Sample records for solvent-dependent conformational transitions

  1. Solvent dependence of dynamic transitions in protein solutions

    PubMed Central

    Réat, Valerie; Dunn, Rachel; Ferrand, Michel; Finney, John L.; Daniel, Roy M.; Smith, Jeremy C.

    2000-01-01

    A transition as a function of increasing temperature from harmonic to anharmonic dynamics has been observed in globular proteins by using spectroscopic, scattering, and computer simulation techniques. We present here results of a dynamic neutron scattering analysis of the solvent dependence of the picosecond-time scale dynamic transition behavior of solutions of a simple single-subunit enzyme, xylanase. The protein is examined in powder form, in D2O, and in four two-component perdeuterated single-phase cryosolvents in which it is active and stable. The scattering profiles of the mixed solvent systems in the absence of protein are also determined. The general features of the dynamic transition behavior of the protein solutions follow those of the solvents. The dynamic transition in all of the mixed cryosolvent–protein systems is much more gradual than in pure D2O, consistent with a distribution of energy barriers. The differences between the dynamic behaviors of the various cryosolvent protein solutions themselves are remarkably small. The results are consistent with a picture in which the picosecond-time scale atomic dynamics respond strongly to melting of pure water solvent but are relatively invariant in cryosolvents of differing compositions and melting points. PMID:10963663

  2. Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives.

    PubMed

    Saif, Mari; Widom, Julia R; Xu, Senmiao; Abbey, Eric R; Liu, Shih-Yuan; Marcus, Andrew H

    2015-06-25

    Fluorescent analogues of the indole side chain of tryptophan can be useful spectroscopic probes of protein-protein and protein-DNA interactions. Here we present linear dichroism and solvent-dependent spectroscopic studies of two fluorescent analogues of indole, in which the organic C?C unit is substituted with the isosteric inorganic B-N unit. We studied the so-called "external" BN indole, which has C2v symmetry, and the "fused" BN indole with Cs symmetry. We performed a combination of absorption and fluorescence spectroscopy, ultraviolet linear dichroism (UV-LD) in stretched poly(ethylene) (PE) films, and quantum chemical calculations on both BN indole compounds. Our measurements allowed us to characterize the degree of alignment for both molecules in stretched PE films. We thus determined the orientations and magnitudes of the two lowest energy electric dipole transition moments (EDTMs) for external BN indole, and the two lowest energy EDTMs for fused BN indole within the 30?000-45?000 cm(-1) spectral range. We compared our experimental results to those of quantum chemical calculations using standard density functional theory (DFT). Our theoretical predictions for the low-energy EDTMs are in good agreement with our experimental data. The absorption and fluorescence spectra of the external and the fused BN indoles are sensitive to solvent polarity. Our results indicate that the fused BN indole experiences much greater solvation interactions with polar solvents than does the external BN indole. PMID:26000556

  3. Solvent-dependent rate-limiting steps in the conformational change of sodium channel gating in squid giant axon.

    PubMed Central

    Kukita, F

    1997-01-01

    1. The time course of sodium currents (INa) in squid giant axon was analysed using viscous non-electrolyte solutions on both sides of the axolemma. It slowed reversibly as the non-electrolyte concentration increased. The activation, deactivation (closing) and inactivation processes were slowed in a similar manner. The gating current of the sodium channel was also slowed to the same extent as the activation time constant. 2. The voltage dependence observed in a time constant vs. voltage relationship and a chord conductance vs. voltage relationship (activation curve), did not change significantly. 3. The gating kinetics have a similar temperature dependence in non-electrolyte solutions, showing that the basic gating mechanism did not change in these solutions and only a slight increase in the activation free energy was one of the main causes of slowing. 4. Eight non-electrolytes, formamide, ethylene glycol, glycerol, erythritol, glucose, sorbitol, sucrose and polyethylene glycol (mean molecular weight 600) were used. The amount of slowing was correlated with the gram concentration (g l-1) of non-electrolytes, but not with molar concentration (M) and solution osmolarity (osmol l-1). 5. The percentage changes of the time constant were expressed as a function of the relative change in solution viscosity, eta/eta0. The proportionality constants alpha in the relationship alpha (eta/eta0), and gamma in the relationship 100 (eta/eta0)gamma, obtained using different non-electrolytes, were close to 100% and 1, respectively. The simplest model to explain the results assumes that a slowing of a global conformational change is a consequence of sequential viscosity-dependent movements of local structures (viscosity model). 6. Values of alpha and gamma deviated frequently from those in an ideal case, i.e. 100% for alpha and 1 for gamma, and they scattered, having a tendency to decrease as a function of molecular weight. 7. The slowing was also expressed as an exponential function of the solution osmolarity. A predicted solute-inaccessible volume Va ranged (in nm3 per molecule) between 0.09 and 1.45. The value of Va increased as a logarithmic function of the molecular weight of the non-electrolyte. 8. This solute-inaccessible volume should be distributed in all hydrophilic parts of the sodium channel protein, but is not located in the channel conducting pore itself. The slowing of gating could be explained by a model in which a rate-limiting step is a hydration process that occurs after local small structural changes have exposed new, unhydrated faces (transient hydrated-states model). 9. Considering the opposite dependencies of parameters alpha (or gamma) and beta on the molecular weight, sodium channel gating is likely to reflect a combination of these two models, which are coupled in microscopic segment movements. We emphasize with this combination of models that fluctuating hydrophilic structures play an important role in determining time constants in the gating process. PMID:9023772

  4. Nucleophilic Metal Complexes as Acylation Catalysts: Solvent-Dependent

    E-print Network

    Lectka, Thomas

    is demonstrated. Surprisingly, a solvent-dependent mechanistic "switch" results in a Lewis acid-based acylation operate as Lewis acids, as Lewis bases, or less commonly as a combination of the two.1 Almost unheard acid to a Lewis base or vice versa. For example, complex transition metal salts XmYn, in which both X

  5. Theory of conformational transitions of viral shells

    NASA Astrophysics Data System (ADS)

    Guérin, Thomas; Bruinsma, Robijn

    2007-12-01

    We propose a continuum theory for the conformational transitions of viral shells. Conformational transitions of viral shells, as encountered during viral maturation, are associated with a soft mode instability of the capsid proteins [F. Tama and C. L. Brooks, J. Mol. Biol. 345(2), 299 (2005)]. The continuum theory presented here is an adaptation of the Ginzburg-Landau theory of soft-mode structural phase transitions of solids to viral shells. The theory predicts that the conformational transitions are characterized by a pronounced softening of the shell elasticity in the critical region. We demonstrate that the thermodynamics of the conformational transition can be probed quantitatively by a micromechanical atomic force microscope study. The external force can drive a capsid into a state of phase coexistence characterized by a highly nonlinear force deformation curve.

  6. Conformational Transitions in Model Silk Peptides

    Microsoft Academic Search

    Donna Wilson; Regina Valluzzi; David Kaplan

    2000-01-01

    Protein structural transitions and ?-sheet formation are a common problem both in vivo and in vitro and are of critical relevance in disparate areas such as protein processing and ?-amyloid and prion behavior. Silks provide a “databank” of well-characterized polymorphic sequences, acting as a window onto structural transitions. Peptides with conformationally polymorphic silk-like sequences, expected to exhibit an intractable ?-sheet

  7. Conformational transition of native and modified gellan.

    PubMed

    Mazen, F; Milas, M; Rinaudo, M

    1999-11-01

    This paper concerns the characterisation of native gellan by differential scanning calorimetry (DSC) and rheology. The stability of the double helix is characterised by Tm and the enthalpy of conformational change. The role of the external salt concentration is investigated; it is shown that Tm is only slightly modified. At ambient temperature, in 10(-2) M NaCl, native gellan behaves as a loose gel (G' > G''). This behaviour disappears when temperature is larger than 60 degrees C. The comparison with deacylated gellan (commercial sample) shows that the position of conformational transition is much more influenced by the salt concentration; the helical structure is less stable and the conformational transition presents a hysteresis between heating and cooling runs when the external salt concentration increases. The rheological behaviour is that corresponding to a solution (G' < G'') at ambient temperature and in 10(-2) M NaCl. When the salt excess increases, then a stronger gel is formed. The differences between the two types of samples are clearly established as well as the relations between the conformation and the rheology of the systems. PMID:10517517

  8. Conformational transitions of a weak polyampholyte.

    PubMed

    Narayanan Nair, Arun Kumar; Uyaver, Sahin; Sun, Shuyu

    2014-10-01

    Using grand canonical Monte Carlo simulations of a flexible polyelectrolyte where the charges are in contact with a reservoir of constant chemical potential given by the solution pH, we study the behavior of weak polyelectrolytes in poor and good solvent conditions for polymer backbone. We address the titration behavior and conformational properties of a flexible diblock polyampholyte chain formed of two oppositely charged weak polyelectrolyte blocks, each containing equal number of identical monomers. The change of solution pH induces charge asymmetry in a diblock polyampholyte. For diblock polyampholyte chains in poor solvents, we demonstrate that a discontinuous transition between extended (tadpole) and collapsed (globular) conformational states is attainable by varying the solution pH. The double-minima structure in the probability distribution of the free energy provides direct evidence for the first-order like nature of this transition. At the isoelectric point electrostatically driven coil-globule transition of diblock polyampholytes in good solvents is found to consist of different regimes identified with increasing electrostatic interaction strength. At pH values above or below the isoelectric point diblock chains are found to have polyelectrolyte-like behavior due to repulsion between uncompensated charges along the chain. PMID:25296835

  9. Assessing Iterative Normal Modes on Representing Protein Conformational Transitions

    Microsoft Academic Search

    Cheng Peng; Liqing Zhang

    2009-01-01

    How to capture biologically important conformational transitions from structures have been of key interest in computational biology. It is generally recognized that normal modes derived from structure-based potentials can well represent functional movements in lots of biomolecules. Recently normal mode analysis was successfully used in an iterative manner to explore protein conformational transition pathway, but the impact of these iterative

  10. Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations

    E-print Network

    de Groot, Bert

    Conformational Transitions upon Ligand Binding: Holo- Structure Prediction from Apo Conformations design. Hence, if only an unbound (apo) structure is available distinct from the ligand of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration

  11. Atomistic simulations of the MS2 coat protein conformational transition

    NASA Astrophysics Data System (ADS)

    Perkett, Matthew; Pontiggia, Francesco; Hagan, Michael

    2012-02-01

    During the replication of many viruses, hundreds to thousands of proteins self-assemble to form a protective protein coat, called a capsid, around the viral nucleic acid. Often these proteins have identical amino acid sequences with slightly different, or quasi-equivalent, conformations, which join in precise spatial arrangements. Although the structure of completed capsids is known to atomic resolution, little is known about the assembly intermediates and how protein conformations are selected during assembly. In this talk, we will use all-atom simulations to investigate how protein-RNA interactions guide conformational transitions of capsid proteins from the single-stranded RNA bacteriophage MS2. Since conformational changes occur on timescales which are not accessible to all-atom simulations, we use enhanced sampling methods to sample probable transition pathways and corresponding free energy profiles. Specifically, we will present free energy profiles associated with the MS2 capsid protein conformation in the presence and absence of RNA.

  12. Mapping the conformational transition in Src activation by cumulating the information from

    E-print Network

    Yang, Sichun

    Mapping the conformational transition in Src activation by cumulating the information from multiple solvent is combined together to assemble a connectivity map of the conformational transition. Two. conformational landscape connectivity map intermediate kinase inhibitor Non-receptor Src tyrosine kinases

  13. Water-Peptide Dynamics during Conformational Transitions Dmitry Nerukh*,

    E-print Network

    Nerukh, Dmitry

    Water-Peptide Dynamics during Conformational Transitions Dmitry Nerukh*, and Sergey Karabasov are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water

  14. Solvent-Dependent Lithium Bridging in Allenyl-Propargyllithium Reagents

    E-print Network

    Reich, Hans J.

    , the equilib- rium isotope shifts are independent of the number of bonds separating the site of isotopicSolvent-Dependent Lithium Bridging in Allenyl-Propargyllithium Reagents Hans J. Reich* and Jennifer and propargyl isomers have been studied by the Saunders isotope perturbation technique. Variable equilibrium

  15. Conformal microstrip patch circular array with orthogonal conformal stripline feed and all-angle transition

    Microsoft Academic Search

    R. T. Cock; R. D. Cook

    1997-01-01

    A prototype Ku-band, 32-element, circular microstrip patch array connected to a conformal stripline feed with an orthogonal all-angle transition was designed, fabricated and tested. The low cost antenna uses standard printed circuit technology. The antenna consists of a stripline feed conformally encased in a metal ring orthogonal to microstrip patch radiating elements which are etched on the front Duriod 5880

  16. Intrinsic correlations between dynamic heterogeneity and conformational transition in polymers during glass transition.

    PubMed

    Nie, Yijing; Ye, Xubo; Zhou, Zhiping; Yang, Wenming; Tao, Lu

    2014-08-21

    We performed dynamic Monte Carlo simulation to investigate the micro-structural evolutions of polymers during glass transition. A new parameter, probability of segment movement, was proposed to probe the heterogeneity of local segment dynamics. A microscopic picture of spatial distribution of dynamic heterogeneity was obtained. A conformational transition was also detected. Further analysis demonstrated the existence of intrinsic links between the two phenomena. Compared with chain segments with gauche-conformation, segments with trans-conformation were packed more closely, and thus easier to be frozen. This difference in segmental mobility between the gauche- and trans-conformations results in the emergence of dynamic heterogeneity. Our simulation results reveal the underlying mechanism controlling the dynamic heterogeneity during glass transition from the viewpoint of local conformational changes. PMID:25149811

  17. Conformational transitions in semiflexible dendrimers induced by bond orientations

    NASA Astrophysics Data System (ADS)

    Kumar, Amit; Biswas, Parbati

    2012-09-01

    We theoretically investigate the conformational properties of semiflexible dendrimers where the semiflexibility is implemented by topologically restricting the bond directions and orientations of the respective bond vectors. Molecular size (radius of gyration, Rg and Wiener index, W), shape factor ?, configurational free energy F, and the static structure factor, S(q) of semiflexible dendrimers are analyzed as a function of the bond orientation angle, ?. The size of the lower generation dendrimers decreases with increasing ? throughout the entire range of ?, ? ? (0, ?). The higher generation dendrimers show a non-uniform behavior, for compressed conformations the size decreases with increasing ?, while for the expanded ones it increases with the increase in ?. A conformational transition occurs for the higher generation dendrimers from the limiting value of the hard sphere to an ideal chain with the change in ?. This conformational transition at ? = ?/2 is also reflected in the configurational free energy. The configurational free energy exhibits a discontinuous behavior with the variation of ?, and this discontinuity occurs at ? = ?/2. However, no such conformational transition is observed with the variation of the bond direction angle, ?, generation, G and functionality, f of the semiflexible dendrimers. The flexible dendrimer, i.e., at ? = ?/2 is flanked between the compressed and expanded conformations of the semiflexible dendrimers resembling a hard sphere. The Kratky plot of the structure factor of all conformations quantitatively match with the results obtained from experiments and simulations in the low q-region in respect to the position of the major Kratky peak. For higher wave numbers, the Kratky plots for all conformations of semiflexible dendrimers agree with earlier theoretical results of model dendrimers [R. La Ferla, J. Chem. Phys. 106, 688 (1997), 10.1063/1.473405; F. Ganazzoli, R. La Ferla, and G. Raffaini, Macromolecules 34, 4222 (2001), 10.1021/ma001613z] but are in sharp contrast to the experimental [S. Rathgeber et al., J. Chem. Phys. 117, 4047 (2002), 10.1063/1.1493771; S. Rathgeber, T. Pakula, and V. Urban, J. Chem. Phys. 121, 3840 (2004), 10.1063/1.1768516] and simulated [M. L. Mansfield and L. I. Klushin, Macromolecules 26, 4262 (1993), 10.1021/ma00068a029] scattering curves for the higher generation dendrimers. All compressed conformations (0 < ? < ?/2) behave as compact hard spheres, while the expanded conformations (?/2 < ? < ?) are relatively more open, partially decongesting the steric crowding among the monomers with increasing ?.

  18. Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

    PubMed Central

    McCammon, J. Andrew

    2009-01-01

    Ras mediates signaling pathways controlling cell proliferation and development by cycling between GTP- and GDP-bound active and inactive conformational states. Understanding the complete reaction path of this conformational change and its intermediary structures is critical to understanding Ras signaling. We characterize nucleotide-dependent conformational transition using multiple-barrier-crossing accelerated molecular dynamics (aMD) simulations. These transitions, achieved for the first time for wild-type Ras, are impossible to observe with classical molecular dynamics (cMD) simulations due to the large energetic barrier between end states. Mapping the reaction path onto a conformer plot describing the distribution of the crystallographic structures enabled identification of highly populated intermediate structures. These structures have unique switch orientations (residues 25–40 and 57–75) intermediate between GTP and GDP states, or distinct loop3 (46–49), loop7 (105–110), and ?5 C-terminus (159–166) conformations distal from the nucleotide-binding site. In addition, these barrier-crossing trajectories predict novel nucleotide-dependent correlated motions, including correlations of ?2 (residues 66–74) with ?3-loop7 (93–110), loop2 (26–37) with loop10 (145–151), and loop3 (46–49) with ?5 (152–167). The interconversion between newly identified Ras conformations revealed by this study advances our mechanistic understanding of Ras function. In addition, the pattern of correlated motions provides new evidence for a dynamic linkage between the nucleotide-binding site and the membrane interacting C-terminus critical for the signaling function of Ras. Furthermore, normal mode analysis indicates that the dominant collective motion that occurs during nucleotide-dependent conformational exchange, and captured in aMD (but absent in cMD) simulations, is a low-frequency motion intrinsic to the structure. PMID:19300489

  19. Targeted Molecular Dynamics Simulation of Conformational Change-Application to the T ? R Transition in Insulin

    Microsoft Academic Search

    J. Schlitter; M. Engels; P. Krtiger; E. Jacoby; A. Wollmer

    1993-01-01

    A novel method to calculate transition pathways between two known protein conformations is presented. It is based on a molecular dynamics simulation starting from one conformational state as initial structure and using the other for a directing constraint. The method is exemplified with the T ? R transition of insulin. The most striking difference between these conformational states is that

  20. Conformation transitions of eukaryotic polyribosomes during multi-round translation

    PubMed Central

    Afonina, Zhanna A.; Myasnikov, Alexander G.; Shirokov, Vladimir A.; Klaholz, Bruno P.; Spirin, Alexander S.

    2015-01-01

    Using sedimentation and cryo electron tomography techniques, the conformations of eukaryotic polyribosomes formed in a long-term cell-free translation system were analyzed over all the active system lifetime (20–30 translation rounds during 6–8 h in wheat germ extract at 25°C). Three distinct types of the conformations were observed: (i) circular polyribosomes, varying from ring-shaped forms to circles collapsed into double rows, (ii) linear polyribosomes, tending to acquire planar zigzag-like forms and (iii) densely packed 3D helices. At the start, during the first two rounds of translation mostly the circular (ring-shaped and double-row) polyribosomes and the linear (free-shaped and zigzag-like) polyribosomes were formed (‘juvenile phase’). The progressive loading of the polyribosomes with translating ribosomes induced the opening of the circular polyribosomes and the transformation of a major part of the linear polyribosomes into the dense 3D helices (‘transitional phase’). After 2 h from the beginning (about 8–10 rounds of translation) this compact form of polyribosomes became predominant, whereas the circular and linear polyribosome fractions together contained less than half of polysomal ribosomes (‘steady-state phase’). The latter proportions did not change for several hours. Functional tests showed a reduced translational activity in the fraction of the 3D helical polyribosomes. PMID:25520190

  1. Thermally induced conformational transitions in nascent branched amphiphilic peptide capsules.

    PubMed

    Sukthankar, Pinakin; Whitaker, Susan K; Garcia, Macy; Herrera, Alvaro; Boatwright, Mark; Prakash, Om; Tomich, John M

    2015-03-17

    Branched amphiphilic peptide capsules (BAPCs) are biocompatible, bilayer delimited polycationic nanospheres that spontaneously form at room temperature through the coassembly of two amphiphilic branched peptides: bis(FLIVI)-K-K4 and bis(FLIVIGSII)-K-K4. BAPCs are readily taken up by cells in culture, where they escape and/or evade the endocytic pathway and accumulate in the perinuclear region, persisting there without apparent degradation or extravasation. Drugs, small proteins, and solutes as well as ? particle emitting radionuclides are stably encapsulated for extended periods of time. BAPC formation at room temperature proceeds via a fusogenic process and after 48 h a range of BAPCs sizes are observed, from 50 nm to a few microns in diameter. It was previously reported that cooling BAPCs from 25 to 4 °C and then back to 25 °C eliminated their fusogenic property. In this report, biophysical techniques reveal that BAPCs undergo thermosensitive conformational transitions as a function of both time and temperature and that the properties of BAPCs vary based on the temperature of assembly. The solvent dissociation properties of BAPCs were studied as well as the contributions of specific amino acid residues to the observed conformations. The roles of the potential stabilizing forces present within the bilayer that bestow the unusal stability of the BAPCs are discussed. Ultimately this study presents revised assembly protocols for preparing BAPCs with discrete sizes and solvent-induced extravasation properties. PMID:25719598

  2. Molecular Dynamical Approach to the Conformational Transition in Peptide Nanorings and Masato Teranishi, Hajime Okamoto, and Kyozaburo Takeda*

    E-print Network

    Southern California, University of

    Molecular Dynamical Approach to the Conformational Transition in Peptide Nanorings and NanotubesVed: October 30, 2008 We study the conformational transition in D,L-peptide nanorings (PNRs) and nanotubes the transition process from E-type to B-type and vice versa. The conformational transition occurs easily from E

  3. Effect of electrolyte concentration on DNA AB conformational transition: An unrestrained molecular dynamics simulation study

    Microsoft Academic Search

    Fujimoto Shintaro; Yang-Xin Yu

    2010-01-01

    The DNA conformational transition depends on both the DNA sequences and environment such as solvent as well as electrolyte in the solution. This paper uses the AMBER8 package to investigate the electrolyte concentration influence on the dynamics of the A --> B conformational transition of DNA duplex d(CGCGAATTCGCG)2. The results from the restrained molecular dynamics (MD) simulations indicate that the

  4. Investigating conformational transitions of proteins by coarse-grained elastic network models

    NASA Astrophysics Data System (ADS)

    Tekpinar, Mustafa

    Proteins are large molecular machines. Many of these machines carry out conformational transitions to perform function. It is very difficult to determine all metastable protein conformations experimentally. Therefore, computational methods have been developed to investigate metastable protein conformations and conformational transitions. For most of proteins, atomistic molecular dynamics cannot reach the time scales of conformational transitions, which are typically beyond microseconds. The large size of proteins is another obstacle in atomistic molecular dynamics simulations. Coarse-grained elastic network models can provide an alternative to overcome the time scale and size problems. In this dissertation, we have investigated conformational transitions of proteins by using modified elastic network models. These models can be applied in two ways. First, they allow us to analyze conformational transition pathways and deduce the dynamic order of structural events. Second, they enable us to build models for unknown protein conformations by incorporating experimental data. For the first application, a transition pathway modeling method called iENM will be presented in Chapter 2. For the second application, a flexible fitting method based on small angle X-ray scattering (SAXS) data will be discussed in Chapter 3. Our methods will be compared to alternative methods and they will be validated by experimental data.

  5. Sequence Recognition of DNA by Protein-Induced Conformational Transitions

    SciTech Connect

    Watkins, Derrick; Mohan, Srividya; Koudelka, Gerald B.; Williams, Loren Dean (GIT); (SUNYB)

    2010-11-09

    The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA functional groups) and indirect readout (sensing DNA conformation and deformability). Previously we showed that the P22 c2 repressor N-terminal domain (P22R NTD) forces the central non-contacted 5{prime}-ATAT-3{prime} sequence of the DNA operator into the B{prime} state, a state known to affect DNA hydration, rigidity and bending. Usually the B{prime} state, with a narrow minor groove and a spine of hydration, is reserved for A-tract DNA (TpA steps disrupt A-tracts). Here, we have co-crystallized P22R NTD with an operator containing a central 5{prime}-ACGT-3{prime} sequence in the non-contacted region. C {center_dot} G base pairs have not previously been observed in the B{prime} state and are thought to prevent it. However, P22R NTD induces a narrow minor groove and a spine of hydration to 5{prime}-ACGT-3{prime}. We observe that C {center_dot} G base pairs have distinctive destabilizing and disordering effects on the spine of hydration. It appears that the reduced stability of the spine results in a higher energy cost for the B to B{prime} transition. The differential effect of DNA sequence on the barrier to this transition allows the protein to sense the non-contacted DNA sequence.

  6. Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

    Microsoft Academic Search

    Nigar Kantarci-Carsibasi; Turkan Haliloglu; Pemra Doruker

    2008-01-01

    Conformational transitions between open\\/closed or free\\/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative

  7. Conformational transition in signal transduction: metastable States and transition pathways in the activation of a signaling protein.

    PubMed

    Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

    2015-06-01

    Signal transduction is of vital importance to the growth and adaptation of living organisms. The key to understand mechanisms of biological signal transduction is elucidation of the conformational dynamics of its signaling proteins, as the activation of a signaling protein is fundamentally a process of conformational transition from an inactive to an active state. A predominant form of signal transduction for bacterial sensing of environmental changes in the wild or inside their hosts is a variety of two-component systems, in which the conformational transition of a response regulator (RR) from an inactive to an active state initiates responses to the environmental changes. Here, RR activation has been investigated using RR468 as a model system by extensive unbiased all-atom molecular dynamics (MD) simulations in explicit solvent, starting from snapshots along a targeted MD trajectory that covers the conformational transition. Markov state modeling, transition path theory, and geometric analyses of the wealth of the MD data have provided a comprehensive description of the RR activation. It involves a network of metastable states, with one metastable state essentially the same as the inactive state and another very similar to the active state that are connected via a small set of intermediates. Five major pathways account for >75% of the fluxes of the conformational transition from the inactive to the active-like state. The thermodynamic stability of the states and the activation barriers between states are found, to identify rate-limiting steps. The conformal transition is initiated predominantly by movements of the ?3?3 loop, followed by movements of the ?4?4-loop and neighboring ?4 helix region, and capped by additional movements of the ?3?3 loop. A number of transient hydrophobic and hydrogen bond interactions are revealed, and they may be important for the conformational transition. PMID:25945797

  8. Identification of key residues for protein conformational transition using elastic network model

    NASA Astrophysics Data System (ADS)

    Su, Ji Guo; Jin Xu, Xian; Hua Li, Chun; Chen, Wei Zu; Wang, Cun Xin

    2011-11-01

    Proteins usually undergo conformational transitions between structurally disparate states to fulfill their functions. The large-scale allosteric conformational transitions are believed to involve some key residues that mediate the conformational movements between different regions of the protein. In the present work, a thermodynamic method based on the elastic network model is proposed to predict the key residues involved in protein conformational transitions. In our method, the key functional sites are identified as the residues whose perturbations largely influence the free energy difference between the protein states before and after transition. Two proteins, nucleotide binding domain of the heat shock protein 70 and human/rat DNA polymerase ?, are used as case studies to identify the critical residues responsible for their open-closed conformational transitions. The results show that the functionally important residues mainly locate at the following regions for these two proteins: (1) the bridging point at the interface between the subdomains that control the opening and closure of the binding cleft; (2) the hinge region between different subdomains, which mediates the cooperative motions between the corresponding subdomains; and (3) the substrate binding sites. The similarity in the positions of the key residues for these two proteins may indicate a common mechanism in their conformational transitions.

  9. Capturing transition paths and transition states for conformational rearrangements in the ribosome.

    PubMed

    Noel, Jeffrey K; Chahine, Jorge; Leite, Vitor B P; Whitford, Paul Charles

    2014-12-16

    To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-transfer RNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. Although a commonly used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome. PMID:25517153

  10. Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

    NASA Astrophysics Data System (ADS)

    Noel, Jeffrey; Chahine, Jorge; Leite, Vitor; Whitford, Paul

    2015-03-01

    To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-tRNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally-accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. While a currently-used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome. More details can be found at doi:10.1529/biophysj.106.090944.

  11. Monte Carlo analysis of conformational transitions in superhelical DNA Hongzhi Sun

    E-print Network

    Benham, Craig J.

    Monte Carlo analysis of conformational transitions in superhelical DNA Hongzhi Sun Department August 1995 Metropolis­Monte Carlo algorithms are developed to analyze the strand separation transition the results of Monte Carlo calculations that use shuffling operations are compared with those from statistical

  12. Generating conformational transitions using the euclidean distance matrix.

    PubMed

    Li, Xiao-Bo; Burkowski, Forbes

    2015-03-01

    Elastic network interpolation (ENI) is an efficient method for generating intermediate conformations between two end protein conformations. Its current formulation uses interatomic distance. We show how this can be generalized to interatomic distances-squared. This generalization is part of an effort to study protein dynamics on the set of positive semidefinite (PSD) matrices, which has a rich mathematical structure. We use lattice structures to test this interpolation scheme, and discuss some limitations observed. We conclude with some suggestions for future research. PMID:25608309

  13. The effect of salt concentration on DNA conformation transition: a molecular-dynamics study

    Microsoft Academic Search

    Chen Song; Yueyuan Xia; Mingwen Zhao; Xiangdong Liu; Feng Li; Yanju Ji; Boda Huang; Yanyan Yin

    2006-01-01

    We performed three 3-ns molecular dynamics simulations of d(CGCGAATTCGCG)2 using the AMBER 8 package to determine the effect of salt concentration on DNA conformational transitions. All the simulations\\u000a were started with A-DNA, with different salt concentrations, and converged with B-DNA with similar conformational parameters.\\u000a However, the dynamic processes of the three MD simulations were very different. We found that the

  14. Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

    NASA Astrophysics Data System (ADS)

    Zhang, Zheling; Huang, Weimin; Wang, Erkang; Dong, Shaojun

    2003-01-01

    Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

  15. Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels

    PubMed Central

    Mowrey, David; Cheng, Mary Hongying; Liu, Lu Tian; Willenbring, Dan; Lu, Xinghua; Wymore, Troy; Xu, Yan; Tang, Pei

    2013-01-01

    The anesthetic propofol inhibits the currents of the homo-pentameric ligand-gated ion channel GLIC, yet the crystal structure of GLIC with five propofol molecules bound symmetrically shows an open-channel conformation. To address this dilemma and determine if symmetry of propofol binding sites affects the channel conformational transition, we performed a total of 1.5 As of molecular dynamics simulations for different GLIC systems with propofol occupancies of 0, 1, 2, 3, and 5. GLIC without propofol binding or with five propofol molecules bound symmetrically showed similar channel conformation and hydration status over multiple replicates of 100-ns simulations. In contrast, asymmetric binding to one, two or three equivalent sites in different subunits accelerated the channel dehydration, which was accompanied by increased conformational heterogeneity of the pore and shifted the lateral and radial tilting angles of the pore-lining TM2 towards a closed-channel conformation. The results differentiate two groups of systems based on the propofol binding symmetry. The difference between symmetric and asymmetric groups is correlated with the variance in the propofol-binding cavity adjacent to the hydrophobic gate and the force imposed by the bound propofol. Asymmetrically bound propofol produced greater variance in the cavity size that could further elevate the conformation heterogeneity. The force trajectory generated by propofol in each subunit over the course of a simulation exhibits an ellipsoidal shape, which has the larger component tangential to the pore. Asymmetric propofol binding creates an unbalanced force that expedites the channel conformation transitions. The findings from this study not only suggest that asymmetric binding underlies the propofol functional inhibition of GLIC, but also advocate for the role of symmetry breaking in facilitating channel conformational transitions. PMID:23339564

  16. Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding

    E-print Network

    Dai, Yang

    Constrained Proper Sampling of Conformations of Transition State Ensemble during Protein Folding) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al40 to study TSE to understand how proteins fold to its native state8,29,37 . Protein folding is a complex process that involves

  17. Mapping the structure and conformational movements of proteins with transition metal ion FRET

    E-print Network

    Cai, Long

    Mapping the structure and conformational movements of proteins with transition metal ion FRET of most allosteric proteins are unknown. Here we report that fluorescence resonance energy transfer (FRET structural rearrangements in proteins. This method provides several key advantages over classical FRET

  18. Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.

    PubMed

    Das, Avisek; Gur, Mert; Cheng, Mary Hongying; Jo, Sunhwan; Bahar, Ivet; Roux, Benoît

    2014-04-01

    Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. PMID:24699246

  19. Solvent-dependent optical limiting response of platinum nanoparticles stabilized by [60] fullerene derivative

    NASA Astrophysics Data System (ADS)

    Gao, Y. C.; He, C. Y.

    2015-05-01

    The optical limiting performance of platinum nanoparticle protected by C60 derivative in chloroform, ethanol and dimethylformamide (DMF) was measured with 532nm, 8ns duration laser pulses. Experiments showed that the optical limiting is solvent-dependent. The origins and solvent effect of the optical limiting were analyzed. It was proposed that the absorption-induced scattering is the main mechanism causing the optical limiting behavior and solvent effect.

  20. A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition

    NASA Astrophysics Data System (ADS)

    Dalgicdir, Cahit; Sensoy, Ozge; Peter, Christine; Sayar, Mehmet

    2013-12-01

    One of the major challenges in the development of coarse grained (CG) simulation models that aim at biomolecular structure formation processes is the correct representation of an environment-driven conformational change, for example, a folding/unfolding event upon interaction with an interface or upon aggregation. In the present study, we investigate this transferability challenge for a CG model using the example of diphenylalanine. This dipeptide displays a transition from a trans-like to a cis-like conformation upon aggregation as well as upon transfer from bulk water to the cyclohexane/water interface. Here, we show that one can construct a single CG model that can reproduce both the bulk and interface conformational behavior and the segregation between hydrophobic/hydrophilic medium. While the general strategy to obtain nonbonded interactions in the present CG model is to reproduce solvation free energies of small molecules representing the CG beads in the respective solvents, the success of the model strongly depends on nontrivial decisions one has to make to capture the delicate balance between the bonded and nonbonded interactions. In particular, we found that the peptide's conformational behavior is qualitatively affected by the cyclohexane/water interaction potential, an interaction that does not directly involve the peptide at all but merely influences the properties of the hydrophobic/hydrophilic interface. Furthermore, we show that a small modification to improve the structural/conformational properties of the CG model could dramatically alter the thermodynamic properties.

  1. Solid-to-hybrid transitioning armature railgun with non-conforming-to-prejudice bore profile

    DOEpatents

    Solberg, Jerome Michael

    2012-12-04

    An improved railgun, railgun barrel, railgun projectile, and railgun system for accelerating a solid-to-hybrid transitioning armature projectile using a barrel having a bore that does not conform to a cross-sectional profile of the projectile, to contact and guide the projectile only by the rails in a low pressure bore volume so as to minimize damage, failure, and/or underperformance caused by plasma armatures, insulator ablation, and/or restrikes.

  2. Molecular dynamical approach to the conformational transition in peptide nanorings and nanotubes.

    PubMed

    Teranishi, Masato; Okamoto, Hajime; Takeda, Kyozaburo; Nomura, Ken-ichi; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya; Shimojo, Fuyuki

    2009-02-01

    We study the conformational transition in d,l-peptide nanorings (PNRs) and nanotubes (PNTs) computationally based on the total energy calculation. Ab initio energy calculation has been carried out to investigate the static states of PNRs, whereas the molecular dynamics (MD) calculation has been employed to examine PNRs' dynamical states. We, then, discuss the time-dependent (TD) feature via the transition process from E-type to B-type and vice versa. The conformational transition occurs easily from E-type equatorial (Eeq) to B-type axial (Bax) but is unreversible for the opposite direction because of a larger activation energy. The TD tracing of the two dihedral angles in the individual amino acid residues reveals that the conformational change propagates along the peptide skeleton ring nearly at the sound velocity. We further expand our study to the tubular forms and reveal that the PNT has an ability to produce the two kinds of homogeneous tubes, being composed of E rings (E-tube) and of B rings (B-tube), and also that these two PNRs should be mixed to produce a binary alloyed PNT. PMID:19133731

  3. The solvent dependent shift of the amide I band of a fully solvated peptide in methanol/water mixtures as a local probe for the solvent composition in the peptide/solvent interface

    SciTech Connect

    Gnanakaran, S [Los Alamos National Laboratory

    2008-01-01

    We determine the shift and line-shape of the amide I band of a model AK-peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR-spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, taking both the effect of hydrogen bonding, as well as intramolecular vibrational coupling into account. We consider a single isolated AK-peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, varying from pure water to the pure methanol solvent, a monotonous blue-shift of the IR amide I band of about 8 wavenumbers is observed. The shift is found to be caused by two counter-compensating effects: An intramolecular red-shift of about 1.2 wavenumbers, due to stronger intramolecular hydrogen-bonding in a methanol-rich environment. Dominating, however, is the intermolecular solvent-dependent blue-shift of about 10 wavenumbers, being attributed to the less effective hydrogen bond donor capabilities of methanol compared to water. The importance of solvent-contribution to the IR-shift, as well as the significantly different hydrogen formation capabilities of water and methanol make the amide I band sensitive to composition changes in the local environment close the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK-peptide case they observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent-interface, supposedly promoted by the partially hydrophobic character of the AK-peptide's solvent accessible surface.

  4. An investigation of the solvent dependence on the ultrafast intersystem crossing kinetics of xanthone

    NASA Astrophysics Data System (ADS)

    Cavaleri, Joseph J.; Prater, Katherine; Bowman, Robert M.

    1996-09-01

    The photophysics of xanthone in solution are measured using femtosecond pump-probe techniques. A kinetic model which includes intersystem crossing from both the 1?? ? and 1n? ? electronic states accurately represents the non-single exponential growth of the triplet-triplet absorption after excitation into the 1?? ? state at 310 nm. The intersystem crossing rate constants are consistent with an 'inverse' gap effect due to solvent polarity induced shifts in the electronic states. The branching between intersystem crossing from the 1?? ? and 1n? ? electronic states is also solvent dependent and is determined by the rate constant for internal conversion in the singlet electronic state.

  5. The 'order-to-disorder' conformational transition in CD44 protein: an umbrella sampling analysis.

    PubMed

    Plazinski, Wojciech; Knys-Dzieciuch, Agnieszka

    2013-09-01

    The molecule of CD44, a membrane protein being the major cell surface receptor for hyaluronan, is postulated to undergo the conformational rearrangement called the 'order-to-disorder' transition. The experimental studies suggest that the Tyr161 residue is crucial for maintaining the equilibrium between the 'ordered' (O) and 'partially disordered' (PD) forms of CD44. The molecular modeling study based on the umbrella sampling protocol was carried out separately for the wild-type CD44 and Tyr161Ala mutant in order to gain more insight into the molecular mechanism of the O-PD transition and to clarify the role of the Tyr161 amino acid residue. The calculated free energy profiles associated with the initial stages of the O-PD conformational transition allow to identify the crucial steps of this process and their molecular details. The differences between the wild-type CD44 and the Tyr161Ala mutant are very insignificant which allows for speculating that, surprisingly, the role of Tyr161 in the O-PD transition is not connected with disrupting the attractive Glu48-Tyr161 and Leu52-Tyr161 interactions but with other types of (unknown yet) interactions located outside the ?7-?8 loop or with the existence of the PD-like structure in which the terminal lobe remains located under the ?7-?8 loop. PMID:24012974

  6. Perturbation of planarity as the possible mechanism of solvent-dependent variations of fluorescence quantum yield in 2-aryl-3-hydroxychromones

    NASA Astrophysics Data System (ADS)

    Klymchenko, Andrey S.; Pivovarenko, Vasyl G.; Demchenko, Alexander P.

    2003-03-01

    In order to understand the unexpectedly low quantum yields of 3-hydroxyflavones (3-HFs) in certain solvents, such as acetonitrile or ethyl acetate, the comparative study of solvent-dependent properties of parent 3-HF, 2-furyl-3-hydroxychromone and 2-benzofuryl-3-hydroxychromone derivatives have been performed. The results suggest that the formation of intermolecular hydrogen bond of 3-hydroxy group with the solvent favors non-planar conformations of phenyl group with respect to chromone system. This steric hindrance is not observed in the case of furan- and benzofuran-substituted 3-hydroxychromones (3-HCs). These results suggesting a new strategy for dramatic improvement of fluorescence properties of 3-HCs as two-wavelength ratiometric fluorescence probes.

  7. Solvent-dependent luminescent Cu(I) framework based on 5-(4-pyridyl)tetrazole

    SciTech Connect

    Wang Fei; Yu Rongmin; Zhang Qisheng; Zhao Zhenguo; Wu Xiaoyuan; Xie Yiming; Qin Li; Chen Shanci [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35002 (China); Lu Canzhong, E-mail: czlu@fjirsm.ac.c [State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35002 (China)

    2009-09-15

    A new Cu(IOTA) coordination compound, Cu{sub 4}(L){sub 4}.2EtOH (1), has been obtained from the solvothermal reaction of CuBr, HL (L=5-(4-pyridyl) tetrazole), EtOH and NH{sub 3}.H{sub 2}O. The structure determination reveals that 1 has a 2D network, where each Cu(I) atom adopts a trigonal coordination mode. The 2D networks stacked in an ABAB sequence through the pi-pi interaction to form a 3D supramolecular framework, giving a 1D channel along the b-axis. The TGA and powder XRD measurements reveal that the framework is stable after removal of the guest molecules. Gas (N{sub 2}) adsorption measurement was carried out for the framework. Framework 1 shows II sorption profile with N{sub 2}, which indicates that N{sub 2} molecules cannot diffuse into the micropore and only surface adsorption occurs. The photoluminescent research shows that compound 1 displays an interesting solvent-dependent luminescence. - Abstract: A new Cu(I) compound, Cu{sub 4}(L){sub 4}.2EtOH (1) (L=5-(4-pyridyl) tetrazole), was synthesized under solvothermal method, which displays an interesting solvent-dependent luminescence. Display Omitted

  8. An Investigation of the Solvent Dependence on the Ultrafast Intersystem Crossing Kinetics of Xanthone

    NASA Astrophysics Data System (ADS)

    Cavaleri, Joseph J.; Prater, Katherine; Bowman, Robert M.

    1997-03-01

    The kinetics of internal conversion and intersystem crossing of xanthone in solution are measured using femtosecond pump-probe techniques. The growth of the triplet-triplet absorption is non-single exponential in nature and has a strong dependence on solvent polarity. A kinetic model which includes intersystem crossing from both the ^1 n ?^* and ^1 ? ?^* electronic states accurately represents the experimental results. The solvent dependence on the intersystem rate constants can be explained by taking into account the change in the singlet-triplet energy gap as a result of the stabilization of the ? ?^* electronic states with increasing solvent polarity. The intersystem crossing rates from the ^1 ? ?^* and ^1 n ?^* electronic states are consistent with an "inverse" gap effect where the rate constants increase as the singlet-triplet energy gap increases. Due to the proximity in energy of the singlet and triplet electronic states, the kinetics are governed by the change in the density of vibronic states resulting from a change in the singlet-triplet energy gap. The branching between intersystem crossing from the ^1 ? ?^* and ^1 n ?^* electronic states is also highly solvent dependent and is determined by the rate of internal conversion in the singlet electronic state.

  9. Conformational transitions of plasmid ds-DNA on ultrathin films of alkylamines on graphite

    NASA Astrophysics Data System (ADS)

    Falk, Caroline; Liang, Hua; Severin, Nikolai; Zhuang, Wei; Zauscher, Stefan; Rabe, Jürgen P.

    2015-03-01

    DNA replication is an important process in the human body. Replication of double-stranded (ds)-DNA requires its local melting into two single strands. DNA, when stretched in solution, overwinds and melts. This was argued to give insight onto the replication mechanism. It is difficult, however, to access the direct conformational changes during stretching in solution. Recent work demonstrated that this transition can be imaged with scanning force microscopy on a graphite surface that is coated with an alkylamine layer. ds-DNA can be controlled by an amphiphilic layer, since the DNA conformation depends on the amphiphile concentration. In particular we analyzed different DNA lengths on the same surface, and we found that at a specific concentration of octadecylamine the ds-DNA pUC19 plasmid ring splits into two single strands at one position. We will discuss methods to mark the DNA to determine the exact location at which the plasmid ring splits.

  10. Single tryptophan mutants of FtsZ: nucleotide binding/exchange and conformational transitions.

    PubMed

    Montecinos-Franjola, Felipe; James, Nicholas G; Concha-Marambio, Luis; Brunet, Juan E; Lagos, Rosalba; Monasterio, Octavio; Jameson, David M

    2014-07-01

    Cell division protein FtsZ cooperatively self-assembles into straight filaments when bound to GTP. A set of conformational changes that are linked to FtsZ GTPase activity are involved in the transition from straight to curved filaments that eventually disassemble. In this work, we characterized the fluorescence of single Trp mutants as a reporter of the predicted conformational changes between the GDP- and GTP-states of Escherichia coli FtsZ. Steady-state fluorescence characterization showed the Trp senses different environments and displays low solvent accessibility. Time-resolved fluorescence data indicated that the main conformational changes in FtsZ occur at the interaction surface between the N and C domains, but also minor rearrangements were detected in the bulk of the N domain. Surprisingly, despite its location near the bottom protofilament interface at the C domain, the Trp 275 fluorescence lifetime did not report changes between the GDP and GTP states. The equilibrium unfolding of FtsZ features an intermediate that is stabilized by the nucleotide bound in the N-domain as well as by quaternary protein-protein interactions. In this context, we characterized the unfolding of the Trp mutants using time-resolved fluorescence and phasor plot analysis. A novel picture of the structural transition from the native state in the absence of denaturant, to the solvent-exposed unfolded state is presented. Taken together our results show that conformational changes between the GDP and GTP states of FtsZ, such as those observed in FtsZ unfolding, are restricted to the interaction surface between the N and C domains. PMID:24704635

  11. Equilibrium transitions between side-chain conformations in leucine and isoleucine.

    PubMed

    Caballero, Diego; Smith, W Wendell; O'Hern, Corey S; Regan, Lynne

    2015-08-01

    Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different ?1 and ?2 dihedral angle combinations as a function of the backbone dihedral angles ? and ?. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of ?2 , the Leu side-chain bond angles ?1 and ?2 must increase, whereas to transition in ?1 , the Ile bond angles ?1 and ?2 must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design. Proteins 2015; 83:1488-1499. © 2015 Wiley Periodicals, Inc. PMID:26018846

  12. Conformational transition of polyelectrolyte chains extending over the de Gennes regime in slitlike nanochannels

    NASA Astrophysics Data System (ADS)

    Chun, Myung-Suk

    2012-09-01

    The confinement-induced conformational transitions of the polyelectrolyte chain are characterized with the coarse-grained Brownian dynamics simulations and the blob theory. Submicron-sized biopolymer xanthan is chosen as a model polyelectrolyte taking into account both flexible and semiflexible chains for comparison. Confined flexible and semiflexible chains exhibit a nonmonotonic variation in size in weak confinements, where the relative radius of gyration shows a dip and then increases when decreasing the channel width. The rigid chain, realized at low screening, exhibits a sigmoidal transition without minima in size. Major attention should be on the dependence of scaling law exponents on the screening effect of the solution in the moderate confinement of the de Gennes regime. Our findings are expected to provide useful information and new insight into the confined polyelectrolytes when relevant micro/nanochannels are designed and fabricated.

  13. Thermodynamic and conformational insights into the phase transition of a single flexible homopolymer chain using replica exchange Monte Carlo method.

    PubMed

    Wang, Lei; Li, Ningning; Xiao, Shiyan; Liang, Haojun

    2014-07-01

    The phase transition of a single flexible homopolymer chain in the limit condition of dilute solution is systematically investigated using a coarse-grained model. Replica exchange Monte Carlo method is used to enhance the performance of the conformation space exploration, and thus detailed investigation of phase behavior of the system can be provided. With the designed potentials, the coil-globule transition and the liquid-solid-like transition are identified, and the transition temperatures are measured with the conformational and thermodynamic analyses. Additionally, by extrapolating the coil-globule transition temperature, T ? , and the liquid-solid-like transition temperature T(L ? S) to the thermodynamic limit, N????, we found no "tri-critical" point in the current model. PMID:24961896

  14. Solvent Dependence of Vacuum-Dried C60 Thin-Film Transistors

    NASA Astrophysics Data System (ADS)

    Kang, Woogun; Kitamura, Masatoshi; Kamura, Masakazu; Aomori, Shigeru; Arakawa, Yasuhiko

    2012-02-01

    We demonstrated solution-processed C60 thin-film transistors with high electron mobility. C60 solutions in various organic solvents were dried in a vacuum chamber to obtain uniform thin films. While C60 solution dried under atmospheric pressure produced a large number of crystals, vacuum-dried C60 solution provided flat and uniform thin films of sufficiently high quality to fabricate thin-film transistors. In spite of amorphous-like thin-film formation, C60 transistors showed strong solvent dependence. High performance C60 thin-film transistors with field-effect mobility of 0.86 cm2 V-1 s-1, threshold voltage of 1.5 V, subthreshold slope of 0.67 V/decade and a current on/off ratio of 3.9 ×106 were obtained from 1,2,4-trichlorobenzene C60 solution.

  15. Morphologies and conformation transition of lentinan in aqueous NaOH solution.

    PubMed

    Zhang, Xufeng; Zhang, Lina; Xu, Xiaojuan

    2004-10-01

    Molecular morphologies and conformation transition of lentinan, a beta-(1-->3)-D-glucan from Lentinus edodes, were studied in aqueous NaOH solution by atomic force microscopy (AFM), viscometry, multiangle laser light scattering, and optical rotation measurements. The results revealed that lentinan exists as triple-helical chains and as single random-coil chains at NaOH concentration lower than 0.05M and higher than 0.08M, respectively. Moreover, the dramatic changes in weight-average molecular weight Mw, radius of gyration [s2](1/2), intrinsic viscosity [eta], as well as specific optical rotation at 589 nm [alpha]589 occurred in a narrow range of NaOH concentration between 0.05 and 0.08M NaOH, indicating that the helix-coil conformation transition of lentinan was carried out more easily than that of native schizophyllan and scleroglucan, and was irreversible. For the first time, we confirmed that the denatured lentinan molecule, which was dissolved in 0.15M NaOH to be disrupted into single coil chains, could be renatured as triple helical chain by dialyzing against abundant water in the regenerated cellulose tube at ambient temperature (15 degrees C). In view of the AFM image, lentinan in aqueous solution exhibited the linear, circular, and branched species of triple helix compared with native linear schizophyllan or scleroglucan. PMID:15356872

  16. Conformational and phase transitions in DNA-photosensitive surfactant solutions: Experiment and modeling.

    PubMed

    Kasyanenko, N; Lysyakova, L; Ramazanov, R; Nesterenko, A; Yaroshevich, I; Titov, E; Alexeev, G; Lezov, A; Unksov, I

    2015-02-01

    DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 mM NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown. © 2014 Wiley Periodicals, Inc. Biopolymers 103: 109-122, 2015. PMID:25302479

  17. Inherent flexibility and protein function: The open/closed conformational transition in the N-terminal domain of calmodulin

    NASA Astrophysics Data System (ADS)

    Tripathi, Swarnendu; Portman, John J.

    2008-05-01

    The key to understand a protein's function often lies in its conformational dynamics. We develop a coarse-grained variational model to investigate the interplay between structural transitions, conformational flexibility, and function of the N-terminal calmodulin domain (nCaM). In this model, two energy basins corresponding to the ``closed'' apo conformation and ``open'' holo conformation of nCaM are coupled by a uniform interpolation parameter. The resulting detailed transition route from our model is largely consistent with the recently proposed EF?-scaffold mechanism in EF-hand family proteins. We find that the N-terminal parts of the calcium binding loops shows higher flexibility than the C-terminal parts which form this EF?-scaffold structure. The structural transition of binding loops I and II are compared in detail. Our model predicts that binding loop II, with higher flexibility and earlier structural change than binding loop I, dominates the open/closed conformational transition in nCaM.

  18. Conformational transition of membrane-associated terminally-acylated HIV-1 Nef

    PubMed Central

    Akgun, Bulent; Satija, Sushil; Nanda, Hirsh; Pirrone, Gregory F.; Shi, Xiaomeng; Engen, John R.; Kent, Michael S.

    2013-01-01

    Many proteins are post-translationally modified by acylation targetting them to lipid membranes. While methods such as X-ray crystallography and NMR are available to determine the structure of folded proteins in solution, the precise position of folded domains relative to a membrane remains largely unknown. We used neutron and X-ray reflection methods to measure the displacement of the core domain of HIV Nef from lipid membranes upon insertion of the N-terminal myristate group. Nef is one of several HIV-1 accessory proteins and an essential factor in AIDS progression. Upon insertion of the myristate and residues from the N-terminal arm, Nef transitions from a closed to open conformation that positions the core domain 70 Å from the lipid headgroups. This work rules out speculation that the Nef core remains closely associated with the membrane to optimize interactions with the cytoplasmic domain of MHC-1. PMID:24035710

  19. Diepoxide-triggered conformational transition of silk fibroin: formation of hydrogels.

    PubMed

    Karakutuk, Ilknur; Ak, Fatih; Okay, Oguz

    2012-04-01

    Silk fibroin hydrogels with tunable properties could be obtained from aqueous fibroin solutions (4.2 w/v %) in a short period of time. This was achieved by the addition of ethylene glycol diglycidyl ether (EGDE) into the reaction solution. Introduction of EGDE cross-links between the fibroin molecules decreases the mobility of the chains, which triggers the conformational transition from random-coil to ?-sheet structure and hence fibroin gelation. Dynamic rheological measurements conducted at 50 °C show the formation of strong to weak hydrogels depending on the pH of the reaction solution. Although EGDE attacks the amino groups of fibroin and forms interstrand cross-links, ?-sheets acting as physical cross-links dominate the elasticity of the hydrogels. Mechanical response of low-modulus fibroin hydrogels formed above pH 9.7 is highly nonlinear with strong strain hardening behavior (700%) arising from the alignment of the crystallizable amino acid segments. PMID:22360530

  20. Solvent-dependent properties of poly(vinylidene fluoride) monolayers at the air-water interface.

    PubMed

    Zhu, Huie; Matsui, Jun; Yamamoto, Shunsuke; Miyashita, Tokuji; Mitsuishi, Masaya

    2015-03-14

    The present work addresses the solvent-dependent properties of Langmuir films of poly(vinylidene fluoride) (PVDF) and amphiphilic poly(N-dodecylacrylamide) (pDDA) at different mixing ratios. After introducing pDDA nanosheets, PVDF Langmuir films obtain a tremendously enhanced modulus as well as high transfer ratios using the vertical dipping method caused by the support of the pDDA two-dimensional hydrogen bonding network. Brewster angle microscopy (BAM) was used to investigate PVDF monolayers at the air-water interface in situ. Spreading from different solvents, the PVDF molecules take completely different aggregation states at the air-water interface. The PVDF molecules aggregate to become large domains when spread from N-methyl-2-pyrrolidone (NMP). However, the volatile and low-polarity methylethyl ketone (MEK) made the PVDF molecules more dispersive on the water surface. This study also discovers a versatile crystallization control of PVDF homopolymer from complete ? phase (NMP) to complete ? phase (MEK) at the air-water interface, thereby eliciting useful information for further manipulation of film morphologies and film applications. PMID:25622932

  1. Distinct Conformational Transition Patterns of Noncoding 7SK snRNA and HIV TAR RNAs upon Tat Binding

    PubMed Central

    2015-01-01

    Noncoding 7SK snRNA is believed to play an important role in the recruitment of P-TEFb by viral protein Tat to stimulate HIV processive transcription. Because HIV-2 TAR RNA and 7SK both evolved to feature a dinucleotide bulge region, compared to the trinucleotide bulge for HIV-1 TAR, ultrafast time-resolved fluorescence spectroscopy has been used to probe the conformational landscape of HIV-2 TAR and 7SK-SL4 RNA to monitor the conformational changes upon Tat binding. Our studies demonstrate that both HIV-1/2 TAR and 7SK-SL4 sample heterogeneous ensembles in the free state and undergo distinct conformational transitions upon Tat binding. These findings provide exquisite knowledge on the conformational complexity and intricate mechanism of molecular recognition and pave the way for drug design and discovery that incorporate dynamics information. PMID:24422492

  2. Conformational transition pathway and free energy analyses of proteins by parallel cascade selection molecular dynamics (PaCS-MD)

    NASA Astrophysics Data System (ADS)

    Harada, Ryuhei; Nishihara, Yasutaka; Wakai, Nobuhiko; Kitao, Akio

    2014-10-01

    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) was recently proposed to generate conformational transition pathways of proteins under the condition that a certain target quantity to be reached is introduced (R. Harada and A. Kitao, J. Chem. Phys., 139, 035103 2013). In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the target quantity for the next cycle are repeated until the simulated structures move sufficiently close to the target. Conformational sampling efficiency is demonstrated in the cases of mini-protein folding/unfolding and protein large conformational transitions. The result of PaCS-MD was further utilized to calculate free energy landscape by the combination with weighted-histogram analysis method or Markov state model.

  3. Identification of the Conformational transition pathway in PIP2 Opening Kir Channels

    PubMed Central

    Li, Junwei; Lü, Shouqin; Liu, Yuzhi; Pang, Chunli; Chen, Yafei; Zhang, Suhua; Yu, Hui; Long, Mian; Zhang, Hailin; Logothetis, Diomedes E.; Zhan, Yong; An, Hailong

    2015-01-01

    The gating of Kir channels depends critically on phosphatidylinositol 4,5-bisphosphate (PIP2), but the detailed mechanism by which PIP2 regulates Kir channels remains obscure. Here, we performed a series of Targeted molecular dynamics simulations on the full-length Kir2.1 channel and, for the first time, were able to achieve the transition from the closed to the open state. Our data show that with the upward motion of the cytoplasmic domain (CTD) the structure of the C-Linker changes from a loop to a helix. The twisting of the C-linker triggers the rotation of the CTD, which induces a small downward movement of the CTD and an upward motion of the slide helix toward the membrane that pulls the inner helix gate open. At the same time, the rotation of the CTD breaks the interaction between the CD- and G-loops thus releasing the G-loop. The G-loop then bounces away from the CD-loop, which leads to the opening of the G-loop gate and the full opening of the pore. We identified a series of interaction networks, between the N-terminus, CD loop, C linker and G loop one by one, which exquisitely regulates the global conformational changes during the opening of Kir channels by PIP2. PMID:26063437

  4. Identification of the Conformational transition pathway in PIP2 Opening Kir Channels.

    PubMed

    Li, Junwei; Lü, Shouqin; Liu, Yuzhi; Pang, Chunli; Chen, Yafei; Zhang, Suhua; Yu, Hui; Long, Mian; Zhang, Hailin; Logothetis, Diomedes E; Zhan, Yong; An, Hailong

    2015-01-01

    The gating of Kir channels depends critically on phosphatidylinositol 4,5-bisphosphate (PIP2), but the detailed mechanism by which PIP2 regulates Kir channels remains obscure. Here, we performed a series of Targeted molecular dynamics simulations on the full-length Kir2.1 channel and, for the first time, were able to achieve the transition from the closed to the open state. Our data show that with the upward motion of the cytoplasmic domain (CTD) the structure of the C-Linker changes from a loop to a helix. The twisting of the C-linker triggers the rotation of the CTD, which induces a small downward movement of the CTD and an upward motion of the slide helix toward the membrane that pulls the inner helix gate open. At the same time, the rotation of the CTD breaks the interaction between the CD- and G-loops thus releasing the G-loop. The G-loop then bounces away from the CD-loop, which leads to the opening of the G-loop gate and the full opening of the pore. We identified a series of interaction networks, between the N-terminus, CD loop, C linker and G loop one by one, which exquisitely regulates the global conformational changes during the opening of Kir channels by PIP2. PMID:26063437

  5. An analysis of stable forms of CL-20: A DFT study of conformational transitions, infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Kholod, Yana; Okovytyy, Sergiy; Kuramshina, Gulnara; Qasim, Mohammad; Gorb, Leonid; Leszczynski, Jerzy

    2007-10-01

    The most stable forms of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) were analyzed at the B3LYP/6-31G+(d,p) level of theory. The mechanism of conformational transformations was clarified. The activation energies of those transitions were found to be quite low and lie in the range 1.2-4.0 kcal mol -1. IR and Raman spectra of the studied CL-20 forms were simulated. The predicted vibrational modes were used for comparison with the experimental values. The unique peaks for each of the conformers in IR and Raman spectra were found. These peaks can be used as the "signatures" of the studied conformers and for identification of different polymorphs of CL-20 in mixtures.

  6. Autoantigenicity of human C1q is associated with increased hydrophobicity due to conformational transitions in the globular heads.

    PubMed

    Stoyanova, Vishnya; Bogoeva, Vanya; Petrova, Lidiya; Tchorbadjieva, Magdalena; Petrova, Svetla; Georgieva, Ventsislava; Georgiev, George; Deliyska, Boriana; Vasilev, Vasil; Tsacheva, Ivanka

    2015-04-21

    We analyzed the structural features of C1q that underlie its autoantigenicity by means of a model system using the amphiphilic polyzwitterion (PZ), poly(ethylene oxide-b-N,N-dimethyl(methacryloyloxyethyl) ammonium propanesulfonate) in the process of C1q immobilization. The source of anti-C1q autoantibodies was human sera from patients with Lupus Nephritis (LN). Both analyzed concentrations of PZ, 25 mM and 50 mM, were found to be applicable for inducing conformational transitions which resulted in increased recognition of C1q and the globular domain of its B polypeptide chain, designated ghB, by the LN autoantibodies. The registered conformational transitions displayed a hydrophobic enhancement of the protein microenvironment due to the presence of hydrophobic binding sites in ghB which consequently affected the autoantigenicity of the whole C1q molecule. PMID:25813365

  7. All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition

    E-print Network

    Ayako Yamada; Koji Kubo; Tonau Nakai; Kanta Tsumoto; Kenichi Yoshikawa

    2004-08-18

    Recently, it has been confirmed that long duplex DNA molecules with sizes larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an elongated coil state to a compact globule state upon the addition of various kinds of chemical species that usually induce DNA condensation. In this study, we performed a single-molecule observation on a large DNA, Lambda ZAP II DNA (ca. 41 kbp), in a solution containing RNA polymerase and substrates along with spermine, a tetravalent cation, at different concentrations, by use of fluorescence staining of both DNA and RNA. We found that transcription, or RNA production, is completely inhibited in the compact state, but is actively performed in the unfolded coil state. Such an all-or-none effect on transcriptional activity induced by the discrete conformational transition of single DNA molecules is discussed in relation to the mechanism of the regulation of large-scale genetic activity.

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

    Microsoft Academic Search

    Guo Chen; Benjamin H Mcmahon; Chang-Shung Tung

    2008-01-01

    Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from

  9. Conformational Transitions in Protein-Protein Association: Binding of Fasciculin-2 to Acetylcholinesterase

    Microsoft Academic Search

    Jennifer M. Bui; Zoran Radic; Palmer Taylor; J. Andrew McCammon

    2006-01-01

    The neurotoxin fasciculin-2 (FAS2) is a picomolar inhibitor of synaptic acetylcholinesterase (AChE). The dynamics of binding between FAS2 and AChE is influenced by conformational fluctuations both before and after protein encounter. Submicrosecond molecular dynamics trajectories of apo forms of fasciculin, corresponding to different conformational substates, are reported here with reference to the conformational changes of loop I of this three-fingered

  10. Conformational transitions of poly(dA-dT)poly(dA-dT) in ethanolic solutions.

    PubMed Central

    Vorlícková, M; Sedlácek, P; Kypr, J; Sponar, J

    1982-01-01

    Examination of circular dichroic and phosphorus nuclear magnetic resonance spectra showed that poly(dA-dT)-poly(dA-dT) exhibited an ethanol-induced transition to the A form in an Na+ containing medium like natural DNAs. A mere replacement of the Na+ by Cs+ counterions meant that the polynucleotide was with a little cooperativity transformed into a novel conformation displaying a deep negative band in the long wavelength part of the CD spectrum. The presence of very low concentration of Cs2+ shifted the midpoint of the transition to a lower content of ethanol. PMID:7177855

  11. Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

    PubMed Central

    Ovchinnikov, Victor; Karplus, Martin; Vanden-Eijnden, Eric

    2011-01-01

    A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepowerstroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS?R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. PMID:21361558

  12. Cytochrome c conformations resolved by the photon counting histogram: Watching the alkaline transition

    E-print Network

    Zare, Richard N.

    Cytochrome c conformations resolved by the photon counting histogram: Watching the alkaline-molecule sensitivity, to study pH- induced conformational changes of cytochrome c. PCH is able to distinguish different label cytochrome c through its single free cysteine with tetramethylrho- damine-5-maleimide (TMR

  13. ?-Fluorophosphonates reveal how a phosphomutase conserves transition state conformation over hexose recognition in its two-step reaction

    PubMed Central

    Jin, Yi; Bhattasali, Debabrata; Pellegrini, Erika; Forget, Stephanie M.; Baxter, Nicola J.; Cliff, Matthew J.; Bowler, Matthew W.; Jakeman, David L.; Blackburn, G. Michael; Waltho, Jonathan P.

    2014-01-01

    ?-Phosphoglucomutase (?PGM) catalyzes isomerization of ?-d-glucose 1-phosphate (?G1P) into d-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a ?-d-glucose 1,6-bisphosphate (?G16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of ?G1P deliver novel step 1 transition state analog (TSA) complexes for ?PGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the ?-d-glucopyranose ring in the ?G1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O–P bond orientation for binding the phosphate in the inert phosphate site differs by ?30° between steps 1 and 2. By contrast, the orientations for the axial O–Mg–O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ?5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of ?G16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein. PMID:25104750

  14. Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions

    E-print Network

    Kirchenbuechler, Inka; Kurniawan, Nicholas A; Koenderink, Gijsje H; Lettinga, M Paul

    2015-01-01

    While semi-flexible polymers and fibers are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behavior of entangl...

  15. Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using Allosteric Transitions in Myosin II

    E-print Network

    Thirumalai, Devarajan

    Coupling between Normal Modes Drives Protein Conformational Dynamics: Illustrations Using, University of Maryland, College Park, Maryland ABSTRACT Structure-based elastic network models (ENMs) have interactions between residues in contact in a given protein structure with a uniform force constant. To explore

  16. Molecular Dynamics Simulation of Conformational Transition and Frictional Performance Modulation of Densely Packed Self-Assembled Monolayers Based on Electrostatic Stimulation.

    PubMed

    Ma, Xiao; Shrotriya, Pranav

    2015-06-23

    Self-assembled monolayers (SAMs) terminated with functional end groups such as polyethylene glycols (PEG) have attracted considerable attention because of their unique and flexible structure that exhibits conformational transition under electrostatic stimulation. Molecular dynamics simulations are used to investigate the conformational transition and associated modulation of frictional performance of densely packed PEG-terminated SAMs subjected to electrical field stimulation. Previously reported empirical potentials and atomic charges were used to model the intrachain bonds and electrostatic and interchain interactions. Simulation results indicate that significant conformational transition is generated because of the electrostatic forces. Under positive electrical fields, PEG groups are compressed and twisted into the helical form, "gauche" state, whereas under negative electrical fields, PEG groups are stretched into the straight form, "all-trans" state. Such conformational transition may lead to substantial alteration of frictional response upon SAMs. By shallow penetration and sliding using a repulsive indenter, the SAMs under positive electrical fields exhibit a level of frictional response that is comparatively lower than those under zero and negative potentials, which may be attributed to reduced interchain space for deformation, limited conformational transition, and less energy absorption. The simulation results demonstrate that with appropriate selection of functional end groups attached to SAM backbone chains it is possible to modulate frictional performance of densely packed SAMs via electrostatic stimuli. PMID:26053128

  17. Solvent Dependence of the N-Methylacetamide Structure and Force Field

    NASA Astrophysics Data System (ADS)

    Andrushchenko, Valery; Pavel, Mat?jka; Anderson, David T.; Kaminský, Jakub; Horní?ek, Jan; Paulson, Leif O.; Bou?, Petr

    2009-08-01

    The N-methylacetamide molecule (NMA) is an important model for peptide and protein vibrational spectroscopy as it contains the main amide chromophore. In the past, some observed NMA geometry and spectral features could not be entirely explained at the harmonic level or by a single-conformer model. In particular, the spectra were found to be very dependent on molecular environment. In this work NMA Raman and infrared (IR) spectra in a variety of conditions were remeasured and simulated theoretically to separate the fundamental, dimer, and anharmonic bands. Under vacuum the MP2, MP4, and CCSD(T) wave function methods predicted a broad anharmonic potential energy well or even a double-well for the amide nitrogen out of plane motion, which density functional methods failed to reproduce. However, eventual nonplanar minima cannot support an asymmetric quantum state or explain band splittings observed in some experiments. In polar solvents the potential becomes more harmonic and the amide plane more rigid. On the other hand, solvent polarity enhances other anharmonic phenomena, such as the coupling between the carbonyl stretching (amide I) and lower frequency amide bending modes. The amide I band splitting is commonly observed experimentally. The influence of the CH3 group rotations modeled by a rigid rotor model was found to be important for explaining some features of the spectra in a solid parahydrogen matrix. At room temperature the methyl rotation contributes to a nonspecific inhomogeneous band broadening. The dependence of the amide group flexibility on the environment polarity may have interesting consequences for peptide and protein folding studies.

  18. Conformational transitions of flexible hydrophobic polyelectrolytes in solutions of monovalent and multivalent salts and their mixtures.

    PubMed

    Trotsenko, Oleksandr; Roiter, Yuri; Minko, Sergiy

    2012-04-10

    Conformations of cationic polyelectrolytes (PEs), a weak poly(2-vinylpyridine) (P2VP) and a strong poly(N-methyl-2-vinylpyridinium iodide) (qP2VP), adsorbed on mica from saline solutions in the presence of counterions of different valences are studied using in situ atomic force microscopy (AFM). Quantitative characteristics of chain conformations are analyzed using AFM images of the adsorbed molecules. The results of the statistical analysis of the chain contour reveal collapse of the PE coils when ionic strength is in a range from tens to hundreds of millimoles per kilogram and re-expansion of the coils with a further increase of ionic strength up to a region of the saturated saline solutions. The competition between monovalent and multivalent counterions simultaneously present in solutions strongly affects conformations of PE chains even at a very small fraction of multivalent counterions. Shrinkage of PE coils is steeper for multivalent counterions than for monovalent counterions. However, the re-expansion is only incremental in the presence of multivalent counterions. Extended adsorbed coils at low salt concentrations and at very high concentrations of monovalent salt exhibit conformation corresponding to a 2D coil with 0.95 fraction of bound segments (segments in "trains") in the regime of diluted surface concentration of the PE. Shrunken coils in the intermediate range of ionic strength resemble 3D-globules with 0.8 fraction of trains. The incrementally re-expanded PE coils at a high ionic strength remain unchanged at higher multivalent salt concentrations up to the solubility limit of the salt. The formation of a strong PE complex with multivalent counterions at high ionic strength is not well understood yet. A speculative explanation of the observed experimental result is based on possible stabilization of the complex due to hydrophobic interactions of the backbone. PMID:22413781

  19. Conformation and dynamics of biopharmaceuticals: Transition of mass spectrometry-based tools from academe to industry

    Microsoft Academic Search

    Igor A. Kaltashov; Cedric E. Bobst; Rinat R. Abzalimov; Steven A. Berkowitz; Damian Houde

    2010-01-01

    Mass spectrometry plays a very visible role in biopharmaceutical industry, although its use in development, characterization,\\u000a and quality control of protein drugs is mostly limited to the analysis of covalent structure (amino acid sequence and post-translational\\u000a modifications). Despite the centrality of protein conformation to biological activity, stability, and safety of biopharmaceutical\\u000a products, the expanding arsenal of mass spectrometry-based methods that

  20. Understanding the conformation transition in the activation pathway of ?2 adrenergic receptor via a targeted molecular dynamics simulation.

    PubMed

    Xiao, Xiuchan; Zeng, Xiaojun; Yuan, Yuan; Gao, Nan; Guo, Yanzhi; Pu, Xuemei; Li, Menglong

    2015-01-28

    G protein coupled receptors (GPCRs) play a crucial role in regulating signal recognition and transduction through their activation. The conformation transition in the activation pathway is of particular importance for their function. However, it has been poorly elucidated due to experimental difficulties in determining the conformations and the time limitation of conventional molecular dynamics (CMD) simulation. Thus, in this work, we employed a targeted molecular dynamic (TMD) simulation to study the activation process from an inactive structure to a fully active one for ?2 adrenergic receptor (?2AR). As a reference, 110 ns CMD simulations on wild ?2AR and its D130N mutant were also carried out. TMD results show that there is at least an intermediate conformation cluster in the activation process, evidenced by the principal component analysis and the structural and dynamic differences of some important motifs. It is noteworthy that the activation of the ligand binding site lags the G-protein binding site, displaying uncoupled correlation. Comparisons between the CMD and TMD results show that the D130N mutation significantly speeds up ICL2 and key ionic lock to enter into the intermediate state, which to some extent facilitates the activation involved in the NPxxY, DRY region and the separation between TM3 and TM6. However, the contribution from the D130N mutation to the activation of the ligand binding site could not be observed within the scale of 110 ns time. These observations could provide novel insights into previous studies for better understanding of the activation mechanism for ?2AR. PMID:25494239

  1. Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry

    PubMed Central

    Kaltashov, Igor A.; Bobst, Cedric E.; Abzalimov, Rinat R.; Berkowitz, Steven A.; Houde, Damian

    2009-01-01

    Mass spectrometry plays a very visible role in biopharmaceutical industry, although its use in development, characterization and quality control of protein drugs is mostly limited to the analysis of covalent structure (amino acid sequence and post-translational modifications). Despite the centrality of protein conformation to biological activity, stability and safety of biopharmaceutical products, the expanding arsenal of mass spectrometry-based methods that are currently available to probe higher order structure and conformational dynamics of biopolymers did not enjoy until recently much attention in the industry. This is beginning to change as a result of recent work demonstrating the utility of these experimental tools for various aspects of biopharmaceutical product development and manufacturing. In this work we use a paradigmatic protein drug interferon ?-1a as an example to illustrate the utility of mass spectrometry as a powerful tool not only to assess the integrity of higher order structure of a protein drug, but also to predict consequences of its degradation at a variety of levels. PMID:19963397

  2. Conformation and dynamics of biopharmaceuticals: transition of mass spectrometry-based tools from academe to industry.

    PubMed

    Kaltashov, Igor A; Bobst, Cedric E; Abzalimov, Rinat R; Berkowitz, Steven A; Houde, Damian

    2010-03-01

    Mass spectrometry plays a very visible role in biopharmaceutical industry, although its use in development, characterization, and quality control of protein drugs is mostly limited to the analysis of covalent structure (amino acid sequence and post-translational modifications). Despite the centrality of protein conformation to biological activity, stability, and safety of biopharmaceutical products, the expanding arsenal of mass spectrometry-based methods that are currently available to probe higher order structure and conformational dynamics of biopolymers did not, until recently, enjoy much attention in the industry. This is beginning to change as a result of recent work demonstrating the utility of these experimental tools for various aspects of biopharmaceutical product development and manufacturing. In this work, we use a paradigmatic protein drug interferon beta-1a as an example to illustrate the utility of mass spectrometry as a powerful tool not only to assess the integrity of higher order structure of a protein drug, but also to predict consequences of its degradation at a variety of levels. PMID:19963397

  3. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

    PubMed Central

    Malinverni, Duccio; Marsili, Simone; Barducci, Alessandro; De Los Rios, Paolo

    2015-01-01

    Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex biochemical cycle involving large-scale structural rearrangements. Here we show that an analysis of coevolution at the residue level fully captures the characteristic large-scale conformational transitions of this protein family, and predicts an evolutionary conserved–and thus functional–homo-dimeric arrangement. Furthermore, we highlight that the features encoding the Hsp70 dimer are more conserved in bacterial than in eukaryotic sequences, suggesting that the known Hsp70/Hsp110 hetero-dimer is a eukaryotic specialization built on a pre-existing template. PMID:26046683

  4. Conformational transitions of nucleic acids studied by IR and Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Taillandier, E.; Liquier, J.; Ghomi, M.

    1989-12-01

    In this short review we first summarize briefly the comparative results obtained in our laboratory by IR and Raman spectroscopies on the right-handed B and the left-handed Z geometries of polynucleotides. The marker IR bands and Raman lines of these conformations are used to present new results concerning the polymorphism of several oligonucleotidic sequences, studied in crystal, solutions and hydrated films by Raman, IR, microRaman and, for the first time, microIR spectroscopies. Finally we give an example of how vibrational spectroscopy can help in the study of interactions between DNAs and drugs. This experimental work has been performed in parallel with a normal coordinate analysis of the DNA marker peaks and this review includes some of the results concerning these calculations and in particular those recently obtained involved with sugar pucker and phosphate backbone markers.

  5. Structural Characterization and pH-Induced Conformational Transition of Full-Length KcsA

    PubMed Central

    Zimmer, Jochen; Doyle, Declan A.; Grossmann, J. Günter

    2006-01-01

    The bacterial K+ channel KcsA from Streptomyces lividans was analyzed by neutron and x-ray small-angle solution scattering. The C-terminally truncated version of KcsA, amenable to crystallographic studies, was compared with the full-length channel. Analyzing the scattering data in terms of radius of gyration reveals differences between both KcsA species of up to 13.2 Å. Equally, the real-space distance distribution identifies a 40 to 50 Å extension of full-length KcsA compared to its C-terminally truncated counterpart. We show that the x-ray and neutron scattering data are amenable for molecular shape reconstruction of full-length KcsA. The molecular envelopes calculated display an hourglass-shaped structure within the C-terminal intracellular domain. The C-terminus extends the membrane spanning region of KcsA by 54–70 Å, with a central constriction 10–30 Å wide. Solution scattering techniques were further employed to characterize the KcsA channel under acidic conditions favoring its open conformation. The full-length KcsA at pH 5.0 shows the characteristics of a dumbbell-shaped macromolecular structure, originating from dimerization of the tetrameric K+ channel. Since C-terminally truncated KcsA measured under the same low pH conditions remains tetrameric, oligomerization of full-length KcsA seems to proceed via structurally changed C-terminal domains. The determined maximum dimensions of the newly formed complex increase by 50–60%. Shape reconstruction of the pseudooctameric complex indicates the pH-induced conformational reorganization of the intracellular C-terminal domain. PMID:16339887

  6. A Conformational Phase Transition in a Langmuir Film of an Amphiphilic Azacrown David Gidalevitz, Oksana Y. Mindyuk, MacKenzie R. Stetzer, and Paul A. Heiney*

    E-print Network

    Kurnaz, Levent

    A Conformational Phase Transition in a Langmuir Film of an Amphiphilic Azacrown David Gidalevitz to study an amphiphilic azacrown derivative at the air-water interface. The compound studied has a ring with this rearrangement, the film develops long-range in-plane structural order. 1. Introduction Amphiphilic rod

  7. Solvent-dependent self-assembly behaviour and speciation control of Pd6L8 metallo-supramolecular cages.

    PubMed

    Henkelis, James J; Fisher, Julie; Warriner, Stuart L; Hardie, Michaele J

    2014-04-01

    The C3-symmetric chiral propylated host-type ligands (±)-tris(isonicotinoyl)-tris(propyl)-cyclotricatechylene (L1) and (±)-tris(4-pyridyl-4-benzoxy)-tris(propyl)-cyclotricatechylene (L2) self-assemble with Pd(II) into [Pd6L8](12+) metallo-cages that resemble a stella octangula. The self-assembly of the [Pd6(L1)8](12+) cage is solvent-dependent; broad NMR resonances and a disordered crystal structure indicate no chiral self-sorting of the ligand enantiomers in DMSO solution, but sharp NMR resonances occur in MeCN or MeNO2. The [Pd6(L1)8](12+) cage is observed to be less favourable in the presence of additional ligand, than is its counterpart, where L=(±)-tris(isonicotinoyl)cyclotriguaiacylene (L1?a). The stoichiometry of reactant mixtures and chemical triggers can be used to control formation of mixtures of homoleptic or heteroleptic [Pd6L8](12+) metallo-cages where L=L1 and L1?a. PMID:24591034

  8. The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation.

    PubMed

    Cecchini, Marco; Changeux, Jean-Pierre

    2015-09-01

    Pentameric ligand-gated ion channels (pLGICs) play a central role in intercellular communications in the nervous system by converting the binding of a chemical messenger - a neurotransmitter - into an ion flux through the postsynaptic membrane. Here, we present an overview of the most recent advances on the signal transduction mechanism boosted by X-ray crystallography of both prokaryotic and eukaryotic homologues of the nicotinic acetylcholine receptor (nAChR) in conjunction with time-resolved analyses based on single-channel electrophysiology and Molecular Dynamics simulations. The available data consistently point to a global mechanism of gating that involves a large reorganization of the receptor mediated by two distinct quaternary transitions: a global twisting and a radial expansion/contraction of the extracellular domain. These transitions profoundly modify the organization of the interface between subunits, which host several sites for orthosteric and allosteric modulatory ligands. The same mechanism may thus mediate both positive and negative allosteric modulations of pLGICs ligand binding at topographically distinct sites. The emerging picture of signal transduction is expected to pave the way to new pharmacological strategies for the development of allosteric modulators of nAChR and pLGICs in general. This article is part of the Special Issue entitled 'The Nicotinic Acetylcholine Receptor: From Molecular Biology to Cognition'. PMID:25529272

  9. Conformal or Confining

    E-print Network

    da Silva, Tiago Nunes; Robroek, Lasse

    2015-01-01

    We present a lattice study of the zero-temperature line of chiral symmetry breaking phase transitions in the conformal window of QCD for varying number of flavors. We argue that it is consistent with a lower edge of the conformal window at $N_fpoint merging as a mechanism for the loss of conformality.

  10. Time-resolved infrared absorption studies of the solvent-dependent vibrational relaxation dynamics of chlorine dioxide.

    PubMed

    Bolinger, Joshua C; Bixby, Teresa J; Reid, Philip J

    2005-08-22

    We report a series of time-resolved infrared absorption studies on chlorine dioxide (OClO) dissolved in H2O, D2O, and acetonitrile. Following the photoexcitation at 401 nm, the evolution in optical density for frequencies corresponding to asymmetric stretch of OClO is measured with a time resolution of 120+/-50 fs. The experimentally determined optical-density evolution is compared with theoretical models of OClO vibrational relaxation derived from collisional models as well as classical molecular-dynamics (MD) studies. The vibrational relaxation rates in D2O are reduced by a factor of 3 relative to H2O consistent with the predictions of MD. This difference reflects modification of the frequency-dependent solvent-solute coupling accompanying isotopic substitution of the solvent. Also, the geminate-recombination quantum yield for the primary photofragments resulting in the reformation of ground-state OClO is reduced in D2O relative to H2O. It is proposed that this reduction reflects enhancement of the dissociation rate accompanying vibrational excitation along the asymmetric-stretch coordinate. In contrast to H2O and D2O, the vibrational-relaxation dynamics in acetonitrile are not well described by the theoretical models. Reproduction of the optical-density evolution in acetonitrile requires significant modification of the frequency-dependent solvent-solute coupling derived from MD. It is proposed that this modification reflects vibrational-energy transfer from the asymmetric stretch of OClO to the methyl rock of acetonitrile. In total, the results presented here provide a detailed description of the solvent-dependent geminate-recombination and vibrational-relaxation dynamics of OClO in solution. PMID:16164308

  11. Push-Pull Type Oligo(N-annulated perylene)quinodimethanes: Chain Length and Solvent-Dependent Ground States and Physical Properties.

    PubMed

    Zeng, Zebing; Lee, Sangsu; Son, Minjung; Fukuda, Kotaro; Burrezo, Paula Mayorga; Zhu, Xiaojian; Qi, Qingbiao; Li, Run-Wei; Navarrete, Juan T López; Ding, Jun; Casado, Juan; Nakano, Masayoshi; Kim, Dongho; Wu, Jishan

    2015-07-01

    Research on stable open-shell singlet diradicaloids recently became a hot topic because of their unique optical, electronic, and magnetic properties and promising applications in materials science. So far, most reported singlet diradicaloid molecules have a symmetric structure, while asymmetric diradicaloids with an additional contribution of a dipolar zwitterionic form to the ground state were rarely studied. In this Article, a series of new push-pull type oligo(N-annulated perylene)quinodimethanes were synthesized. Their chain length and solvent-dependent ground states and physical properties were systematically investigated by various experimental methods such as steady-state and transient absorption, two-photon absorption, X-ray crystallographic analysis, electron spin resonance, superconducting quantum interference device, Raman spectroscopy, and electrochemistry. It was found that with extension of the chain length, the diradical character increases while the contribution of the zwitterionic form to the ground state becomes smaller. Because of the intramolecular charge transfer character, the physical properties of this push-pull system showed solvent dependence. In addition, density functional theory calculations on the diradical character and Hirshfeld charge were conducted to understand the chain length and solvent dependence of both symmetric and asymmetric systems. Our studies provided a comprehensive understanding on the fundamental structure- and environment-property relationships in the new asymmetric diradicaloid systems. PMID:26062868

  12. Evidence of PPII-like helical conformation and glass transition in a self-assembled solid-state polypeptide-surfactant complex: poly(L-histidine)/docylbenzenesulfonic acid.

    PubMed

    Ramani, Ramasubbu; Hanski, Sirkku; Laiho, Ari; Tuma, Roman; Kilpeläinen, Simo; Tuomisto, Filip; Ruokolainen, Janne; Ikkala, Olli

    2008-05-01

    We present lamellar self-assembly of cationic poly(L-histidine) (PLH) stoichiometrically complexed with an anionic surfactant, dodecyl benzenesulfonic acid (DBSA), which allows a stabilized conformation reminiscent of polyproline type II (PPII) left-handed helices. Such a conformation has no intrapeptide hydrogen bonds, and it has previously been found to be one source of flexibility, e.g., in collagen and elastin, as well as an intermediate in silk processing. PLH(DBSA)1.0 complexes were characterized by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and differential scanning calorimetry (DSC). The PPII-like conformation in PLH(DBSA)1.0 is revealed by characteristic CD and FTIR spectra, where the latter indicates absence of intrachain peptide hydrogen bonds. In addition, a glass transition was directly verified by DSC at ca. 135 degrees C for PLH(DBSA)1.0 and indirectly by SAXS and TEM in comparison to pure PLH at 165 degrees C, thus indicating plasticization. Glass transitions have not been observed before in polypeptide-surfactant complexes. The present results show that surfactant binding can be a simple scheme to provide steric crowding to stabilize PPII conformation to tune the polypeptide properties, plasticization and flexibility. PMID:18419152

  13. Unusual solvent-dependent photophysical and self-assembly properties of NO2 substituted T-shaped phenazines.

    PubMed

    Lee, Dong-Chan; Brownell, Lacie V; Jang, Kyoungmi; Han, Seung Ju; Robins, Kathleen A

    2015-01-28

    This paper investigates the importance of substituent placement when designing low-molecular mass ?-organogelators. The electron-deficient NO2 substituent was systematically added to novel T-shaped phenazines to examine electronic as well as assembly properties. This T-shaped molecular platform promotes selective electronic tuning, which can be theoretically analyzed by examining the system's frontier molecular orbitals. Electronic properties were characterized by UV-vis spectroscopy and cyclic voltammetry, and comparisons were made based on number and placement of the NO2 group. Computational chemistry (B3LYP/6-31G*) was employed for geometry optimizations, and to generate molecular orbital diagrams for all systems. The most noticeable influence of NO2 position was found for two molecules with four NO2 groups placed at different locations about the molecule (T-34dNT and T-35dNT). A 0.13 eV difference in ELUMO was observed while EHOMO was not significantly impacted by this change only in NO2 placement. Interestingly and unexpectedly, the photophysical properties and solvent-dependent gelation properties were considerably different for T-34dNT and T-35dNT. T-34dNT exhibited a unique fluorescence (FL) solvatochromism, with FL intensity and maxima dependent on solvent polarity. This result is indicative of intramolecular charge transfer. In addition, long tailing at the solid-state absorption of T-34dNT suggests the presence of intermolecular charge transfer. The gelation of T-34dNT produced chromism ranging from red to orange to yellow when the solvents changed from acetonitrile to ethyl acetate to cyclohexane, respectively. T-35dNT gels in these solvents did not exhibit any of the same properties. Xerogel morphology characterizations were carried out using three different solvents for both T-34dNT and T-35dNT. In the case of T-34dNT, striking differences in the morphology were detected by field-emission scanning electron microscopy (FE-SEM). We conclude that numbers of substituents are not the only consideration in effective molecular design for organogelators, but that substituent position plays a critical role in certain fundamental properties of these systems. PMID:25491727

  14. Conformality lost

    SciTech Connect

    Kaplan, David B.; Lee, Jong-Wan; Son, Dam T.; Stephanov, Mikhail A. [Institute for Nuclear Theory, University of Washington, Seattle, Washington 98195-1550 (United States); Department of Physics, University of Illinois, Chicago, Illinois 60607-7059 (United States)

    2009-12-15

    We consider zero-temperature transitions from conformal to nonconformal phases in quantum theories. We argue that there are three generic mechanisms for the loss of conformality in any number of dimensions: (i) fixed point goes to zero coupling, (ii) fixed point runs off to infinite coupling, or (iii) an IR fixed point annihilates with a UV fixed point and they both disappear into the complex plane. We give both relativistic and nonrelativistic examples of the last case in various dimensions and show that the critical behavior of the mass gap behaves similarly to the correlation length in the finite temperature Berezinskii-Kosterlitz-Thouless (BKT) phase transition in two dimensions, {xi}{approx}exp(c/|T-T{sub c}|{sup 1/2}). We speculate that the chiral phase transition in QCD at large number of fermion flavors belongs to this universality class, and attempt to identify the UV fixed point that annihilates with the Banks-Zaks fixed point at the lower end of the conformal window.

  15. Structure Transition in PSS/Lysozyme Complexes: A Chain-Conformation-Driven Process, as Directly Seen by Small Angle Neutron Scattering

    E-print Network

    Jérémie Gummel; Fabrice Cousin; François Boué

    2009-03-30

    Measurements of chain conformation in proteins/polyelectrolytes complexes (lysozyme and PSSNa) show that the crossover observed between an open structure -a chain network crosslinked by the proteins, and a globular one - dense globules of ~ 10 nm aggregated in a fractal way, results from a conformation modification prior to the transition. Before showing this, we have widened the parameters range for the observation of the transition. We had shown before that the two structures can be formed depending on chain length (for a given [PSS]/[lysozyme] ratio): gel for large chains, globules for short chains. We show here that the crossover between these two regimes can also be reached as a function of chains concentration or salinity of the buffer. Since all these crossover parameters act on chains overlapping concentration c*, we reinforce the idea of a transition from the dilute to the semi-dilute regime, but c* is shifted compared to pure PSS solutions. In order to understand this, we have measured by SANS the conformation of a single chain of PSS in presence of proteins within the complexes. This is achieved by a specific labeling trick where we take advantage of the fact that lysozyme and hydrogenated PSS chains have the same neutron scattering length density. In the gel structure, the PSS chains keep a wormlike structure as in pure solutions, but their persistence length is strongly reduced, from 50 {\\AA} without proteins to 20 {\\AA} in average with lysozyme. With this value of 20 {\\AA}, we calculate new overlapping thresholds (concentration, mass, ionic strength) in agreement with observed ones. In a second stage, after the globular structure is formed, the PSS chains get a third conformation, no longer wormlike, but more collapsed, within the globules.

  16. Solvent dependence of two-photon absorption spectra of the enhanced green fluorescent protein (eGFP) chromophore

    NASA Astrophysics Data System (ADS)

    Hosoi, Haruko; Tayama, Ryo; Takeuchi, Satoshi; Tahara, Tahei

    2015-06-01

    Two-photon absorption spectra of 4?-hydroxybenzylidene-2,3-dimethylimidazolinone, a model chromophore of enhanced green fluorescent protein (eGFP), were measured in various solvents. The two-photon absorption band of its anionic form is markedly blue-shifted from the corresponding one-photon absorption band in all solvents. Moreover, the magnitude of the blue shift varies largely depending on the solvent, which does not accord with the assignment of the two-photon absorption band to the transitions to the vibrationally excited S1 state. Our finding is readily rationalized by considering overlapping contributions of the S1 ? S0 and S2 ? S0 transitions, suggesting the involvement of the S2 state also in two-photon fluorescence of eGFP.

  17. Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene

    NASA Astrophysics Data System (ADS)

    Shankla, Manish; Aksimentiev, Aleksei

    2014-10-01

    Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.

  18. Solvent Dependency in the Quantum Efficiency of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] Aniline Hydrochloride.

    PubMed

    Pathrose, Bini; Nampoori, V P N; Radhakrishnan, P; Sahira, H; Mujeeb, A

    2015-05-01

    In the present work dual beam thermal lens technique is used for studying the solvent dependency on the quantum efficiency of a novel dye used for biomedical applications. The role of solvent in the absolute fluorescence quantum yield of 4-[(4-Aminophenyl)-(4-imino-1-cyclohexa-2, 5- dienylidene) methyl] aniline hydrochloride is studied using thermal lens technique. It is observed that the variation in solvents and its concentration results considerable variations in the fluorescence quantum yield. These variations are due to the non-radiative relaxation of the absorbed energy and because of the different solvent properties. The highest quantum yield of the dye is observed in the polar protic solvent-water. PMID:25820872

  19. Nucleotide- and substrate-induced conformational transitions in the CBS domain-containing pyrophosphatase of Moorella thermoacetica.

    PubMed

    Jämsen, Joonas; Baykov, Alexander A; Lahti, Reijo

    2010-02-01

    In contrast to all other known pyrophosphatases, Moorella thermoacetica pyrophosphatase (mtCBS-PPase) contains nucleotide-binding CBS domains and is thus strongly regulated by adenine nucleotides. Stopped-flow measurements using a fluorescent AMP analogue, 2'(3')-O-(N-methylanthranoyl)-AMP (Mant-AMP), reveal that nucleotide binding to mtCBS-PPase involves a three-step increase in Mant-AMP fluorescence with relaxation times from 0.01 to 100 s, implying conformational changes in the complex. This effect is reversed by AMP. Metal cofactors (Co(2+) and Mg(2+)) enhance the fluorescence signal but are not absolutely required, unlike what is seen when the catalytic reaction is examined. The relaxation times and amplitudes of the fluorescence signals depend on Mant-AMP concentration in a manner suggestive of the presence of a second binding site for Mant-AMP on the protein. Equilibrium fluorescence titration experiments additionally support the presence of two types of AMP binding sites with different affinities, whereas equilibrium dialysis and membrane filtration measurements reveal binding of one AMP molecule per enzyme monomer, implying negative cooperativity in nucleotide binding. The substrate (PP(i)) modulates Mant-AMP binding, leading to a further conformational change in the enzyme-Mant-AMP complex, and stimulates mtCBS-PPase in alkaline medium within a time scale of minutes, via conversion to a more active form. This active form initially comprises only a third of the enzyme, as estimated from kinetic titration with ADP. AMP inhibits both enzyme forms but is unable to independently induce interconversion. Our results collectively suggest that nucleotides and the substrate induce multiple conformational changes in mtCBS-PPase occurring over a wide time scale; the changes are distinct and almost independent. PMID:20038140

  20. Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers.

    PubMed

    Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H; Nilges, Michael; Francetic, Olivera

    2014-05-01

    The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility, or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here, we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3,900 pilus models suggested a transition path toward low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of interprotomer contacts along this path were tested by site-directed mutagenesis, pilus assembly, and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. PMID:24685147

  1. Distinct docking and stabilization steps of the pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers

    PubMed Central

    Nivaskumar, Mangayarkarasi; Bouvier, Guillaume; Campos, Manuel; Nadeau, Nathalie; Yu, Xiong; Egelman, Edward H.; Nilges, Michael; Francetic, Olivera

    2014-01-01

    SUMMARY The closely related bacterial type II secretion (T2S) and type IV pilus (T4P) systems are sophisticated machines that assemble dynamic fibers promoting protein transport, motility or adhesion. Despite their essential role in virulence, the molecular mechanisms underlying helical fiber assembly remain unknown. Here we use electron microscopy and flexible modeling to study conformational changes of PulG pili assembled by the Klebsiella oxytoca T2SS. Neural network analysis of 3900 pilus models suggested a transition path towards low-energy conformations driven by progressive increase in fiber helical twist. Detailed predictions of inter-protomer contacts along this path were tested by site-directed mutagenesis, pilus assembly and protein secretion analyses. We demonstrate that electrostatic interactions between adjacent protomers (P-P+1) in the membrane drive pseudopilin docking, while P-P+3 and P-P+4 contacts determine downstream fiber stabilization steps. These results support a new model of a spool-like assembly mechanism for fibers of the T2SS-T4P superfamily. PMID:24685147

  2. Observation of the A-x electronic transition of the isomers and conformers of pentyl peroxy radical using cavity ringdown spectroscopy.

    PubMed

    Sharp, Erin N; Rupper, Patrick; Miller, Terry A

    2008-02-21

    Cavity ringdown spectra of the A-X electronic transition of all eight isomers of the pentyl peroxy radical are reported. Using the corresponding assignments from previously studied smaller alkyl peroxy radicals, assignments of origin bands are made for the pentyl peroxy isomers including some conformer-specific assignments for bands of a given isomer. Ab initio calculations also were performed to aid in the spectral assignments for neopentyl, t-butyl, and t-pentyl peroxies. In addition to the origins, vibrational bands have also been assigned for some species. Using the analyzed spectra, the relative reactivity of the primary, secondary, and tertiary hydrogen atoms in isopentane could be determined semiquantitatively. PMID:18211043

  3. Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

    Microsoft Academic Search

    G. Sieger; H. Hofmann; J. Förtsch; H. J. Gross; J. W. Randies; H. L. Sänger; D. Riesner

    1984-01-01

    Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermodynamic, kinetic and hydrodynamic methods.

  4. Conformational behavior of pyrazine-bridged and mixed-bridged cavitands: a general model for solvent effects on thermal "vase-kite" switching.

    PubMed

    Roncucci, Pamela; Pirondini, Laura; Paderni, Giuseppe; Massera, Chiara; Dalcanale, Enrico; Azov, Vladimir A; Diederich, François

    2006-06-14

    The controllable switching of suitably bridged resorcin[4]arene cavitands between a "vase" conformation, with a cavity capable of guest inclusion, and a "kite" conformation, featuring an extended flattened surface, provides the basis for ongoing developments of dynamic molecular receptors, sensors, and molecular machines. This paper describes the synthesis, X-ray crystallographic characterization, and NMR analysis of the "vase-kite" switching behavior of a fully pyrazine-bridged cavitand and five other mixed-bridged quinoxaline-bridged cavitands with one methylene, phosphonate, or phosphate bridge. The pyrazine-bridged resorcin[4]arene cavitand displayed an unexpectedly high preference for the kite conformation in nonpolar solvents, relative to the quinoxaline-bridged analogue. This observation led to extensive solvent-dependent switching studies that provide a detailed picture of how solvent affects the thermal vase-kite equilibration. As for any thermodynamic process in the liquid phase, the conformational equilibrium is affected by how the solvent stabilizes the two individual states. Suitably sized solvents (benzene and derivatives) solvate the cavity of the vase form and reduce the propensity for the vase-to-kite transition. Correspondingly, the kite geometry becomes preferred in bulky solvents such as mesitylene, incapable of penetrating the vase cavity. As proposed earlier by Cram, the kite form is preferred at low temperatures due to the more favorable enthalpy of solvation of the enlarged surface. Furthermore, the kite conformation is more preferred in solvents with substantial hydrogen-bonding acidity: weak hydrogen-bonding interactions between the mildly basic quinoxaline and pyrazine nitrogen atoms and solvent molecules are more efficient in the open kite than in the closed vase form. Vase-to-kite conversion is entirely absent in dipolar aprotic solvents lacking any H-bonding acidity. Thermal vase-kite switching requires fully quinoxaline- or pyrazine-bridged cavitands, whereas pH-controlled switching is also applicable to systems incorporating only two or three such bridges. PMID:16671048

  5. Transitions.

    ERIC Educational Resources Information Center

    Nathanson, Jeanne H., Ed.

    1993-01-01

    This theme issue on transitions for individuals with disabilities contains nine papers discussing transition programs and issues. "Transition Issues for the 1990s," by Michael J. Ward and William D. Halloran, discusses self-determination, school responsibility for transition, continued educational engagement of at-risk students, and service…

  6. Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data.

    PubMed

    Steger, G; Hofmann, H; Förtsch, J; Gross, H J; Randles, J W; Sänger, H L; Riesner, D

    1984-12-01

    Viroids are single-stranded circular RNA molecules of 240 to 400 nucleotides which are pathogens of certain higher plants and replicate autonomously in the host cell. Virusoids are similar to viroids in respect to size and circularity but replicate only as genomic part of a plant virus. Their structure and structural transitions have been investigated by thermo-dynamic, kinetic and hydrodynamic methods. The special features of the sequences of these RNAs, which are the basis for their secondary structures and structural flexibility, are investigated with theoretical methods. A set of thermodynamic parameters for helix growth and loop formation is selected from the literature to calculate secondary structures and structural transitions of single-stranded RNAs. Appropriate modifications of the chosen parameter set are discussed. For calculations we used either Tinoco-plots and the model of "cooperative helices" or the Zuker-program based on the exact algorithm of Nussinov et al, or both. Calculations were done for viroids and virusoids. As both are single-stranded, circular RNAs we had to modify the Zuker-program as described in the appendix. Calculations are done for different viroids, i.e. potato spindle tuber, citrus exocortis, chrysanthemum stunt, coconut cadang-cadang, and avocado sunblotch, and for two virusoids, i.e. the circular RNAs of Solanum nodiflorum mottle virus, and velvet tobacco mottle virus. For viroids the calculations confirm our earlier theoretical and experimental results about the extended native structure and the highly cooperative transition into a branched structure. Virusoids show less base pairing, branching in the native secondary structure, and only low cooperativity during denaturation. They resemble more closely the properties of random sequences with length, G:C content, and circularity as in viroids but statistical sequences. The comparison of viroids, virusoids, and circular RNA or random sequences confirms the uniqueness of viroid structure. PMID:6086063

  7. Transitions.

    ERIC Educational Resources Information Center

    Field, David; And Others

    1992-01-01

    Includes four articles: "Career Aspirations" (Field); "Making the Transition to a New Curriculum" (Baker, Householder); "How about a 'Work to School' Transition?" (Glasberg); and "Technological Improvisation: Bringing CNC to Woodworking" (Charles, McDuffie). (SK)

  8. Temperature-dependence of UV laser one-electron oxidative guanine modifications as a probe of local stacking fluctuations and conformational transitions.

    PubMed

    Spassky, Annick; Angelov, Dimitar

    2002-10-11

    By monitoring R(pip)/R(Fpg), i.e. the relative sensitivity to hot piperidine and to formamidopyrimidine DNA glycosylase (Fpg protein) of the guanine lesions induced in DNA exposed to UV laser irradiation, we have previously observed that the formation of the two major types of one-electron oxidative guanine modifications, oxazolone and 7,8-dihydro-8-oxoguanine (8-oxodG), depends on DNA conformational features. While oxazolone is largely predominant at each site of single-stranded DNA (R(pip)>R(Fpg)), 8-oxodG is the major lesion at most of the sites of double-stranded DNA (R(pip)transition between the double-stranded and the melted random coiled states. The striking result is that the transition curves of the ratio R(pip)/R(Fpg) display a shape similar to the helix-coil melting profile of the DNA fragment determined from UV absorbance measurements with, at individual sites, subtle differences in the slope of the curves and in the temperature at the mid-point of the transitions. At a few guanine residues of the DNA duplex, R(pip)>R(Fpg) at 20 degrees C and the ratio R(pip)/R(Fpg) does not vary significantly during the melting process. Interestingly, these guanine residues display a high sensitivity to dimethyl sulfoxide methylation while the opposite cytosine residues are unsensitive, suggesting that the prevalence of R(pip) over R(Fpg) is related not to base-pairing disruption but rather to the local helical alteration of the B-DNA stacking geometry. This leads us to propose that the slight variations in the ratios R(pip)/R(Fpg) observed, at individual sites, at temperatures below the helix-coil transition reflect local small-scale breathing motions, unstacking single dinucleotide steps prior to opening. Our results thus support the view that the temperature dependence of the ratio of R(pip)/R(Fpg) at sites of B-DNA provides a sensitive probe of the DNA internal local thermal stability and are discussed in relation with the mechanisms proposed for the intramolecular rearrangement of the guanyl radical. PMID:12368094

  9. Interactions of the Escherichia coli DnaB–DnaC Protein Complex with Nucleotide Cofactors. 1. Allosteric Conformational Transitions of the Complex†

    PubMed Central

    Roychowdhury, Anasuya; Szymanski, Michal R.; Jezewska, Maria J.; Bujalowski, Wlodzimierz

    2011-01-01

    Interactions of nucleotide cofactors with both protein components of the Escherichia coli DnaB helicase complex with the replication factor, the DnaC protein, have been examined using MANT-nucleotide analogues. At saturation, in all examined stationary complexes, including the binary, DnaB–DnaC, and tertiary, DnaB–DnaC–ssDNA, complexes, the helicase binds six cofactor molecules. Thus, protein–protein and protein–DNA interactions do not affect the maximum stoichiometry of the helicase–nucleotide interactions. The single-stranded DNA dramatically increases the ATP analogue affinity, while it has little effect on the affinity of the NDP analogues, indicating that stationary complexes reflect allosteric interactions between the DNA- and NTP-binding site prior to the cofactor hydrolysis step and subsequent to product release. In the binary complex, the DnaC protein diminishes the intrinsic affinity and increases the negative cooperativity in the cofactor binding to the helicase; an opposite effect of the protein on the cofactor–helicase interactions occurs in the tertiary complex. The DnaC protein retains its nucleotide binding capability in the binary and tertiary complexes with the helicase. Surprisingly, the DnaC protein–nucleotide interactions, in the binary and tertiary complexes, are characterized by positive cooperativity. The DnaC assembles on the helicase as a hexamer, which exists in two conformational states and undergoes an allosteric transition, induced by the cofactor. Cooperativity of the allosteric transition depends on the structure of the phosphate group of the nucleotide. The significance of the results for the DnaB–DnaC complex activities is discussed. PMID:19569622

  10. Coupling of Conformational Transitions in the N-terminal Domain of the 51-kDa FK506-binding Protein (FKBP51) Near Its Site of Interaction with the Steroid Receptor Proteins.

    PubMed

    LeMaster, David M; Mustafi, Sourajit M; Brecher, Matthew; Zhang, Jing; Héroux, Annie; Li, Hongmin; Hernández, Griselda

    2015-06-19

    Interchanging Leu-119 for Pro-119 at the tip of the ?4-?5 loop in the first FK506 binding domain (FK1) of the FKBP51 and FKBP52 proteins, respectively, has been reported to largely reverse the inhibitory (FKBP51) or stimulatory (FKBP52) effects of these co-chaperones on the transcriptional activity of glucocorticoid and androgen receptor-protein complexes. Previous NMR relaxation studies have identified exchange line broadening, indicative of submillisecond conformational motion, throughout the ?4-?5 loop in the FK1 domain of FKBP51, which are suppressed by the FKBP52-like L119P substitution. This substitution also attenuates exchange line broadening in the underlying ?2 and ?3a strands that is centered near a bifurcated main chain hydrogen bond interaction between these two strands. The present study demonstrates that these exchange line broadening effects arise from two distinct coupled conformational transitions, and the transition within the ?2 and ?3a strands samples a transient conformation that resembles the crystal structures of the selectively inhibited FK1 domain of FKBP51 recently reported. Although the crystal structures for their series of inhibitors were interpreted as evidence for an induced fit mechanism of association, the presence of a similar conformation being significantly populated in the unliganded FKBP51 domain is more consistent with a conformational selection binding process. The contrastingly reduced conformational plasticity of the corresponding FK1 domain of FKBP52 is consistent with the current model in which FKBP51 binds to both the apo- and hormone-bound forms of the steroid receptor to modulate its affinity for ligand, whereas FKBP52 binds selectively to the latter state. PMID:25953903

  11. Accounting for conformational flexibility and torsional anharmonicity in the H + CH{sub 3}CH{sub 2}OH hydrogen abstraction reactions: A multi-path variational transition state theory study

    SciTech Connect

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio, E-mail: qf.ramos@usc.es [Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)] [Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)

    2014-05-07

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

  12. Förster resonance energy transfer confirms the bacterial-induced conformational transition in highly-branched poly(N-isopropyl acrylamide with vancomycin end groups on binding to Staphylococcus aureus.

    PubMed

    Sarker, Prodip; Swindells, Kathryn; Douglas, C W Ian; MacNeil, Sheila; Rimmer, Stephen; Swanson, Linda

    2014-08-21

    We describe a series of experiments designed to investigate the conformational transition that highly-branched polymers with ligands undergo when interacting with bacteria, a process that may provide a new sensing mechanism for bacterial detection. Fluorescent highly-branched poly(N-isopropyl acrylamide)s (HB-PNIPAM) were prepared by sequential self-condensing radical copolymerizations, using anthrylmethyl methacrylate (AMMA) and fluorescein-O-acrylate (FA) as fluorescent comonomers and 4-vinylbenzyl pyrrole carbodithioate as a branch forming monomer. Differences in reactivity necessitated to first copolymerize AMMA then react with FA in a separate sequential monomer feed step. Modifications of the chain ends produced vancomycin-functional derivatives (HB-PNIPAM-Van). The AMMA and FA labels allow probing of the conformational behaviour of the polymers in solution via Förster resonance energy transfer experiments. It was shown that interaction of this polymer's end groups with Staphylococcus aureus induced a macromolecular collapse. The data thus provide conclusive evidence for a conformational transition that is driven by binding to a bacterium. PMID:24974819

  13. Conformal House

    NASA Astrophysics Data System (ADS)

    Ryttov, Thomas A.; Sannino, Francesco

    We investigate the gauge dynamics of nonsupersymmetric SU(N) gauge theories featuring the simultaneous presence of fermionic matter transforming according to two distinct representations of the underlying gauge group. We bound the regions of flavors and colors which can yield a physical infrared fixed point. As a consistency check we recover the previously investigated bounds of the conformal windows when restricting to a single matter representation. The earlier conformal windows can be imagined to be part now of the new conformal house. We predict the nonperturbative anomalous dimensions at the infrared fixed points. We further investigate the effects of adding mass terms to the condensates on the conformal house chiral dynamics and construct the simplest instanton induced effective Lagrangian terms.

  14. Conformational changes in biopolymers

    NASA Astrophysics Data System (ADS)

    Ivanov, Vassili

    2005-12-01

    Biopolymer conformational changes are involved in many biological processes. This thesis summarizes some theoretical and experimental approaches which I have taken at UCLA to explore conformational changes in biopolymers. The reversible thermal denaturation of the DNA double helix is, perhaps, the simplest example of biopolymer conformational change. I have developed a statistical mechanics model of DNA melting with reduced degrees of freedom, which allows base stacking interaction to be taken into account and treat base pairing and stacking separately. Unlike previous models, this model describes both the unpairing and unstacking parts of the experimental melting curves and explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. I developed a basic kinetic model for irreversible thermal denaturation of F-actin, which incorporates depolymerization of F-actin from the ends and breaking of F-actin fiber in the middle. The model explains the cooperativity of F-actin thermal denaturation observed by D. Pavlov et al. in differential calorimetry measurements. CG-rich DNA sequences form left-handed Z-DNA at high ionic strength or upon binding of polyvalent ions and some proteins. I studied experimentally the B-to-Z transition of the (CG)6 dodecamer. Improvement of the locally linearized model used to interpret the data gives evidence for an intermediate state in the B-to-Z transition of DNA, contrary to previous research on this subject. In the past 15 years it has become possible to study the conformational changes of biomolecules using single-molecule techniques. In collaboration with other lab members I performed a single-molecule experiment, where we monitored the displacement of a micrometer-size bead tethered to a surface by a DNA probe undergoing the conformational change. This technique allows probing of conformational changes with subnanometer accuracy. We applied the method to detect, for the first time, single hybridization events of label-free target oligomers. This demonstrates a new paradigm of molecule detection where, hybridization of the target is detected through the conformational change of the probe.

  15. Effect of pH and Copper(II) on the Conformation Transitions of Silk Fibroin Based on EPR, NMR, and Raman Spectroscopy †

    Microsoft Academic Search

    Xiao-Hong Zong; Ping Zhou; Zheng-Zhong Shao; Shi-Ming Chen; Xin Chen; Bing-Wen Hu; Feng Deng; Wen-Hua Yao

    2004-01-01

    Much attention has been paid to the natural mechanism of silkworm spinning due to the impressive mechanical properties of the natural fibers. Our results in the present work show that the fractional changes of the conformational components in regenerated silk fibroin (SF) extracted from Bombyx mori fibers is remarkably pH- and Cu(II)-dependent as demonstrated by Cu(II) EPR, 13C NMR, and

  16. Self-assembly in a near-frictionless granular material: conformational structures and transitions in uniaxial cyclic compression of hydrogel spheres.

    PubMed

    Walker, David M; Tordesillas, Antoinette; Brodu, Nicolas; Dijksman, Joshua A; Behringer, Robert P; Froyland, Gary

    2015-03-21

    We use a Markov transition matrix-based analysis to explore the structures and structural transitions in a three-dimensional assembly of hydrogel spheres under cyclic uniaxial compression. We apply these methods on experimental data obtained from a packing of nearly frictionless hydrogel balls. This allows an exploration of the emergence and evolution of mesoscale internal structures - a key micromechanical property that governs self-assembly and self-organization in dense granular media. To probe the mesoscopic force network structure, we consider two structural state spaces: (i) a particle and its contacting neighbours, and (ii) a particle's local minimal cycle topology summarized by a cycle vector. In both spaces, our analysis of the transition dynamics reveals which structures and which sets of structures are most prevalent and most likely to transform into each other during the compression/decompression of the material. In compressed states, structures rich in 3-cycle or triangle topologies form in abundance. In contrast, in uncompressed states, transitions comprising poorly connected structures are dominant. An almost-invariant transition set within the cycle vector space is discovered that identifies an intermediate set of structures crucial to the material's transition from weakly jammed to strongly jammed, and vice versa. Preferred transition pathways are also highlighted and discussed with respect to thermo-micro-mechanical constitutive formulations. PMID:25634109

  17. A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA.

    PubMed

    Kannan, Arvind; Camilloni, Carlo; Sahakyan, Aleksandr B; Cavalli, Andrea; Vendruscolo, Michele

    2014-02-12

    Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. Such advances also suggest the possibility of using chemical shifts to characterize the conformational fluctuations of these molecules. Here we describe a method of using methyl chemical shifts as restraints in replica-averaged molecular dynamics (MD) simulations, which enables us to determine the conformational ensemble of the HU dimer and characterize the range of motions accessible to its flexible ?-arms. Our analysis suggests that the bending action of HU on DNA is mediated by a mechanical clamping mechanism, in which metastable structural intermediates sampled during the hinge motions of the ?-arms in the free state are presculpted to bind DNA. These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms. PMID:24517490

  18. Induced plasma expander-like properties as a function of PEG-chains on extension arm facilitated PEGylation of albumin: "mushroom to brush-like" conformational transition of the PEG-albumin conjugate.

    PubMed

    Sahu, Ranjit K; Nacharaju, Parimala; Manjula, Belur N; Acharya, Seetharama A

    2009-01-01

    Plasma expander-like properties of albumin induced on hexa as well as dodecacPEGylation using Extension Arm Facilitated PEGylation platform make it an excellent resuscitation fluid. PEGylation induced changes in the structure, drug binding, and plasma expander-like properties of bovine serum albumin has been now investigated as a function of PEGylation. The molecular volume of albumin increases on PEGylation nearly linearly; in the beginning up to about six PEG chains are conjugated, then plateau off, while the viscosity and colloidal osmotic pressure change very little initially and then increase exponentially as a function of PEG chains conjugated. PEGylation has essentially no influence on the secondary structure or drug properties of albumin. Tryphtophyl fluorescence of albumin is quenched on PEGylation as a direct correlate of the changes in molecular radius of PEG-albumin. It is concluded that hexaPEGylated and dodecaPEGylated albumin belong to two different configurational states of PEG-albumin in terms of packing of PEG-chains on the molecular surface of the protein. The results suggest a transition of PEGylated albumin from the initial mushroom-like conformation to brush conformation as the PEGylation increases. The therapeutic efficacy of the two PEGylated species is needed to establish the optimum level of PEGylation to function as resuscitation fluids. PMID:19922165

  19. Conformational Dynamics of the Cytochrome P450 BM3/N-Palmitoylglycine Complex: The Proposed "Proximal-Distal" Transition Probed by Temperature-Jump Spectroscopy

    E-print Network

    "Proximal-Distal" Transition Probed by Temperature-Jump Spectroscopy Sibylle Brenner, Sam Hay, Hazel M450 BM3 and its F87G mutant by using temperature (T)-jump relaxation spectroscopy in combination with static equilibrium experiments. No relaxation process was measurable in the substrate-free enzyme

  20. Solvent dependent branching between C-I and C-Br bond cleavage following 266 nm excitation of CH{sub 2}BrI

    SciTech Connect

    Anderson, Christopher P.; Spears, Kenneth G.; Wilson, Kaitlynn R.; Sension, Roseanne J. [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)] [Department of Chemistry and Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States)

    2013-11-21

    It is well known that ultraviolet photoexcitation of halomethanes results in halogen-carbon bond cleavage. Each halogen-carbon bond has a dominant ultraviolet (UV) absorption that promotes an electron from a nonbonding halogen orbital (n{sub X}) to a carbon-halogen antibonding orbital (?*{sub C-X}). UV absorption into specific transitions in the gas phase results primarily in selective cleavage of the corresponding carbon-halogen bond. In the present work, broadband ultrafast UV-visible transient absorption studies of CH{sub 2}BrI reveal a more complex photochemistry in solution. Transient absorption spectra are reported spanning the range from 275 nm to 750 nm and 300 fs to 3 ns following excitation of CH{sub 2}BrI at 266 nm in acetonitrile, 2-butanol, and cyclohexane. Channels involving formation of CH{sub 2}Br + I radical pairs, iso-CH{sub 2}Br-I, and iso-CH{sub 2}I-Br are identified. The solvent environment has a significant influence on the branching ratios, and on the formation and stability of iso-CH{sub 2}Br-I. Both iso-CH{sub 2}Br-I and iso-CH{sub 2}I-Br are observed in cyclohexane with a ratio of ?2.8:1. In acetonitrile this ratio is 7:1 or larger. The observation of formation of iso-CH{sub 2}I-Br photoproduct as well as iso-CH{sub 2}Br-I following 266 nm excitation is a novel result that suggests complexity in the dissociation mechanism. We also report a solvent and concentration dependent lifetime of iso-CH{sub 2}Br-I. At low concentrations the lifetime is >4 ns in acetonitrile, 1.9 ns in 2-butanol and ?1.4 ns in cyclohexane. These lifetimes decrease with higher initial concentrations of CH{sub 2}BrI. The concentration dependence highlights the role that intermolecular interactions can play in the quenching of unstable isomers of dihalomethanes.

  1. Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis

    Microsoft Academic Search

    Lin Chen; Qing-Chuan Zheng; Li-Ying Yu; Wen-Ting Chu; Ji-Long Zhang; Qiao Xue; Hong-Xing Zhang; Chia-Chung Sun

    2012-01-01

    In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics\\/Poisson–Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA

  2. DFT Study of Solvent Effects on Conformational Equilibria and Vibrational Spectra of 4-(1-PYRROLIDINYL)PIPERAZINE

    NASA Astrophysics Data System (ADS)

    Baglayan, O.; Kesan, G.; Parlak, C.; Senyel, M.

    2012-06-01

    The optimized structural parameters (bond lengths, bond and dihedral angles), conformational equilibria and normal mode frequencies and corresponding vibrational assignments of 4-(1-Pyrrolidinyl)piperazine (4-pypp) have been examined by means of B3LYP hybrid density functional theory (DFT) method with 6-31++G(d,p) basis set. Furthermore, reliable vibrational assignments have made on the basis of potential energy distribution (PED) calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of 4-pypp (C_8H17N_3) have been predicted. Calculations are employed for different conformations of 4-pypp both in gas phase and in solution. Solvent effects are investigated using chloroform and dimethylsulfoxide. Results from the theoretical values are showed that the structural parameters, mole fractions of stable conformers, vibrational frequencies, IR intensities and Raman activities of 4-pypp are solvent dependent. {Keywords}: 4-(1-Pyrrolidinyl)piperazine, vibrational spectra, solvent effect, DFT.

  3. STEADY-STATE AND TIME-RESOLVED FLUORESCENCE QUENCHING WITH TRANSITION METAL IONS AS SHORT-DISTANCE PROBES FOR PROTEIN CONFORMATION

    PubMed Central

    Posokhov, Yevgen O.; Kyrychenko, Alexander; Ladokhin, Alexey S.

    2011-01-01

    A series of model dye-labeled histidine-containing peptides was used to investigate the nature of the quenching mechanism with Cu2+ and Ni2+. The strong reduction in steady-state fluorescence was found to be unaccompanied by any noticeable changes in lifetime kinetics. This static nature of quenching is not consistent with the dynamic FRET phenomenon, which was assumed to dominate the quenching mechanism, and is likely caused by shorter range orbital coupling. Our results indicate that the FRET-like 6th power of distance dependence of quenching cannot be automatically assumed for transition metal ions, and time-resolved measurements should be used to distinguish various quenching mechanisms. PMID:20707982

  4. Viscoelasticity, Conformational Transition and Ultrastructure of Kappa-Carrageenan in the Presence of Potassium Ion around the Critical Total Ion Concentration

    NASA Astrophysics Data System (ADS)

    Núñez-Santiago, María C.; Tecante, Alberto; Durand, Sylvie; Garnier, Catherine; Doublier, Jean L.

    2008-07-01

    Rheology, microDSC, and confocal laser scanning microscopy were used to study the effect of potassium ion on the viscoelastic behavior, disorder-order transition and the ultrastructure, respectively, of kappa-carrageenan in aqueous medium in the vicinity of the critical total ionic concentration (C*). The rheological tests showed a "weak" gel behavior, with G'>G? and both moduli dependent on frequency. However, during heating, microDSC showed two zones: one attributed to the presence of ordered double helices without aggregation, and another to the fusion of aggregated double helices. Microscopy showed a three-dimensional network whose continuity depends of the concentration of added potassium ions. For a gel to be formed, a sufficient amount of potassium ion is necessary to promote complete aggregation of double helices so they can form a continuous three-dimensional network.

  5. Solvent dependent photophysical properties of dimethoxy curcumin

    NASA Astrophysics Data System (ADS)

    Barik, Atanu; Indira Priyadarsini, K.

    2013-03-01

    Dimethoxy curcumin (DMC) is a methylated derivative of curcumin. In order to know the effect of ring substitution on photophysical properties of curcumin, steady state absorption and fluorescence spectra of DMC were recorded in organic solvents with different polarity and compared with those of curcumin. The absorption and fluorescence spectra of DMC, like curcumin, are strongly dependent on solvent polarity and the maxima of DMC showed red shift with increase in solvent polarity function (?f), but the above effect is prominently observed in case of fluorescence maxima. From the dependence of Stokes' shift on solvent polarity function the difference between the excited state and ground state dipole moment was estimated as 4.9 D. Fluorescence quantum yield (?f) and fluorescence lifetime (?f) of DMC were also measured in different solvents at room temperature. The results indicated that with increasing solvent polarity, ?f increased linearly, which has been accounted for the decrease in non-radiative rate by intersystem crossing (ISC) processes.

  6. Conformational Properties of ?-PrP*

    PubMed Central

    Hosszu, Laszlo L. P.; Trevitt, Clare R.; Jones, Samantha; Batchelor, Mark; Scott, David J.; Jackson, Graham S.; Collinge, John; Waltho, Jonathan P.; Clarke, Anthony R.

    2009-01-01

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly ?-helical conformation to one dominated by ?-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91–231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant ?-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a ?-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126–227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state. PMID:19369250

  7. 40 CFR 93.129 - Special exemptions from conformity requirements for pilot program areas.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit Laws § 93.129 Special exemptions from conformity...

  8. 40 CFR 93.129 - Special exemptions from conformity requirements for pilot program areas.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit Laws § 93.129 Special exemptions from conformity...

  9. 40 CFR 93.129 - Special exemptions from conformity requirements for pilot program areas.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit Laws § 93.129 Special exemptions from conformity...

  10. 40 CFR 93.129 - Special exemptions from conformity requirements for pilot program areas.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit Laws § 93.129 Special exemptions from conformity...

  11. 40 CFR 93.129 - Special exemptions from conformity requirements for pilot program areas.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...PLANS Conformity to State or Federal Implementation Plans of Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit Laws § 93.129 Special exemptions from conformity...

  12. Conformational studies of 3-hexyne

    NASA Astrophysics Data System (ADS)

    Churchill, Geoffrey B.; Wiberg, Kenneth B.; Bohn, Robert K.; Michels, H. Harvey

    The microwave spectrum of 3-hexyne has recently been observed and can be assigned unambiguously to a syn-eclipsed C2v conformation. Owing to its nonpolar nature, a trans-conformer (C2h) would not be observable in microwave studies. A gauche conformer (C2), which would exhibit tunneling splittings because there are two equivalent structures corresponding to a torsional angle of ±?, was also not experimentally observed. In the present study, we determine whether computational studies can be carried out with sufficient accuracy to support these experimental observations. The torsional barrier to rotation in this molecule is expected to be of the order of 10-20 cal/mol, similar to that observed in 2-butyne. This very low barrier offers a significant computational challenge. In an attempt to find a rigorous explanation for the observed stability of the C2v conformer, ab initio calculations were carried out at the Hartree-Fock (HF) and second-order Møller-Plesset (MP2) levels of theory with several basis sets, ranging from 6-311+G(d,p) to aug-cc-pVQZ. We find that the calculated potential energy surface for 3-hexyne is extremely flat for variation of the torsional angle. The relative stability of the conformers of 3-hexyne is quite dependent on the size of the basis set and tight convergence criteria must be used in the search for stable minima. Stable structures of nearly identical energy were found for the syn-eclipsed C2v conformation and a gauche C2 structure. The trans-C2h structure is found to be a transition state for the basis sets that were used in this study. The C2v structure has the lowest calculated energy using the aug-cc-pVQZ basis, in agreement with experiment.

  13. Time-resolved fluorescence studies of tryptophan mutants of Escherichia coli glutamine synthetase: conformational analysis of intermediates and transition-state complexes.

    PubMed Central

    Atkins, W. M.; Villafranca, J. J.

    1992-01-01

    Single tryptophan-containing mutants of low adenylylation state Escherichia coli glutamine synthetase have been studied by frequency-domain fluorescence spectroscopy in the presence of various substrates and inhibitors. At pH 6.5, the Mn-bound wild-type enzyme (wild type has two tryptophans/subunit) and the mutant enzymes exhibit heterogeneous fluorescence decay kinetics; the individual tryptophans are adequately described by a triple exponential decay scheme. The recovered lifetime values are 5.9 ns, 2.6 ns, and 0.4 ns for Trp-57 and 5.8 ns, 2.3 ns, and 0.4 ns for Trp-158. These values are nearly identical to the previously reported results at pH 7.5 (Atkins, W.M., Stayton, P.S., & Villafranca, J.J., 1991, Biochemistry 30, 3406-3416). In addition, Trp-57 and Trp-158 both exhibit an ATP-induced increase in the relative fraction of the long lifetime component, whereas only Trp-57 is affected by this ligand at pH 7.5. The transition-state analogue L-methionine-(R,S)-sulfoximine (MSOX) causes a dramatic increase in the fractional intensity of the long lifetime component of Trp-158. This ligand has no effect on the W158S mutant protein and causes a small increase in the fractional intensity of the long lifetime component of the W158F mutant protein. Addition of glutamate to the ATP complex, which affords the gamma-glutamylphosphate-ADP complex, results in the presence of new lifetime components at 7, 3.2, and 0.5 ns for Trp-158, but has no effect on Trp-57. Similar results were obtained when ATP was added to the MSOX complex; Trp-57 exhibits heterogeneous fluorescence decay with lifetimes of 7, 3.5, and 0.8 ns. Decay kinetics of Trp-158 are best fit to a nearly homogeneous decay with a lifetime of 5.5 ns in the MSOX-ATP inactivated complex. These results provide a model for the sequence of structural and dynamic changes that take place at the Trp-57 loop and the central loop (Trp-158) during several intermediate stages of catalysis. PMID:1363912

  14. Global conformal surface parameterization

    Microsoft Academic Search

    Xianfeng Gu; Shing-tung Yau

    2003-01-01

    We solve the problem of computing global conformal parameterizations for surfaces with nontrivial topologies. The parameterization is global in the sense that it preserves the conformality everywhere except for a few points, and has no boundary of discontinuity. We analyze the structure of the space of all global conformal parameterizations of a given surface and find all possible solutions by

  15. Irrational conformal field theory

    Microsoft Academic Search

    M. B. Halpern; E. Kiritsis; N. A. Obers; K. Clubok

    1996-01-01

    This is a review of irrational conformal field theory, which includes rational conformal field theory as a small subspace. Central topics of the review include the Virasoro master equation, its solutions and the dynamics of irrational conformal field theory. Discussion of the dynamics includes the generalized Knizhnik-Zamolodchikov equations on the sphere, the corresponding heat-like systems on the torus and the

  16. Toward TeV Conformality

    SciTech Connect

    Appelquist, T; Avakian, A; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Soltz, R; Vranas, P

    2009-11-30

    We study the chiral condensate <{bar {psi}}{psi}> for an SU(3) gauge theory with N{sub f} massless Dirac fermions in the fundamental representation when N{sub f} is increased from 2 to 6. For N{sub f} = 2, our lattice simulations of <{bar {psi}}{psi}>/F{sup 3}, where F is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For N{sub f} = 6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{sub f} increases further, toward the critical value for transition from confinement to infrared conformality.

  17. Transition States, analogues, and drug development.

    PubMed

    Schramm, Vern L

    2013-01-18

    Enzymes achieve their transition states by dynamic conformational searches on the femtosecond to picosecond time scale. Mimics of reactants at enzymatic transition states bind tightly to enzymes by stabilizing the conformation optimized through evolution for transition state formation. Instead of forming the transient transition state geometry, transition state analogues convert the short-lived transition state to a stable thermodynamic state. Enzymatic transition states are understood by combining kinetic isotope effects and computational chemistry. Analogues of the transition state can bind millions of times more tightly than substrates and show promise for drug development for several targets. PMID:23259601

  18. Conformational kinetics of triligated hemoglobin.

    PubMed Central

    Ferrone, F A; Martino, A J; Basak, S

    1985-01-01

    We have used the method of modulated excitation (Ferrone, F.A., and J.J. Hopfield, 1976, Proc. Natl. Acad. Sci. USA. 73:4497-4501), with an improved apparatus and a revised analytical procedure, to measure the rate of conformational change between the oxy (R) and deoxy (T) conformations of triligated carboxy-hemoglobin A at pH 6.5 and 7.0. We have found the rates to be kRT = 1.2 X 10(3) s-1 and kTR = 3.5 X 10(3) s-1 for pH 6.5, while for pH 7.0, kRT = 1.0 X 10(3) s-1, and kTR = 3.0 X 10(3) s-1. The value for L3, the equilibrium constant between conformations, was virtually unchanged between pH 6.5 and 7.0. While the rates measured here differ from those obtained in the original use of this method, these new rates are fully consistent with the original data when analyzed by the revised procedures presented here. When taken with other kinetic and equilibrium data, our measurements suggest that the transition state between structures is dominated by the behavior of the T quaternary structure. Finally, a spectral feature near the HbCO Soret peak has been observed that we ascribe to an allosteric perturbation of the spectra of the liganded hemes. PMID:4052561

  19. Conformational properties of polymers

    NASA Astrophysics Data System (ADS)

    Lee, Namkyoung

    In this thesis, I study the conformational properties of polymers in non-stationary and stationary states. In the first part of my thesis, I study the conformations of polymers in non-stationary state. I consider two cases: (1) the motion of a polymer penetrating a membrane and (2) the dynamics of DNA molecules in a gel. In the first case, I assume that a polymer crosses a membrane several times during the process of penetration. The polymer reptates along its own contour. The mobility of the polymer chain is related to its configurations which are characterized by the number of crossings with the membrane. I find the configurations which give the main contribution to the transport and calculate the overall permeability in the case of both Zimm and Rouse dynamics. As a second system, I consider the motion of a long DNA molecule confined in a gel. When a strong electric field is applied, the electric field forces the DNA into a tree-like structure. The dynamics of large segments of DNA is almost deterministic and can be described by a set of simple mechanical equations. This allows the numerical study of gel electrophoresis of DNA. I confirm the hypothesis of the statistical self-similarity of a moving polymer. In the second part of the thesis, there are three major sections all dealing with configurational properties of a single isolated charged polymer. (1) I study the configurational statistics of a ring polyampholyte chain. In addition to the cascade like transitions similar to that in a linear chain, I found that a ring polyampholyte has a metastable phase where the configurations are controlled by the randomness in the charge distribution. (2) I study new exact solution of the nonlinear Poisson-Boltzmann equation describing counterion condensation on a strongly charged polymer in the dilute regime. The counterion has to be brought from three-dimensional space and the entropy loss is 3/2 times larger than in the picture of Manning. The condensation occurs at a critical line charge density lambda=3/2, which is 3/2 times larger than in Manning's theory. (3) I study the rigidity of the charged polymer in the presence of counterion condensation. I show that the condensation of counterions changes the local structure of the charged polymer more than in the Debye-Huckel approximation. By solving the Poisson Boltzmann equation in cylindrical coordinates in the vicinity of charged polymer, I show that the persistence length lsb{p} of a strongly charged polymer is proportional to the Debye radius lsb{p}˜ Rsb{d}.

  20. Discovering Conformational Sub-States Relevant to Protein Function

    PubMed Central

    Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2011-01-01

    Background Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. Methods and Findings To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function. Conclusions Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function. PMID:21297978

  1. Intrinsically disordered proteins and conformational noise

    PubMed Central

    Mahmoudabadi, Gita; Rajagopalan, Krithika; Getzenberg, Robert H.; Hannenhalli, Sridhar; Rangarajan, Govindan; Kulkarni, Prakash

    2013-01-01

    Intrinsically disordered proteins, IDPs, are proteins that lack a rigid 3D structure under physiological conditions, at least in vitro. Despite the lack of structure, IDPs play important roles in biological processes and transition from disorder to order upon binding to their targets. With multiple conformational states and rapid conformational dynamics, they engage in myriad and often “promiscuous” interactions. These stochastic interactions between IDPs and their partners, defined here as conformational noise, is an inherent characteristic of IDP interactions. The collective effect of conformational noise is an ensemble of protein network configurations, from which the most suitable can be explored in response to perturbations, conferring protein networks with remarkable flexibility and resilience. Moreover, the ubiquitous presence of IDPs as transcriptional factors and, more generally, as hubs in protein networks, is indicative of their role in propagation of transcriptional (genetic) noise. As effectors of transcriptional and conformational noise, IDPs rewire protein networks and unmask latent interactions in response to perturbations. Thus, noise-driven activation of latent pathways could underlie state-switching events such as cellular transformation in cancer. To test this hypothesis, we created a model of a protein network with the topological characteristics of a cancer protein network and tested its response to a perturbation in presence of IDP hubs and conformational noise. Because numerous IDPs are found to be epigenetic modifiers and chromatin remodelers, we hypothesize that they could further channel noise into stable, heritable genotypic changes. PMID:23255110

  2. Vibrational Spectroscopic Investigation and Conformational Analysis of 1-HEPTYLAMINE: a Comparative Density Functional Study

    NASA Astrophysics Data System (ADS)

    Tursun, Mahir; Kesan, Gurkan; Parlak, Cemal; Senyel, Mustafa

    2013-06-01

    FT-IR and Raman spectra of 1-heptylamine (1-ha) were experimentally reported in the region of 4000-10 cm-1 and 4000-100 cm-1, respectively. The conformational analysis, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 1-ha (C7H17N) were theoretically examined by means of Becke-3-Lee-Yang-Parr (B3-LYP) density functional theory (DFT) method together with 6-31++G(d,p) basis set. Furthermore, reliable vibrational assignments were made on the basis of potential energy distribution (PED) calculated and the thermodynamics functions, highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO) of 1-ha were predicted. Calculations were carried out with the possible ten conformational isomers (TT, TG, GT, GT1, GG1, GG2, GG3, GG4, GG5, GG6; T and G denote trans and gauge) of 1-ha, both in gas phase and in solution. Solvent effects were investigated using benzene and methanol. All results indicates that B3-LYP method provides satisfactory results for the prediction vibrational wavenumbers, TT isomer is the most stable form of 1-ha and the conformational energy barrier is independent of the solvent whereas the vibrational frequencies and assignments, IR and Raman intensities of 1-ha are solvent dependent.

  3. Conformal Carroll groups

    E-print Network

    C. Duval; G. W. Gibbons; P. A. Horvathy

    2014-07-02

    Conformal extensions of Levy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labelled by an integer $k$. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to Conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by "Carrollian photons". Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

  4. Conformal Carroll groups

    NASA Astrophysics Data System (ADS)

    Duval, C.; Gibbons, G. W.; Horvathy, P. A.

    2014-08-01

    Conformal extensions of Lévy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labeled by an integer k. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by ‘Carrollian photons’. Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

  5. Transport in non-conformal holographic fluids

    E-print Network

    Shailesh Kulkarni; Bum-Hoon Lee; Jae-Hyuk Oh; Chanyong Park; Raju Roychowdhury

    2013-03-06

    We have considered non-conformal fluid dynamics whose gravity dual is a certain Einstein dilaton system with Liouville type dilaton potential, characterized by an intrinsic parameter $\\eta$. We have discussed the Hawking-Page transition in this framework using hard-wall model and it turns out that the critical temperature of the Hawking-Page transition encapsulates a non-trivial dependence on $\\eta$. We also obtained transport coefficients such as AC conductivity, shear viscosity and diffusion constant in the hydrodynamic limit, which show non-trivial $\\eta$ dependent deviations from those in conformal fluids, although the ratio of the shear viscosity to entropy density is found to saturate the universal bound. Some of the retarded correlators are also computed in the high frequency limit for case study.

  6. Microwave Spectrum of Allyl Isothiocyanate: gauche Conformer

    NASA Astrophysics Data System (ADS)

    Maiti, S.; Jaman, A. I.; Nandi, R. N.

    1994-05-01

    The ground state microwave rotational spectrum of allyl isothiocyanate (H 2C?CHCH 2NCS) has been observed and analyzed in the frequency range 12.4-26.0 GHz. Analysis of a-type R-branch transitions gives the rotational constants A = 7918.32, B = 1252.95, and C = 1123.66 MHz, which are consistent with the C- gauche conformer of the molecule having the NCS group cis with respect to the C?C bond.

  7. [Conformers of carnosine].

    PubMed

    Kliuev, S A

    2006-01-01

    The geometric and energetic parameters of most stable conformations of carnosine were calculated by the semiempirical guantum-chemical method PM3. The carnosine-water-zinc (II) clusters were simulated. PMID:16909845

  8. Assemblies of Conformal Tanks

    NASA Technical Reports Server (NTRS)

    DeLay, Tom

    2009-01-01

    Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.

  9. Conformal invariance of curvature perturbation

    E-print Network

    Jinn-Ouk Gong; Jai-chan Hwang; Wan Il Park; Misao Sasaki; Yong-Seon Song

    2011-07-10

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the delta N formalism, and show its conformal invariance.

  10. Ambient connections realising conformal Tractor

    E-print Network

    Olver, Peter

    Ambient connections realising conformal Tractor holonomy Thomas Leistner, University of Adelaide 17-August 4, Poster session, July 24, 2006 #12;Conformal Structures and Tractor bundles A conformal is the normal conformal Tractor bundle. It is a vector bundle which is associated to the principle fibre bundle

  11. Protein Conformational Populations and Functionally Relevant Sub-states

    SciTech Connect

    Agarwal, Pratul K [ORNL; Burger, Virginia [University of Pittsburgh School of Medicine, Pittsburgh PA; Savol, Andrej [University of Pittsburgh School of Medicine, Pittsburgh PA; Ramanathan, Arvind [ORNL; Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA

    2013-01-01

    Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.

  12. Killing Tensors and Conformal Killing Tensors from Conformal Killing Vectors

    E-print Network

    Raffaele Rani; S. Brian Edgar; Alan Barnes

    2003-03-12

    Koutras has proposed some methods to construct reducible proper conformal Killing tensors and Killing tensors (which are, in general, irreducible) when a pair of orthogonal conformal Killing vectors exist in a given space. We give the completely general result demonstrating that this severe restriction of orthogonality is unnecessary. In addition we correct and extend some results concerning Killing tensors constructed from a single conformal Killing vector. A number of examples demonstrate how it is possible to construct a much larger class of reducible proper conformal Killing tensors and Killing tensors than permitted by the Koutras algorithms. In particular, by showing that all conformal Killing tensors are reducible in conformally flat spaces, we have a method of constructing all conformal Killing tensors (including all the Killing tensors which will in general be irreducible) of conformally flat spaces using their conformal Killing vectors.

  13. Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms

    PubMed Central

    Yang, Sichun; Roux, Benoît

    2008-01-01

    Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the ?C helix, the activation-loop, and the ? strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the ?C helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation. PMID:18369437

  14. Electronically Rich N-Substituted Tetrahydroisoquinoline 3-Carboxylic Acid Esters: Concise Synthesis and Conformational Studies

    PubMed Central

    Al-Horani, Rami A.; Desai, Umesh R.

    2012-01-01

    Recent work in our laboratory has shown that the highly substituted, electronically rich 1,2,3,4–tetrahydroisoquinoline–3–carboxylic acid (THIQ3CA) scaffold is a key building block for a novel class of promising anticoagulants (Al-Horani et al. J. Med. Chem. 2011, 54, 6125–6138). The synthesis of THIQ3CA analogs, especially containing specific, electronically rich substituents, has been a challenge and essentially no efficient methods have been reported in the literature. We describe three complementary, glycine donor-based strategies for high yielding synthesis of highly substituted, electronically rich THIQ3CA esters. Three glycine donors studied herein include hydantoin 1, (±)-Boc-?-phosphonoglycine trimethyl ester 2 and (±)-Z-?-phosphonoglycine trimethyl ester 3. Although the synthesis of THIQ3CA analogs could be achieved using either of the three, an optimal, high yielding approach for the desired THIQ3CA esters was best achieved using 3 in three mild, efficient steps. Using this approach, a focused library of advanced N-arylacyl, N-arylalkyl, and bis-THIQ3CA analogs was synthesized. Variable temperature and solvent-dependent NMR chemical shift studies indicated the presence of two major conformational rotamers in 3:1 proportion for N–arylacyl–THIQ3CA analogs, which were separated by a high kinetic barrier of ~17 kcal/mol. In contrast, N–arylalkyl and bis–THIQ3CA variants displayed no rotamerism, which implicates restricted rotation around the amide bond as the origin for high-barrier conformational interconversion. This phenomenon is of major significance because structure-based drug design typically utilizes only one conformation. Overall, the work presents fundamental studies on the synthesis and conformational properties of highly substituted, electronically rich THIQ3CA analogs. PMID:22665943

  15. Characterization of DNA conformation inside bacterial viruses

    NASA Astrophysics Data System (ADS)

    Petrov, Anton S.; Locker, C. Rebecca; Harvey, Stephen C.

    2009-08-01

    In this study we develop a formalism to describe the organization of DNA inside bacteriophage capsids during genome packaging. We have previously shown that DNA inside bacteriophage phi29 (?29) is organized into folded toroids [A. S. Petrov and S. C. Harvey, Structure 15, 21 (2007)], whereas epsilon15 (?15) reveals the coaxial organization of the genetic material [A. S. Petrov, K. Lim-Hing, and S. C. Harvey, Structure 15, 807 (2007)]. We now show that each system undergoes two consecutive transitions. The first transition corresponds to the formation of global conformations and is analogous to a disorder-order conformational transition. The second transition is characterized by a significant loss of DNA mobility at the local level leading to glasslike dynamic behavior. Packing genetic material inside bacteriophages can be used as a general model to study the behavior of semiflexible chains inside confined spaces, and the proposed formalism developed here can be used to study other systems of linear polymer chains confined to closed spaces.

  16. Conformal General Relativity

    E-print Network

    V. Pervushin; D. Proskurin

    2001-06-03

    The inflation-free solution of problems of the modern cosmology (horizon, cosmic initial data, Planck era, arrow of time, singularity,homogeneity, and so on) is considered in the conformal-invariant unified theory given in the space with geometry of similarity where we can measure only the conformal-invariant ratio of all quantities. Conformal General Relativity is defined as the $SU_c(3)\\times SU(2)\\times U(1)$-Standard Model where the dimensional parameter in the Higgs potential is replaced by a dilaton scalar field described by the negative Penrose-Chernikov-Tagirov action. Spontaneous SU(2) symmetry breaking is made on the level of the conformal-invariant angle of the dilaton-Higgs mixing, and it allows us to keep the structure of Einstein's theory with the equivalence principle. We show that the lowest order of the linearized equations of motion solves the problems mentioned above and describes the Cold Universe Scenario with the constant temperature T and z-history of all masses with respect to an observable conformal time. A new fact is the intensive cosmic creation of $W,Z$-vector bosons due to their mass singularity. In the rigid state, this effect is determined by the integral of motion $(m_w^2H_{\\rm hubble})^{1/3}=2.7 K k_B$ that coincides with the CMB temperature and has the meaning of the primordial Hubble parameter. The created bosons are enough to consider their decay as an origin of the CMB radiation and all observational matter with the observational element abundances and the baryon asymmetry. Recent Supernova data on the relation between the luminosity distance and redshift (including the point $z=1.7$) do not contradict the dominance of the rigid state of the dark matter in the Conformal Cosmology.

  17. Charged Conformal Killing Spinors

    E-print Network

    Andree Lischewski

    2014-08-10

    We study the twistor equation on pseudo-Riemannian $Spin^c-$manifolds whose solutions we call charged conformal Killing spinors (CCKS). We derive several integrability conditions for the existence of CCKS and study their relations to spinor bilinears. A construction principle for Lorentzian manifolds admitting CCKS with nontrivial charge starting from CR-geometry is presented. We obtain a partial classification result in the Lorentzian case under the additional assumption that the associated Dirac current is normal conformal and complete the Classification of manifolds admitting CCKS in all dimensions and signatures $\\leq 5$ which has recently been initiated in the study of supersymmetric field theories on curved space.

  18. Conformally coupled dark matter

    E-print Network

    Mark Israelit

    1996-08-15

    Dark matter is obtained from a scalar field coupled conformally to gravitation; the scalar being a relict of Dirac's gauge function. This conformally coupled dark matter includes a gas of very light ($m\\approx 2.25\\times 10^{-34} eV$) neutral bosons having spin 0, as well as a time-dependent global scalar field, both pervading all of the cosmic space. The time-development of this dark matter in the expanding F-R-W universe is investigated, and an acceptable cosmological behaviour is obtained.

  19. Conformation of Oligo(Ethylene Glycol) grafted Poly(Norbornene) in solutions: A Small Angle Neutron Scattering Study

    SciTech Connect

    Cheng, Gang [ORNL; Melnichenko, Yuri B [ORNL; Hua, Fengjun [ORNL; Hong, Kunlun [ORNL; Wignall, George D [ORNL; Hammouda, B. [National Institute of Standards and Technology (NIST); Mays, Jimmy [ORNL

    2008-01-01

    The structure of thermo sensitive poly(methoxyoligo(ethylene glycol) norbornenyl esters) homopolymers in dilute solution was investigated by Small Angle Neutron Scattering (SANS). The homopolymers consist of a polynorbornene (PNB) backbone with a degree of polymerization (DP) of 50, and each backbone monomer has a grafted Ethylene Glycol (EG) side chain with an average DP of 6.6. The hydrophobic backbone and hydrophilic side chains interact differently with solvents depending on their polarity, which makes the conformation very sensitive to the solvent quality. The polymer conformation was studied in two solvents, d-toluene and D2O, with the aim of understanding the influence of solvent/polymer interactions on the resulting structures. It was found that in a 0.5 wt. % solution in d-toluene the polymers assume wormlike chains and gradually contract with increasing polymer concentration. In a 0.5 wt. % solution in D2O, the polymers are partially contracted at room temperature and their conformation can be described by the form factor of a rigid cylinder. The volume of the cylinder shows no concentration dependence. Furthermore, the polymers in D2O collapse at higher temperatures due to decreasing solubility of the side chains in water.

  20. Galilean conformal and superconformal symmetries

    SciTech Connect

    Lukierski, J., E-mail: lukier@ift.uni.wroc.pl [University of Wroclaw, Institute for Theoretical Physics (Poland)

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  1. Characterizing the conformational ensemble of monomeric polyglutamine.

    PubMed

    Wang, Xiaoling; Vitalis, Andreas; Wyczalkowski, Matthew A; Pappu, Rohit V

    2006-05-01

    Studies of synthetic polyglutamine peptides in vitro have established that polyglutamine peptides aggregate via a classic nucleation and growth mechanism. Chen and colleagues [Proc Natl Acad Sci U S A 2002;99:11884-11889] have found that monomeric polyglutamine, which is a disordered statistical coil in solution, is the critical nucleus for aggregation. Therefore, nucleation of beta-sheet-rich aggregates requires an initial disorder to order transition, which is a highly unfavorable thermodynamic reaction. The questions of interest to us are as follows: What are the statistical fluctuations that drive beta-sheet formation in monomeric polyglutamine? How do these fluctuations vary with chain length? And why is this process thermodynamically unfavorable, that is, why is monomeric polyglutamine disordered? To answer these questions we use multiple molecular dynamics simulations to provide quantitative characterization of conformational ensembles for two short polyglutamine peptides. We find that the ensemble for polyglutamine is indeed disordered. However, the disorder is inherently different from that of denatured proteins and the average compactness and magnitude of conformational fluctuations increase with chain length. Most importantly, the effective concentration of sidechain primary amides around backbone units is inherently high and peptide units are solvated either by hydrogen bonds to sidechains or surrounding water molecules. Due to the multiplicity of backbone solvation modes the probability associated with any specific backbone conformation is small, resulting in a conformational entropy bottleneck which makes beta-sheet formation in monomeric polyglutamine thermodynamically unfavorable. PMID:16299774

  2. Conforming quadrilaterals meshes on the cubed sphere.

    SciTech Connect

    Taylor, Mark A.; Levy, Michael Nathan; Overfelt, James Robert

    2010-08-01

    The cubed sphere geometry, obtained by inscribing a cube in a sphere and mapping points between the two surfaces using a gnomonic (central) projection, is commonly used in atmospheric models because it is free of polar singularities and is well-suited for parallel computing. Global meshes on the cubed-sphere typically project uniform (square) grids from each face of the cube onto the sphere, and if refinement is desired then it is done with non-conforming meshes - overlaying the area of interest with a finer uniform mesh, which introduces so-called hanging nodes on edges along the boundary of the fine resolution area. An alternate technique is to tile each face of the cube with quadrilaterals without requiring the quads to be rectangular. These meshes allow for refinement in areas of interest with a conforming mesh, providing a smoother transition between high and low resolution portions of the grid than non-conforming refinement. The conforming meshes are demonstrated in HOMME, NCAR's High Order Method Modeling Environment, where two modifications have been made: the dependence on uniform meshes has been removed, and the ability to read arbitrary quadrilateral meshes from a previously-generated file has been added. Numerical results come from a conservative spectral element method modeling a selection of the standard shallow water test cases.

  3. Atomic cranks and levers control sugar ring conformations

    NASA Astrophysics Data System (ADS)

    Zhang, Qingmin; Lee, Gwangrog; Marszalek, Piotr E.

    2005-05-01

    In this paper we review the conformational analysis of sugar rings placed under tension during mechanical manipulations of single polysaccharide molecules with the atomic force microscope and during steered molecular dynamics simulations. We examine the role of various chemical bonds and linkages between sugar rings in inhibiting or promoting their conformational transitions by means of external forces. Small differences in the orientation of one chemical bond on the sugar ring can produce significantly different mechanical properties at the polymer level as exemplified by two polysaccharides: cellulose, composed of ?-1\\to 4 -linked D-glucose, and amylose, composed of ?-1\\to 4 -linked D-glucose. In contrast to ?-glucose rings, which are mechanically stable and produce simple entropic elasticity of the chain, ?-glucose rings flip under tension from their chair to a boat-like structure and these transitions produce deviations of amylose elasticity from the freely jointed chain model. We also examine the deformation of two mechanically complementary 1 \\to 6 -linked polysaccharides: pustulan, a ?-1\\to 6 -linked glucan, and dextran, a ?-1\\to 6 -linked glucan. Forced rotations about the C5-C6 bonds govern the elasticity of pustulan, and complex conformational transitions that involve simultaneous C5-C6 rotations and chair-boat transitions govern the elasticity of dextran. Finally, we discuss the likelihood of various conformational transitions in sugar rings in biological settings and speculate on their significance.

  4. Simple, yet powerful methodologies for conformational sampling of proteins.

    PubMed

    Harada, Ryuhei; Takano, Yu; Baba, Takeshi; Shigeta, Yasuteru

    2015-03-01

    Several biological functions, such as molecular recognition, enzyme catalysis, signal transduction, allosteric regulation, and protein folding, are strongly related to conformational transitions of proteins. These conformational transitions are generally induced as slow dynamics upon collective motions, including biologically relevant large-amplitude fluctuations of proteins. Although molecular dynamics (MD) simulation has become a powerful tool for extracting conformational transitions of proteins, it might still be difficult to reach time scales of the biological functions because the accessible time scales of MD simulations are far from biological time scales, even if straightforward conventional MD (CMD) simulations using massively parallel computers are employed. Thus, it is desirable to develop efficient methods to achieve canonical ensembles with low computational costs. From this perspective, we review several enhanced conformational sampling techniques of biomolecules developed by us. In our methods, multiple independent short-time MD simulations are employed instead of single straightforward long-time CMD simulations. Our basic strategy is as follows: (i) selection of initial seeds (initial structures) for the conformational sampling in restarting MD simulations. Here, the seeds should be selected as candidates with high potential to transit. (ii) Resampling from the selected seeds by initializing velocities in restarting short-time MD simulations. A cycle of these simple protocols might drastically promote the conformational transitions of biomolecules. (iii) Once reactive trajectories extracted from the cycles of short-time MD simulations are obtained, a free energy profile is evaluated by means of umbrella sampling (US) techniques with the weighted histogram analysis method (WHAM) as a post-processing technique. For the selection of the initial seeds, we proposed four different choices: (1) Parallel CaScade molecular dynamics (PaCS-MD), (2) Fluctuation Flooding Method (FFM), (3) Outlier FLOODing (OFLOOD) method, and (4) TaBoo SeArch (TBSA) method. We demonstrate applications of our methods to several biological systems, such as domain motions of proteins with large-amplitude fluctuations, conformational transitions upon ligand binding, and protein folding/refolding to native structures of proteins. Finally, we show the conformational sampling efficiencies of our methods compared with those by CMD simulations and other previously developed enhanced conformational sampling methods. PMID:25659594

  5. Taming the conformal zoo

    Microsoft Academic Search

    Gregory Moore; Nathan Seiberg

    1989-01-01

    All known rational conformal field theories may be obtained from (2+1) dimensional Chern-Simons gauge theories by appropriate choice of gauge group. We conjecture that all rational field theories are classified by groups via (2+1)-dimensional Chern-Simons gauge theories. On leave of absence from the Department of Physics, Weizmann Institute of Science, Rehovot 76100, Israel.

  6. Metamaterials with conformational nonlinearity

    E-print Network

    Metamaterials with conformational nonlinearity Mikhail Lapine1,2 , Ilya V. Shadrivov1,2 , David A development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer

  7. Massive conformal gravity

    E-print Network

    F. F. Faria

    2014-12-15

    In this article we construct a massive theory of gravity that is invariant under conformal transformations. The massive action of the theory depend on the metric tensor and a scalar field, which are considered as the only field variables. We find the vacuum field equations of the theory and the solution of its Newtonian limit.

  8. Solid state NMR measurements of conformation and conformational

    E-print Network

    Weliky, David

    Solid state NMR measurements of conformation and conformational distributions in the membrane Lansing, MI, USA The solid state NMR lineshape of a protein backbone carbonyl nucleus is a general conformation in the distri- bution. These types of solid state NMR methodologies have been applied

  9. Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling

    NASA Astrophysics Data System (ADS)

    Wang, Jun; Gu, Yan; Liu, Haiyan

    2006-09-01

    We improve the multidimensional adaptive umbrella sampling method for the computation of conformational free energies of biomolecules. The conformational transition between the ?-helical and ?-hairpin conformational states of an alanine decapeptide is used as an example. Convergence properties of the weighted-histogram-analysis-based adaptive umbrella sampling can be improved by using multiple replicas in each adaptive iteration and by using adaptive updating of the bounds of the umbrella potential. Using positional root-mean-square deviations from structures of the ?-helical and ?-hairpin reference states as reaction coordinates, we obtained well-converged free energy surfaces of both the in-vacuum and in-solution decapeptide systems. From the free energy surfaces well-converged relative free energies between the two conformational states can be derived. Advantages and disadvantages of different methods for obtaining conformational free energies as well as implications of our results in studying conformational transitions of proteins and in improving force field are discussed.

  10. An Expression of Periodic Phenomena of Fashion on Sexual Selection Model with Conformity Genes and Memes

    NASA Astrophysics Data System (ADS)

    Mutoh, Atsuko; Tokuhara, Shinya; Kanoh, Masayoshi; Oboshi, Tamon; Kato, Shohei; Itoh, Hidenori

    It is generally thought that living things have trends in their preferences. The mechanism of occurrence of another trends in successive periods is concerned in their conformity. According to social impact theory, the minority is always exists in the group. There is a possibility that the minority make the transition to the majority by conforming agents. Because of agent's promotion of their conform actions, the majority can make the transition. We proposed an evolutionary model with both genes and memes, and elucidated the interaction between genes and memes on sexual selection. In this paper, we propose an agent model for sexual selection imported the concept of conformity. Using this model we try an environment where male agents and female agents are existed, we find that periodic phenomena of fashion are expressed. And we report the influence of conformity and differentiation on the transition of their preferences.

  11. Relaxation time of non-conformal plasma

    E-print Network

    Alex Buchel

    2009-11-27

    We study effective relaxation time of viscous hydrodynamics of strongly coupled non-conformal gauge theory plasma using gauge theory/string theory correspondence. We compute leading corrections to the conformal plasma relaxation time from the relevant deformations due to dim-2 and dim-3 operators. We discuss in details the relaxation time tau_eff of N=2^* plasma. For a certain choice of masses this theory undergoes a phase transition with divergent specific heat c_V ~ |1-T_c/T|^(-1/2). Although the bulk viscosity remains finite all the way to the critical temperature, we find that tau_eff diverges near the critical point as tau_eff ~ |1-T_c/T|^(-1/2).

  12. Loop Virasoro Lie conformal algebra

    SciTech Connect

    Wu, Henan, E-mail: wuhenanby@163.com; Chen, Qiufan; Yue, Xiaoqing [Department of Mathematics, Tongji University, Shanghai 200092 (China)] [Department of Mathematics, Tongji University, Shanghai 200092 (China)

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[?]-basis (L{sub i} | i?Z) and ?-brackets [L{sub i}?{sub ?}?L{sub j}] = (???2?)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  13. Conformal mappings involving curvilinear quadrangles

    E-print Network

    Craster, Richard

    1 Conformal mappings involving curvilinear quadrangles By R.V. Craster Department of Theoretical Mechanics, University of Nottingham, Nottingham, NG7 2RD, U.K. Conformally mapping a curvilinear quadrangle and there are usually no obvious solutions. In this paper conformal mappings involving a special class of curvilinear

  14. Conformal Complementarity Maps

    E-print Network

    Jose L. F. Barbon; Eliezer Rabinovici

    2013-08-08

    We study quantum cosmological models for certain classes of bang/crunch singularities, using the duality between expanding bubbles in AdS with a FRW interior cosmology and perturbed CFTs on de Sitter space-time. It is pointed out that horizon complementarity in the AdS bulk geometries is realized as a conformal transformation in the dual deformed CFT. The quantum version of this map is described in full detail in a toy model involving conformal quantum mechanics. In this system the complementarity map acts as an exact duality between eternal and apocalyptic Hamiltonian evolutions. We calculate the commutation relation between the Hamiltonians corresponding to the different frames. It vanishes only on scale invariant states.

  15. Intramolecular Conformational Changes Optimize Protein Kinase C Signaling#

    PubMed Central

    Antal, Corina E.; Violin, Jonathan D.; Kunkel, Maya T.; Skovsø, Søs

    2014-01-01

    Summary Optimal tuning of enzyme signaling is critical for cellular homeostasis. We use fluorescence resonance energy transfer reporters in live cells to follow conformational transitions that tune the affinity of a multi-domain signal transducer, protein kinase C, for optimal response to second messengers. This enzyme comprises two diacylglycerol sensors, the C1A and C1B domains, whose intrinsic affinity for ligand is sufficiently high that the enzyme would be in a ligand-engaged, active state if not for mechanisms that mask its domains. We show that both diacylglycerol sensors are exposed in newly-synthesized protein kinase C and that conformational transitions following priming phosphorylations mask the domains such that the lower affinity sensor, the C1B domain, is the primary diacylglycerol binder. Protein kinase C's conformational rearrangements serve as a paradigm for how multi-module transducers optimize their dynamic range of signaling. PMID:24631122

  16. 40 CFR 93.114 - Criteria and procedures: Currently conforming transportation plan and TIP.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit...currently conforming TIP at the time of project approval, or a project must meet the requirements in §...

  17. 40 CFR 93.114 - Criteria and procedures: Currently conforming transportation plan and TIP.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit...currently conforming TIP at the time of project approval, or a project must meet the requirements in §...

  18. 40 CFR 93.114 - Criteria and procedures: Currently conforming transportation plan and TIP.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit...currently conforming TIP at the time of project approval, or a project must meet the requirements in §...

  19. The Observation and Study of ELP V5-120 Conformational Changes 

    E-print Network

    Zhou, Qian

    2012-10-24

    and secondary/tertiary structure formation. In this thesis, the collapse process of ELP was studied with differential scanning calorimetry (DSC). In DSC thermal cycling, a clear conformational transition was observed. Also, a transiently stable state of ELP V5...

  20. 40 CFR 93.114 - Criteria and procedures: Currently conforming transportation plan and TIP.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...Transportation Plans, Programs, and Projects Developed, Funded or Approved Under Title 23 U.S.C. or the Federal Transit...currently conforming TIP at the time of project approval, or a project must meet the requirements in §...

  1. Conformational distributions of unfolded polypeptides from novel NMR techniques

    NASA Astrophysics Data System (ADS)

    Meier, Sebastian; Blackledge, Martin; Grzesiek, Stephan

    2008-02-01

    How the information content of an unfolded polypeptide sequence directs a protein towards a well-formed three-dimensional structure during protein folding remains one of the fundamental questions in structural biology. Unfolded proteins have recently attracted further interest due to their surprising prevalence in the cellular milieu, where they fulfill not only central regulatory functions, but also are implicated in diseases involving protein aggregation. The understanding of both the protein folding transition and these often natively unfolded proteins hinges on a more detailed experimental characterization of the conformations and conformational transitions in the unfolded state. This description is intrinsically very difficult due to the very large size of the conformational space. In principle, solution NMR can monitor unfolded polypeptide conformations and their transitions at atomic resolution. However, traditional NMR parameters such as chemical shifts, J couplings, and nuclear Overhauser enhancements yield only rather limited and often qualitative descriptions. This situation has changed in recent years by the introduction of residual dipolar couplings and paramagnetic relaxation enhancements, which yield a high number of well-defined, quantitative parameters reporting on the averages of local conformations and long-range interactions even under strongly denaturing conditions. This information has been used to obtain plausible all-atom models of the unfolded state at increasing accuracy. Currently, the best working model is the coil model, which derives amino acid specific local conformations from the distribution of amino acid torsion angles in the nonsecondary structure conformations of the protein data bank. Deviations from the predictions of such models can often be interpreted as increased order resulting from long-range contacts within the unfolded ensemble.

  2. Conformal anomaly of some 2-d Z (n) models

    NASA Astrophysics Data System (ADS)

    William, Peter

    1991-01-01

    We describe a numerical calculation of the conformal anomaly in the case of some two-dimensional statistical models undergoing a second-order phase transition, utilizing a recently developed method to compute the partition function exactly. This computation is carried out on a massively parallel CM2 machine, using the finite size scaling behaviour of the free energy.

  3. Integrating Formal Verification and Conformance Testing for Reactive Systems

    E-print Network

    Paris-Sud XI, Université de

    verified on the specification using automatic techniques based on approximated state-space exploration of properties. Because of this incompleteness and of state-space explosion, the verification may not succeed a conformance testing theory based on IOLTS (input- output labeled transition systems) and the ioco con

  4. Conformations of amphiphilic polyelectrolyte stars with diblock copolymer arms

    E-print Network

    Alexey A. Polotsky; Tatiana M. Birshtein; Mohamed Daoud; Oleg V. Borisov

    2012-05-12

    We consider conformations and intra-molecular conformational transitions in amphiphilic starlike polymers formed by diblock copolymer arms with inner hydrophobic and outer polyelectrolyte blocks. A combination of an analytical mean-field theory with the assumption-free numerical self-consistent field (SCF) modeling approach is applied. It is demonstrated that unimolecular micelles with collapsed hydrophobic cores and swollen polyelectrolyte coronae are formed in dilute aqueous solutions at high ionic strength or/and low degree of ionization of the outer hydrophilic block. An intra-molecular conformational transition related to the unfolding of the hydrophobic core of the unimolecular micelles can be triggered by a decrease in the ionic strength of the solution or/and increase in the degree of ionization of the coronal blocks. In the stars with large number of diblock copolymer arms the transition between conformations with collapsed or stretched core-forming blocks occurs continuously by progressive unfolding of the core domain. By contrast, in the stars with relatively small number of arms the continuous unfolding of the core is interrupted by an abrupt unravelling transition. A detailed SCF analysis indicates that under both unfolding scenario the arms of the star are extended fairly equally, i.e., no intra-molecular disproportionation occurs.

  5. Conformal superalgebras via tractor calculus

    E-print Network

    Andree Lischewski

    2014-08-10

    We use the manifestly conformally invariant description of a Lorentzian conformal structure in terms of a parabolic Cartan geometry in order to introduce a superalgebra structure on the space of twistor spinors and normal conformal vector fields formulated in purely algebraic terms on parallel sections in tractor bundles. Via a fixed metric in the conformal class, one reproduces a conformal superalgebra structure which has been considered in the literature before. The tractor approach, however, makes clear that the failure of this object to be a Lie superalgebra in certain cases is due to purely algebraic identities on the spinor module and to special properties of the conformal holonomy representation. Moreover, it naturally generalizes to higher signatures. This yields new formulas for constructing new twistor spinors and higher order normal conformal Killing forms out of existing ones, generalizing the well-known spinorial Lie derivative. Moreover, we derive restrictions on the possible dimension of the space of twistor spinors in any metric signature.

  6. Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions.

    PubMed

    Zacharias, M; Sklenar, H

    1997-12-01

    A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form. PMID:9414214

  7. Subtleties Concerning Conformal Tractor Bundles

    E-print Network

    Graham, C Robin

    2012-01-01

    The realization of tractor bundles as associated bundles in conformal geometry is studied. It is shown that different natural choices of principal bundle with normal Cartan connection corresponding to a given conformal manifold can give rise to topologically distinct associated tractor bundles for the same inducing representation. Consequences for homogeneous models and conformal holonomy are described. A careful presentation is made of background material concerning standard tractor bundles and equivalence between parabolic geometries and underlying structures.

  8. A Threaded Loop Conformation Adopted by a Family of Peptoid Nonamers

    PubMed Central

    Huang, Kai; Wu, Cindy W.; Sanborn, Tracy J.; Patch, James A.; Kirshenbaum, Kent; Zuckermann, Ronald N.; Barron, Annelise E.; Radhakrishnan, Ishwar

    2008-01-01

    Non-natural polymers with well-defined three-dimensional folds offer considerable potential for engineering novel functions that are outside the scope of biological polymers. Here we describe a family of N-substituted glycine or ‘peptoid’ nonamers that folds into an unusual ‘threaded loop’ structure of exceptional thermal stability and conformational homogeneity in acetonitrile. The structure is chain length-specific and relies on bulky, chiral side chains and chain-terminating functional groups for stability. Notable elements of the structure include the engagement of the positively charged amino-terminus by carbonyl groups of the backbone through hydrogen bonding interactions, and shielding of polar groups from and near-complete exposure of hydrophobic groups to solvent, in a manner resembling a folded polypeptide globular domain turned ‘inside-out’. The structure is stable in a variety of organic solvents but is readily denatured in any solvent/cosolvent milieu with hydrogen bonding potential. The structure could serve as a scaffold for the elaboration of novel functions and could be used to test methodologies for predicting solvent-dependent polymer folding. PMID:16448149

  9. A Conformational Intermediate in Glutamate Receptor Activation

    PubMed Central

    Lau, Albert Y.; Salazar, Héctor; Blachowicz, Lydia; Ghisi, Valentina; Plested, Andrew J.R.; Roux, Benoît

    2013-01-01

    SUMMARY Ionotropic glutamate receptors (iGluRs) transduce the chemical signal of neurotransmitter release into membrane depolarization at excitatory synapses in the brain. The opening of the transmembrane ion channel of these ligand-gated receptors is driven by conformational transitions that are induced by the association of glutamate molecules to the ligand-binding domains (LBDs). Here, we describe the crystal structure of a GluA2 LBD tetramer in a configuration that involves an ~30° rotation of the LBD dimers relative to the crystal structure of the full-length receptor. The configuration is stabilized by an engineered disulfide crosslink. Biochemical and electrophysiological studies on full-length receptors incorporating either this crosslink or an engineered metal bridge show that this LBD configuration corresponds to an intermediate state of receptor activation. GluA2 activation therefore involves a combination of both intra-LBD (cleft closure) and inter-LBD dimer conformational transitions. Overall, these results provide a comprehensive structural characterization of an iGluR intermediate state. PMID:23931998

  10. Ethanol monomers and dimers revisited: a Raman study of conformational preferences and argon nanocoating effects.

    PubMed

    Wassermann, Tobias N; Suhm, Martin A

    2010-08-19

    The gauche-trans conformational distribution in ethanol can be determined from the OH stretching Raman spectrum of seeded supersonic jet expansions, which thus provides a sensitive conformational thermometer. Depending on the rare gas mixture, one, two or four ethanol dimer conformations are abundant. Their conformational assignment is facilitated by the observation of hydrogen bond acceptor modes, which have similar Raman cross sections but much inferior infrared intensities than donor modes. Ethanol monomers and dimers can be progressively Ar-coated, and the resulting spectra may be compared with those in a bulk argon matrix. The low frequency range of torsional transitions provides some evidence for conformation-changing transitions in Raman jet spectra. PMID:20701332

  11. TRANSIENT MESH ADAPTATION USING CONFORMING AND NON CONFORMING MESH MODIFICATIONS

    E-print Network

    Frey, Pascal

    TRANSIENT MESH ADAPTATION USING CONFORMING AND NON CONFORMING MESH MODIFICATIONS Jean refinements, both in 2D and 3D. Keywords: mesh adaptation, discontinuous Galerkin, anisotropy 1. INTRODUCTION multiple mesh adaptations in order to follow complex features of the flow. The discontinuous Galerkin

  12. Holographic dual of a boundary conformal field theory.

    PubMed

    Takayanagi, Tadashi

    2011-09-01

    We propose a holographic dual of a conformal field theory defined on a manifold with boundaries, i.e., boundary conformal field theory (BCFT). Our new holography, which may be called anti-de Sitter BCFT, successfully calculates the boundary entropy or g function in two-dimensional BCFTs and it agrees with the finite part of the holographic entanglement entropy. Moreover, we can naturally derive a holographic g theorem. We also analyze the holographic dual of an interval at finite temperature and show that there is a first order phase transition. PMID:21981491

  13. Replacement between conformity and counter-conformity in consumption decisions.

    PubMed

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future. PMID:23654033

  14. Capturing Chromosome Conformation

    NASA Astrophysics Data System (ADS)

    Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

    2002-02-01

    We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

  15. Conformal Aspects of QCD

    SciTech Connect

    Brodsky, S

    2003-11-19

    Theoretical and phenomenological evidence is now accumulating that the QCD coupling becomes constant at small virtuality; i.e., {alpha}{sub s}(Q{sup 2}) develops an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. For example, the hadronic decays of the {tau} lepton can be used to determine the effective charge {alpha}{sub {tau}}(m{sub {tau}{prime}}{sup 2}) for a hypothetical {tau}-lepton with mass in the range 0 < m{sub {tau}{prime}} < m{sub {tau}}. The {tau} decay data at low mass scales indicates that the effective charge freezes at a value of s = m{sub {tau}{prime}}{sup 2} of order 1 GeV{sup 2} with a magnitude {alpha}{sub {tau}} {approx} 0.9 {+-} 0.1. The near-constant behavior of effective couplings suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer and why there are no significant running coupling corrections to quark counting rules for exclusive processes. The AdS/CFT correspondence of large N{sub c} supergravity theory in higher-dimensional anti-de Sitter space with supersymmetric QCD in 4-dimensional space-time also has interesting implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for exclusive processes and light-front wavefunctions. The utility of light-front quantization and light-front Fock wavefunctions for analyzing nonperturbative QCD and representing the dynamics of QCD bound states is also discussed.

  16. Algebraic orbifold conformal field theories

    Microsoft Academic Search

    Feng Xu

    2000-01-01

    The unitary rational orbifold conformal field theories in the algebraic quantum field theory and subfactor theory framework are formulated. Under general conditions, it is shown that the orbifold of a given unitary rational conformal field theory generates a unitary modular category. Many new unitary modular categories are obtained. It is also shown that the irreducible representations of orbifolds of rank

  17. Methods for Numerical Conformal Mapping

    Microsoft Academic Search

    Ralph Menikoff; Charles Zemach

    1980-01-01

    Nonlinear integral equations for the boundary functions which determine conformal transformations in two dimensions are developed and analyzed. One of these equations has a nonsingular logarithmic kernel and is especially well suited for numerical computations of conformal maps including those which deal with regions having highly distorted boundaries. Numerical procedures based on interspersed Gaussian quadrature for approximating the integrals and

  18. Conformal mapping: Methods and applications

    Microsoft Academic Search

    R. Schinzinger; P. A. A. Laura

    1991-01-01

    This book exhibits its best qualities as a readily accessible, desk-top source reference on conformal mapping applications for the practicing engineer and applied scientist who may beunfamiliar with the topic or uninformed about its utility in solving problems of contemporary interest. On the other hand, it is not an applied or operational mathematics textbook on conformal transformation methods. The authors

  19. Counselor Identity: Conformity or Distinction?

    ERIC Educational Resources Information Center

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  20. Conformal Transformations and Space Travel

    Microsoft Academic Search

    Suraj N. Gupta

    1961-01-01

    Conformal transformations are applied to the motion of a space ship experiencing a constant acceleration. The role of proper time is interpreted in terms of atomic periods, and the relationship between the conformal transformations and the general theory of relativity is clarified.

  1. Conformational flexibility in dodecasubstituted porphyrins

    SciTech Connect

    Nurco, D.J.; Medford, C.J.; Forsyth, T.P.; Olmstead, M.M.; Smith, K.M. [Univ. of California, Davis, CA (United States)] [Univ. of California, Davis, CA (United States)

    1996-11-06

    In contrast to regular porphyrins, dodecasubstituted porphyrins have not so far been demonstrated to possess a high degree of conformational flexibility. To determine if this is a general feature of dodecasubstituted porphyrins, we have undertaken an investigation of the conformational properties of the dodecaarylporphyrins 4-6. We show herein that crystal structures of these porphyrins provide ample evidence of the significant conformational flexibility that can be observed for dodecasubstituted porphyrins; the structures we report include the first highly ruffled dodecasubstituted porphyrin, the first examples of multiple conformations in a single dodecasubstituted porphyrin, and the first `wave` core structure of a dodecasubstituted porphyrin, which is also the most nonplanar wave structure reported to date for any porphyrin. The structure reported herein for nickel(II) complexes and metal-free porphyrins 4-6 clearly indicate that these porphyrins possess a higher degree of conformational flexibility than has previously been observed for other dodecasubstituted porphyrins. 6 refs., 2 figs.

  2. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity...the Transportation Conformity SIP from Indiana. [75 FR 50710, Aug. 17,...

  3. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity...the Transportation Conformity SIP from Indiana. [75 FR 50710, Aug. 17,...

  4. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity...the Transportation Conformity SIP from Indiana. [75 FR 50710, Aug. 17,...

  5. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity...the Transportation Conformity SIP from Indiana. [75 FR 50710, Aug. 17,...

  6. Scattering in conformally invariant quantum mechanics

    SciTech Connect

    Oksak, A.I.

    1986-08-01

    The S matrix conformally invariant quantum mechanics is determined by the multiple valuedness of the representation of the conformal group (i.e., by the operator that realizes conformal rotation through angle 2..pi..).

  7. Generalized Koebe's Method for Conformal Mapping

    E-print Network

    Generalized Koebe's Method for Conformal Mapping Multiply Connected Domains Wei Zeng 1 Xiaotian Yin Francisco, California #12;Problem · Circular conformal mapping for Multiply connected domains 2009 SIAM #12;Highlights · A practical algorithm to explicitly construct conformal mappings for multiply

  8. Conformational activation of visual rhodopsin in native disc membranes.

    PubMed

    Malmerberg, Erik; M Bovee-Geurts, Petra H; Katona, Gergely; Deupi, Xavier; Arnlund, David; Wickstrand, Cecilia; Johansson, Linda C; Westenhoff, Sebastian; Nazarenko, Elena; Schertler, Gebhard F X; Menzel, Andreas; de Grip, Willem J; Neutze, Richard

    2015-03-10

    Rhodopsin is the G protein-coupled receptor (GPCR) that serves as a dim-light receptor for vision in vertebrates. We probed light-induced conformational changes in rhodopsin in its native membrane environment at room temperature using time-resolved wide-angle x-ray scattering. We observed a rapid conformational transition that is consistent with an outward tilt of the cytoplasmic portion of transmembrane helix 6 concomitant with an inward movement of the cytoplasmic portion of transmembrane helix 5. These movements were considerably larger than those reported from the basis of crystal structures of activated rhodopsin, implying that light activation of rhodopsin involves a more extended conformational change than was previously suggested. PMID:25759477

  9. Conformal gravity and time

    NASA Astrophysics Data System (ADS)

    Hazboun, Jeffrey Shafiq

    Cartan geometry provides a rich formalism from which to look at various geometrically motivated extensions to general relativity. In this manuscript, we start by motivating reasons to extend the theory of general relativity. We then introduce the reader to our technique, called the quotient manifold method, for extending the geometry of spacetime. We will specifically look at the class of theories formed from the various quotients of the conformal group. Starting with the conformal symmetries of Euclidean space, we construct a manifold where time manifests as a part of the geometry. Though there is no matter present in the geome- try studied here, geometric terms analogous to dark energy and dark matter appear when we write down the Einstein tensor. Specifically, the quotient of the conformal group of Euclidean four-space by its Weyl subgroup results in a geometry possessing many of the properties of relativistic phase space, including both a natural symplectic form and nondegenerate Killing metric. We show the general solution possesses orthogonal Lagrangian submanifolds, with the induced metric and the spin connection on the submanifolds necessarily Lorentzian, despite the Euclidean starting point. By examining the structure equations of the biconformal space in an orthonormal frame adapted to its phase space properties, we also find two new tensor fields exist in this geometry, not present in Riemannian geometry. The first is a combination of the Weyl vector with the scale factor on the metric, and determines the time-like directions on the submanifolds. The second comes from the components of the spin connection, symmetric with respect to the new metric. Though this field comes from the spin connection, it transforms ho- mogeneously. Finally, we show in the absence of Cartan curvature or sources, the configuration space has geometric terms equivalent to a perfect fluid and a cosmological constant. We complete the analysis of this homogeneous space by transforming the known, general solution of the Maurer-Cartan equations into the orthogonal, Lagrangian basis. This results in a signature-changing metric, just as in the work of Spencer and Wheeler, however without any conditions on the curvature of the momentum sector. The Riemannian curvatures of the two submanifolds are directly related. We investigate the case where the curvature on the momentum submanifold vanishes, while the curvature of the configuration submanifold gives an effective energy-momentum tensor corresponding to a perfect fluid. In the second part of this manuscript, we look at the most general curved biconformal geometry dictated by the Wehner-Wheeler action. We use the assemblage of structure equations, Bianchi identities, and field equations to show how the geometry of the manifolds self-organizes into trivial Weyl geometries, which can then be gauged to Riemannian geometries. The Bianchi identities reveal the strong relationships between the various curvatures, torsions, and cotorsions. The discussion of the curved case culminates in a number of simplifying restrictions that show general relativity as the base of the more general theory.

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

    PubMed Central

    Wang, Kai; Long, Shiyang; Tian, Pu

    2015-01-01

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

  11. Conformational polymorphism in bicalutamide.

    PubMed

    Vega, Daniel R; Polla, Griselda; Martinez, Andrea; Mendioroz, Elsa; Reinoso, María

    2007-01-10

    Two crystalline forms (forms I and II) and an amorphous phase of bicalutamide were fully characterized through combined results of differential scanning calorimetry, X-ray powder and single crystal diffraction and Raman spectroscopy. Each polymorph crystallizes with one molecule in the asymmetric unit and the molecular conformations are quite different between them. The main difference is provided by C12-C11-S8-C5 torsion angle, which assumes a value of -88.3(4) degrees (-Syn-Clinal) and 72.5(4) degrees (+Syn-Clinal) in forms I and II, respectively. Consequently, molecules in form I show an open folding and molecules in form II a closed one. The relative stability between forms I and II is presented in an energy versus temperature diagram, where forms I and II are considered as a monotropic system, being form I the more stable one. The amorphous phase was observed very metastable and it converts to form II spontaneously at RT in around a week. PMID:16978811

  12. The Conformal Standard Model

    E-print Network

    Latosinski, Adam; Meissner, Krzysztof A; Nicolai, Hermann

    2015-01-01

    We present an extended version of the Conformal Standard Model (characterized by the absence of any new intermediate scales between the electroweak scale and the Planck scale) with an enlarged scalar sector coupling to right-chiral neutrinos in such a way that the scalar potential and the Yukawa couplings involving only right-chiral neutrinos are invariant under a new global symmetry SU(3)$_N$ which is broken explicitly only by the Yukawa interaction coupling right-chiral neutrinos and the electroweak lepton doublets. We point out four main advantages of such an enlargement, namely: (1) the economy of the (non-supersymmetric) Standard Model, and thus its observational success, is preserved; (2) thanks to the enlarged scalar sector the RG improved one-loop effective potential is everywhere positive with a stable global minimum, thereby avoiding the notorious instability of the Standard Model vacuum; (3) the pseudo-Goldstone bosons resulting from spontaneous breaking of the SU(3)$_N$ symmetry are natural Dark M...

  13. Conformal Fermi Coordinates

    E-print Network

    Liang Dai; Enrico Pajer; Fabian Schmidt

    2015-04-14

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable effects and "projection" terms.

  14. 6d Conformal matter

    NASA Astrophysics Data System (ADS)

    Del Zotto, Michele; Heckman, Jonathan J.; Tomasiello, Alessandro; Vafa, Cumrun

    2015-02-01

    A single M5-brane probing G, an ADE-type singularity, leads to a system which has G × G global symmetry and can be viewed as "bifundamental" ( G, G) matter. For the A N series, this leads to the usual notion of bifundamental matter. For the other cases it corresponds to a strongly interacting (1 , 0) superconformal system in six dimensions. Similarly, an ADE singularity intersecting the Ho?ava-Witten wall leads to a superconformal matter system with E 8 × G global symmetry. Using the F-theory realization of these theories, we elucidate the Coulomb/tensor branch of ( G, G') conformal matter. This leads to the notion of fractionalization of an M5-brane on an ADE singularity as well as fractionalization of the intersection point of the ADE singularity with the Ho?ava-Witten wall. Partial Higgsing of these theories leads to new 6d SCFTs in the infrared, which we also characterize. This generalizes the class of (1 , 0) theories which can be perturbatively realized by suspended branes in IIA string theory. By reducing on a circle, we arrive at novel duals for 5d affine quiver theories. Introducing many M5-branes leads to large N gravity duals.

  15. Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols

    E-print Network

    Allosteric transitions of Torpedo acetylcholine receptor in lipids, detergent and amphipols, in the detergent CHAPS, and after complexation by amphipathic polymers (`amphipols'). Binding kinetics was similar: Nicotinic acetylcholine receptor; Conformational transition; Membrane protein; Detergent; Amphipol 1

  16. Folding kinetics for the conformational switch between alternative RNA structures.

    PubMed

    Cao, Song; Fürtig, Boris; Schwalbe, Harald; Chen, Shi-Jie

    2010-10-28

    Transitions between different conformational states, so-called conformational switching, are intrinsic to RNA catalytic and regulatory functions. Often, conformational switching occurs on time scales of several seconds. In combination with the recent real-time NMR experiments (Wenter et al. Angew. Chem. Int. Ed. 2005, 44, 2600; Wenter et al. ChemBioChem 2006, 7, 417) for the transitions between bistable RNA conformations, we combine the master equation method with the kinetic cluster method to investigate the detailed kinetic mechanism and the factors that govern the folding kinetics. We propose that heat capacity change (?C(p)) upon RNA folding may be important for RNA folding kinetics. In addition, we find that, for tetraloop hairpins, noncanonical (tertiary) intraloop interactions are important to determine the folding kinetics. Furthermore, through theory-experiment comparisons, we find that the different rate models for the fundamental steps (i.e., formation/disruption of a base pair or stack) can cause contrasting results in the theoretical predictions. PMID:20886868

  17. Conformational Landscape of Nicotinoids: Solving the "conformational - Rity" of Anabasine

    NASA Astrophysics Data System (ADS)

    Lesarri, Alberto; Cocinero, Emilio J.; Evangelisti, Luca; Suenram, Richard D.; Caminati, Walther; Grabow, Jens-Uwe

    2010-06-01

    The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N-H equatorial stereochemistry at the piperidine ring (Eq-Eq). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing in a ca. 180° rotation of the pyridine subunit, denoted either Syn or Anti. The preference of anabasine for the Eq-Eq-Syn conformation has been established by relative intensity measurements (Syn/Anti˜5(2)). The conformational preferences of free anabasine are directed by a N\\cdot\\cdot\\cdotH-C weak hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest hydrogen bond in pyridine, with N\\cdot\\cdot\\cdotN distances ranging from 4.750 Å (Syn) to 4.233 Å (Anti). R. J. Lavrich, R. D. Suenram, D. F. Plusquellic and S. Davis, 58^th OSU Int. Symp. on Mol. Spectrosc., Columbus, OH, 2003, Comm. RH13.

  18. A novel approach to the study of conformality in the SU(3) theory with multiple flavors

    E-print Network

    Richard Brower; Anna Hasenfratz; Claudio Rebbi; Evan Weinberg; Oliver Witzel

    2014-10-16

    We investigate the transition between spontaneous chiral symmetry breaking and conformal behavior in the SU(3) theory with multiple fermion flavors. We propose a new strategy for studying this transition. Instead of changing the number of flavors, we lift the mass of a subset of the fermions, keeping the rest of the fermions near to the massless chiral limit in order to probe the transition. Dedicated to the 60th birthday of Academician Valery Rubakov.

  19. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap

    NASA Astrophysics Data System (ADS)

    Spiwok, Vojt?ch; Králová, Blanka

    2011-12-01

    Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.

  20. FRET-based detection of different conformations of MK2

    Microsoft Academic Search

    Armin Neininger; Heiko Thielemann; Matthias Gaestel

    2001-01-01

    MAP kinase-activated protein kinase 2 (MK2 or MAPKAP K2) is a stress-activated enzyme downstream to p38 MAPK. By fusion of green fluorescent protein variants to the N- and C-terminus we analysed conformational changes in the kinase molecule in vitro and in vivo. Activation of MK2 is accompanied by a decrease in fluorescence resonance energy transfer, indicating a transition from an

  1. Graphene-based conformal devices.

    PubMed

    Park, Yong Ju; Lee, Seoung-Ki; Kim, Min-Seok; Kim, Hyunmin; Ahn, Jong-Hyun

    2014-08-26

    Despite recent progress in bendable and stretchable thin-film transistors using novel designs and materials, the development of conformal devices remains limited by the insufficient flexibility of devices. Here, we demonstrate the fabrication of graphene-based conformal and stretchable devices such as transistor and tactile sensor on a substrate with a convoluted surface by scaling down the device thickness. The 70 nm thick graphene-based conformal devices displayed a much lower bending stiffness than reported previously. The demonstrated devices provided excellent conformal coverage over an uneven animal hide surface without the need for an adhesive. In addition, the ultrathin graphene devices formed on the three-dimensionally curved animal hide exhibited stable electrical characteristics, even under repetitive bending and twisting. The advanced performance and flexibility demonstrated here show promise for the development and adoption of wearable electronics in a wide range of future applications. PMID:25073058

  2. Conformal mapping of rectangular heptagons

    SciTech Connect

    Bogatyrev, Andrei B

    2012-12-31

    A new effective approach to calculating the direct and inverse conformal mapping of rectangular polygons onto a half-plane is put forward; it is based on the use of Riemann theta functions. Bibliography: 14 titles.

  3. Lattice Simulations and Infrared Conformality

    DOE PAGESBeta

    Appelquist, Thomas; Fleming, George T.; Lin, Meifeng; Neil, Ethan T.; Schaich, David A.

    2011-09-01

    We examine several recent lattice-simulation data sets, asking whether they are consistent with infrared conformality. We observe, in particular, that for an SU(3) gauge theory with 12 Dirac fermions in the fundamental representation, recent simulation data can be described assuming infrared conformality. Lattice simulations include a fermion mass m which is then extrapolated to zero, and we note that this data can be fit by a small-m expansion, allowing a controlled extrapolation. We also note that the conformal hypothesis does not work well for two theories that are known or expected to be confining and chirally broken, and that itmore »does work well for another theory expected to be infrared conformal.« less

  4. Einstein Gravity from Conformal Gravity

    E-print Network

    Juan Maldacena

    2011-06-09

    We show that that four dimensional conformal gravity plus a simple Neumann boundary condition can be used to get the semiclassical (or tree level) wavefunction of the universe of four dimensional asymptotically de-Sitter or Euclidean anti-de Sitter spacetimes. This simple Neumann boundary condition selects the Einstein solution out of the more numerous solutions of conformal gravity. It thus removes the ghosts of conformal gravity from this computation. In the case of a five dimensional pure gravity theory with a positive cosmological constant we show that the late time superhorizon tree level probability measure, $|\\Psi [ g ]|^2$, for its four dimensional spatial slices is given by the action of Euclidean four dimensional conformal gravity.

  5. Statistical Mechanics of Membrane Protein Conformation: A Homopolymer Model

    E-print Network

    Pyeong Jun Park; W. Sung

    1998-07-01

    The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\\alpha$-helix integration into the membrane that results depending upon membrane permeability and polymer adsorptivity. For a membrane with the permeability larger than a critical value, the integration becomes the second order transition that occurs at the same temperature as that of the adsorption transition. For a nonadsorbing membrane, the integration is of the first order due to the aggregation of $\\alpha$-helices.

  6. Indomethacin polymorphs: Experimental and conformational analysis.

    PubMed

    Aceves-Hernandez, J M; Nicolás-Vázquez, I; Aceves, F J; Hinojosa-Torres, J; Paz, M; Castaño, V M

    2009-07-01

    Thermal analysis of indomethacin alpha and gamma polymorphs presents a temperature transition at 429.2 and 435.8 K, respectively, although with X-ray diffraction or near infra-red spectroscopy phase transformations were not registered. DSC method for the indomethacin amorphous solid shows an endothermic event; however, the conformational analysis at higher temperature shows a rotational change which may explain such endothermic peak. By heating the gamma polymorph at 483 K (210 degrees C) for 30 min and then quenching into liquid nitrogen the amorphous solid was obtained. The alpha form shows the highest intrinsic dissolution rate, while the lowest rate was for the amorphous indomethacin. Theoretical calculations (ab initio, Hartree-Fock and density functional theory, DFT) indicate that the double interaction is responsible for the observed difference in solubility. PMID:19199282

  7. Scale invariance vs conformal invariance

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2015-03-01

    In this review article, we discuss the distinction and possible equivalence between scale invariance and conformal invariance in relativistic quantum field theories. Under some technical assumptions, we can prove that scale invariant quantum field theories in d = 2 space-time dimensions necessarily possess the enhanced conformal symmetry. The use of the conformal symmetry is well appreciated in the literature, but the fact that all the scale invariant phenomena in d = 2 space-time dimensions enjoy the conformal property relies on the deep structure of the renormalization group. The outstanding question is whether this feature is specific to d = 2 space-time dimensions or it holds in higher dimensions, too. As of January 2014, our consensus is that there is no known example of scale invariant but non-conformal field theories in d = 4 space-time dimensions under the assumptions of (1) unitarity, (2) Poincaré invariance (causality), (3) discrete spectrum in scaling dimensions, (4) existence of scale current and (5) unbroken scale invariance in the vacuum. We have a perturbative proof of the enhancement of conformal invariance from scale invariance based on the higher dimensional analogue of Zamolodchikov's c-theorem, but the non-perturbative proof is yet to come. As a reference we have tried to collect as many interesting examples of scale invariance in relativistic quantum field theories as possible in this article. We give a complementary holographic argument based on the energy-condition of the gravitational system and the space-time diffeomorphism in order to support the claim of the symmetry enhancement. We believe that the possible enhancement of conformal invariance from scale invariance reveals the sublime nature of the renormalization group and space-time with holography. This review is based on a lecture note on scale invariance vs conformal invariance, on which the author gave lectures at Taiwan Central University for the 5th Taiwan School on Strings and Fields.

  8. Falsification of Mannheim's conformal gravity

    E-print Network

    Yoon, Youngsub

    2013-01-01

    We show that Mannheim's conformal gravity, whose potential has a term proportional to $1/r$ and another term proportional to $r$, doesn't reduce to Newtonian gravity at short distances. Therefore, despite the claim that it successfully explains galaxy rotation curves, it seems falsified by numerous Cavendish-type experiments performed at laboratories on Earth whose work haven't found any deviations from Newton's theory. Moreover, when Mannheim used his potential to fit the galaxy rotation curve, he used the Newtonian formula to calculate the effects of the term proportional to $1/r$, not the conformal gravity one. So, he lacked consistency. After all, he would not have been able to use the conformal gravity one either since it deviates so much from the Newtonian one, which the conformal gravity one should reduce to. We also give a couple of other similar reasons why Mannheim's conformal gravity is wrong. For example, the gravitational potential of conformal gravity doesn't reduce to the Newtonian one even in ...

  9. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection

    PubMed Central

    Buscaglia, Robert; Miller, M. Clarke; Dean, William L.; Gray, Robert D.; Lane, Andrew N.; Trent, John O.; Chaires, Jonathan B.

    2013-01-01

    Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation. PMID:23804761

  10. Electron microscopy of xanthan: Topology and strandedness of the ordered and disordered conformation

    SciTech Connect

    Stokke, B.T.; Elgsaeter, A.; Smidsrod, O.

    1988-05-01

    The usefulness of xanthan in polymer flooding for enhanced oil recovery is based on its ability to yield large increase in viscosity at low polymer concentration under high-temperature and high-salinity conditions. This important property of xanthan is to a large extent determined by the conformational properties of the macromolecule. Xanthan is reported to undergo a chiro-optically detected temperature or salt-driven conformational change from an ordered conformation at high salt, low temperature to a disordered conformation at low salt, high temperature. The primary structure of xanthan has been known for about a decade, but several different structures have been suggested both for the ordered and disordered conformation. Several workers conclude that the ordered conformation is double-stranded or double-helix, but others claim that a single stranded description can account for the observed data. Measurements of molecular weight and radius of gyration through the conformational transition and into the disordered conformation indicate no major changes occur in molecular weight nor in hydrodynamic volume. Use of cadoxen as solvent is the only disordering condition reported to give complete strand separation into single strands. In this study, the authors use electron microscopy (EM) to study xanthan strandedness and topology both in the ordered and disordered conformation. EM data are compared with structural implications of the reported solution behavior of some of the samples.

  11. 40 CFR 93.154 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...subpart must make its own conformity determination...requirements of this subpart. In making its conformity determination...agency or develop its own analysis in order to make...subpart must make its own conformity determination...requirements of this subpart. In making its conformity...

  12. Physical studies of conformational plasticity in a recombinant prion protein.

    PubMed

    Zhang, H; Stockel, J; Mehlhorn, I; Groth, D; Baldwin, M A; Prusiner, S B; James, T L; Cohen, F E

    1997-03-25

    PrP(Sc) is known to be the major, if not the only, component of the infectious prion. Limited proteolysis of PrP(Sc) produces an N-terminally truncated polypeptide of about 142 residues, designated PrP 27-30. Recently, a recombinant protein (rPrP) of 142 residues corresponding to the Syrian hamster PrP 27-30 was expressed in Escherichia coli and purified (Mehlhorn et al., 1996). rPrP has been refolded into both alpha-helical and beta-sheet structures as well as various intermediates in aqueous buffers. The beta-sheet state and two pH-dependent alpha-helical states were characterized by CD and NMR. The alpha-helical conformation occurred only after the formation of an intramolecular disulfide bond, whereas the beta-sheet form was accessible either with or without the disulfide. Of the different alpha-helical forms studied, only those refolded in the pH range 5-8 were substantially soluble at physiological pH, exhibiting similar conformations and monomeric analytical sedimentation profiles throughout the above pH range. Furthermore, refolded alpha-rPrP showed NMR chemical shift dispersion typical of proteins with native conformations, although 2D NMR indicated large segments of conformational flexibility. It displayed a cooperative thermal denaturation transition; at elevated temperatures, it converted rapidly and irreversibly to the thermodynamically more stable beta-sheet form. Unfolding of alpha-rPrP by GdnHCl revealed a two-phase transition with a relatively stable folding intermediate at 2 M GdnHCl. The deltaG values were estimated to be 1.9 +/- 0.4 kcal/mol for the first phase and 6.5 +/- 1.2 kcal/mol for the second, consistent with a folding core surrounded by significant segments of flexible conformation. By NMR, alpha-rPrP(acid) isolated at pH 2 without refolding exhibited heterogeneous line widths, consistent with an acid-denatured molten globular state. We conclude that to the extent that rPrP constitutes a relevant folding domain of PrP(C), the various conformations exhibited by rPrP suggest that the PrP sequence may be intrinsically plastic in its conformations; indeed, portions of PrP(C) may possess a relatively open conformation which makes it susceptible to conversion into PrP(Sc) under appropriate conditions. PMID:9132005

  13. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate, (3) using partially formed gels, (4) using combinations of high and low molecular weight (Mw) polymers, (5) using secondary crosslinking reactions, (6) injecting un-hydrated polymer particles, and (7) incorporating particulates. All of these methods showed promise in some aspects, but required performance improvements in other aspects. All materials investigated to date showed significant performance variations with fracture width. High pressure gradients and limited distance of penetration are common problems in tight fractures. Gravity segregation and low resistance to breaching are common problems in wide fractures. These will be key issues to address in future work. Although gels can exhibit disproportionate permeability reduction in fractures, the levels of permeability reduction for oil flow are too high to allow practical exploitation in most circumstances. In contrast, disproportionate permeability reduction provided by gels that form in porous rock (adjacent to the fractures) has considerable potential in fractured systems.

  14. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-03-01

    This technical progress report describes work performed from September 1, 2003, through February 29, 2004, for the project, ''Conformance Improvement Using Gels.'' We examined the properties of several ''partially formed'' gels that were formulated with a combination of high and low molecular weight HPAM polymers. After placement in 4-mm-wide fractures, these gels required about 25 psi/ft for brine to breach the gel (the best performance to date in fractures this wide). After this breach, stabilized residual resistance factors decreased significantly with increased flow rate. Also, residual resistance factors were up to 9 times greater for water than for oil. Nevertheless, permeability reduction factors were substantial for both water and oil flow. Gel with 2.5% chopped fiberglass effectively plugged 4-mm-wide fractures if a 0.5-mm-wide constriction was present. The ability to screen-out at a constriction appears crucial for particulate incorporation to be useful in plugging fractures. In addition to fiberglass, we examined incorporation of polypropylene fibers into gels. Once dispersed in brine or gelant, the polypropylene fibers exhibited the least gravity segregation of any particulate that we have tested to date. In fractures with widths of at least 2 mm, 24-hr-old gels (0.5% high molecular weight HPAM) with 0.5% fiber did not exhibit progressive plugging during placement and showed extrusion pressure gradients similar to those of gels without the fiber. The presence of the fiber roughly doubled the gel's resistance to first breach by brine flow. The breaching pressure gradients were not as large as for gels made with high and low molecular weight polymers (mentioned above). However, their material requirements and costs (i.e., polymer and/or particulate concentrations) were substantially lower than for those gels. A partially formed gel made with 0.5% HPAM did not enter a 0.052-mm-wide fracture when applying a pressure gradient of 65 psi/ft. This result suggests a lower limit of fracture width for entry of formed or partially formed gels (when reasonable pressure gradients are applied). In unfractured porous rock, we investigated the time dependence of oil and water permeabilities during various cycles of oil and water injection after placement of a Cr(III)-acetate-HPAM gel. Permeability to water stabilized rapidly (within 1 pore volume, PV), while permeability to oil stabilized gradually over the course of 100 PV. The behavior was surprisingly insensitive to core material (strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene), core permeability (740 to 10,000 md), and applied pressure gradient (10 to 100 psi/ft).

  15. Monitoring membrane protein conformational heterogeneity by fluorescence lifetime distribution analysis using the maximum entropy method.

    PubMed

    Haldar, Sourav; Kombrabail, Mamata; Krishnamoorthy, G; Chattopadhyay, Amitabha

    2010-01-01

    Due to the inherent difficulty in crystallizing membrane proteins, approaches based on fluorescence spectroscopy have proved useful in elucidating their conformational characteristics. The ion channel peptide gramicidin serves as an excellent prototype for monitoring membrane protein conformation and dynamics due to a number of reasons. We have analyzed conformational heterogeneity in membrane-bound gramicidin using fluorescence lifetime distribution analysis of tryptophan residues by the maximum entropy method (MEM). MEM represents a model-free and robust approach for analyzing fluorescence lifetime distribution. In this paper, we show for the first time, that fluorescence lifetime distribution analysis using MEM could be a convenient approach to monitor conformational heterogeneity in membrane-bound gramicidin in particular and membrane proteins in general. Lifetime distribution analysis by MEM therefore provides a novel window to monitor conformational transitions in membrane proteins. PMID:19816758

  16. Conformational transformations of sulfur-containing rings: 2-methyltetrahydrothiophene gas-phase structures.

    PubMed

    Van, Vinh; Dindic, Christina; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

    2015-02-01

    Stable conformations of five-member rings with the prototype cyclopentane are well-known to exist as twist or envelope structures and are of general interest in chemistry. Here, we report on the conformational analysis of the sulfur-containing ring 2-methyltetrahydrothiophene studied by a combination of molecular beam Fourier transform microwave (MB-FTMW) spectroscopy and quantum chemistry. Two twist conformers were observed, whereby highly accurate molecular parameters could be determined. In addition, the (34) S-isotopologue of the most stable conformer was assigned in natural abundances. Geometry optimizations were performed at different levels of theory and the calculated rotational constants were compared with experimental values. Two transition states optimized at the MP2/6-311++G(d,p) level using the Berny algorithm could illustrate the intramolecular conversion between both conformers. PMID:25376652

  17. Conformations of n-butyl imidazole: matrix isolation infrared and DFT studies.

    PubMed

    Ramanathan, N; Sundararajan, K; Sankaran, K

    2015-03-15

    Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg(±)tt, tg(±)g(?)t, tg(±)g(±)t, tg(±)tg(±), tg(±)tg(?), tg(±)g(?)g(?), tg(±)g(±)g(±), tg(±)g(?)g(±) and tg(±)g(±)g(?) structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg(±)tt structure were carried out. The barriers for the conformer inter-conversion were found to be ?2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID. PMID:25554955

  18. Conformations of n-butyl imidazole: Matrix isolation infrared and DFT studies

    NASA Astrophysics Data System (ADS)

    Ramanathan, N.; Sundararajan, K.; Sankaran, K.

    2015-03-01

    Conformations of n-butyl imidazole (B-IMID) were studied using matrix isolation infrared spectroscopy by trapping in argon, xenon and nitrogen matrixes using an effusive nozzle source. The experimental studies were supported by DFT computations performed at the B3LYP/6-311++G(d,p) level. Computations identified nine unique minima for B-IMID, corresponding to conformers with tg±tt, tg±g?t, tg±g±t, tg±tg±, tg±tg?, tg±g?g?, tg±g±g±, tg±g?g± and tg±g±g? structures, given in order of increasing energy. Computations of the transition state structures connecting the higher energy conformers to the global minimum, tg±tt structure were carried out. The barriers for the conformer inter-conversion were found to be ?2 kcal/mol. Natural Bond Orbital (NBO) analysis was performed to understand the reasons for conformational preferences in B-IMID.

  19. Conformational isomerization dynamics of flexible molecules and their water containing complexes

    Microsoft Academic Search

    Jasper R Clarkson

    2006-01-01

    Molecules with several flexible coordinates have potential energy surfaces with a large number of minima and many transition states separating them. A general experimental protocol, based on conformation-specific ultraviolet and infrared spectroscopy, has been developed and described which is capable of studying conformational isomerization in such circumstances, measuring energy thresholds for isomerization of specific X?Y reactant-product isomer pairs following excitation

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

    PubMed Central

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

    2014-01-01

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

  1. Pyrene: a probe to study protein conformation and conformational changes.

    PubMed

    Bains, Gursharan; Patel, Arti B; Narayanaswami, Vasanthy

    2011-01-01

    The review focuses on the unique spectral features of pyrene that can be utilized to investigate protein structure and conformation. Pyrene is a fluorescent probe that can be attached covalently to protein side chains, such as sulfhydryl groups. The spectral features of pyrene are exquisitely sensitive to the microenvironment of the probe: it exhibits an ensemble of monomer fluorescence emission peaks that report on the polarity of the probe microenvironment, and an additional band at longer wavelengths, the appearance of which reflects the presence of another pyrene molecule in spatial proximity (~10 Å). Its high extinction coefficient allows us to study labeled proteins in solution at physiologically relevant concentrations. The environmentally- and spatially-sensitive features of pyrene allow monitoring protein conformation, conformational changes, protein folding and unfolding, protein-protein, protein-lipid and protein-membrane interactions. PMID:22143550

  2. Conformal Killing-Yano tensors for the Plebanski-Demianski family of solutions

    SciTech Connect

    Kubiznak, David [Theoretical Physics Institute, University of Alberta, Edmonton, Alberta, T6G 2G7 (Canada); Institute of Theoretical Physics, Charles University, V Holesovickach 2, Prague (Czech Republic); Krtous, Pavel [Institute of Theoretical Physics, Charles University, V Holesovickach 2, Prague (Czech Republic)

    2007-10-15

    We present explicit expressions for the conformal Killing-Yano tensors for the Plebanski-Demianski family of type D solutions in four dimensions. Some physically important special cases are discussed in more detail. In particular, it is demonstrated how the conformal Killing-Yano tensor becomes the Killing-Yano tensor for the solutions without acceleration. A possible generalization into higher dimensions is studied. Whereas the transition from the nonaccelerating to accelerating solutions in four dimensions is achieved by the conformal rescaling of the metric, we show that such a procedure is not sufficiently general in higher dimensions - only the maximally symmetric spacetimes in 'accelerated' coordinates are obtained.

  3. IR-IR-UV hole-burning: conformation specific IR spectra in the face of UV spectral overlap.

    PubMed

    Shubert, V Alvin; Zwier, Timothy S

    2007-12-27

    A new technique, IR-IR-UV hole-burning, is reported for obtaining conformation specific IR spectra when the electronic spectra are too closely overlapped to obtain clean spectra free from interference from other conformations via standard ion dip or fluorescence dip methods. The 4'-aminobenzo-15-crown-5 ether-(HDO) complex is used as an example, on which the method was applied to prove the presence of two conformations having overlapped electronic spectra and to assign IR transitions belonging to the same conformation. PMID:18047306

  4. Enzymatic Detoxication, Conformational Selection, and the Role of Molten Globule Active Sites*

    PubMed Central

    Honaker, Matthew T.; Acchione, Mauro; Zhang, Wei; Mannervik, Bengt; Atkins, William M.

    2013-01-01

    The role of conformational ensembles in enzymatic reactions remains unclear. Discussion concerning “induced fit” versus “conformational selection” has, however, ignored detoxication enzymes, which exhibit catalytic promiscuity. These enzymes dominate drug metabolism and determine drug-drug interactions. The detoxication enzyme glutathione transferase A1–1 (GSTA1–1), exploits a molten globule-like active site to achieve remarkable catalytic promiscuity wherein the substrate-free conformational ensemble is broad with barrierless transitions between states. A quantitative index of catalytic promiscuity is used to compare engineered variants of GSTA1–1 and the catalytic promiscuity correlates strongly with characteristics of the thermodynamic partition function, for the substrate-free enzymes. Access to chemically disparate transition states is encoded by the substrate-free conformational ensemble. Pre-steady state catalytic data confirm an extension of the conformational selection model, wherein different substrates select different starting conformations. The kinetic liability of the conformational breadth is minimized by a smooth landscape. We propose that “local” molten globule behavior optimizes detoxication enzymes. PMID:23649628

  5. NMR Mapping of Protein Conformational Landscapes using Coordinated Behavior of Chemical Shifts upon Ligand Binding

    PubMed Central

    Cembran, Alessandro; Kim, Jonggul; Gao, Jiali; Veglia, Gianluigi

    2014-01-01

    Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria following linear trajectories of NMR chemical shifts. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues’ response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein’s approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins. PMID:24604024

  6. NMR mapping of protein conformational landscapes using coordinated behavior of chemical shifts upon ligand binding.

    PubMed

    Cembran, Alessandro; Kim, Jonggul; Gao, Jiali; Veglia, Gianluigi

    2014-04-14

    Proteins exist as an ensemble of conformers that are distributed on free energy landscapes resembling folding funnels. While the most stable conformers populate low energy basins, protein function is often carried out through low-populated conformational states that occupy high energy basins. Ligand binding shifts the populations of these states, changing the distribution of these conformers. Understanding how the equilibrium among the states is altered upon ligand binding, interaction with other binding partners, and/or mutations and post-translational modifications is of critical importance for explaining allosteric signaling in proteins. Here, we propose a statistical analysis of the linear trajectories of NMR chemical shifts (CONCISE, COordiNated ChemIcal Shifts bEhavior) for the interpretation of protein conformational equilibria. CONCISE enables one to quantitatively measure the population shifts associated with ligand titrations and estimate the degree of collectiveness of the protein residues' response to ligand binding, giving a concise view of the structural transitions. The combination of CONCISE with thermocalorimetric and kinetic data allows one to depict a protein's approximate conformational energy landscape. We tested this method with the catalytic subunit of cAMP-dependent protein kinase A, a ubiquitous enzyme that undergoes conformational transitions upon both nucleotide and pseudo-substrate binding. When complemented with chemical shift covariance analysis (CHESCA), this new method offers both collective response and residue-specific correlations for ligand binding to proteins. PMID:24604024

  7. Patterns and conformations in molecularly thin films

    NASA Astrophysics Data System (ADS)

    Basnet, Prem B.

    Molecularly thin films have been a subject of great interest for the last several years because of their large variety of industrial applications ranging from micro-electronics to bio-medicine. Additionally, molecularly thin films can be used as good models for biomembrane and other systems where surfaces are critical. Many different kinds of molecules can make stable films. My research has considered three such molecules: a polymerizable phospholipid, a bent-core molecules, and a polymer. One common theme of these three molecules is chirality. The phospolipid molecules studied here are strongly chiral, which can be due to intrinsically chiral centers on the molecules and also due to chiral conformations. We find that these molecules give rise to chiral patterns. Bent-core molecules are not intrinsically chiral, but individual molecules and groups of molecules can show chiral structures, which can be changed by surface interactions. One major, unconfirmed hypothesis for the polymer conformation at surface is that it forms helices, which would be chiral. Most experiments were carried out at the air/water interface, in what are called Langmuir films. Our major tools for studying these films are Brewster Angle Microscopy (BAM) coupled with the thermodynamic information that can be deduced from surface pressure isotherms. Phospholipids are one of the important constituents of liposomes -- a spherical vesicle com-posed of a bilayer membrane, typically composed of a phospholipid and cholesterol bilayer. The application of liposomes in drug delivery is well-known. Crumpling of vesicles of polymerizable phospholipids has been observed. With BAM, on Langmuir films of such phospholipids, we see novel spiral/target patterns during compression. We have found that both the patterns and the critical pressure at which they formed depend on temperature (below the transition to a i¬‘uid layer). Bent-core liquid crystals, sometimes knows as banana liquid crystals, have drawn increasing attention because of the richness in phases that they exhibit. Due to the unique coupling between dipole properties and the packing constraints placed by the bent shape, these molecules are emerging as strong candidates in electromechanical devices. However, most applications require that the molecules be aligned, which has proved difficult. Our group has tested such molecules both as Langmuir layers and, when transferred to a solid, as alignment layers with some limited success. However, these molecules do not behave well with the surfaces and the domains at the air/water interface tend to form ill-controlled multilayer structures since attraction with the surfaces is relatively weak. New bent-core molecules obtained from Prof. Dr. C. Tsehiemke from Department of Chemistry Institute of Organic Chemistry, Martin-Luther-University, Germany, have a hydrophilic group at one end. We expect this molecule to behave better on the surface because of the stronger attraction of the hydrophilic group towards the surface than for the bent-core molecules without the hydrophilic group. Polydimethylsiloxane (PDMS) is a polymer which finds many applications in modifying surface properties. It is used in manufacturing lubricants, protective coatings, hair conditioner and glass-coating. However its properties are not well understood. This polymer has been proposed to follow either helical or caterpillar conformations on a surface. The orientational order of CH3 side groups can test for these conformations (they would be predominantly up/down for the caterpillar conformation, but rotating through the entire 360 degree for the helical one). Thus previous work on the Langmuir polymer films at the air/water interface were complemented by deuterium NMR studies to probe their conformations at a surface. These experiments were performed using humid porous solids, in order to provide sufficient surface area for the technique. Previous tests in this group at room temperature were suggestive but inconclusive because of the rapid averaging motion of the molecules. Here, we attempt t

  8. Conformal curvature flows: From phase transitions to active vision

    Microsoft Academic Search

    Satyanad Kichenassamy; Arun Kumar; Peter Olver; Allen Tannenbaum; Anthony Yezzi

    1996-01-01

    In this paper, we analyze geometric active contour models from a curve evolution point of view and propose some modifications based on gradient flows relative to certain new feature-based Riemannian metrics. This leads to a novel edge-detection paradigm in which the feature of interest may be considered to lie at the bottom of a potential well. Thus an edge-seeking curve

  9. Conformal Curvature Flows: From Phase Transitions to Active Vision

    Microsoft Academic Search

    Satyanad Kichenassamy; Arun Kumar

    1995-01-01

    In this paper, we analyze geometric active contour models from a curve evolutionpoint of view and propose some modifications based on gradient flows relative to certainnew feature-based Riemannian metrics. This leads to a novel edge-detection paradigmin which the feature of interest may be considered to lie at the bottom of a potentialwell. Thus an edge-seeking curve is attracted very naturally

  10. Geometry-Based Sampling of Conformational Transitions in Proteins

    E-print Network

    de Groot, Bert

    design (SBDD) (Knegtel et al., 1997; Carlson, 2002; Meagher and Carlson, 2004; McGovern and Shoichet structure or pro- tein model (McGovern and Shoichet, 2003). Among the computational approaches used

  11. Phase transformation in conformational polymorphs of nimesulide.

    PubMed

    Sanphui, Palash; Sarma, Bipul; Nangia, Ashwini

    2011-06-01

    Nimesulide is a nonsteroidal anti-inflammatory drug (NSAID) and a COX-2 inhibitor. The native crystal structure of nimesulide (or Form I) has been characterized in the literature by X-ray powder diffraction (XRPD) lines, whereas full three-dimensional coordinates are known for a second polymorph (Form II). A detailed structural characterization and phase stability of nimesulide polymorphs were carried out. Rod-like crystals of Form I (space group Pca2(1); number of symmetry-independent molecules, Z' = 2) were crystallized from EtOH concomitantly with Form II (C2/c, Z' = 1). These conformational polymorphs have different torsion angles at the phenoxy and sulfonamide groups. The crystal structures are stabilized by N-H · · · O hydrogen bonds and C-H · · · O, C-H · · · ? interactions. Phase transition from the metastable Form (II) to the stable modification (I) was studied using differential scanning calorimetry, hot-stage microscopy, solid-state grinding, solvent-drop grinding, and slurry crystallization. The phase transition was monitored by infrared, Raman, and ss-nuclear magnetic resonance spectroscopy; and XRPD and single-crystal X-ray diffraction. The stable polymorph I was obtained in excess during solution crystallization, grinding, and slurry methods. Intrinsic dissolution and equilibrium solubility experiments showed that the metastable Form II dissolves much faster than the stable Form I. PMID:21491446

  12. Analysing the visible conformational substates of the FK506-binding protein FKBP12

    PubMed Central

    Mustafi, Sourajit M.; Chen, Hui; Li, Hongmin; LeMaster, David M.; Hernández, Griselda

    2013-01-01

    The 1H-15N 2D NMR correlation spectrum of the widely studied FK506-binding protein FKBP12 (FK506-binding protein of 12 kDa) contains previously unreported peak doublings for at least 31 residues that arise from a minor conformational state (12% of total) which exchanges with the major conformation with a time constant of 3.0 s at 43°C. The largest differences in chemical shift occur for the 80?s loop that forms critical recognition interactions with many of the protein partners for the FKBP family. The residues exhibiting doubling extend into the adjacent strands of the ?-sheet, across the active site to the ?-helix and into the 50?s loop. Each of the seven proline residues adopts a trans-peptide linkage in both the major and minor conformations, indicating that this slow transition is not the result of prolyl isomerization. Many of the residues exhibiting resonance doubling also participate in conformational line-broadening transition(s) that occur ~105-fold more rapidly, proposed previously to arise from a single global process. The 1.70 Å (1 Å=0.1 nm) resolution X-ray structure of the H87V variant is strikingly similar to that of FKBP12, yet this substitution quenches the slow conformational transition throughout the protein while quenching the line-broadening transition for residues near the 80?s loop. Line-broadening was also decreased for the residues in the ?-helix and 50?s loop, whereas line-broadening in the 40?s loop was unaffected. The K44V mutation selectively reduces the line-broadening in the 40?s loop, verifying that at least three distinct conformational transitions underlie the line-broadening processes of FKBP12. PMID:23688288

  13. Universality class in conformal inflation

    SciTech Connect

    Kallosh, Renata; Linde, Andrei, E-mail: kallosh@stanford.edu, E-mail: alinde@stanford.edu [Department of Physics and SITP, Stanford University, Stanford, California 94305 (United States)

    2013-07-01

    We develop a new class of chaotic inflation models with spontaneously broken conformal invariance. Observational consequences of a broad class of such models are stable with respect to strong deformations of the scalar potential. This universality is a critical phenomenon near the point of enhanced symmetry, SO(1,1), in case of conformal inflation. It appears because of the exponential stretching of the moduli space and the resulting exponential flattening of scalar potentials upon switching from the Jordan frame to the Einstein frame in this class of models. This result resembles stretching and flattening of inhomogeneities during inflationary expansion. It has a simple interpretation in terms of velocity versus rapidity near the Kähler cone in the moduli space, similar to the light cone of special theory of relativity. This effect makes inflation possible even in the models with very steep potentials. We describe conformal and superconformal versions of this cosmological attractor mechanism.

  14. Transit Tracks

    NSDL National Science Digital Library

    Lawrence Hall of Science

    2008-01-01

    In this space science activity, learners explore transits and the conditions when a transit may be seen. Learners use models to investigate how a planet's size and distance from its star affects the behavior of transits. Learners also use mathematics to interpret graphs of brightness vs. time to deduce information about planet-star systems. This lesson includes educator instructions, photocopy masters for Transit Light Curves, Option Math for Transit Tracks, Kepler’s 3rd Law graphs, cube root tables, an account of Jeremiah Horrocks' 1639 observation of the transit of Venus, and an answer key for the Transit Tracks Light Curves.

  15. Killing Tensors from Conformal Killing Vectors

    E-print Network

    A. Barnes; S. B. Edgar; R. Rani

    2002-12-03

    Some years ago Koutras presented a method of constructing a conformal Killing tensor from a pair of orthogonal conformal Killing vectors. When the vector associated with the conformal Killing tensor is a gradient, a Killing tensor (in general irreducible) can then be constructed. In this paper it is shown that the severe restriction of orthogonality is unnecessary and thus it is possible that many more Killing tensors can be constructed in this way. We also extend, and in one case correct, some results on Killing tensors constructed from a single conformal Killing vector. Weir's result that, for flat space, there are 84 independent conformal Killing tensors, all of which are reducible, is extended to conformally flat spacetimes. In conformally flat spacetimes it is thus possible to construct all the conformal Killing tensors and in particular all the Killing tensors (which in general will not be reducible) from conformal Killing vectors.

  16. Transitions of tethered chain molecules under tension

    E-print Network

    Jutta Luettmer-Strathmann; Kurt Binder

    2014-09-09

    An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent quality and surface attraction are reflected in equilibrium force-extension curves that can be measured in experiments. To investigate these effects theoretically, we study tethered chains under tension with Wang-Landau simulations of a bond-fluctuation lattice model. Applying our model to pulling experiments on biological molecules we obtain a good description of experimental data in the intermediate force range, where universal features dominate and finite size effects are small. For tethered chains in poor solvent, we observe the predicted two-phase coexistence at transitions from the globule to stretched conformations and also discover direct transitions from crystalline to stretched conformations. A phase portrait for finite chains constructed by evaluating the density of states for a broad range of solvent conditions and tensions shows how increasing tension leads to a disappearance of the globular phase. For chains in good solvents tethered to hard and attractive surfaces we find the predicted scaling with the chain length in the low-force regime and show that our results are well described by an analytical, independent-bond approximation for the bond-fluctuation model for the highest tensions. Finally, for a hard or slightly attractive surface the stretching of a tethered chain is a conformational change that does not correspond to a phase transition. However, when the surface attraction is sufficient to adsorb a chain it will undergo a desorption transition at a critical value of the applied force. Our results for force-induced desorption show the transition to be discontinuous with partially desorbed conformations in the coexistence region.

  17. Epigenetic Dominance of Prion Conformers

    PubMed Central

    Saijo, Eri; Kang, Hae-Eun; Bian, Jifeng; Bowling, Kristi G.; Browning, Shawn; Kim, Sehun; Hunter, Nora; Telling, Glenn C.

    2013-01-01

    Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders such as bovine spongiform encephalopathy, sheep scrapie, and human Creutzfeldt Jakob disease, propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems, including other protein misfolding disorders such as those causing Alzheimer's and Parkinson's diseases. To address the poorly understood mechanism by which host prion protein (PrP) primary structures interact with distinct prion conformations to influence pathogenesis, we produced transgenic (Tg) mice expressing different sheep scrapie susceptibility alleles, varying only at a single amino acid at PrP residue 136. Tg mice expressing ovine PrP with alanine (A) at (OvPrP-A136) infected with SSBP/1 scrapie prions propagated a relatively stable (S) prion conformation, which accumulated as punctate aggregates in the brain, and produced prolonged incubation times. In contrast, Tg mice expressing OvPrP with valine (V) at 136 (OvPrP-V136) infected with the same prions developed disease rapidly, and the converted prion was comprised of an unstable (U), diffusely distributed conformer. Infected Tg mice co-expressing both alleles manifested properties consistent with the U conformer, suggesting a dominant effect resulting from exclusive conversion of OvPrP-V136 but not OvPrP-A136. Surprisingly, however, studies with monoclonal antibody (mAb) PRC5, which discriminates OvPrP-A136 from OvPrP-V136, revealed substantial conversion of OvPrP-A136. Moreover, the resulting OvPrP-A136 prion acquired the characteristics of the U conformer. These results, substantiated by in vitro analyses, indicated that co-expression of OvPrP-V136 altered the conversion potential of OvPrP-A136 from the S to the otherwise unfavorable U conformer. This epigenetic mechanism thus expands the range of selectable conformations that can be adopted by PrP, and therefore the variety of options for strain propagation. PMID:24204258

  18. Rydberg electrons spy conformational dynamics of hot molecules

    NASA Astrophysics Data System (ADS)

    Weber, Peter M.

    2007-03-01

    The observation of structural dynamics of flexible molecules at high temperatures is arguably one of the most challenging problems of molecular dynamics. We succeeded in observing conformational dynamics by using electrons in Rydberg orbits as spies of the molecular structure. The time-resolved photoionization from the Rydberg states, providing a purely electronic spectrum that serves to characterize the molecular structure, allows us to follow the molecular motions in real time. The internal rotation about carbon-carbon bonds affords the unsaturated hydrocarbon chain molecules N,N-dimethyl-2-butanamine (DM2BA) and N,N-dimethyl-3-hexanamine (DM3HA) an opportunity to assume multiple conformeric structures. We explore the equilibrium compositions and the dynamics of transitions between such structures. An ultrashort laser pulse rapidly increases the molecule's internal energy and changes the potential energy landscape. The molecules respond by adjusting their shape, i.e. by converting between conformeric molecular structures. For DM2BA at a total internal energy of 1.79 eV, the time constants for interconversion between conformers are 19 ps and 66 ps, respectively. In DM3HA, the respective time constants are 23 and 41 ps. Comparison with a calculated conformational energy landscape reveals the conformeric forms of DM2BA involved in the molecular shape transformation. Thus, for the first time a time-resolved and quantitative view of the conformational dynamics of a flexible hydrocarbon chain at high temperature is revealed.

  19. Finding Transition Pathways on Manifolds

    E-print Network

    Tiejun Li; Xiaoguang Li; Xiang Zhou

    2014-08-13

    We consider noise-induced transition paths in randomly perturbed dynami- cal systems on a smooth manifold. The classical Freidlin-Wentzell large devia- tion theory in Euclidean spaces is generalized and new forms of action functionals are derived in the spaces of functions and the space of curves to accommodate the intrinsic constraints associated with the manifold. Numerical meth- ods are proposed to compute the minimum action paths for the systems with constraints. The examples of conformational transition paths for a single and double rod molecules arising in polymer science are numerically investigated.

  20. Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter

    PubMed Central

    Song, Hyun Deok; Zhu, Fangqiang

    2015-01-01

    Mhp1 is a bacterial secondary transporter with high-resolution crystal structures available for both the outward- and inward-facing conformations. Through molecular dynamics simulations of the ligand-free Mhp1 as well as analysis of its crystal structures, here we show that two inter-helical loops, respectively located at the extra- and intracellular ends of the “hash motif” in the protein, play important roles in the conformational transition. In the outward- and inward-facing states of the protein, the loops adopt different secondary structures, either wrapped to the end of an alpha-helix, or unwrapped to extended conformations. In equilibrium simulations of 100 ns with Mhp1 in explicit lipids and water, the loop conformations remain largely stable. In targeted molecular dynamics simulations with the protein structure driven from one state to the other, the loops exhibit resistance and only undergo abrupt changes when other parts of the protein already approach the target conformation. Free energy calculations on the isolated loops further confirm that the wrapping/unwrapping transitions are associated with substantial energetic barriers, and consist of multiple sequential steps involving the rotation of certain backbone torsion angles. Furthermore, in simulations with the loops driven from one state to the other, a large part of the protein follows the loops to the target conformation. Taken together, our simulations suggest that changes of the loop secondary structures would be among the slow degrees of freedom in the conformational transition of the entire protein. Incorporation of detailed loop structures into the reaction coordinate, therefore, should improve the convergence and relevance of the resulting conformational free energy. PMID:26186341

  1. Quasilocal rotating conformal Killing horizons

    E-print Network

    Chatterjee, Ayan

    2015-01-01

    The formulation of quasi-local conformal Killling horizons(CKH) is extended to include rotation. This necessitates that the horizon be foliated by 2-spheres which may be distorted. Matter degrees of freedom which fall through the horizon is taken to be a real scalar field. We show that these rotating CKHs also admit a first law in differential form.

  2. Parsimony in Protein Conformational Change.

    PubMed

    Chapman, Brynmor K; Davulcu, Omar; Skalicky, Jack J; Brüschweiler, Rafael P; Chapman, Michael S

    2015-07-01

    Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ?(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (?, ?) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within ? helices and ? sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium. PMID:26095029

  3. Correct Representation of Conformational Equilibria.

    ERIC Educational Resources Information Center

    Fulop, F.; And Others

    1983-01-01

    In representing conformational equilibria of compounds having only one chiral center, erroneous formulas showing different antipodes on the two sides of the equilibrium are rare. In contrast, with compounds having two or more chiral centers especially with saturated heterocycles, this erroneous representation occurs frequently in the chemical…

  4. Temperature: Human Regulating, Ants Conforming

    ERIC Educational Resources Information Center

    Clopton, Joe R.

    2007-01-01

    Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

  5. Hierarchical Least Squares Conformal Map

    Microsoft Academic Search

    Nicolas Ray; Bruno Lévy

    2003-01-01

    A texture atlas is an efficient way to represent informa- tion (like colors, normals, displacement maps ...) on trian- gulated surfaces. The LSCM method (Least Squares Con- formal Maps) automatically generates a texture atlas from a meshed model. For large charts (over 100k facets), the convergence of the numerical solver may be slow. It is well known that the conformality

  6. Electrostatic imaging via conformal mapping

    Microsoft Academic Search

    Ibrahim Akduman; Rainer Kress

    2002-01-01

    We present the solution of an inverse boundary value problem for harmonic functions arising in electrostatic imaging through conformal mapping techniques. The numerical method consists of two parts. In a first step, by successive approximations a nonlinear equation is solved to determine the boundary values of a holomorphic function on the outer boundary circle of an annulus. Then in a

  7. Bondi metric and conformal motions

    SciTech Connect

    Di Prisco, A.; Herrera, L.; Jimenez, J.; Galina, V.; Ibanez, J.

    1987-11-01

    It is shown that there exist no physically significant solutions of the Einstein vacuum field equations, except the trivial one (i.e., Minkowski), for axially and reflection symmetric space-times (Bondi metric) admitting a one-parameter group of conformal motions globally defined on S/sup 2/.

  8. Logarithmic exotic conformal Galilean algebras

    NASA Astrophysics Data System (ADS)

    Henkel, Malte; Hosseiny, Ali; Rouhani, Shahin

    2014-02-01

    Logarithmic representations of the conformal Galilean algebra (CGA) and the Exotic Conformal Galilean algebra (ECGA) are constructed. This can be achieved by non-decomposable representations of the scaling dimensions or the rapidity indices, specific to conformal Galilean algebras. Logarithmic representations of the non-exotic CGA lead to the expected constraints on scaling dimensions and rapidities and also on the logarithmic contributions in the co-variant two-point functions. On the other hand, the ECGA admits several distinct situations which are distinguished by different sets of constraints and distinct scaling forms of the two-point functions. Two distinct realisations for the spatial rotations are identified as well. This is the first concrete example of a reducible, but non-decomposable representation, without logarithmic terms. Such cases had been anticipated before. One may try to generalise (1.3) further by extending the projective conformal (or Möbius) transformations in the time t to arbitrary conformal transformations. Taking the projective terms describing the transformation of the wave functions into account, the only cases with local generators which close as a Lie algebra are, besides evidently conformal transformations in space-time, the cases l=1/2 >,1 of the Schrödinger algebra and the CGA [12]. When considering the non-relativistic limit of space-time conformal transformations and assuming the existence of a dynamical exponent z, restriction to time-like and light-like geodesics reproduces exactly the Schrödinger algebra and the CGA, for z=2 and z=1, respectively [16]. Physical applications either refer to strongly anisotropic systems at equilibrium, where the ‘time' t is just a name for a peculiar spatial direction with strongly modified interactions such that z=? is better referred to as an ‘anisotropy exponent' (paradigmatic examples are uniaxial Lifshitz points in lattice spin models with competing interactions); or else to real dynamics, at or far away from equilibrium. In the first case, co-variant n-point functions (such as we shall calculate later on) will represent physical correlators; the second case, causality constraints

  9. Conformal Killing forms on Riemannian manifolds Habilitationsschrift

    E-print Network

    Semmelmann, Uwe

    Conformal Killing forms on Riemannian manifolds Habilitationsschrift zur Feststellung der Lehrbef Conformal Killing Forms 9 1.1 Definition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 1.2 Killing tensors and first integrals . . . . . . . . . . . . . . . . . . . . . . . . 14 2

  10. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity...Conformity regulations adopted into the South Carolina State Implementation Plan which...submitted on November 8, 1996. South Carolina incorporated by reference...

  11. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity...Conformity regulations adopted into the South Carolina State Implementation Plan which...submitted on November 8, 1996. South Carolina incorporated by reference...

  12. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity...Conformity regulations adopted into the South Carolina State Implementation Plan which...submitted on November 8, 1996. South Carolina incorporated by reference...

  13. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity...Conformity regulations adopted into the South Carolina State Implementation Plan which...submitted on November 8, 1996. South Carolina incorporated by reference...

  14. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity...Conformity regulations adopted into the South Carolina State Implementation Plan which...submitted on November 8, 1996. South Carolina incorporated by reference...

  15. Systematic conformational search with constraint satisfaction

    E-print Network

    Tucker-Kellogg, Lisa, 1969-

    2002-01-01

    Determining the conformations of biological molecules is a high scientific priority for biochemists and for the pharmaceutical industry. This thesis describes a systematic method for conformational search, an application ...

  16. Differential conformal superalgebras and their forms

    E-print Network

    Kac, Victor

    We introduce the formalism of differential conformal superalgebras, which we show leads to the “correct” automorphism group functor and accompanying descent theory in the conformal setting. As an application, we classify ...

  17. Gravity Duals for Nonrelativistic Conformal Field Theories

    E-print Network

    McGreevy, John

    We attempt to generalize the anti–de Sitter/conformal field theory correspondence to nonrelativistic conformal field theories which are invariant under Galilean transformations. Such systems govern ultracold atoms at ...

  18. 40 CFR 51.854 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...action subject to this subpart must make its own conformity determination consistent with the requirements of this subpart. In making its conformity determination, a Federal...of another Federal agency or develop its own analysis in order to make its...

  19. Targeting the conformal window with 4+8 flavors

    E-print Network

    Rich Brower; Anna Hasenfratz; Claudio Rebbi; Evan Weinberg; Oliver Witzel

    2014-11-12

    We study the transition between spontaneous chiral symmetry breaking and conformal behavior in the SU(3) theory with multiple fermion flavors. Instead of the traditional approach of changing the number of flavors, we keep the number of fermions fixed but lift the mass of a subset, keeping the remaining fermions near to the massless chiral limit. This way we can interpolate continuously between the conformal and chirally broken dynamics. In particular, we consider four light and eight heavy flavors and investigate the running/walking gauge coupling and the low energy meson spectrum, including the 0++ iso-singlet scalar state in this system. Our preliminary data reveal an iso-singlet scalar that is considerably lighter than the pion at large fermion mass but becomes heavier at smaller masses. This behavior is of particular phenomenological interest.

  20. Geodesics and submanifold structures in conformal geometry

    NASA Astrophysics Data System (ADS)

    Belgun, Florin

    2015-05-01

    A conformal structure on a manifold Mn induces natural second order conformally invariant operators, called Möbius and Laplace structures, acting on specific weight bundles of M, provided that n ? 3. By extending the notions of Möbius and Laplace structures to the case of surfaces and curves, we develop here the theory of extrinsic conformal geometry for submanifolds, find tensorial invariants of a conformal embedding, and use these invariants to characterize various notions of geodesic submanifolds.

  1. An extension theorem for conformal gauge singularities

    SciTech Connect

    Luebbe, Christian [Mathematical Institute, Oxford OX1 3LB (United Kingdom); Queen Mary University of London, London E1 4NS (United Kingdom); Tod, Paul [Mathematical Institute, Oxford OX1 3LB (United Kingdom); St. John's College, Oxford OX1 3JP (United Kingdom)

    2009-11-15

    We analyze conformal gauge, or isotropic, singularities in cosmological models in general relativity. Using the calculus of tractors, we find conditions in terms of tractor curvature for a local extension of the conformal structure through a cosmological singularity and prove a local extension theorem along a congruence of timelike conformal geodesics.

  2. Flexible ligand docking using conformational ensembles.

    PubMed Central

    Lorber, D. M.; Shoichet, B. K.

    1998-01-01

    Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre-calculated in the same frame of reference, so that each conformer shares a common rigid fragment with all other conformations. The ligand conformers are then docked together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the same molecule. The algorithm was tested using three organic ligand protein systems and two protein-protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method found conformations that resembled those determined in X-ray crystal structures (RMS values typically less than 1.5 A). To test the method's usefulness for inhibitor discovery, multi-compound and multi-conformer databases were screened for compounds known to bind to dihydrofolate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conformations resembling those observed experimentally. The ligand ensemble method was 100-fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation. PMID:9568900

  3. Optimization of Brain Conformal Mapping with Landmarks

    E-print Network

    Wang, Yalin

    Optimization of Brain Conformal Mapping with Landmarks 1Yalin Wang , 1Lok Ming Lui, 1Tony F. Chan. Objective: One way to analyze and compare brain data from multiple subjects is to map them conformally the conformal parametrization of cortical surfaces. Our algorithm can compute a map from the cortical surface

  4. Reinforcement Learning Signal Predicts Social Conformity

    Microsoft Academic Search

    Vasily Klucharev; Kaisa Hytönen; Mark Rijpkema; Ale Smidts; Guillén Fernández

    2009-01-01

    SUMMARY We often change our decisions and judgments to conform with normative group behavior. However, the neural mechanisms of social conformity remain unclear. Here we show, using functional magnetic resonance imaging, that conformity is based on mechanisms that comply with principles of reinforce- ment learning. We found that individual judgments of facial attractiveness are adjusted in line with group opinion.

  5. Producing Compliant Interactions: Conformance, Coverage, and Interoperability

    E-print Network

    Producing Compliant Interactions: Conformance, Coverage, and Interoperability Amit K. Chopra to produce only compliant executions, first and foremost the agent must be conformant; second, it must also and Interoperability For an agent to be compliant with a protocol, first and foremost it must be conformant

  6. Serpin latency transition at atomic resolution

    PubMed Central

    Cazzolli, Giorgia; Wang, Fang; a Beccara, Silvio; Gershenson, Anne; Faccioli, Pietro; Wintrode, Patrick L.

    2014-01-01

    Protease inhibition by serpins requires a large conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular dynamics simulations. Using a variational path sampling algorithm, we simulated the entire serpin active-to-latent transition in all-atom detail with a physically realistic force field using a standard computing cluster. These simulations provide a unifying picture explaining existing experimental data for the latency transition of the serpin plasminogen activator inhibitor-1 (PAI-1). They predict a long-lived intermediate that resembles a previously proposed, partially loop-inserted, prelatent state; correctly predict the effects of PAI-1 mutations on the kinetics; and provide a potential means to identify ligands able to accelerate the latency transition. Interestingly, although all of the simulated PAI-1 variants readily access the prelatent intermediate, this conformation is not populated in the active-to-latent transition of another serpin, ?1-antitrypsin, which does not readily go latent. Thus, these simulations also help elucidate why some inhibitory serpin families are more conformationally labile than others. PMID:25313058

  7. Brain Surface Conformal MappingBrain Surface Conformal Mapping XianfengXianfeng GuGu11

    E-print Network

    Wang, Yalin

    Brain Surface Conformal MappingBrain Surface Conformal Mapping XianfengXianfeng GuGu11 ,, Yalin constraints are added to ensure that the conformal map is unique. Empirical tests on MRI data show to differences in data triangulation, and resolution. Compared with other brain surface conformal mapping

  8. Infrared and ultraviolet spectral signatures and conformational preferences of jet-cooled serotonin.

    PubMed

    LeGreve, Tracy A; Baquero, Esteban E; Zwier, Timothy S

    2007-04-01

    The ultraviolet and infrared spectroscopy of single conformations of neutral serotonin (5-hydroxytryptamine) have been studied in the gas phase using a combination of methods including laser-induced fluorescence, resonance-enhanced two-photon ionization, UV-UV hole-burning spectroscopy, and resonant ion-dip infrared spectroscopy. By comparison to its close analogue tryptamine, for which firm assignments to seven low-energy conformations have been made, UV and IR transitions due to eight conformations of serotonin are observed and assigned. The ultraviolet spectrum divides into two subsets of transitions separated from one another by approximately 230 cm-1 ascribable to syn and anti conformations of the 5-OH group. These two subsets are also distinguishable via their 5-OH stretch fundamentals, with the anti-OH subset shifted by approximately 4-5 cm-1 to lower frequency than those due to syn-OH conformers. The existing firm assignments for tryptamine play a decisive role in assignments in serotonin, where the alkyl CH stretch infrared spectrum is diagnostic of the conformation of the ethylamine side chain. Conformer A of serotonin (SERO(A)), with S1 <-- S0 origin transition at 32584 cm-1, is assigned to Gpy(out)/anti-OH, SERO(B) at 32548 cm-1 to Gpy(up)/anti, SERO(C) at 32545 cm-1 to Gph(out)/anti, SERO(D) at 32560 cm-1 to Anti(py)/anti, SERO(E) at 32537 cm-1 to Anti(up)/anti, SERO(F) at 32353 cm-1 to Gpy(out)/syn, SERO(G) at 32313 cm-1 to Gpy(up)/syn, and SERO(H) at 32282 cm-1 to Gph(out)/syn. The conformational preferences of serotonin differ from those of tryptamine most notably in the selective stabilization observed for the Gph(out)/anti-OH conformer SERO(C), which makes it the second-most intense transition in the ultraviolet spectrum, surpassed only by the Gpy(out)/anti-OH conformer SERO(A). PMID:17355134

  9. Measuring Conformational Dynamics of Single Biomolecules Using Nanoscale Electronic Devices

    NASA Astrophysics Data System (ADS)

    Akhterov, Maxim V.; Choi, Yongki; Sims, Patrick C.; Olsen, Tivoli J.; Gul, O. Tolga; Corso, Brad L.; Weiss, Gregory A.; Collins, Philip G.

    2014-03-01

    Molecular motion can be a rate-limiting step of enzyme catalysis, but motions are typically too quick to resolve with fluorescent single molecule techniques. Recently, we demonstrated a label-free technique that replaced fluorophores with nano-electronic circuits to monitor protein motions. The solid-state electronic technique used single-walled carbon nanotube (SWNT) transistors to monitor conformational motions of a single molecule of T4 lysozyme while processing its substrate, peptidoglycan. As lysozyme catalyzes the hydrolysis of glycosidic bonds, two protein domains undergo 8 Å hinge bending motion that generates an electronic signal in the SWNT transistor. We describe improvements to the system that have extended our temporal resolution to 2 ?s . Electronic recordings at this level of detail directly resolve not just transitions between open and closed conformations but also the durations for those transition events. Statistical analysis of many events determines transition timescales characteristic of enzyme activity and shows a high degree of variability within nominally identical chemical events. The high resolution technique can be readily applied to other complex biomolecules to gain insights into their kinetic parameters and catalytic function.

  10. Solitonic Phase Transitions of Galilean Black Holes

    E-print Network

    R. B. Mann

    2009-03-25

    Planar black holes with Galilean asymptotics have been proposed as the holographic dual of a non-relativistic conformal field theory at finite temperature. I show that these objects can undergo a phase transition at low temperature to a new type of soliton with the same asymptotic structure. The strength of the chemical potential is induced by the scale of the soliton.

  11. Conformation and intramolecular relaxation dynamics of semiflexible randomly hyperbranched polymers

    NASA Astrophysics Data System (ADS)

    Kumar, Amit; Rai, Gobind Ji; Biswas, Parbati

    2013-03-01

    The conformational and dynamic properties of semiflexible randomly hyperbranched polymers are investigated in dilute solutions within the framework of optimized Rouse-Zimm formalism. Semiflexibility is incorporated by restricting the directions and orientations of the respective bond vectors, while hydrodynamic interactions are modeled through the preaveraged Oseen tensor. The effect of semiflexibility is typically reflected in the intermediate frequency regime of the viscoelastic relaxation moduli where the bond orientation angle restores the characteristic power-law scaling in fractal structures, as in randomly hyperbranched polymers. Despite the absence of this power-law scaling regime in flexible randomly hyperbranched polymers and in earlier models of semiflexible randomly branched polymers due to weak disorder [C. von Ferber and A. Blumen, J. Chem. Phys. 116, 8616 (2002)], 10.1063/1.1470198, this power-law behavior may be reinstated by explicitly modeling hyperbranched polymers as a Vicsek fractals. The length of this power-law zone in the intermediate frequency region is a combined function of the number of monomers and the degree of semiflexibility. A clear conformational transition from compact to open structures is facilitated by changing the bond orientation angle, where the compressed conformations are compact, while the expanded ones are relatively non-compact. The extent of compactness in the compressed conformations are much less compared to the semiflexible dendrimers, which resemble hard spheres. The fractal dimensions of the compressed and expanded conformations calculated from the Porod's scaling law vary as a function of the bond orientation angle, spanning the entire range of three distinct scaling regimes of linear polymers in three-dimensions. The results confirm that semiflexibility exactly accounts for the excluded volume interactions which are expected to be significant for such polymers with complex topologies.

  12. Conformation and intramolecular relaxation dynamics of semiflexible randomly hyperbranched polymers.

    PubMed

    Kumar, Amit; Rai, Gobind Ji; Biswas, Parbati

    2013-03-14

    The conformational and dynamic properties of semiflexible randomly hyperbranched polymers are investigated in dilute solutions within the framework of optimized Rouse-Zimm formalism. Semiflexibility is incorporated by restricting the directions and orientations of the respective bond vectors, while hydrodynamic interactions are modeled through the preaveraged Oseen tensor. The effect of semiflexibility is typically reflected in the intermediate frequency regime of the viscoelastic relaxation moduli where the bond orientation angle restores the characteristic power-law scaling in fractal structures, as in randomly hyperbranched polymers. Despite the absence of this power-law scaling regime in flexible randomly hyperbranched polymers and in earlier models of semiflexible randomly branched polymers due to weak disorder [C. von Ferber and A. Blumen, J. Chem. Phys. 116, 8616 (2002)], this power-law behavior may be reinstated by explicitly modeling hyperbranched polymers as a Vicsek fractals. The length of this power-law zone in the intermediate frequency region is a combined function of the number of monomers and the degree of semiflexibility. A clear conformational transition from compact to open structures is facilitated by changing the bond orientation angle, where the compressed conformations are compact, while the expanded ones are relatively non-compact. The extent of compactness in the compressed conformations are much less compared to the semiflexible dendrimers, which resemble hard spheres. The fractal dimensions of the compressed and expanded conformations calculated from the Porod's scaling law vary as a function of the bond orientation angle, spanning the entire range of three distinct scaling regimes of linear polymers in three-dimensions. The results confirm that semiflexibility exactly accounts for the excluded volume interactions which are expected to be significant for such polymers with complex topologies. PMID:23514514

  13. New criterion for conformational polymorphism

    SciTech Connect

    Serezhkin, V. N., E-mail: serezhkin@ssu.samara.ru; Serezhkina, L. B. [Samara State University (Russian Federation)

    2012-01-15

    An analysis of nonvalent interactions in 29 crystal structures of compounds that have the C{sub a}H{sub b}N{sub c}O{sub d} composition (salicylaldoxime, glycine, and 2,4,6,8,10,12-hexaazaisowurzitane) and form polymorphic modifications is performed using molecular Voronoi-Dirichlet polyhedra. It is found that each conformational polymorph is characterized by a unique combination of the types of intramolecular and intermolecular nonvalent interactions. It is shown that a criterion which takes into account the total number of intramolecular nonvalent contacts and their distribution depending on the nature of neighboring atoms and the rank of faces of molecular Voronoi-Dirichlet polyhedra can be used to reveal conformational polymorphs.

  14. The Conformational Behaviour of Glucosamine

    NASA Astrophysics Data System (ADS)

    Peña, Isabel; Kolesniková, Lucie; Cabezas, Carlos; Bermúdez, Celina; Berdakin, Matías; Simao, Alcides; Alonso, José L.

    2014-06-01

    A laser ablation method has been successfully used to vaporize the bioactive amino monosaccharide D-glucosamine. Three cyclic ?-4C1 pyranose forms have been identified using a combination of CP-FTMW and LA-MB-FTMW spectroscopy. Stereoelectronic hyperconjugative factors, like those associated with anomeric or gauche effects, as well as the cooperative OH\\cdotsO, OH\\cdotsN and NH\\cdotsO chains, extended along the entire molecule, are the main factors driving the conformational behavior. All observed conformers exhibit a counter-clockwise arrangement (cc) of the network of intramolecular hydrogen bonds. The results are compared with those recently obtained for D-glucose. J. L. Alonso, M. A. Lozoya, I. Peña, J. C. López, C. Cabezas, S. Mata, S. Blanco, Chem. Sci. 2014, 5, 515.

  15. Conformal FDTD modeling wake fields

    SciTech Connect

    Jurgens, T.; Harfoush, F.

    1991-05-01

    Many computer codes have been written to model wake fields. Here we describe the use of the Conformal Finite Difference Time Domain (CFDTD) method to model the wake fields generated by a rigid beam traveling through various accelerating structures. The non- cylindrical symmetry of some of the problems considered here requires the use of a three dimensional code. In traditional FDTD codes, curved surfaces are approximated by rectangular steps. The errors introduced in wake field calculations by such an approximation can be reduced by increasing the mesh size, therefore increasing the cost of computing. Another approach, validated here, deforms Ampere and Faraday contours near a media interface so as to conform to the interface. These improvements of the FDTD method result in better accuracy of the fields at asymptotically no computational cost. This method is also capable of modeling thin wires as found in beam profile monitors, and slots and cracks as found in resistive wall motions. 4 refs., 5 figs.

  16. Exchanging conformations of a hydroformylation catalyst structurally characterized using two-dimensional vibrational spectroscopy.

    PubMed

    Panman, Matthijs R; Vos, Jannie; Bocoki?, Vladica; Bellini, Rosalba; de Bruin, Bas; Reek, Joost H N; Woutersen, Sander

    2013-12-16

    Catalytic transition-metal complexes often occur in several conformations that exchange rapidly (conformations of the hydroformylation catalyst (xantphos)Rh(CO)2H using two-dimensional vibrational spectroscopy, a method that can be applied to any catalyst provided that the exchange between its conformers occurs on a time scale of a few picoseconds or slower. We find that, in one of the conformations, the OC-Rh-CO angle deviates significantly from the canonical value in a trigonal-bipyramidal structure. On the basis of complementary density functional calculations, we ascribe this effect to attractive van der Waals interaction between the CO and the xantphos ligand. PMID:24256078

  17. Sub-Angstrom Conformational Changes of a Single Molecule Captured by AFM Variance Analysis

    PubMed Central

    Walther, Kirstin A.; Bruji?, Jasna; Li, Hongbin; Fernández, Julio M.

    2006-01-01

    A system's equilibrium variance can be analyzed to probe its underlying dynamics at higher resolution. Here, using single-molecule atomic-force microscope techniques, we show how the variance in the length of a single dextran molecule can be used to establish thermodynamic equilibrium and to detect conformational changes not directly observable with other methods. Dextran is comprised of a chain of pyranose rings that each undergoes an Angstrom-scale transition from a chair to boat conformation under a stretching force. Our analysis of the variance of the molecule's fluctuations verifies equilibrium throughout the force-extension curve, consistent with the expected thermodynamic ensemble. This validates further analysis of the variance in the transition region, which reveals an intermediate conformation between the chair and the boat on the sub-Angstrom scale. Our test of thermal equilibrium as well as our variance analysis can be readily extended to a wide variety of molecules, including proteins. PMID:16500987

  18. Conformational Substates of Myoglobin Intermediate Resolved by Picosecond X-ray Solution Scattering

    PubMed Central

    2015-01-01

    Conformational substates of proteins are generally considered to play important roles in regulating protein functions, but an understanding of how they influence the structural dynamics and functions of the proteins has been elusive. Here, we investigate the structural dynamics of sperm whale myoglobin associated with the conformational substates using picosecond X-ray solution scattering. By applying kinetic analysis considering all of the plausible candidate models, we establish a kinetic model for the entire cycle of the protein transition in a wide time range from 100 ps to 10 ms. Four structurally distinct intermediates are formed during the cycle, and most importantly, the transition from the first intermediate to the second one (B ? C) occurs biphasically. We attribute the biphasic kinetics to the involvement of two conformational substates of the first intermediate, which are generated by the interplay between the distal histidine and the photodissociated CO. PMID:24761190

  19. Neutrinos, axions and conformal symmetry

    Microsoft Academic Search

    Krzysztof A. Meissner; Hermann Nicolai

    2008-01-01

    We demonstrate that radiative breaking of conformal symmetry (and simultaneously electroweak symmetry) in the standard model\\u000a with right-chiral neutrinos and a minimally enlarged scalar sector induces spontaneous breaking of lepton number symmetry,\\u000a which naturally gives rise to an axion-like particle with some unusual features. The couplings of this ‘axion’ to standard\\u000a model particles, in particular photons and gluons, are entirely

  20. Conformal Maps and Integrable Hierarchies

    Microsoft Academic Search

    P. B. Wiegmann; A. Zabrodin

    2000-01-01

    :   We show that conformal maps of simply connected domains with an analytic boundary to a unit disk have an intimate relation\\u000a to the dispersionless 2D Toda integrable hierarchy. The maps are determined by a particular solution to the hierarchy singled\\u000a out by the conditions known as “string equations”. The same hierarchy locally solves the 2D inverse potential problem, i.e.,

  1. Exceptional and Spinorial Conformal Windows

    E-print Network

    Matin Mojaza; Claudio Pica; Thomas A. Ryttov; Francesco Sannino

    2012-06-12

    We study the conformal window of gauge theories containing fermionic matter fields, where the gauge group is any of the exceptional groups with the fermions transforming according to the fundamental and adjoint representations and the orthogonal groups where the fermions transform according to a spinorial representation. We investigate the phase diagram using a purely perturbative four loop analysis, the all-orders beta function and the ladder approximation.

  2. Dark energy from conformal symmetry breaking

    E-print Network

    F. Darabi

    2013-06-18

    The breakdown of conformal symmetry in a conformally invariant scalar-tensor gravitational model is revisited in the cosmological context. Although the old scenario of conformal symmetry breaking in cosmology containing scalar field has already been used in many earlier works, it seems that no special attention has been paid for the investigation on the possible connection between the breakdown of conformal symmetry and the existence of dark energy. In this paper, it is shown that the old scenario of conformal symmetry breaking in cosmology, if properly interpreted, not only has a potential ability to describe the origin of dark energy as a symmetry breaking effect, but also may resolve the coincidence problem.

  3. Dynamical conformal transformation and classical Euclidean wormholes

    E-print Network

    F. Darabi

    2011-01-21

    We investigate the necessary condition for the existence of classical Euclidean wormholes in a conformally non-invariant gravitational model minimally coupled to an scalar field. It is shown that while the original Ricci tensor with positive eigenvalues does not allow the Euclidean wormholes to occur, under dynamical conformal transformations the Ricci tensor, with respect to the original metric, is dynamically coupled with the conformal field and its eigenvalues may become negative allowing the Euclidean wormholes to occur. Therefore, it is conjectured that dynamical conformal transformations may provide us with {\\it effective} forms of matter sources leading to Euclidean wormholes in conformally non-invariant systems.

  4. The Conformational Landscape of Serinol

    NASA Astrophysics Data System (ADS)

    Sanz, M. Eugenia; Loru, Donatella; Peña, Isabel; Alonso, José L.

    2014-06-01

    The rotational spectrum of the amino alcohol serinol CH_2OH--CH(NH_2)--CH_2OH, which constitutes the hydrophilic head of the lipid sphingosine, has been investigated using chirped-pulsed Fourier transform microwave spectroscopy in combination with laser ablation Five different forms of serinol have been observed and conclusively identified by the comparison between the experimental values of their rotational and 14N quadrupole coupling constants and those predicted by ab initio calculations. In all observed conformers several hydrogen bonds are established between the two hydroxyl groups and the amino groups in a chain or circular arrangement. The most abundant conformer is stabilised by O--H···N and N--H···O hydrogen bonds forming a chain rather than a cycle. One of the detected conformers presents a tunnelling motion of the hydrogen atoms of the functional groups similar to that observed in glycerol. S. Mata, I. Peña, C. Cabezas, J. C. López, J. L. Alonso, J. Mol. Spectrosc. 2012, 280, 91 V. V. Ilyushin, R. A. Motiyenko, F. J. Lovas, D. F. Plusquellic, J. Mol. Spectrosc. 2008, 251, 129.

  5. Exploring protein native states and large-scale conformational changes with a modified generalized born model

    Microsoft Academic Search

    Alexey Onufriev; Donald Bashford; David A. Case

    2004-01-01

    Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the elec- trostatics of aqueous solvation. Here, a popular analytical Generalized Born (GB) solvation model is modified to improve its accuracy in calculating the solvent polarization part of free energy changes in large-scale conformational transitions, such as pro- tein folding. In contrast to an

  6. STUDY OF LIQUID CRYSTAL CONFORMATION BY MULTIPLE QUANTUM NMR: n-PENTYL CYANOBIPHENYL

    SciTech Connect

    Sinton, S.; Pines, A.

    1980-09-01

    The multiple quantum NMR spectrum of 4-cyano-4'-n-pentyl-d{sub 11}-biphenyl in the nematic phase is presented. The sub-spectra of the higher quantum transitions are easier to interpret than the single quantum spectrum. A preliminary analysis of the biphenyl conformation indicates that the dihedral angle is 32° ± 1°.

  7. Centrifugal distortion analysis of the microwave spectrum of allyl isothiocyanate (C-gauche conformer)

    NASA Astrophysics Data System (ADS)

    Jaman, A. I.

    1999-11-01

    The ground state microwave rotational spectrum of the C-gauche conformer of allyl isothiocyanate has been reinvestigated by extending the frequency range up to 37.0 GHz. A detailed centrifugal distortion analysis has been carried out with previously reported and newly assigned microwave rotational transition frequencies. The evaluated rotational and centrifugal distortion constants are presented.

  8. TRAVEL DEMAND MODELING AND CONFORMITY DETERMINATION: ATLANTA REGIONAL COMMISSION CASE STUDY

    Microsoft Academic Search

    Guy Rousseau; Tracy Clymer

    2002-01-01

    The Atlanta Regional Commission (ARC) regional travel demand model is described as it relates to its link-based emissions postprocessor. In addition to conformity determination, an overview of other elements is given. The transit networks include the walk and highway access links. Trip generation addresses trip production, trip attraction, reconciliation of productions and attractions, and special adjustments made for Hartsfield Atlanta

  9. Gramicidin conformational studies with mixed-chain unsaturated phospholipid bilayer systems

    SciTech Connect

    Cox, K.J.; Ho, Cojen; Lombardi, J.V.; Stubbs, C.D. (Thomas Jefferson Univ., Philadelphia, PA (United States))

    1992-02-04

    The transition of gramicidin from a nonchannel to a channel form was investigated using mixed-chain phosphatidylcholine lipid bilayers. Gramicidin and phospholipids were codispersed, after removal of the solvents chloroform/methanol or trifluoroethanol which resulted in nonchannel and channel conformations, respectively, as confirmed using circular dichroism (CD). The fluorescence emission maxima of the nonchannel form were shifted toward shorter wavelengths by heating at 60C (for 0-12 h), which converted it to a channel form, again as confirmed by CD. The channel form did not respond to heat treatment. Heat treatment also increased the fluorescence anisotropy of the nonchannel gramicidin tryptophans. The rate of transition from the nonchannel to channel conformation was found to be faster is phosphatidylethanolamine was present in combination with phosphatidylcholine compared to phosphatidylcholine alone. Using the fluorescence anisotropy of the membrane lipid probe, 1,6-diphenyl-1,3,5-hexatriene, it was also shown that the motional properties of the surrounding lipid acyl chains differed for the channel and nonchannel gramicidin conformations. The possibility that lipids tending to favor the hexagonal phase (H{sub II}) would enhance the rate of the nonchannel to channel transition was supported by {sup 31}P NMR which revealed the presence of some H{sub II} lipids in the channel preparations. The results of this study suggest that gramicidin may serve as a useful model for similar conformational transitions in other more complex membrane proteins.

  10. Conformally equivariant quantization for spinning particles

    E-print Network

    Jean-Philippe Michel

    2015-01-06

    This work takes place over a conformally flat spin manifold (M,g). We prove existence and uniqueness of the conformally equivariant quantization valued in spinor differential operators, and provide an explicit formula for it when restricted to first order operators. The Poisson algebra of symbols is realized as a space of functions on the supercotangent bundle, endowed with a symplectic form depending on the metric g. It admits two different actions of the conformal Lie algebra, one tensorial and one Hamiltonian. They are intertwined by the uniquely defined conformally equivariant superization, for which an explicit formula is given. This map allows us to classify all the conformal supercharges of the spinning particle in terms of conformal Killing tensors with mixed symmetry, generated by the totally symmetric and skew-symmetric ones. Higher symmetries of the Dirac operator are obtained by quantization of the conformal supercharges.

  11. Logarithmic conformal field theory: a lattice approach

    NASA Astrophysics Data System (ADS)

    Gainutdinov, A. M.; Jacobsen, J. L.; Read, N.; Saleur, H.; Vasseur, R.

    2013-12-01

    Logarithmic conformal field theories (LCFT) play a key role, for instance, in the description of critical geometrical problems (percolation, self-avoiding walks, etc), or of critical points in several classes of disordered systems (transition between plateaux in the integer and spin quantum Hall effects). Much progress in their understanding has been obtained by studying algebraic features of their lattice regularizations. For reasons which are not entirely understood, the non-semi-simple associative algebras underlying these lattice models—such as the Temperley-Lieb algebra or the blob algebra—indeed exhibit, in finite size, properties that are in full correspondence with those of their continuum limits. This applies not only to the structure of indecomposable modules, but also to fusion rules, and provides an ‘experimental’ way of measuring couplings, such as the ‘number b’ quantifying the logarithmic coupling of the stress-energy tensor with its partner. Most results obtained so far have concerned boundary LCFTs and the associated indecomposability in the chiral sector. While the bulk case is considerably more involved (mixing in general left and right moving sectors), progress has also recently been made in this direction, uncovering fascinating structures. This study provides a short general review of our work in this area.

  12. Use of Chou-Fasman amino acid conformational parameters to analyze the organization of the genetic code and to construct protein genealogies

    Microsoft Academic Search

    Morris Goodman; G. William Moore

    1977-01-01

    Summary Chou-Fasman parameters, measuring preferences of each amino acid for different conformational regions in proteins, were used to obtain an amino acid difference index of conformational parameter distance (CPD) values. CPD values were found to be significantly lower for amino acid exchanges representing in the genetic code transitions of purines, G?A than for exchanges representing either transitions of pyrimidines, C?U,

  13. Low-frequency vibrations specific for conformers of 1-aminoindan studied by UV-UV hole-burning spectroscopy.

    PubMed

    Isozaki, Tasuku; Iga, Hiroshi; Suzuki, Tadashi; Ichimura, Teijiro

    2007-06-01

    The UV-UV hole-burning spectra of the jet-cooled 1-aminoindan were measured for the first time. Complicated spectral features observed in the laser-induced fluorescence excitation spectrum due to two conformers, R and B, were firmly separated. On the basis of fluorescence measurements and B3LYP/cc-pVTZ calculations, low-frequency ring twisting and ring puckering modes were assigned. These modes are coupled in the S1 state due to the Duschinsky rotation. The Duschinsky matrix was calculated from the normal modes predicted by quantum chemical calculations. The coupling between the twisting and puckering modes for conformer B is stronger than that for conformer R. The twisting mode was observed at 0+99 cm(-1) in the S1 state for conformer B, while not for conformer R. The Franck-Condon activity of the twisting mode substantially differs between the two conformers. The transition to the twisting level for conformer B would be allowed by the Duschinsky rotation. The fluorescence lifetime of conformer vibronic levels was also measured and differed for each conformer. PMID:17567193

  14. Conformal invariance and the conformal-traceless decomposition of the gravitational field

    E-print Network

    David Brown

    2005-05-05

    Einstein's theory of general relativity is written in terms of the variables obtained from a conformal--traceless decomposition of the spatial metric and extrinsic curvature. The determinant of the conformal metric is not restricted, so the action functional and equations of motion are invariant under conformal transformations. With this approach the conformal--traceless variables remain free of density weights. The conformal invariance of the equations of motion can be broken by imposing an evolution equation for the determinant of the conformal metric g. Two conditions are considered, one in which g is constant in time and one in which g is constant along the unit normal to the spacelike hypersurfaces. This approach is used to write the Baumgarte--Shapiro--Shibata--Nakamura system of evolution equations in conformally invariant form. The presentation includes a discussion of the conformal thin sandwich construction of gravitational initial data, and the conformal flatness condition as an approximation to the evolution equations.

  15. Conformation and structure of polymeric contrast agents for medical imaging.

    PubMed

    Uzgiris, E E; Cline, Harvey; Moasser, Bahram; Grimmond, Brian; Amaratunga, Mohan; Smith, Joanne F; Goddard, Gregory

    2004-01-01

    The structure of Gd-DTPA-polylysine, Gd-DOTA-polylysine, Gd-SCN-Bz-DOTA-polylysine, and Gd-DTPA-poly(glu:lys) was investigated with circular dichroism, gel permeation chromatography, low angle light scattering, and proton longitudinal relaxivity. Molecular modeling calculations were performed and predicted helical secondary structure for charged Gd-chelator residues, i.e., Gd-DTPA, when the DTPA conjugation levels reached 90% and higher. This helical secondary structure was observed with circular dichroism. The conformational transition from coiled to extended linear was observed also by gel permeation chromatography and by proton relaxivity measurements. The helical secondary structure was not observed when the chelator was changed to DOTA. The residue charge interactions were eliminated in this case since the Gd-DOTA complex had no net charge. For this construct, the gel permeation and relaxivity measurements indicated a coiled conformation. An extended linear conformation was regained when the chelator complex was changed to Gd-SCN-Bz-DOTA, which had a net negative charge. The functional aspects of these structures were investigated by MR imaging of an animal tumor model. The linear extended polymer constructs gave 10-fold higher tumor signals then the coiled-collapsed constructs, indicating a much higher degree of trans-endothelial transport in the tumors. PMID:14715008

  16. Conformational dependence of a protein kinase phosphate transfer reaction

    PubMed Central

    Henkelman, Graeme; LaBute, Montiago X.; Tung, Chang-Shung; Fenimore, P. W.; McMahon, Benjamin H.

    2005-01-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. With the protein in TC, the motions involved in reaction are small, with only P? and the catalytic proton moving >0.5 Å. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site. PMID:16227439

  17. Conformal mapping of Unruh temperature

    E-print Network

    Pierre Martinetti

    2009-05-02

    Thanks to a local interpetation of the KMS condition, the mapping from (unbounded) wedge regions of Minkowski space-time to (bounded) double-cone regions is extended to the Unruh temperature associated to relevant observers in both regions. A previous result, the diamond's temperature, is shown to be proportional to the inverse of the conformal factor (Weyl rescaling of the metric) of this map. One thus explains from a mathematical point of view why an observer with finite lifetime experiences the vacuum as a thermal state whatever his acceleration, even vanishing.

  18. Conformance Verification of Privacy Policies

    NASA Astrophysics Data System (ADS)

    Fu, Xiang

    Web applications are both the consumers and providers of information. To increase customer confidence, many websites choose to publish their privacy protection policies. However, policy conformance is often neglected. We propose a logic based framework for formally specifying and reasoning about the implementation of privacy protection by a web application. A first order extension of computation tree logic is used to specify a policy. A verification paradigm, built upon a static control/data flow analysis, is presented to verify if a policy is satisfied.

  19. Scale Invariance + Unitarity => Conformal Invariance?

    E-print Network

    Dorigoni, Daniele

    2009-01-01

    We revisit the long-standing conjecture that in unitary field theories, scale invariance implies conformality. We explain why the Zamolodchikov-Polchinski proof in D=2 does not work in higher dimensions. We speculate which new ideas might be helpful in a future proof. We also search for possible counterexamples. We consider a general multi-field scalar-fermion theory with quartic and Yukawa interactions. We show that there are no counterexamples among fixed points of such models in 4-epsilon dimensions. We also discuss fake counterexamples, which exist among theories without a stress tensor.

  20. Combined effect of confinement and affinity of crowded environment on conformation switching of adenylate kinase.

    PubMed

    Li, Min; Xu, Weixin; Zhang, John Z H; Xia, Fei

    2014-12-01

    The actual conformation switching of proteins in the crowded cellular environment is completely different from that in vitro. Proteins in cytoplasm are continually subject to confinement and/or attraction to other molecules in their surroundings due to the existence of various biological species. To gain insight into the nature of crowded environments, we investigated the effects of confinement and affinity on the conformation switching of adenylate kinase (ADK) in a spherical cavity. It was found that even a small degree of confinement reduces the entropy of the open state and stabilizes the closed state, which leads to increased energy barriers for transition. Furthermore, the analysis of transition temperatures and mean first passage times indicates that the proper affinity can promote the transition of ADK from closed state to open state. This study reveals that the crowded cellular environment plays an important role in the thermodynamics and kinetics of proteins in vivo. PMID:25432855

  1. Magnetically-conformed, Variable Area Discharge Chamber for Hall Thruster, and Method

    NASA Technical Reports Server (NTRS)

    Hofer, Richard R. (Inventor)

    2013-01-01

    The invention is a Hall thruster that incorporates a discharge chamber having a variable area channel including an ionization zone, a transition region, and an acceleration zone. The variable area channel is wider through the acceleration zone than through the ionization zone. An anode is located in a vicinity of the ionization zone and a cathode is located in a vicinity of the acceleration zone. The Hall thruster includes a magnetic circuit which is capable of forming a local magnetic field having a curvature within the transition region of the variable area channel whereby the transition region conforms to the curvature of the local magnetic field. The Hall thruster optimizes the ionization and acceleration efficiencies by the combined effects of the variable area channel and magnetic conformity.

  2. Conformal gravity in the Schwarzschild metric

    E-print Network

    R. K. Nesbet

    2014-10-30

    Conformal gravity theory is a version of general relativity based on replacing Ricci scalar R in the Einstein-Hilbert variational action integral by the conformal Weyl Lagrangian density. In the Schwarzschild metric, relevant to a static spherically symmetric galactic model, conformal gravity has recently been shown to imply a remarkable fit to anomalous rotation data for 138 galaxies. Recent criticism suggests failure of this formalism to reproduce standard subgalactic phenomenology and to account for the relative signs of implied Newtonian and nonclassical acceleration parameters inferred from galactic rotational velocity data. These problems are resolved here by combining conformal gravity with a conformal modification of the Higgs scalar field model, relevant to Hubble expansion. The resulting universal conformal theory establishes relationships between parameters for distinct phenomena that are shown here to be consistent with observed data.

  3. The conformation of P450cam in complex with putidaredoxin is dependent on oxidation state

    PubMed Central

    Myers, William K.; Lee, Young-Tae; Britt, R. David; Goodin, David B.

    2013-01-01

    Double electron-electron resonance (DEER) spectroscopy was used to determine the conformational state in solution for the heme monooxygenase P450cam when bound to its natural redox partner, putidaredoxin (Pdx). When oxidized Pdx was titrated into substrate-bound ferric P450cam, the enzyme shifted from the closed to the open conformation. In sharp contrast however, the enzyme remained in the closed conformation when ferrous-CO P450cam was titrated with reduced Pdx. This result fully supports the proposal that binding of oxidized Pdx to P450cam opposes the open to closed transition induced by substrate binding. However, the data strongly suggest that, in solution, binding of reduced Pdx to P450cam does not favor the open conformation. This supports a model in which substrate recognition is associated with the open-to-closed transition and electron transfer from Pdx occurs in the closed conformation. The opening of the enzyme in the ferric-hydroperoxo state following electron transfer from Pdx would provide for efficient O2 bond activation, substrate oxidation and product release. PMID:23901883

  4. Bootstrapping phase transitions in QCD and frustrated spin systems

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu; Ohtsuki, Tomoki

    2015-01-01

    In view of its physical importance in predicting the order of chiral phase transitions in QCD and frustrated spin systems, we perform the conformal bootstrap program of [O (n )×O (2 ) ]-symmetric conformal field theories in d =3 dimensions with a special focus on n =3 and 4. The existence of renormalization group fixed points with these symmetries has been controversial over the years, but our conformal bootstrap program provides nonperturbative evidence. In both the n =3 and 4 cases, we find singular behaviors in the bounds of scaling dimensions of operators in two different sectors, which we claim correspond to chiral and collinear fixed points, respectively. In contrast to the cases with larger values of n , we find no evidence for the antichiral fixed point. Our results indicate the possibility that the chiral phase transitions in QCD and frustrated spin systems are continuous with the critical exponents that we predict from the conformal bootstrap program.

  5. Exploration trees and conformal loop ensembles

    E-print Network

    Scott Sheffield

    2006-11-23

    We construct and study the conformal loop ensembles CLE(kappa), defined for all kappa between 8/3 and 8, using branching variants of SLE(kappa) called exploration trees. The conformal loop ensembles are random collections of countably many loops in a planar domain that are characterized by certain conformal invariance and Markov properties. We conjecture that they are the scaling limits of various random loop models from statistical physics, including the O(n) loop models.

  6. Computing conformational free energy by deactivated morphing.

    SciTech Connect

    Park, S.; Lau, A. Y.; Roux, B.; Univ. of Chicago

    2008-10-07

    Despite the significant advances in free-energy computations for biomolecules, there exists no general method to evaluate the free-energy difference between two conformations of a macromolecule that differ significantly from each other. A crucial ingredient of such a method is the ability to find a path between different conformations that allows an efficient computation of the free energy. In this paper, we introduce a method called 'deactivated morphing', in which one conformation is morphed into another after the internal interactions are completely turned off. An important feature of this method is the (shameless) use of nonphysical paths, which makes the method robustly applicable to conformational changes of arbitrary complexity.

  7. Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline

    NASA Astrophysics Data System (ADS)

    Cabezas, C.; Cortijo, V.; Mata, S.; Lopez, J. C.; Alonso, J. L.

    2013-06-01

    Recent improvements in our LA-MB-FTMW instrumentation have allowed the characterization of eleven and eight conformers for the neurotransmitters adrenaline and noradrenaline respectively. The observation of this rich conformational behavior is in accordance with the recent observation of seven conformers for dopamine and in sharp contrast with the conformational reduction proposed for catecholamines. C. Cabezas, I. Peña, J. C. López, J. L. Alonso J. Phys. Chem. Lett. 2013, 4, 486. H. Mitsuda, M. Miyazaki, I. B. Nielsen, P. Carcabal,C. Dedonder, C. Jouvet, S. Ishiuchi, M. Fujii J. Phys. Chem. Lett. 2010, 1, 1130.

  8. Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC.

    PubMed

    Kinde, Monica N; Chen, Qiang; Lawless, Matthew J; Mowrey, David D; Xu, Jiawei; Saxena, Sunil; Xu, Yan; Tang, Pei

    2015-06-01

    Structural rearrangements underlying functional transitions of pentameric ligand-gated ion channels (pLGICs) are not fully understood. Using (19)F nuclear magnetic resonance and electron spin resonance spectroscopy, we found that ELIC, a pLGIC from Erwinia chrysanthemi, expanded the extracellular end and contracted the intracellular end of its pore during transition from the resting to an apparent desensitized state. Importantly, the contraction at the intracellular end of the pore likely forms a gate to restrict ion transport in the desensitized state. This gate differs from the hydrophobic gate present in the resting state. Conformational changes of the TM2-TM3 loop were limited to the N-terminal end. The TM4 helices and the TM3-TM4 loop appeared relatively insensitive to agonist-mediated structural rearrangement. These results indicate that conformational changes accompanying functional transitions are not uniform among different ELIC regions. This work also revealed the co-existence of multiple conformations for a given state and suggested asymmetric conformational arrangements in a homomeric pLGIC. PMID:25960405

  9. ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece.

    PubMed

    Grycova, Lenka; Sklenovsky, Petr; Lansky, Zdenek; Janovska, Marika; Otyepka, Michal; Amler, Evzen; Teisinger, Jan; Kubala, Martin

    2009-05-01

    Conformational changes of the Na(+)/K(+)-ATPase isolated large cytoplasmic segment connecting transmembrane helices M4 and M5 (C45) induced by the interaction with enzyme ligands (i.e. Mg(2+) and/or ATP) were investigated by means of the intrinsic tryptophan fluorescence measurement and molecular dynamic simulations. Our data revealed that this model system consisting of only two domains retained the ability to adopt open or closed conformation, i.e. behavior, which is expected from the crystal structures of relative Ca(2+)-ATPase from sarco(endo)plasmic reticulum for the corresponding part of the entire enzyme. Our data revealed that the C45 is found in the closed conformation in the absence of any ligand, in the presence of Mg(2+) only, or in the simultaneous presence of Mg(2+) and ATP. Binding of the ATP alone (i.e. in the absence of Mg(2+)) induced open conformation of the C45. The fact that the transmembrane part of the enzyme was absent in our experiments suggested that the observed conformational changes are consequences only of the interaction with ATP or Mg(2+) and may not be related to the transported cations binding/release, as generally believed. Our data are consistent with the model, where ATP binding to the low-affinity site induces conformational change of the cytoplasmic part of the enzyme, traditionally attributed to E2-->E1 transition, and subsequent Mg(2+) binding to the enzyme-ATP complex induces in turn conformational change traditionally attributed to E1-->E2 transition. PMID:19232513

  10. Conformal mapping techniques in string field theory. January 1986-April 1989 (Citations from the INSPEC: Information Services for the Physics and Engineering Communities data base). Report for January 1986-April 1989

    SciTech Connect

    Not Available

    1989-04-01

    This bibliography contains citations concerning recent developments of conformal-mapping techniques in string theories and superstring theories for elementary particle physics and unified fields. Conformal field theories for bosonic strings, fermionic strings, and heterotic strings are presented. Topics include construction of vertex operators for the development of string theories, conformal invariance and string dynamics, conformal gauge theory of strings, closed string and open string transitions, string propagation in background fields, conformal string compactification, string quantization on Riemann surfaces, supergravity, and superconformal algebras. (Contains 98 citations fully indexed and including a title list.)

  11. Exact spectra of conformal supersymmetric nonlinear sigma models in two dimensions

    NASA Astrophysics Data System (ADS)

    Read, N.; Saleur, H.

    2001-10-01

    We study two-dimensional nonlinear sigma models in which the target spaces are the coset supermanifolds U(n+m|n)/[ U(1)× U(n+m-1|n)]? CP n+m-1|n (projective superspaces) and OSp(2 n+ m|2 n)/OSp(2 n+ m-1|2 n)? S2 n+ m-1|2 n (superspheres), n, m integers, -2? m?2; these quantum field theories live in Hilbert spaces with indefinite inner products. These theories possess non-trivial conformally-invariant renormalization-group fixed points, or in some cases, lines of fixed points. Some of the conformal fixed-point theories can also be obtained within Landau-Ginzburg theories. We obtain the complete spectra (with multiplicities) of exact conformal weights of states (or corresponding local operators) in the isolated fixed-point conformal field theories, and at one special point on each of the lines of fixed points. Although the conformal weights are rational, the conformal field theories are not, and (with one exception) do not contain the affine versions of their superalgebras in their chiral algebras. The method involves lattice models that represent the strong-coupling region, which can be mapped to loop models, and then to a Coulomb gas with modified boundary conditions. The results apply to percolation, dilute and dense polymers, and other statistical mechanics models, and also to the spin quantum Hall transition in non-interacting fermions with quenched disorder.

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

    PubMed

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

    2010-08-01

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

  13. Large conformational changes in MutS during DNA scanning, mismatch recognition and repair signalling

    PubMed Central

    Qiu, Ruoyi; DeRocco, Vanessa C; Harris, Credle; Sharma, Anushi; Hingorani, Manju M; Erie, Dorothy A; Weninger, Keith R

    2012-01-01

    MutS protein recognizes mispaired bases in DNA and targets them for mismatch repair. Little is known about the transient conformations of MutS as it signals initiation of repair. We have used single-molecule fluorescence resonance energy transfer (FRET) measurements to report the conformational dynamics of MutS during this process. We find that the DNA-binding domains of MutS dynamically interconvert among multiple conformations when the protein is free and while it scans homoduplex DNA. Mismatch recognition restricts MutS conformation to a single state. Steady-state measurements in the presence of nucleotides suggest that both ATP and ADP must be bound to MutS during its conversion to a sliding clamp form that signals repair. The transition from mismatch recognition to the sliding clamp occurs via two sequential conformational changes. These intermediate conformations of the MutS:DNA complex persist for seconds, providing ample opportunity for interaction with downstream proteins required for repair. PMID:22505031

  14. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion

    PubMed Central

    Hohlbein, Johannes; Aigrain, Louise; Craggs, Timothy D.; Bermek, Oya; Potapova, Olga; Shoolizadeh, Pouya; Grindley, Nigel D. F.; Joyce, Catherine M.; Kapanidis, Achillefs N.

    2013-01-01

    The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides before phosphoryl transfer. Here, we combine single-molecule FRET with the use of DNA polymerase I and various fidelity mutants to highlight mechanisms by which active-site side chains influence the conformational transitions and free-energy landscape that underlie fidelity decisions in DNA synthesis. Ternary complexes of high fidelity derivatives with complementary dNTPs adopt mainly a fully closed conformation, whereas a conformation with a FRET value between those of open and closed is sparsely populated. This intermediate-FRET state, which we attribute to a partially closed conformation, is also predominant in ternary complexes with incorrect nucleotides and, strikingly, in most ternary complexes of low-fidelity derivatives for both correct and incorrect nucleotides. The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection. PMID:23831915

  15. Weinhold geometry and Ruppeiner geometry of black holes with conformal anomaly

    NASA Astrophysics Data System (ADS)

    Mo, Jie-Xiong

    2015-03-01

    The thermodynamic geometry of black holes with conformal anomaly has been investigated in this paper. We study two classical kinds of thermodynamic geometry. Namely, Weinhold geometry and Ruppeiner geometry. It is shown that the condition when Weinhold scalar curvature diverges is the same as the phase transition condition characterized by the divergence of specific heat. It is also shown that Ruppeiner scalar curvature not only reveals the phase structure but also contains the information of Hawking temperature. In a word, both Weinhold metric and Ruppeiner metric can correctly reproduce the phase structure of black holes even when conformal anomaly is taken into consideration.

  16. Using Solutes and Kinetics to Probe Large Conformational Changes in the Steps of Transcription Initiation

    PubMed Central

    Ruff, Emily; Kontur, Wayne S.; Record, M. Thomas

    2014-01-01

    Summary Small solutes are useful probes of large conformational changes in RNA polymerase (RNAP)-promoter interactions and other biopolymer processes. In general, a large effect of a solute on an equilibrium constant (or rate constant) indicates a large change in water-accessible biopolymer surface area in the corresponding step (or transition state), resulting from conformational changes, interface formation, or both. Here, we describe nitrocellulose filter binding assays from series used to determine the urea dependence of open complex formation and dissociation with Escherichia coli RNAP and ?PR promoter DNA. Then, we describe the subsequent data analysis and interpretation of these solute effects. PMID:25665568

  17. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

    NASA Astrophysics Data System (ADS)

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

    2015-06-01

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

  18. On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein.

    PubMed

    Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E; Fernandez-Alberti, Sebastian

    2015-06-28

    The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data. PMID:26133456

  19. Open to closed transition in apo maltose-binding protein visualized by paramagnetic NMR

    E-print Network

    Clore, G. Marius

    Open to closed transition in apo maltose-binding protein visualized by paramagnetic NMR Chun Tang,1 of holo (maltotriose-bound) conformation on the agreement between observed and calculated RDCs for apo MBP, assuming only a single conformation represented by the crystal structure of apo MBP. Fig. S1. Agreement

  20. From Stability to Mobility: African Secondary School Aged Adolescents' Transition to Mainstream Schooling

    ERIC Educational Resources Information Center

    Gunasekera, Sashya; Houghton, Stephen; Glasgow, Kenneth; Boyle, Christopher

    2014-01-01

    Setting clear achievable goals that enhance reputational status has been shown to direct the energies of adolescents into socially conforming or non-conforming activities. It appears to be the case that following transition from Intensive English Centres (IECs) into mainstream schooling, students from African refugee backgrounds experience…

  1. Observing the unfolding transition of [beta]-hairpin peptides with nonlinear infrared spectroscopy

    E-print Network

    Smith, Adam Wilcox, 1977-

    2008-01-01

    The biological function of a protein is in large measure determined by its three-dimensional structure. To date, however, the transition of the protein between the native and non-native conformations is not well-understood. ...

  2. Conformational Analysis and Molecular Dynamics Simulation of Glucose, Cellobiose and Cellulose Oligomers.

    NASA Astrophysics Data System (ADS)

    Hardy, Barry John

    1990-01-01

    The conformational behavior of beta -D- and alpha-D-glucose, cellobiose and cellulose oligomers was studied by a combination of energy minimization and molecular dynamics simulation in vacuo and in water, using models based on molecular mechanics force fields. Calculations were carried out with different modeling strategies to ascertain the sensitivity of conformational behavior to force field, lone-pairs of electrons, charges and dielectric constant. Glucose and cellobiose rings remained in the ^4C_1 conformation at all times in all simulations. Rotational O6 transitions were observed for all structures between gg, gt and gt conformations with gg and tg conformations favored. Charged models enhanced the intramolecular hydrogen -bonding and tg occupancy of the structures and reduced molecular flexibility. The hydrogen-bonding patterns were dependent on O6 conformation. The cellobiose and cellooligomer structures moved between a number of local minima on the Phi , Psi conformational map. Two of the minima, located in the region of observed crystal structures, were favored with a few transitions to higher energy minima also occurring. The dependence of both molecular energy and dynamics on Phi, Psi and O6 conformation was found to be primarily sensitive to charge assignments and dielectric constant. A solvation energy contribution of less than 1 kcal/mole would be sufficient to match the experimental anomeric ratio of glucose in water for any of the models. Experimental optical rotation and vicinal coupling constant data on cellobiose in solution could be fit--to varying degrees for different models--by the predicted distribution of conformations. The cellooligomers were observed to have considerable flexibility and exhibited a variety of different motions, more so than had been observed in dimer models. These motions included ring flipping, chain folding and pseudorotation. Simulations in water showed that both the average conformation and flexibility of cellobiose was affected slightly by solvating water. All dimer hydroxyl groups participated in both intermolecular hydrogen bonds with water and intramolecular hydrogen bonds. Approximately eight intermolecular hydrogen bonds were formed per dimer residue. The vector-concurrent optimization and performance of the force field code used for simulation is described. A computer graphics and animation video, illustrating a selection of simulation results, accompanies the dissertation.

  3. Conformal structures The ambient metric in complex analysis

    E-print Network

    Drmota, Michael

    Conformal structures The ambient metric in complex analysis The conformal ambient metric, November 2009 Andreas Cap Ambient metric #12;Conformal structures The ambient metric in complex analysis Ambient metric #12;Conformal structures The ambient metric in complex analysis The conformal ambient

  4. Electromagnetic characterization of conformal antennas

    NASA Technical Reports Server (NTRS)

    Volakis, John L.; Kempel, Leo C.; Alexanian, Angelos; Jin, J. M.; Yu, C. L.; Woo, Alex C.

    1992-01-01

    The ultimate objective of this project is to develop a new technique which permits an accurate simulation of microstrip patch antennas or arrays with various feed, superstrate and/or substrate configurations residing in a recessed cavity whose aperture is planar, cylindrical or otherwise conformed to the substructure. The technique combines the finite element and boundary integral methods to formulate a system suitable for solution via the conjugate gradient method in conjunction with the fast Fourier transform. The final code is intended to compute both scattering and radiation patterns of the structure with an affordable memory demand. With upgraded capabilities, the four included papers examined the radar cross section (RCS), input impedance, gain, and resonant frequency of several rectangular configurations using different loading and substrate/superstrate configurations.

  5. Charged gravastars admitting conformal motion

    E-print Network

    A A Usmani; Farook Rahaman; Saibal Ray; K K Nandi; Peter K. F. Kuhfittig; Sk. A Rakib; Z Hasan

    2011-06-03

    We propose a new model of a {\\it gravastar} admitting conformal motion. While retaining the framework of the Mazur-Mottola model, the gravastar is assumed to be internally charged, with an exterior defined by a Reissner-Nordstr{\\"o}m rather than a Schwarzschild line element. The solutions obtained involve (i) the interior region, (ii) the shell, and (iii) the exterior region of the sphere. Of these three cases the first case is of primary interest since the total gravitational mass vanishes for vanishing charge and turns the total gravitational mass into an {\\it electromagnetic mass} under certain conditions. This suggests that the interior de Sitter vacuum of a charged gravastar is essentially an electromagnetic mass model that must generate the gravitational mass. We have also analyzed various other aspects such as the stress energy tensor in the thin shell and the entropy of the system.

  6. Approaching Conformality with Ten Flavors

    SciTech Connect

    Appelquist, Thomas; Brower, Richard C.; Buchoff, Michael I.; Cheng, Michael; Cohen, Saul D.; Fleming, George T.; Kiskis, Joe; Lin, Meifeng; Na, Heechang; Neil, Ethan T.; Osborn, James C.

    2012-04-01

    We present first results for lattice simulations, on a single volume, of the low-lying spectrum of an SU(3) Yang-Mills gauge theory with N{sub f} = 10 light fermions in the fundamental representation. Fits to the fermion mass dependence of various observables are found to be globally consistent with the hypothesis that this theory is within or just outside the strongly-coupled edge of the conformal window, with mass anomalous dimension {gamma}* {approx} 1 over the range of scales simulated. We stress that we cannot rule out the possibility of spontaneous chiral-symmetry breaking at scales well below our infrared cutoff. We discuss important systematic effects, including finite-volume corrections, and consider directions for future improvement.

  7. Thermodynamic and conformational studies on an immunoglobulin light chain which reversibly precipitates at low temperatures.

    PubMed

    Klein, M; Kells, D I; Tinker, D O; Dorrington, K J

    1977-02-01

    A lambda light chain, isolated from an immunoglobulin G molecule, was found to reversibly precipitate at low temperatures. This cryoprecipitation was a function of pH, ionic strength, protein concentration, and time as well as temperature. The lambda chain underwent a cooperative conformational change as the temperature was lowered from 26 to 0 degrees C as judged by ultraviolet difference spectroscopy and circular dichroism. Normal lambda chains showed no conformational change. By difference spectroscopy it was possible to calculate the equilibrium constant governing the conformational change. The change was strongly exothermic (delta H approximately -80 kcal mol-1) and accompanied by a large decrease in entropy (delta S approximately -280 eu). The midpoint of the transition was dependent on the initial protein concentration, suggesting that only the noncovalent dimer of the lambda chain exhibited the conformational change. The existence of a monomer-dimer eqiulibrium (KA approximately 4 X 10(5) M-1) was confirmed by sedimentation velocity. No conformational change was observed by circular dichroism at concentrations where greater than 95% of lambda chain was in the form of a monomer. Although high ionic strength inhibited cryoprecipitation, it had no effect on the conformational change. Stabilization of the dimer by forming an interchain disulfide bond between two monomers abolished both the conformational change and cryoprecipitation. A fragment corresponding to the constant region was isolated from both peptic and tryptic digests of the lambda chain. This fragment neither cryoprecipitated nor showed temperature dependence conformational changes. It proved impossible to isolate a fragment corresponding to the variable region. Both qualitative and quantitative models are presented to account for the behavior of the lambda chain at low temperatures. PMID:13819

  8. Conformal Mapping in Wing Aerodynamics Thomas Johnson

    E-print Network

    Morrow, James A.

    Conformal Mapping in Wing Aerodynamics Thomas Johnson June 4, 2013 Contents 1 Introduction 1 2 the first complete treatment of conformal mapping in aerodynamics. Near the beginning of the twentieth and aerodynamics. The purpose of this exposition is to give the reader an elementary intro- duction to the use

  9. Mapping chromatin conformation Peter J Shaw

    E-print Network

    Shaw, Peter

    Mapping chromatin conformation Peter J Shaw Address: Department of Cell and Developmental Biology and can be found at: http://f1000.com/reports/biology/content/2/18 Abstract Chromatin conformation capture using high-throughput DNA sequencing to generate global interaction maps for the entire genome

  10. Tomographic patient registration and conformal avoidance tomotherapy

    Microsoft Academic Search

    Jennifer Stacy Aldridge

    1999-01-01

    Development of tomotherapy has led to the emergence of several processes, providing the basis for many unique investigative opportunities. These processes include setup verification, tomographic verification, megavoltage dose reconstruction, and conformal avoidance tomotherapy. Setup verification and conformal avoidance tomotherapy, in particular, are two closely intertwined matters. In order to avoid critical structures located within or adjacent to indistinct tumor regions,

  11. Regulatory Conformance Checking: Logic and Logical Form

    ERIC Educational Resources Information Center

    Dinesh, Nikhil

    2010-01-01

    We consider the problem of checking whether an organization conforms to a body of regulation. Conformance is studied in a runtime verification setting. The regulation is translated to a logic, from which we synthesize monitors. The monitors are evaluated as the state of an organization evolves over time, raising an alarm if a violation is…

  12. Conformal invariance, supersymmetry and string theory

    Microsoft Academic Search

    Daniel Friedan; Emil Martinec; Stephen Shenker

    1986-01-01

    Covariant quantization of string theories is developed in the context of conformal field theory and the BRST quantization procedure. The BRST method is used to covariantly quantize superstrings, and in particular to construct the vertex operators for string emission as well as the supersymmetry charge. The calculation of string loop diagrams is sketched. We discuss how conformal methods can be

  13. Brain Surface Conformal Parameterization with Algebraic Functions

    E-print Network

    Wang, Yalin

    Brain Surface Conformal Parameterization with Algebraic Functions 1,2Yalin Wang , 3Xianfeng Gu, 1 Angeles, CA, USA. 2Laboratory of Neuro Imaging, Brain Mapping Division, Department of Neurology, UCLA previous work conformally parameterizes various brain anatomical surfaces with several planar

  14. Conformity to Peer Pressure in Preschool Children

    ERIC Educational Resources Information Center

    Haun, Daniel B. M.; Tomasello, Michael

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous…

  15. Dirac fields in massive conformal gravity

    E-print Network

    F. F. Faria

    2014-10-19

    In this article we show that the gravitational field in massive conformal gravity couples consistently with Dirac spinor fields. We solve the problem of consistency by considering that the Dirac spinor fields couple with both the metric field and a scalar field, which are the gravitational field variables of massive conformal gravity.

  16. Conformational Sampling of Peptides in Cellular Environments?

    PubMed Central

    Tanizaki, Seiichiro; Clifford, Jacob; Connelly, Brian D.; Feig, Michael

    2008-01-01

    Abstract Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over ?-helical conformations at the dipeptide level at and below dielectric constants of 5–10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at ? = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response. PMID:17905846

  17. Transition & Beyond

    MedlinePLUS

    ... Transition & Beyond Aging Matters Research NDSS en Español Finances Ways to Give Ways to Donate NDSS Your ... Bienestar Emocional y Psiquiátrico La Enfermedad de Alzheimer Finances SSI Special Needs Trusts e-newsletter signup New & ...

  18. Performance of Conformable Ablators in Aerothermal Environments

    NASA Technical Reports Server (NTRS)

    Thornton, J.; Fan, W.; Skokova, K.; Stackpoole, M.; Beck, R.; Chavez-Garcia, J.

    2012-01-01

    Conformable Phenolic Impregnated Carbon Ablator, a cousin of Phenolic Impregnated Carbon Ablator (PICA), was developed at NASA Ames Research Center as a lightweight thermal protection system under the Fundamental Aeronautics Program. PICA is made using a brittle carbon substrate, which has a very low strain to failure. Conformable PICA is made using a flexible carbon substrate, a felt in this case. The flexible felt significantly increases the strain to failure of the ablator. PICA is limited by its thermal mechanical properties. Future NASA missions will require heatshields that are more fracture resistant than PICA and, as a result, NASA Ames is working to improve PICAs performance by developing conformable PICA to meet these needs. Research efforts include tailoring the chemistry of conformable PICA with varying amounts of additives to enhance mechanical properties and testing them in aerothermal environments. This poster shows the performance of conformable PICA variants in arc jets tests. Some mechanical and thermal properties will also be presented.

  19. Conformal nets III: fusion of defects

    E-print Network

    Arthur Bartels; Christopher L. Douglas; André Henriques

    2015-02-21

    Conformal nets provides a mathematical model for conformal field theory. We define a notion of defect between conformal nets, formalizing the idea of an interaction between two conformal field theories. We introduce an operation of fusion of defects, and prove that the fusion of two defects is again a defect, provided the fusion occurs over a conformal net of finite index. There is a notion of sector (or bimodule) between two defects, and operations of horizontal and vertical fusion of such sectors. Our most difficult technical result is that the horizontal fusion of the vacuum sectors of two defects is isomorphic to the vacuum sector of the fused defect. Equipped with this isomorphism, we construct the basic interchange isomorphism between the horizontal fusion of two vertical fusions and the vertical fusion of two horizontal fusions of sectors.

  20. Vibrational and vibronic spectra of tryptamine conformers.

    PubMed

    Mayorkas, Nitzan; Bernat, Amir; Izbitski, Shay; Bar, Ilana

    2013-03-28

    Conformation-specific ionization-detected stimulated Raman spectra, including both Raman loss and Raman gain lines, along with visible-visible-ultraviolet hole-burning spectra of tryptamine (TRA) conformers have been measured simultaneously, with the aim of obtaining new data for identifying them. The slightly different orientations of the ethylamine side chain relative to the indole lead to unique spectral signatures, pointing to the presence of seven TRA conformers in the molecular beam. Comparison of ionization-loss stimulated Raman spectra to computationally scaled harmonic Raman spectra, especially in the alkyl C-H and amine N-H stretch regions together with the retrieved information on the stabilities of the TRA conformers assisted their characterization and structural identification. The prospects and limitations of using these spectroscopic methods as potential conformational probes of flexible molecules are discussed. PMID:23556728

  1. Vibrational and vibronic spectra of tryptamine conformers

    NASA Astrophysics Data System (ADS)

    Mayorkas, Nitzan; Bernat, Amir; Izbitski, Shay; Bar, Ilana

    2013-03-01

    Conformation-specific ionization-detected stimulated Raman spectra, including both Raman loss and Raman gain lines, along with visible-visible-ultraviolet hole-burning spectra of tryptamine (TRA) conformers have been measured simultaneously, with the aim of obtaining new data for identifying them. The slightly different orientations of the ethylamine side chain relative to the indole lead to unique spectral signatures, pointing to the presence of seven TRA conformers in the molecular beam. Comparison of ionization-loss stimulated Raman spectra to computationally scaled harmonic Raman spectra, especially in the alkyl C-H and amine N-H stretch regions together with the retrieved information on the stabilities of the TRA conformers assisted their characterization and structural identification. The prospects and limitations of using these spectroscopic methods as potential conformational probes of flexible molecules are discussed.

  2. BOUNDARY INTERPOLATION SETS FOR CONFORMAL MAPS CHRISTOPHER J. BISHOP

    E-print Network

    Bishop, Christopher

    BOUNDARY INTERPOLATION SETS FOR CONFORMAL MAPS CHRISTOPHER J set for conformal mappings iff it has logarithmic capacity zero. __________ Date: August 25, 2004. 1 #12; BOUNDARY INTERPOLATION SETS FOR CONFORMAL MAPS 1

  3. Analysis of the conformational dependence of mass-metric tensor determinants in serial polymers with constraints

    NASA Astrophysics Data System (ADS)

    Patriciu, Alexandru; Chirikjian, Gregory S.; Pappu, Rohit V.

    2004-12-01

    It is well known that mass-metric tensor determinants det(Gs) influence the equilibrium statistics and the rates of conformational transitions for polymers with constrained bond lengths and bond angles. It is now standard practice to include a Fixman-style compensating potential of the form Uc(qs)?(-kBT/2)ln[det(Gs)] as part of algorithms for torsional space molecular dynamics. This elegant strategy helps eliminate unwarranted biases that arise due to the imposition of holonomic constraints. However, the precise nature and extent of variation of det(Gs) and hence ln[det(Gs)] with chain conformation and chain length has never been quantified. This type of analysis is crucial for understanding the nature of the conformational bias that the introduction of a Fixman potential aims to eliminate. Additionally, a detailed analysis of the conformational dependence of det(Gs) will help resolve ambiguities regarding suggestions for incorporating terms related to det(Gs) in the design of move sets in torsional space Monte Carlo simulations. In this work, we present results from a systematic study of the variation of det(Gs) for a serial polymer with fixed bond lengths and bond angles as a function of chain conformation and chain length. This analysis requires an algorithm designed for rapid computation of det(Gs) which simultaneously allows for a physical/geometric interpretation of the conformational dependence of det(Gs). Consequently, we provide a detailed discussion of our adaptation of an O(n) algorithm from the robotics literature, which leads to simple recursion relations for direct evaluation of det(Gs). Our analysis of the conformational dependence of det(Gs) yields the following insights. (1) det(Gs) is maximized for spatial conformers and minimized for planar conformations. (2) Previous work suggests that it is logical to expect that the conformational dependence of det(Gs) becomes more pronounced with increase in chain length. Confirming this expectation, we provide systematic quantification of the nature of this dependency and show that the difference in det(Gs) between spatial and planar conformers, i.e., between the maxima and minima of det(Gs) grows systematically with chain length. Finally, we provide a brief discussion of implications of our analysis for the design of move sets in Monte Carlo simulations.

  4. Real-time observation of the conformational dynamics of mitochondrial Hsp70 by spFRET

    PubMed Central

    Sikor, Martin; Mapa, Koyeli; von Voithenberg, Lena Voith; Mokranjac, Dejana; Lamb, Don C

    2013-01-01

    The numerous functions of the important class of molecular chaperones, heat shock proteins 70 (Hsp70), rely on cycles of intricate conformational changes driven by ATP-hydrolysis and regulated by cochaperones and substrates. Here, we used Förster resonance energy transfer to study the conformational dynamics of individual molecules of Ssc1, a mitochondrial Hsp70, in real time. The intrinsic dynamics of the substrate-binding domain of Ssc1 was observed to be uncoupled from the dynamic interactions between substrate- and nucleotide-binding domains. Analysis of the fluctuations in the interdomain separation revealed frequent transitions to a nucleotide-free state. The nucleotide-exchange factor Mge1 did not induce ADP release, as expected, but rather facilitated binding of ATP. These results indicate that the conformational cycle of Ssc1 is more elaborate than previously thought and provide insight into how the Hsp70s can perform a wide variety of functions. PMID:23624933

  5. Surface Quasi-Conformal Mapping by Solving Beltrami Equations

    E-print Network

    ,Luo,Yau,Gu Quasi-Conformal Mapping #12;Theoretic Background Definition (Conformal Atlas) suppose S is a surface, then the atlas A is a conformal atlas. U U S (U) (U) Zeng,Luo,Yau,Gu Quasi-Conformal Mapping #12;Theoretic-conformal map, with Beltrami coefficient µ(z), w ¯z = µ(z) w z . Then we construct another conformal atlas ~A1

  6. Technidilaton at the conformal edge

    SciTech Connect

    Hashimoto, Michio; Yamawaki, Koichi [Maskawa Institute for Science and Culture, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto 603-8555 (Japan); Kobayashi-Maskawa Institute for the Origin of Particles and the Universe (KMI), Nagoya University, Nagoya 464-8602 (Japan)

    2011-01-01

    Technidilaton (TD) was proposed long ago in the technicolor near criticality/conformality. To reveal the critical behavior of TD, we explicitly compute the nonperturbative contributions to the scale anomaly <{theta}{sub {mu}}{sup {mu}>} and to the technigluon condensate <{alpha}G{sub {mu}{nu}}{sup 2}>, which are generated by the dynamical mass m of the technifermions. Our computation is based on the (improved) ladder Schwinger-Dyson equation, with the gauge coupling {alpha} replaced by the two-loop running coupling {alpha}({mu}) having the Caswell-Banks-Zaks infrared fixed point {alpha}{sub *}: {alpha}({mu}){approx_equal}{alpha}={alpha}{sub *} for the infrared region m<{mu}<{Lambda}{sub TC}, where {Lambda}{sub TC} is the intrinsic scale (analogue of {Lambda}{sub QCD} of QCD) relevant to the perturbative scale anomaly. We find that -<{theta}{sub {mu}}{sup {mu}}>/m{sup 4}{yields}const{ne}0 and <{alpha}G{sub {mu}}{nu}{sup 2}>/m{sup 4}{yields}({alpha}/{alpha}{sub cr}-1){sup -3/2}{yields}{infinity} in the criticality limit m/{Lambda}{sub TC}{approx}exp(-{pi}/({alpha}/{alpha}{sub cr}-1){sup 1/2}){yields}0 ({alpha}={alpha}{sub *}=>{alpha}{sub cr}, or N{sub f} approaches N{sub f}{sup cr}) ('conformal edge'). Our result precisely reproduces the formal identity <{theta}{sub {mu}}{sup {mu}>}=({beta}({alpha})/4{alpha}{sup 2})<{alpha}G{sub {mu}{nu}}{sup 2}>, where {beta}({alpha})={Lambda}{sub TC}({partial_derivative}{alpha}/{partial_derivative}{Lambda}{sub TC})=-(2{alpha}{sub cr}/{pi}){center_dot}({alpha}/{alpha}{sub cr}-1){sup 3/2} is the nonperturbative beta function corresponding to the above essential singularity scaling of m/{Lambda}{sub TC}. Accordingly, the partially conserved dilatation current implies (M{sub TD}/m){sup 2}(F{sub TD}/m){sup 2}=-4<{theta}{sub {mu}}{sup {mu}}>/m{sup 4}{yields}const{ne}0 at criticality limit, where M{sub TD} is the mass of TD and F{sub TD} the decay constant of TD. We thus conclude that at criticality limit the TD could become a ''true (massless) Nambu-Goldstone boson'' M{sub TD}/m{yields}0, only when m/F{sub TD}{yields}0, namely, getting decoupled, as was the case of ''holographic technidilaton'' of Haba-Matsuzaki-Yamawaki. The decoupled TD can be a candidate of dark matter.

  7. Understanding modern magnets through conformal mapping

    SciTech Connect

    Halbach, K.

    1989-10-01

    I want to show with the help of a number of examples that conformal mapping is a unique and enormously powerful tool for thinking about, and solving, problems. Usually one has to write down only a few equations, and sometimes none at all When I started getting involved in work for which conformal mapping seemed to be a powerful tool, I did not think that I would ever be able to use that technique successfully because it seemed to require a nearly encyclopedic memory, an impression that was strengthened when I saw K. Kober's Dictionary of Conformal Representations. This attitude changed when I started to realize that beyond the basics of the theory of a function of a complex variable, I needed to know only about a handful of conformal maps and procedures. Consequently, my second goal for this talk is to show that in most cases conformal mapping functions can be obtained by formulating the underlying physics appropriately. This means particularly that encyclopedic knowledge of conformal maps is not necessary for successful use of conformal mapping techniques. To demonstrate these facts I have chosen examples from an area of physics/engineering in which I am active, namely accelerator physics. In order to do that successfully I start with a brief introduction into high energy charged particle storage ring technology, even though not all examples used in this paper to elucidate my points come directly from this particular field of accelerator technology.

  8. The conformal Killing equation on forms -- prolongations and applications

    E-print Network

    A. Rod Gover; Josef Silhan

    2006-01-31

    We construct a conformally invariant vector bundle connection such that its equation of parallel transport is a first order system that gives a prolongation of the conformal Killing equation on differential forms. Parallel sections of this connection are related bijectively to solutions of the conformal Killing equation. We construct other conformally invariant connections, also giving prolongations of the conformal Killing equation, that bijectively relate solutions of the conformal Killing equation on $k$-forms to a twisting of the conformal Killing equation on (k - l)-forms for various integers l. These tools are used to develop a helicity raising and lowering construction in the general setting and on conformally Einstein manifolds.

  9. Conformational flexibility in biochemical regulation

    SciTech Connect

    Trewhella, J.

    1993-09-01

    Small-angle X-ray and neutron scattering have proven extremely useful for studying the evolutionarily related dumbbell-shaped Ca {sup 2+} -binding proteins calmodulin and troponin C and their interactions with the target proteins whose activity they regulate. Calmodulin contracts about target enzyme binding domains with the common characteristic of having a high propensity for forming a basic, amphipathic a-helix. The contraction is achieved via flexibility in the interconnecting helix region of the molecule that links its two globular domains. This flexibility allows calmodulin to optimize its binding to different arrangements of hydrophobic and charged residues important in forming these complexes. In contrast calmodulin remains extended in its interaction with the catalytic subunit of phosphorylase kinase. There are structural and functional similarities between this interaction and that of troponin C and troponin I. Our most recent neutron scattering experiments confirm our prediction that troponin C also remains extended in this complex. The ability of the dumbbell-shaped Ca {sup 2+} -binding proteins to modulate their conformations via flexibility in the interconnecting helix region in order to accommodate different target binding domains is a remarkable example nature building functional diversity as well as specificity into a compact and unusual shape.

  10. Transition Resources

    NSDL National Science Digital Library

    Transition

    2011-11-23

    This is a site for teachers that work with students with disabilities at the secondary level. This site is broken down into categories to help you with the transition aspect of the IEP. The categories are as follows: Employment/Training, For Students - Career Exploration and Profiles, Independent Living, Learning Styles & Trainings, Level 1 Assessments, Self-Determination, and Transition Resources. All of the resources included in this site are free! TRANSITION RESOURCES: 1.) Adult Career and Continuing Education Services (ACCES-VR) This website takes you directly to the ACCES-VR website, where you can find information about vocational rehabilitation and the referral process. 2,) Guide to Quality Individualized Education Program (IEP) Development and Implementation Created by the New York State Special Education Department to help answer questions regarding the New IEP. Great resource! Gives examples!! 3.) Indicator 13 Checklist Use this ...

  11. Single molecule conformational memory extraction: p5ab RNA hairpin.

    PubMed

    Pressé, Steve; Peterson, Jack; Lee, Julian; Elms, Phillip; MacCallum, Justin L; Marqusee, Susan; Bustamante, Carlos; Dill, Ken

    2014-06-19

    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

  12. Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin

    PubMed Central

    2015-01-01

    Extracting kinetic models from single molecule data is an important route to mechanistic insight in biophysics, chemistry, and biology. Data collected from force spectroscopy can probe discrete hops of a single molecule between different conformational states. Model extraction from such data is a challenging inverse problem because single molecule data are noisy and rich in structure. Standard modeling methods normally assume (i) a prespecified number of discrete states and (ii) that transitions between states are Markovian. The data set is then fit to this predetermined model to find a handful of rates describing the transitions between states. We show that it is unnecessary to assume either (i) or (ii) and focus our analysis on the zipping/unzipping transitions of an RNA hairpin. The key is in starting with a very broad class of non-Markov models in order to let the data guide us toward the best model from this very broad class. Our method suggests that there exists a folding intermediate for the P5ab RNA hairpin whose zipping/unzipping is monitored by force spectroscopy experiments. This intermediate would not have been resolved if a Markov model had been assumed from the onset. We compare the merits of our method with those of others. PMID:24898871

  13. Conformity and Dissonance in Generalized Voter Models

    NASA Astrophysics Data System (ADS)

    Page, Scott E.; Sander, Leonard M.; Schneider-Mizell, Casey M.

    2007-09-01

    We generalize the voter model to include social forces that produce conformity among voters and avoidance of cognitive dissonance of opinions within a voter. The time for both conformity and consistency (which we call the exit time) is, in general, much longer than for either process alone. We show that our generalized model can be applied quite widely: it is a form of Wright's island model of population genetics, and is related to problems in the physical sciences. We give scaling arguments, numerical simulations, and analytic estimates for the exit time for a range of relative strengths in the tendency to conform and to avoid dissonance.

  14. Structure, Intent and Conformance Monitoring in ATC

    NASA Technical Reports Server (NTRS)

    Reynolds, Tom G.; Histon, Jonathan M.; Davison, Hayley J.; Hansman, R. John

    2004-01-01

    Infield studies of current Air Traffic Control operations it is found that controllers rely on underlying airspace structure to reduce the complexity of the planning and conformance monitoring tasks. The structure appears to influence the controller's working mental model through abstractions that reduce the apparent cognitive complexity. These structure-based abstractions are useful for the controller's key tasks of planning, implementing, monitoring, and evaluating tactical situations. In addition, the structure-based abstractions appear to be important in the maintenance of Situation Awareness. The process of conformance monitoring is analyzed in more detail and an approach to conformance monitoring which utilizes both the structure-based abstractions and intent is presented.

  15. Conformational and Vibrational Studies of Triclosan

    NASA Astrophysics Data System (ADS)

    Özi?ik, Haci; Bayari, S. Haman; Sa?lam, Semran

    2010-01-01

    The conformational equilibrium of triclosan (5-chloro-2-(2, 4-dichlorophenoxy) phenol) have been calculated using density functional theory (DFTe/B3LYP/6-311++G(d, p)) method. Four different geometries were found to correspond to energy minimum conformations. The IR spectrum of triclosan was measured in the 4000-400 cm-1 region. We calculated the harmonic frequencies and intensities of the most stable conformers in order to assist in the assignment of the vibrational bands in the experimental spectrum. The fundamental vibrational modes were characterized depending on their total energy distribution (TED%) using scaled quantum mechanical (SQM) force field method.

  16. Conformal field theory on the plane

    E-print Network

    Sylvain Ribault

    2014-09-19

    We provide an introduction to conformal field theory on the plane in the conformal bootstrap approach. We introduce the main ideas of the bootstrap approach to quantum field theory, and how they apply to two-dimensional theories with local conformal symmetry. We describe the mathematical structures which appear in such theories, from the Virasoro algebra and its representations, to the BPZ equations and their solutions. As examples, we study a number of models: Liouville theory, (generalized) minimal models, free bosonic theories, the $H_3^+$ model, and the $SU_2$ and $\\widetilde{SL}_2(\\mathbb{R})$ WZW models.

  17. On Conformal Conic Mappings of Spherical Domains

    PubMed Central

    Bourchtein, Ludmila

    2014-01-01

    The problem of the generation of homogeneous grids for spherical domains is considered in the class of conformal conic mappings. The equivalence between secant and tangent projections is shown and splitting the set of conformal conic mappings into equivalence classes is presented. The problem of minimization of the mapping factor variation is solved in the class of conformal conic mappings. Obtained results can be used in applied sciences, such as geophysical fluid dynamics and cartography, where the flattening of the Earth surface is required. PMID:24558337

  18. Role of Electrostatic Repulsion in Controlling pH-dependent Conformational Changes of Viral Fusion Proteins

    PubMed Central

    Harrison, Joseph S.; Higgins, Chelsea D.; O'Meara, Matthew J.; Koellhoffer, Jayne F.; Kuhlman, Brian A.; Lai, Jonathan R.

    2013-01-01

    Viral fusion proteins undergo dramatic conformational transitions during membrane fusion. For viruses that enter through the endosome, these conformational rearrangements are typically pH sensitive. Here we provide a comprehensive review of the molecular interactions that govern pH-dependent rearrangements and introduce a novel paradigm for electrostatic residue pairings that regulate progress through the viral fusion coordinate. Analysis of structural data demonstrates a significant role for side chain protonation in triggering conformational change. To characterize this behavior we identify two distinct residue pairings, which we define as Histidine-Cation (HisCat) and Anion-Anion (AniAni) interactions. These side chain pairings destabilize a particular conformation via electrostatic repulsion through side chain protonation. Furthermore, two energetic control mechanisms, thermodynamic and kinetic, regulate these structural transitions. This review expands on the current literature by identification of these residue clusters, discussion of data demonstrating their function, and speculation of how these residue pairings contribute to the energetic controls. PMID:23823327

  19. Venus Transit

    NSDL National Science Digital Library

    2012-08-03

    This is an activity about the Venus Transit and how it helped astronomers determine the scale of the solar system. Learners will use measurement, ratios, and graphing to construct a model of the solar system and determine the relationship of each planet to the Sun. They will explore the scales needed to represent the size of the planets and the distances to the Sun. This activity corresponds to the NASA CONNECT video, titled Venus Transit, and has supplemental questions to support the video viewing.

  20. Distinct contracted conformations of the Tcra/Tcrd locus during Tcra and Tcrd recombination

    PubMed Central

    Shih, Han-Yu

    2010-01-01

    Studies have suggested that antigen receptor loci adopt contracted conformations to promote long-distance interactions between gene segments during V(D)J recombination. The Tcra/Tcrd locus is unique because it undergoes highly divergent Tcrd and Tcra recombination programs in CD4?CD8? double negative (DN) and CD4+CD8+ double positive (DP) thymocytes, respectively. Using three-dimensional fluorescence in situ hybridization, we asked whether these divergent recombination programs are supported by distinct conformational states of the Tcra/Tcrd locus. We found that the 3? portion of the locus is contracted in DN and DP thymocytes but not in B cells. Remarkably, the 5? portion of the locus is contracted in DN thymocytes but is decontracted in DP thymocytes. We propose that the fully contracted conformation in DN thymocytes allows Tcrd rearrangements involving V? gene segments distributed over 1 Mb, whereas the unique 3?-contracted, 5?-decontracted conformation in DP thymocytes biases initial Tcra rearrangements to the most 3? of the available V? gene segments. This would maintain a large pool of distal 5? V? gene segments for subsequent rounds of recombination. Thus, distinct contracted conformations of the Tcra/Tcrd locus may facilitate a transition from a Tcrd to a Tcra mode of recombination during thymocyte development. PMID:20696701

  1. Intrinsic ?-helical and ?-sheet conformational preferences: a computational case study of alanine.

    PubMed

    Caballero, Diego; Määttä, Jukka; Zhou, Alice Qinhua; Sammalkorpi, Maria; O'Hern, Corey S; Regan, Lynne

    2014-07-01

    A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an ?-helix, ?-sheet, or other backbone dihedral angle ( ?-?) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for ?-helical structures, while experiments on small peptides observe that ?-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model for Ala dipeptide mimetics that includes steric interactions between nonbonded atoms and bond length and angle constraints with the goal of evaluating the role of steric interactions in determining protein backbone conformational preferences. We find four key results. For the hard-sphere MD simulations, we show that (1) ?-sheet structures are roughly three and half times more probable than ?-helical structures, (2) transitions between ?-helix and ?-sheet structures only occur when the backbone bond angle ? (N?C? ?C) is greater than 110°, and (3) the probability distribution of ? for Ala conformations in the "bridge" region of ?-? space is shifted to larger angles compared to other regions. In contrast, (4) the distributions obtained from Amber and CHARMM MD simulations in the bridge regions are broader and have increased ? compared to those for hard sphere simulations and from high-resolution protein crystal structures. Our results emphasize the importance of hard-sphere interactions and local stereochemical constraints that yield strong correlations between ?-? conformations and ?. PMID:24753338

  2. Intrinsic ?-helical and ?-sheet conformational preferences: A computational case study of alanine

    PubMed Central

    Caballero, Diego; Määttä, Jukka; Zhou, Alice Qinhua; Sammalkorpi, Maria; O'Hern, Corey S; Regan, Lynne

    2014-01-01

    A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an ?-helix, ?-sheet, or other backbone dihedral angle (-?) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for ?-helical structures, while experiments on small peptides observe that ?-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model for Ala dipeptide mimetics that includes steric interactions between nonbonded atoms and bond length and angle constraints with the goal of evaluating the role of steric interactions in determining protein backbone conformational preferences. We find four key results. For the hard-sphere MD simulations, we show that (1) ?-sheet structures are roughly three and half times more probable than ?-helical structures, (2) transitions between ?-helix and ?-sheet structures only occur when the backbone bond angle ? (N–C?–C) is greater than 110°, and (3) the probability distribution of ? for Ala conformations in the “bridge” region of-? space is shifted to larger angles compared to other regions. In contrast, (4) the distributions obtained from Amber and CHARMM MD simulations in the bridge regions are broader and have increased ? compared to those for hard sphere simulations and from high-resolution protein crystal structures. Our results emphasize the importance of hard-sphere interactions and local stereochemical constraints that yield strong correlations between -? conformations and ?. PMID:24753338

  3. Conformations within soluble oligomers and insoluble aggregates revealed by resonance energy transfer.

    PubMed

    Digambaranath, Jyothi L; Dang, Loan; Dembinska, Monika; Vasyluk, Andrew; Finke, John M

    2010-04-01

    A fluorescently labeled 20-residue polyglutamic acid (polyE) peptide 20 amino acid length polyglutamic acid (E(20)) was used to study structural changes which occur in E(20) as it co-aggregates with other unlabeled polyE peptides. Resonance energy transfer (RET) was performed using an o-aminobenzamide donor at the N-terminus and 3-nitrotyrosine acceptor at the C-terminus of E(20). PolyE aggregates were not defined as amyloid, as they were nonfibrillar and did not bind congo red. Circular dichroism measurements indicate that polyE aggregation involves a transition from alpha-helical monomers to aggregated beta-sheets. Soluble oligomers are also produced along with aggregates in the reaction, as determined through size exclusion chromatography. Time-resolved and steady-state RET measurements reveal four dominant E(20) conformations: (1) a partially collapsed conformation (24 A donor-acceptor distance) in monomers, (2) an extended conformation in soluble oligomers (>29 A donor-acceptor distance), (3) a minor partially collapsed conformation (22 A donor-acceptor distance) in aggregates, and (4) a major highly collapsed conformation (13 A donor-acceptor distance) in aggregates. These findings demonstrate the use of RET as a means of determining angstrom-level structural details of soluble oligomer and aggregated states of proteins. PMID:19927295

  4. 75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-26

    ...Transportation Conformity Guidance for Quantitative Hot- spot Analyses in PM 2.5 and PM...quantitative PM 2.5 and PM 10 hot-spot analyses for project- level transportation...certain highway and transit projects. A hot-spot analysis includes an estimation...

  5. Steady-State Coupling of Ion-Channel Conformations to a Transmembrane Ion Gradient

    NASA Astrophysics Data System (ADS)

    Richard, Edwin A.; Miller, Christopher

    1990-03-01

    Under stationary conditions, opening and closing of single Torpedo electroplax chloride channels show that the number of transitions per unit time between inactivated and conducting states are unequal in opposite directions. This asymmetry, which increases with transmembrane electrochemical gradient for the chloride ion, violates the principle of microscopic reversibility and thus demonstrates that the channel-gating process is not at thermodynamic equilibrium. The results imply that the channel's conformational states are coupled to the transmembrane electrochemical gradient of the chloride ion.

  6. Revised conformational assignments and conformational evolution of tyrosine by laser desorption supersonic jet laser spectroscopy.

    PubMed

    Shimozono, Yoko; Yamada, Kohei; Ishiuchi, Shun-ichi; Tsukiyama, Koichi; Fujii, Masaaki

    2013-04-14

    The number of conformers and their structures of tyrosine are reassigned on the basis of resonance enhanced multiphoton ionization (REMPI), ultraviolet-ultraviolet hole burning (UV-UV HB), infrared (IR) dip spectra, and quantum chemical calculations. From comparison between REMPI and UV-UV HB spectra, it was found that 12 conformers coexist in the supersonic jet. The structures of these conformers are determined by the IR spectra and theoretical calculations. The number of conformers is more than that reported in the previous reports (8 conformers), and is rationalized by the systematic formation of conformers from simpler molecules without substituents, just like evolution. The importance of dipole-dipole interaction between an amino-acid chain and hydroxyl group at the benzene ring was also discussed. PMID:23455039

  7. The folding transition state theory in simple model systems

    NASA Astrophysics Data System (ADS)

    Niewieczerza?, Szymon; Cieplak, Marek

    2008-06-01

    We present the results of an exact analysis of several model free energy landscapes of a protein to clarify the notion of the transition state and the physical meaning of the phi values determined in protein engineering experiments. We argue that a proper search strategy for the transition state in more realistic models should involve identification of a common part of various methods. Two of the models considered involve explicit conformations instead of just points on the free energy axis. These models are minimalistic as they are endowed only with five or 36 states to enumerate folding paths and to identify the transition state easily. Even though they display much of the two-state behavior, the phi values are found not to correspond to the conformation of the transition state.

  8. Hidden conformal symmetry of extremal black holes

    SciTech Connect

    Chen Bin; Long Jiang; Zhang Jiaju [Department of Physics, and State Key Laboratory of Nuclear Physics Technology, and Center for High Energy Physics, Peking University, Beijing 100871 (China); Department of Physics, and State Key Laboratory of Nuclear Physics Technology, Peking University, Beijing 100871 (China)

    2010-11-15

    We study the hidden conformal symmetry of extremal black holes. We introduce a new set of conformal coordinates to write the SL(2,R) generators. We find that the Laplacian of the scalar field in many extremal black holes, including Kerr(-Newman), Reissner-Nordstrom, warped AdS{sub 3}, and null warped black holes, could be written in terms of the SL(2,R) quadratic Casimir. This suggests that there exist dual conformal field theory (CFT) descriptions of these black holes. From the conformal coordinates, the temperatures of the dual CFTs could be read directly. For the extremal black hole, the Hawking temperature is vanishing. Correspondingly, only the left (right) temperature of the dual CFT is nonvanishing, and the excitations of the other sector are suppressed. In the probe limit, we compute the scattering amplitudes of the scalar off the extremal black holes and find perfect agreement with the CFT prediction.

  9. Conformational Electroresistance and Hysteresis in Nanoclusters

    SciTech Connect

    Li, Xiangguo [University of Florida, Gainesville; Zhang, Xiaoguang [ORNL; Cheng, Hai-Ping [University of Florida

    2014-01-01

    Among many mechanisms proposed for electroresistance, ones involving structural changes are the least understood because of challenges of controllability and repeatability. Yet structural changes can cause dramatic changes in electronic properties, leading to multiple ways in which conduction paths can be opened and closed, not limited to filament movement or variation in molecular conductance. Here we show at least another way: conformational dependence of the Coulomb charging energy of a nanocluster, where charging induced conformational distortion changes the blockade voltage, which in turn leads to a giant electroresistance. This intricate interplay between charging and conformation change is demonstrated in a nanocluster Zn3O4 by combining a first-principles calculation with a temperature dependent transport model. The predicted hysteretic Coulomb blockade staircase in the current-voltage curve adds another dimension to the rich phenomenon of tunneling electroresistance. The new mechanism also provides a better controlled and repeatable platform to study conformational electroresistance.

  10. W symmetry in conformal field theory

    Microsoft Academic Search

    Peter Bouwknegt; Kareljan Schoutens

    1993-01-01

    We review various aspects of W algebra symmetry in two-dimensional conformal field theory and string theory. We pay particular attention to the construction of W algebras through the quantum Drinfeld-Sokolov reduction and through the coset construction.

  11. Aluminized fiberglass insulation conforms to curved surfaces

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Layers of fiber glass with outer reflective films of vacuum-deposited aluminum or other reflective metal, provide thermal insulation which conforms to curved surfaces. This insulation has good potential for cryogenic systems.

  12. Excision boundary conditions for the conformal metric

    SciTech Connect

    Cook, Gregory B.; Baumgarte, Thomas W. [Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109 (United States); Department of Physics and Astronomy, Bowdoin College, Brunswick, Maine 04011 (United States)

    2008-11-15

    Shibata, Uryu and Friedman recently suggested a new decomposition of Einstein's equations that is useful for constructing initial data. In contrast to previous decompositions, the conformal metric is no longer treated as a freely specifiable variable, but rather is determined as a solution to the field equations. The new set of freely specifiable variables includes only time derivatives of metric quantities, which makes this decomposition very attractive for the construction of quasiequilibrium solutions. To date, this new formalism has only been used for binary neutron stars. Applications involving black holes require new boundary conditions for the conformal metric on the domain boundaries. In this paper we demonstrate how these boundary conditions follow naturally from the conformal geometry of the boundary surfaces and the inherent gauge freedom of the conformal metric.

  13. Excision boundary conditions for the conformal metric

    E-print Network

    Gregory B. Cook; Thomas W. Baumgarte

    2008-10-24

    Shibata, Ury\\=u and Friedman recently suggested a new decomposition of Einstein's equations that is useful for constructing initial data. In contrast to previous decompositions, the conformal metric is no longer treated as a freely-specifiable variable, but rather is determined as a solution to the field equations. The new set of freely-specifiable variables includes only time-derivatives of metric quantities, which makes this decomposition very attractive for the construction of quasiequilibrium solutions. To date, this new formalism has only been used for binary neutron stars. Applications involving black holes require new boundary conditions for the conformal metric on the domain boundaries. In this paper we demonstrate how these boundary conditions follow naturally from the conformal geometry of the boundary surfaces and the inherent gauge freedom of the conformal metric.

  14. Mesh generation by conformal and quasiconformal mappings

    NASA Technical Reports Server (NTRS)

    Mastin, C. W.; Thompson, J. F.

    1981-01-01

    It is pointed out that many recent advances in the finite-difference solution of elliptic equations have been limited to regions whose boundary contours coincide with coordinate lines of the Cartesian coordinate system. The reason for this is related to the fact that in the case of an arbitrary curvilinear coordinate system the original equation becomes much more complex. However, there is no added complexity if an orthogonal coordinate system is generated from a conformal mapping. In the present investigation, a finite difference method developed for the construction of conformal mappings has been generalized to construct quasi-conformal mappings. It is expected that the use of more sophisticated numerical algorithms could lead to improvements in both speed and accuracy. Quasi-conformal mappings have applications not only in the solution of elliptic equations but also in other areas such as orthogonal mesh generation on surfaces and the solution of certain fluid flow problems.

  15. Cosmological Creation of Matter in Conformal Cosmology

    Microsoft Academic Search

    V. V. Papoyan; V. N. Pervushin; D. V. Proskurin

    2003-01-01

    The effect of rapid cosmological creation of vector W and Z bosons is studied in the framework of conformal cosmology, which unifies the general theory of relativity and the standard model for strong and electroweak interactions.

  16. BRAIN SURFACE CONFORMAL PARAMETERIZATION Mathematics Department, UCLA

    E-print Network

    Wang, Yalin

    BRAIN SURFACE CONFORMAL PARAMETERIZATION Yalin Wang Mathematics Department, UCLA email: ylwang scans of the brain, including the cortex, hip- pocampus, and lateral ventricles. We found. KEY WORDS Brain Mapping, Riemann Surface Structure, Conforaml Net, Critical Graph 1 Introduction

  17. Social conformity despite individual preferences for distinctiveness

    PubMed Central

    Smaldino, Paul E.; Epstein, Joshua M.

    2015-01-01

    We demonstrate that individual behaviours directed at the attainment of distinctiveness can in fact produce complete social conformity. We thus offer an unexpected generative mechanism for this central social phenomenon. Specifically, we establish that agents who have fixed needs to be distinct and adapt their positions to achieve distinctiveness goals, can nevertheless self-organize to a limiting state of absolute conformity. This seemingly paradoxical result is deduced formally from a small number of natural assumptions and is then explored at length computationally. Interesting departures from this conformity equilibrium are also possible, including divergence in positions. The effect of extremist minorities on these dynamics is discussed. A simple extension is then introduced, which allows the model to generate and maintain social diversity, including multimodal distinctiveness distributions. The paper contributes formal definitions, analytical deductions and counterintuitive findings to the literature on individual distinctiveness and social conformity.

  18. Conformable apparatus in a drill string

    DOEpatents

    Hall, David R. (Provo, UT); Hall, Jr., H. Tracy (Provo, UT); Pixton, David S. (Lehi, UT); Fox, Joe (Spanish Fork, UT)

    2007-08-28

    An apparatus in a drill string comprises an internally upset drill pipe. The drill pipe comprises a first end, a second end, and an elongate tube intermediate the first and second ends. The elongate tube and the ends comprising a continuous an inside surface with a plurality of diameters. A conformable metal tube is disposed within the drill pipe intermediate the ends thereof and terminating adjacent to the ends of the drill pipe. The conformable metal tube substantially conforms to the continuous inside surface of the metal tube. The metal tube may comprise a non-uniform section which is expanded to conform to the inside surface of the drill pipe. The non-uniform section may comprise protrusions selected from the group consisting of convolutions, corrugations, flutes, and dimples. The non-uniform section extends generally longitudinally along the length of the tube. The metal tube may be adapted to stretch as the drill pipes stretch.

  19. Glass Transition

    Microsoft Academic Search

    Fumiko Yonezawa; Shoichi Sakamoto; Shuichi Nosé

    1990-01-01

    Computer simulations of melting, crystallization, glass transition, and annealing for a model system of 864 Lennard-Jones (LJ) atoms under a periodic boundary condition are carried out using constant-pressure molec ular dynamics techniques with temperature control. When an fcc crystal of LJ atoms is heated, melting occurs; however, an LJ liquid, when quenched slowly, crystallizes into layers with stacking faults. Each

  20. Radioactive Transitions

    NSDL National Science Digital Library

    This resource provides an interactive activity demonstrating how radioactive transitions (photon absorption and stimulated emission) occur in an optical field. Many important phenomena are emergent behaviors of this dynamic model. An interactive diagram is presented allowing students to experiment and watch a simulation of the result.

  1. Intrinsic optical activity and conformational flexibility: the role of size-dependent ring morphology in model cycloketones.

    PubMed

    Lahiri, Priyanka; Wiberg, Kenneth B; Vaccaro, Patrick H

    2013-11-27

    The optical rotatory dispersion of two monocyclic ketones, (R)-3-methylcyclopentanone [R-3MCP] and (R)-3-methylcyclohexanone [R-3MCH], has been investigated under isolated and solvated conditions to explore the role of ring size/morphology and to elucidate the impact of environmental perturbations. Vapor-phase measurements of specific rotation, [?]?T, were performed at 355/633 nm by means of cavity ring-down polarimetry while complementary solution-phase work employed a canonical discrete-wavelength polarimeter to probe five distinct solvents. The magnitude of [?]?T was found to increase upon solvation, albeit to different extents for the two species of interest, with the attendant sign switching between the solution and vapor phases for ? ? 510.7 nm in the case of R-3MCH. Quantum-chemical analyses suggest two low-lying conformers to exist for each ketone, distinguished by an equatorial or axial arrangement of the methyl substituent. Linear-response calculations built upon density-functional [DFT(B3LYP)/aug-cc-pVTZ] and coupled-cluster [CCSD/aug-cc-pVDZ] frameworks gave antagonistic chiroptical parameters for these isomers, which were combined with various energy metrics in a conformer-averaging ansatz to simulate the response for a thermally equilibrated ensemble. The intrinsic behavior of R-3MCP was reproduced best by averaging DFT optical-activity predictions according to relative populations deduced from free-energy differences; however, less satisfactory agreement was realized for isolated R-3MCH molecules. The sizable circular birefringence of R-3MCP can be attributed to inherent chirality of its twisted carbon ring whereas the more modest response of R-3MCH stems mainly from the lone stereogenic center. The implicit polarizable continuum model treated solvation effects in R-3MCP with moderate success, but failed to replicate solvent-dependent trends in R-3MCH. The relationship of dispersive optical activity to bulk characteristics of the surrounding medium, including dielectric constant, refractive index, and polarizability, is discussed with the goal of bridging the gap between isolated and solvated chiroptical properties. PMID:24224892

  2. Human Meibum Lipid Conformation and Thermodynamic Changes with Meibomian-Gland Dysfunction

    PubMed Central

    Borchman, Douglas; Yappert, Marta C.; Bell, James; Wells, Emily; Neravetla, Shantanu; Greenstone, Victoria

    2011-01-01

    Purpose. Instability of the tear film with rapid tear break-up time is a common feature of aqueous-deficient and evaporative dry eye diseases, suggesting that there may be a shared structural abnormality of the tear film that is responsible for the instability. It may be that a change in the normal meibum lipid composition and conformation causes this abnormality. Principle component analyses of infrared spectra of human meibum indicate that human meibum collected from normal donors (Mn) is less ordered than meibum from donors with meibomian gland dysfunction (Md). In this study the conformation of Md was quantified to test this finding. Methods. Changes in lipid conformation with temperature were measured by infrared spectroscopy. There were two phases to our study. In phase 1, the phase transitions of human samples, Mn and Md, were measured. In phase 2, the phase transitions of model lipid standards composed of different waxes and cholesterol esters were measured. Results. The phase-transition temperature was significantly higher (4°C) for the Md compared with the Mn of age-matched donors with no history of dry-eye symptoms. Most (82%) of the phase-transition temperatures measured for Md were above the values for Mn. The small change in the transition temperature was amplified in the average lipid order (stiffness) at 33.4°C. The average lipid order at 33.4°C for Md was significantly higher (30%, P = 0.004) than for Mn. The strength of lipid–lipid interactions was 72% higher for Md than for Mn. The ability of one lipid to influence the melting of adjacent lipids is termed cooperativity. There were no significant differences between Mn and Md in phase-transition cooperativity, nor was there a difference between Mn and Md in the minimum order or maximum order that Mn and Md achieved at very low and very high temperatures, respectively. The model wax studies showed that the phase transition of complex mixtures of natural lipids was set by the level of unsaturation. A double bond decreased the phase-transition temperature by approximately 40°C. The addition of a second CHCH moiety decreased the phase-transition temperature by approximately 19°C. Unsaturated waxes were miscible with saturated waxes. When a saturated wax was mixed with an unsaturated one, the saturated wax disproportionately increased the phase transition of the mixture by approximately 30°C compared with the saturated wax alone. Cholesterol ester had little effect on the phase-transition temperature of the waxes. Model studies indicated that changes in the amount of lipid saturation, rather than the amount of cholesterol esters, could be a factor in the observed conformational changes. Conclusions. Meibum lipid compositional changes with meibomian gland dysfunction reflect changes in hydrocarbon chain conformation and lipid–lipid interaction strength. Spectroscopic techniques are useful in studying the lipid–lipid interactions and conformation of lipid from individual patients. (ClinicalTrials.gov number, NCT00803452.) PMID:21398284

  3. Influence of backbone conformational rigidity in temperature-sensitive amphiphilic supramolecular assemblies.

    PubMed

    Raghupathi, Krishna R; Sridhar, Uma; Byrne, Kevin; Raghupathi, Kishore; Thayumanavan, S

    2015-04-29

    Molecular design features that endow amphiphilic supramolecular assemblies with a unique temperature-sensitive transition have been investigated. We find that conformational rigidity in the backbone is an important feature for eliciting this feature. We also find that intramolecular hydrogen-bonding can induce such rigidity in amphiphile backbone. Guest encapsulation stability of these assemblies was found to be significantly altered within a narrow temperature window, which correlates with the temperature-sensitive size transition of the molecular assembly. Molecular design principles demonstrated here could have broad implications in developing future temperature-responsive systems. PMID:25893806

  4. Mechanism of Nucleated Conformational Conversion of A?42.

    PubMed

    Fu, Ziao; Aucoin, Darryl; Davis, Judianne; Van Nostrand, William E; Smith, Steven O

    2015-07-14

    Soluble oligomers and protofibrils of the A?42 peptide are neurotoxic intermediates in the conversion of monomeric A?42 into the amyloid fibrils associated with Alzheimer's disease. Nuclear magnetic resonance and Fourier transform infrared spectroscopy, along with single-touch atomic force microscopy, are used to establish the structural transitions involved in fibril formation. We show that under conditions favorable for the nucleated conformation conversion, the A?42 peptide aggregates into largely unstructured low-molecular weight (MW) oligomers that are able to stack to form high-MW oligomers and to laterally associate to form protofibrils. ?-Sheet secondary structure develops during the irreversible lateral association of the oligomers. The first step in this conversion is the formation of an antiparallel ?-hairpin stabilized by intramonomer hydrogen bonding. The antiparallel ?-hairpins then associate into a cross ?-sheet structure with parallel and in-register ?-strands having intermonomer hydrogen bonding. PMID:26069943

  5. Conformity of LINAC-Based Stereotactic Radiosurgery Using Dynamic Conformal Arcs and Micro-Multileaf Collimator

    Microsoft Academic Search

    Lisa J. Hazard; Brian Wang; Thomas B. Skidmore; Shyh-Shi Chern; Bill J. Salter; Randy L. Jensen; Dennis C. Shrieve

    2009-01-01

    Purpose: To assess the conformity of dynamic conformal arc linear accelerator-based stereotactic radiosurgery and to describe a standardized method of isodose surface (IDS) selection. Methods and Materials: In 174 targets, the conformity index (CI) at the prescription IDS used for treatment was calculated as CI = (PIV\\/PVTV)\\/(PVTV\\/TV), where TV is the target volume, PIV (prescription isodose volume) is the total

  6. Conformal phased array antenna pattern corrector

    NASA Astrophysics Data System (ADS)

    Antonucci, J. D.

    1984-11-01

    The present invention relates to radar antenna systems and particularly to a pattern corrector for a conformal phased array monopulse antenna system. In certain monopulse radar applications, such as aboard aircraft, it becomes advantageous to mount a phased array antenna onto the curved exterior surface of the host vehicle. Such a conformal phased array antenna, however, produces a distorted radiation pattern when the beam is scanned off of broadside.

  7. Coordinate systems for conformal cerebellar flat maps

    Microsoft Academic Search

    Monica K. Hurdal; Ken Stephenson; Phil Bowers; De Witt Sumners; David A. Rottenberg

    2000-01-01

    Methods Quasi-conformal flat maps of the human cerebellum (1,4) were created from a high-resolution Tl-weighted MRI volume (5). A topologically correct surface was produced from a cerebellar volume defined by a plane parallel to the posterior commisure-obex line and orthogonal to a plane passing through the vermal midline. Our quasi-conformal flattening procedure (2,3) was applied to this surface to produce

  8. Scale-invariant breaking of conformal symmetry

    E-print Network

    Dymarsky, Anatoly

    2015-01-01

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  9. Scale-invariant breaking of conformal symmetry

    E-print Network

    Anatoly Dymarsky; Alexander Zhiboedov

    2015-05-05

    Known examples of unitary relativistic scale but not conformal-invariant field theories (SFTs) can be embedded into conventional conformal field theories (CFTs). We show that any SFT which is a subsector of a unitary CFT is a free theory. Our discussion applies to an arbitrary number of spacetime dimensions and explains triviality of known SFTs in four spacetime dimensions. We comment on examples of unitary SFTs which are not captured by our construction.

  10. The research of conformal optical design

    NASA Astrophysics Data System (ADS)

    Li, Lin; Li, Yan; Huang, Yi-fan; Du, Bao-lin

    2009-07-01

    Conformal optical domes are characterized as having external more elongated optical surfaces that are optimized to minimize drag, increased missile velocity and extended operational range. The outer surface of the conformal domes typically deviate greatly from spherical surface descriptions, so the inherent asymmetry of conformal surfaces leads to variations in the aberration content presented to the optical sensor as it is gimbaled across the field of regard, which degrades the sensor's ability to properly image targets of interest and then undermine the overall system performance. Consequently, the aerodynamic advantages of conformal domes cannot be realized in practical systems unless the dynamic aberration correction techniques are developed to restore adequate optical imaging capabilities. Up to now, many optical correction solutions have been researched in conformal optical design, including static aberrations corrections and dynamic aberrations corrections. There are three parts in this paper. Firstly, the combination of static and dynamic aberration correction is introduced. A system for correcting optical aberration created by a conformal dome has an outer surface and an inner surface. The optimization of the inner surface is regard as the static aberration correction; moreover, a deformable mirror is placed at the position of the secondary mirror in the two-mirror all reflective imaging system, which is the dynamic aberration correction. Secondly, the using of appropriate surface types is very important in conformal dome design. Better performing optical systems can result from surface types with adequate degrees of freedom to describe the proper corrector shape. Two surface types and the methods of using them are described, including Zernike polynomial surfaces used in correct elements and user-defined surfaces used in deformable mirror (DM). Finally, the Adaptive optics (AO) correction is presented. In order to correct the dynamical residual aberration in conformal optical design, the SPGD optimization algorithm is operated at each zoom position to calculate the optimized surface shape of the MEMS DM. The communication between MATLAB and Code V established via ActiveX technique is applied in simulation analysis.

  11. Conformal universe as false vacuum decay

    NASA Astrophysics Data System (ADS)

    Libanov, M.; Rubakov, V.

    2015-05-01

    We point out that the (pseudo)conformal universe scenario may be realized as the decay of a conformally invariant, metastable vacuum, which proceeds via spontaneous nucleation and subsequent growth of a bubble of a putative new phase. We study perturbations about the bubble and show that their leading late-time properties coincide with those inherent in the original models with homogeneously rolling backgrounds. In particular, the perturbations of a spectator dimension-zero field have a flat power spectrum.

  12. Conformal Symmetry as a Template for QCD

    SciTech Connect

    Brodsky, S

    2004-08-04

    Conformal symmetry is broken in physical QCD; nevertheless, one can use conformal symmetry as a template, systematically correcting for its nonzero {beta} function as well as higher-twist effects. For example, commensurate scale relations which relate QCD observables to each other, such as the generalized Crewther relation, have no renormalization scale or scheme ambiguity and retain a convergent perturbative structure which reflects the underlying conformal symmetry of the classical theory. The ''conformal correspondence principle'' also dictates the form of the expansion basis for hadronic distribution amplitudes. The AdS/CFT correspondence connecting superstring theory to superconformal gauge theory has important implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for hard exclusive processes as well as determining essential aspects of hadronic light-front wavefunctions. Theoretical and phenomenological evidence is now accumulating that QCD couplings based on physical observables such as {tau} decay become constant at small virtuality; i.e., effective charges develop an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. The near-constant behavior of effective couplings also suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer. The importance of using an analytic effective charge such as the pinch scheme for unifying the electroweak and strong couplings and forces is also emphasized.

  13. Conformational rearrangements upon Syk auto-phosphorylation

    PubMed Central

    Arias-Palomo, Ernesto; Recuero-Checa, María A.; Bustelo, Xosé R.; Llorca, Oscar

    2009-01-01

    Syk is a cytoplasmic tyrosine kinase that is activated after recruitment to immune receptors, triggering the phopshorylation of downstream targets. The kinase activity of Syk is controlled by an auto-inhibited conformation consisting of a regulatory region that contains two N-terminal Src homology 2 (SH2) domains inhibiting the catalytic activity of the kinase domain located at the C-terminus. The atomic structure of the related Zap-70 kinase and an electron microscopy (EM) model of Syk have revealed the structural mechanism of this auto-inhibition based on the formation of a compact conformation sustained by interactions between the regulatory and catalytic domains. On the other hand, the structural basis of Syk activation is not fully understood due to the lack of a 3D structure of full length Syk in an active conformation. Here, we have used single particle electron microscopy to analyse the conformational changes taken place in an activated form of Syk induced by auto-phosphorylation. The conformation of phosphorylated Syk is reminiscent of the compact structure of the inhibited protein but significant conformational changes are observed in the regulatory region. These rearrangements could be sufficient to disrupt the inhibitory interactions, contributing to Syk activation. These results suggest that the regulation of the activation of Syk might be modulated by subtle changes in the positioning of the regulatory domains rather than a full opening mechanism as proposed for the Src kinases. PMID:19409513

  14. A Kinesin Motor In A Force-producing Conformation

    SciTech Connect

    Heuston, E.; Bronner, C; Kull, F; Endow, S

    2010-01-01

    Kinesin motors hydrolyze ATP to produce force and move along microtubules, converting chemical energy into work by a mechanism that is only poorly understood. Key transitions and intermediate states in the process are still structurally uncharacterized, and remain outstanding questions in the field. Perturbing the motor by introducing point mutations could stabilize transitional or unstable states, providing critical information about these rarer states. Here we show that mutation of a single residue in the kinesin-14 Ncd causes the motor to release ADP and hydrolyze ATP faster than wild type, but move more slowly along microtubules in gliding assays, uncoupling nucleotide hydrolysis from force generation. A crystal structure of the motor shows a large rotation of the stalk, a conformation representing a force-producing stroke of Ncd. Three C-terminal residues of Ncd, visible for the first time, interact with the central {beta}-sheet and dock onto the motor core, forming a structure resembling the kinesin-1 neck linker, which has been proposed to be the primary force-generating mechanical element of kinesin-1. Force generation by minus-end Ncd involves docking of the C-terminus, which forms a structure resembling the kinesin-1 neck linker. The mechanism by which the plus- and minus-end motors produce force to move to opposite ends of the microtubule appears to involve the same conformational changes, but distinct structural linkers. Unstable ADP binding may destabilize the motor-ADP state, triggering Ncd stalk rotation and C-terminus docking, producing a working stroke of the motor.

  15. TRANSITION DE MOTT METAL-INSULATOR TRANSITIONS

    E-print Network

    Paris-Sud XI, Université de

    TRANSITION DE MOTT METAL-INSULATOR TRANSITIONS IN TRANSITION METAL OXIDES by D. B. McWHAN, A. MENTH with increasing number of d elec- trons in the transition metal oxides. In the (V1-~Cr~)203system a Mott predominantly non-trivalent ions favor the metallicstate. I. Introduction. -Transition metal oxides form a class

  16. ON CONFORMAL KILLING SYMMETRIC TENSOR FIELDS ON RIEMANNIAN MANIFOLDS

    E-print Network

    Sharafutdinov, Vladimir

    ON CONFORMAL KILLING SYMMETRIC TENSOR FIELDS ON RIEMANNIAN MANIFOLDS N. S. DAIRBEKOV AND V. A. SHARAFUTDINOV Abstract. A vector field on a Riemannian manifold is called conformal Killing if it gen- erates one-parameter group of conformal transformation. The class of conformal Killing symmetric tensor

  17. Conformal Killing forms on Riemannian manifolds Uwe Semmelmann

    E-print Network

    Semmelmann, Uwe

    Conformal Killing forms on Riemannian manifolds Uwe Semmelmann February 19, 2012 Abstract Conformal Killing forms are a natural generalization of conformal vector fields on Riemannian manifolds the existence of conformal Killing forms on nearly K¨ahler and weak G2-manifolds. Moreover, we give a complete

  18. Conformal Killing symmetric tensor fields on a Riemannian manifold

    E-print Network

    Sharafutdinov, Vladimir

    Conformal Killing symmetric tensor fields on a Riemannian manifold Vladimir Sharafutdinov Sobolev Abstract A conformal Killing vector field on a Riemannian manifold is a vector field generating a one-parameter group of conformal transformations. We generalize the differential equation of conformal Killing vector

  19. Optimization of Brain Conformal Mapping with Yalin Wang1

    E-print Network

    Wang, Yalin

    Optimization of Brain Conformal Mapping with Landmarks Yalin Wang1 , Lok Ming Lui1 , Tony F. Chan1 into a canonical space. One method to do this is to conformally map cortical surfaces to the sphere. It is well known that any genus zero Riemann surface can be conformally mapped to a sphere. Therefore, conformal

  20. A Complete Conformational Map for RNA Venkatesh L. Murthy1

    E-print Network

    Fleming, Patrick

    A Complete Conformational Map for RNA Venkatesh L. Murthy1 , Rajgopal Srinivasan1 , David E. Draper for understanding RNA structure has remained elusive to date. We present a comprehensive conformation- al map a predictive conformational map for RNA. # 1999 Academic Press Keywords: RNA conformation; RNA folding; RNA

  1. Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR–NMR correlation

    Microsoft Academic Search

    Qing-Xia Ruan; Ping Zhou

    2008-01-01

    In the present work, we investigated Na+ ion effect on the silk fibroin (SF) conformation. Samples are Na+-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na+] increases, partial silk fibroin conformation transit from helix-form to ?-form at certain Na+ ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR–NMR

  2. Eliminating Transitions

    ERIC Educational Resources Information Center

    Gallick, Barb; Lee, Lisa

    2010-01-01

    Adults often find themselves transitioning from one activity to another in a short time span. Most of the time, they do not feel they have a lot of control over their schedules, but wish that they could carve out extended time to relax and focus on one project. Picture a group of children in the block area who have spent 15 or 20 minutes building…

  3. Fractal to Nonfractal Phase Transition in the Dielectric Breakdown Model

    SciTech Connect

    Hastings, M. B.

    2001-10-22

    A fast method is presented for simulating the dielectric-breakdown model using iterated conformal mappings. Numerical results for the dimension and for corrections to scaling are in good agreement with the recent renormalization group prediction of an upper critical {eta}{sub c}=4 , at which a transition occurs between branching fractal clusters and one-dimensional nonfractal clusters.

  4. Phase transition in ethylenetetrafluoroethylene (ETFE) alternating copolymer. A spectroscopic study

    Microsoft Academic Search

    G. Zerbi

    1997-01-01

    The study of temperature dependent infrared (i.r.) and Raman spectra of alternating ethylenetetrafluoroethylene (ETFE) copolymer suggests that the transition from orthorhombic to hexagonal phases may be driven by the generation and propagation of conformational solitons (gentle mobile chain twist).

  5. Beyond the Boundaries of School: Transition Considerations in Gifted Education.

    ERIC Educational Resources Information Center

    Higgins, Kyle; Boone, Randall

    2003-01-01

    This article discusses components of instruction for gifted students that stress real-world-based, school-to-work transition learning. Student needs are noted such as multi-potentiality, personal expectations versus those of others, and pressure to conform. Recommendations address mentoring, career education, self-determination, leadership skills,…

  6. Cyclic Constraints on Conformational Flexibility in ?-PEPTIDES: Conformation-Specific IR and UV Spectroscopy

    NASA Astrophysics Data System (ADS)

    Walsh, Patrick S.; Kusaka, Ryoji; Zwier, Timothy S.; Fisher, Brian F.; Gellman, Samuel H.

    2013-06-01

    Spectroscopic studies of flexible peptides in the gas phase can provide insight to their inherent structural preferences in the absence of solvent. Recently, there has been increased attention paid to synthetic foldamers containing non-natural residues that can be specifically engineered to robustly form particular secondary structures. These engineered peptides have potential in therapeutic drug design because they are resistant to enzymatic degradation. Specifically, the Gellman group has synthesized a ?-peptide with a six membered cyclic constraint in the ?^{4}-?^{3} position and an ethyl group at the ?^{2} position (?_{ACHC}). The three stereocenters have a well-defined chirality [S,S,S]. These two features constrain the relative orientation of adjacent amide groups, thereby favoring a particular "pitch" to the turn. Solution phase results indicate that constrained ?-peptides induce the formation of a 14-helix. Ac-?_{ACHC}-NHBz, its monohydrate and Ac-?_{ACHC}-?_{ACHC}-NHBz have been studied using ultraviolet (UV) and infrared (IR) double-resonance methods to obtain conformation-specific spectra under jet-cooled conditions in the gas phase. IR spectra in the hydride stretch (3300-3750 cm^{-1}), amide I/II and OH bend (1400-1800 cm^{-1}) were recorded and compared to predictions using density functional methods (DFT) and harmonic frequency calculations. We will compare the present results on constrained ?-peptides with corresponding results on unconstrained analogs. Data obtained for the monohydrated water cluster of Ac-?_{ACHC}-NHBz will also be presented, including assignment of the water bend fundamental, which appears in the midst of transitions due to the amide II vibrations. L. Guo, W. Zhang, A. G. Reidenbach, M. W. Giuliano, I. A. Guzei, L. C. Spencer and S. H. Gellman Angew. Chem. Int. Ed. 2011, 50, 5843-5846

  7. Probing the Role of Hydration in the Unfolding Transitions of Carbonmonoxy Myoglobin and Apomyoglobin

    E-print Network

    Shorter, James

    Probing the Role of Hydration in the Unfolding Transitions of Carbonmonoxy Myoglobin unfolding transition of horse carbonmonoxy myoglobin monitored by the stretching vibration of the CO ligand conformational reporters. In addition, the denatured protein exhibits an A0- like CO band. We hypothesize

  8. Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer

    E-print Network

    Thirumalai, Devarajan

    Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer Alexander ABSTRACT: We investigate the structural transitions in a polymer induced by spherical and nonspherical crowding particles over a wide range of conditions. The polymer conformations are specified by the radius

  9. Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS)

    PubMed Central

    Widom, Julia R.; Johnson, Neil P.; von Hippel, Peter H.; Marcus, Andrew H.

    2013-01-01

    We have observed the conformation-dependent electronic coupling between the monomeric subunits of a dinucleotide of 2-aminopurine (2-AP), a fluorescent analog of the nucleic acid base adenine. This was accomplished by extending two-dimensional fluorescence spectroscopy (2D FS) – a fluorescence-detected variation of 2D electronic spectroscopy – to excite molecular transitions in the ultraviolet (UV) regime. A collinear sequence of four ultrafast laser pulses centered at 323 nm was used to resonantly excite the coupled transitions of 2-AP dinucleotide. The phases of the optical pulses were continuously swept at kilohertz frequencies, and the ensuing nonlinear fluorescence was phase-synchronously detected at 370 nm. Upon optimization of a point-dipole coupling model to our data, we found that in aqueous buffer the 2-AP dinucleotide adopts an average conformation in which the purine bases are non-helically stacked (center-to-center distance R12 = 3.5 Å ± 0.5 Å, twist angle ?12 = 5° ± 5°), which differs from the conformation of such adjacent bases in duplex DNA. These experiments establish UV-2D FS as a method for examining the local conformations of an adjacent pair of fluorescent nucleotides substituted into specific DNA or RNA constructs, which will serve as a powerful probe to interpret, in structural terms, biologically significant local conformational changes within the nucleic acid framework of protein-nucleic acid complexes. PMID:24223491

  10. Conformal anomaly of super Wilson loop

    NASA Astrophysics Data System (ADS)

    Belitsky, A. V.

    2012-09-01

    Classically supersymmetric Wilson loop on a null polygonal contour possesses all symmetries required to match it onto non-MHV amplitudes in maximally supersymmetric Yang-Mills theory. However, to define it quantum mechanically, one is forced to regularize it since perturbative loop diagrams are not well defined due to presence of ultraviolet divergences stemming from integration in the vicinity of the cusps. A regularization that is adopted by practitioners by allowing one to use spinor helicity formalism, on the one hand, and systematically go to higher orders of perturbation theory is based on a version of dimensional regularization, known as Four-Dimensional Helicity scheme. Recently it was demonstrated that its use for the super Wilson loop at one loop breaks both conformal symmetry and Poincaré supersymmetry. Presently, we exhibit the origin for these effects and demonstrate how one can undo this breaking. The phenomenon is alike the one emerging in renormalization group mixing of conformal operators in conformal theories when one uses dimensional regularization. The rotation matrix to the diagonal basis is found by means of computing the anomaly in the Ward identity for the conformal boost. Presently, we apply this ideology to the super Wilson loop. We compute the one-loop conformal anomaly for the super Wilson loop and find that the anomaly depends on its Grassmann coordinates. By subtracting this anomalous contribution from the super Wilson loop we restore its interpretation as a dual description for reduced non-MHV amplitudes which are expressed in terms of superconformal invariants.

  11. Arcjet Testing of Advanced Conformal Ablative TPS

    NASA Technical Reports Server (NTRS)

    Gasch, Matthew; Beck, Robin; Agrawal, Parul

    2014-01-01

    A conformable TPS over a rigid aeroshell has the potential to solve a number of challenges faced by traditional rigid TPS materials (such as tiled Phenolic Impregnated Carbon Ablator (PICA) system on MSL. The compliant (high strain to failure) nature of the conformable ablative materials will allow integration of the TPS with the underlying aeroshell structure much easier and enable monolithic-like configuration and larger segments (or parts) to be used. In May of 2013 the CA250 project executed an arcjet test series in the Ames IHF facility to evaluate a phenolic-based conformal system (named Conformal-PICA) over a range of test conditions from 40-400Wcm2. The test series consisted of four runs in the 13-inch diameter nozzle. Test models were based on SPRITE configuration (a 55-deg sphere cone), as it was able to provide a combination of required heat flux, pressure and shear within a single entry. The preliminary in-depth TC data acquired during that test series allowed a mid-fidelity thermal response model for conformal-PICA to be created while testing of seam models began to address TPS attachment and joining of multiple segments for future fabrication of large-scale aeroshells. Discussed in this paper are the results.

  12. Nonparametric Clustering for Studying RNA Conformations

    PubMed Central

    Le Faucheur, Xavier; Hershkovits, Eli; Tannenbaum, Rina; Tannenbaum, Allen

    2013-01-01

    The local conformation of RNA molecules is an important factor in determining their catalytic and binding properties. The analysis of such conformations is particularly difficult due to the large number of degrees of freedom, such as the measured torsion angles per residue and the interatomic distances among interacting residues. In this work, we use a nearest-neighbor search method based on the statistical mechanical Potts model to find clusters in the RNA conformational space. The proposed technique is mostly automatic and may be applied to problems, where there is no prior knowledge on the structure of the data space in contrast to many other clustering techniques. Results are reported for both single residue conformations, where the parameter set of the data space includes four to seven torsional angles, and base pair geometries, where the data space is reduced to two dimensions. Moreover, new results are reported for base stacking geometries. For the first two cases, i.e., single residue conformations and base pair geometries, we get a very good match between the results of the proposed clustering method and the known classifications with only few exceptions. For the case of base stacking geometries, we validate our classification with respect to geometrical constraints and describe the content, and the geometry of the new clusters. PMID:21173460

  13. Global attractors of complete conformal foliations

    SciTech Connect

    Zhukova, Nina I [N.I. Lobachevsky Nizhni Novgorod State University, Nizhnii Novgorod (Russian Federation)

    2012-03-31

    We prove that every complete conformal foliation (M,F) of codimension q{>=}3 is either Riemannian or a (Conf(S{sup q}), S{sup q})-foliation. We further prove that if (M,F) is not Riemannian, it has a global attractor which is either a nontrivial minimal set or a closed leaf or a union of two closed leaves. In this theorem we do not assume that the manifold M is compact. In particular, every proper conformal non-Riemannian foliation (M,F) has a global attractor which is either a closed leaf or a union of two closed leaves, and the space of all nonclosed leaves is a connected q-dimensional orbifold. We show that every countable group of conformal transformations of the sphere S{sup q} can be realized as the global holonomy group of a complete conformal foliation. Examples of complete conformal foliations with exceptional and exotic minimal sets as global attractors are constructed. Bibliography: 20 titles.

  14. Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

    NASA Astrophysics Data System (ADS)

    Ruan, Qing-Xia; Zhou, Ping

    2008-07-01

    In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to ?-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil ? helix-like ? ?-sheet-like ? ?-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of ?-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

  15. Microwave, structural, conformational, vibrational studies and ab initio calculations of fluoroacetyl chloride.

    PubMed

    Deodhar, Bhushan S; Brenner, Reid E; Klaassen, Joshua J; Tubergen, Michael J; Durig, James R

    2015-09-01

    The infrared and Raman spectra (3200-50cm(-1)) of the gas, liquid or solution, and solid of fluoroacetyl chloride, FCH2COCl have been recorded. FT-microwave studies have also been carried out and 22 transitions were recorded for the trans conformer. Variable temperature (-50 to -105°C) studies of the infrared and Raman spectra (3200-50cm(-1)) of xenon solutions have been carried out. From these data, the trans, cis and gauche conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 159±11cm(-1) (1.90±0.14kJmol(-1)) with the trans conformer the more stable form than the cis. The energy difference between the cis and gauche form is 222±18cm(-1) (2.66±0.21kJ/mol) and the energy difference between the trans and gauche forms is 386±13cm(-1) (4.61±0.16kJ/mol). Vibrational assignments have been made for the observed bands for the three conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, and Raman activities for the three conformers. By utilizing the microwave rotational constants of two isotopomers for trans, combined with the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for the trans conformer. The results are discussed and compared to the corresponding properties of some related molecules. PMID:25909903

  16. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    SciTech Connect

    Forneris, Federico; Burnley, B. Tom; Gros, Piet, E-mail: p.gros@uu.nl [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands)

    2014-03-01

    Ensemble-refinement analysis of native and mutant factor D (FD) crystal structures indicates a dynamical transition in FD from a self-inhibited inactive conformation to a substrate-bound active conformation that is reminiscent of the allostery in thrombin. Comparison with previously observed dynamics in thrombin using NMR data supports the crystallographic ensembles. Human factor D (FD) is a self-inhibited thrombin-like serine proteinase that is critical for amplification of the complement immune response. FD is activated by its substrate through interactions outside the active site. The substrate-binding, or ‘exosite’, region displays a well defined and rigid conformation in FD. In contrast, remarkable flexibility is observed in thrombin and related proteinases, in which Na{sup +} and ligand binding is implied in allosteric regulation of enzymatic activity through protein dynamics. Here, ensemble refinement (ER) of FD and thrombin crystal structures is used to evaluate structure and dynamics simultaneously. A comparison with previously published NMR data for thrombin supports the ER analysis. The R202A FD variant has enhanced activity towards artificial peptides and simultaneously displays active and inactive conformations of the active site. ER revealed pronounced disorder in the exosite loops for this FD variant, reminiscent of thrombin in the absence of the stabilizing Na{sup +} ion. These data indicate that FD exhibits conformational dynamics like thrombin, but unlike in thrombin a mechanism has evolved in FD that locks the unbound native state into an ordered inactive conformation via the self-inhibitory loop. Thus, ensemble refinement of X-ray crystal structures may represent an approach alternative to spectroscopy to explore protein dynamics in atomic detail.

  17. Conformal Higgs model: predicted dark energy density

    E-print Network

    R. K. Nesbet

    2014-11-03

    Postulated universal Weyl conformal scaling symmetry provides an alternative to the $\\Lambda$CDM paradigm for cosmology. Recent applications to galactic rotation velocities, Hubble expansion, and a model of dark galactic halos explain qualitative phenomena and fit observed data without invoking dark matter. Significant revision of theory relevant to galactic collisions and clusters is implied, but not yet tested. Dark energy is found to be a consequence of conformal symmetry for the Higgs scalar field of electroweak physics. The present paper tests this implication. The conformal Higgs model acquires a gravitational effect described by a modified Friedmann cosmic evolution equation, shown to fit cosmological data going back to the cosmic microwave background epoch. The tachyonic mass parameter of the Higgs model becomes dark energy in the Friedmann equation. A dynamical model of this parameter, analogous to the Higgs mechanism for gauge boson mass, is derived and tested here. An approximate calculation yields a result consistent with the empirical magnitude inferred from Hubble expansion.

  18. QCD evolution equations from conformal symmetry

    E-print Network

    V. M. Braun; A. N. Manashov

    2014-08-28

    QCD evolution equations in $\\text{MS}$-like schemes can be recovered from the same equations in a modified theory, QCD in non-integer $d=4-2\\epsilon$ dimensions, which enjoys exact scale and conformal invariance at the critical point. Restrictions imposed by the conformal symmetry of the modified theory allow one to obtain complete evolution kernels in integer (physical) dimensions at the given order of perturbation theory from the spectrum of anomalous dimensions added by the calculation of the special conformal anomaly at one order less. We use this technique to derive two-loop evolution equations for flavor-nonsinglet quark-antiquark light-ray operators that encode the scale dependence of generalized hadron parton distributions.

  19. Conformal Symmetry for General Black Holes

    E-print Network

    Mirjam Cveti?; Finn Larsen

    2011-06-16

    We show that the warp factor of a generic asymptotically flat black hole in five dimensions can be adjusted such that a conformal symmetry emerges. The construction preserves all near horizon properties of the black holes, such as the thermodynamic potentials and the entropy. We interpret the geometry with modified asymptotic behavior as the "bare" black hole, with the ambient flat space removed. Our warp factor subtraction generalizes hidden conformal symmetry and applies whether or not rotation is significant. We also find a relation to standard AdS/CFT correspondence by embedding the black holes in six dimensions. The asymptotic conformal symmetry guarantees a dual CFT description of the general rotating black holes.

  20. Multi-field conformal cosmological attractors

    NASA Astrophysics Data System (ADS)

    Kallosh, Renata; Linde, Andrei

    2013-12-01

    We describe a broad class of multi-field inflationary models with spontaneously broken conformal invariance. It generalizes the recently discovered class of cosmological attractors with a single inflaton field [1]. In the new multi-field theories, just as in the single-field models of [1], the moduli space has a boundary (Kähler cone) in terms of the original homogeneous conformal variables. Upon spontaneous breaking of the conformal invariance and switching to the Einstein frame, this boundary moves to infinity in terms of the canonically normalized inflaton field. This results in the exponential stretching and flattening of scalar potentials in the vicinity of the boundary of the moduli space, which makes even very steep potentials perfectly suitable for the slow-roll inflation. These theories, just like their single-field versions, typically lead to inflationary perturbations with ns = 1-2/N and r = 12/N2, where N is the number of e-foldings.

  1. Lorentzian Einstein metrics with prescribed conformal infinity

    E-print Network

    Alberto Enciso; Niky Kamran

    2014-12-14

    We prove that there are asymptotically anti-de Sitter Einstein metrics with prescribed conformal infinity. More precisely we show that, given any suitably small perturbation $\\hat g$ of the conformal metric of the $(n+1)$-dimensional anti-de Sitter space at timelike infinity, which is given by the canonical Lorentzian metric on the $n$-dimensional cylinder, there is a Lorentzian Einstein metric on $(-T,T)\\times \\mathbb{B}^n$ whose conformal geometry is given by $\\hat g$. This is a Lorentzian counterpart of the Graham-Lee theorem in Riemannian geometry and is motivated by the holographic prescription problem in the context of the AdS/CFT correspondence in string theory.

  2. Infrared modification of gravity from conformal symmetry

    E-print Network

    Jack Gegenberg; Shohreh Rahmati; Sanjeev S. Seahra

    2015-05-22

    We reconsider a gauge theory of gravity in which the gauge group is the conformal group SO(4,2) and the action is of the Yang-Mills form, quadratic in the curvature. The resulting gravitational theory exhibits local conformal symmetry and reduces to Weyl-squared gravity under certain conditions. When the theory is linearized about flat spacetime, we find that matter which couples to the generators of special conformal transformations reproduces Newton's inverse square law. Conversely, matter which couples to generators of translations induces a constant and possibly repulsive force far from the source, which may be relevant for explaining the late time acceleration of the universe. The coupling constant of theory is dimensionless, which means that it is potentially renormalizable.

  3. Infrared modification of gravity from conformal symmetry

    E-print Network

    Gegenberg, Jack; Seahra, Sanjeev S

    2015-01-01

    We reconsider a gauge theory of gravity in which the gauge group is the conformal group SO(4,2) and the action is of the Yang-Mills form, quadratic in the curvature. The resulting gravitational theory exhibits local conformal symmetry and reduces to Weyl-squared gravity under certain conditions. When the theory is linearized about flat spacetime, we find that matter which couples to the generators of special conformal transformations reproduces Newton's inverse square law. Conversely, matter which couples to generators of translations induces a constant and possibly repulsive force far from the source, which may be relevant for explaining the late time acceleration of the universe. The coupling constant of theory is dimensionless, which means that it is potentially renormalizable.

  4. Improved Conformal Mapping of the Borel Plane

    E-print Network

    U. D. Jentschura; G. Soff

    2000-07-12

    The conformal mapping of the Borel plane can be utilized for the analytic continuation of the Borel transform to the entire positive real semi-axis and is thus helpful in the resummation of divergent perturbation series in quantum field theory. We observe that the rate of convergence can be improved by the application of Pad\\'{e} approximants to the Borel transform expressed as a function of the conformal variable, i.e. by a combination of the analytic continuation via conformal mapping and a subsequent numerical approximation by rational approximants. The method is primarily useful in those cases where the leading (but not sub-leading) large-order asymptotics of the perturbative coefficients are known.

  5. QCD Evolution Equations from Conformal Symmetry

    NASA Astrophysics Data System (ADS)

    Braun, V. M.; Manashov, A. N.

    2015-02-01

    QCD evolution equations in MS-like schemes can be recovered from the same equations in a modified theory, QCD in non-integer d = 4 - 2? dimensions, which enjoys exact scale and conformal invariance at the critical point. Restrictions imposed by the conformal symmetry of the modified theory allow one to obtain complete evolution kernels in integer (physical) dimensions at the given order of perturbation theory from the spectrum of anomalous dimensions added by the calculation of the special conformal anomaly at one order less. We use this technique to derive two-loop evolution equations for flavor-nonsinglet quark-antiquark light-ray operators that encode the scale dependence of generalized hadron parton distributions.

  6. Computational conformal mapping for surface grid generation

    SciTech Connect

    Khamayseh, A. [Los Alamos National Laboratory, NM (United States)] [Los Alamos National Laboratory, NM (United States); Mastin, C.W. [NASA Langley Research Center, Hampton, VA (United States)] [NASA Langley Research Center, Hampton, VA (United States)

    1996-02-01

    The paper describes the development and application of a new approach for formulating an elliptic generation system on parametrically defined surfaces. The present derivation of the surface equations proceeds in two steps: First, conformal mapping of smooth surfaces onto rectangular regions is utilized to derive a first-order system of partial differential equations analogous to Beltrami`s system for quasi-conformal mapping of planar regions. Second, a general elliptic generation system for three-dimensional surfaces, including forcing functions, is formulated based on Beltrami`s system and quasi-conformal mapping. The resulting elliptic system is solved using an iterative method on arbitrary surfaces represented analytically by rational B-splines. The overall effect of this approach is a reliable and versatile elliptic method for generating and improving surface grids. Examples will be presented to demonstrate the application of the method in constructing practical grids. 21 refs., 5 figs.

  7. Conformal invariance in three dimensional percolation

    E-print Network

    Gori, G

    2015-01-01

    The aim of the paper is to present numerical results supporting the presence of conformal invariance in three dimensional statistical mechanics models at criticality and to elucidate the geometric aspects of universality. As a case study we study three dimensional percolation at criticality in bounded domains. Both on discrete and continuous models of critical percolation, we test by numerical experiments the invariance of quantities in finite domains under conformal transformations focusing on crossing probabilities. Our results show clear evidence of the onset of conformal invariance in finite realizations especially for the continuum percolation models. Finally we propose a simple analytical function approximating the crossing probability among two spherical caps on the surface of a sphere and confront it with the numerical results.

  8. Conformal coatings : challenging environments lead to growth.

    SciTech Connect

    Challener, Cynthia A.

    2005-08-01

    Advances in technology have resulted in the need for electronic devices to continue functioning even when placed in harsh environments. Widespread use of cell phones, laptop computers, and other personal electronic devices, the increased number of electronic controls in home appliances, and the ever more extensive utilization of digital technology in the automotive industry have led to a growing demand for printed circuit boards (PCBs) that can perform under difficult conditions. Conformal coatings provide a protective barrier that enables the PCBs to function in these demanding environments. This growth in demand comes despite the cost and numerous difficulties associated with the application of these coatings. Many conformal coatings manufacturers are investing in the development of new technologies that minimize these difficulties. Others are involved in developing disruptive technologies that will serve as alternatives to traditional conformal coatings processes.

  9. Supersymmetric extension of Galilean conformal algebras

    SciTech Connect

    Bagchi, Arjun; Mandal, Ipsita [Harish-Chandra Research Institute, Chhatnag Road, Jhusi, Allahabad 211019 (India)

    2009-10-15

    The Galilean conformal algebra has recently been realized in the study of the nonrelativistic limit of the AdS/CFT conjecture. This was obtained by a systematic parametric group contraction of the parent relativistic conformal field theory. In this paper, we extend the analysis to include supersymmetry. We work at the level of the coordinates in superspace to construct the N=1 super-Galilean conformal algebra. One of the interesting outcomes of the analysis is that one is able to naturally extend the finite algebra to an infinite one. This looks structurally similar to the N=1 superconformal algebra in two dimensions, but is different. We also comment on the extension of our construction to cases of higher N.

  10. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems

    PubMed Central

    2015-01-01

    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach. PMID:25018675

  11. Conformal Anomaly Actions and Dilaton Interactions

    E-print Network

    Mirko Serino

    2014-08-01

    A number of computational results concerning quantum conformal symmetry is presented. After a review of the connection between conformal symmetry for a Lagrangian field theory in flat space and Weyl symmetry for the same system embedded in a gravitational background, which is discussed in chapter 1, in chapter 2 the 3 energy momentum tensors correlation function is explicitly computed in three free field theories in 4 dimensions; the result is given for two of the three operators on the mass-shell. In chapter 3 a general method to map Green functions built in position space on the ground of symmetry requirements to momentum space, where they can be computed in terms of Feynman diagrams, is developed and discussed: an "integrability" condition, allowing to decide whether a certain correlator can exist within a Lagrangian theory, is derived. Chapter 4 discusses the possible phenomenological implications of the conformal anomaly pole which shows up in the 3 point Green function of one energy momentum tensor with two gauge currents and is interpreted as the perturbative signature of the pseudo-Goldstone boson of conformal symmetry, the dilaton. In chapter 5 we present the computation of the completely traced 4 point function of the energy momentum tensor with a method that exploits the relation between 1-loop counterterms and conformal anomalies, completely bypassing perturbative computations with Feynman diagrams. Later in chapter 6, an algorithm is developed which allows to compute recursively the completely traced Green functions of any number of energy momentum tensors in any renormalization scheme, starting from the dilaton Wess-Zumino action for conformal anomalies. This is derived by applying the Weyl-gauging procedure to the 1-loop counterterms in dimensional regularization. The result is explicitly derived and tested in 2, 4 and 6 dimensions.

  12. Theoretical conformational analysis of thiacrown macrocycles

    SciTech Connect

    Hill, S.E.; Feller, D.

    2000-01-27

    A gas phase conformational analysis was performed on four sulfur-containing macrocycles (i-thiacrown-3, 12-thiacrown-4, 15-thiacrown-5, and 19-thiacrown-6) using a combination of empirical and ab initio methods. Candidates for low-lying conformers were initially generated from high-temperature molecular dynamics simulations. A more computationally manageable subset of conformations was selected for further study based on their relative energies at successively higher levels of ab initio theory. The highest level of theory included second-order perturbation theory with the aug-cc-pVDZ basis set. The lowest conformation of 9-thiacrown-3 was found to have an exodentate C{sub 2} structure with an electronic energy that is 4 kcal/mol below the C{sub 3} crystal structure. For 12-thiacrown-4, the lowest energy structure possesses D{sub 4} structure in both the gas and crystal phase. In the case of 15-thiacrown-5 the lowest energy conformer possesses an oblong, partially exodentate, gas phase structure with C{sub 2} symmetry. The crystal structure has C{sub 1} symmetry and lies 3 kcal/mol higher in energy. 18-Thiacrown-6 has an exodentate C{sub 2} symmetry, which is estimated with a large uncertainty to be 1 kcal/mol below the folded C{sub 2} structure of the crystal. Zero-point vibrational effects shift relative energies by up to 0.3 kcal/mol across an energy span of 5--7 kcal/mol, but the effect on close-lying conformers is less.

  13. The Conformal Stealth of any Standard Cosmology

    E-print Network

    Eloy Ayón-Beato; Alberto A. García; Pedro Isaac Ramírez-Baca; Cesar A. Terrero-Escalante

    2013-09-14

    It is shown that any homogeneous and isotropic universe, independently of its spatial topology and matter content, allows for the presence of a conformal stealth, i.e. a nontrivial conformally invariant scalar field with vanishing energy-momentum tensor, which evolves along with the universe without causing even the smallest backreaction. Surprisingly, this gravitationally invisible universal witness is inhomogeneous with zero consequences for the underlying cosmology. Additionally, it is shown that these results are not exclusive of a four-dimensional universe by generalizing them to higher dimensions.

  14. The Conformal Stealth of any Standard Cosmology

    E-print Network

    Ayón-Beato, Eloy; Ramírez-Baca, Pedro Isaac; Terrero-Escalante, Cesar A

    2013-01-01

    It is shown that any homogeneous and isotropic universe, independently of its spatial topology and matter content, allows for the presence of a conformal stealth, i.e. a nontrivial conformally invariant scalar field with vanishing energy-momentum tensor, which evolves along with the universe without causing even the smallest backreaction. Surprisingly, this gravitationally invisible universal witness is inhomogeneous with zero consequences for the underlying cosmology. Additionally, it is shown that these results are not exclusive of a four-dimensional universe by generalizing them to higher dimensions.

  15. Conformal Field Theory and black hole physics

    NASA Astrophysics Data System (ADS)

    Sidhu, Steve

    2012-01-01

    This thesis reviews the use of 2-dimensional conformal field theory applied to gravity, specifically calculating Bekenstein-Hawking entropy of black holes in (2+1) dimensions. A brief review of general relativity, Conformal Field Theory, energy extraction from black holes, and black hole thermodynamics will be given. The Cardy formula, which calculates the entropy of a black hole from the AdS/CFT duality, will be shown to calculate the correct Bekenstein-Hawking entropy of the static and rotating BTZ black holes. The first law of black hole thermodynamics of the static, rotating, and charged-rotating BTZ black holes will be verified.

  16. Collisions of Einstein-Conformal Scalar Waves

    E-print Network

    C. Klim?{\\'?}k; P. Koln{\\'?}k

    1992-12-18

    A large class of solutions of the Einstein-conformal scalar equations in D=2+1 and D=3+1 is identified. They describe the collisions of asymptotic conformal scalar waves and are generated from Einstein-minimally coupled scalar spacetimes via a (generalized) Bekenstein transformation. Particular emphasis is given to the study of the global properties and the singularity structure of the obtained solutions. It is shown, that in the case of the absence of pure gravitational radiation in the initial data, the formation of the final singularity is not only generic, but is even inevitable.

  17. Conformal coordinates associated with uniformly accelerated motion

    NASA Technical Reports Server (NTRS)

    Jones, R. T.

    1976-01-01

    Specific problems in the theory of relativity are often simplified by an appropriate choice of the coordinate system. Restricted conformal coordinates provide an especially simple analysis of motion with uniform acceleration, known as hyperbolic motion. Conformal coordinates x', t' may be obtained from Cartesian coordinates x, t by the transformation x'+ct'=F(x+ct) and x'-ct'=G(x-ct), where c is the velocity of light. A variable motion of the x' system is determined by the choice of the functions F and G.

  18. Conformal Gravity Holography in Four Dimensions

    NASA Astrophysics Data System (ADS)

    Grumiller, Daniel; Irakleidou, Maria; Lovrekovic, Iva; McNees, Robert

    2014-03-01

    We formulate four-dimensional conformal gravity with (anti-)de Sitter boundary conditions that are weaker than Starobinsky boundary conditions, allowing for an asymptotically subleading Rindler term concurrent with a recent model for gravity at large distances. We prove the consistency of the variational principle and derive the holographic response functions. One of them is the conformal gravity version of the Brown-York stress tensor, the other is a "partially massless response". The on shell action and response functions are finite and do not require holographic renormalization. Finally, we discuss phenomenologically interesting examples, including the most general spherically symmetric solutions and rotating black hole solutions with partially massless hair.

  19. Metastable supersymmetry breaking vacua from conformal dynamics

    E-print Network

    Hiroyuki Abe; Tatsuo Kobayashi; Yuji Omura

    2007-12-26

    We study the scenario that conformal dynamics leads to metastable supersymmetry breaking vacua. At a high energy scale, the superpotential is not R-symmetric, and has a supersymmetric minimum. However, conformal dynamics suppresses several operators along renormalization group flow toward the infrared fixed point. Then we can find an approximately R-symmetric superpotential, which has a metastable supersymmetry breaking vacuum, and the supersymmetric vacuum moves far away from the metastable supersymmetry breaking vacuum. We show a 4D simple model. Furthermore, we can construct 5D models with the same behavior, because of the AdS/CFT dual.

  20. Metastable supersymmetry breaking vacua from conformal dynamics

    E-print Network

    Yuji Omura

    2008-09-18

    We study the scenario that conformal dynamics leads to metastable supersymmetry breaking vacua. At a high energy scale, the superpotential is not R-symmetric, and has a supersymmetric minimum. However, conformal dynamics suppresses several operators along renormalization group flow toward the infrared fixed point. Then we can find an approximately R-symmetric superpotential, which has a metastable supersymmetry breaking vacuum, and the supersymmetric vacuum moves far away from the metastable supersymmetry breaking vacuum. We show a 4D simple model. Furthermore, we can construct 5D models with the same behavior, because of the AdS/CFT dual.

  1. Vacuum energy sequestering and conformal symmetry

    E-print Network

    Ido Ben-Dayan; Robert Richter; Fabian Ruehle; Alexander Westphal

    2015-07-15

    In a series of recent papers Kaloper and Padilla proposed a mechanism to sequester standard model vacuum contributions to the cosmological constant. We study the consequences of embedding their proposal into a fully local quantum theory. In the original work, the bare cosmological constant $\\Lambda$ and a scaling parameter $\\lambda$ are introduced as global fields. We find that in the local case the resulting Lagrangian is that of a spontaneously broken conformal field theory where $\\lambda$ plays the role of the dilaton. A vanishing or a small cosmological constant is thus a consequence of the underlying conformal field theory structure.

  2. Vacuum energy sequestering and conformal symmetry

    E-print Network

    Ben-Dayan, Ido; Ruehle, Fabian; Westphal, Alexander

    2015-01-01

    In a series of recent papers Kaloper and Padilla proposed a mechanism to sequester standard model vacuum contributions to the cosmological constant. We study the consequences of embedding their proposal into a fully local quantum theory. In the original work, the bare cosmological constant $\\Lambda$ and a scaling parameter $\\lambda$ are introduced as global fields. We find that in the local case the resulting Lagrangian is that of a spontaneously broken conformal field theory where $\\lambda$ plays the role of the dilaton. A vanishing or a small cosmological constant is thus a consequence of the underlying conformal field theory structure.

  3. Randomized ligation control for chromosome conformation capture.

    PubMed

    Belton, Jon-Matthew; Dekker, Job

    2015-01-01

    In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes, and length of restriction fragment can cause variations in primer or probe performance and fragment ligation efficiency. Bias can be measured empirically by production of a random control library, as described here, to be used with the 3C library of interest. PMID:26034305

  4. Black hole temperature: Minimal coupling vs conformal coupling

    SciTech Connect

    Fazel, Mohamadreza, E-mail: m.fazel@ph.iut.ac.ir [Department of Physics, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Department of Physics, University of Tehran, North Kargar Avenue, Teharn 14395-547 (Iran, Islamic Republic of); Mirza, Behrouz, E-mail: b.mirza@cc.iut.ac.ir [Department of Physics, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Mansoori, Seyed Ali Hosseini, E-mail: sa.hosseinimansoori@ph.iut.ac.ir [Department of Physics, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of)

    2014-05-15

    In this article, we discuss the propagation of scalar fields in conformally transformed spacetimes with either minimal or conformal coupling. The conformally coupled equation of motion is transformed into a one-dimensional Schrödinger-like equation with an invariant potential under conformal transformation. In a second stage, we argue that calculations based on conformal coupling yield the same Hawking temperature as those based on minimal coupling. Finally, it is conjectured that the quasi normal modes of black holes are invariant under conformal transformation.

  5. Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca²?-ATPase.

    PubMed

    Kobayashi, Chigusa; Koike, Ryotaro; Ota, Motonori; Sugita, Yuji

    2015-04-01

    Sarco(endo)plasmic reticulum Ca(2+)-ATPase transports two Ca(2+) per ATP-hydrolyzed across biological membranes against a large concentration gradient by undergoing large conformational changes. Structural studies with X-ray crystallography revealed functional roles of coupled motions between the cytoplasmic domains and the transmembrane helices in individual reaction steps. Here, we employed "Motion Tree (MT)," a tree diagram that describes a conformational change between two structures, and applied it to representative Ca(2+) -ATPase structures. MT provides information of coupled rigid-body motions of the ATPase in individual reaction steps. Fourteen rigid structural units, "common rigid domains (CRDs)" are identified from seven MTs throughout the whole enzymatic reaction cycle. CRDs likely act as not only the structural units, but also the functional units. Some of the functional importance has been newly revealed by the analysis. Stability of each CRD is examined on the morphing trajectories that cover seven conformational transitions. We confirmed that the large conformational changes are realized by the motions only in the flexible regions that connect CRDs. The Ca(2+) -ATPase efficiently utilizes its intrinsic flexibility and rigidity to response different switches like ligand binding/dissociation or ATP hydrolysis. The analysis detects functional motions without extensive biological knowledge of experts, suggesting its general applicability to domain movements in other membrane proteins to deepen the understanding of protein structure and function. PMID:25641564

  6. Iterative derivation of effective potentials to sample the conformational space of proteins at atomistic scale

    SciTech Connect

    Capelli, Riccardo [Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy)] [Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milano (Italy); Paissoni, Cristina [Department of Chemistry, Università degli Studi di Milano, via Venezian 21, 20133 Milano (Italy) [Department of Chemistry, Università degli Studi di Milano, via Venezian 21, 20133 Milano (Italy); Biomolecular NMR Unit, S. Raffaele Scientific Institute, via Olgettina 58, 20132 Milano (Italy); Sormanni, Pietro [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)] [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Tiana, Guido, E-mail: guido.tiana@unimi.it [Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, 20133 Milano (Italy)] [Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, 20133 Milano (Italy)

    2014-05-21

    The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behavior of large systems or to perform systematic scans of smaller systems. While powerful algorithms are available to facilitate the sampling of the conformational space, successful applications of such models are hindered by the availability of simple enough potentials able to satisfactorily reproduce known properties of the system. We develop an interatomic potential to account for a number of properties of proteins in a computationally economic way. The potential is defined within an all-atom, implicit solvent model by contact functions between the different atom types. The associated numerical values can be optimized by an iterative Monte Carlo scheme on any available experimental data, provided that they are expressible as thermal averages of some conformational properties. We test this model on three different proteins, for which we also perform a scan of all possible point mutations with explicit conformational sampling. The resulting models, optimized solely on a subset of native distances, not only reproduce the native conformations within a few Angstroms from the experimental ones, but show the cooperative transition between native and denatured state and correctly predict the measured free-energy changes associated with point mutations. Moreover, differently from other structure-based models, our method leaves a residual degree of frustration, which is known to be present in protein molecules.

  7. Species-Dependent Ensembles of Conserved Conformational States Define the Hsp90 Chaperone ATPase Cycle

    PubMed Central

    Southworth, Daniel R.; Agard, David A.

    2008-01-01

    Summary The molecular chaperone Heat Shock Protein 90 (Hsp90) is required for the folding and activation of numerous essential signaling proteins. Hsp90 is generally thought to transition between an open, apo and a closed, ‘ATP’ conformation in response to nucleotide. Here, 3D single particle reconstructions of E. coli and yeast Hsp90 homologs establish the existence of two distinct nucleotide-stabilized conformations (ATP, ADP) in addition to an apo extended state, supporting previous structural work. However, single particle matching methods reveal that, rather than being irreversibly determined by nucleotide, a species-dependent dynamic conformational equilibrium exists between states. Using crosslinking methods we trap transient nucleotide-specific states of yeast and human Hsp90 and establish that the apo, ATP and ADP states are universal. These data support a conserved three-state chaperone cycle where the conformational equilibrium varies between species, implicating evolutionary tuning to meet the particular client protein and metabolic environment of an organism. PMID:19061638

  8. New Conformational State of NHERF1-CXCR2 Signaling Complex Captured by Crystal Lattice Trapping

    PubMed Central

    Jiang, Yuanyuan; Lu, Guorong; Trescott, Laura R.; Hou, Yuning; Guan, Xiaoqing; Wang, Shuo; Stamenkovich, Angelique; Brunzelle, Joseph; Sirinupong, Nualpun; Li, Chunying; Yang, Zhe

    2013-01-01

    NHERF1 is a PDZ adaptor protein that scaffolds the assembly of diverse signaling complexes and has been implicated in many cancers. However, little is known about the mechanism responsible for its scaffolding promiscuity or its ability to bind to multiple targets. Computational studies have indicated that PDZ promiscuity may be attributed to its conformational dynamics, but experimental evidence for this relationship remains very limited. Here we examine the conformational flexibility of the NHERF1 PDZ1 domain using crystal lattice trapping via solving PDZ1 structure of a new crystal form. The structure, together with prior PDZ1 structures of a different space group, reveals that 4 of 11 ligand-interacting residues undergo significant crystal packing-induced structural changes. Most of these residues correspond to the residues involved in allosteric transition when a peptide ligand binds. In addition, a subtle difference in ligand conformations causes the same peptide to bind in slightly different modes in different crystal forms. These findings indicate that substantial structural flexibility is present in the PDZ1 peptide-binding pocket, and the structural substate trapped in the present crystal form can be utilized to represent the conformational space accessible to the protein. Such knowledge will be critical for drug design against the NHERF1 PDZ1 domain, highlighting the continued need for experimentally determined PDZ1-ligand complexes. PMID:24339979

  9. Conformational changes of ?2-human glycoprotein I and lipid order in lipid-protein complexes.

    PubMed

    Paolorossi, Mariana; Montich, Guillermo G

    2011-09-01

    We studied the conformation of ?2-human glycoprotein (?2GPI) in solution and bound to the anionic lipids palmitoyl oleoyl phosphatidylglycerol (POPG), dimiristoyl phosphatidylglycerol (DMPG) and dipalmitoyl phosphatidylglycerol (DPPG) as a function of the temperature. We used the infrared amide I' band to study the protein conformation, and the position of the antisymmetric stretching band of the methylene groups in the lipid hydrocarbon chains to study the lipid order. Lipid-protein complexes were studied in media of low and high ionic strengths. In solution, ?2GPI displayed a conformational pre-transition in the range 47-50°C, characterized by a shift in the band of ? secondary structure, previous to the main unfolding at 64°C. When the protein was bound to the anionic lipid membranes at 25°C, a similar shift as in the pre-transition in solution was observed, together with an increase in the band corresponding to ?-helix secondary structure. Lipid-protein complexes formed large aggregates within the temperature range 10?60°C. At temperatures above the protein unfolding, the complexes were disrupted to yield vesicles with bound protein. This finding indicated that the native fold was required for the formation of the lipid-protein aggregates. Cycles of heating and cooling showed hysteresis in the formation of aggregates. PMID:21600190

  10. ATP Alone Triggers the Outward Facing Conformation of the Maltose ATP-binding Cassette Transporter*

    PubMed Central

    Bao, Huan; Duong, Franck

    2013-01-01

    The maltose transporter MalFGK2 is a study prototype for ABC importers. During catalysis, the MalFG membrane domain alternates between inward and outward facing conformations when the MalK dimer closes and hydrolyzes ATP. Because a rapid ATP hydrolysis depends on MalE and maltose, it has been proposed that closed liganded MalE facilitates the transition to the outward facing conformation. Here we find that, in contrast to the expected, ATP is sufficient for the closure of MalK and for the conversion of MalFG to the outward facing state. The outward facing transporter binds MalE with nanomolar affinity, yet neither MalE nor maltose is necessary or facilitates the transition. Thus, the rapid hydrolysis of ATP observed in the presence of MalE and maltose is not because closed liganded MalE accelerates the formation of the outward facing conformation. These findings have fundamental implications for the description of the transport reaction. PMID:23243313

  11. The Solubilization of Model Alzheimer Tangles: Reversing the ?-Sheet Conformation Induced by Aluminum with Silicates

    NASA Astrophysics Data System (ADS)

    Fasman, Gerald D.; Moore, Cathy D.

    1994-11-01

    Neurofibrillary tangles are one of two lesions found in the brain of Alzheimer disease victims. With synthetic peptide fragments of human neurofilament NF-M17 (Glu-Glu-Lys-Gly-Lys-Ser-Pro-Val-Pro-Lys-Ser-Pro-Val-Glu-Glu-Lys-Gly, phosphorylated and unphosphorylated), CD studies were done to examine the effect of sodium orthosilicate on the conformational state produced by Al3+ on fragments of neuronal proteins. Previous studies had shown a conformational transition from ?-helix and random to ?-pleated sheet upon addition of Al3+ to both phosphorylated and unphosphorylated peptides. If sufficient quantities of Al3+ are added, the peptide precipitates from solution. The ability to reverse or slow the progression of aggregation was examined. Al3+ binding was reversed with 1-2 molar equivalents of sodium orthosilicate (with respect to Al3+), altering the conformation from ?-sheet to random coil and resulting in a CD spectrum similar to that of the initial peptide. The tight binding of the SiO4-_4 with the Al3+ provides the mechanism for this transition. These results provide additional information toward understanding the role of aluminum in the Alzheimer diseased brain and suggest the investigation of the possible use of silicates as a therapeutic agent.

  12. Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution.

    PubMed

    Hernández, Griselda; Anderson, Janet S; LeMaster, David M

    2012-04-01

    The acute sensitivity to conformation exhibited by amide hydrogen exchange reactivity provides a valuable test for the physical accuracy of model ensembles developed to represent the Boltzmann distribution of the protein native state. A number of molecular dynamics studies of ubiquitin have predicted a well-populated transition in the tight turn immediately preceding the primary site of proteasome-directed polyubiquitylation Lys 48. Amide exchange reactivity analysis demonstrates that this transition is 10(3)-fold rarer than these predictions. More strikingly, for the most populated novel conformational basin predicted from a recent 1 ms MD simulation of bovine pancreatic trypsin inhibitor (at 13% of total), experimental hydrogen exchange data indicates a population below 10(-6). The most sophisticated efforts to directly incorporate experimental constraints into the derivation of model protein ensembles have been applied to ubiquitin, as illustrated by three recently deposited studies (PDB codes 2NR2, 2K39 and 2KOX2K392KOX). Utilizing the extensive set of experimental NOE constraints, each of these three ensembles yields a modestly more accurate prediction of the exchange rates for the highly exposed amides than does a standard unconstrained molecular simulation. However, for the less frequently exposed amide hydrogens, the 2NR2 ensemble offers no improvement in rate predictions as compared to the unconstrained MD ensemble. The other two NMR-constrained ensembles performed markedly worse, either underestimating (2KOX) or overestimating (2K39) the extent of conformational diversity. PMID:22425325

  13. Pattern synthesis for a conformal wing array

    Microsoft Academic Search

    Hans Steyskal; Hanscom AFB

    2002-01-01

    Future aircraft may utilize the large aerodynamic areas of the wings also for electrodynamics by structurally embedding conformal phased array antennas. We explore this concept with a computer model for a line array wrapped around a wing. The model uses a realistic wing profile and array element patterns which include the effects of mutual coupling and the local radius of

  14. Measurement Processes in Conformity Assessment Systems

    Microsoft Academic Search

    Roman Aleksander Tabisz

    A key role of metrology in the realization of the concept of sustainable development of the regions and countries of the world, is underlined. In particular, are those developing regions\\/countries and those in the process of an economical transformation in their economic systems. The most important influence of the measurement process validation in all kinds of conformity assessment systems, is

  15. Brain Surface Conformal Parameterization with Algebraic Functions

    E-print Network

    Wang, Yalin

    Brain Surface Conformal Parameterization with Algebraic Functions Yalin Wang1,2 , Xianfeng Gu3 a brain surface to a multi-hole disk. The re- sulting parameterizations do not have any singularities of anatomical surfaces in MRI scans of the brain, in- cluding the hippocampi and the cerebral cortices

  16. Raman characterization of polyaniline induced conformational changes

    Microsoft Academic Search

    J. E. Pereira da Silva; S. I. Córdoba de Torresi; D. L. A. de Faria; M. L. A. Temperini

    1999-01-01

    Conformational changes induced by temperature and secondary doping process, were followed by Raman resonance spectroscopy and ESR measurements. Raman results give complementary data about the secondary doping process showing that together with the structural change of the polymeric chains, there is also a chemical transformation of quinoid segments into scmiquinoid units. When the temperature is raised, changes in Raman spectra

  17. G Protein-Coupled Receptors: Conformational ``Gatekeepers''

    E-print Network

    Goddard III, William A.

    CHAPTER 11 G Protein-Coupled Receptors: Conformational ``Gatekeepers'' of Transmembrane Signal of different proteins that enable and drive the amazing plethora of functions necessary for growth, survival) or the environment (e.g. photons, tastants, etc.). Cellular signaling proteins have evolved to sense this diverse set

  18. A nonconforming multigrid method using conforming subspaces

    NASA Technical Reports Server (NTRS)

    Lee, Chang Ock

    1993-01-01

    For second-order elliptic boundary value problems, we develop a nonconforming multigrid method using the coarser-grid correction on the conforming finite element subspaces. The convergence proof with an arbitrary number of smoothing steps for nu-cycle is presented.

  19. Synthesis of Conformal Arrays With Optimized Polarization

    Microsoft Academic Search

    Christof Dohmen; Johann W. Odendaal; Johan Joubert

    2007-01-01

    Adaptive array theory is applied to a conformal antenna array to synthesize a main beam with optimized polarization employing dual polarized patch antennas as radiators. The required polarization in the main beam region of the array is realized by combining the weighted individual feeding ports of the patch antennas before the beam forming optimization is performed. This significantly reduces the

  20. Conformational order in aggregates of conjugated polymers.

    PubMed

    Jackson, Nicholas E; Kohlstedt, Kevin L; Savoie, Brett M; Olvera de la Cruz, Monica; Schatz, George C; Chen, Lin X; Ratner, Mark A

    2015-05-20

    With the abundant variety and increasing chemical complexity of conjugated polymers proliferating the field of organic semiconductors, it has become increasingly important to correlate the polymer molecular structure with its mesoscale conformational and morphological attributes. For instance, it is unknown which combinations of chemical moieties and periodicities predictably produce mesoscale ordering. Interestingly, not all ordered morphologies result in efficient devices. In this work we have parametrized accurate classical force-fields and used these to compute the conformational and aggregation characteristics of single strands of common conjugated polymers. Molecular dynamics trajectories are shown to reproduce experimentally observed polymeric ordering, concluding that efficient organic photovoltaic devices span a range of polymer conformational classes, and suggesting that the solution-phase morphologies have far-reaching effects. Encouragingly, these simulations indicate that despite the wide-range of conformational classes present in successful devices, local molecular ordering, and not long-range crystallinity, appears to be the necessary requirement for efficient devices. Finally, we examine what makes a "good" solvent for conjugated polymers, concluding that dispersive ?-electron solvent-polymer interactions, and not the electrostatic potential of the backbone interacting with the solvent, are what primarily determine a polymer's solubility in a particular solvent, and consequently its morphological characteristics. PMID:25920989

  1. Discrete conformal mappings via circle patterns

    Microsoft Academic Search

    Liliya Kharevych; Boris Springborn; Peter Schröder

    2006-01-01

    We introduce a novel method for the construction of discrete conformal mappings from surface meshes of arbitrary topology to the plane. Our approach is based on circle patterns, that is, arrangements of circles—one for each face—with prescribed intersection angles. Given these angles, the circle radii follow as the unique minimizer of a convex energy. The method supports very flexible boundary

  2. An integral equation method in conformal mapping

    Microsoft Academic Search

    George T. Symm

    1966-01-01

    This paper describes an integral equation method for computing the conformal mapping of a given simply-connected domain onto the interior of the unit circle. Simple error estimates are available when the given domain possesses symmetry, and results are presented for a number of trial problems of this form.

  3. Conformal mapping methods for interfacial dynamics

    E-print Network

    Martin Z. Bazant; Darren Crowdy

    2004-09-17

    The article provides a pedagogical review aimed at graduate students in materials science, physics, and applied mathematics, focusing on recent developments in the subject. Following a brief summary of concepts from complex analysis, the article begins with an overview of continuous conformal-map dynamics. This includes problems of interfacial motion driven by harmonic fields (such as viscous fingering and void electromigration), bi-harmonic fields (such as viscous sintering and elastic pore evolution), and non-harmonic, conformally invariant fields (such as growth by advection-diffusion and electro-deposition). The second part of the article is devoted to iterated conformal maps for analogous problems in stochastic interfacial dynamics (such as diffusion-limited aggregation, dielectric breakdown, brittle fracture, and advection-diffusion-limited aggregation). The third part notes that all of these models can be extended to curved surfaces by an auxilliary conformal mapping from the complex plane, such as stereographic projection to a sphere. The article concludes with an outlook for further research.

  4. Conformational Variability of Benzamidinium Based Inhibitors

    PubMed Central

    Li, Xue; He, Xiao; Wang, Bing; Merz, Kenneth

    2009-01-01

    Determining the structure of a small molecule bound to a biological receptor (e.g., a protein implicated in a disease state) is a necessary step in structure-based drug design. The preferred conformation of a small molecule can change when bound to a protein, and a detailed knowledge of the preferred conformation(s) of a bound ligand can help in optimizing the affinity of a molecule for its receptor. However, the quality of a protein/ligand complex determined using X-ray crystallography is dependent on the size of the protein, crystal quality and the realized resolution. The energy restraints used in traditional X-ray refinement procedures typically use “reduced” (i.e., neglect of electrostatics and dispersion interactions) Engh and Huber force field models that, while quite suitable for modeling proteins often are less suitable for small molecule structures due to a lack of validated parameters. Through the use of ab initio QM/MM based X-ray refinement procedures this shortcoming can be overcome especially in the active site or binding site of a small molecule inhibitor. Herein, we demonstrate that ab initio QM/MM refinement of an inhibitor/protein complex provides insights into the binding of small molecules beyond what is available using more traditional refinement protocols. In particular, QM/MM refinement studies of benzamidinium derivatives show variable conformational preferences depending on the refinement protocol used and the nature of the active site region. PMID:19435349

  5. Conformational properties of polymers in anisotropic environments

    E-print Network

    K. Haydukivska; V. Blavatska

    2014-07-11

    We analyze the conformational properties of polymer macromolecules in solutions in presence of extended structural obstacles of (fractal) dimension $\\varepsilon_d$ causing the anisotropy of environment. Applying the pruned-enriched Rosenbluth method (PERM), we obtain numerical estimates for scaling exponents and universal shape parameters of polymers in such environments for a wide range $0parallel and perpendicular to the extended defects.

  6. Multiple Sequence Alignment by Conformational Space Annealing

    Microsoft Academic Search

    Keehyoung Joo; Jinwoo Lee; Ilsoo Kim; Sung Jong Lee; Jooyoung Lee

    2008-01-01

    We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA databases, the 82 families from the BAliBASE reference

  7. PERSPECTIVES Chromatin Conformation of Yeast Centromeres

    E-print Network

    PERSPECTIVES Chromatin Conformation of Yeast Centromeres KERRY S. BLOOM, ENRIQUE AMAYA, JOHN CARBON The centromere region of Saccharomyces cerevisiae chromosome III has been replaced by various DNA fragments from the centromere regions of yeast chromosomes III and Xl. A 289-base pair centromere (CEN3) sequence can stabilize

  8. Conformally flat polytropes for anisotropic matter

    E-print Network

    L. Herrera; A. Di Prisco; W. Barreto; J. Ospino

    2014-11-05

    We analyze in detail conformally flat spherically symmetric fluid distributions, satisfying a polytropic equation of state. Among the two possible families of relativistic polytropes, only one contains models which satisfy all the required physical conditions. The ensuing configurations are necessarily anisotropic and show interesting physical properties. Prospective applications of the presented models to the study of super-Chandrasekhar white dwarfs, are discussed.

  9. Recent Applications of Conformal Geometric Anthony Lasenby

    E-print Network

    Cambridge, University of

    to Euclidean geometry. We also assume that the reader is familiar with the extension of this to non-Euclidean in the conformal representation of Euclidean geometry introduced by Hestenes [1]), we will see that covariance techniques and notation can be used seamlessly in all of spherical, hyperbolic and Euclidean geometry, has

  10. de Sitter entropy from conformal field theory

    Microsoft Academic Search

    Daniel Kabat; Gilad Lifschytz

    2002-01-01

    We propose that the entropy of de Sitter space can be identified with the mutual entropy of a dual conformal field theory. We argue that unitary time evolution in de Sitter space restricts the total number of excited degrees of freedom to be bounded by the de Sitter entropy, and we give a CFT interpretation of this restriction. We also

  11. Extreme nesting in the conformal loop ensemble

    E-print Network

    Jason Miller; Samuel S. Watson; David B. Wilson

    2014-12-21

    The conformal loop ensemble CLE$_\\kappa$ with parameter $8/3 compute the almost-sure Hausdorff dimension of the set of points $z$ for which the number of CLE loops surrounding the disk of radius $\\varepsilon$ centered at $z$ has asymptotic growth $\

  12. Surveillance and conformity in competitive youth swimming

    Microsoft Academic Search

    Melanie Lang

    2010-01-01

    Underpinned by a Foucauldian analysis of sporting practices, this paper identifies the disciplinary mechanism of surveillance at work in competitive youth swimming. It highlights the ways in which swimmers and their coaches are subject to and apply this mechanism to produce embodied conformity to normative behaviour and obedient, docile bodies. The data were drawn from a wider ethnographic study of

  13. Lobachevsky geometry of (super)conformal mechanics

    E-print Network

    Tigran Hakobyan; Armen Nersessian

    2008-03-15

    We give a simple geometric explanation for the similarity transformation mapping one-dimensional conformal mechanics to free-particle system. Namely, we show that this transformation corresponds to the inversion of the Klein model of Lobachevsky space (non-compact complex projective plane). We also extend this picture to the N=2k superconformal mechanics described in terms of Lobachevsky superspace.

  14. Logarithmic correlators in nonrelativistic conformal field theory

    SciTech Connect

    Hosseiny, Ali; Rouhani, Shahin [Department of Physics, Sharif University of Technology, Tehran 11165-9161 (Iran, Islamic Republic of)

    2010-10-15

    We show how logarithmic terms may arise in the correlators of fields which belong to the representation of the Schroedinger-Virasoro algebra or the affine Galilean conformal algebra (GCA). We show that in GCA, only scaling operator can have a Jordan form and rapidity cannot. We observe that in both algebras, logarithmic dependence appears along the time direction alone.

  15. Surveillance and Conformity in Competitive Youth Swimming

    ERIC Educational Resources Information Center

    Lang, Melanie

    2010-01-01

    Underpinned by a Foucauldian analysis of sporting practices, this paper identifies the disciplinary mechanism of surveillance at work in competitive youth swimming. It highlights the ways in which swimmers and their coaches are subject to and apply this mechanism to produce embodied conformity to normative behaviour and obedient, docile bodies.…

  16. Finite Size Scaling and Conformal Curves

    E-print Network

    M. A. Rajabpour; S. Moghimi-Araghi

    2005-11-06

    In this letter we investigate the finite size scaling effect on SLE($\\kappa,\\rho$) and boundary conformal field theories and find the effect of fixing some boundary conditions on the free energy per length of SLE($\\kappa,\\rho$). As an application, we will derive the entanglement entropy of quantum systems in critical regime in presence of boundary operators.

  17. Submaximal conformal symmetry superalgebras for Lorentzian manifolds of low dimension

    E-print Network

    Paul de Medeiros

    2014-06-19

    We consider a class of smooth oriented Lorentzian manifolds in dimensions three and four which admit a nowhere vanishing conformal Killing vector and a closed two-form that is invariant under the Lie algebra of conformal Killing vectors. The invariant two-form is constrained in a particular way by the conformal geometry of the manifold. In three dimensions, the conformal Killing vector must be everywhere causal (or null if the invariant two-form vanishes identically). In four dimensions, the conformal Killing vector must be everywhere null and the invariant two-form vanishes identically if the geometry is everywhere of Petrov type N or O. To the conformal class of any such geometry, it is possible to assign a particular Lie superalgebra structure, called a conformal symmetry superalgebra. The even part of this superalgebra contains conformal Killing vectors and constant R-symmetries while the odd part contains (charged) twistor spinors. The largest possible dimension of a conformal symmetry superalgebra is realised only for geometries that are locally conformally flat. We determine precisely which non-trivial conformal classes of metrics admit a conformal symmetry superalgebra with the next largest possible dimension, and compute all the associated submaximal conformal symmetry superalgebras. In four dimensions, we also compute symmetry superalgebras for a class of Ricci-flat Lorentzian geometries not of Petrov type N or O which admit a null Killing vector.

  18. The investigation on the pressure-induced phase transition in linoleic acid by in situ Raman spectroscopy.

    PubMed

    Ya, Fan; Jing, Zhou; Da-Peng, Xu

    2014-08-14

    With diamond anvil cell as a high-pressure apparatus, the in situ Raman spectra of linoleic acid from normal pressure to 1.29 GPa were measured to investigate the effect of pressure on the structural changes. In the pressure ranges of 0.07-0.12 GPa and 0.31-0.53 GPa, the significant changes in Raman spectra show that linoleic acid undergoes two pressure-induced phase transitions. Spectral analysis indicates that the polymethylene chain of linoleic acid molecule transforms from the disordered gauche conformation to the ordered trans conformation in the range of 0.07-0.12 GPa. And the polymethylene chain of linoleic acid molecule remains the ordered trans conformation whereas the conformation of the olefin group significantly changes and the degree of conformational order increases in the range of 0.31-0.53 GPa. The pressure-induced phase transitions in linoleic acid are reversible. PMID:24727173

  19. DNA fragment conformations in adducts with Kiteplatin.

    PubMed

    Margiotta, Nicola; Petruzzella, Emanuele; Platts, James A; Mutter, Shaun T; Deeth, Robert J; Ranaldo, Rosa; Papadia, Paride; Marzilli, Patricia A; Marzilli, Luigi G; Hoeschele, James D; Natile, Giovanni

    2015-02-28

    The anticancer activity of cisplatin is triggered by its formation of intrastrand adducts involving adjacent G residues of DNA. To obtain information on the different conformers that can be formed, carrier ligands such as 2,2'-bipiperidine, which provide large steric bulk near the platinum coordination plane and decrease the dynamic motion about the Pt-N7 bonds, were introduced ("retro-modelling" approach). In the present study we investigate the effect of cis-1,4-diaminocyclohexane (cis-1,4-DACH) on the formation, stability, and stereochemistry of (cis-1,4-DACH)Pt(ss-oligo) adducts (ss-oligo = d(GpG) with 3'- and/or 5'-substituents). Interesting features of this ligand, absent in previous retro-modelling studies, include the large bite angle (expected to impede the ease of interconversion between possible conformers), the presence of two protons on each nitrogen (a characteristic associated with antitumor activity), and the absence of chiral centres. The use of cis-1,4-DACH has made it possible to detect different conformers in a system containing a primary diamine carrier ligand associated with anticancer activity and to confirm the previous hypothesis that the coexistence of different conformers established in studies of retro models having relatively bulky ligands is not an artefact resulting from carrier-ligand bulk. Moreover, the data for the (cis-1,4-DACH)Pt(d(GpG)) and (cis-1,4-DACH)Pt(d(GGTTT)) adducts indicate that at a temperature close to the physiological one (40 °C) HH1 and ?HT1 conformers are present in comparable amounts. In contrast, at low temperature (close to 0 °C) the equilibrium shifts dramatically toward the more stable HH1 conformer (for the (cis-1,4-DACH)Pt(d(TGGT)) adduct the HH1 conformer is always dominant, even at high temperature). Notably, (cis-1,4-DACH)PtCl2 (Kiteplatin) has been recently reinvestigated and found to be particularly active against colorectal cancer (including oxaliplatin-resistant phenotypes). PMID:25144401

  20. Excitonic splitting and vibronic coupling in 1,2-diphenoxyethane: Conformation-specific effects in the weak coupling limit

    NASA Astrophysics Data System (ADS)

    Buchanan, Evan G.; Walsh, Patrick S.; Plusquellic, David F.; Zwier, Timothy S.

    2013-05-01

    Vibrationally and rotationally resolved electronic spectra of 1,2-diphenoxyethane (C6H5-O-CH2-CH2-O-C6H5, DPOE) are reported for the isolated molecule under jet-cooled conditions. The spectra demonstrate that the two excited surfaces are within a few cm-1 of one another over significant regions of the torsional potential energy surfaces that modulate the position and orientation of the two aromatic rings with respect to one another. Two-color resonant two-photon ionization (2C-R2PI) and laser-induced fluorescence excitation spectra were recorded in the near-ultraviolet in the region of the close-lying S0-S1 and S0-S2 states (36 400-36 750 cm-1). In previous work, double resonance spectroscopy in the ultraviolet and alkyl CH stretch regions of the infrared was used to identify and assign transitions to two conformational isomers differing primarily in the central C-C dihedral angle, a tgt conformation with C2 symmetry and a ttt conformation with C2h symmetry [E. G. Buchanan, E. L. Sibert, and T. S. Zwier, J. Phys. Chem. A 117, 2800 (2013)], 10.1021/jp400691a. Comparison of 2C-R2PI spectra recorded in the m/z 214 (all 12C) and m/z 215 (one 13C) mass channels demonstrate the close proximity of the S1 and S2 excited states for both conformations, with an upper bound of 4 cm-1 between them. High resolution spectra of the origin band of the tgt conformer reveal it to consist of two transitions at 36 422.91 and 36 423.93 cm-1, with transition dipole moments perpendicular to one another. These are assigned to the S0-S1 and S0-S2 origin transitions with excited states of A and B symmetry, respectively, and an excitonic splitting of only 1.02 cm-1. The excited state rotational constants and transition dipole coupling model directions prove that the electronic excitation is delocalized over the two rings. The ttt conformer has only one dipole-allowed electronic transition (Ag?Bu) giving rise to a pure b-type band at 36 508.77 cm-1. Here, the asymmetry induced by a single 13C atom in one of the rings is sufficient to localize the electronic excitation in one or the other ring. Dispersed fluorescence (DFL) spectra are used to provide assignments for all vibronic structure in the first 200 cm-1of both conformers. In the tgt conformer, both "a" and "b" symmetry fundamentals are observed, consistent with extensive vibronic coupling between the two dipole-allowed, nearly degenerate excited states. In the ttt conformer, the lowest frequency vibronic transition located 46 cm-1 above the Bu origin is assigned to a bu fundamental (labeled bar R) built off the dipole-forbidden Ag state origin. The DFL spectrum of the Ag(bar R^1) level contains strong transitions to v?(bar R) = 0, 1, and 2, seemingly at odds with vibronic coupling models. Studies of the DFL spectrum of this band as a function of distance from the nozzle reveal that much of the intensity in v? = 1 arises from collisions of DPOE while in the excited state Ag(vb' = 1) level with He, producing Bu(bar R = 1) levels with large collision cross section. The remaining intensity in the fundamental at large x/D is ascribed to emission from the 13C isotopomer, for which this emission is dipole-allowed.