleran, Sinead A.; Ashbaugh, Henry S.; Pratt, Lawrence R.

    2013-01-01

    The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 < 0) and become more attractive with increasing temperature (ΔB2/ΔT < 0) in the temperature range 300 K ≤ T ≤ 360 K. Thus, these hydrophobic interactions are attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes. PMID:24297918

  10. Protozoan HSP90-heterocomplex: molecular interaction network and biological significance.

    PubMed

    Figueras, Maria J; Echeverria, Pablo C; Angel, Sergio O

    2014-05-01

    The HSP90 chaperone is a highly conserved protein from bacteria to higher eukaryotes. In eukaryotes, this chaperone participates in different large complexes, such as the HSP90 heterocomplex, which has important biological roles in cell homeostasis and differentiation. The HSP90-heterocomplex is also named the HSP90/HSP70 cycle because different co-chaperones (HIP, HSP40, HOP, p23, AHA1, immunophilins, PP5) participate in this complex by assembling sequentially, from the early to the mature complex. In this review, we analyze the conservation and relevance of HSP90 and the HSP90-heterocomplex in several protozoan parasites, with emphasis in Plasmodium spp., Toxoplasma spp., Leishmania spp. and Trypanosoma spp. In the last years, there has been an outburst of studies based on yeast two-hybrid methodology, co-immunoprecipitation-mass spectrometry and bioinformatics, which have generated a most comprehensive protein-protein interaction (PPI) network of HSP90 and its co-chaperones. This review analyzes the existing PPI networks of HSP90 and its co-chaperones of some protozoan parasites and discusses the usefulness of these powerful tools to analyze the biological role of the HSP90-heterocomplex in these parasites. The generation of a T. gondii HSP90 heterocomplex PPI network based on experimental data and a recent Plasmodium HSP90 heterocomplex PPI network are also included and discussed. As an example, the putative implication of nuclear transport and chromatin (histones and Sir2) as HSP90-heterocomplex interactors is here discussed.

  11. Cellular regulation and molecular interactions of the ferritins.

    PubMed

    Hintze, K J; Theil, E C

    2006-03-01

    Controlling iron/oxygen chemistry in biology depends on multiple genes, regulatory messenger RNA (mRNA) structures, signaling pathways and protein catalysts. Ferritin, a protein nanocage around an iron/oxy mineral, centralizes the control. Complementary DNA (antioxidant responsive element/Maf recognition element) and mRNA (iron responsive element) responses regulate ferritin synthesis rates. Multiple iron-protein interactions control iron and oxygen substrate movement through the protein cage, from dynamic gated pores to catalytic sites related to di-iron oxygenase cofactor sites. Maxi-ferritins concentrate iron for the bio-synthesis of iron/heme proteins, trapping oxygen; bacterial mini-ferritins, DNA protection during starvation proteins, reverse the substrate roles, destroying oxidants, trapping iron and protecting DNA. Ferritin is nature's unique and conserved approach to controlled, safe use of iron and oxygen, with protein synthesis in animals adjusted by dual, genetic DNA and mRNA sequences that selectively respond to iron or oxidant signals and link ferritin to proteins of iron, oxygen and antioxidant metabolism.

  12. Long-range interactions and parallel scalability in molecular simulations

    NASA Astrophysics Data System (ADS)

    Patra, Michael; Hyvönen, Marja T.; Falck, Emma; Sabouri-Ghomi, Mohsen; Vattulainen, Ilpo; Karttunen, Mikko

    2007-01-01

    Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform extensive benchmarking of different commonly used electrostatic schemes on a range of computer architectures (Pentium-4, IBM Power 4, and Apple/IBM G5) for single processor and parallel performance up to 8 nodes—we have also tested the scalability on four different networks, namely Infiniband, GigaBit Ethernet, Fast Ethernet, and nearly uniform memory architecture, i.e. communication between CPUs is possible by directly reading from or writing to other CPUs' local memory. It turns out that the particle-mesh Ewald method (PME) performs surprisingly well and offers competitive performance unless parallel runs on PC hardware with older network infrastructure are needed. Lipid bilayers of sizes 128, 512 and 2048 lipid molecules were used as the test systems representing typical cases encountered in biomolecular simulations. Our results enable an accurate prediction of computational speed on most current computing systems, both for serial and parallel runs. These results should be helpful in, for example, choosing the most suitable configuration for a small departmental computer cluster.

  13. Advances in the molecular understanding of gonadotropins-receptors interactions.

    PubMed

    el Tayar, N

    1996-12-20

    The extracellular domain (ECD) of gonadotropin receptors belong to the leucine-rich repeat (LRR) protein superfamily and their transmembrane domain (TMD) is characteristic of the seven alpha-helices G-protein-coupled receptors (GPCR). The availability of the X-ray structures of porcine ribonuclease inhibitor (RI), a LRR protein, and bacteriorhodopsin (bR) allows the construction of 3D models of the ECD and the TMD of gonadotropin receptors, respectively. The predicted models are to a large extent consistent with currently available biochemical and mutational data. The models provide a reliable basis for understanding how the hormone binds and activates its receptor. The ECD, in particular the LRR region, serves as a baseball glove which efficiently catches the large hormone and optimally orient the appropriate parts of it for interaction with the seven-transmembrane-helix domain of the receptor. This in turn is expected to lead to a conformational change to be sensed by the appropriate G-protein complex leading to the stimulation of cAMP synthesis and steroids production.

  14. Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept.

    PubMed

    Allec, Nicholas; Choi, Mina; Yesupriya, Nikhil; Szychowski, Brian; White, Michael R; Kann, Maricel G; Garcin, Elsa D; Daniel, Marie-Christine; Badano, Aldo

    2015-07-10

    Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species.

  15. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide.

    PubMed

    Ding, Jing-Na; Zhang, Yan-Jun; Zhong, Hui; Ao, Cheng-Cheng; Han, Ju-Guang

    2017-03-15

    Ebola viruses (EBOV) will induce acute hemorrhagic fever fatally to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations. Conformational analysis of the systems demonstrate that combination with VP35 may lead to the conformational transition of NPNTD from "open" to "closed" state. According to the analyses of binding free energies and their decomposition, VP35 residue R37 plays crucial role in wild type (WT) as well as mutant systems. Mutations of I29 and L33 to aspartate as well as M34 to proline affect binding affinity mainly through influencing electrostatic interaction, which is closely related to H-bonds formation. In addition, mutations mainly affect β-hairpin and loop regions, among which, M34P may has the greatest influence to the binding. This study may provide specific binding mechanisms between VP35 peptide and NPNTD, especially some important residues concerning binding.

  16. Investigating Conversational Dynamics: Interactive Alignment, Interpersonal Synergy, and Collective Task Performance

    ERIC Educational Resources Information Center

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    This study investigates interpersonal processes underlying dialog by comparing two approaches, "interactive alignment" and "interpersonal synergy", and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between interlocutors, the synergy…

  17. Interaction Between Molecular Iodine in a Gas Phase and Paints Aged in a Nuclear Power Plant

    SciTech Connect

    Zoulalian, Andre; Belval-Haltier, Edith

    2000-06-15

    The interactions of gaseous molecular iodine with painted surfaces aged in French nuclear pressurized water reactors (PWRs) were carried out in an experimental facility consisting of a molecular iodine generator, a mixing chamber, a sampling chamber, a specimen holder, and a gamma-counting probe [Cristal NaI(Tl)]. The same experimental facility was used to precisely measure the gaseous molecular iodine interactions with epoxy-painted coupons conditioned by two artificial hydrothermal treatments, either by heating at 130degC in a dry atmosphere or by heating at 130 deg. C in a saturated water atmosphere. Then, a kinetic model was developed to represent these experimental results.This paper examines if the previous kinetic model can be used to interpret the gaseous molecular iodine interactions with aged paints. With the rate constant values found for the artificially conditioned paints, the kinetic model agrees with experimental results. Moreover, for the three studied temperatures (95, 110, and 125 deg. C), the values of initial adsorbed water concentration onto the paint and the adsorbed water concentration in equilibrium with the steam of the carrier gas are intermediate between the values found for the two artificial hydrothermal treatments.Finally, a kinetic model is available, allowing the evaluation of precise assessments of the gaseous molecular iodine interactions with aged epoxy paints in the case of a severe PWR accident.

  18. The role of molecular epidemiology in contact investigations: a US perspective.

    PubMed

    Daley, C L; Kawamura, L M

    2003-12-01

    Preventing tuberculosis (TB) transmission through treatment of active cases and contact investigation is the highest priority of TB control programs in the United States. The role of contact investigation is becoming increasingly important as the number of TB cases declines nationally. However, the effectiveness of contact investigation has been difficult to assess because, prior to the availability of molecular genotyping techniques, levels of transmission were crudely measurable. Epidemiological links within and outside the traditional concentric circle approach are limited by the quality of the contact investigation, the skill and knowledge of the investigator and the information provided by the patient. Molecular epidemiology has added a new dimension by enabling the recognition of unsuspected transmission, likely locations of transmission, and quantification of the extent of transmission that is occurring within a given population. In the future, as real-time genotyping becomes more available, the role of molecular epidemiology is likely to expand.

  19. Investigating the interactions of yeast prions: [SWI+], [PSI+], and [PIN+].

    PubMed

    Du, Zhiqiang; Li, Liming

    2014-06-01

    Multiple prion elements, which are transmitted as heritable protein conformations and often linked to distinct phenotypes, have been identified in the budding yeast, Saccharomyces cerevisiae. It has been shown that overproduction of a prion protein Swi1 can promote the de novo conversion of another yeast prion [PSI(+)] when Sup35 is co-overproduced. However, the mechanism underlying this Pin(+) ([PSI(+)] inducible) activity is not clear. Moreover, how the Swi1 prion ([SWI(+)]) interacts with other yeast prions is unknown. Here, we demonstrate that the Pin(+) activity associated with Swi1 overproduction is independent of Rnq1 expression or [PIN(+)] conversion. We also show that [SWI(+)] enhances the appearance of [PSI(+)] and [PIN(+)]. However, [SWI(+)] significantly compromises the Pin(+) activity of [PIN(+)] when they coexist. We further demonstrate that a single yeast cell can harbor three prions, [PSI(+)], [PIN(+)], and [SWI(+)], simultaneously. However, under this condition, [SWI(+)] is significantly destabilized. While the propensity to aggregate underlies prionogenesis, Swi1 and Rnq1 aggregates resulting from overproduction are usually nonheritable. Conversely, prion protein aggregates formed in nonoverexpressing conditions or induced by preexisting prion(s) are more prionogenic. For [PSI(+)] and [PIN(+)] de novo formation, heterologous "facilitators," such as preexisting [SWI(+)] aggregates, colocalize only with the newly formed ring-/rod-shaped Sup35 or Rnq1 aggregates, but not with the dot-shaped mature prion aggregates. Their colocalization frequency is coordinated with their prion inducibility, indicating that prion-prion interactions mainly occur at the early initiation stage. Our results provide supportive evidence for the cross-seeding model of prionogenesis and highlight a complex interaction network among prions in yeast.

  20. Infrared Spectroscopy of Transition Metal-Molecular interactions in the Gas Phase

    SciTech Connect

    Duncan, Michael A.

    2008-11-14

    Transition metal-molecular complexes produced in a molecular beam are mass-selected and studied with infrared laser photodissociation spectroscopy. Metal complexes with carbon monoxide, carbon dioxide, nitrogen, water, acetylene or benzene are studied for a variety of metals. The number and intensity of infrared active bands are compared to the predictions of density functional theory calculations to derive structures, spin states and coordination numbers in these systems. These studied provide new insights into subtle details of metal-molecular interactions important in heterogeneous catalysis, metal-ligand bonding and metal ion solvation.

  1. Investigation of ODE integrators using interactive graphics. [Ordinary Differential Equations

    NASA Technical Reports Server (NTRS)

    Brown, R. L.

    1978-01-01

    Two FORTRAN programs using an interactive graphic terminal to generate accuracy and stability plots for given multistep ordinary differential equation (ODE) integrators are described. The first treats the fixed stepsize linear case with complex variable solutions, and generates plots to show accuracy and error response to step driving function of a numerical solution, as well as the linear stability region. The second generates an analog to the stability region for classes of non-linear ODE's as well as accuracy plots. Both systems can compute method coefficients from a simple specification of the method. Example plots are given.

  2. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    PubMed

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  3. Investigation of radiative interactions in supersonic internal flows

    NASA Technical Reports Server (NTRS)

    Tiwari, Surendra N.; Thomas, A. M.

    1991-01-01

    Analyses and numerical procedures are presented to study the radiative interactions of absorbing emitting species in chemically reacting supersonic flow in various ducts. The 2-D time dependent Navier-Stokes equations in conjunction with radiative flux equation are used to study supersonic flows undergoing finite rate chemical reaction in a hydrogen air system. The specific problem considered is the flow of premixed radiating gas between parallel plates. Specific attention was directed toward studying the radiative contribution of H2O, OH, and NO under realistic physical and flow conditions. Results are presented for the radiative flux obtained for different gases and for various combination of these gases. The problem of chemically reacting and radiating flows was solved for the flow of premixed hydrogen-air through a 10 deg compression ramp. Results demonstrate that the radiative interaction increases with an increase in pressure, temperature, amount of participating species, plate spacing, and Mach number. Most of the energy, however, is transferred by convection in the flow direction. In general the results indicate that radiation can have a significant effect on the entire flow field.

  4. A preliminary investigation of affective interaction in chronic pain couples.

    PubMed

    Johansen, Ayna Beate; Cano, Annmarie

    2007-11-01

    The objective of this preliminary study was to examine the extent to which affective marital interaction related to depressive symptoms in persons with chronic pain and their spouses and to pain severity in persons with pain. Couples from the community completed self-report surveys and engaged in a videotaped conversation on a topic of mutual disagreement that was coded for three affect types (i.e., anger/contempt, sadness, humor). Humor was positively related to marital satisfaction in both partners. Spouse anger/contempt and sadness were positively related to depressive symptoms in spouses. Several significant interaction effects between couple pain status (i.e., whether one or both partners reported pain) and affect also emerged. Specifically, sadness in the participant designated as the person with pain was associated with greater depressive symptoms and pain severity when only he or she reported pain whereas sadness was related to fewer depressive symptoms and less pain severity when both partners reported pain. The relationships between spouse anger and spouse depressive symptoms and between spouse humor and pain severity in the person with pain were also moderated by couple pain status. These exploratory findings can be interpreted in light of emotion regulation and pain empathy theories. For example, partners who have not experienced pain themselves may fail to empathize with persons in pain, thus preventing effective emotion regulation. When both spouses report chronic pain, expressions of negative affect may instead promote emotion regulation because the affect is experienced with a spouse who may be more empathetic.

  5. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA.

    PubMed

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-15

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  6. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

    NASA Astrophysics Data System (ADS)

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-01

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  7. Molecular mechanics and dynamics studies on the interaction of gallic acid with collagen-like peptides

    NASA Astrophysics Data System (ADS)

    Madhan, B.; Thanikaivelan, P.; Subramanian, V.; Raghava Rao, J.; Unni Nair, Balachandran; Ramasami, T.

    2001-10-01

    Molecular modelling approaches have been used to understand the interaction of collagen-like peptides with gallic acid, which mimic vegetable tanning processes involved in protein stabilization. Several interaction sites have been identified and the binding energies of the complexes have been calculated. The calculated binding energies for various geometries are in the range 6-13 kcal/mol. It is found that some complexes exhibit hydrogen bonding, and electrostatic interaction plays a dominant role in the stabilization of the peptide by gallic acid. The π-OH type of interaction is also observed in the peptide stabilization. Molecular dynamics (MD) simulation for 600 ps revealed the possibility of hydrogen bonding between the collagen-like peptide and gallic acid.

  8. DyNet: visualization and analysis of dynamic molecular interaction networks

    PubMed Central

    Goenawan, Ivan H.; Lynn, David J.

    2016-01-01

    Summary: The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most ‘rewired’ nodes across many network states. Availability and Implementation: DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). Contact: david.lynn@sahmri.com. Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:27153624

  9. Investigating molecular structures: Rapidly examining molecular fingerprints through fast passage broadband fourier transform microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Grubbs, Garry Smith Smitty, II

    Microwave spectroscopy is a gas phase technique typically geared toward measuring the rotational transitions of molecules. The information contained in this type of spectroscopy pertains to a molecules structure, both geometric and electronic, which give insight into a molecule's chemistry. Typically this type of spectroscopy is high resolution, but narrowband ≤1 MHz in frequency. This is achieved by tuning a cavity, exciting a molecule with electromagnetic radiation in the microwave region, turning the electromagnetic radiation off, and measuring a signal from the molecular relaxation in the form of a free induction decay (FID). The FID is then Fourier transformed to give a frequency of the transition. "Fast passage" is defined as a sweeping of frequencies through a transition at a time much shorter (≤10 mus) than the molecular relaxation (≈100 mus). Recent advancements in technology have allowed for the creation of these fast frequency sweeps, known as "chirps", which allow for broadband capabilities. This work presents the design, construction, and implementation of one such novel, high-resolution microwave spectrometer with broadband capabilities. The manuscript also provides the theory, technique, and motivations behind building of such an instrument. In this manuscript it is demonstrated that, although a gas phase technique, solids, liquids, and transient species may be studied with the spectrometer with high sensitivity, making it a viable option for many molecules wanting to be rotationally studied. The spectrometer has a relative correct intensity feature that, when coupled with theory, may ease the difficulty in transition assignment and facilitate dynamic chemical studies of the experiment. Molecules studied on this spectrometer have, in turn, been analyzed and assigned using common rotational spectroscopic analysis. Detailed theory on the analysis of these molecules has been provided. Structural parameters such as rotational constants and

  10. [From Purkinje's pharmacologic observations to molecular drug interactions].

    PubMed

    Kvĕtina, J

    1998-11-01

    The 650th anniversary of the foundation of Charles University (7 April 1348) in Prague has initiated a number of historical surveys of the subjects which has been taught at the University for a longer period of time. The disciplines connected with pharmacotherapy were being developed in an empirical conception at the University from the second half of the 14th century but the beginnings of experimental drug research date as late as the mid-19th century. The present survey of the history of "the sciences of medicaments" therefore attempts to outline in short entries the developmental stages of pharmaceutical and pharmacological investigations in the territory of Bohemia and Moravia in about recent 150 years. The arrangement of data is chronological; in the part covering the second half of the 20th century the research of a predominantly exploratory character (universities and academic institutions and their representatives) and research aimed primarily to innovate medicaments (research institutions of pharmaceutical industry and clinical pharmacology and some of their representatives) are treated separately.

  11. Real-time investigation of nucleic acids phosphorylation process using molecular beacons

    PubMed Central

    Tang, Zhiwen; Wang, Kemin; Tan, Weihong; Ma, Changbei; Li, Jun; Liu, Lingfeng; Guo, Qiuping; Meng, Xiangxian

    2005-01-01

    Phosphorylation of nucleic acids is an indispensable process to repair strand interruption of nucleic acids. We have studied the process of phosphorylation using molecular beacon (MB) DNA probes in real-time and with high selectivity. The MB employed in this method is devised to sense the product of a ‘phosphorylation–ligation’ coupled enzyme reaction. Compared with the current assays, this novel method is convenient, fast, selective, highly sensitive and capable of real-time monitoring in a homogenous solution. The preference of T4 polynucleotide kinase (T4 PNK) has been investigated using this approach. The results revealed that a single-stranded oligonucleotide containing guanine at the 5′ termini is most preferred, while those utilizing cytosine in this location are least preferred. The preference of (T)9 was reduced greatly when phosphoryl was modified at the 5′ end, implying that T4 PNK could discern the phosphorylated/unphosphorylated oligonucleotides. The increase of oligonucleotide DNA length leads to an enhancement in preference. A fast and accurate method for assaying the kinase activity of T4 PNK has been developed with a wide linear detection range from 0.002 to 4.0 U/ml in 3 min. The effects of certain factors, such as NTP, ADP, (NH4)2SO4 and Na2HPO4, on phosphorylation have been investigated. This novel approach enables us to investigate the interactions between proteins and nucleic acids in a homogenous solution, such as those found in DNA repair or in drug development. PMID:15961728

  12. Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods

    NASA Astrophysics Data System (ADS)

    Shen, Liangliang; Xu, Hong; Huang, Fengwen; Li, Yi; Xiao, Huafeng; Yang, Zhen; Hu, Zhangli; He, Zhendan; Zeng, Zheling; Li, Yinong

    2015-01-01

    Ligupurpuroside A is one of the major glycoside in Ku-Din-Cha, a type of Chinese functional tea. In order to better understand its digestion and metabolism in humans, the interaction between Ligupurpuroside A and pepsin has been investigated by fluorescence spectra, UV-vis absorption spectra and synchronous fluorescence spectra along with molecular docking method. The fluorescence experiments indicate that Ligupurpuroside A can effectively quench the intrinsic fluorescence of pepsin through a combined quenching way at the low concentration of Ligupurpuroside A, and a static quenching procedure at the high concentration. The binding constant, binding sites of Ligupurpuroside A with pepsin have been calculated. The thermodynamic analysis suggests that non-covalent reactions, including electrostatic force, hydrophobic interaction and hydrogen bond are the main forces stabilizing the complex. According to the Förster's non-radiation energy transfer theory, the binding distance between pepsin and Ligupurpuroside A was calculated to be 3.15 nm, which implies that energy transfer occurs between pepsin and Ligupurpuroside A. Conformation change of pepsin was observed from UV-vis absorption spectra and synchronous fluorescence spectra under experimental conditions. In addition, all these experimental results have been validated by the protein-ligand docking studies which show that Ligupurpuroside A is located in the cleft between the domains of pepsin.

  13. Investigation on interaction between Ligupurpuroside A and pepsin by spectroscopic and docking methods.

    PubMed

    Shen, Liangliang; Xu, Hong; Huang, Fengwen; Li, Yi; Xiao, Huafeng; Yang, Zhen; Hu, Zhangli; He, Zhendan; Zeng, Zheling; Li, Yinong

    2015-01-25

    Ligupurpuroside A is one of the major glycoside in Ku-Din-Cha, a type of Chinese functional tea. In order to better understand its digestion and metabolism in humans, the interaction between Ligupurpuroside A and pepsin has been investigated by fluorescence spectra, UV-vis absorption spectra and synchronous fluorescence spectra along with molecular docking method. The fluorescence experiments indicate that Ligupurpuroside A can effectively quench the intrinsic fluorescence of pepsin through a combined quenching way at the low concentration of Ligupurpuroside A, and a static quenching procedure at the high concentration. The binding constant, binding sites of Ligupurpuroside A with pepsin have been calculated. The thermodynamic analysis suggests that non-covalent reactions, including electrostatic force, hydrophobic interaction and hydrogen bond are the main forces stabilizing the complex. According to the Förster's non-radiation energy transfer theory, the binding distance between pepsin and Ligupurpuroside A was calculated to be 3.15 nm, which implies that energy transfer occurs between pepsin and Ligupurpuroside A. Conformation change of pepsin was observed from UV-vis absorption spectra and synchronous fluorescence spectra under experimental conditions. In addition, all these experimental results have been validated by the protein-ligand docking studies which show that Ligupurpuroside A is located in the cleft between the domains of pepsin.

  14. Water-ionomer interfacial interactions investigated by infrared spectroscopy and computational methods.

    PubMed

    Liu, Shu; Aquino, Adelia J A; Korzeniewski, Carol

    2013-11-12

    Structures for interfacial water condensed in pores and channels of the fluorinated ionomer Nafion from low relative humidity atmosphere were probed through the use of Fourier transform infrared (FTIR) spectroscopy and support from classical and quantum chemical calculations. Modern FTIR spectra of H2O and the O-H stretching region for the deuterium-substituted HOD species interacting at the water-ionomer interface in Nafion exchanged by sodium cations are reported and compared to characteristics observed in the earlier studies that employed a dispersive infrared spectrometer and unspecified spectral resolution. Molecular simulations that examine the orientations of water molecules in the vicinity of ionomer were applied to understand the appearance of multiple free O-H stretching bands and the effect of HOD addition. One computational approach was based on a classical force field model, and the other employed density functional theory (DFT) to investigate atomic-scale interactions of water with regions of different hydrophobicity and charge on a perfluorosulfonate ionomer segment. The results suggest hydrogen bonding stabilizes the types of water-ionomer environments that can lead to multiple free O-H stretching vibrational features in experimental spectra. The studies shed light on the structure of H2O at interfaces inside ion conducting membrane materials and have potential for application in elucidating structure at different types of water interfaces.

  15. An experimental investigation of interaction between projectiles and flames

    NASA Astrophysics Data System (ADS)

    Baryshnikov, A. S.; Basargin, I. V.; Bobashev, S. V.; Monakhov, N. A.; Popov, P. A.; Sakharov, V. A.; Chistyakova, M. V.

    2015-12-01

    This investigation is devoted to the influence of a heated area of gas on model stability with the supersonic motion during free-flying operation. The conditions of the maximum influence on aerodynamics of body flight in an inhomogeneous heated area are ascertained.

  16. The impact of long-range electron-hole interaction on the charge separation yield of molecular photocells

    NASA Astrophysics Data System (ADS)

    Nemati Aram, Tahereh; Ernzerhof, Matthias; Asgari, Asghar; Mayou, Didier

    2017-01-01

    We discuss the effects of charge carrier interaction and recombination on the operation of molecular photocells. Molecular photocells are devices where the energy conversion process takes place in a single molecular donor-acceptor complex attached to electrodes. Our investigation is based on the quantum scattering theory, in particular on the Lippmann-Schwinger equation; this minimizes the complexity of the problem while providing useful and non-trivial insight into the mechanism governing photocell operation. In this study, both exciton pair creation and dissociation are treated in the energy domain, and therefore there is access to detailed spectral information, which can be used as a framework to interpret the charge separation yield. We demonstrate that the charge carrier separation is a complex process that is affected by different parameters, such as the strength of the electron-hole interaction and the non-radiative recombination rate. Our analysis helps to optimize the charge separation process and the energy transfer in organic solar cells and in molecular photocells.

  17. Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process.

    PubMed

    Venclovas, Ceslovas; Colvin, Michael E; Thelen, Michael P

    2002-10-01

    Replication and related processes in eukaryotic cells require replication factor C (RFC) to load a molecular clamp for DNA polymerase in an ATP-driven process, involving multiple molecular interactions. The detailed understanding of this mechanism is hindered by the lack of data regarding structure, mutual arrangement, and dynamics of the players involved. In this study, we analyzed interactions that take place during loading onto DNA of either the PCNA clamp or the Rad9-Rad1-Hus1 checkpoint complex, using computationally derived molecular models. Combining the modeled structures for each RFC subunit with known structural, biochemical, and genetic data, we propose detailed models of how two of the RFC subunits, RFC1 and RFC3, interact with the C-terminal regions of PCNA. RFC1 is predicted to bind PCNA similarly to the p21-PCNA interaction, while the RFC3-PCNA binding is proposed to be similar to the E. coli delta-beta interaction. Additional sequence and structure analysis, supported by experimental data, suggests that RFC5 might be the third clamp loader subunit to bind the equivalent PCNA region. We discuss functional implications stemming from the proposed model of the RFC1-PCNA interaction and compare putative clamp-interacting regions in RFC1 and its paralogs, Rad17 and Ctf18. Based on the individual intermolecular interactions, we propose RFC and PCNA arrangement that places three RFC subunits in association with each of the three C-terminal regions in PCNA. The two other RFC subunits are positioned at the two PCNA interfaces, with the third PCNA interface left unobstructed. In addition, we map interactions at the level of individual subunits between the alternative clamp loader/clamp system, Rad17-RFC(2-5)/Rad9-Rad1-Hus1. The proposed models of interaction between two clamp/clamp loader pairs provide both structural framework for interpretation of existing experimental data and a number of specific findings that can be subjected to direct experimental

  18. Elizabethkingia anophelis: molecular manipulation and interactions with mosquito hosts.

    PubMed

    Chen, Shicheng; Bagdasarian, Michael; Walker, Edward D

    2015-03-01

    Flavobacteria (members of the family Flavobacteriaceae) dominate the bacterial community in the Anopheles mosquito midgut. One such commensal, Elizabethkingia anophelis, is closely associated with Anopheles mosquitoes through transstadial persistence (i.e., from one life stage to the next); these and other properties favor its development for paratransgenic applications in control of malaria parasite transmission. However, the physiological requirements of E. anophelis have not been investigated, nor has its capacity to perpetuate despite digestion pressure in the gut been quantified. To this end, we first developed techniques for genetic manipulation of E. anophelis, including selectable markers, reporter systems (green fluorescent protein [GFP] and NanoLuc), and transposons that function in E. anophelis. A flavobacterial expression system based on the promoter PompA was integrated into the E. anophelis chromosome and showed strong promoter activity to drive GFP and NanoLuc reporter production. Introduced, GFP-tagged E. anophelis associated with mosquitoes at successive developmental stages and propagated in Anopheles gambiae and Anopheles stephensi but not in Aedes triseriatus mosquitoes. Feeding NanoLuc-tagged cells to A. gambiae and A. stephensi in the larval stage led to infection rates of 71% and 82%, respectively. In contrast, a very low infection rate (3%) was detected in Aedes triseriatus mosquitoes under the same conditions. Of the initial E. anophelis cells provided to larvae, 23%, 71%, and 85% were digested in A. stephensi, A. gambiae, and Aedes triseriatus, respectively, demonstrating that E. anophelis adapted to various mosquito midgut environments differently. Bacterial cell growth increased up to 3-fold when arginine was supplemented in the defined medium. Furthermore, the number of NanoLuc-tagged cells in A. stephensi significantly increased when arginine was added to a sugar diet, showing it to be an important amino acid for E. anophelis. Animal

  19. Elizabethkingia anophelis: Molecular Manipulation and Interactions with Mosquito Hosts

    PubMed Central

    Bagdasarian, Michael; Walker, Edward D.

    2015-01-01

    Flavobacteria (members of the family Flavobacteriaceae) dominate the bacterial community in the Anopheles mosquito midgut. One such commensal, Elizabethkingia anophelis, is closely associated with Anopheles mosquitoes through transstadial persistence (i.e., from one life stage to the next); these and other properties favor its development for paratransgenic applications in control of malaria parasite transmission. However, the physiological requirements of E. anophelis have not been investigated, nor has its capacity to perpetuate despite digestion pressure in the gut been quantified. To this end, we first developed techniques for genetic manipulation of E. anophelis, including selectable markers, reporter systems (green fluorescent protein [GFP] and NanoLuc), and transposons that function in E. anophelis. A flavobacterial expression system based on the promoter PompA was integrated into the E. anophelis chromosome and showed strong promoter activity to drive GFP and NanoLuc reporter production. Introduced, GFP-tagged E. anophelis associated with mosquitoes at successive developmental stages and propagated in Anopheles gambiae and Anopheles stephensi but not in Aedes triseriatus mosquitoes. Feeding NanoLuc-tagged cells to A. gambiae and A. stephensi in the larval stage led to infection rates of 71% and 82%, respectively. In contrast, a very low infection rate (3%) was detected in Aedes triseriatus mosquitoes under the same conditions. Of the initial E. anophelis cells provided to larvae, 23%, 71%, and 85% were digested in A. stephensi, A. gambiae, and Aedes triseriatus, respectively, demonstrating that E. anophelis adapted to various mosquito midgut environments differently. Bacterial cell growth increased up to 3-fold when arginine was supplemented in the defined medium. Furthermore, the number of NanoLuc-tagged cells in A. stephensi significantly increased when arginine was added to a sugar diet, showing it to be an important amino acid for E. anophelis. Animal

  20. Characterization of intermolecular interaction between cyanidin-3-glucoside and bovine serum albumin: spectroscopic and molecular docking methods.

    PubMed

    Shi, Jie-hua; Wang, Jing; Zhu, Ying-yao; Chen, Jun

    2014-08-01

    The intermolecular interaction between cyanidin-3-glucoside (Cy-3-G) and bovine serum albumin (BSA) was investigated using fluorescence, circular dichroism and molecular docking methods. The experimental results revealed that the fluorescence quenching of BSA at 338 nm by Cy-3-G resulted from the formation of Cy-3-G-BSA complex. The number of binding sites (n) for Cy-3-G binding on BSA was approximately equal to 1. The experimental and molecular docking results revealed that after binding Cy-3-G to BSA, Cy-3-G is closer to the Tyr residue than the Trp residue, the secondary structure of BSA almost not change, the binding process of Cy-3-G with BSA is spontaneous, and Cy-3-G can be inserted into the hydrophobic cavity of BSA (site II') in the binding process of Cy-3-G with BSA. Moreover, based on the sign and magnitude of the enthalpy and entropy changes (ΔH(0)  = - 29.64 kcal/mol and ΔS(0)  = - 69.51 cal/mol K) and the molecular docking results, it can be suggested that the main interaction forces of Cy-3-G with BSA are Van der Waals and hydrogen bonding interactions.

  1. Homogeneous nucleation and growth in supersaturated zinc vapor investigated by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Römer, F.; Kraska, T.

    2007-12-01

    Homogeneous nucleation and growth of zinc from supersaturated vapor are investigated by nonequilibrium molecular dynamics simulations in the temperature range from 400to800K and for a supersaturation ranging from logS =2 to 11. Argon is added to the vapor phase as carrier gas to remove the latent heat from the forming zinc clusters. A new parametrization of the embedded atom method for zinc is employed for the interaction potential model. The simulation data are analyzed with respect to the nucleation rates and the critical cluster sizes by two different methods, namely, the threshold method of Yasuoka and Matsumoto [J. Chem. Phys. 109, 8451 (1998)] and the mean first passage time method for nucleation by Wedekind et al. [J. Chem. Phys. 126, 134103 (2007)]. The nucleation rates obtained by these methods differ approximately by one order of magnitude. Classical nucleation theory fails to describe the simulation data as well as the experimental data. The size of the critical cluster obtained by the mean first passage time method is significantly larger than that obtained from the nucleation theorem.

  2. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    SciTech Connect

    Sun, Hui-Yong; Ji, Feng-Qin

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. Black-Right-Pointing-Pointer C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. Black-Right-Pointing-Pointer The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  3. Theoretical investigation of the molecular structures and excitation spectra of triphenylamine and its derivatives

    NASA Astrophysics Data System (ADS)

    Sumimoto, Michinori; Yokogawa, Daisuke; Komeda, Masahiro; Yamamoto, Hidetoshi; Hori, Kenji; Fujimoto, Hitoshi

    2011-10-01

    The molecular geometries, electronic structures, and excitation energies of NPh 3, NPh 2Me, NPhMe 2, and NMe 3, were investigated using DFT and post-Hartree Fock methods. When the structural stabilities of these compounds were compared to results obtained by using MP4(SDQ) method, it was confirmed that the optimized geometries by using MP2 method were sufficiently reliable. The excited states with large oscillator strengths consisted of transition components from the HOMO. It should be noted that the orbitals of the nitrogen atom mix with the π-orbital of the phenyl group in an anti-bonding way in the HOMO, and the orbital energy increases with this mixing. The unoccupied orbitals are generated from bonding and anti-bonding type interactions between the π-orbitals of the phenyl groups; therefore, the number of phenyl groups strongly affects the energy diagram of the compounds studied. The differences in the energy diagram cause a spectral change in these compounds in the ultraviolet region.

  4. Mechanistic investigations and molecular medicine applications of gold nanoparticle mediated (GNOME) laser transfection

    NASA Astrophysics Data System (ADS)

    Schomaker, M.; Heinemann, D.; Kalies, S.; Willenbrock, S.; Murua Escobar, H.; Buch, A.; Sodeik, B.; Ripken, T.; Meyer, H.

    2014-03-01

    Alternative high throughput transfection methods are required to understand the molecular network of the cell, which is linked to the evaluation of target genes as therapeutic agents. Besides diagnostic purposes, the transfection of primary- and stem cells is of high interest for therapeutic use. Here, the cell release of trans- or exogene proteins is used to develop immune cancer therapies. The basic requirement to accomplish manipulation of cells is an efficient and gentle transfection method. Therefore, we developed an automatized cell manipulation platform providing high throughput by using GNOME laser transfection. Herein, the interaction of moderately focused laser pulses with gold nanoparticles in close vicinity to the cell membrane mediate transient membrane permeabilization. The exact nature of the involved permeabilization effects depends on the applied particles and laser parameters. Hereinafter, we describe investigations considering the parameter regime, the permeabilization mechanism and the safety profile of GNOME laser transfection. The experimental and calculated results imply a combined permeabilization mechanism consisting of both photochemical and photothermal effects. Furthermore, paramount spatial control achieved either by laser illumination with micrometer precision or targeted gold nanoparticle binding to the cells was demonstrated, allowing selective cell manipulation and destruction. Additionally, the possibility to manipulate difficult to transfect primary cells (neurons) is shown. These results give insights in the basic mechanisms involved in GNOME laser transfection and serve as a strong basis to deliver different molecules for therapeutic (e.g. proteins) and diagnostic (siRNA) use.

  5. Adaptive GPU-accelerated force calculation for interactive rigid molecular docking using haptics.

    PubMed

    Iakovou, Georgios; Hayward, Steven; Laycock, Stephen D

    2015-09-01

    Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loop should run at rates of 500Hz to 1kHz. We present an adaptive force calculation approach that can be executed in parallel on a wide range of Graphics Processing Units (GPUs) for interactive haptics-assisted docking with wider applicability to molecular simulations. Prior to the interactive session either a regular grid or an octree is selected according to the available GPU memory to determine the set of interatomic interactions within a cutoff distance. The total force is then calculated from this set. The approach can achieve force updates in less than 2ms for molecular structures comprising hundreds of thousands of atoms each, with performance improvements of up to 90 times the speed of current CPU-based force calculation approaches used in interactive docking. Furthermore, it overcomes several computational limitations of previous approaches such as pre-computed force grids, and could potentially be used to model receptor flexibility at haptic refresh rates.

  6. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Zeidler, Anita; Salmon, Philip S.; Fischer, Henry E.; Neuefeind, Jörg C.; Simonson, J. Mike; Markland, Thomas E.

    2012-07-01

    The structures of heavy and light water at 300 K were investigated by using a joint approach in which the method of neutron diffraction with oxygen isotope substitution was complemented by path integral molecular dynamics simulations. The diffraction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) Å, were found to be in best agreement with those obtained by using the flexible anharmonic TTM3-F water model. Both techniques show a difference of ≃ 0.5% between the O-D and O-H intra-molecular bond lengths, and the results support a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  7. How does the molecular linker in dynamic force spectroscopy affect probing molecular interactions at the single-molecule level?

    NASA Astrophysics Data System (ADS)

    Taninaka, Atsushi; Aizawa, Kota; Hanyu, Tatsuya; Hirano, Yuuichi; Takeuchi, Osamu; Shigekawa, Hidemi

    2016-08-01

    Dynamic force spectroscopy (DFS) based on atomic force microscopy, which enables us to obtain information on the interaction potential between molecules such as antigen-antibody complexes at the single-molecule level, is a key technique for advancing molecular science and technology. However, to ensure the reliability of DFS measurement, its basic mechanism must be well understood. We examined the effect of the molecular linker used to fix the target molecule to the atomic force microscope cantilever, i.e., the force direction during measurement, for the first time, which has not been discussed until now despite its importance. The effect on the lifetime and barrier position, which can be obtained by DFS, was found to be ˜10 and ˜50%, respectively, confirming the high potential of DFS.

  8. Investigating interactions between UK horse owners and prescribers of anthelmintics.

    PubMed

    Easton, Stephanie; Pinchbeck, Gina L; Tzelos, Thomas; Bartley, David J; Hotchkiss, Emily; Hodgkinson, Jane E; Matthews, Jacqueline B

    2016-12-01

    Helminths are common pathogens of equids and anthelmintic resistance is a major issue in cyathostomin species and Parascaris equorum. At the heart of mitigating the impact of increasing anthelmintic resistance levels, is the responsible dissemination and use of these medicines following best practice principles. There is a paucity of information on interactions between horse owners and anthelmintic prescribers and how this shapes control. Here, a study was undertaken to determine opinions and experiences of horse owners as they relate to anthelmintics purchase and implementation of best practice control. An online survey was distributed via email and social media to explore owners' experiences of purchasing anthelmintics from United Kingdom prescribers, these being veterinarians, suitably qualified persons (SQPs) and pharmacists. Owner responses (n=494) were analysed statistically to compare answers of respondents grouped according to: (i) from whom they bought anthelmintics (Veterinarians n=60; SQPs n=256; Pharmacists n=42; More than one channel n=136), and (ii) by which route (Face-to-face n=234; Telephone n=31; Online n=226) they purchased. Owners who purchased from veterinarians predominantly did so face-to-face (81.3%), whilst those that bought from SQPs purchased via face-to-face (48.8%) and online (46.0%) interactions. Those who purchased from pharmacists predominantly bought anthelmintics online (76.2%). Participants who bought from veterinarians were more likely to view certain factors (i.e. time to talk to the supplier, supplier knowledge) as more important than those who purchased from other prescribers. Those who purchased from veterinarians were more likely to be recommended faecal egg count (FEC) test analysis; however, there was high uptake of FEC testing across all groups. There was a low uptake of anthelmintic efficacy testing; regardless of the prescriber type from whom anthelmintics were purchased. Those who purchased from veterinarians were more

  9. Investigation of Hydrodynamic and Depletion Interactions in Binary Colloidal Dispersions

    NASA Astrophysics Data System (ADS)

    James, Gregory K.

    Within a colloidal dispersion, the presence of negatively adsorbing material can produce a variety of effects on the dispersion properties and interactions. With increasing concentration, the negatively adsorbing material induces both depletion and structural forces on the dispersion, which can dramatically affect both colloidal stability and near-contact hydrodynamics. This project focused on expanding our understanding of the effects of such negatively adsorbing materials on both equilibrium and dynamic interactions between particles. The effects of charged, hard spheres (silica nanoparticle) on the hydrodynamic drag force a particle experiences as it approaches a flat plate were measured experimentally using colloid probe atomic force microscopy (CP-AFM). Deviation was found between the measured drag force and predictions for the drag force in a simple, Newtonian fluid. The measured drag force was always smaller than the predicted drag force as the particle approached contact with the plate. An effective viscosity, that approached the dispersing fluid viscosity at contact and the bulk viscosity at large separations, was determined for the system. This effective viscosity displayed similar characteristics to those predicted theoretically by Bhattacharya and Blawzdziewicz ( J. Chem. Phys. 2008, 128, 214704.). The effects of both anionic and cationic micelles on the depletion and structural forces in a colloidal dispersion were studied both experimentally (with CP-AFM) and theoretically. The depletion and structural forces between a microparticle and a flat plate were measured and compared with the depletion force predicted by the force-balance model of Walz and Sharma (J. Colloid Interface Sci. 1994, 168, 485-496.). Consistent with previous work, the measured depletion force for both micelles was smaller in magnitude than that predicted by the Walz and Sharma model for hard, charged spheres. It is theorized that rearrangement of the micelle surfaces charges or

  10. Numerical investigation of fluid-particle interactions for embolic stroke

    NASA Astrophysics Data System (ADS)

    Mukherjee, Debanjan; Padilla, Jose; Shadden, Shawn C.

    2016-04-01

    Roughly one-third of all strokes are caused by an embolus traveling to a cerebral artery and blocking blood flow in the brain. The objective of this study is to gain a detailed understanding of the dynamics of embolic particles within arteries. Patient computed tomography image is used to construct a three-dimensional model of the carotid bifurcation. An idealized carotid bifurcation model of same vessel diameters was also constructed for comparison. Blood flow velocities and embolic particle trajectories are resolved using a coupled Euler-Lagrange approach. Blood is modeled as a Newtonian fluid, discretized using the finite volume method, with physiologically appropriate inflow and outflow boundary conditions. The embolus trajectory is modeled using Lagrangian particle equations accounting for embolus interaction with blood as well as vessel wall. Both one- and two-way fluid-particle coupling are considered, the latter being implemented using momentum sources augmented to the discretized flow equations. It was observed that for small-to-moderate particle sizes (relative to vessel diameters), the estimated particle distribution ratio—with and without the inclusion of two-way fluid-particle momentum exchange—were found to be similar. The maximum observed differences in distribution ratio with and without the coupling were found to be higher for the idealized bifurcation model. Additionally, the distribution was found to be reasonably matching the volumetric flow distribution for the idealized model, while a notable deviation from volumetric flow was observed in the anatomical model. It was also observed from an analysis of particle path lines that particle interaction with helical flow, characteristic of anatomical vasculature models, could play a prominent role in transport of embolic particle. The results indicate therefore that flow helicity could be an important hemodynamic indicator for analysis of embolus particle transport. Additionally, in the presence

  11. Interplay between Long-Range Crystal Order and Short-Range Molecular Interactions Tunes Carrier Mobility in Liquid Crystal Dyes

    PubMed Central

    2017-01-01

    We investigated the influence of molecular packing on the optical and electrical properties of the liquid crystalline dye 4,7-bis[5-(2-fluoro-4-pentyl-phenyl)-2-thienyl]-2,1,3-benzothiadiazole (FPPTB). FPPTB is crystalline at room temperature, exhibits a nematic phase at temperatures above 149 °C and is in an isotropic melt at temperatures above 230 °C. Solution processed FPPTB films were subject to thermal annealing through these phase transition temperatures and characterized with X-ray diffraction and polarized optical microscopy. Cooling FPPTB films from the nematic and isotropic phases increased crystal domain size, but also induced local structural variations in the molecular packing of crystalline FPPTB. The decrease in long-range order was correlated with an increase in short-range π–π interactions, leading to changes in molecular aggregation which persisted even when the FPPTB films were cooled to room temperature. Annealing-induced changes in molecular aggregation were confirmed with optical spectroscopy. The carrier mobility in FPPTB films increased over 2 orders of magnitude from (2.2 ± 0.4) × 10–5 cm2 V–1 s–1 in as-spun films to μ = (5.0 ± 0.8) × 10–3 cm2 V–1 s–1 in films cooled from the isotropic melt. We discuss the relationship between thermal stability and high carrier mobility values in terms of the interplay between long-range molecular order and increased π–π interactions between molecular pairs in the FPPTB film. PMID:28139915

  12. Exploring the Molecular Interactions of 7,8-Dihydroxyflavone and Its Derivatives with TrkB and VEGFR2 Proteins

    PubMed Central

    Chitranshi, Nitin; Gupta, Vivek; Kumar, Sanjay; Graham, Stuart L.

    2015-01-01

    7,8-Dihydroxyflavone (7,8-DHF) is a TrkB receptor agonist, and treatment with this flavonoid derivative brings about an enhanced TrkB phosphorylation and promotes downstream cellular signalling. Flavonoids are also known to exert an inhibitory effect on the vascular endothelial growth factor receptor (VEGFR) family of tyrosine kinase receptors. VEGFR2 is one of the important receptors involved in the regulation of vasculogenesis and angiogenesis and has also been implicated to exhibit various neuroprotective roles. Its upregulation and uncontrolled activity is associated with a range of pathological conditions such as age-related macular degeneration and various proliferative disorders. In this study, we investigated molecular interactions of 7,8-DHF and its derivatives with both the TrkB receptor as well as VEGFR2. Using a combination of molecular docking and computational mapping tools involving molecular dynamics approaches we have elucidated additional residues and binding energies involved in 7,8-DHF interactions with the TrkB Ig2 domain and VEGFR2. Our investigations have revealed for the first time that 7,8-DHF has dual biochemical action and its treatment may have divergent effects on the TrkB via its extracellular Ig2 domain and on the VEGFR2 receptor through the intracellular kinase domain. Contrary to its agonistic effects on the TrkB receptor, 7,8-DHF was found to downregulate VEGFR2 phosphorylation both in 661W photoreceptor cells and in retinal tissue. PMID:26404256

  13. Delineating solute-solvent interactions in binary mixtures of ionic liquids in molecular solvents and preferential solvation approach.

    PubMed

    Khupse, Nageshwar D; Kumar, Anil

    2011-02-03

    The effect of solute-solvent and solvent-solvent interactions on the preferential solvation of solvatochromic indicators in binary mixtures of ionic liquids with molecular solvents has been investigated. The binary mixtures of the pyridinium-based ionic liquids 1-butylpyridinium tetrafluoroborate ([BP][BF4]), 1-butyl-3-methylpyridinium tetrafluoroborate ([3-MBP][BF4]), and 1-butyl-4-methylpyridinium tetrafluoroborate ([4-MBP][BF4]) with molecular solvents like water, methanol, and dichloromethane have been selected for this investigation. The effect of addition of ionic liquids to molecular solvents on the polarity parameters E(T)(N), Kamlet-Taft parameters, hydrogen bond donor ability (HBD) (α), hydrogen bond acceptor ability (HBA) (β), and polarizability (π*) was obtained. The polarity parameters of the mixture display nonideality on addition of ionic liquids to water and dichloromethane. On the other hand, strong synergetic effects were seen in the ionic liquid-methanol binary mixtures. The preferential solvation models have been employed to analyze the collected data in order to achieve information on solute-solvent interactions in these binary mixtures.

  14. Investigation of the radiation-stimulated oxidation of sulfide by molecular oxygen

    SciTech Connect

    Muratbekov, M.B.; Beremzhanov, B.A.; Koroleva, G.Y.

    1986-07-01

    In order to determine the possibility of radiation stimulation of the oxidation of dissolved sulfide by molecular oxygen and to consider the mechanism from the standpoint of radiation chemical concepts, the authors investigated the radiation-stimulated oxidation of sulfide by molecular oxygen at pH 13. The kinetics were studied according to the decrease in oxygen with the aid of a gasometric set up.

  15. Theoretical Investigation Leading to Energy Storage in Atomic and Molecular Systems

    DTIC Science & Technology

    1990-12-01

    maintenance of equivalent quality of calculation for nuclear geometries differing in the nature or number of chemical bonds ; (iii) ability to describe...function. In order to calculate properties for such states, or to investigate the formation of molecular bonds , one often needs multiconfiguration wave...of calculating one-electron properties and analyzing molecular charge distributions, and various ’post-SCF’ stages, beginning with a 4- index

  16. Investigation of limb-sidestick dynamic interaction with roll control

    NASA Technical Reports Server (NTRS)

    Johnston, D. E.; Mcruer, D. T.

    1986-01-01

    A fixed-base simulation was performed to identify and quantify interactions between the pilot's hand/arm neuromuscular subsystem and such features of typical modern fighter aircraft roll rate command control system mechanization as: (1) force sensing side-stick type manipulator; (2) vehicle effective roll time constant; and (3) flight control system effective time delay. The simulation results provide insight to high frequency pilot induced oscillations (PIO) (roll ratchet), low frequency PIO, and roll-to-right control and handling problems previously observed in experimental and production fly-by-wire control systems. The simulation configurations encompass and/or duplicate several actual flight situations, reproduce control problems observed in flight, and validate the concept that the high frequency nuisance mode known as roll ratchet derives primarily from the pilot's neuromuscular subsystem. The simulations show that force-sensing side-stick manipulator force/displacement/command gradients, command prefilters, and flight control system time delays need to be carefully adjusted to minimize neuromuscular mode amplitude peaking (roll ratchet tendency) without restricting roll control bandwidth (with resulting sluggish or PIO prone control).

  17. Molecular Dynamics Study on the Biophysical Interactions of Seven Green Tea Catechins with Cell Membranes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular dynamics simulations were performed to study the interactions of bioactive catechins (flavonoids) commonly found in green tea with lipid bilayers, as model for cell membranes. Previously, a number of experimental studies rationalized catechin’s anticarcinogenic, antibacterial, and other be...

  18. Experimental investigation of particle surface interactions for turbomachinery application

    NASA Astrophysics Data System (ADS)

    Hamed, A.; Tabakoff, W.

    This paper describes an experimental investigation to determine the particle restitution characteristics after impacting solid targets in a particulate flow wind tunnel. The tests simulate the two phase flow conditions encountered in turbomachinery operating in particle laden flow environments. Both incoming and rebounding velocities are measured using a three color Argon Ion laser in backward scattered mode through a window in the tunnel section containing the impact target. The experimental results are presented for ash particles impinging on RENE 41 targets at different impact conditions. The presented results are applicable to particle dynamics simulations in gas turbine engines and to the prediction of the associated blade surface erosion.

  19. A surface site interaction point methodology for macromolecules and huge molecular databases.

    PubMed

    Oliver, Antoni; Hunter, Christopher A; Prohens, Rafel; Rosselló, Josep L

    2017-03-15

    Determining the position and magnitude of Surface Site Interaction Points (SSIP) is a useful technique for understanding intermolecular interactions. SSIPs have been used for the prediction of solvation properties and for virtual co-crystal screening. To determine the SSIPs for a molecule, the Molecular Electrostatic Potential Surface (MEPS) is first calculated using ab initio methods such as Density Functional Theory. This leads to a high cost in terms of computation time and is not compatible with the analysis of huge molecular databases. Herein, we present a method for the fast estimation of SSIPs, which is based on the MEPS calculated from MMFF94 atomic partial charges. The results show that this method can be used to calculate SSIPs for large molecular databases with a much higher speed than the original ab initio methodology. © 2017 Wiley Periodicals, Inc.

  20. Molecular interactions on single-walled carbon nanotubes revealed by high-resolution transmission microscopy

    PubMed Central

    Umeyama, Tomokazu; Baek, Jinseok; Sato, Yuta; Suenaga, Kazu; Abou-Chahine, Fawzi; Tkachenko, Nikolai V.; Lemmetyinen, Helge; Imahori, Hiroshi

    2015-01-01

    The close solid-state structure–property relationships of organic π−aromatic molecules have attracted interest due to their implications for the design of organic functional materials. In particular, a dimeric structure, that is, a unit consisting of two molecules, is required for precisely evaluating intermolecular interactions. Here, we show that the sidewall of a single-walled carbon nanotube (SWNT) represents a unique molecular dimer platform that can be directly visualized using high-resolution transmission electron microscopy. Pyrene is chosen as the π−aromatic molecule; its dimer is covalently linked to the SWNT sidewalls by aryl addition. Reflecting the orientation and separation of the two molecules, the pyrene dimer on the SWNT exhibits characteristic optical and photophysical properties. The methodology discussed here—form and probe molecular dimers—is highly promising for the creation of unique models and provides indispensable and fundamental information regarding molecular interactions. PMID:26173983

  1. Strong Hydrogen Bonded Molecular Interactions between Atmospheric Diamines and Sulfuric Acid.

    PubMed

    Elm, Jonas; Jen, Coty N; Kurtén, Theo; Vehkamäki, Hanna

    2016-05-26

    We investigate the molecular interaction between methyl-substituted N,N,N',N'-ethylenediamines, propane-1,3-diamine, butane-1,4-diamine, and sulfuric acid using computational methods. Molecular structure of the diamines and their dimer clusters with sulfuric acid is studied using three density functional theory methods (PW91, M06-2X, and ωB97X-D) with the 6-31++G(d,p) basis set. A high level explicitly correlated CCSD(T)-F12a/VDZ-F12 method is used to obtain accurate binding energies. The reaction Gibbs free energies are evaluated and compared with values for reactions involving ammonia and atmospherically relevant monoamines (methylamine, dimethylamine, and trimethylamine). We find that the complex formation between sulfuric acid and the studied diamines provides similar or more favorable reaction free energies than dimethylamine. Diamines that contain one or more secondary amino groups are found to stabilize sulfuric acid complexes more efficiently. Elongating the carbon backbone from ethylenediamine to propane-1,3-diamine or butane-1,4-diamine further stabilizes the complex formation with sulfuric acid by up to 4.3 kcal/mol. Dimethyl-substituted butane-1,4-diamine yields a staggering formation free energy of -19.1 kcal/mol for the clustering with sulfuric acid, indicating that such diamines could potentially be a key species in the initial step in the formation of new particles. For studying larger clusters consisting of a diamine molecule with up to four sulfuric acid molecules, we benchmark and utilize a domain local pair natural orbital coupled cluster (DLPNO-CCSD(T)) method. We find that a single diamine is capable of efficiently stabilizing sulfuric acid clusters with up to four acid molecules, whereas monoamines such as dimethylamine are capable of stabilizing at most 2-3 sulfuric acid molecules.

  2. Rotational Spectromicroscopy: Imaging the Orbital Interaction between Molecular Hydrogen and an Adsorbed Molecule

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Yuan, Dingwang; Yu, Arthur; Czap, Gregory; Wu, Ruqian; Ho, W.

    2015-05-01

    A hydrogen molecule can diffuse freely on the surface and be trapped above an adsorbed molecule within the junction of a scanning tunneling microscope. The trapped dihydrogen exhibits the properties of a free rotor. Here we show that the intermolecular interaction between dihydrogen and Mg-porphyrin (MgP) can be visualized by imaging j =0 to 2 rotational excitation of dihydrogen. The interaction leads to a weakened H-H bond and modest electron donation from the dihydrogen to the lowest unoccupied molecular orbital of MgP, a process similarly observed for the interaction between dihydrogen and an adsorbed Au atom.

  3. Antiretroviral Drug Interactions: Overview of Interactions Involving New and Investigational Agents and the Role of Therapeutic Drug Monitoring for Management

    PubMed Central

    Rathbun, R. Chris; Liedtke, Michelle D.

    2011-01-01

    Antiretrovirals are prone to drug-drug and drug-food interactions that can result in subtherapeutic or supratherapeutic concentrations. Interactions between antiretrovirals and medications for other diseases are common due to shared metabolism through cytochrome P450 (CYP450) and uridine diphosphate glucuronosyltransferase (UGT) enzymes and transport by membrane proteins (e.g., p-glycoprotein, organic anion-transporting polypeptide). The clinical significance of antiretroviral drug interactions is reviewed, with a focus on new and investigational agents. An overview of the mechanistic basis for drug interactions and the effect of individual antiretrovirals on CYP450 and UGT isoforms are provided. Interactions between antiretrovirals and medications for other co-morbidities are summarized. The role of therapeutic drug monitoring in the detection and management of antiretroviral drug interactions is also briefly discussed. PMID:24309307

  4. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    SciTech Connect

    Carnevale, V.; Raugei, S.

    2009-12-14

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  5. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation.

    PubMed

    Carnevale, V; Raugei, S

    2009-12-14

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  6. 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.

  7. Investigations of the intermolecular forces between RDX and polyethylene by force-distance spectroscopy and molecular dynamics simulations.

    PubMed

    Taylor, D E; Strawhecker, K E; Shanholtz, E R; Sorescu, D C; Sausa, R C

    2014-07-10

    The development of novel nanoenergetic materials with enhanced bulk properties requires an understanding of the intermolecular interactions occurring between molecular components. We investigate the surface interactions between 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and polyethylene (PE) crystals on the basis of combined use of molecular dynamics (MD) simulations and force-distance spectroscopy, in conjunction with Lifshitz macroscopic theory of van der Waals forces between continuous materials. The binding energy in the RDX-PE system depends both on the degree of PE crystallinity and on the RDX crystal face. Our MD simulations yield binding energies of approximately 132 and 120 mJ/m(2) for 100% amorphous and 100% crystalline PE on RDX (210), respectively. The average value is about 36% greater than our experimental value of 81 ± 15 mJ/m(2) for PE (∼48% amorphous) on RDX (210). By comparison, Liftshitz theory predicts a value of about 79 mJ/m(2) for PE interacting with RDX. Our MD simulations also predict larger binding energies for both amorphous and crystalline PE on RDX (210) compared to the RDX (001) surface. Analysis of the interaction potential indicates that about 60% of the binding energy in the PE-RDX system is due to attractive interactions between HPE-ORDX and CPE-NRDX pairs of atoms. Further, amorphous PE shows a much longer interaction distance than crystalline PE with the (210) and (001) RDX surfaces due to the possibility of larger polymer elongations in the case of amorphous PE as strain is applied. Also, we report estimates of the binding energies of energetic materials RDX and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) with PE, propylene, polystyrene, and several fluorine-containing polymers using Lifshitz theory and compare these with reported MD calculations.

  8. Investigation of ethanol infiltration into demineralized dentin collagen fibrils using molecular dynamics simulations.

    PubMed

    Jee, Sang Eun; Zhou, Jienfeng; Tan, Jianquo; Breschi, Lorenzo; Tay, Franklin R; Grégoire, Geneviève; Pashley, David H; Jang, Seung Soon

    2016-05-01

    The purpose of this study is to investigate the interaction of neat ethanol with bound and non-bound water in completely demineralized dentin that is fully hydrated, using molecular dynamics (MD) simulation method. The key to creating ideal resin-dentin bonds is the removal of residual free water layers and its replacement by ethanol solvent in which resin monomers are soluble, using the ethanol wet-bonding technique. The test null hypotheses were that ethanol cannot remove any collagen-bound water, and that ethanol cannot infiltrate into the spacing between collagen triple helix due to narrow interlayer spacing. Collagen fibrillar structures of overlap and gap regions were constructed by aligning the collagen triple helix of infinite length in hexagonal packing. Three layers of the water molecules were specified as the layers of 0.15-0.22nm, 0.22-0.43nm and 0.43-0.63nm from collagen atoms by investigating the water distribution surrounding collagen molecules. Our simulation results show that ethanol molecules infiltrated into the intermolecular spacing in the gap region, which increased due to the lateral shrinkage of the collagen structures in contact with ethanol solution, while there was no ethanol infiltration observed in the overlap region. Infiltrated ethanol molecules in the gap region removed residual water molecules via modifying mostly the third water layer (50% decrease), which would be considered as a loosely-bound water layer. The first and second hydration layers, which would be considered as tightly bound water layers, were not removed by the ethanol molecules, thus maintaining the helical structures of the collagen molecules.

  9. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    PubMed

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments.

  10. Interaction of anticancer drug clofarabine with human serum albumin and human α-1 acid glycoprotein. Spectroscopic and molecular docking approach.

    PubMed

    Ajmal, Mohammad Rehan; Nusrat, Saima; Alam, Parvez; Zaidi, Nida; Khan, Mohsin Vahid; Zaman, Masihuz; Shahein, Yasser E; Mahmoud, Mohamed H; Badr, Gamal; Khan, Rizwan Hasan

    2017-02-20

    The binding interaction between clofarabine, an important anticancer drug and two important carrier proteins found abundantly in human plasma, Human Serum Albumin (HSA) and α-1 acid glycoprotein (AAG) was investigated by spectroscopic and molecular modeling methods. The results obtained from fluorescence quenching experiments demonstrated that the fluorescence intensity of HSA and AAG is quenched by clofarabine and the static mode of fluorescence quenching is operative. UV-vis spectroscopy deciphered the formation of ground state complex between anticancer drug and the two studied proteins. Clofarabine was found to bind at 298K with both AAG and HSA with the binding constant of 8.128×10(3) and 4.120×10(3) for AAG and HSA, respectively. There is stronger interaction of clofarabine with AAG as compared to HSA. The Gibbs free energy change was found to be negative for the interaction of clofarabine with AAG and HSA indicating that the binding process is spontaneous. Binding of clofarabine with HSA and AAG induced ordered structures in both proteins and lead to molecular compaction. Clofarabine binds to HSA near to drug site II. Hydrogen bonding and hydrophobic interactions were the main bonding forces between HSA-clofarabine and AAG-clofarabine as revealed by docking results. This study suggests the importance of binding of anticancer drug to AAG spatially in the diseases like cancers where the plasma concentration of AAG increases many folds. Design of drug dosage can be adjusted accordingly to achieve optimal treatment outcome.

  11. Interaction of an antiepileptic drug, lamotrigine with human serum albumin (HSA): Application of spectroscopic techniques and molecular modeling methods.

    PubMed

    Poureshghi, Fatemeh; Ghandforoushan, Parisa; Safarnejad, Azam; Soltani, Somaieh

    2017-01-01

    Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (Kb) of 5.74×10(3) and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism. Negative standard enthalpy (ΔH) and standard entropy (ΔS) changes indicated that van der Waals interactions and hydrogen bonds were dominant forces which facilitate the binding of Lamotrigine to HSA, the results were confirmed by molecular docking studies which showed no hydrogen binding. The FRET studies showed that there is a possibility of energy transfer between Trp214 and lamotrigine. Also the binding of lamotrigine to HSA in the studied concentrations was not as much as many other drugs, but the secondary structure of the HSA was significantly changed following the interaction in a way that α-helix percentage was reduced from 67% to 57% after the addition of lamotrigine in the molar ratio of 4:1 to HSA. According to the docking studies, lamotrigine binds to IB site preferably.

  12. Final Report on Investigation of the Electron Interactions in Graphene

    SciTech Connect

    Kim, Philip

    2015-02-14

    In graphene, combined with the real spin degree of freedom, which exhibits SU(2) symmetry, the total internal degrees of freedom of graphene carriers is thus described by a larger SU(4) symmetry, which produces a richer space for potential phenomena of emergent correlated electron phenomena. The major part of this proposal is exploring this unique multicomponent correlated system in the quantum limit. In the current period of DOE BES support we have made several key advances that will serve as a foundation for the new studies in this proposal. Employing the high-mobility encapsulated graphene heterostructures developed during the current phase of research, we have investigated spin and valley quantum Hall ferromagnetism in graphene and discovered a spin phase transition leading to a quantum spin Hall analogue. We have also observed the fractal quantum Hall effect arising from the Hofstadter’s butterfly energy spectrum. In addition, we have discovered multiband transport phenomena in bilayer graphene at high carrier densities.

  13. [Investigation of ultrasonic wave interaction with porous saturated rocks

    SciTech Connect

    Not Available

    1993-07-01

    During the last year we have continued our investigation of ultrasonic wave propagation in fluid-filled porous materials. Previously, we studied the feasibility of using different surface modes to characterize both synthetic and natural rocks. We introduced a novel experimental technique based on the direct generation of surface waves by edge excitation. At first, we used two low-frequency (100--500 kHz) shear transducers in pitch-catch mode to launch and receive the ultrasonic surface wave. The contact transducers were coupled to the opposite edges of the porous specimens with normal polarization relative to the surface. The same technique was successfully used to generate Rayleigh-type surface modes on the free surface of both dry and water-saturated specimens, as well as Stoneley-type interface modes on the fluid-loaded surfaces of immersed samples. Recently, we developed a special interferometric technique for non-contact detection of ultrasonic vibrations on diffusely reflecting rough surfaces. This method was found to be more suitable for surface wave inspection of porous ceramics and natural rocks than the previously used contact techniques. Beside investigating guided acoustic waves in water-saturated porous materials, we also studied bulk wave propagation in air-saturated specimens. We further developed our experimental technique which is based on the transmission of airborne ultrasonic waves through air-filled porous plates. This method can be readily used to study the frequency-dependent propagation properties of slow compressional waves in different porous materials including natural rocks. By simple technical improvements, we extended the measuring range so that we could continuously cover both low-frequency (diffuse) and high-frequency (propagating) regimes of slow wave propagation.

  14. Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions

    PubMed Central

    Vagenende, Vincent; Han, Alvin X.; Pek, Han B.; Loo, Bernard L. W.

    2013-01-01

    Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments. PMID:23696727

  15. Multispectroscopic and molecular modeling studies on the interaction of two curcuminoids with β-lactoglobulin

    NASA Astrophysics Data System (ADS)

    Mohammadi, F.; Sahihi, M.; Bordbar, A. Khalegh

    2015-04-01

    This study demonstrates the binding properties of bisdemethoxycurcumin (BDMC) and diacetylbisdemethoxycurcumin (DABC) as bioactive curcuminoids with bovine β-lactoglobulin (BLG) variant B using fluorescence and circular dichroism (CD) spectroscopy; molecular docking, and molecular dynamics simulation methods. The estimated binding constants for BLG-BDMC and BLG-DABC complexes were (8.99 ± 0.10) × 104 M-1 and (1.87 ± 0.10) × 102 M-1, respectively. The distances between BLG and these curcuminoids were obtained based on the Förster's theory of non-radiative energy transfer. Molecular docking studies revealed the binding of BDMC and DABC to the protein surface cleft of protein by formation of four and one hydrogen bonds, respectively. Finally, molecular dynamics simulation results represent the conformational changes of BLG due to its interaction with BDMC. Also, the profiles of atomic fluctuations signified the rigidity of ligand binding site during the simulation.

  16. Effects of cholesterol concentration on the interaction of cytarabine with lipid membranes: a molecular dynamics simulation study.

    PubMed

    Karami, Leila; Jalili, Seifollah

    2015-01-01

    Liposomal cytarabine, DepoCyt, is a chemotherapy agent which is used in cancer treatment. This form of cytarabine has more efficacy and fewer side effects relative to the other forms. Since DepoCyt contains the cytarabine encapsulated within phosphatidylcholine and the sterol molecules, we modeled dioleoylphosphatidylcholine (DOPC)/cholesterol bilayer membrane as a carrier for cytarabine to study drug-bilayer interactions. For this purpose, we performed a series of united-atom molecular dynamics (MD) simulations for 25 ns to investigate the interactions between cytarabine and cholesterol-containing DOPC lipid bilayers. Only the uncharged form of cytarabine molecule was investigated. In this study, different levels of the cholesterol content (0, 20, and 40%) were used. MD simulations allowed us to determine dynamical and structural properties of the bilayer membrane and to estimate the preferred location and orientation of the cytarabine molecule inside the bilayer membrane. Properties such as membrane thickness, area per lipid, diffusion coefficient, mass density, bilayer packing, order parameters, and intermolecular interactions were examined. The results show that by increasing the cholesterol concentration in the lipid bilayers, the bilayer thickness increases and area per lipid decreases. Moreover, in accordance with the experiments, our calculations show that cholesterol molecules have ordering effect on the hydrocarbon acyl chains. Furthermore, the cytarabine molecule preferentially occupies the polar region of the lipid head groups to form specific interactions (hydrogen bonds). Our results fully support the experimental data. Our finding about drug-bilayer interaction is crucial for the liposomal drug design.

  17. Theoretical investigation of energy storage in atomic and molecular systems: Metastable molecular fuels

    NASA Astrophysics Data System (ADS)

    Saxon, Roberta P.

    1990-12-01

    Ion-pair species bound by the coulomb attraction between a stable positive and stable negative ion have been investigated theoretically as candidate high-energy fuels that could form the basis of new propulsion schemes. Theoretical results for H3O, Li3H, and H3F are presented along with specific impulse, I(sub sp), predictions based on calculated energies. The ion-pair local minimum on the first excited potential surface of H3O is found to be unstable with respect to dissociation to H2 + H + O. The ion-pair state of H3F has a double degenerate imaginary frequency. These results support the general conclusion that ion-pair states based on the H3 cation will not be stable because back-charge transfer to H3(+) leads to neutral H3, which is unstable with respect to H2 + H. However, the ion-pair state of Li3H is found to be a local minimum with a very small barrier to conversion to the lower energy planar form. Even the lowest energy form of Li3H as an additive to hydrogen is predicted to provide a 16 percent improvement in I(sub sp).

  18. Interaction of Curcumin with PEO-PPO-PEO block copolymers: a molecular dynamics study.

    PubMed

    Samanta, Susruta; Roccatano, Danilo

    2013-03-21

    Curcumin, a naturally occurring drug molecule, has been extensively investigated for its various potential usages in medicine. Its water insolubility and high metabolism rate require the use of drug delivery systems to make it effective in the human body. Among various types of nanocarriers, block copolymer based ones are the most effective. These polymers are broadly used as drug-delivery systems, but the nature of this process is poorly understood. In this paper, we propose a molecular dynamics simulation study of the interaction of Curcumin with block copolymer based on polyethylene oxide (PEO) and polypropylene oxide (PPO). The study has been conducted considering the smallest PEO and PPO oligomers and multiple chains of the block copolymer Pluronic P85. Our study shows that the more hydrophobic 1,2-dimethoxypropane (DMP) molecules and PPO block preferentially coat the Curcumin molecule. In the case of the Pluronic P85, simulation shows formation of a drug-polymer aggregate within 50 ns. This process leaves exposed the PEO part of the polymers, resulting in better solvation and stability of the drug in water.

  19. Molecular Dynamics Simulations of the Interactions Between Tungsten Dust and Beryllium Plasma-Facing Material

    NASA Astrophysics Data System (ADS)

    Niu, Guojian; Li, Xiaochun; Xu, Qian; Yang, Zhongshi; Luo, Guangnan

    2015-12-01

    In the present research, molecular dynamics simulation is applied to study the interactions between tungsten dusts and a beryllium plasma-facing material surface. Calculation results show that it is quite difficult for nanometer-size dust particles to damage the plasma-facing material surface, which is different from the micrometer-size ones. The reason may be the size difference between dust and crystal grains. The depth of dust penetration into plasma-facing materials is closely related to the incident velocity, and the impacting angle also plays an important role. Dust and material surface damage is also investigated. Results show that both incident velocity and angle can significantly influence the damage. supported by the National Magnetic Confinement Fusion Science Program of China (Nos. 2013GB105001, 2013GB105002, and 2015GB109001), National Natural Science Foundation of China (Nos. 11205198, 11305213 and 11405201), as well as Technological Development Grant of Hefei Science Center of CAS (No. 2014TDG-HSC003)

  20. Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study.

    PubMed

    Baler, K; Martin, O A; Carignano, M A; Ameer, G A; Vila, J A; Szleifer, I

    2014-01-30

    A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation.

  1. Investigation of mechanisms governing electrowetting and hydrodynamic interactions in the presence of draining channels

    NASA Astrophysics Data System (ADS)

    Gupta, Rohini

    Modulation of solid-liquid interfacial interactions via electric field (or electrowetting) is an effective method to deform and move liquid drops on solid surfaces in micro-/nanoscale systems. The deformation and motion of a liquid drop on a solid surface in response to an external driving force is hindered by pinning of triple contact line. A better understanding of the mechanisms and limitations of electrowetting is warranted for design and optimization of active micro-/nanoscale systems. Modulation of hydrodynamic interactions via surface structures may contribute to the adhesion and locomotion mechanisms employed by tree frogs under flooded conditions: a better understanding of which will facilitate design of biomimetic systems inspired by the same. This thesis summarizes the results of investigation of the mechanisms and limitations of electrowetting (electrowetting on dielectric and potential-induced molecular reorganization) and the hydrodynamic interactions in the presence of draining channels. The mechanism at play during electrowetting on dielectric is probed via capillary condensation inside surface force apparatus. Height of a nanometer-sized annular water meniscus is measured and observed to be independent of the applied potential. These nanoscale electrowetting measurements unequivocally demonstrate that spreading of a liquid conductive drop on a charged dielectric is driven by electromechanics and not by a change in solid-liquid interfacial energy. Macroscopic electrowetting response of substrates with a range of contact angle hysteresis is characterized to quantify the relationship between contact angle hysteresis, threshold potential for liquid actuation, and electrowetting hysteresis. These results are interpreted within the electromechanical framework corrected for pinning of the moving triple contact line and demonstrate that the electrowetting hysteresis and the contact angle hysteresis are equal in magnitude. Alternatively, potential

  2. An Experimental Investigation To Determine Interaction Between Rotating Bodies

    NASA Technical Reports Server (NTRS)

    Grugel, R. N.; Volz, M. P.; Mazuruk, K.

    2003-01-01

    A brass (copper+zinc) wheel, with a 4-in diameter and 1.4 in thick, was used for this investigation. Ceramic ball bearings were used to safely spin the wheel up to 40,000 rpm. The wheel was also electrically insulated from the rest of the armature. For spinning, an air turbine was used. The rotational velocity was measured by two methods: (1) A simple strobe light and (2) a photodiode that detected laser beam pulses as they passed through a slot in the rotating shaft. The magnetic sensor is based on a giant magnetoresistivity, and consists of a balanced bridge circuitry. The position of the sensor was as close as possible to the rim of the wheel. The linear dimension of the sensor is approximately equal to 8 mm so that the offset from the surface is on the order of 15 percent. We did not use any goniometer system, so the accuracy of the angular position is not high, being estimated within a few degrees, with the main uncertainty being the direction of Earth's magnetic field. We attempted to fit the experimental data with the presented theory by selecting the best value for the electrical conductivity of the wheel. The results of this procedure are displayed, where the black dots represent experimental values. A slight misfit on the right shoulder can be due to slight angular misalignment from a 90 degree position. The obtained value for the resistivity is 43 n(OMEGA)m, which compares well with those listed. We can conclude, based on these measurements, that the proposed theory satisfactorily explains our experiments.

  3. Investigating hadronic resonances in pp interactions with HADES

    NASA Astrophysics Data System (ADS)

    Przygoda, Witold

    2015-06-01

    In this paper we report on the investigation of baryonic resonance production in proton-proton collisions at the kinetic energies of 1.25 GeV and 3.5 GeV, based on data measured with HADES. Exclusive channels npπ+ and ppπ0 as well as ppe+e- were studied simultaneously in the framework of a one-boson exchange model. The resonance cross sections were determined from the one-pion channels for Δ(1232) and N(1440) (1.25 GeV) as well as further Δ and N* resonances up to 2 GeV/c2 for the 3.5 GeV data. The data at 1.25 GeV energy were also analysed within the framework of the partial wave analysis together with the set of several other measurements at lower energies. The obtained solutions provided the evolution of resonance production with the beam energy, showing a sizeable non-resonant contribution but with still dominating contribution of Δ(1232)P33. In the case of 3.5 GeV data, the study of the ppe+e- channel gave the insight on the Dalitz decays of the baryon resonances and, in particular, on the electromagnetic transition form-factors in the time-like region. We show that the assumption of a constant electromagnetic transition form-factors leads to underestimation of the yield in the dielectron invariant mass spectrum below the vector mesons pole. On the other hand, a comparison with various transport models shows the important role of intermediate ρ production, though with a large model dependency. The exclusive channels analysis done by the HADES collaboration provides new stringent restrictions on the parameterizations used in the models.

  4. Interaction between a Functionalized Single-Walled Carbon Nanotube and the YAP65WW Protein Domain: a Molecular Dynamics Simulation Study

    NASA Astrophysics Data System (ADS)

    Dou, Quan-Tao; Zuo, Guang-Hong; Fang, Hai-Ping

    2012-06-01

    The interaction between a functionalized single-walled carbon nanotube (f-SWCNT) and the YAP65WW protein domain is investigated by using molecular dynamics simulations. It is found that the f-SWCNT binds onto the active site of the YAP65WW domain and leads to a substantial conformational change of the protein domain, which may securely affect the original function of protein. Both the hydrophobic interaction and the long lifetime hydrogen bonds play important roles in the binding.

  5. Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations.

    PubMed

    Liu, Ya-Lin; Jang, Soonmin; Wang, Shih-Min; Chen, Chiu-Hao; Li, Feng-Yin

    2016-06-01

    The glucocorticoid receptor (GR), a transcription factor regulating gene expression in a ligand-dependent fashion, is known for flexibility in adapting various ligands with their structures ranging from steroid to non-steroid. However, in our previous study, GR shows a stringent discrimination against a set of steroid ligands with highly similar structures for triggering its nuclear migration. In order to resolve this puzzle, we employed molecular docking simulations to investigate the origin of this structural discrimination. By analyzing the docking orientations and the related ligand-GR interaction patterns, we found that the hydrophilicity mismatch between the docking ligand and the GR ligand-binding site is the main cause combined with the steric hindrance and structural rigidness of these steroid ligands. Furthermore, we utilized this knowledge to rationalize how the structure-binding interaction of non-steroid ligands triggers GR nuclear migration with their structures available in Protein Data Bank.

  6. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    PubMed Central

    Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus

    2016-01-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short. PMID:27004867

  7. Molecular docking simulation analysis of the interaction of dietary flavonols with heat shock protein 90

    PubMed Central

    Singh, Salam Pradeep; Deb, Chitta Ranjan; Ahmed, Sharif Udin; Saratchandra, Yenisetti; Konwar, Bolin Kumar

    2016-01-01

    Abstract Hsp90 is a major protein involved in the stabilization of various proteins in cancer cells. The present investigation focused on the molecular docking simulation studies of flavanols as inhibitors of Hsp90 at the high affinity adenosine triphosphate (ATP) binding site and analyzed absorption, distribution, metabolism, excretion and toxicity (ADME-toxicity). The molecular docking analysis revealed that the flavanols showed competitive inhibition with ATP molecule at the active site and enhanced pharmacological parameters.

  8. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations.

    PubMed

    Dal Peraro, Matteo; Ruggerone, Paolo; Raugei, Simone; Gervasio, Francesco Luigi; Carloni, Paolo

    2007-04-01

    Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

  9. Molecular Dynamics Simulation and NMR Investigation of the Association of the β-Blockers Atenolol and Propranolol with a Chiral Molecular Micelle

    PubMed Central

    Morris, Kevin F.; Billiot, Eugene J.; Billiot, Fereshteh H.; Hoffman, Charlene B.; Gladis, Ashley A.; Lipkowitz, Kenny B.; Southerland, William M.; Fang, Yayin

    2015-01-01

    Molecular dynamics simulations and NMR spectroscopy were used to compare the binding of two β-blocker drugs to the chiral molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The molecular micelle is used as a chiral selector in capillary electrophoresis. This study is part of a larger effort to understand the mechanism of chiral recognition in capillary electrophoresis by characterizing the molecular micelle binding of chiral compounds with different geometries and charges. Propranolol and atenolol were chosen because their structures are similar, but their chiral interactions with the molecular micelle are different. Molecular dynamics simulations showed both propranolol enantiomers inserted their aromatic rings into the molecular micelle core and that (S)-propranolol associated more strongly with the molecular micelle than (R)-propranolol. This difference was attributed to stronger molecular micelle hydrogen bonding interactions experienced by (S)-propranolol. Atenolol enantiomers were found to bind near the molecular micelle surface and to have similar molecular micelle binding free energies. PMID:26257464

  10. Study on Interaction between 5-Bromo-4-thio-2‧-deoxyuridine and human serum albumin by spectroscopy and molecular docking

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaohui; Gao, Ruiqi; Li, Depeng; Yin, Hongyan; Zhang, Juling; Cao, Hongyu; Zheng, Xuefang

    2015-02-01

    The interaction between 5-Bromo-4-thio-2‧-deoxyuridine (4-SBrdU) and human serum albumin (HSA) was investigated by the methods of UV-vis absorbance, fluorescence and circular dichroism (CD) spectroscopy and molecular docking under simulative physiological conditions. The results showed that the quenching mechanism of HAS by 4-SBrdU was dynamic fluorescence quenching, hydrophobic interaction was the main intermolecular force based on thermodynamic data, the fluorescence experimental results were in agreement with results obtained by the molecular docking study.

  11. Kinematics of the ionized and molecular gas in nearby luminous infrared interacting galaxies

    NASA Astrophysics Data System (ADS)

    Zaragoza-Cardiel, Javier; Beckman, John; Font, Joan; Rosado, Margarita; Camps-Fariña, Artemi; Borlaff, Alejandro

    2017-03-01

    We have observed three luminous infrared galaxy systems which are pairs of interacting galaxies, with the Galaxy Hα Fabry-Perot system mounted on the 4.2 m William Herschel Telescope at the Roque de los Muchachos Observatory, and combined the observations with the Atacama Large Millimeter Array observations of these systems in CO emission to compare the physical properties of the star formation regions and the molecular gas clouds, and specifically the internal kinematics of the star-forming regions. We identified 88 star-forming regions in the Hα emission data cubes, and 27 molecular cloud complexes in the CO emission data cubes. The surface densities of the star formation rate and the molecular gas are significantly higher in these systems than in non-interacting galaxies and the Galaxy, and are closer to the surface densities of the star formation rate and the molecular gas of extreme star-forming galaxies at higher redshifts. The large values of the velocity dispersion also show the enhanced gas surface density. The H II regions are situated on the SFR - σv envelope, and so are also in virial equilibrium. Since the virial parameter decreases with the surface densities of both the star formation rate and the molecular gas, we claim that the clouds presented here are gravitationally dominated rather than being in equilibrium with the external pressure.

  12. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin

    2007-09-13

    An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

  13. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method.

    PubMed

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-15

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔH(θ)) and entropy change (ΔS(θ)) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  14. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    NASA Astrophysics Data System (ADS)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  15. Investigation on the interaction behavior between bisphenol A and pepsin by spectral and docking studies

    NASA Astrophysics Data System (ADS)

    Zhang, Hongmei; Cao, Jian; Fei, Zhenghao; Wang, Yanqing

    2012-08-01

    In this report, the binding interaction of BPA with pepsin has been explored by spectroscopic and molecular modeling methods. Quenching of fluorescence of pepsin with increasing BPA concentration is a useful tool in the analysis of thermodynamic parameters. The results showed that the hydrophobic, steric contacts and hydrogen bonds interactions played major roles in stabilizing the complex. The binding of BPA to pepsin induced some micro-environmental and conformational changes in pepsin. The docking studies results showed that BPA entered into the hydrophobic cavity of pepsin. The interaction of pepsin with BPA occurs in the area between domain I and domain III.

  16. GAMMA-RAY EMISSION FROM SUPERNOVA REMNANT INTERACTION WITH MOLECULAR CLUMPS

    NASA Astrophysics Data System (ADS)

    Tang, Xiaping; Chevalier, R.

    2014-01-01

    Observations of the middle-aged supernova remnants IC 443, W28, and W51C indicate that the brightnesses at GeV and TeV energies are correlated with each other and with regions of molecular clump interaction, but not with the radio synchrotron brightness. We suggest that the radio emission is primarily associated with a radiative shell in the interclump medium of a molecular cloud, while the Gamma-ray emission is primarily associated with the interaction of the radiative shell with molecular clumps. The shell interaction produces a high pressure region, so that the Gamma-ray luminosity can be approximately reproduced even if shock acceleration of particles is not efficient, provided that energetic particles are trapped in the cooling shell. In addition, the GeV through TeV emission can be produced in the interaction region if the trapping occurs to sufficiently high energies. Alternatively, diffusive acceleration may be efficient; in this case the observed GeV emission can be approximately reproduced, but not the TeV emission.

  17. Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

    NASA Astrophysics Data System (ADS)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2012-10-01

    Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

  18. Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

    SciTech Connect

    Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A; Mostofian, Barmak; Kucerka, Norbert; Drazba, Paul; Katsaras, John

    2012-01-01

    Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.

  19. Molecular composites via ionic interactions and their deformation/fracture properties

    SciTech Connect

    Parker, G.; Chen, W.; Hara, M.

    1995-12-01

    Homogeneous molecular composites have been made from ionic PPTA and PVP, in which a good dispersion of rod molecules is achieved via ion-dipole interactions. Appearance of a single T{sub g} as well as morphological observations by TEM have indicated good dispersion of the rigid-rod PPTA molecules. The deformation mode of the matrix polymer is modified significantly with the addition of rod molecules: while crazing is the only deformation mechanism of PVP, an addition of ionic PPTA molecules into the PVP matrix induces shear deformation. This suggests better fracture properties of these molecular composites. Initial studies have indicated significant enhancement in mechanical properties.

  20. Band formation in a molecular quantum well via 2D superatom orbital interactions.

    PubMed

    Dougherty, Daniel B; Feng, Min; Petek, Hrvoje; Yates, John T; Zhao, Jin

    2012-12-28

    By scanning tunneling microscopy and spectroscopy, we study nearly free electron band formation of the σ* lowest unoccupied