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1

Solvent dependence of dynamic transitions in protein solutions.  

PubMed

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 D(2)O, 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 D(2)O, 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

Réat, V; Dunn, R; Ferrand, M; Finney, J L; Daniel, R M; Smith, J C

2000-08-29

2

Cranklike conformational transitions in polyethylene  

NASA Astrophysics Data System (ADS)

Molecular dynamics simulations of a variety of polymeric systems provide the evidence for two different kinds of conformational transitions: independent single bond transitions and cranklike transitions (or correlated bond transitions). While single bond transitions can be rationalized according to standard theories of activated processes controlled by the saddle point crossing, a more complex description is required for the other type of transitions. In a recent work devoted to the analysis of the simplified chain model with three rotors [B. Nigro and G. J. Moro, J. Phys. Chem. B 106, 7365 (2002)], a theory has been proposed for cranklike transitions represented as a kinetic process between equilibrium states differing by two torsional angles (i.e., two bond transitions). Moreover their rate coefficients were estimated on the basis of a local expansion about the bifurcation of the separatrices departing from the potential function maximum. In the present work the same theory is applied to a model for long alkyl chains in solution, in order to rationalize the behavior of cranklike transitions in polyethylene and to recognize the molecular features controlling them. We obtain probabilities of occurrence of cranklike transitions in substantial agreement with simulation results. Furthermore, the theory is capable of explaining the dependence of the rate on the separation between the two reactive bonds, as well as the dependence on the conformational state of the starting configuration. In particular, selection rules for next-to-nearest neighbor transitions are recovered from the shape of the separatrices and the location of the corresponding bifurcations.

Nigro, B.; di Stefano, D.; Rassu, A.; Moro, G. J.

2004-09-01

3

Mechanism of the conformational transition of melittin.  

PubMed

It is known that, while melittin at micromolar concentrations is unfolded under conditions of low ionic strength at neutral pH, it adopts a tetrameric alpha-helical structure under conditions of high ionic strength, at alkaline pH, or at high peptide concentrations. To understand the mechanism of the conformational transition of melittin, we examined in detail the conformation of melittin under various conditions by far-UV circular dichroism at 20 degrees C. We found that the helical conformation is also stabilized by strong acids such as perchloric acid. The effects of various acids varied largely and were similar to those of the corresponding salts, indicating that the anions are responsible for the salt- or acid-induced transitions. The order of effectiveness of various monovalent anions was consistent with the electroselectivity series of anions toward anion-exchange resins, indicating that the anion binding is responsible for the salt- or acid-induced transitions. From the NaCl-, HCl-, and alkaline pH-induced conformational transitions, we constructed a phase diagram of the anion- and pH-dependent conformational transition. The phase diagram was similar in shape to that of acid-denatured apomyoglobin [Goto, Y., & Fink, A.L. (1990) J. Mol. Biol. 214, 803-805] or that of the amphiphilic Lys, Leu model polypeptide [Goto, Y., & Aimoto, S. (1991) J. Mol. Biol. 218, 387-396], suggesting a common mechanism of the conformational transition. The anion-, pH-, and peptide concentration-dependent conformational transition of melittin was explained on the basis of an equation in which the conformational transition is linked to proton and anion binding to the titratable groups. PMID:1731930

Goto, Y; Hagihara, Y

1992-01-28

4

Conformational transitions of a weak polyampholyte.  

PubMed

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

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

2014-10-01

5

Conformational transitions of a weak polyampholyte  

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

6

Transitions to catalytically inactive conformations in EGFR kinase.  

PubMed

The epidermal growth factor receptor (EGFR) is a key protein in cellular signaling, and its kinase domain (EGFR kinase) is an intensely pursued target of small-molecule drugs. Although both catalytically active and inactive conformations of EGFR kinase have been resolved crystallographically, experimental characterization of the transitions between these conformations remains difficult. Using unbiased, all-atom molecular dynamics simulations, we observed EGFR kinase spontaneously transition from the active to the so-called "Src-like inactive" conformation by way of two sets of intermediate conformations: One corresponds to a previously identified locally disordered state and the other to previously undescribed "extended" conformations, marked by the opening of the ATP-binding site between the two lobes of the kinase domain. We also simulated the protonation-dependent transition of EGFR kinase to another ["Asp-Phe-Gly-out" ("DFG-out")] inactive conformation and observed similar intermediate conformations. A key element observed in the simulated transitions is local unfolding, or "cracking," which supports a prediction of energy landscape theory. We used hydrogen-deuterium (H/D) exchange measurements to corroborate our simulations and found that the simulated intermediate conformations correlate better with the H/D exchange data than existing active or inactive EGFR kinase crystal structures. The intermediate conformations revealed by our simulations of the transition process differ significantly from the existing crystal structures and may provide unique possibilities for structure-based drug discovery. PMID:23576739

Shan, Yibing; Arkhipov, Anton; Kim, Eric T; Pan, Albert C; Shaw, David E

2013-04-30

7

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA  

Microsoft Academic Search

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible.

Dina Zhabinskaya; Craig J. Benham

2012-01-01

8

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

E-print Network

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

de Groot, Bert

9

Atomistic simulations of the MS2 coat protein conformational transition  

NASA Astrophysics Data System (ADS)

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.

Perkett, Matthew; Pontiggia, Francesco; Hagan, Michael

2012-02-01

10

Water-Peptide Dynamics during Conformational Transitions Dmitry Nerukh*,  

E-print Network

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

Nerukh, Dmitry

11

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins  

NASA Astrophysics Data System (ADS)

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-?s canonical MD simulation failed to sample such a rare event.

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-01

12

Maximum Flux Transition Paths of Conformational Change  

PubMed Central

Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space. The computational task becomes that of computing the “center” of such a cluster. A good way to define the center employs the concept of a committor, whose value at a point in collective variable space is the probability that a trajectory at that point will reach B before A. The committor “foliates” the transition region into a set of isocommittors. The maximum flux transition path is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories. This path is based on the same principle as the minimum resistance path of Berkowitz et al (1983), but it has two advantages: (i) the path is invariant with respect to a change of coordinates in collective variable space and (ii) the differential equations that define the path are simpler. It is argued that such a path is nearer to an ideal path than others that have been proposed with the possible exception of the finite-temperature string method path. To make the calculation tractable, three approximations are introduced, yielding a path that is the solution of a nonsingular two-point boundary-value problem. For such a problem, one can construct a simple and robust algorithm. One such algorithm and its performance is discussed. PMID:20890401

Zhao, Ruijun; Shen, Juanfang; Skeel, Robert D.

2010-01-01

13

de Sitter transitivity, conformal transformations and conservation laws  

E-print Network

Minkowski spacetime is transitive under ordinary translations, a transformation that do not have matrix representations. The de Sitter spacetime, on the other hand, is transitive under a combination of translations and proper conformal transformations, which do have a matrix representation. Such matrix, however, is not by itself a de Sitter generator: it gives rise to a conformal re-scaling of the metric, a transformation not belonging to the de Sitter group, and in general not associated with diffeomorphisms in spacetime. When dealing with variational principles and Noether's theorem in de Sitter spacetime, therefore, it turns out necessary to regularise the transformations in order to eliminate the conformal re-scaling of the metric.

J. G. Pereira; A. C. Sampson; L. L. Savi

2013-12-11

14

Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations  

PubMed Central

The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on ? -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

2011-01-01

15

Conformational Transition of H-shaped Branched Polymers  

E-print Network

We report dynamic Monte Carlo simulation on conformational transition of H-shaped branched polymers by varying main chain (backbone) and side chain (branch) length. H-shaped polymers in comparison with equivalent linear polymers exhibit a depression of theta temperature accompanying with smaller chain dimensions. We observed that the effect of branches on backbone dimension is more pronounced than the reverse, and is attributed to the conformational heterogeneity prevails within the molecule. With increase in branch length, backbone is slightly stretched out in coil and globule state. However, in the pre-collapsed (cf. crumpled globule) state, backbone size decreases with the increase of branch length. We attribute this non-monotonic behavior as the interplay between excluded volume interaction and intra-chain bead-bead attractive interaction during collapse transition. Structural analysis reveals that the inherent conformational heterogeneity promotes the formation of a collapsed structure with segregated backbone and branch units (resembles to 'sandwich' or 'Janus' morphology) rather an evenly distributed structure comprising of all the units. The shape of the collapsed globule becomes more spherical with increasing either backbone or branch length.

Ashok Kumar Dasmahapatra; Venkata Mahanth Sanka

2013-10-15

16

Surface Immobilization of antibody on silk fibroin through conformational transition  

PubMed Central

In recent studies silk fibroin has been explored as a new material platform for biosensors. Based on these developments a procedure for the immobilization of antibodies on silk fibroin substrates was developed as a route to functionalizing these biosensor systems. By controlling the conformational transition of the silk fibroin, a primary antibody was immobilized and enriched at the surface of silk fibroin substrates under mild reaction conditions to maintain antibody function. Compared to chemical crosslinking, the immobilization efficiency in the present approach was increased significantly. This method, achieving high loading of antibody while retaining function, improves the feasibility of silk fibroin as a platform material for biosensor applications. PMID:21382528

Lu, Qiang; Wang, Xiaoqin; Zhu, Hesun; Kaplan, David L.

2011-01-01

17

Efficient generation of feasible pathways for protein conformational transitions.  

PubMed Central

We develop a computationally efficient method to simulate the transition of a protein between two conformations. Our method is based on a coarse-grained elastic network model in which distances between spatially proximal amino acids are interpolated between the values specified by the two end conformations. The computational speed of this method depends strongly on the choice of cutoff distance used to define interactions as measured by the density of entries of the constant linking/contact matrix. To circumvent this problem we introduce the concept of using a cutoff based on a maximum number of nearest neighbors. This generates linking matrices that are both sparse and uniform, hence allowing for efficient computations that are independent of the arbitrariness of cutoff distance choices. Simulation results demonstrate that the method developed here reliably generates feasible intermediate conformations, because our method observes steric constraints and produces monotonic changes in virtual bond and torsion angles. Applications are readily made to large proteins, and we demonstrate our method on lactate dehydrogenase, citrate synthase, and lactoferrin. We also illustrate how this framework can be used to complement experimental techniques that partially observe protein motions. PMID:12202386

Kim, Moon K; Jernigan, Robert L; Chirikjian, Gregory S

2002-01-01

18

Broadband transition between microstrip line and conformal surface plasmon waveguide  

NASA Astrophysics Data System (ADS)

We propose a broadband and high-efficiency transition from a microstrip line to a conformal surface plasmon (CSP) waveguide that is made of an ultrathin corrugated metallic strip, to transform the guide wave into a spoof surface plasmon polariton (SPP) in the microwave region. The transition consists of three parts: a convertor which converts the direction of the electric field from perpendicular to parallel to the strip, a matching area with gradient corrugations and a flaring metallic line to match both the momentum and impedance, and a CSP waveguide to support the SPP waves. A back-to-back transition sample is fabricated using the proposed method. Experimental results of S parameters and near-field distributions verify the excellent performance of the sample to transform guided waves to SPPs and transmit SPP waves in a wide band. The sample exhibits low energy loss when the CSP waveguide is bent or even twisted. The proposed transition may have potential applications in integrating conventional microwave devices with the SPP devices.

Liao, Zhen; Zhao, Jie; Cao Pan, Bai; Shen, Xiao Peng; Cui, Tie Jun

2014-08-01

19

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

PubMed Central

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

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

2013-01-01

20

The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: A TEE-REX Molecular Dynamics Study  

Microsoft Academic Search

SUMMARY We report on an atomistic molecular dynamics simu- lation of the complete conformational transition of Escherichia coli adenylate kinase (ADK) using the re- cently developed TEE-REX algorithm. Two phases characterize the transition pathway of ADK, which folds into the domains CORE and LID and the AMP binding domain AMPbd. Starting from the closed conformation, half-opening of the AMPbd precedes

Marcus B. Kubitzki; Bert L. de Groot

2008-01-01

21

Sequence Recognition of DNA by Protein-Induced Conformational Transitions  

SciTech Connect

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.

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

2010-11-09

22

Conformational transitions of subunit epsilon in ATP synthase from thermophilic Bacillus PS3.  

PubMed

Subunit epsilon of bacterial and chloroplast F(O)F(1)-ATP synthase is responsible for inhibition of ATPase activity. In Bacillus PS3 enzyme, subunit epsilon can adopt two conformations. In the "extended", inhibitory conformation, its two C-terminal alpha-helices are stretched along subunit gamma. In the "contracted", noninhibitory conformation, these helices form a hairpin. The transition of subunit epsilon from an extended to a contracted state was studied in ATP synthase incorporated in Bacillus PS3 membranes at 59 degrees C. Fluorescence energy resonance transfer between fluorophores introduced in the C-terminus of subunit epsilon and in the N-terminus of subunit gamma was used to follow the conformational transition in real time. It was found that ATP induced the conformational transition from the extended to the contracted state (half-maximum transition extent at 140 microM ATP). ADP could neither prevent nor reverse the ATP-induced conformational change, but it did slow it down. Acid residues in the DELSEED region of subunit beta were found to stabilize the extended conformation of epsilon. Binding of ATP directly to epsilon was not essential for the ATP-induced conformational change. The ATP concentration necessary for the half-maximal transition (140 microM) suggests that subunit epsilon probably adopts the extended state and strongly inhibits ATP hydrolysis only when the intracellular ATP level drops significantly below the normal value. PMID:20141757

Feniouk, Boris A; Kato-Yamada, Yasuyuki; Yoshida, Masasuke; Suzuki, Toshiharu

2010-02-01

23

Solvent-dependent photophysical properties of borondipyrromethene dyes in solution  

NASA Astrophysics Data System (ADS)

Four fluorescent dyes derived from 4,4-difluoro-4-bora-3a,4a-diaza- s-indacene (BODIPY) with unusual substituents (chloro, methoxy, and malonate) at the 3,5-positions have been synthesized by a novel nucleophilic substitution reaction of 3,5-dichloroBODIPY. Their solvent-dependent photophysical properties have been investigated by means of UV/Vis absorption, steady-state and time-resolved fluorimetry. For each compound, the fluorescence quantum yield and lifetime are lower in solvents with higher polarity due to an increase in the rate of nonradiative deactivation. The fluorescence rate constants are in the (1.6-2.0) × 10 8 s -1 range. The borondipyrromethene derivatives show small Stokes shifts (between 440 and 490 cm -1) and narrow absorption (FWHM between 710 and 820 cm -1) and emission bands.

Qin, Wenwu; Rohand, Taoufik; Baruah, Mukulesh; Stefan, Alina; der Auweraer, Mark Van; Dehaen, Wim; Boens, Noël

2006-03-01

24

Monte Carlo analysis of conformational transitions in superhelical DNA Hongzhi Sun  

E-print Network

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

Benham, Craig J.

25

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

PubMed Central

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

Yu, Jin; Ha, Taekjip; Schulten, Klaus

2004-01-01

26

Artificial accelerators of the molecular chaperone hsp90 facilitate rate-limiting conformational transitions.  

PubMed

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

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

2014-11-01

27

Conformational transitions in human translin enable nucleic acid binding  

PubMed Central

Translin is a highly conserved RNA- and DNA-binding protein that plays essential roles in eukaryotic cells. Human translin functions as an octamer, but in the octameric crystallographic structure, the residues responsible for nucleic acid binding are not accessible. Moreover, electron microscopy data reveal very different octameric configurations. Consequently, the functional assembly and the mechanism of nucleic acid binding by the protein remain unclear. Here, we present an integrative study combining small-angle X-ray scattering (SAXS), site-directed mutagenesis, biochemical analysis and computational techniques to address these questions. Our data indicate a significant conformational heterogeneity for translin in solution, formed by a lesser-populated compact octameric state resembling the previously solved X-ray structure, and a highly populated open octameric state that had not been previously identified. On the other hand, our SAXS data and computational analyses of translin in complex with the RNA oligonucleotide (GU)12 show that the internal cavity found in the octameric assemblies can accommodate different nucleic acid conformations. According to this model, the nucleic acid binding residues become accessible for binding, which facilitates the entrance of the nucleic acids into the cavity. Our data thus provide a structural basis for the functions that translin performs in RNA metabolism and transport. PMID:23980029

Perez-Cano, Laura; Eliahoo, Elad; Lasker, Keren; Wolfson, Haim J.; Glaser, Fabian; Manor, Haim; Bernado, Pau; Fernandez-Recio, Juan

2013-01-01

28

Molecular Dynamics Simulations of Forced Conformational Transitions in 1,6-Linked Polysaccharides  

PubMed Central

Recent atomic force microscopy stretching measurements of single polysaccharide molecules suggest that their elasticity is governed by force-induced conformational transitions of the pyranose ring. However, the mechanism of these transitions and the mechanics of the pyranose ring are not fully understood. Here we use steered molecular dynamics simulations of the stretching process to unravel the mechanism of forced conformational transitions in 1,6 linked polysaccharides. In contrast to most sugars, 1,6 linked polysaccharides have an extra bond in their inter-residue linkage, C5–C6, around which restricted rotations occur and this additional degree of freedom increases the mechanical complexity of these polymers. By comparing the computational results with the atomic force microscopy data we determine that forced rotations around the C5–C6 bond have a significant and different impact on the elasticity of ?- and ?-linked polysaccharides. ?-linkages of a polysaccharide pustulan force the rotation around the C5–C6 bonds and produce a Hookean-like elasticity but do not affect the conformation of the pyranose rings. However, ?-linkages of dextran induce compound conformational transitions that include simultaneous rotations around the C5–C6 bonds and chair-boat transitions of the pyranose rings. These previously not-recognized transitions are responsible for the characteristic plateau in the force-extension relationship of dextran. PMID:15345528

Lee, Gwangrog; Nowak, Wies?aw; Jaroniec, Justyna; Zhang, Qingmin; Marszalek, Piotr E.

2004-01-01

29

Anomalous conformational transitions in cytochrome C adsorbing to Langmuir-Blodgett films  

NASA Astrophysics Data System (ADS)

Helix to beta conformational transitions in proteins has attracted much attention due to their relevance to fibril formation which is implicated in many neurological diseases. This study reports on unusual conformational transition of cytochrome C adsorbing to hydrophilic surface containing pure cationic lipid and mixed Langmuir-Blodgett films (LB films) of cationic and neutral lipids. Evidence for conformational changes of the protein from its native helical state to beta sheet comes from Circular dichroic spectroscopy (CD spectroscopy). Analysis of these samples using High resolution TEM (HRTEM) shows a typical fibrillar pattern with each strand spacing of about 0.41 nm across which can be attributed to the repeat distance of interdigitated neighboring hydrogen-bonded ribbons in a beta sheet. Changes in contact angles of protein adsorbing to the LB films together with the increased mass uptake of water using quartz crystal microbalance (QCM) confirm the role of positive charges in the conformational transition. Dehydration of the protein resulting from the excess water entrainment in the polar planes of the cationic lipid in hydrophilic surface seems to trigger the refolding of the protein to beta sheet while it retains its native conformation in hydrophobic films. The results suggest that drastic conformational changes in CytC adsorbing to cationic lipids may be of significance in its role as a peripheral membrane protein.

Sankaranarayanan, Kamatchi; Nair, B. U.; Dhathathreyan, A.

2013-05-01

30

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

PubMed

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

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

2014-01-01

31

Dehydration-induced conformational transitions in proteins and their inhibition by stabilizers.  

PubMed Central

Dehydration of proteins results in significant, measurable conformational changes as observed using Fourier-transform infrared spectroscopy and resolution-enhancement techniques. For several proteins these conformational changes are at least partially irreversible, since, upon rehydration, denaturation and aggregation are observed. The presence of certain stabilizers inhibited these dehydration-induced transitions; the native structure was preserved in the dried state and upon reconstitution. Conformational transitions were also observed in a model polypeptide, poly-L-lysine, after lyophilization and were inhibited with the addition of stabilizing cosolutes. The ability of a particular additive to preserve the aqueous structure of dehydrated proteins and poly-L-lysine upon dehydration correlates directly with its ability to preserve the activity of lactate dehydrogenase, a labile enzyme, during drying. PMID:7693001

Prestrelski, S J; Tedeschi, N; Arakawa, T; Carpenter, J F

1993-01-01

32

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

NASA Astrophysics Data System (ADS)

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

Harada, Ryuhei; Kitao, Akio

2013-07-01

33

Conformational Transitions as Determinants of Specificity for the DNA Methyltransferase EcoRI*  

E-print Network

­19275). The direct measurement of the kinetic rate con- stants for DNA bending, intercalation, and base flippingConformational Transitions as Determinants of Specificity for the DNA Methyltransferase Eco of California, Santa Barbara, California 93106-9510 Changes in DNA bending and base flipping in a previously

Reich, Norbert O.

34

The impact of N-terminal phosphorylation on LHCII conformation in state transition  

NASA Astrophysics Data System (ADS)

State transition is an important protection mechanism of plants for maintaining optimal efficiency through redistributing unbalanced excitation energy between photo-system II (PSII) and photosystem I (PSI). This process depends on the reversible phosphorylation/dephosphorylation of the major light-harvesting complex II (LHCII) and its bi-directional migration between PSII and PSI. But it remains unclear how phosphorylation/dephosphorylation modulates the LHCII conformation and further regulates its reversible migration. Here molecular dynamics simulations (MDS) were employed to elucidate the impact of phosphorylation on LHCII conformation. The results indicated that N-terminal phosphorylation loosened LHCII trimer with decreased hydrogen bond (H-bond) interactions and extended the distances between neighboring monomers, which stemmed from the conformational adjustment of each monomer itself. Global conformational change of LHCII monomer started from its stromal Nterminal (including the phosphorylation sites) by enhancing its interaction to lipid membrane and by adjusting the interaction network with surrounded inter-monomer and intra-monomer transmembrane helixes of B, C, and A, and finally triggered the reorientation of transmembrane helixes and transferred the conformational change to luminal side helixes and loops. These results further our understanding in molecular mechanism of LHCII migration during state transition from the phosphorylation-induced microstructural feature of LHCII.

Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lü, Shou-Qin; Long, Mian

2014-06-01

35

Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model  

PubMed Central

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

Jo, Sunhwan; Bahar, Ivet; Roux, Benoit

2014-01-01

36

Finite-Size Conformational Transitions: A Unifying Concept Underlying Chromosome Dynamics  

NASA Astrophysics Data System (ADS)

Investigating average thermodynamic quantities is not sufficient to understand conformational transitions of a finite-size polymer. We propose that such transitions are better described in terms of the probability distribution of some finite-size order parameter, and the evolution of this distribution as a control parameter varies. We demonstrate this claim for the coil-globule transition of a linear polymer and its mapping onto a two-state model. In a biological context, polymer models delineate the physical constraints experienced by the genome at different levels of organization, from DNA to chromatin to chromosome. We apply our finite-size approach to the formation of plectonemes in a DNA segment submitted to an applied torque and the ensuing helix-coil transition that can be numerically observed, with a coexistence of the helix and coil states in a range of parameters. Polymer models are also essential to analyze recent in vivo experiments providing the frequency of pairwise contacts between genomic loci. The probability distribution of these contacts yields quantitative information on the conformational fluctuations of chromosome regions. The changes observed in the shape of the distribution when the cell type or the physiological conditions vary may reveal an epigenetic modulation of the conformational constraints experienced by the chromosomes.

Bertrand, R. Caré; Pascal, Carrivain; Thierry, Forné; Jean-Marc, Victor; Annick, Lesne

2014-10-01

37

Mechanistic picture for conformational transition of a membrane transporter at atomic resolution.  

PubMed

During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods. PMID:24191018

Moradi, Mahmoud; Tajkhorshid, Emad

2013-11-19

38

Mechanistic picture for conformational transition of a membrane transporter at atomic resolution  

PubMed Central

During their transport cycle, ATP-binding cassette (ABC) transporters undergo large-scale conformational changes between inward- and outward-facing states. Using an approach based on designing system-specific reaction coordinates and using nonequilibrium work relations, we have performed extensive all-atom molecular dynamics simulations in the presence of explicit membrane/solvent to sample a large number of mechanistically distinct pathways for the conformational transition of MsbA, a bacterial ABC exporter whose structure has been solved in multiple functional states. The computational approach developed here is based on (i) extensive exploration of system-specific biasing protocols (e.g., using collective variables designed based on available low-resolution crystal structures) and (ii) using nonequilibrium work relations for comparing the relevance of the transition pathways. The most relevant transition pathway identified using this approach involves several distinct stages reflecting the complex nature of the structural changes associated with the function of the protein. The opening of the cytoplasmic gate during the outward- to inward-facing transition of apo MsbA is found to be disfavored when the periplasmic gate is open and facilitated by a twisting motion of the nucleotide-binding domains that involves a dramatic change in their relative orientation. These results highlight the cooperativity between the transmembrane and the nucleotide-binding domains in the conformational transition of ABC exporters. The approach introduced here provides a framework to study large-scale conformational changes of other membrane transporters whose computational investigation at an atomic resolution may not be currently feasible using conventional methods. PMID:24191018

Moradi, Mahmoud; Tajkhorshid, Emad

2013-01-01

39

The discontinuities of conformal transitions and mass spectra of V-QCD  

NASA Astrophysics Data System (ADS)

Zero temperature spectra of mesons and glueballs are analyzed in a class of holographic bottom-up models for QCD in the Veneziano limit, N c ? ?, N f ? ?, with x = N f /N c fixed(V-QCD).The back reaction of flavor on color is fully included. It is found that spectra are discrete and gapped (modulo the pions) in the QCD regime, for x below the critical value x c where the conformal transition takes place. The masses uniformly converge to zero in the walking region due to Miransky scaling. All the ratios of masses asymptote to non-zero constants as and therefore there is no "dilaton" in the spectrum. The S-parameter is computed and found to be of in units of N f N c in the walking regime, while it is always an increasing function of x. This indicates the presence of a subtle discontinuity of correlation functions across the conformal transition at x = x c .

Areán, Daniel; Iatrakis, Ioannis; Järvinen, Matti; Kiritsis, Elias

2013-11-01

40

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

SciTech Connect

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.

Dalgicdir, Cahit; Sensoy, Ozge; Sayar, Mehmet, E-mail: msayar@ku.edu.tr [College of Engineering, Koç University, 34450 Istanbul (Turkey)] [College of Engineering, Koç University, 34450 Istanbul (Turkey); Peter, Christine [Max Planck Institute for Polymer Research, 55128 Mainz (Germany) [Max Planck Institute for Polymer Research, 55128 Mainz (Germany); Department of Chemistry, University of Konstanz, 78547 Konstanz (Germany)

2013-12-21

41

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

DOEpatents

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.

Solberg, Jerome Michael

2012-12-04

42

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores.  

PubMed

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green's function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA via transverse electronic conductance can widen the potential use of graphene-based nanosensors for DNA detection. PMID:25325530

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus

2014-11-01

43

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores  

NASA Astrophysics Data System (ADS)

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green?s function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA via transverse electronic conductance can widen the potential use of graphene-based nanosensors for DNA detection.

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus

2014-11-01

44

How and why do transition dipole moment orientations depend on conformer structure?  

PubMed

A remarkable influence of the orientation of a polar side chain on the direction of the S(1) ? S(0) transition dipole moment of monosubstituted benzenes was previously reported from high-resolution electronic spectroscopy. In search for a more general understanding of this non-Condon behavior, we investigated ethylamino-substituted indole and benzene (tryptamine and 2-phenylethylamine) using ab initio theory and compared the results to rotationally resolved laser-induced fluorescence measurements. The interaction of the ethylamino side chain with the benzene chromophore can evoke a rotation and a change of ordering of the molecular orbitals involved in the excitation, leading to state mixing and large changes in the orientation of the excited-state transition dipole moment. These changes are much less pronounced in tryptamine with the indole chromophore, where a rotation of the transition dipole moment is attributed to Rydberg contributions of the nitrogen atom of the chromophore. For phenylethylamine, a strong dependence of the oscillator strengths of the lowest two singlet states from the conformation of the side chain is found, which makes the use of experimental vibronic intensities for assessment of relative conformer stabilities at least questionable. PMID:21500787

Brand, Christian; Meerts, W Leo; Schmitt, Michael

2011-09-01

45

A Conformational Transition Observed in Single HIV-1 Gag Molecules during In Vitro Assembly of Virus-Like Particles  

PubMed Central

ABSTRACT The conformational changes within single HIV-1 Gag molecules that occur during assembly into immature viruses are poorly understood. Using an in vitro assembly assay, it has been proposed that HIV-1 Gag undergoes a conformational transition from a compact conformation in solution to an extended rod-like conformation in virus-like particles (VLPs). Here we used single-molecule Förster resonance energy transfer (smFRET) to test this model by directly probing the conformation of single HIV-1 Gag molecules. We demonstrate that monomeric HIV-1 Gag lacking the p6 domain and the N-terminal myristoyl moiety is found in solution predominantly in a compact conformation. Gag in this conformation, and in the presence of nucleic acid, assembles into 30-nm-diameter particles. However, with the addition of inositol hexakisphosphate, Gag adopts a linear conformation and assembles into full-sized ?100-to-150-nm-diameter VLPs. Parallel fluorescence correlation spectroscopy measurements show that this conformational transition occurs early in the assembly process when Gag oligomers are small, perhaps as early as upon dimerization. Thus, smFRET measurements confirm that HIV-1 Gag transitions from a compact to a linear conformation during the formation of VLPs. Our results are consistent with a model whereby binding of HIV-1 Gag to phosphoinositides at the plasma membrane stabilizes an extended conformation and promotes oligomerization into the radially aligned immature capsid. IMPORTANCE The establishment of single-molecule fluorescence techniques reveals the conformational state of individual HIV-1 Gag molecules prior to and during in vitro assembly into virus-like particles. The data demonstrate that Gag in distinct conformations forms particles with different morphologies. In the compact conformation, in the presence of nucleic acid, Gag forms spherical particles of a diameter of approximately 30 nm. In the extended conformation, Gag forms spherical virus-like particles of approximately 100-nm diameter. The adoption of the extended conformation required the presence of inositol hexakisphosphate in addition to nucleic acid. Our results are consistent with a model whereby binding of HIV-1 Gag to phosphoinositides at the plasma membrane stabilizes an extended conformation and promotes oligomerization into the radially aligned immature capsid. PMID:24403576

Nath, Abhinav; Farber, Michael; Datta, Siddhartha A. K.; Rein, Alan; Rhoades, Elizabeth

2014-01-01

46

Free energy of transition for the individual alkaline conformers of yeast iso-1-cytochrome c.  

PubMed

Direct protein electrochemistry was used to obtain the thermodynamic parameters of transition from the native (state III) to the alkaline (state IV) conformer for untrimethylated Saccharomyces cerevisiae iso-1-cytochrome c expressed in E. coli and its single and multiple lysine-depleted variants. In these variants, one or more of the lysine residues involved in axial Met substitution (Lys72, Lys73, and Lys79) was mutated to alanine. The aim of this work is to determine the thermodynamic affinity of each of the substituting lysines for the heme iron and evaluate the interplay of enthalpic and entropic factors. The equilibrium constants for the deprotonation reaction of Lys72, 73, and 79 were computed for the minimized MD average structures of the wild-type and mutated proteins, applying a modified Tanford-Kirkwood calculation. Solvent accessibility calculations for the substituting lysines in all variants were also performed. The transition enthalpy and entropy values within the protein series show a compensatory behavior, typical of a process involving extensive solvent reorganization effects. The experimental and theoretical data indicate that Lys72 most readily deprotonates and replaces M80 as the axial heme iron ligand, whereas Lys73 and Lys79 show comparably higher pKa values and larger transition free energies. A good correlation is found within the series between the lowest calculated Lys pKa value and the corresponding experimental pKa value, which can be interpreted as indicative of the deprotonating lysine itself acting as the triggering group for the conformational transition. The triple Lys to Ala mutant, in which no lysine residues are available for heme iron binding, features transition thermodynamics consistent with a hydroxide ion replacing the axial methionine ligand. PMID:17243773

Battistuzzi, Gianantonio; Borsari, Marco; De Rienzo, Francesca; Di Rocco, Giulia; Ranieri, Antonio; Sola, Marco

2007-02-13

47

Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods  

PubMed Central

Background Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important for understanding the mechanisms of interaction of many proteins. Methods This paper presents a computationally efficient approach, combining methods originating from robotics and computational biophysics, to model protein conformational transitions. The ability of normal mode analysis to predict directions of collective, large-amplitude motions is applied to bias the conformational exploration performed by a motion planning algorithm. To reduce the dimension of the problem, normal modes are computed for a coarse-grained elastic network model built on short fragments of three residues. Nevertheless, the validity of intermediate conformations is checked using the all-atom model, which is accurately reconstructed from the coarse-grained one using closed-form inverse kinematics. Results Tests on a set of ten proteins demonstrate the ability of the method to model conformational transitions of proteins within a few hours of computing time on a single processor. These results also show that the computing time scales linearly with the protein size, independently of the protein topology. Further experiments on adenylate kinase show that main features of the transition between the open and closed conformations of this protein are well captured in the computed path. Conclusions The proposed method enables the simulation of large-amplitude conformational transitions in proteins using very few computational resources. The resulting paths are a first approximation that can directly provide important information on the molecular mechanisms involved in the conformational transition. This approximation can be subsequently refined and analyzed using state-of-the-art energy models and molecular modeling methods. PMID:24564964

2013-01-01

48

Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects  

E-print Network

Lithium Diisopropylamide-Mediated Enolizations: Solvent-Dependent Mixed Aggregation Effects Xiufeng spectroscopic investigations of lithium diisopropylamide-mediated ester enolization in THF, t-BuOMe, HMPA that the metalations by lithium diisopropylamide (LDA) homonuclear dimers proceed at nearly solvent-independent rates

Collum, David B.

49

Correlation of acid-induced conformational transition of ferricytochrome c with cyanide binding kinetics.  

PubMed

A relation between pH-induced conformational transitions of horse heart ferricytochrome c and the kinetics of external ligand coordination to heme iron was investigated by optical spectroscopy, circular dichroism and viscometry. The dependencies of both the association, k (a), and dissociation rate constants of cyanide binding on pH were determined from kinetic measurements. The association rate constant exhibits a bell-shaped form of dependence on pH in the region where this protein unfolds. The maximum of the dependence of k (a) on pH is found to be coincident with the pK values of conformational transitions of ferricytochrome c in solutions with both low and high ionic strengths. This observation is explained in terms of ferricytochrome c unfolding, which is characterized by two processes: the gradual opening of the heme crevice accompanied by the detachment of the axial Met80 and its replacement with a water molecule. The former process enhances the rate, whereas the latter results in the inhibition of the rate of cyanide binding. PMID:18317818

Varhac, Rastislav; Antalík, Marián

2008-06-01

50

Conformational transitions of cytochrome C in sub-micron-sized capsules at air/buffer interface.  

PubMed

This work presents the design of sub-micron-sized capsules of Cytochrome c (cyt c) in the range 300-350 nm and the conformational transitions of the protein that occur when the films of these capsules spread at the air/buffer interface are subjected to repeated compression-expansion cycles. Steady state fluorescence, time-resolved fluorescence, and circular dichroic (CD) spectra have been used to study the highly compact native conformation (70% helicity) of the protein in the capsules and its stability has been analyzed using cyclic voltammetry. The capsules have been characterized using zeta sizer and high resolution transmission electron microscopy (HRTEM). Surface concentration-surface pressure (?-?) isotherms of the films of the capsules spread at air/buffer interface following compression-expansion show destabilizing effect on cyt c. FTIR and CD spectra of these films skimmed from the surface show that the protein transitions gradually from its native helical to an anomalous beta sheet aggregated state. This results from a competition between stabilizing hydrated polar segments of the protein in the capsule and destabilizing nonspecific hydrophobic interactions arising at the air/buffer interface. This 2D model could further our understanding of the spatial and temporal roles of proteins in confined spaces and also in the design of new drug delivery vehicles using proteins. PMID:25233344

Jaganathan, Maheshkumar; Dhathathreyan, Aruna

2014-09-30

51

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

PubMed Central

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

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

2013-01-01

52

Conformational transitions of macromolecules in an eluent flow and their manifestation in the chromatography of polymers  

NASA Astrophysics Data System (ADS)

The behaviour of macromolecules in a free eluent flow, in a confined space, and in a flow passing through a pore system is considered. It is shown that the behaviour of macromolecules can be described by different theories such as the De Gennes theory and the theory of A DiMarzio and C M Guttman. Specific features of chromatographic fractionation and separation processes with the use of membranes formed from ultrahigh-molecular-mass polymers, which are widely used as constructional materials, are discussed. To account for these features, theoretical models considering conformational transitions of macromolecules in the eluent flow and taking into account possible degradation of macromolecules under the influence of the flow are applied. The current state of theoretical and experimental studies of the behaviour of macromolecules in a fluid flow is surveyed. The bibliography includes 152 references.

Kurganov, A. A.; Kanateva, A. Yu; Orekhov, V. A.

2014-07-01

53

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

PubMed

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

Karakutuk, Ilknur; Ak, Fatih; Okay, Oguz

2012-04-01

54

Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation  

PubMed Central

The role that DNA conformation plays in the biochemistry of cells has been the subject of intensive research since DNA polymorphism was discovered. B-DNA has long been considered the native form of DNA in cells although alternative conformations of DNA are thought to occur transiently and along short tracts. Here, we report the first direct observation of a fully reversible en masse conformational transition between B- and A-DNA within live bacterial cells using Fourier transform infrared (FTIR) spectroscopy. This biospectroscopic technique allows for non-invasive and reagent-free examination of the holistic biochemistry of samples. For this reason, we have been able to observe the previously unknown conformational transition in all four species of bacteria investigated. Detection of this transition is evidence of a previously unexplored biological significance for A-DNA and highlights the need for new research into the role that A-DNA plays as a cellular defence mechanism and in stabilizing the DNA conformation. Such studies are pivotal in understanding the role of A-DNA in the evolutionary pathway of nucleic acids. Furthermore, this discovery demonstrates the exquisite capabilities of FTIR spectroscopy and opens the door for further investigations of cell biochemistry with this under-used technique. PMID:24898023

Whelan, Donna R.; Hiscox, Thomas J.; Rood, Julian I.; Bambery, Keith R.; McNaughton, Don; Wood, Bayden R.

2014-01-01

55

Synaptotagmin's role in neurotransmitter release likely involves Ca(2+)-induced conformational transition.  

PubMed

Neuronal exocytosis is mediated by a Ca(2+)-triggered membrane fusion event that joins synaptic vesicles and presynaptic membrane. In this event, synaptotagmin I plays a key role as a Ca(2+) sensor protein that binds to and bends the presynaptic membrane with its C2B domain, and thereby initiates membrane fusion. We report free energy calculations according to which C2B-induced membrane bending is preceded by a Ca(2+)- and membrane-dependent conformational transition. In this transition C2B attaches to the membrane, moves its C-terminal helix from the orientation seen in the available (but membrane-free) crystal/NMR structures as pointing away from the membrane (helix-up), to an orientation pointing toward the membrane (helix-down). In the C2B helix-down state, lipid tails in the proximal membrane bilayer leaflet interact with the moved helix and become disordered, whereas tails in the distal leaflet, to keep in contact with the proximal leaflet, become stretched and ordered. The difference in lipid tail packing between the two leaflets results in an imbalance of pressure across the membrane, and thereby causes membrane bending. The lipid-disordering monitored in the simulations is well suited to facilitate Ca(2+)-triggered membrane fusion. PMID:25185551

Wu, Zhe; Schulten, Klaus

2014-09-01

56

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

NASA Astrophysics Data System (ADS)

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.

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

2014-10-01

57

Structure transition in PSS-lysozyme complexes: a chain conformation driven process, as directly seen by Small  

E-print Network

, results from a conformation modification prior to the transition. Before showing this, we have widened and progressing, prompted by its importance in real life (food, biotechnology and biology, personal care], progress has been done via techniques at scales characteristic of the structure. We have shown recently

Paris-Sud XI, Université de

58

Expression of Mutant ?1 Na/K-ATPase Defective in Conformational Transition Attenuates Src-mediated Signal Transduction*  

PubMed Central

The ?1 Na/K-ATPase possesses both pumping and signaling functions. Using purified enzyme we found that the ?1 Na/K-ATPase might interact with and regulate Src activity in a conformation-dependent manner. Here we further explored the importance of the conformational transition capability of ?1 Na/K-ATPase in regulation of Src-related signal transduction in cell culture. We first rescued the ?1-knockdown cells by wild-type rat ?1 or ?1 mutants (I279A and F286A) that are known to be defective in conformational transition. Stable cell lines with comparable expression of wild type ?1, I279A, and F286A were characterized. As expected, the defects in conformation transition resulted in comparable degree of inhibition of pumping activity in the mutant-rescued cell lines. However, I279A was more effective in inhibiting basal Src activity than either the wild-type or the F286A. Although much higher ouabain concentration was required to stimulate Src in I279A-rescued cells, extracellular K+ was comparably effective in regulating Src in both control and I279A cells. In contrast, ouabain and extracellular K+ failed to produce detectable changes in Src activity in F286A-rescued cells. Furthermore, expression of either mutant inhibited integrin-induced activation of Src/FAK pathways and slowed cell spreading processes. Finally, the expression of these mutants inhibited cell growth, with I279A being more potent than that of F286A. Taken together, the new findings suggest that the ?1 Na/K-ATPase may be a key player in dynamic regulation of cellular Src activity and that the capability of normal conformation transition is essential for both pumping and signaling functions of ?1 Na/K-ATPase. PMID:23288841

Ye, Qiqi; Lai, Fangfang; Banerjee, Moumita; Duan, Qiming; Li, Zhichuan; Si, Shuyi; Xie, Zijian

2013-01-01

59

Expression of mutant ?1 Na/K-ATPase defective in conformational transition attenuates Src-mediated signal transduction.  

PubMed

The ?1 Na/K-ATPase possesses both pumping and signaling functions. Using purified enzyme we found that the ?1 Na/K-ATPase might interact with and regulate Src activity in a conformation-dependent manner. Here we further explored the importance of the conformational transition capability of ?1 Na/K-ATPase in regulation of Src-related signal transduction in cell culture. We first rescued the ?1-knockdown cells by wild-type rat ?1 or ?1 mutants (I279A and F286A) that are known to be defective in conformational transition. Stable cell lines with comparable expression of wild type ?1, I279A, and F286A were characterized. As expected, the defects in conformation transition resulted in comparable degree of inhibition of pumping activity in the mutant-rescued cell lines. However, I279A was more effective in inhibiting basal Src activity than either the wild-type or the F286A. Although much higher ouabain concentration was required to stimulate Src in I279A-rescued cells, extracellular K(+) was comparably effective in regulating Src in both control and I279A cells. In contrast, ouabain and extracellular K(+) failed to produce detectable changes in Src activity in F286A-rescued cells. Furthermore, expression of either mutant inhibited integrin-induced activation of Src/FAK pathways and slowed cell spreading processes. Finally, the expression of these mutants inhibited cell growth, with I279A being more potent than that of F286A. Taken together, the new findings suggest that the ?1 Na/K-ATPase may be a key player in dynamic regulation of cellular Src activity and that the capability of normal conformation transition is essential for both pumping and signaling functions of ?1 Na/K-ATPase. PMID:23288841

Ye, Qiqi; Lai, Fangfang; Banerjee, Moumita; Duan, Qiming; Li, Zhichuan; Si, Shuyi; Xie, Zijian

2013-02-22

60

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

SciTech Connect

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

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

61

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

NASA Astrophysics Data System (ADS)

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.

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

2007-10-01

62

Theoretical study on structure, conformation, stability and electronic transition of C4 and C5 anions of ascorbic acid stereoisomers  

NASA Astrophysics Data System (ADS)

The structures, stabilities, conformational analysis and electronic transitions of L-ascorbic acid anions (four stereoisomers) were studied theoretically. These anions are produced from the de-protonation of C4-H and C5-H sites of L-ascorbic acid stereoisomers. The geometries of these anions were fully optimized in gas phase and aqueous phase in order to determine their relative stabilities. It was observed that the de-protonation at C5 site of two stereoisomers leads to the ring opening in both phases. Isomerization of the L-form to one of the D-form was observed during the optimization of the anions at C5. Conformational analysis (potential energy surface scan) of the opened ring anions was performed in search of energy minima and/or maxima. The absorption electronic transitions of the anions in the UV region were calculated using Time-Dependent Density Functional Theory (TD-DFT).

Dabbagh, Hossein A.; Azami, Fatemeh; Farrokhpour, Hossein; Chermahini, Alireza Najafi

2014-03-01

63

Conformational changes at mesophase transitions in a ferroelectric liquid crystal by comparative DFT computational and (13)C NMR study.  

PubMed

In this work, we report a detailed investigation on both the conformational and the orientational ordering properties of a ferroelectric liquid crystal mesogen, namely, M10/**, through the combination of high resolution solid state (13)C NMR and density functional theory (DFT) computational methods. The trends of the observed (13)C chemical shift in the blue, cholesteric, and ferroelectric SmC* phases of M10/** were analyzed in terms of conformational changes occurring in the flexible parts of the molecule. In particular, we focused on the aliphatic alpha methylenoxy carbons because of their high sensitivity to mesophase environment, as evidenced by experimental (13)C chemical shift anisotropy (CSA). DFT computation of the chemical shift tensors as a function of geometrical parameters, such as dihedral angles, put in evidence significant changes in the average conformation at the mesophase transitions. The conformations predicted by DFT have been validated by comparing the calculated (13)C chemical shifts with those experimentally observed for the alkoxylic carbons, whose relative orientation plays a key role in establishing the overall conformation of the molecule in each liquid crystalline phase. Furthermore, the orientational order parameters of the relevant flexible fragments were calculated and found to be in good agreement with those characterizing similar systems, thus validating our approach. PMID:20701374

Marini, Alberto; Domenici, Valentina

2010-08-19

64

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

PubMed Central

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

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

2011-01-01

65

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

NASA Astrophysics Data System (ADS)

A new Cu(?) coordination compound, Cu 4(L) 4·2EtOH ( 1), has been obtained from the solvothermal reaction of CuBr, HL (L=5-(4-pyridyl) tetrazole), EtOH and NH 3·H 2O. 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 ?-? 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 2) adsorption measurement was carried out for the framework. Framework 1 shows II sorption profile with N 2, which indicates that N 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.

Wang, Fei; Yu, Rongmin; Zhang, Qi-Sheng; Zhao, Zhen-Guo; Wu, Xiao-Yuan; Xie, Yi-Ming; Qin, Li; Chen, Shan-Ci; Lu, Can-Zhong

2009-09-01

66

Large scale conformational transitions in ?-structural motif of gramicidin A: kinetic analysis based on CD and FT-IR data.  

PubMed

Gramicidin A (gA) is a polypeptide antibiotic, which forms dimeric channels specific for monovalent cations in artificial and biological membranes. It is a polymorphic molecule that adopts a unique variety of helical conformations, including antiparallel double-stranded ???5.6 or ???7.2 helices (number of residues per turn) and a single-stranded ?6.3 helix (the 'channel form'). The behavior of gA-Cs(+) complex in the micelles of TX-100 was studied in this work. Transfer of the complex into the micelles activates a cascade of sequential conformational transitions monitored by CD and FT-IR spectroscopy: [Formula: see text] At the first step after Cs(+) removal, the RH ???5.6 helix is formed, which has been discussed so far only hypothetically. Kinetics of the transitions was measured, and the activation parameters were determined. The activation energies of the ???5.6????-helical monomer transition in dioxane and dioxane/water solutions were also measured for comparison. The presence of water raises the transition rate constant ~10(3) times but does not lead to crucial fall of the activation energy. All activation energies were found in the 20-25?kcal/mol range, i.e. much lower than would be expected for unwinding of the double helix (when 28 H-bonds are broken simultaneously). These results can be accounted for in the light of local unfolding (or 'cracking') model for large scale conformational transitions developed by the P.?G.Wolynes team [Miyashita O, Onuchic JN, Wolynes PG. Proc. Natl. Acad. Sci. USA 2003; 100: 12570-12575.]. PMID:24788525

Sychev, Sergei V; Ivanov, Vadim T

2014-08-01

67

Conformation transition in the protein of a photosynthetic reaction center observed at the nanometer range of distances at cryogenic temperatures  

NASA Astrophysics Data System (ADS)

Electron spin echo (ESE) spectroscopy is applied to study magnetic dipolar interaction between electron spins in the transient P +Q A- radical pairs (P is the primary donor, a bacteriochlorophyll dimer, and Q A is the primary quinone acceptor) and the 3PQ A- triplet-radical pairs in bacterial photosynthetic reaction centers of Rhodobacter sphaeroides R26. Distance separation in both pairs is about 29 Å. A well-resolved reversible conformational transition of the reaction center protein holding the P and Q A cofactors was observed between 13 and 20 K. This transition results in a narrowing of the distribution of protein conformations with decreasing temperature, with the width of distance distribution between P and Q A dropping from ca. 4 Å at 20 K to ca. 1 Å at 13 K. This transition implies the existence of low barriers in the protein energy landscape and the presence of cooperatively rearranging domains of the size of several nm both in the protein and in the surrounding glassy environment.

Borovykh, I. V.; Kulik, L. V.; Gast, P.; Dzuba, S. A.

2003-11-01

68

Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions  

Microsoft Academic Search

Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on

Haw Yang

2011-01-01

69

Phosphorylation Induces a Conformational Transition near the Lipid-Water Interface of Phospholamban Reconstituted with the Ca-ATPase  

SciTech Connect

We have measured conformational changes of phospholamban (PLB) induced both by its interaction with the SR Ca-ATPase and by phosphorylation of Ser-16 by cAMP-dependent protein kinase (PKA) using an engineered PLB having a single cysteine (Cys-24) derivatized with the fluorophore 2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid (ANSmal). This modified mutant PLB is fully functional when co-reconstituted with the affinity-purified Ca-ATPase in liposomes. ANSmal emission properties and its solvent accessibility indicate that Cys-24 is in an aqueous environment outside the membrane. Fluorescence quenching and time-resolved anisotropy measurements of ANSmal-PLB demonstrate distinct structures for PLB in the free and Ca-ATPase-bound state. Both solvent exposure and probe motions of ANSmal are enhanced upon interaction of PLB with the Ca-ATPase. This conformational transition entails conversion of free PLB in a conformation which is insensitive to one which is sensitive to the phosphorylation state of PLB. Upon phosphorylation of Ca-ATPase-bound PLB, a decreased level of solvent exposure of ANSmal is observed, suggesting that the amino acid sequence of PLB near the lipid-water interface acts as a conformational switch in response to the phosphorylation of PLB. A longer correlation time, resolved by anisotropy measurements, corresponding to polypeptide chain fluctuations, is substantially restricted by interaction of PLB with the Ca-ATPase. This restriction is not reversed by phosphorylation of PLB, indicating that the region around Cys-24 near the lipid-water interface does not undergo dissociation from the Ca-ATPase. These results suggest that the phosphorylation by PKA induces a redistribution of PLB-Ca-ATPase protein contacts to relieve the inhibitory effect of PLB for the activation of calcium transport.

Chen, Baowei; Bigelow, Diana J.

2002-11-26

70

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

NASA Astrophysics Data System (ADS)

While semi-flexible polymers and fibres 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 behaviour of entangled F-actin solutions, which aids the understanding of the flow behaviour of complex fluids containing semi-flexible polymers.

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

2014-10-01

71

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

PubMed

While semi-flexible polymers and fibres 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 behaviour of entangled F-actin solutions, which aids the understanding of the flow behaviour of complex fluids containing semi-flexible polymers. PMID:25297898

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

2014-01-01

72

P-glycoprotein function involves conformational transitions detectable by differential immunoreactivity  

PubMed Central

The MDR1 P-glycoprotein (Pgp), a member of the ATP-binding cassette family of transporters, is a transmembrane ATPase efflux pump for various lipophilic compounds, including many anti-cancer drugs. mAb UIC2, reactive with the extracellular moiety of Pgp, inhibits Pgp-mediated efflux. UIC2 reactivity with Pgp was increased by the addition of several Pgp-transported compounds or ATP-depleting agents, and by mutational inactivation of both nucleotide-binding domains (NBDs) of Pgp. UIC2 binding to Pgp mutated in both NBDs was unaffected in the presence of Pgp transport substrates or in ATP-depleted cells, whereas the reactivities of the wild-type Pgp and Pgps mutated in a single NBD were increased by these treatments to the level of the double mutant. These results indicate the existence of different Pgp conformations associated with different stages of transport-associated ATP hydrolysis and suggest trapping in a transient conformation as a mechanism for antibody-mediated inhibition of?Pgp. PMID:9371774

Mechetner, Eugene B.; Schott, Brigitte; Morse, Brian S.; Stein, Wilfred D.; Druley, Todd; Davis, Kenneth A.; Tsuruo, Takashi; Roninson, Igor B.

1997-01-01

73

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

SciTech Connect

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

Chen, Guo [Los Alamos National Laboratory; Mcmahon, Benjamin H [Los Alamos National Laboratory; Tung, Chang - Shung [Los Alamos National Laboratory

2008-01-01

74

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

E-print Network

Allosteric Transitions in Myosin II Wenjun Zheng * and D. Thirumalai * Physics Department, University illustrate the new concepts using myosin II motor protein as an example. The biological implications of mode, and the force-generating converter and lever arm in myosin isoforms are discussed. We evaluate the robustness

Thirumalai, Devarajan

75

Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies  

NASA Astrophysics Data System (ADS)

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV-vis, fluorescence, circular dichroism (CD) spectroscopy, UV-melting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation. The fluorescence quenching of TB by ctDNA was static and due to electron transfer from bases to the excited singlet state of TB. At low [TB]/[DNA] ratio, TB mainly partially intercalated into ctDNA resulting in the slight increase of base stacking degree; at high [TB]/[DNA] ratio, excessive TB externally stacked along the helix surface via coupling with partially intercalated ones, thereby inducing B-A transition of ctDNA. The conformational transition of DNA was confirmed by the obvious improvement of the thermal stability of ctDNA. The SERS spectra suggest that TB could partially intercalate into DNA basepairs with its ring C 1NC 1' side buried.

Wang, Juan; Yang, Xiurong

2009-10-01

76

K U R S A R A h D H O L Z W A R T H Backbone Conformational Change in the A -B Transition of  

E-print Network

K U R S A R A h D H O L Z W A R T H Backbone Conformational Change in the A -B Transition of Deoxyribonucleic Acidt Tom Kursar and G. Holzwarth*,t ABSTRACT: Infrared linear dichroism studies of A- and B (Fraser and Fraser, 1951;Sutherland and Tsuboi, 1957; Bradbury et al., 1961; Falk et al., 1963;Tsuboi

Coley, Phyllis

77

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

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

Kurnaz, Levent

78

Na(+) transport, and the E(1)P-E(2)P conformational transition of the Na(+)/K(+)-ATPase.  

PubMed Central

We have used admittance analysis together with the black lipid membrane technique to analyze electrogenic reactions within the Na(+) branch of the reaction cycle of the Na(+)/K(+)-ATPase. ATP release by flash photolysis of caged ATP induced changes in the admittance of the compound membrane system that are associated with partial reactions of the Na(+)/K(+)-ATPase. Frequency spectra and the Na(+) dependence of the capacitive signal are consistent with an electrogenic or electroneutral E(1)P <--> E(2)P conformational transition which is rate limiting for a faster electrogenic Na(+) dissociation reaction. We determine the relaxation rate of the rate-limiting reaction and the equilibrium constants for both reactions at pH 6.2-8.5. The relaxation rate has a maximum value at pH 7.4 (approximately 320 s(-1)), which drops to acidic (approximately 190 s(-1)) and basic (approximately 110 s(-1)) pH. The E(1)P <--> E(2)P equilibrium is approximately at a midpoint position at pH 6.2 (equilibrium constant approximately 0.8) but moves more to the E(1)P side at basic pH 8.5 (equilibrium constant approximately 0.4). The Na(+) affinity at the extracellular binding site decreases from approximately 900 mM at pH 6.2 to approximately 200 mM at pH 8.5. The results suggest that during Na(+) transport the free energy supplied by the hydrolysis of ATP is mainly used for the generation of a low-affinity extracellular Na(+) discharge site. Ionic strength and lyotropic anions both decrease the relaxation rate. However, while ionic strength does not change the position of the conformational equilibrium E(1)P <--> E(2)P, lyotropic anions shift it to E(1)P. PMID:11053130

Babes, A; Fendler, K

2000-01-01

79

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft  

PubMed Central

Background The N-terminal SH2 domain (N-SH2) of the non-receptor tyrosine phosphatase SHP-2 is involved both in localization of SHP-2 by recognition of phosphotyrosine (pY) peptides and self-inhibition of SHP-2 phosphatase activity through the formation of a protein – protein interface with the phosphatase domain. Mutations that disrupt this interface break the coupling between pY-peptide binding cleft conformation and self-inhibition, thereby increasing both SHP-2 phosphatase activity and pY-peptide binding affinity, and are associated with the congenital condition Noonan syndrome and various pediatric leukemias. To better characterize the molecular process involved in N-SH2 pY-dependent binding, we have applied explicit-solvent molecular dynamics simulations to study the closed-to-open transition of the N-SH2 pY-peptide binding cleft. Results The existence of stable conformations in the left-handed helical and the extended regions of Tyr66 ?/? space prevent rapid interconversion of the backbone and create a conformational switch such that Tyr66 in a left-handed helical backbone conformation results in an open cleft and in an extended backbone conformation results in a closed cleft. The stable conformations arise from deep, well-localized free-energy minima in the left-handed helical and extended regions of the Tyr66 ?/? map. Changing the Tyr66 backbone conformation from extended to left-handed helical induces a closed-to-open transition in the cleft, and the reverse change in backbone conformation induces the reverse, open-to-closed transition. In the open-cleft state, weak solvent-exposed interactions involving the sidechains of Tyr66, Asp40, Lys55, and Gln57 serve to anchor the Tyr66 sidechain to the surface of the protein and away from the binding cleft entrance, thereby facilitating pY-peptide access to the binding cleft. Conclusion The simulations point to a regulatory role for Tyr66 and surrounding residues in SHP-2 function: mutations at Tyr66, Asp40, Lys55, and/or Gln57 are predicted to break the switching mechanism and negatively impact pY-peptide binding. This in turn would interfere with cellular localization and the coupled SHP-2 phosphatase activity. The structurally well-defined binding cleft conformations resulting from the switch-like transition suggest the possibility of applying structure-based methods to develop inhibitors of N-SH2 pY-peptide binding to serve as research tools for signal transduction and precursors to therapeutics for SHP-2-related diseases. PMID:17378938

Guvench, Olgun; Qu, Cheng-Kui; MacKerell, Alexander D

2007-01-01

80

Unusually Strong Dependence of Conformation on Solvent  

Microsoft Academic Search

Relative partition coefficients between aqueous methanol and pentane of the two stereoisomers of a series of 4-tert-butylcyclohexylamines were measured by NMR. The cis isomer shows a larger partition coefficient, with a ¢¢G°orgfaq up to 1.4 kcal\\/mol. A thermodynamic cycle relates these values to a solvent dependence of the A value for conformational equilibrium of an amino substituent. The variation with

Charles L. Perrin; Miles A. Fabian; Ignacio A. Rivero

1998-01-01

81

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

E-print Network

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.

Jérémie Gummel; Fabrice Cousin; François Boué

2009-03-30

82

Solvent annealing induced phase separation and dewetting in PMMA/SAN blend film: Film thickness and solvent dependence  

NASA Astrophysics Data System (ADS)

The competition between ``dewetting'' and ``phase separation'' behaviors in polymer blend films attracts significant attention in the last decade. The simultaneous phase separation and dewetting in PMMA/SAN [poly(methyl methacrylate) and poly(styrene-ran-acrylonitrile)] blend ultrathin films upon solvent annealing have been observed for the first time in our previous work. In this work, film thickness and annealing solvent dependence of phase behaviors in this system has been investigated using atomic force microscopy and grazing incidence small-angle X-ray scattering (GISAXS). On one hand, both vertical phase separation and dewetting take place upon selective solvent vapor annealing, leading to the formation of droplet/mimic-film structures with various sizes (depending on original film thickness). On the other hand, the whole blend film dewets the substrate and produces dispersed droplets on the silicon oxide upon common solvent annealing. GISAXS results demonstrate the phase separation in the big dewetted droplets resulted from the thicker film (39.8 nm). In contrast, no period structure is detected in small droplets from the thinner film (5.1 nm and 9.7 nm). This investigation indicates that dewetting and phase separation in PMMA/SAN blend film upon solvent annealing depend crucially on the film thickness and the atmosphere during annealing.

You, Jichun; Zhang, Shuangshuang; Huang, Gang; Shi, Tongfei; Li, Yongjin

2013-06-01

83

The Spectral Properties of (-)-Epigallocatechin 3-O-Gallate (EGCG) Fluorescence in Different Solvents: Dependence on Solvent Polarity  

PubMed Central

(-)-Epigallocatechin 3-O-gallate (EGCG) a molecule found in green tea and known for a plethora of bioactive properties is an inhibitor of heat shock protein 90 (HSP90), a protein of interest as a target for cancer and neuroprotection. Determination of the spectral properties of EGCG fluorescence in environments similar to those of binding sites found in proteins provides an important tool to directly study protein-EGCG interactions. The goal of this study is to examine the spectral properties of EGCG fluorescence in an aqueous buffer (AB) at pH=7.0, acetonitrile (AN) (a polar aprotic solvent), dimethylsulfoxide (DMSO) (a polar aprotic solvent), and ethanol (EtOH) (a polar protic solvent). We demonstrate that EGCG is a highly fluorescent molecule when excited at approximately 275 nm with emission maxima between 350 and 400 nm depending on solvent. Another smaller excitation peak was found when EGCG is excited at approximately 235 nm with maximum emission between 340 and 400 nm. We found that the fluorescence intensity (FI) of EGCG in AB at pH=7.0 is significantly quenched, and that it is about 85 times higher in an aprotic solvent DMSO. The Stokes shifts of EGCG fluorescence were determined by solvent polarity. In addition, while the emission maxima of EGCG fluorescence in AB, DMSO, and EtOH follow the Lippert-Mataga equation, its fluorescence in AN points to non-specific solvent effects on EGCG fluorescence. We conclude that significant solvent-dependent changes in both fluorescence intensity and fluorescence emission shifts can be effectively used to distinguish EGCG in aqueous solutions from EGCG in environments of different polarity, and, thus, can be used to study specific EGCG binding to protein binding sites where the environment is often different from aqueous in terms of polarity. PMID:24278192

Snitsarev, Vladislav; Young, Michael N.; Miller, Ross M. S.; Rotella, David P.

2013-01-01

84

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

PubMed

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. PMID:25296960

Shankla, Manish; Aksimentiev, Aleksei

2014-01-01

85

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

NASA Astrophysics Data System (ADS)

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.

Shankla, Manish; Aksimentiev, Aleksei

2014-10-01

86

A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution  

SciTech Connect

Crystal structures of A-form and B-form DNA duplexes containing 2'-S-methyl-uridines reveal that the modified residues adopt a RNA-like C3'-endo pucker, illustrating that the replacement of electronegative oxygen at the 2'-carbon of RNA by sulfur does not appear to fundamentally alter the conformational preference of the sugar in the oligonucleotide context and sterics trump stereoelectronics.

Pallan, Pradeep S.; Prakash, Thazha P.; Li, Feng; Eoff, Robert L.; Manoharan, Muthiah; Egli, Martin; (Isis Pharm.); (Alnylam Pharm.); (Vanderbilt)

2009-06-17

87

Detecting Solvent-Driven Transitions of poly(A) to Double-Stranded Conformations by Atomic Force Microscopy  

PubMed Central

We report the results of direct measurements by atomic force microscopy of solvent-driven structural transitions within polyadenylic acid (poly(A)). Both atomic force microscopy imaging and pulling measurements reveal complex strand arrangements within poly(A) induced by acidic pH conditions, with a clear fraction of double-stranded molecules that increases as pH decreases. Among these complex structures, force spectroscopy identified molecules that, upon stretching, displayed two distinct plateau features in the force-extension curves. These plateaus exhibit transition forces similar to those previously observed in native double-stranded DNA (dsDNA). However, the width of the first plateau in the force-extension curves of poly(A) varies significantly, and on average is shorter than the canonical 70% of initial length corresponding to the B-S transition of dsDNA. Also, similar to findings in dsDNA, stretching and relaxing elasticity profiles of dspoly(A) at forces below the mechanical melting transition overlap but reveal hysteresis when the molecules are stretched above the mechanical melting transition. These results strongly suggest that under acidic pH conditions, poly(A) can form duplexes that are mechanically stable. We hypothesize that under acidic conditions, similar structures may be formed by the cellular poly(A) tails on mRNA. PMID:19348773

Ke, Changhong; Loksztejn, Anna; Jiang, Yong; Kim, Minkyu; Humeniuk, Michael; Rabbi, Mahir; Marszalek, Piotr E.

2009-01-01

88

Binding, Conformational Transition and Dimerization of Amyloid-? Peptide on GM1-Containing Ternary Membrane: Insights from Molecular Dynamics Simulation  

PubMed Central

Interactions of amyloid-? (A?) with neuronal membrane are associated with the progression of Alzheimer’s disease (AD). Ganglioside GM1 has been shown to promote the structural conversion of A? and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs) to investigate the behavior of A? monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for A?-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a ?-hairpin motif was formed at the C-terminus of the GM1-bound A?-monomer; that didn’t appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium) within the simulation time span. For A?-dimers, the ?-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of A? to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D23-K28 salt-bridge and a turn at V24GSN27 region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide atomistic details of A?-GM1 and A?-A? interactions and demonstrate their importance in the early-stages of GM1-mediated A?-oligomerisation on membrane surface. PMID:23951128

Manna, Moutusi; Mukhopadhyay, Chaitali

2013-01-01

89

Characterization of a Small Molecule Inhibitor of Plasminogen Activator Inhibitor Type 1 That Accelerates the Transition into the Latent Conformation*  

PubMed Central

A novel class of small molecule inhibitors for plasminogen activator inhibitor type 1 (PAI-1), represented by AZ3976, was identified in a high throughput screening campaign. AZ3976 displayed an IC50 value of 26 ?m in an enzymatic chromogenic assay. In a plasma clot lysis assay, the compound was active with an IC50 of 16 ?m. Surprisingly, AZ3976 did not bind to active PAI-1 but bound to latent PAI-1 with a KD of 0.29 ?m at 35 °C and a binding stoichiometry of 0.94, as measured by isothermal calorimetry. Reversible binding was confirmed by surface plasmon resonance direct binding experiments. The x-ray structure of AZ3976 in complex with latent PAI-1 was determined at 2.4 ? resolution. The inhibitor was bound in the flexible joint region with the entrance to the cavity located between ?-helix D and ?-strand 2A. A set of surface plasmon resonance experiments revealed that AZ3976 inhibited PAI-1 by enhancing the latency transition of active PAI-1. Because AZ3976 only had measurable affinity for latent PAI-1, we propose that its mechanism of inhibition is based on binding to a small fraction in equilibrium with active PAI-1, a latent-like prelatent form, from which latent PAI-1 is then generated more rapidly. This mode of action, with induced accelerated latency transition of active PAI-1 may, together with supporting x-ray data, provide improved opportunities for small molecule drug design in the hunt for therapeutically useful PAI-1 inhibitors. PMID:23155046

Fjellstrom, Ola; Deinum, Johanna; Sjogren, Tove; Johansson, Carina; Geschwindner, Stefan; Nerme, Viveca; Legnehed, Anne; McPheat, Jane; Olsson, Karolina; Bodin, Cristian; Paunovic, Amalia; Gustafsson, David

2013-01-01

90

310-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State  

PubMed Central

The activation of voltage-gated ion channels is controlled by the S4 helix, with arginines every third residue. The x-ray structures are believed to reflect an open-inactivated state, and models propose combinations of translation, rotation, and tilt to reach the resting state. Recently, experiments and simulations have independently observed occurrence of 310-helix in S4. This suggests S4 might make a transition from ?- to 310-helix in the gating process. Here, we show 310-helix structure between Q1 and R3 in the S4 segment of a voltage sensor appears to facilitate the early stage of the motion toward a down state. We use multiple microsecond-steered molecular simulations to calculate the work required for translating S4 both as ?-helix and transformed to 310-helix. The barrier appears to be caused by salt-bridge reformation simultaneous to R4 passing the F233 hydrophobic lock, and it is almost a factor-two lower with 310-helix. The latter facilitates translation because R2/R3 line up to face E183/E226, which reduces the requirement to rotate S4. This is also reflected in a lower root mean-square deviation distortion of the rest of the voltage sensor. This supports the 310 hypothesis, and could explain some of the differences between the open-inactivated- versus activated-states. PMID:21402026

Schwaiger, Christine S.; Bjelkmar, Par; Hess, Berk; Lindahl, Erik

2011-01-01

91

Transits  

Microsoft Academic Search

Transits of the planets Mercury and especially Venus have been exciting events in the development of astronomy over the past few hundred years. Just two years ago the first transiting extra-solar planet, HD 209458b, was discovered, and subsequent studies during transit have contributed fundamental new knowledge. From the photometric light curve during transit one obtains a basic confirmation that the

Ronald L. Gilliland

2005-01-01

92

Mechanistic Studies of Ce(IV)-Mediated Oxidation of ?-Dicarbonyls: Solvent-Dependent Behavior of Radical Cation Intermediates  

PubMed Central

The Ce(IV) initiated oxidation of synthetically relevant ?-diketones and ?-keto silyl enol ethers were explored in three solvents: acetonitrile, methylene chloride, and methanol. The studies presented herein show that the rate of reaction between Ce(IV) and the substrates is dependent upon the polarity of the solvent. Thermochemical studies and analysis are interpreted to be consistent with transition state stabilization by solvent being primarily responsible for the rate of substrate oxidation. Kinetic investigation of radical cations obtained from oxidations of ?-diketones reveal that a more ordered transition state for the radical cation decay is achieved through the direct involvement of methanol in the deprotonation of the intermediate. In the case of radical cations derived from ?-keto silyl enol ethers, experimental data supports a mechanism involving unimolecular decay of the intermediate. Remarkably, radical cations derived from ?-diketones and ?-keto silyl enol ethers are surprisingly stable in methylene chloride. PMID:17602587

Jiao, Jingliang; Zhang, Yang; Devery, James J.; Xu, Luna; Deng, Jennifer; Flowers, Robert A.

2008-01-01

93

Solvent-dependent switch of ligand donor ability and catalytic activity of ruthenium(II) complexes containing pyridinylidene amide (PYA) N-heterocyclic carbene hybrid ligands.  

PubMed

Chelating ligands incorporating both N-[1-alkylpyridin-4(1H)-ylidene]amide (PYA) and N-heterocyclic carbene (NHC) donor sites were prepared and used for the synthesis of ruthenium(II) complexes. Cyclic voltammetry, NMR, and UV-vis spectroscopy of the complexes indicate a solvent-dependent contribution of the limiting resonance structures associated with the ligand in solution. The neutral pyridylidene imine structure is more pronounced in apolar solvents (CH2Cl2), while the mesoionic pyridinium amide form is predominant in polar solvents (MeOH, DMSO). The distinct electronic properties of these hybrid PYA-NHC ligands in different solvents have a direct influence on the catalytic activity of the ruthenium center, e.g., in the dehydrogenation of benzyl alcohol to benzaldehyde. The activity in different solvents qualitatively correlates with the solvent permittivity. PMID:25046249

Leigh, Vivienne; Carleton, Daniel J; Olguin, Juan; Mueller-Bunz, Helge; Wright, L James; Albrecht, Martin

2014-08-01

94

The Transition from Closed to Open Conformation of Treponema pallidum Outer Membrane-associated Lipoprotein TP0453 Involves Membrane Sensing and Integration by Two Amphipathic Helices*  

PubMed Central

The molecular architecture and composition of the outer membrane (OM) of Treponema pallidum (Tp), the noncultivable agent of venereal syphilis, differ considerably from those of typical Gram-negative bacteria. Several years ago we described TP0453, the only lipoprotein associated with the inner leaflet of the Tp OM. Whereas polypeptides of other treponemal lipoproteins are hydrophilic, non-lipidated TP0453 can integrate into membranes, a property attributed to its multiple amphipathic helices (AHs). Furthermore, membrane integration of the TP0453 polypeptide was found to increase membrane permeability, suggesting the molecule functions in a porin-like manner. To better understand the mechanism of membrane integration of TP0453 and its physiological role in Tp OM biogenesis, we solved its crystal structure and used mutagenesis to identify membrane insertion elements. The crystal structure of TP0453 consists of an ?/?/?-fold and includes five stably folded AHs. In high concentrations of detergent, TP0453 transitions from a closed to open conformation by lateral movement of two groups of AHs, exposing a large hydrophobic cavity. Triton X-114 phase partitioning, liposome floatation assay, and bis-1-anilino-8-naphthalenesulfonate binding revealed that two adjacent AHs are critical for membrane sensing/integration. Using terbium-dipicolinic acid complex-loaded large unilamellar vesicles, we found that TP0453 increased efflux of fluorophore only at acidic pH. Gel filtration and cross-linking experiments demonstrated that one AH critical for membrane sensing/insertion also forms a dimeric interface. Based on structural dynamics and comparison with Mycobacterium tuberculosis lipoproteins LprG and LppX, we propose that TP0453 functions as a carrier of lipids, glycolipids, and/or derivatives during OM biogenesis. PMID:21965687

Luthra, Amit; Zhu, Guangyu; Desrosiers, Daniel C.; Eggers, Christian H.; Mulay, Vishwaroop; Anand, Arvind; McArthur, Fiona A.; Romano, Fabian B.; Caimano, Melissa J.; Heuck, Alejandro P.; Malkowski, Michael G.; Radolf, Justin D.

2011-01-01

95

Slow conformational changes in MutS and DNA direct ordered transitions between mismatch search, recognition and signaling of DNA repair  

PubMed Central

MutS functions in mismatch repair (MMR) to scan DNA for errors, identify a target site and trigger subsequent events in the pathway leading to error removal and DNA re-synthesis. These actions, enabled by the ATPase activity of MutS, are now beginning to be analyzed from the perspective of the protein itself. This study provides the first ensemble transient kinetic data on MutS conformational dynamics as it works with DNA and ATP in MMR. Using a combination of fluorescence probes (on T. aquaticus MutS and DNA) and signals (intensity, anisotropy and resonance energy transfer), we have monitored the timing of key conformational changes in MutS that are coupled to mismatch binding and recognition, ATP binding and hydrolysis, as well as sliding clamp formation and signaling of repair. Significant findings include: (a) a slow step that follows weak initial interaction between MutS and DNA, in which concerted conformational changes in both macromolecules control mismatch recognition, (b) rapid, binary switching of MutS conformations that is concerted with ATP binding and hydrolysis, and (c) is stalled after mismatch recognition to control formation of the ATP-bound MutS sliding clamp. These rate-limiting pre- and post-mismatch recognition events outline the mechanism of action of MutS on DNA during initiation of MMR. PMID:23973435

Sharma, Anushi; Doucette, Christopher; Biro, F. Noah; Hingorani, Manju M.

2013-01-01

96

Conformable seal  

DOEpatents

Sealing apparatus and method, comprising first and second surfaces or membranes, at least one of which surfaces is deformable, placed in proximity to one another. Urging means cause these surfaces to contact one another in a manner such that the deformable surface deforms to conform to the geometry of the other surface, thereby creating a seal. The seal is capable of undergoing multiple cycles of sealing and unsealing.

Neef, W.S.; Lambert, D.R.

1982-08-10

97

Conformational selection in protein binding and function.  

PubMed

Protein binding and function often involves conformational changes. Advanced nuclear magnetic resonance (NMR) experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may "select" protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational-selection and induced-change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational-selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced-change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on- and off-rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single-molecule fluorescence resonance energy transfer experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational-selection and induced-change processes in both binding and unbinding direction. PMID:25155241

Weikl, Thomas R; Paul, Fabian

2014-11-01

98

A quantitative measure for protein conformational heterogeneity  

PubMed Central

Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs. PMID:24089719

Lyle, Nicholas; Das, Rahul K.; Pappu, Rohit V.

2013-01-01

99

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

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

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

2014-02-12

100

Conformational dynamics through an intermediate  

NASA Astrophysics Data System (ADS)

The self-assembly of biological and synthetic nanostructures commonly proceeds via intermediate states. In living systems in particular, the intermediates have the capacity to tilt the balance between functional and potentially fatal behavior. This work develops a statistical mechanical treatment of conformational dynamics through an intermediate under a variable force. An analytical solution is derived for the key experimentally measurable quantity—the distribution of forces at which a conformational transition occurs. The solution reveals rich kinetics over a broad range of parameters and enables one to locate the intermediate and extract the activation barriers and rate constants.

Garai, Ashok; Zhang, Yaojun; Dudko, Olga K.

2014-04-01

101

Conformation analysis and computation of energy barrier to rotation about Csbnd N bond in para-methylphenyl carbamate and its solvent dependence in comparison with tertiary carbamates and tertiary amides  

NASA Astrophysics Data System (ADS)

Barrier to rotation about conjugated Csbnd N bond in p-Methyl phenyl carbamate (PMPC) was computed 14-16 kcal/mol at three levels of HF, B3LYP and MP2 using 6-311++G?? basis set. The solvent effect and energy barriers about Csbnd N bond in PMPC were compared to the case of tertiary carbamates and tertiary amides. Moreover, it is shown that in primary carbamates such as PMPC and tertiary amides isomerisation process passes through TS2 and TS1 respectively, while in tertiary carbamates goes through a combination of both TSs. Furthermore, X-ray analysis which is reported for the first time for primary aryl carbamates demonstrated that the inclusive plane of carbamate functional group is perpendicular to the plane of phenyl ring. The results of computations are completely in agreement with the X-ray data.

Modarresi-Alam, Ali Reza; Nowroozi, Alireza; Najafi, Parisa; Movahedifar, Fahimeh; Hajiabadi, Hossein

2014-11-01

102

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)

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.

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

2008-07-01

103

Holographic multiverse and conformal invariance  

NASA Astrophysics Data System (ADS)

We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

Garriga, Jaume; Vilenkin, Alexander

2009-11-01

104

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

PubMed Central

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

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

1992-01-01

105

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

SciTech Connect

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.

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

106

Conformational isomers of linear rotaxanes.  

PubMed

We examine a simple model of rotaxane structure, with 3 asymmetric rings interacting via repulsive power-law forces. This interlocked molecule exhibits conformational isomerisation which is different from that of molecules whose connectedness is through covalent bonds. The rings are free to translate along and rotate around the axle, and hence weak interaction forces between the rings can lead to distinct rotamer states. We use energy minimisation to determine these states exactly, and show that there can be transitions from asymmetric to symmetric states by varying the bond lengths. We also use classical statistical mechanics to show the effect of thermal noise. PMID:25240369

Sevick, Edith M; Williams, David R M

2014-09-21

107

Conformational isomers of linear rotaxanes  

NASA Astrophysics Data System (ADS)

We examine a simple model of rotaxane structure, with 3 asymmetric rings interacting via repulsive power-law forces. This interlocked molecule exhibits conformational isomerisation which is different from that of molecules whose connectedness is through covalent bonds. The rings are free to translate along and rotate around the axle, and hence weak interaction forces between the rings can lead to distinct rotamer states. We use energy minimisation to determine these states exactly, and show that there can be transitions from asymmetric to symmetric states by varying the bond lengths. We also use classical statistical mechanics to show the effect of thermal noise.

Sevick, Edith M.; Williams, David R. M.

2014-09-01

108

Toward TeV Conformality  

SciTech Connect

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.

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

109

Conformational Dynamics in DNA Replication Selectivity  

NASA Astrophysics Data System (ADS)

Replicative DNA polymerases are remarkable molecular machines that carry out DNA synthesis accordingly to the Watson and Crick rules (Guanine pairs with Cytosine and Adenine with Thymidine) with high specificity or fidelity. The biochemical mechanism that dictates polymerase fidelity has its fundaments in the tight active site of replicative polymerases and the shape and size of the Watson-Crick base pairs. Pre-steady state kinetic analysis have shown that during polymerase nucleotide addition, the chemical reaction is not the rate limiting step and it was postulated that DNA polymerases suffer a conformational change from an "open" to a "closed" conformation before chemistry which is also the step responsible for their high fidelity. Crystal structures of replicative DNA polymerases demonstrated that the fingers subdomain suffers a large conformational change during catalysis and that this conformational transition aligns the polymerase active site in a proper conformation for catalysis. Recent studies using single molecule techniques and Fluorescence Resonance Energy Transfer analysis also shown that at least in the case of T7 DNA polymerase, the closure of the fingers subdomain is in part the rate limiting step associated with the high fidelity of DNA polymerases, although the overall fidelity of the reaction maybe involves an assemble of chemical steps and several conformational changes. Our current knowledge indicates that the mechanisms of enzyme specificity in DNA replication involve several energy landscapes that maybe correlated with conformational changes and active site assemblies.

Brieba, Luis G.

2007-11-01

110

Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations  

PubMed Central

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843

Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-01-01

111

Conformal Transformations of Pseudo-Rie-mannian manifolds  

E-print Network

. Conformal vector fields can be considered as a natural generalization of Killing vector fields, pp-wave, Penrose limit, twistor spinor Contents 1 Introduction 2 2 Basic concepts 3 3 Flat 9 The transition to the Penrose limit 27 10 Conformal vector fields and twistor spinors 29 This work

Kuehnel, Wolfgang

112

Conformal Transformations of PseudoRie mannian manifolds  

E-print Network

generalization of Killing vector fields. They are also called conformal Killing fields or infinitesimal confor, pp­wave, Penrose limit, twistor spinor Contents 1 Introduction 2 2 Basic concepts 3 3 Flat 9 The transition to the Penrose limit 27 10 Conformal vector fields and twistor spinors 29

Kuehnel, Wolfgang

113

Conformal Radii for Conformal Loop Ensembles  

NASA Astrophysics Data System (ADS)

The conformal loop ensembles CLE ? , defined for 8/3 ? ? ? 8, are random collections of loops in a planar domain which are conjectured scaling limits of the O( n) loop models. We calculate the distribution of the conformal radii of the nested loops surrounding a deterministic point. Our results agree with predictions made by Cardy and Ziff and by Kenyon and Wilson for the O( n) model. We also compute the expectation dimension of the CLE ? gasket, which consists of points not surrounded by any loop, to be 2 - {(8 - kappa)(3kappa - 8)}/{32kappa} , which agrees with the fractal dimension given by Duplantier for the O( n) model gasket.

Schramm, Oded; Sheffield, Scott; Wilson, David B.

2009-05-01

114

Conformations of Substituted Ethanes.  

ERIC Educational Resources Information Center

Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

Kingsbury, Charles A.

1979-01-01

115

Crime and Conformism  

Microsoft Academic Search

We propose a simple conformism model that explains how parental education and peer pressure impact on criminal activities. We then test the model using the U.S. National Longitudinal Survey of Adolescent Health (AddHealth), which contains unique information on friendship relationships among delinquent teenagers. We find that conformity is very strong within groups of delinquents and that the higher the taste

Eleonora Patacchini; Yves Zenou

2005-01-01

116

Conformal radii for conformal loop ensembles  

E-print Network

The conformal loop ensembles CLE(k), defined for k in [8/3, 8], are random collections of loops in a planar domain which are conjectured scaling limits of the O(n) loop models. We calculate the distribution of the conformal radii of the nested loops surrounding a deterministic point. Our results agree with predictions made by Cardy and Ziff and by Kenyon and Wilson for the O(n) model. We also compute the expectation dimension of the CLE(k) gasket, which consists of points not surrounded by any loop, to be 2-(8-k)(3k-8)/32k, which agrees with the fractal dimension given by Duplantier for the O(n) model gasket.

Oded Schramm; Scott Sheffield; David B. Wilson

2006-11-22

117

Discovering conformational sub-states relevant to protein function  

SciTech Connect

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. 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. Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function.

Agarwal, Pratul K [ORNL; Ramanathan, Arvind [ORNL

2011-01-01

118

Conformal Carroll groups  

NASA Astrophysics Data System (ADS)

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.

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

2014-08-01

119

Conformal and non conformal dilaton gravity  

NASA Astrophysics Data System (ADS)

The quantum dynamics of the gravitational field non-minimally coupled to an (also dynamical) scalar field is studied in the broken phase. For a particular value of the coupling the system is classically conformal, and can actually be understood as the group averaging of Einstein-Hilbert's action under conformal transformations. Conformal invariance implies a simple Ward identity asserting that the trace of the equation of motion for the graviton is the equation of motion of the scalar field. We perform an explicit one-loop computation to show that the DeWitt effective action is not UV divergent on shell and to find that the Weyl symmetry Ward identity is preserved on shell at that level. We also discuss the fate of this Ward identity at the two-loop level — under the assumption that the two-loop UV divergent part of the effective action can be retrieved from the Goroff-Sagnotti counterterm — and show that its preservation in the renormalized theory requires the introduction of counterterms which exhibit a logarithmic dependence on the dilaton field.

Alvarez, Enrique; Herrero-Valea, Mario; Martín, C. P.

2014-10-01

120

Transition States, Analogues and Drug Development  

PubMed Central

Enzymes achieve their transition states by dynamic conformational searches on the fsec to psec timescale. 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 tighter than substrates and show promise for drug development for several targets. PMID:23259601

Schramm, Vern L.

2013-01-01

121

The conformal window of deformed conformal field theories in the planar limit  

SciTech Connect

We discuss in the planar approximation the effect of double-trace deformations on conformal field theories. We show that this large class of models posses a conformal window describing a nontrivial flow between two fixed points of the renormalization group and reveal the presence of a resonance which we associate to the remnant of a dilaton pole. As the conformal window shrinks to zero measure, the theory undergoes a conformal phase transition separating a symmetric from a nonsymmetric phase. The recently conjectured strongly coupled branch of nonsupersymmetric, non-Abelian gauge theories with a large number of flavors is analyzed in light of these results, and a model for the strong branch is proposed. Some phenomenological implications in the context of unparticle physics are also emphasized.

Vecchi, Luca [Theoretical Division T-2, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2010-08-15

122

Characterizing Protein Conformation Space  

E-print Network

In this work, we propose a radical approach for exploring the space of all possible protein structures. We present techniques to explore the clash-free conformation space, which comprises all protein structures whose atoms ...

Nigham, Anshul

123

Assemblies of Conformal Tanks  

NASA Technical Reports Server (NTRS)

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.

DeLay, Tom

2009-01-01

124

Essential role of conformational selection in ligand binding.  

PubMed

Two competing and mutually exclusive mechanisms of ligand recognition - conformational selection and induced fit - have dominated our interpretation of ligand binding in biological macromolecules for almost six decades. Conformational selection posits the pre-existence of multiple conformations of the macromolecule from which the ligand selects the optimal one. Induced fit, on the other hand, postulates the existence of conformational rearrangements of the original conformation into an optimal one that are induced by binding of the ligand. In the former case, conformational transitions precede the binding event; in the latter, conformational changes follow the binding step. Kineticists have used a facile criterion to distinguish between the two mechanisms based on the dependence of the rate of relaxation to equilibrium, kobs, on the ligand concentration, [L]. A value of kobs decreasing hyperbolically with [L] has been seen as diagnostic of conformational selection, while a value of kobs increasing hyperbolically with [L] has been considered diagnostic of induced fit. However, this simple conclusion is only valid under the rather unrealistic assumption of conformational transitions being much slower than binding and dissociation events. In general, induced fit only produces values of kobs that increase with [L] but conformational selection is more versatile and is associated with values of kobs that increase with, decrease with or are independent of [L]. The richer repertoire of kinetic properties of conformational selection applies to kinetic mechanisms with single or multiple saturable relaxations and explains the behavior of nearly all experimental systems reported in the literature thus far. Conformational selection is always sufficient and often necessary to account for the relaxation kinetics of ligand binding to a biological macromolecule and is therefore an essential component of any binding mechanism. On the other hand, induced fit is never necessary and only sufficient in a few cases. Therefore, the long assumed importance and preponderance of induced fit as a mechanism of ligand binding should be reconsidered. PMID:24113284

Vogt, Austin D; Pozzi, Nicola; Chen, Zhiwei; Di Cera, Enrico

2014-02-01

125

Conformational heterogeneity of ?-synuclein in membrane.  

PubMed

?-Synuclein (?S) is a natively disordered protein in solution, thought to be involved in the fusion of neurotransmitter vesicles to cellular membranes during neurotransmission. Monomeric ?S has been previously characterized in two distinct membrane-associated conformations: a broken-helix structure, and an extended helix. By employing atomistic molecular dynamics and a novel membrane representation with significantly enhanced lipid mobility (HMMM), we investigate the process of spontaneous membrane binding of ?S and the conformational dynamics of monomeric ?S in its membrane-bound form. By repeatedly placing helical ?S monomers in solution above a planar lipid bilayer and observing their spontaneous association and its spontaneous insertion into the membrane during twenty independent unbiased simulations, we are able to characterize ?S in its membrane-bound state, suggesting that ?S has a highly variable membrane insertion depth at equilibrium. Our simulations also capture two distinct states of ?S, the starting broken-helix conformation seen in the micelle bound NMR structures, and a semi-extended helix. Analysis of lipid distributions near ?S monomers indicates that the transition to a semi-extended helix is facilitated by concentration of phosphatidyl-serine headgroups along the inner edge of the protein. Such a lipid-mediated transition between helix-turn-helix and extended conformations of ?S may also occur in vivo, and may be important for the physiological function of ?S. PMID:25135664

Vermaas, Josh V; Tajkhorshid, Emad

2014-12-01

126

Conformal equivalence of triangle meshes  

Microsoft Academic Search

We present a new algorithm for conformal mesh parameterization. It is based on a precise notion of discrete conformal equivalence for triangle meshes which mimics the notion of conformal equivalence for smooth surfaces. The problem of finding a flat mesh that is discretely conformally equivalent to a given mesh can be solved efficiently by minimizing a convex energy function, whose

Boris Springborn; Peter Schröder; Ulrich Pinkall

2008-01-01

127

Random Conformal Weldings  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\beta$ is in the "high temperature" regime $\\betawelding problem is solved by studying a non-uniformly elliptic Beltrami equation with a random complex dilatation. For the existence a method of Lehto is used. This requires sharp probabilistic estimates to control conformal moduli of annuli and they are proven by decomposing the free field as a sum of independent fixed scale fields and controlling the correlations of the complex dilation restricted to dyadic cells of various scales. For uniqueness we invoke a result by Jones and Smirnov on conformal removability of H\\"older curves. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

Astala, K; Kupiainen, A; Saksman, E

2009-01-01

128

Random Conformal Weldings  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\beta$ is in the "high temperature" regime $\\betawelding problem is solved by studying a non-uniformly elliptic Beltrami equation with a random complex dilatation. For the existence a method of Lehto is used. This requires sharp probabilistic estimates to control conformal moduli of annuli and they are proven by decomposing the free field as a sum of independent fixed scale fields and controlling the correlations of the complex dilation restricted to dyadic cells of various scales. For uniqueness we invoke a result by Jones and Smirnov on conformal removability of H\\"older curves. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-09-07

129

Gravity on Conformal Superspace  

NASA Astrophysics Data System (ADS)

The configuration space of general relativity is superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms. However, it has been argued that the configuration space for gravity should be conformal superspace - the space of all Riemannian 3-metrics modulo diffeomorphisms and conformal transformations. Taking this conformal nature seriously leads to a new theory of gravity which although very similar to general relativity has some very different features particularly in cosmology and quantisation. It should reproduce the standard tests of general relativity. The cosmology is studied in some detail. The theory is incredibly restrictive and as a result admits an extremely limited number of possible solutions. The problems of the standard cosmology are addressed and most remarkably the cosmological constant problem is resolved in a natural way. The theory also has several attractive features with regard to quantisation particularly regarding the problem of time.

Kelleher, Bryan

2003-11-01

130

Conformal Orthosymplectic Quantum Mechanics  

E-print Network

We present the most general curvature obstruction to the deformed parabolic orthosymplectic symmetry subalgebra of the supersymmetric quantum mechanical models recently developed to describe Lichnerowicz wave operators acting on arbitrary tensors and spinors. For geometries possessing a hypersurface-orthogonal homothetic conformal Killing vector we show that the parabolic subalgebra is enhanced to a (curvature-obstructed) orthosymplectic algebra. The new symmetries correspond to time-dependent conformal symmetries of the underlying particle model. We also comment on generalizations germane to three dimensions and new Chern--Simons-like particle models.

J. Burkart; A. Waldron

2008-12-20

131

Conformal orthosymplectic quantum mechanics  

NASA Astrophysics Data System (ADS)

We present the most general curvature obstruction to the deformed parabolic orthosymplectic symmetry subalgebra of the supersymmetric quantum mechanical models recently developed to describe Lichnerowicz wave operators acting on arbitrary tensors and spinors. For geometries possessing a hypersurface-orthogonal homothetic conformal Killing vector we show that the parabolic subalgebra is enhanced to a (curvature-obstructed) orthosymplectic algebra. The new symmetries correspond to time-dependent conformal symmetries of the underlying particle model. We also comment on generalizations germane to three dimensions and new Chern-Simons-like particle models.

Burkart, Joshua; Waldron, Andrew

2009-05-01

132

Random Conformal Weldings  

Microsoft Academic Search

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle. The homeomorphism is constructed using the exponential of $\\\\beta X$ where $X$ is the restriction of the two dimensional free field on the circle and the parameter $\\\\beta$ is in the \\

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-01-01

133

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

134

CHAPTER TWO Conformational Ensemble  

E-print Network

35 3. Generating Starting Structures Based on Templates 36 4. BiHelix: TM Bundle Conformational Sampling of Helix Rotation Angles 38 5. SuperBiHelix TM Bundle Sampling of All Helix Orientation Angles 40 to control G protein-mediated pathways, which gave them their original name. Overwhelming evidence has shown

Goddard III, William A.

135

Taming the conformal zoo  

Microsoft Academic Search

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.

Gregory Moore; Nathan Seiberg

1989-01-01

136

Galilean conformal and superconformal symmetries  

SciTech Connect

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.

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

2012-10-15

137

Conforming quadrilaterals meshes on the cubed sphere.  

SciTech Connect

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.

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

2010-08-01

138

Conformal superspace ?-models  

NASA Astrophysics Data System (ADS)

We review recent developments in the context of two-dimensional conformally invariant ?-models. These quantum field theories play a prominent role in the covariant superstring quantization in flux backgrounds and in the analysis of disordered systems. We present supergroup WZW models as primary examples of logarithmic conformal field theories, whose structure is almost entirely determined by the underlying supergeometry. In particular, we discuss the harmonic analysis on supergroups and supercosets and point out the subtleties of Lie superalgebra representation theory that are responsible for the emergence of logarithmic representations. Furthermore, special types of marginal deformations of supergroup WZW models are studied which only exist if the Killing form is vanishing. We show how exact expressions for anomalous dimensions of boundary fields can be derived using quasi-abelian perturbation theory. Finally, the knowledge of the exact spectrum is used to motivate a duality between the OSP(4|2) symmetric Gross-Neveu model and the S supersphere ?-model.

Mitev, Vladimir; Quella, Thomas; Schomerus, Volker

2011-09-01

139

Quantum conformal fluctuations revisited  

Microsoft Academic Search

The conformal quantization method of Narlikar and Padmanabhan is reformulated with a view to take into account theexact propagator and to provide explicitnumerical estimates of various predictions for dust cosmologies. It is found that in spite of the divergence of quantum fluctuations at the big-bang epoch it is possible to construct wave packets which remain sharp fromt=10?70s, say, up to

J. Lahiri; V. J. Menon

1988-01-01

140

Conformal scalar field wormholes  

NASA Technical Reports Server (NTRS)

The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

Halliwell, Jonathan J.; Laflamme, Raymond

1989-01-01

141

Conformational analysis and stereoelectronic effects in trans-1,2-dihalocyclohexanes: 1H NMR and theoretical investigation  

NASA Astrophysics Data System (ADS)

The conformational equilibrium of trans-1,2-difluoro- ( 1), trans-1,2-dichloro- ( 2) and trans-1,2-dibromo-cyclohexane ( 3) was studied through a combined method of NMR, theoretical calculations and solvation theory. The solvent dependence of the JH,H3 NMR coupling constants together with theoretical calculations allow the direct determination of the conformational equilibria without recourse to model compounds. The coupling constants were obtained with the aid of spectrum simulation, since these symmetric molecules present complex coupling systems. The observed couplings, when analysed by solvation theory and utilising DFT geometries (B3LYP/6-311+G**), gave energy values of Eee - Eaa of 0.10, 0.95 and 1.40 kcal mol -1 in the vapour phase for 1, 2 and 3, respectively, decreasing to -0.63, 0.36 and 0.93 kcal mol -1 in CCl 4 and to -1.91, -0.80 and -0.05 kcal mol -1 in DMSO solution. The diaxial preference for all compounds is explained by natural bond orbital (NBO) analysis, which shows important hyperconjugative effects in this conformation. The " gauche effect" for compounds with more electronegative substituents, which are in gauche arrangement in the ee conformation, also plays a relevant role in more polar solvents.

Freitas, Matheus P.; Rittner, Roberto; Tormena, Cláudio F.; Abraham, Raymond J.

2005-06-01

142

Relaxation time of non-conformal plasma  

E-print Network

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).

Alex Buchel

2009-08-03

143

Mapping L1 Ligase ribozyme conformational switch  

PubMed Central

L1 Ligase (L1L)molecular switch is an in vitro optimized synthetic allosteric ribozyme that catalyzes the regioselective formation of a 5’-to-3’ phosphodiester bond, a reaction for which there is no known naturally occurring RNA catalyst. L1L serves as a proof of principle that RNA can catalyze a critical reaction for prebiotic RNA self-replication according to the RNA World hypothesis. L1L crystal structure captures two distinct conformations that differ by a re-orientation of one of the stems by around 80 Å and are presumed to correspond to the active and inactive state, respectively. It is of great interest to understand the nature of these two states in solution, and the pathway for their interconversion. In this study, we use explicit solvent molecular simulation together with a novel enhanced sampling method that utilizes concepts from network theory to map out the conformational transition between active and inactive states of L1L. We find that the overall switching mechanism can be described as a 3-state/2-step process. The first step involves a large-amplitude swing that re-orients stem C. The second step involves the allosteric activation of the catalytic site through distant contacts with stem C. Using a conformational space network representation of the L1L switch transition, it is shown that the connection between the three states follows different topographical patterns: the stem C swing step passes through a narrow region of the conformational space network, whereas the allosteric activation step covers a much wider region and a more diverse set of pathways through the network. PMID:22771572

Giambasu, George M.; Lee, Tai-Sung; Scott, William G.; York, Darrin M.

2012-01-01

144

Conformal superalgebras via tractor calculus  

E-print Network

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.

Andree Lischewski

2014-08-10

145

Conformal Fluid Dynamics  

E-print Network

We present a conformal theory of a dissipationless relativistic fluid in 2 space-time dimensions. The theory carries with it a representation of the algebra of 2-$D$ area-preserving diffeomorphisms in the target space of the complex scalar potentials. A complete canonical description is given, and the central charge of the current algebra is calculated. The passage to the quantum theory is discussed in some detail; as a result of operator ordering problems, full quantization at the level of the fields is as yet an open problem.

P. D. Jarvis; J. W. van Holten

2005-01-28

146

Higgs effect in Conformal Cosmology & Supernova Data  

E-print Network

The formulation of the Higgs effect is studied in the Glashow--Weinberg--Salam Standard Model, where the constant part of the Higgs potential is identified with the zeroth mode of the Higgs field. In this model, the Coleman--Weinberg effective potential obtained from the vacuum--vacuum transition amplitude is equal to unity at the extremum. This extremum immediately removes tremendous vacuum cosmological density and predicts mass of Higgs field. In this model, the kinetic energy density of the Higgs field and any scalar field can be treated as the rigid state origin that explains Supernova data in the conformal cosmology without the $\\Lambda$ term.

B. M. Barbashov; L. A. Glinka; V. N. Pervushin; A. F. Zakharov

2007-04-30

147

Modeling active GPCR conformations.  

PubMed

The most significant advance in modeling GPCR active states has been the ?(2)-adrenergic receptor-Gs complex as this essentially transforms active-state modeling into homology modeling. Various different molecular dynamics-based approaches for modeling active states are presented, and a number of key applications discussed. These simulations have given insights into the activation pathway, conformational changes, dimerization, hydration, the ionic lock, ligand binding, protonation, and sodium binding. Crystallography and simulations have shown that the presence of agonist alone is unlikely to be sufficient to form the active state and that restraints applied to the G protein-binding region are required. The role of various microswitches in activation is discussed, including the controversial rotamer toggle switch. The importance of explicitly simulating experimental molecular probes to understand activation is highlighted, along with the need to ensure that such molecules are well parameterized. Approaches to loop modeling are discussed. We argue that the role of successful virtual screening against active models should not be overestimated as the main conformational changes on activation occur in the intracellular region. PMID:23374178

Taddese, Bruck; Simpson, Lisa M; Wall, Ian D; Blaney, Frank E; Reynolds, Christopher A

2013-01-01

148

Dissecting conformational contributions to glycosidase catalysis and inhibition  

PubMed Central

Glycoside hydrolases (GHs) are classified into >100 sequence-based families. These enzymes process a wide variety of complex carbohydrates with varying stereochemistry at the anomeric and other ring positions. The shapes that these sugars adopt upon binding to their cognate GHs, and the conformational changes that occur along the catalysis reaction coordinate is termed the conformational itinerary. Efforts to define the conformational itineraries of GHs have focussed upon the critical points of the reaction: substrate-bound (Michaelis), transition state, intermediate (if relevant) and product-bound. Recent approaches to defining conformational itineraries that marry X-ray crystallography of enzymes bound to ligands that mimic the critical points, along with advanced computational methods and kinetic isotope effects are discussed. PMID:25016573

Speciale, Gaetano; Thompson, Andrew J; Davies, Gideon J; Williams, Spencer J

2014-01-01

149

Intramolecular conformational changes optimize protein kinase C signaling.  

PubMed

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 multidomain signal transducer, protein kinase C (PKC), for optimal response to second messengers. This enzyme comprises two diacylglycerol sensors, the C1A and C1B domains, that have a sufficiently high intrinsic affinity for ligand so 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 PKC and that conformational transitions following priming phosphorylations mask the domains so that the lower affinity sensor, the C1B domain, is the primary diacylglycerol binder. The conformational rearrangements of PKC serve as a paradigm for how multimodule transducers optimize their dynamic range of signaling. PMID:24631122

Antal, Corina E; Violin, Jonathan D; Kunkel, Maya T; Skovsø, Søs; Newton, Alexandra C

2014-04-24

150

Ab initio molecular orbital study of conformational properties of cyclohexyne, cycloheptyne, and cyclooctyne  

Microsoft Academic Search

The structures and relative energies for the basic conformations of cyclohexyne (1), cycloheptyne (2), and cyclooctyne (3) have been calculated by the HF\\/6-31G*, MP2\\/6-31G*, and B3LYP\\/6-31G* methods. The C2 symmetric twist conformer of 1 is calculated to be more stable than the planar C2v geometry. Ring inversion of the envelope conformation of 2 takes place via C2 symmetric twist transition

Issa Yavari; Farough Nasiri; Hoorieh Djahaniani; Arash Jabbari

2006-01-01

151

Conformations of amphiphilic polyelectrolyte stars with diblock copolymer arms  

E-print Network

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.

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

2012-05-12

152

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

NASA Astrophysics Data System (ADS)

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.

William, Peter

1991-01-01

153

The QCD string spectrum and conformal field theory  

SciTech Connect

The low energy excitation spectrum of the critical Wilson surface is discussed between the roughening transition and the continuum limit of lattice QCD. The fine structure of the spectrum is interpreted within the framework of two-dimensional conformal field theory.

Keisuke Jimmy Juge; Julius Kuti; Colin Morningstar

2002-12-19

154

The QCD string spectrum and conformal field theory  

Microsoft Academic Search

The low energy excitation spectrum of the critical Wilson surface is discussed between the roughening transition and the continuum limit of lattice QCD. The fine structure of the spectrum is interpreted within the framework of two-dimensional conformal field theory.

Keisuke Jimmy Juge; Julius Kuti; Colin Morningstar

2002-01-01

155

Conformational Properties of Unfolded Proteins Patrick J. Fleming and George D. Rose  

E-print Network

20 Conformational Properties of Unfolded Proteins Patrick J. Fleming and George D. Rose 20 of denaturing solvents; but they fold to uniquely ordered, biologically relevant conformers (N) under physiological condi- tions. This folding transition is highly cooperative such that individual molecules within

Fleming, Patrick

156

Logarithmic Conformal Field Theory Through Nilpotent Conformal Dimensions  

E-print Network

We study logarithmic conformal field theories (LCFTs) through the introduction of nilpotent conformal weights. Using this device, we derive the properties of LCFT's such as the transformation laws, singular vectors and the structure of correlation functions. We discuss the emergence of an extra energy momentum tensor, which is the logarithmic partner of the energy momentum tensor.

Moghimi-Araghi, S; Saadat, M

2001-01-01

157

Fe-heme conformations in ferric myoglobin.  

PubMed Central

X-ray absorption near-edge structure (XANES) spectra of ferric myoglobin from horse heart have been acquired as a function of pH (between 5.3 and 11.3). At pH = 11.3 temperature-dependent spectra (between 20 and 293 K) have been collected as well. Experimental data solve three main conformations of the Fe-heme: the first, at low pH, is related to high-spin aquomet-myoglobin (Mb+OH2). The other two, at pH 11.3, are related to hydroxymet-myoglobin (Mb+OH-), and are in thermal equilibrium, corresponding to high- and low-spin Mb+OH-. The structure of the three Fe-heme conformations has been assigned according to spin-resolved multiple scattering simulations and fitting of the XANES data. The chemical transition between Mb+OH2 and high-spin Mb+OH-, and the spin transition of Mb+OH-, are accompanied by changes of the Fe coordination sphere due to its movement toward the heme plane, coupled to an increase of the axial asymmetry. PMID:9826636

Longa, S D; Pin, S; Cortes, R; Soldatov, A V; Alpert, B

1998-01-01

158

Replacement between conformity and counter-conformity in consumption decisions.  

PubMed

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

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

2013-02-01

159

The Principle of Maximum Conformality  

SciTech Connect

A key problem in making precise perturbative QCD predictions is the uncertainty in determining the renormalization scale of the running coupling {alpha}{sub s}({mu}{sup 2}). It is common practice to guess a physical scale {mu} = Q which is of order of a typical momentum transfer Q in the process, and then vary the scale over a range Q/2 and 2Q. This procedure is clearly problematic since the resulting fixed-order pQCD prediction will depend on the renormalization scheme, and it can even predict negative QCD cross sections at next-to-leading-order. Other heuristic methods to set the renormalization scale, such as the 'principle of minimal sensitivity', give unphysical results for jet physics, sum physics into the running coupling not associated with renormalization, and violate the transitivity property of the renormalization group. Such scale-setting methods also give incorrect results when applied to Abelian QED. Note that the factorization scale in QCD is introduced to match nonperturbative and perturbative aspects of the parton distributions in hadrons; it is present even in conformal theory and thus is a completely separate issue from renormalization scale setting. The PMC provides a consistent method for determining the renormalization scale in pQCD. The PMC scale-fixed prediction is independent of the choice of renormalization scheme, a key requirement of renormalization group invariance. The results avoid renormalon resummation and agree with QED scale-setting in the Abelian limit. The PMC global scale can be derived efficiently at NLO from basic properties of the PQCD cross section. The elimination of the renormalization scheme ambiguity using the PMC will not only increases the precision of QCD tests, but it will also increase the sensitivity of colliders to new physics beyond the Standard Model.

Brodsky, Stanley J; /SLAC; Giustino, Di; /SLAC

2011-04-05

160

Conformal Transformations and Space Travel  

Microsoft Academic Search

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.

Suraj N. Gupta

1961-01-01

161

Counselor Identity: Conformity or Distinction?  

ERIC Educational Resources Information Center

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.

McLaughlin, Jerry E.; Boettcher, Kathryn

2009-01-01

162

The logarithmic conformal field theories  

E-print Network

We study the correlation functions of logarithmic conformal field theories. First, assuming conformal invariance, we explicitly calculate two- and three- point functions. This calculation is done for the general case of more than one logarithmic field in a block, and more than one set of logarithmic fields. Then we show that one can regard the logarithmic field as a formal derivative of the ordinary field with respect to its conformal weight. This enables one to calculate any n-point function containing the logarithmic field in terms of ordinary n-point functions. At last, we calculate the OPE coefficients of a logarithmic conformal field theory, and show that these can be obtained from the corresponding coefficients of ordinary conformal theory by a simple derivation.

Tabar, M R R; Khorrami, M

1996-01-01

163

Unprecedented conformational variability in main group inorganic chemistry: the tetraazidoarsenite and -antimonite salts A+ [M(N3)4]- (A = NMe4, PPh4, (Ph3P)2N; M = As, Sb), five similar salts, five different anion structures.  

PubMed

A unique example for conformational variability in inorganic main group chemistry has been discovered. The arrangement of the azido ligands in the pseudotrigonal bipyramidal [As(N(3))(4)](-) and [Sb(N(3))(4)](-) anions theoretically can give rise to seven different conformers which have identical MN(4) skeletons but different azido ligand arrangements and very similar energies. We have now synthesized and structurally characterized five of these conformers by subtle variations in the nature of the counterion. Whereas conformational variability is common in organic chemistry, it is rare in inorganic main group chemistry and is usually limited to two. To our best knowledge, the experimental observation of five distinct single conformers for the same type of anion is unprecedented. Theoretical calculations at the M06-2X/cc-pwCVTZ-PP level for all seven possible basic conformers show that (1) the energy differences between the five experimentally observed conformers are about 1 kcal/mol or less, and (2) the free monomeric anions are the energetically favored species in the gas phase and also for [As(N(3))(4)](-) in the solid state, whereas for [Sb(N(3))(4)](-) associated anions are energetically favored in the solid state and possibly in solutions. Raman spectroscopy shows that in the azide antisymmetric stretching region, the solid-state spectra are distinct for the different conformers, and permits their identification. The spectra of solutions are solvent dependent and differ from those of the solids indicating the presence of rapidly exchanging equilibria of different conformers. The only compound for which a solid with a single well-ordered conformer could not be isolated was [N(CH(3))(4)][As(N(3))(4)] which formed a viscous, room-temperature ionic liquid. Its Raman spectrum was identical to that of its CH(3)CN solution indicating the presence of an equilibrium of multiple conformers. PMID:23214472

Haiges, Ralf; Rahm, Martin; Christe, Karl O

2013-01-01

164

6d Conformal Matter  

E-print Network

A single M5-brane probing G, an ADE-type singularity, leads to a system which has G x 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 Horava-Witten wall leads to a superconformal matter system with E_8 x 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 Horava-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.

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

2014-07-23

165

Dynamics of protein conformations  

NASA Astrophysics Data System (ADS)

A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

Stepanova, Maria

2010-10-01

166

Warped conformal field theory  

NASA Astrophysics Data System (ADS)

We study field theories in two spacetime dimensions invariant under a chiral scaling symmetry that acts only on right-movers. The local symmetries include one copy of the Virasoro algebra and a U(1) current algebra. This differs from the two-dimensional conformal group but in some respects is equally powerful in constraining the theory. In particular, the symmetries on a torus lead to modular covariance of the partition function, which is used to derive a universal formula for the asymptotic density of states. For an application we turn to the holographic description of black holes in quantum gravity, motivated by the fact that the symmetries in the near-horizon geometry of any extremal black hole are identical to those of a two-dimensional field theory with chiral scaling. We consider two examples: black holes in warped AdS3 in topologically massive gravity and in string theory. In both cases, the density of states in the two-dimensional field theory reproduces the Bekenstein-Hawking entropy of black holes in the gravity theory.

Detournay, Stéphane; Hartman, Thomas; Hofman, Diego M.

2012-12-01

167

Intrinsically disordered proteins and conformational noise: implications in cancer.  

PubMed

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

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

2013-01-01

168

40 CFR 51.854 - Conformity analysis.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51...OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State...Implementation Plans § 51.854 Conformity analysis. Link to an amendment...

2010-07-01

169

40 CFR 93.154 - Conformity analysis.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

2010-07-01

170

40 CFR 52.2133 - General conformity.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52.2133 Protection...CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South...

2010-07-01

171

40 CFR 52.138 - Conformity procedures.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Conformity procedures. 52.138 Section 52...IMPLEMENTATION PLANS Arizona § 52.138 Conformity procedures. (a) Purpose...organizations (MPOs) to use when determining conformity of transportation plans,...

2010-07-01

172

40 CFR 52.938 - General conformity.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false General conformity. 52.938 Section 52.938 Protection...IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November...

2010-07-01

173

40 CFR 52.799 - Transportation conformity.  

Code of Federal Regulations, 2013 CFR

...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,...

2013-07-01

174

40 CFR 52.799 - Transportation conformity.  

Code of Federal Regulations, 2011 CFR

...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,...

2011-07-01

175

40 CFR 52.799 - Transportation conformity.  

Code of Federal Regulations, 2012 CFR

...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,...

2012-07-01

176

40 CFR 52.799 - Transportation conformity.  

...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,...

2014-07-01

177

Hunting for the Conformal Window  

E-print Network

Undeniably, the imminent activity of LHC and the quest for the nature of physics beyond the standard model have raised renewed interest in the conformal and quasi-conformal behaviour of gauge field theories with matter content. Theoretically driven questions seem to now acquire a strong experimental appeal and might guide us towards a more realistic string theory to field theory connection, originally inspired by the AdS/CFT conjecture. In this brief report, we discuss the state of the art of our search for the conformal window in the SU(3) colour-gauge theory with fermions in the fundamental representation.

A. Deuzeman; M. P. Lombardo; E. Pallante

2008-10-17

178

Lattice Simulations and Infrared Conformality  

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 it does work well for another theory expected to be infrared conformal.

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

2011-09-01

179

Conformal mapping of rectangular heptagons  

SciTech Connect

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.

Bogatyrev, Andrei B

2012-12-31

180

CONFORMANCE IMPROVEMENT USING GELS  

SciTech Connect

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.

Randall S. Seright

2004-09-30

181

Chameleonic dilaton and conformal transformations  

E-print Network

We recently proposed a chameleonic solution to the cosmological constant problem - Phys. Rev. D82 (2010) 044006. One of the results of that paper is a non-equivalence of different conformal frames at the quantum level. In this letter we further discuss our proposal focusing our attention on the conformal transformation. Moreover, we point out that a different choice of parameters is necessary in the model.

Andrea Zanzi

2012-06-20

182

Instability of Human Societies as a Result of Conformity  

NASA Astrophysics Data System (ADS)

We introduce a new model that mimics the strong and sudden effects induced by conformity in tightly interacting human societies. Such effects range from mere crowd phenomena to dramatic political turmoil. The model is a modified version of the Ising Hamiltonian. We have studied the properties of this Hamiltonian using both a Metropolis simulation and analytical derivations. Our study shows that increasing the value of the conformity parameter, results in a first order phase transition. As a result a majority of people begin to honestly support the idea that may contradict the moral principles of a normal human beings though each individual would support the moral principle without tight interaction with the society. Thus, above some critical level of conformity our society destabilizes with respect to ideas that might be doubtful. Our model includes, in a simplified way, human diversity with respect to loyalty to the moral principles.

Efros, A. L.; Désesquelles, P.

183

Extensive conformational heterogeneity within protein cores.  

PubMed

Basic principles of statistical mechanics require that proteins sample an ensemble of conformations at any nonzero temperature. However, it is still common to treat the crystallographic structure of a protein as the structure of its native state, largely because high-resolution structural characterization of protein flexibility remains a profound challenge. To assess the typical degree of conformational heterogeneity within folded proteins, we construct Markov state models describing the thermodynamics and kinetics of proteins ranging from 72 to 263 residues in length. Each of these models is built from hundreds of microseconds of atomically detailed molecular dynamics simulations. Examination of the side-chain degrees of freedom reveals that almost every residue visits at least two rotameric states over this time frame, with rotamer transition rates spanning a wide range of time scales (from nanoseconds to tens of microseconds). We also report substantial backbone dynamics on time scales longer than are typically addressed by experimental measures of protein flexibility, such as NMR order parameters. Finally, we demonstrate that these extensive rearrangements are consistent with NMR and crystallographic data, which supports the validity of our models. Altogether, these results depict the interior of proteins not as well-ordered solids, as is often imagined, but instead as dense fluids, which undergo substantial structural fluctuations despite their high packing fraction. PMID:24564338

Bowman, Gregory R; Geissler, Phillip L

2014-06-19

184

CONFORMANCE IMPROVEMENT USING GELS  

SciTech Connect

This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the flow capacity of fractures (with widths from 1 to 4 mm) during brine and oil flow after placement. Regardless of gel age before placement, very little gel washed out from the fractures during brine or oil flow. However, increased brine or oil flow rate and cyclic injection of oil and water significantly decreased the level of permeability reduction. A particular need exists for gels that can plug large apertures (e.g., wide fractures and vugs). Improved mechanical strength and stability were demonstrated (in 1- to 4-mm-wide fractures) for a gel that contained a combination of high- and low-molecular weight polymers. This gel reduced the flow capacity of 2- and 4-mm-wide fractures by 260,000. In a 1-mm-wide fracture, it withstood 26 psi/ft without allowing any brine flow through the fracture. Cr(III)-acetate-HPAM gels exhibited disproportionate permeability reduction in fractures. The effect was most pronounced when the gel was placed as gelant or partially formed gels. The effect occurred to a modest extent with concentrated gels and with gels that were ''fully formed'' when placed. The effect was not evident in tubes. We explored swelling polymers for plugging fractures. Polymer suspensions were quickly prepared and injected. In concept, the partially dissolved polymer would lodge and swell to plug the fracture. For three types of swelling polymers, behavior was promising. However, additional development is needed before their performance will be superior to that of conventional gels.

Randall S. Seright

2003-09-01

185

Crystal structure of thrombin in a self-inhibited conformation.  

PubMed

The activating effect of Na(+) on thrombin is allosteric and depends on the conformational transition from a low activity Na(+)-free (slow) form to a high activity Na(+)-bound (fast) form. The structures of these active forms have been solved. Recent structures of thrombin obtained in the absence of Na(+) have also documented inactive conformations that presumably exist in equilibrium with the active slow form. The validity of these inactive slow form structures, however, is called into question by the presence of packing interactions involving the Na(+) site and the active site regions. Here, we report a 1.87A resolution structure of thrombin in the absence of inhibitors and salts with a single molecule in the asymmetric unit and devoid of significant packing interactions in regions involved in the allosteric slow --> fast transition. The structure shows an unprecedented self-inhibited conformation where Trp-215 and Arg-221a relocate >10A to occlude the active site and the primary specificity pocket, and the guanidinium group of Arg-187 penetrates the protein core to fill the empty Na(+)-binding site. The extreme mobility of Trp-215 was investigated further with the W215P mutation. Remarkably, the mutation significantly compromises cleavage of the anticoagulant protein C but has no effect on the hydrolysis of fibrinogen and PAR1. These findings demonstrate that thrombin may assume an inactive conformation in the absence of Na(+) and that its procoagulant and anticoagulant activities are closely linked to the mobility of residue 215. PMID:16954215

Pineda, Agustin O; Chen, Zhi-Wei; Bah, Alaji; Garvey, Laura C; Mathews, F Scott; Di Cera, Enrico

2006-10-27

186

Single-conformation spectroscopy in the complexity gap: Synthetic foldamers  

Microsoft Academic Search

A fully predictive model of the sequence-structure-function relationship is a primary goal of biophysical chemistry. In order to realize this goal, a quantitative understanding of all conformational minima, transition states, and isomerization pathways on a molecule’s potential energy surface must be achieved. This effort is hindered by the dramatic increase in complexity exhibited by proteins as the number of residues

William H. James

2009-01-01

187

Self-Dual Conformal Gravity  

E-print Network

We find necessary and sufficient conditions for a Riemannian four-dimensional manifold $(M, g)$ with anti-self-dual Weyl tensor to be locally conformal to a Ricci-flat manifold. These conditions are expressed as vanishing of scalar and tensor conformal invariants. The invariants obstruct the existence of parallel sections of a certain connection on a complex rank-four vector bundle over $M$. They provide a natural generalisation of the Bach tensor which vanishes identically for anti-self-dual conformal structures. We use the obstructions to demonstrate that LeBrun's anti-self-dual metrics on connected sums of $\\CP^2$s are not conformally Ricci-flat on any open set. We analyze both the Riemannian and the neutral signature metrics. In the latter case we find all anti-self-dual metrics with parallel real spinor which are locally conformal to Einstein metrics with non-zero cosmological constant. These metrics admit a hyper-surface orthogonal null Killing vector and thus give rise to projective structures on the s...

Dunajski, Maciej

2013-01-01

188

Self-Dual Conformal Gravity  

E-print Network

We find necessary and sufficient conditions for a Riemannian four-dimensional manifold $(M, g)$ with anti-self-dual Weyl tensor to be locally conformal to a Ricci--flat manifold. These conditions are expressed as the vanishing of scalar and tensor conformal invariants. The invariants obstruct the existence of parallel sections of a certain connection on a complex rank-four vector bundle over $M$. They provide a natural generalisation of the Bach tensor which vanishes identically for anti-self-dual conformal structures. We use the obstructions to demonstrate that LeBrun's anti-self-dual metrics on connected sums of $\\CP^2$s are not conformally Ricci-flat on any open set. We analyze both Riemannian and neutral signature metrics. In the latter case we find all anti-self-dual metrics with a parallel real spinor which are locally conformal to Einstein metrics with non-zero cosmological constant. These metrics admit a hyper-surface orthogonal null Killing vector and thus give rise to projective structures on the space of $\\beta$-surfaces.

Maciej Dunajski; Paul Tod

2013-04-29

189

Self-Dual Conformal Gravity  

NASA Astrophysics Data System (ADS)

We find necessary and sufficient conditions for a Riemannian four-dimensional manifold ( M, g) with anti-self-dual Weyl tensor to be locally conformal to a Ricci-flat manifold. These conditions are expressed as the vanishing of scalar and tensor conformal invariants. The invariants obstruct the existence of parallel sections of a certain connection on a complex rank-four vector bundle over M. They provide a natural generalisation of the Bach tensor which vanishes identically for anti-self-dual conformal structures. We use the obstructions to demonstrate that LeBrun's anti-self-dual metrics on connected sums of s are not conformally Ricci-flat on any open set. We analyze both Riemannian and neutral signature metrics. In the latter case we find all anti-self-dual metrics with a parallel real spinor which are locally conformal to Einstein metrics with non-zero cosmological constant. These metrics admit a hyper-surface orthogonal null Killing vector and thus give rise to projective structures on the space of ?-surfaces.

Dunajski, Maciej; Tod, Paul

2014-10-01

190

Interacting electrons in ballistic conformal billiard quantum dots  

NASA Astrophysics Data System (ADS)

Interacting electrons in a ballistic quantum dot present a novel regime of disorder + interactions. An instability of the ground state towards a spontaneous deformation of the Fermi surface (the Pomeranchuk transition) has been found by the present authors[1], by assuming that Random Matrix Theory describes the states in the Thouless shell near the Fermi energy. However, the question of whether the mesoscopic transition occurs before the bulk transition remains open[2]. Here we describe calculations on the conformal billiard[3] and attempt to see how well RMT assumptions hold, and to what extent the physics of the transition is described by our previous work. 1. G. Murthy, R. Shankar, D. Herman, and H. Mathur, cond-mat/0306529. 2. S. Adam, P. W. Brouwer, and P. Sharma, cond-mat/0309074. 3. M. V. Berry and M. Robnik, J. Phys. A19, 669 (1986).

Murthy, Ganpathy; Mathur, Harsh; Shankar, Ramamurti

2004-03-01

191

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

Microsoft Academic Search

Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein\\/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein\\/ligand complexes if

Daniel Seeliger; Bert L. de Groot

2010-01-01

192

Conformal curvature flows: From phase transitions to active vision  

Microsoft Academic Search

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

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

1996-01-01

193

Conformal Curvature Flows: From Phase Transitions to Active Vision  

Microsoft Academic Search

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

Satyanad Kichenassamy; Arun Kumar

1995-01-01

194

Conformally Invariant Equations for Graviton  

E-print Network

Recent astrophysical data indicate that our universe might currently be in a de Sitter (dS) phase. The importance of dS space has been primarily ignited by the study of the inflationary model of the universe and the quantum gravity. As we know Einstein's theory of gravitation (with a nonzero cosmological constant) can be interpreted as a theory of a metric field; that is, a symmetric tensor field of rank-2 on a fixed de Sitter background. It has been shown that the massless spin-2 Fierz-Pauli wave equation (or the linearized Einstein equation) is not conformally invariant. This result is in contrary with what we used to expect for massless theories. In this thesis we obtain conformally invariant wave equation for the massless spin-2 in the dS space. This study is motivated by the belief that conformal invariance may be the key to a future theory of quantum gravity.

Mohsen Fathi

2012-10-12

195

NIR Laser Radiation Induced Conformational Changes and Tunneling Lifetimes of High-Energy Conformers of Amino Acids in Low-Temperature Matrices  

NASA Astrophysics Data System (ADS)

We review our recent results on combined matrix isolation FT-IR and NIR laser irradiation studies on glycine alanine, and cysteine. The OH and the NH stretching overtones of the low-energy conformers of these amino acids deposited in Ar, Kr, Xe, and N_{2} matrices were irradiated. At the expense of the irradiated conformer, other conformers were enriched and new, high-energy, formerly unobserved conformers were formed in the matrices. This enabled the separation and unambiguous assignment of the vibrational transitions of the different conformers. The main conversion paths and their efficiencies are described qualitatively showing that there are significant differences in different matrices. It was shown that the high-energy conformer decays in the matrix by H-atom tunneling. The lifetimes of the high-energy conformers in different matrices were measured. Based on our results we conclude that some theoretically predicted low-energy conformers of amino acids are likely even absent in low-energy matrices due to fast H-atom tunneling. G. Bazso, G. Magyarfalvi, G. Tarczay J. Mol. Struct. 1025 (Light-Induced Processes in Cryogenic Matrices Special Issue) 33-42 (2012). G. Bazso, G. Magyarfalvi, G. Tarczay J. Phys. Chem. A 116 (43) 10539-10547 (2012). G. Bazso, E. E. Najbauer, G. Magyarfalvi, G. Tarczay J. Phys. Chem. A in press, DOI: 10.1021/jp400196b. E. E. Najbauer, G. Bazso, G. Magyarfalvi, G. Tarczay in preparation.

Bazso, Gabor; Najbauer, Eszter E.; Magyarfalvi, Gabor; Tarczay, Gyorgy

2013-06-01

196

New optimization method for conformational energy calculations on polypeptides: Conformational space annealing  

Microsoft Academic Search

A new optimization method is presented to search for the global minimum-energy conformations of polypeptides. The method combines essential aspects of the build-up procedure and the genetic algorithm, and it introduces the important concept of ''conformational space annealing.'' Instead of considering a single conformation, attention is focused on a population of conformations while new conformations are obtained by modifying a

Jooyoung Lee; Harold A. Scheraga; Shelly Rackovsky

1997-01-01

197

Conformal invariance of domino tiling  

E-print Network

Let U be a multiply-connected region in R^2 with smooth boundary. Let P_epsilon be a polyomino in epsilon Z^2 approximating U as epsilon tends to 0. We show that, for certain boundary conditions on P_epsilon, the height distribution on a random domino tiling (dimer covering) of P_epsilon is conformally invariant in the limit as epsilon tends to 0, in the sense that the distribution of heights of boundary components only depends on the conformal type of U. The mean height and all the moments are explicitly evaluated.

Richard Kenyon

1999-10-01

198

Basics in Conformal Field Theory  

NASA Astrophysics Data System (ADS)

The approach for studying Conformal Field Theories is somewhat different from the usual approach for Quantum Field Theories. Because, instead of starting with a classical action for the fields and quantising them via the canonical quantisation or the path integral method, one employs the symmetries of the theory. In the spirit of the so-called boot-strap approach, for CFTs one defines and for certain cases even solves the theory just by exploiting the consequences of the symmetries. Such a procedure is possible in two dimensions because the algebra of infinitesimal conformal transformations in this case is very special: it is infinite dimensional.

Blumenhagen, Ralph; Plauschinn, Erik

199

Conformal Transformations and Quantum Gravity  

E-print Network

Recently\\cite{BQG}, it was shown that quantum effects of matter could be identified with the conformal degree of freedom of the space-time metric. Accordingly, one can introduce quantum effects either by making a scale transformation (i.e. changing the metric), or by making a conformal transformation (i.e. changing all physical quantities). These two ways are investigated and compared. Also, it is argued that, the ultimate formulation of such a quantum gravity theory should be in the framework of the scalar-tensor theories.

Fatimah Shojai; Ali Shojai; Mehdi Golshani

1999-03-13

200

Social influence: compliance and conformity.  

PubMed

This review covers recent developments in the social influence literature, focusing primarily on compliance and conformity research published between 1997 and 2002. The principles and processes underlying a target's susceptibility to outside influences are considered in light of three goals fundamental to rewarding human functioning. Specifically, targets are motivated to form accurate perceptions of reality and react accordingly, to develop and preserve meaningful social relationships, and to maintain a favorable self-concept. Consistent with the current movement in compliance and conformity research, this review emphasizes the ways in which these goals interact with external forces to engender social influence processes that are subtle, indirect, and outside of awareness. PMID:14744228

Cialdini, Robert B; Goldstein, Noah J

2004-01-01

201

Combined Inhibitor Free-Energy Landscape and Structural Analysis Reports on the Mannosidase Conformational Coordinate**  

PubMed Central

Mannosidases catalyze the hydrolysis of a diverse range of polysaccharides and glycoconjugates, and the various sequence-based mannosidase families have evolved ingenious strategies to overcome the stereoelectronic challenges of mannoside chemistry. Using a combination of computational chemistry, inhibitor design and synthesis, and X-ray crystallography of inhibitor/enzyme complexes, it is demonstrated that mannoimidazole-type inhibitors are energetically poised to report faithfully on mannosidase transition-state conformation, and provide direct evidence for the conformational itinerary used by diverse mannosidases, including ?-mannanases from families GH26 and GH113. Isofagomine-type inhibitors are poor mimics of transition-state conformation, owing to the high energy barriers that must be crossed to attain mechanistically relevant conformations, however, these sugar-shaped heterocycles allow the acquisition of ternary complexes that span the active site, thus providing valuable insight into active-site residues involved in substrate recognition. PMID:24339341

Williams, Rohan J; Iglesias-Fernandez, Javier; Stepper, Judith; Jackson, Adam; Thompson, Andrew J; Lowe, Elisabeth C; White, Jonathan M; Gilbert, Harry J; Rovira, Carme; Davies, Gideon J; Williams, Spencer J

2014-01-01

202

Development of conformity and independence  

Microsoft Academic Search

Investigated age trends in conformity and independence with a total of 366 children from Grades 1, 4, 7, and 10. 3 types of stimuli were used: visual judgments, opinion statements, and delay of gratification preferences. Age trends were found for unanimous peer pressure, adult influence, and peer pressure with social support from a partner. Unanimous peer pressure generally produced decreasing

Vernon L. Allen; Darren Newtson

1972-01-01

203

Correct Representation of Conformational Equilibria.  

ERIC Educational Resources Information Center

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…

Fulop, F.; And Others

1983-01-01

204

Random curves by conformal welding  

Microsoft Academic Search

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE(?) for ?4.

Kari Astala; Peter Jones; Antti Kupiainen; Eero Saksman

2010-01-01

205

Random Curves by Conformal Welding  

Microsoft Academic Search

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\\\kappa)$ for $\\\\kappa<4$.

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-01-01

206

Fragment-based Conformant Planning  

Microsoft Academic Search

With complex systems such as spacecraft, we often need to achieve goals even though failures prevent the exact state of the system from being determined. Conformant planning is the problem of generating a plan that moves a system from any of a number of possible initial states to a goal state, given that actions may have uncertain outcomes and sensing

James Kurien; P. Pandurang Nayak; David E. Smith

2002-01-01

207

Random Curves by Conformal Welding  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

Astala, K; Kupiainen, A; Saksman, E

2009-01-01

208

Conformal Welding And Koebe's Theorem  

Microsoft Academic Search

It is well known that not every orientation preserving homeomorphismof the circle to itself is a conformal welding, but in this paper we prove severalresults which state that every homeomorphism is \\\\almost" a welding in dierentways. The proofs are based on Koebe's circle domain theorem. We also give a newproof, based on Koebe's theorem, of the well known fact that

Christopher J. Bishop

2003-01-01

209

CONFORMAL WELDING OF JORDAN CURVES  

Microsoft Academic Search

This paper gives an alternative description of Lehto's results on homeomorphisms which admit conformal welding (6). A normal families argument is controlled by the action of the homeomorphism as a composition operator on weighted Dirichlet spaces. This point of view admits a discussion of uniqueness.

Gavin L. Jones

210

Random Curves by Conformal Welding  

E-print Network

We construct a conformally invariant random family of closed curves in the plane by welding of random homeomorphisms of the unit circle given in terms of the exponential of Gaussian Free Field. We conjecture that our curves are locally related to SLE$(\\kappa)$ for $\\kappa<4$.

K. Astala; P. Jones; A. Kupiainen; E. Saksman

2009-12-17

211

Air Quality Conformity Trip Generation  

E-print Network

Legislation · Federal Clean Air Act (1963, 1970, 1990) · State Clean Air Act (1969, 1988) #12;Air QualityAir Quality Conformity TTP220 S. Handy 4/30/14 #12;Trip Generation Trip Distribution Mode Split - Air Quality Pollutant Emissions Travel Demand Model + Emissions Model #12;GOAL #12;Air Quality

Handy, Susan L.

212

Temperature: Human Regulating, Ants Conforming  

ERIC Educational Resources Information Center

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.

Clopton, Joe R.

2007-01-01

213

Free fructose is conformationally locked.  

PubMed

Fructose has been examined under isolation conditions using a combination of UV ultrafast laser vaporization and Fourier-transform microwave (FT-MW) spectroscopy. The rotational spectra for the parent, all (six) monosubstituted (13)C species, and two single D species reveal unambiguously that the free hexoketose is conformationally locked in a single dominant ?-pyranose structure. This six-membered-chair skeleton adopts a (2)C(5) configuration (equivalent to (1)C(4) in aldoses). The free-molecule structure sharply contrasts with the furanose form observed in biochemically relevant polysaccharides, like sucrose. The structure of free fructose has been determined experimentally using substitution and effective structures. The enhanced stability of the observed conformation is primarily attributed to a cooperative network of five intramolecular O-H···O hydrogen bonds and stabilization of both endo and exo anomeric effects. Breaking a single intramolecular hydrogen bond destabilizes the free molecule by more than 10 kJ mol(-1). The structural results are compared to ribose, recently examined with rotational resolution, where six different conformations coexist with similar conformational energies. In addition, several DFT and ab initio methods and basis sets are benchmarked with the experimental data. PMID:23346993

Cocinero, Emilio J; Lesarri, Alberto; Écija, Patricia; Cimas, Álvaro; Davis, Benjamin G; Basterretxea, Francisco J; Fernández, José A; Castaño, Fernando

2013-02-20

214

Transition Planning  

ERIC Educational Resources Information Center

Post-school transition is the movement of a child with disabilities from school to activities that occur after the completion of school. This paper provides information about: (1) post-school transition; (2) transition plan; (3) transition services; (4) transition planning; (5) vocational rehabilitation services; (6) services that are available…

Statfeld, Jenna L.

2011-01-01

215

Isothermal titration calorimetric studies of the pH induced conformational changes of bovine serum albumin  

Microsoft Academic Search

Bovine serum albumin (BSA) is a soft globular protein that undergoes conformational changes through several identified transition\\u000a steps in the pH range 2–13.5. The ability to change conformation makes BSA capable of complexing different ligands from fatty\\u000a acids to cations or drugs and carries them in the bloodstream. Microcalorimetric titration of BSA with NaOH solution was performed\\u000a to measure the

Robert Kun; Márta Szekeres; Imre Dékány

2009-01-01

216

Halochromism of a polythiophene derivative induced by conformational changes and its sensing application of carbon dioxide.  

PubMed

We report the design and synthesis of a halochromic polythiophene derivative, whose conformation can be alternated between random coil and rodlike phase by adjusting the pH of the solution. Distinct solution color changes associated with the pH-induced conformational transitions can be used to construct a colorimetric probe for sensing carbon dioxide. This probe can be recovered by bubbling nitrogen gas into carbon dioxide-treated solutions for over 20 cycles. PMID:23705818

Yao, Zhiyi; Hu, Xianping; Huang, Binghuan; Zhang, Li; Liu, Lei; Zhao, Yuliang; Wu, Hai-Chen

2013-06-26

217

Stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification.  

PubMed

It has been appreciated for a long time that enzymes exist as conformational ensembles throughout multiple stages of the reactions they catalyze, but there is renewed interest in the functional implications. The energy landscape that results from conformationlly diverse poteins is a complex surface with an energetic topography in multiple dimensions, even at the transition state(s) leading to product formation, and this represents a new paradigm. At the same time there has been renewed interest in conformational ensembles, a new paradigm concerning enzyme function has emerged, wherein catalytic promiscuity has clear biological advantages in some cases. "Useful", or biologically functional, promiscuity or the related behavior of "multifunctionality" can be found in the immune system, enzymatic detoxification, signal transduction, and the evolution of new function from an existing pool of folded protein scaffolds. Experimental evidence supports the widely held assumption that conformational heterogeneity promotes functional promiscuity. The common link between these coevolving paradigms is the inherent structural plasticity and conformational dynamics of proteins that, on one hand, lead to complex but evolutionarily selected energy landscapes and, on the other hand, promote functional promiscuity. Here we consider a logical extension of the overlap between these two nascent paradigms: functionally promiscuous and multifunctional enzymes such as detoxification enzymes are expected to have an ensemble landscape with more states accessible on multiple time scales than substrate specific enzymes. Two attributes of detoxification enzymes become important in the context of conformational ensembles: these enzymes metabolize multiple substrates, often in substrate mixtures, and they can form multiple products from a single substrate. These properties, combined with complex conformational landscapes, lead to the possibility of interesting time-dependent, or emergent, properties. Here we demonstrate these properties with kinetic simulations of nonequilibrium steady state (NESS) behavior resulting from energy landscapes expected for detoxification enzymes. Analogous scenarios with other promiscuous enzymes may be worthy of consideration. PMID:21473615

Atkins, William M; Qian, Hong

2011-05-17

218

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

PubMed Central

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

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

2014-01-01

219

Laser spectroscopy of a chiral drug in a supersonic beam: conformation and complexation of S-(+)- Naproxen  

NASA Astrophysics Data System (ADS)

The S 0-S 1 electronic transition of jet-cooled Naproxen has been investigated by laser-induced fluorescence excitation and emission spectroscopy. Two electronic transitions separated by 102 cm -1 have been evidenced and attributed to the presence of two conformers. With the help of DFT calculations, the structure of these conformers has been shown to correspond to a rotation by 180° of the chiral substituent with respect to the aromatic plane. When associated with alcohols, both conformers of the chromophore form complexes which give rise to different microscopic solvent shifts of the S 0-S 1 transition. In the case of complexation with R- or S-2-butanol, the hetero- and homo-chiral pairs are characterised by different spectroscopic patterns, which allow a clear discrimination between them.

Lahmani, Françoise; Le Barbu-Debus, Katia; Seurre, Nathalie; Zehnacker-Rentien, Anne

2003-07-01

220

Commuting conformal and dual conformal symmetries in the Regge limit  

NASA Astrophysics Data System (ADS)

In this paper we continue our study of the dual SL(2,C) symmetry of the BFKL equation, analogous to the dual conformal symmetry of N=4 super-Yang-Mills. We find that the ordinary and dual SL(2,C) symmetries do not generate a Yangian, in contrast to the ordinary and dual conformal symmetries in the four-dimensional gauge theory. The algebraic structure is still reminiscent of that of N=4 SYM, however, and one can extract a generator from the dual SL(2,C) close to the bi-local form associated with Yangian algebras. We also discuss the issue of whether the dual SL(2,C) symmetry, which in its original form is broken by IR effects, is broken in a controlled way, similar to the way the dual conformal symmetry of N=4 satisfies an anomalous Ward identity. At least for the lowest orders it seems possible to recover the dual SL(2,C) by deforming its representation, keeping open the possibility that it is an exact symmetry of BFKL. Independently of a possible relation to N=4 scattering amplitudes, this opens an avenue for explaining the integrability of BFKL in terms of two finite-dimensional subalgebras.

Gunnesson, Johan

2011-03-01

221

Conformational effects on optical rotation. 3-substituted 1-butenes.  

PubMed

A calculation of the optical rotation of (R)-(-)-3-chloro-1-butene found a remarkably large dependence on the C=C-C-C torsional angle. At tau = 0 degrees, [alpha](D) = +244 degrees, whereas at tau = 180 degrees, [alpha](D) = -526 degrees. The effect of conformation on the optical rotation was confirmed by a study of the temperature dependence of the rotation. An analysis of the data gave the difference in free energy between the low- and high-energy conformers as 1315 cal/mol and gave the optical rotation of the low-energy conformer and the average of the rotations of the higher energy forms. Although a large effect was found, the observed rotations are a factor of 2.6 smaller than the calculated values, independent of both conformation and wavelength from 589 to 365 nm. The effect of replacing Cl with F, CN, and CCH was examined theoretically. The effects of substituents are remarkably small despite large changes in the calculated electronic transition energies. PMID:12580616

Wiberg, Kenneth B; Vaccaro, Patrick H; Cheeseman, James R

2003-02-19

222

Impact of mutations on the allosteric conformational equilibrium.  

PubMed

Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and effector-unbound protein structures. These simulations can be performed using our web server (http://salilab.org/allosmod/). We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a data set of 10 proteins and 179 mutations, we predict both the magnitude and the sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1k(B)T. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction. PMID:23228330

Weinkam, Patrick; Chen, Yao Chi; Pons, Jaume; Sali, Andrej

2013-02-01

223

Coordinated conformational and compositional dynamics drive ribosome translocation  

PubMed Central

During translation elongation, the compositional factors, elongation factor G (EF-G; encoded by fusA) and transfer RNA (tRNA), alternately bind to the ribosome to direct protein synthesis, in turn regulating the conformation of the ribosome. Here, we use single-molecule fluorescence with zero-mode waveguides to correlate directly ribosome conformations and compositions during multiple rounds of elongation at high factor concentrations in Escherichia coli. Our results show that EF-G-GTP continuously samples both rotational sates of the ribosome, binding with higher affinity to the rotated state. Upon successful accommodation into the rotated ribosome, the EF-G-ribosome complex evolves through several rate-limiting conformational changes and the hydrolysis of GTP, which results in a transition back to the non-rotated state, in turn driving translocation and facilitating both EF-G-GDP and E-site tRNA release. These experiments highlight the power of tracking single-molecule conformation and composition simultaneously in real-time. PMID:23624862

Chen, Jin; Petrov, Alexey; Tsai, Albert; O’Leary, Seán E.; Puglisi, Joseph D.

2013-01-01

224

Killing Initial Data on spacelike conformal boundaries  

E-print Network

We analyze Killing Initial Data on Cauchy surfaces in conformally rescaled vacuum space-times satisfying Friedrich's conformal field equations. As an application, we derive the KID equations on a spacelike $\\mathcal{J}^-$.

Tim-Torben Paetz

2014-03-11

225

Differential conformal superalgebras and their forms  

E-print Network

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 ...

Kac, Victor

226

Conformant Probabilistic Planning via CSPs Nathanael Hyafil  

E-print Network

Conformant Probabilistic Planning via CSPs Nathanael Hyafil Department of Computer Science present a new algorithm for the conformant probabilistic planning problem. This is a planning problem (Kush- merick, Hanks, & Weld 1995), but in modern terminology would more accurately be called

Bacchus, Fahiem

227

Systematic conformational search with constraint satisfaction  

E-print Network

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 ...

Tucker-Kellogg, Lisa, 1969-

2002-01-01

228

Conformal Window and Correlation Functions in Lattice Conformal QCD  

NASA Astrophysics Data System (ADS)

We discuss various aspects of Conformal Field Theories on the Lattice. We mainly investigate the SU(3) gauge theory with Nf degenerate fermions in the fundamental representation, employing the one-plaquette gauge action and the Wilson fermion action. First we make a brief review of our previous works on the phase structure of lattice gauge theories in terms of the gauge coupling constant and the quark mass. We thereby clarify the reason why we conjecture that the conformal window is 7 ? Nf ? 16. Secondly, we introduce a new concept, "conformal theories with IR cutof" and point out that any numerical simulation on a lattice is bounded by an IR cutoff ?IR. Then we make predictions that when Nf is within the conformal window, the propagator of a meson G(t) behaves at large t, as G(t) = c exp (-mHt)/t?, that is, a modified Yukawa-type decay form, instead of the usual exponential decay form exp (-mHt), in the small quark mass region. This holds on an any lattice for any coupling constant g, as far as g is between 0 and g*, where g* is the IR fixed point. We verify that numerical results really satisfy the predictions for the Nf = 7 case and the Nf = 16 case. Thirdly, we discuss small number of flavors (Nf = 2 ˜ 6) QCD at finite temperatures. We point out theoretically and verify numerically that the correlation functions at T/Tc > 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential decay with power correction. Investigating our numerical data by a new method which we call the "local-analysis" of propagators, we observe that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are similar to each other, while the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are similar to each other. Further, we observe our data are consistent with the picture that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are close to the meson unparticle model. On the other hand, the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are close to a free state in the Z(3) twisted vacuum. All results are consistent with naive physical intuition and give clues for long standing issues at high temperatures such as why the free energy at high temperatures does not reach the Stefan-Boltzmann ideal gas limit even at T = 100Tc.

Iwasaki, Y.

229

Modeling the Conformational Changes Underlying Channel Opening in CFTR  

PubMed Central

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator protein (CFTR) cause cystic fibrosis (CF), the most common life-shortening genetic disease among Caucasians. Although general features of the structure of CFTR have been predicted from homology models, the conformational changes that result in channel opening and closing have yet to be resolved. We created new closed- and open-state homology models of CFTR, and performed targeted molecular dynamics simulations of the conformational transitions in a channel opening event. The simulations predict a conformational wave that starts at the nucleotide binding domains and ends with the formation of an open conduction pathway. Changes in side-chain interactions are observed in all major domains of the protein, and experimental confirmation was obtained for a novel intra-protein salt bridge that breaks near the end of the transition. The models and simulation add to our understanding of the mechanism of ATP-dependent gating in this disease-relevant ion channel. PMID:24086355

Rahman, Kazi S.; Cui, Guiying; Harvey, Stephen C.; McCarty, Nael A.

2013-01-01

230

Electrochemical evidence on the molten globule conformation of cytochrome c.  

PubMed

To explore a new approach for characterizing the molten globule conformation, cyclic voltammetric studies of salt induced transitions at acidic pH of cyt c have been carried out. The use of modified electrodes has made the observation of direct electrochemistry in native cyt c possible. However, most of these electrodes do not show reversible responses at acidic pH, due to the fact that, for this system, a deprotonated electrode surface is needed. In these studies, we have used a 6-mercaptopurine and cysteine-modified gold electrodes which are effective for direct rapid electron transfer to cyt c, even in acid solutions. The change in the absorption bands of cyt c are used to monitor the conformational states and, hence, to compare the voltammetric results. Under the experimental conditions where the A state of cyt c is obtained, a reversible voltammetric signal is observed. The midpoint peak potentials are found to be very close to the formal potential of native cyt c. Results are discussed in terms of a cooperative two-state transition between the acid unfolded and the globular acidic states of cyt c. This finding establishes, for the first time, the similarity of both the native and the molten globule-like conformations in terms of its redox properties. PMID:9434113

Pineda, T; Sevilla, J M; Román, A J; Blázquez, M

1997-12-01

231

Nucleophilic Metal Complexes as Acylation Catalysts: Solvent-Dependent  

E-print Network

mechanism in nonpolar media and a nucleophilic mechanism in polar organic media. These observations lead of is the scenario in which a change in solvent fundamentally transforms a catalyst from acting primarily as a Lewis

Lectka, Thomas

232

New criterion for conformational polymorphism  

SciTech Connect

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.

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

2012-01-15

233

Stochastic processes and conformal invariance  

NASA Astrophysics Data System (ADS)

We discuss a one-dimensional model of a fluctuating interface with a dynamic exponent z=1. The events that occur are adsorption, which is local, and desorption which is nonlocal and may take place over regions of the order of the system size. In the thermodynamic limit, the time dependence of the system is given by characters of the c=0 logarithmic conformal field theory of percolation. This implies in a rigorous way, a connection between logarithmic conformal field theory and stochastic processes. The finite-size scaling behavior of the average height, interface width and other observables are obtained. The avalanches produced during desorption are analyzed and we show that the probability distribution of the avalanche sizes obeys finite-size scaling with new critical exponents.

Gier, Jan De; Nienhuis, Bernard; Pearce, Paul A.; Rittenberg, Vladimir

2003-01-01

234

Generative models of conformational dynamics.  

PubMed

Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term 'generative' refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GRAPHICAL MODELS OF ENERGY LANDSCAPES), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc.) from long timescale simulation data. PMID:24446358

Langmead, Christopher James

2014-01-01

235

Guiding light with conformal transformations.  

PubMed

The past decade has seen a revolution in electromagnetics due to the development of metamaterials. These artificial composites have been fashioned to exhibit exotic effects such as a negative index of refraction. However, the full potential of metamaterial devices has only been hinted at. By combining metamaterials with transformation optics (TO), researchers have demonstrated an invisibility cloak. Subsequently, quasi-conformal mapping was used to create a device that exhibited a broadband cloaking effect. Here we extend this latter approach to a strictly conformal mapping to create reflection less, inherently isotropic, and broadband photonic devices. Our method combines the novel effects of TO with the practicality of all-dielectric construction. We show that our structures are capable of guiding light in an almost arbitrary fashion over an unprecedented range of frequencies. PMID:19687966

Landy, Nathan I; Padilla, Willie J

2009-08-17

236

An extension theorem for conformal gauge singularities  

SciTech Connect

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.

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

237

Reinforcement Learning Signal Predicts Social Conformity  

Microsoft Academic Search

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.

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

2009-01-01

238

Forward Conformant Planning via Symbolic Model Checking  

Microsoft Academic Search

Conformant planning is the problem of finding a sequence of actions that is guaranteed to achieve the goal for any pos- sible initial state and nondeterministic behavior of the pl an- ning domain. In this paper we present a new algorithm for conformant planning, returning conformant plans of minimal length if the problem admits a solution, otherwise returnin g with

Alessandro Cimatti; Marco Roveri

2000-01-01

239

Classical and quantum conformal field theory  

Microsoft Academic Search

We define chiral vertex operators and duality matrices and review the fundamental identities they satisfy. In order to understand the meaning of these equations, and therefore of conformal field theory, we define the classical limit of a conformal field theory as a limit in which the conformal weights of all primary fields vanish. The classical limit of the equations for

Gregory Moore; Nathan Seiberg

1989-01-01

240

Transition Invariants  

Microsoft Academic Search

Proof rules for program verification rely on auxiliary assertions. We propose a (sound and relatively complete) proof rule whose auxiliary assertions are transition invari- ants. A transition invariant of a program is a binary rela- tion over program states that contains the transitive closure of the transition relation of the program. A relation is dis- junctively well-founded if it is

Andreas Podelski; Andrey Rybalchenko

2004-01-01

241

Ionization Spectroscopy of Conformational Isomers of Propanal: The Origin of the Conformational Preference  

E-print Network

Ionization Spectroscopy of Conformational Isomers of Propanal: The Origin of the Conformational conformational isomers of propanal, cis and gauche, are investigated by the vacuum-UV mass- analyzed thresholdV and 9.9516 ( 0.0006 eV, respectively. cis-Propanal, which is the more stable conformer in the neutral

Kim, Sang Kyu

242

Transit Tracks  

NSDL National Science Digital Library

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, Keplerâs 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.

Science, Lawrence H.

2008-01-01

243

Essential points of conformal vector fields  

NASA Astrophysics Data System (ADS)

An essential point of a conformal vector field ? on a conformal manifold (M,c) is a point around which the local flow of ? preserves no metric in the conformal class c. It is well-known that a conformal vector field vanishes at each essential point. In this note we show that essential points are isolated. This is a generalization to higher dimensions of the fact that the zeros of a holomorphic function are isolated. As an application, we show that every connected component of the zero set of a conformal vector field is totally umbilical.

Belgun, Florin; Moroianu, Andrei; Ornea, Liviu

2011-03-01

244

DFT study of conformational and spectroscopic properties of yatakemycin.  

PubMed

Molecular structure and conformational preferences of yatakemycin, a novel and exceptionally potent antitumor agent, have been investigated using the density functional theory (DFT) formalism. From the relative stability of various possible conformations, it is found that two conformers are nearly isoenergetic and markedly more stable than the others in the gas phase. To test the effect of polar mediums, the relative energies have been recalculated using the self-consistent reaction field method. Thus, the most stable conformer of the isolated molecule in the gas phase is expected to be still more preferred in solution. The molecular structure of yatakemycin has also been studied by means of its spectroscopic properties. The DFT results satisfactorily reproduce the experimental data and corroborate the reliability of the structural characterization advanced for yatakemycin. The lowest-energy electronic transitions have been interpreted with time-dependent DFT calculations. Notably, the strong IR band observed at 2852 cm(-1) is unambiguously assigned to the O-H stretching of the (C7)O-H...O(C12) fragment, linked by a strong intramolecular H-bond, and may be viewed as a distinctive fingerprint of yatakemycin. Furthermore, the calculated set of NMR chemical shifts of carbonyl carbon atoms and indole protons, the most sensitive to stereoelectronic factors, is consistent with experiment. The effects of both protonation and oxidation on the geometry of the most stable conformer have also been studied. With reference to yatakemycin's DNA alkylation properties, the structure of the yatakemycin-adenine adduct has been theoretically modeled and found to be consistent with experimental spectroscopic evidence. PMID:17564422

Pichierri, Fabio; Galasso, Vinicio

2007-07-01

245

Conformance Testing: Measurement Decision Rules  

NASA Technical Reports Server (NTRS)

The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement decisions rules.

Mimbs, Scott M.

2010-01-01

246

The Biological Bases of Conformity  

PubMed Central

Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects’ behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning. PMID:22712006

Morgan, T. J. H.; Laland, K. N.

2012-01-01

247

Conformational mobility of small molecules in glass-forming solutions studied by FTIR spectroscopy  

NASA Astrophysics Data System (ADS)

Small molecules with two or more stable conformations when embedded in a glass-forming liquid (matrix) serve the role of "conformational probes", i.e., their conformational transitions are used to follow local mobility in the matrix. In the present study, conformational probes were embedded in low-molecular-weight glass-forming liquids, and the molecular mobility was studied in a broad temperature range including the glass transition temperature (Tg). Paraffin oil, dibutylphthalate, bis(2-ethylhexyl)phthalate and isopropylbenzene were used as glass-forming liquids while 1,2-dichloroethane, 1,2-diphenylethane, chlorocyclohexane and bromocyclohexane were used as conformational probes. For some of the matrix/probe systems, the conformational mobility was found to freeze-in at Tg, while for the others it froze-in at certain temperatures Tf < Tg. In the latter case, it was possible to evaluate the activation energies related to mobility of free volume entities in the glassy matrices. In addition, it was possible to estimate the volumes of sub-molecular groups of the matrix that freeze-in at Tf.

Fishman, A. I.; Noskov, A. I.; Stolov, A. A.

2012-06-01

248

Transitions of tethered chain molecules under tension  

E-print Network

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.

Jutta Luettmer-Strathmann; Kurt Binder

2014-09-09

249

Transitions of tethered chain molecules under tension  

NASA Astrophysics Data System (ADS)

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.

Luettmer-Strathmann, Jutta; Binder, Kurt

2014-09-01

250

Conformational Properties of Helical Protein Polymers with Varying Densities of Chemically Reactive Groups  

PubMed Central

Protein engineering strategies have proven valuable for the production of a variety of well-defined macromolecular materials with controlled properties that have enabled their use in a range of materials and biological applications. In this work, such biosynthetic strategies have been employed in the production of monodisperse alanine-rich, helical protein polymers with the sequences [AAAQEAAAAQAAAQAEAAQAAQ]3 and [AAAQAAQAQAAAEAAAQAAQAQ]6. The composition of these protein polymers is similar to that of a previously reported family of alanine-rich protein polymers, but the density and placement of chemically reactive residues has been varied to facilitate the future use of these macromolecules in elucidating polymeric structure-function relationships in biological recognition events. Both protein polymers are readily expressed from E. coli and purified to homogeneity; characterization of their conformational behavior via circular dichroic spectroscopy (CD) indicates that they adopt highly helical conformations under a range of solution conditions. Differential scanning calorimetry, in concert with CD, demonstrates that the conformational transition from helix to coil in these macromolecules can be well-defined, with helicity, conformational transitions, Tm values, and calorimetric enthalpies that vary with the molecular weight of the protein polymers. A combination of infrared spectroscopy and CD also reveals that the macromolecules can adopt ?-sheet structures at elevated temperatures and concentrations and that the existence and kinetics of this conformational transition appear to be related to the density of charged groups on the protein polymer. PMID:19180254

Farmer, Robin S.; Argust, Lindsey M.; Sharp, Jared D.; Kiick, Kristi L.

2008-01-01

251

Finding Transition Pathways on Manifolds  

E-print Network

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.

Tiejun Li; Xiaoguang Li; Xiang Zhou

2014-08-13

252

Parity Doubling and the S Parameter Below the Conformal Window  

SciTech Connect

We describe a lattice simulation of the masses and decay constants of the lowest-lying vector and axial resonances, and the electroweak S parameter, in an SU(3) gauge theory with N{sub f} = 2 and 6 fermions in the fundamental representation. The spectrum becomes more parity doubled and the S parameter per electroweak doublet decreases when N{sub f} is increased from 2 to 6, motivating study of these trends as N{sub f} is increased further, toward the critical value for transition from confinement to infrared conformality.

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

2011-10-21

253

Phase transition in the Sznajd model with independence  

NASA Astrophysics Data System (ADS)

We propose a model of opinion dynamics which describes two major types of social influence —conformity and independence. Conformity in our model is described by the so-called outflow dynamics (known as Sznajd model). According to sociologists' suggestions, we introduce also a second type of social influence, known in social psychology as independence. Various social experiments have shown that the level of conformity depends on the society. We introduce this level as a parameter of the model and show that there is a continuous phase transition between conformity and independence.

Sznajd-Weron, K.; Tabiszewski, M.; Timpanaro, A. M.

2011-11-01

254

Metrics with Galilean conformal isometry  

SciTech Connect

The Galilean conformal algebra (GCA) arises in taking the nonrelativistic limit of the symmetries of a relativistic conformal field theory in any dimensions. It is known to be infinite dimensional in all spacetime dimensions. In particular, the 2d GCA emerges out of a scaling limit of linear combinations of two copies of the Virasoro algebra. In this paper, we find metrics in dimensions greater than 2 which realize the finite 2d GCA (the global part of the infinite algebra) as their isometry by systematically looking at a construction in terms of cosets of this finite algebra. We list all possible subalgebras consistent with some physical considerations motivated by earlier work in this direction and construct all possible higher-dimensional nondegenerate metrics. We briefly study the properties of the metrics obtained. In the standard one higher-dimensional ''holographic'' setting, we find that the only nondegenerate metric is Minkowskian. In four and five dimensions, we find families of nontrivial metrics with a rather exotic signature. A curious feature of these metrics is that all but one of them are Ricci-scalar flat.

Bagchi, Arjun [School of Mathematics, University of Edinburgh, Edinburgh, EH9 3JZ (United Kingdom); Kundu, Arnab [Theory Group, Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States)

2011-03-15

255

Transition & Beyond  

MedlinePLUS

... Education Caring for Your Family Transition & Beyond Aging Matters Research NDSS en Español Ways to Give Ways to ... Education Caring for Your Family Transition & Beyond Aging Matters Research NDSS en Español Ways to Give Ways to ...

256

?-Helical to ?-Helical Conformation Change in the C-Terminal of the Mammalian Prion Protein  

NASA Astrophysics Data System (ADS)

We employ all-atom structure-based models with mixed basis contact maps to explore whether there are any significant geometric or energetic constraints limiting conjectured conformational transitions between the alpha-helical (?H) and the left handed beta helical (LHBH) conformations for the C-terminal (residues 166-226) of the mammalian prion protein. The LHBH structure has been proposed to describe infectious oligomers and one class of in vitro grown fibrils, as well as possibly self- templating the conversion of normal cellular prion protein to the infectious form. Our results confirm that the kinetics of the conformation change are not strongely limited by large scale geometry modification and there exists an overall preference for the LHBH conformation.

Singh, Jesse; Whitford, Paul; Hayre, Natha; Cox, Daniel; Onuchic, José.

2011-03-01

257

VizieR Online Data Catalog: Three conformers of 1,2-propanediol (Bossa+, 2014)  

NASA Astrophysics Data System (ADS)

Three conformers of 1,2-propanediol have been studied in this work, aG'g, gG'a, and g'G'g. 1) The molecules are asymmetric top rotors. Watson's S-reduction was used in the representation Ir. Data below 26GHz are from previous work: Lovas et al., 2009 for all conformers; in the case of the aG'g conformer (table3.dat), the first set of lines between 6 and 18GHz is from Lockley et al., 2002, J. Mol. Struct., 612, 199. All data above 38.5GHz are from this work. The average frequency of blended lines (identical transition frequencies for two or more transitions) is identical to the intensity-weighted average. We therefore omitted the intensity-weighting specified in the line file after the uncertainties in SPFIT. 2) Internal coordinates are given in separate txt files. (6 data files).

Bossa, J. B.; Ordu, M. H.; Muller, H. S. P.; Lewen, F.; Schlemmer, S.

2014-08-01

258

Conformational, spectroscopic, and molecular dynamics DFT study of precursors for new potential antibacterial fluoroquinolone drugs.  

PubMed

Biological activity, functionality, and synthesis of (fluoro)quinolones is closely related to their precursors (for instance 3-fluoroanilinoethylene derivatives) (i.e., their functional groups, conformational behavior, and/or electronic structure). Herein, the theoretical study of 3-fluoroanilinoethylene derivatives is presented. Impact of substituents (acetyl, methyl ester, and ethyl ester) on the conformational analysis and the spectral behavior is investigated. The B3LYP/6-311++G** computational protocol is utilized. It is found that the intramolecular hydrogen bond N-H···O is responsible for the energetic preference of anti (a) conformer (anti position of 3-fluoroanilino group with respect to the C?C double bond). The Boltzmann ratios of the conformers are related to the differences of the particular dipole moments and/or their dependence on the solvent polarity. The studied acetyl, ethyl ester, and methyl ester substituted fluoroquinolone precursors prefer in the solvent either EZa, ZZa, or both conformers equally, respectively. In order to understand the degree of freedom of rotation of the trans ethyl ester group, B3LYP/6-311G** molecular dynamic simulations were carried out. Vibrational frequencies, electron transitions, as well as NMR spectra are analyzed with respect to conformational analysis, including the effect of the substituent. X-ray structures of the precursors are presented and compared with the results of the conformational analysis. PMID:25188903

Dorotíková, Sandra; Plevová, Kristína; Bu?inský, Lukáš; Mal?ek, Michal; Herich, Peter; Kucková, Lenka; Bobeni?ová, Miroslava; Soralová, Stanislava; Kožíšek, Jozef; Fronc, Marek; Milata, Viktor; Dvoranová, Dana

2014-10-01

259

Conformation heterogeneity and mobility of surfactant molecules in intercalated clay minerals studied by solid-state NMR  

SciTech Connect

The conformation heterogeneity and mobility of surfactant molecules in intercalated montmorillonite clay minerals have been investigated using variable-temperature solid-state {sup 13}C NMR and two-dimensional proton wide-line separation (2D WISE) {sup 1}H--{sup 13}C NMR spectroscopy. Previous FTIR studies by Vaia et al. for the first time revealed the existence of a gauche conformation of surfactant molecules in clay minerals and further illustrated the transition from an ordered conformation, to a liquid crystalline state, to completely liquid-like behavior. The NMR study reported in this paper clearly demonstrates the coexistence of order and disordered chain conformations. Two main resonance peaks are resolved and associated with the backbone alkyl chains: the resonance at 33 ppm corresponds to the ordered conformation (all-trans), and the resonance at 30 ppm corresponds to the disordered conformation (mixture of trans and gauche). The NMR technique allows detailed characterization and quantification of the conformational heterogeneity, which is difficult to determine by other techniques. Furthermore, variable-temperature NMR also directly provides quantitative information on the rigidity of the different conformations. Results from cross-polarization time constant T{sub CH} measurements along with 2D WISE NMR suggest that molecules in the ordered all-trans conformation are as rigid as those in solid crystalline materials and that molecules in the disordered conformation are similar to those in liquid crystalline materials. Upon heating, the molecules in the disordered conformation remain more or less unchanged, while the molecules in the ordered conformation become disordered. However, the intercalated molecules in the clay minerals never attained the complete liquid-like behavior even after all the bound surfactant assumed a disordered conformation.

Wang, L.Q.; Liu, J.; Exarhos, G.J.; Flanigan, K.Y.; Bordia, R.

2000-04-06

260

Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin  

E-print Network

Investigations into Sequence and Conformational Dependence of Backbone Entropy, Inter-basin The populations and transitions between Ramachandran basins are stu- died for combinations of the standard 20 and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates

Berry, R. Stephen

261

Geminate Rebinding and Conformational Dynamics of Myoglobin Embedded in a Glass at Room Temperature  

E-print Network

Geminate Rebinding and Conformational Dynamics of Myoglobin Embedded in a Glass at Room Temperature, 5355). As the temperature is increased through the solvent glass transition, the apparent rate have studied ligand rebinding in sperm whale MbCO embedded in a glass at room temperature. Over a wide

Hagen, Stephen J.

262

Conformal gravity in the Schwarzschild metric  

E-print Network

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. The resulting universal conformal theory establishes relationships between parameters for these two distinct phenomena that are shown here to be consistent with observed data.

Nesbet, R K

2014-01-01

263

Opposing auxiliary conformations produce the same torquoselectivity in an oxazolidinone-directed Nazarov cyclization.  

PubMed

Most applications of chiral oxazolidinone auxiliaries in asymmetric synthesis operate through a common set of stereocontrol principles. That is, the oxazolidinone is made to adopt a specific, coplanar conformation with respect to the prochiral substrate, and reaction occurs preferentially at whichever stereoheterotopic face is not blocked by the substituents on the oxazolidinone. In contrast to these principles, we report here the discovery of an alternative mechanism of oxazolidinone-based stereocontrol that does not require coplanarity and is driven instead by allylic strain. This pathway has been uncovered through computational studies of an asymmetric Nazarov cyclization. Chiral oxazolidinone auxiliaries provide essentially complete control over the torquoselectivity of ring closure and the regioselectivity of subsequent deprotonation. Density functional theory calculations (M06-2X//B3LYP) reveal that in the transition state of 4? electrocyclic ring closure, the oxazolidinone ring and the cyclizing pentadienyl cation are distorted from coplanarity in a manner that gives two transition state conformations of similar energy. These two conformers are distinguished by a 180° flip in the auxiliary orientation such that in one conformer the oxazolidinone carbonyl is oriented toward the OH of the pentadienyl cation (syn-conformer) and in the other it is oriented away from this OH (anti-conformer). Surprisingly, both conformations induce the same sense of torquoselectivity, with a 3-5 kcal/mol preference for the C5-? epimer of the ring-closed cation. In both conformations, the conrotatory mode that leads to the C5-? epimer is disfavored due to higher levels of allylic strain between the oxazolidinone substituent and adjacent groups on the pentadienyl cation (R(4) and OH). The excellent torquoselectivities obtained in the oxazolidinone-directed Nazarov cyclization suggest that the allylic strain-driven stereoinduction pathway represents a viable alternative mechanism of stereocontrol for reactions of sterically congested substrates that lie outside of the traditional coplanar (N-acyloxazolidinone) paradigm. PMID:23758343

Flynn, Bernard L; Manchala, Narasimhulu; Krenske, Elizabeth H

2013-06-19

264

Conformational effects on excitonic interactions in a prototypical H-bonded bichromophore: bis(2-hydroxyphenyl)methane.  

PubMed

Laser-induced fluorescence, single-vibronic level fluorescence (SVLF), UV hole burning, and fluorescence dip infrared (FDIR) spectroscopy have been carried out on bis-(2-hydroxyphenyl)methane in order to characterize the ground-state and first excited-state vibronic spectroscopy of this model flexible bichromophore. These studies identified the presence of two conformational isomers. The FDIR spectra in the OH-stretch region determine that conformer A is an OH...O H-bonded conformer, while conformer B is a doubly OH...pi H-bonded conformer with C(2) symmetry. High-resolution ultraviolet spectra ( approximately 50 MHz resolution) of a series of vibronic bands of both conformers confirm and refine these assignments. The transition dipole moment (TDM) direction in conformer A is consistent with electronic excitation that is primarily localized on the donor phenol ring. A tentative assignment of the S(2) origin is made to a set of transitions approximately 400 cm(-1) above S(1). In conformer B, the TDM direction firmly establishes C(2) symmetry for the conformer in its S(1) state and establishes the electronic excitation as delocalized over the two rings, as the lower member of an excitonic pair. The S(2) state has not been clearly identified in the spectrum. Based on CIS calculations, the S(2) state is postulated to be several times weaker than S(1), making it difficult to identify, especially in the midst of overlap from vibronic bands due to conformer A. SVLF spectra show highly unusual vibronic intensity patterns, particularly in conformer B, which cannot be understood by simple harmonic Franck-Condon models, even in the presence of Duschinsky mixing. We postulate that these model flexible bichromophores have TDMs that are extraordinarily sensitive to the distance and orientation of the two aromatic rings, highlighting the need to map out the TDM surface and its dependence on the (up to) five torsional and bending coordinates in order to understand the observations. PMID:19348452

Pillsbury, Nathan R; Müller, Christian W; Meerts, W Leo; Plusquellic, David F; Zwier, Timothy S

2009-04-30

265

Spinor methods in conformal Killing transport  

Microsoft Academic Search

The equations of conformal Killing transport are discussed using tensor and spinor methods. It is shown that, in Minkowski space-time, the equations for a null conformal Killing vector ?a are completely determined by the corresponding spinor ?A and its covariant derivative, which defines a spinor pA'. In conformally flat space-time, the covariant derivative of pA' is also involved. Some applications

Kenza Dighton; Guildford County

1975-01-01

266

Conformal Geodesics on Vacuum Space-times  

Microsoft Academic Search

:  ?We discuss properties of conformal geodesics on general, vacuum, and warped product space-times and derive a system of conformal\\u000a deviation equations. It is then shown how to construct on the Schwarzschild-Kruskal space-time globally defined systems of\\u000a conformal Gauss coordinates which extend smoothly and without degeneracy to future and past null infinity.

Helmut Friedrich

2003-01-01

267

Cooperative relaxations\\/transitions in ferroelectric polymers  

Microsoft Academic Search

Dielectric relaxation and thermal transitions in ?-PVDF have been investigated by Thermo-Stimulated Current spectroscopy and\\u000a Differential Scanning Calorimetry respectively. A comparative study of spectra and thermograms has been performed.\\u000a \\u000a The relaxation mode associated with the glass transition of the true amorphous phase is characterized by relaxation times\\u000a obeying a compensation law due to cooperative molecular movements. A conformationally disordered structure

G. Teyssèdre; A. Bernès; C. Lacabanne

1993-01-01

268

Terbium luminescence-lifetime heterogeneity and protein equilibrium conformational dynamics.  

PubMed Central

The fluorescence decay of the rare earth terbium when bound to the protein calmodulin changes from a simple exponential decay to a complex nonexponential decay as the temperature is lowered below 200 K. We have fit the observed decay curves by assuming that the terbium emission is a forced electric dipole transition and proteins have a distribution of continuous conformational states. Quantitative fits to the data indicate that the root-mean-square configurational deviation of the atoms surrounding the terbium ion is 0.2 A, in good agreement with other measurements. We further point out that because the protein seems to undergo a glass transition yet retains configurational order at room temperature, the proper name for the physical state of a protein at room temperature is the rubber-like state. PMID:3470740

Austin, R H; Stein, D L; Wang, J

1987-01-01

269

Discrete conformal approximation of complex earthquake maps.  

E-print Network

??Using the techniques of circle packing, we construct discrete conformal approximations for complex earthquake maps on the Teichmüller spaces of compact, hyperbolic Riemann surfaces developed… (more)

Murphy, Eric Michael

2005-01-01

270

Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline  

NASA Astrophysics Data System (ADS)

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.

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

2013-06-01

271

Approaching Conformality with Ten Flavors  

SciTech Connect

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.

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

272

Gravitomagnetic effects in conformal gravity  

E-print Network

Gravitomagnetic effects are characterized by two phenomena: first, the geodetic effect which describes the precession of the spin of a gyroscope in a free orbit around a massive object, second, the Lense-Thirring effect which describes the precession of the orbital plane about a rotating source mass. We calculate both these effects in the fourth-order theory of conformal Weyl gravity for the test case of circular orbits. We show that for the geodetic effect a linear term arises which may be interesting for high radial orbits, whereas for the Lense-Thirring effect the additional term has a diminishing effect for most orbits. Circular orbits are also considered in general leading up to a generalization of Kepler's third law.

Said, Jackson Levi; Adami, Kristian Zarb

2014-01-01

273

Gravitomagnetic effects in conformal gravity  

E-print Network

Gravitomagnetic effects are characterized by two phenomena: first, the geodetic effect which describes the precession of the spin of a gyroscope in a free orbit around a massive object, second, the Lense-Thirring effect which describes the precession of the orbital plane about a rotating source mass. We calculate both these effects in the fourth-order theory of conformal Weyl gravity for the test case of circular orbits. We show that for the geodetic effect a linear term arises which may be interesting for high radial orbits, whereas for the Lense-Thirring effect the additional term has a diminishing effect for most orbits. Circular orbits are also considered in general leading up to a generalization of Kepler's third law.

Jackson Levi Said; Joseph Sultana; Kristian Zarb Adami

2014-01-10

274

Serpin latency transition at atomic resolution.  

PubMed

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

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

2014-10-28

275

Simple Model Study of Phase Transition Properties of Isolated and Aggregated Protein  

NASA Astrophysics Data System (ADS)

We investigate the phase transition properties of isolated and aggregated protein by exhaustive numerical study in the confined conformation space with maximally compact lattice model. The study within the confined conformation space shows some general folding properties. Various sequences show different folding properties: two-state folding, three-state folding and prion-like folding behavior. We find that the aggregated protein holds a more evident transition than isolated one and the transition temperature is generally lower than that in isolated case.

Ji, Yong-Yun; Yi, Wei-Qi; Zhang, Lin-Xi

2011-03-01

276

More transition amplitudes on the Riemann sphere  

E-print Network

We consider a conformal field theory for bosons on the Riemann sphere. Correlation functions are defined as singular limits of functional integrals. The main result is that these amplitudes define transition amplitudes, that is multilinear Hilbert-Schmidt functionals on a fixed Hilbert space.

J. Dimock

2008-05-05

277

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

Microsoft Academic Search

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,

Morris Goodman; G. William Moore

1977-01-01

278

Kinetics and conformational stability studies of recombinant leucine aminopeptidase.  

PubMed

Leucine aminopeptidase from Vibrio proteolyticus is a broad specificity N-terminal aminopeptidase that is widely used in pharmaceutical processes where the removal of N-terminal residues in recombinant proteins is required. We previously reported the expression of a heterologous construction of the mature protein fused to a 6-histidine tag that presents a reasonable refolding rate for its use at industrial level. Here, we investigate this recombinant leucine aminopeptidase (rLAP) to explain the gain of activity observed when incubated at 37 °C after its production. Unfolding transitions of rLAP as a function of urea concentration were monitored by circular dichroism (CD) and fluorescence (FL) spectroscopy exhibiting single transitions by both techniques. Free energy change for unfolding measured by CD and FL spectroscopy are 2.8 ± 0.4 and 3.7 ± 0.4 kcal mol(-1), respectively. Thermal stability conformation of rLAP is 2.6 ± 0.1 and 6.1 kcal mol(-1) for CD and Nano-Differential Scanning Calorimetry (Nano-DSC), respectively. Enzyme activity was assessed with L-leucine-p-nitroanilide (L-pNA) as substrate. The catalytic efficiency was 3.87 ± 0.10 min(-1) ?M(-1) at 37 °C and pH 8.0. Kinetic and conformation studies show differences between the enzyme native and rLAP; however rLAP is selective and specific to remove N-terminal groups from amino acids. PMID:24368112

Hernández-Moreno, Ana V; Villaseñor, Francisco; Medina-Rivero, Emilio; Pérez, Néstor O; Flores-Ortiz, Luis F; Saab-Rincón, Gloria; Luna-Bárcenas, Gabriel

2014-03-01

279

Gas-phase conformational distributions for the 2-alkylalcohols 2-pentanol and 2-hexanol from microwave spectroscopy  

NASA Astrophysics Data System (ADS)

Chirped-pulse and cavity Fourier-transform microwave spectrometers were used to record rotational spectra arising from four conformational structures of 2-pentanol and 14 conformations of 2-hexanol. Each conformer's rotational spectrum consists of 10-89 transitions, making the microwave spectra of the alkylalcohols very congested. Assignments of the spectra to conformational structures were made by comparison of the experimental moments of inertia and dipole-selection-rule intensities to predictions from ab initio (MP2/6-311++G ??) model structures. The all-anti configurations of 2-pentanol and 2-hexanol were calculated to have the lowest energies and gave rise to the strongest signals. Spectra were observed from conformers up to 4 kJ mol -1 above these minimum energy structures.

Tubergen, Michael J.; Conrad, Andrew R.; Chavez, Roberto E.; Hwang, Injung; Suenram, Richard D.; Pajski, Jason J.; Pate, Brooks H.

2008-09-01

280

Kramers-Wannier Duality from Conformal Defects  

NASA Astrophysics Data System (ADS)

We demonstrate that the fusion algebra of conformal defects of a two-dimensional conformal field theory contains information about the internal symmetries of the theory and allows one to read off generalizations of Kramers-Wannier duality. We illustrate the general mechanism in the examples of the Ising model and the three-state Potts model.

Fröhlich, Jürg; Fuchs, Jürgen; Runkel, Ingo; Schweigert, Christoph

2004-08-01

281

Conformal Radiation Therapy for Childhood CNS Tumors  

Microsoft Academic Search

Radiation therapy plays a central role in the man- agement of many childhood brain tumors. By combin- ing advances in brain tumor imaging with technology to plan and deliver radiation therapy, pediatric brain tumors can be treated with conformal radiation ther- apy. Through conformal radiation therapy, the radia- tion dose is targeted to the tumor, which can minimize the dose

DAVID G. KIRSCH; NANCY J. TARBELL

282

Differentiating Among Motives for Norm Conformity  

Microsoft Academic Search

Two studies investigated why individuals conform to social norms. The authors propose that individuals conform to social norms to satisfy 3 general motives: accuracy, self-related, and other-related. Building on previous behavior prediction models, Study 1 found that measures of norms that identify specific motivational goals predicted behavior and intention better than did standard measures of social norms that consider only

Gregory J. Pool; Andria F. Schwegler

2007-01-01

283

Conformal Mapping in Wing Aerodynamics Thomas Johnson  

E-print Network

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

Morrow, James A.

284

Conformal Dimension: Cantor Sets and Fuglede Modulus  

Microsoft Academic Search

In this paper we give several conditions for a space to be minimal for conformal dimension. We show that there are sets of zero length and conformal dimension 1 thus answering a question of Bishop and Tyson. Another sucient condition for minimality is given in terms of a modulus of a system of measures in the sense of Fuglede (7).

HRANT HAKOBYAN

2009-01-01

285

Conformant Planning via Heuristic Forward Search  

Microsoft Academic Search

Conformant planning is the task of generating plans given un- certainty about the initial state and action effects, and wi th- out any sensing capabilities during plan execution. The plan should be successful regardless of which particular initia l state we are in. This paper is motivated by the observation that (1) Conformant planning without conditional effects can be handled

Ronen I. Brafman

2004-01-01

286

Matching univalent functions and conformal welding  

Microsoft Academic Search

Given a conformal mapping f of the unit disk D onto a simply connected domain D in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk D? onto the exterior domain D? regarding to D. The answer is expressed in

AlexanderVasil' ev

287

Matching univalent functions and conformal welding  

Microsoft Academic Search

Given a conformal mapping $f$ of the unit disk $\\\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is

Erlend Grong; Pavel Gumenyuk; Alexander Vasil'ev

2008-01-01

288

Hoisting and Rigging Review of Conformance Form  

E-print Network

Hoisting and Rigging Review of Conformance Form (See page 3 for instructions) Hoisting and Rigging standards. List applicable standards Specify structural weld inspection requirement2 Not required Visual of conformance requirements.) Fixed Crane and Hoist Approval Building Inspection Office Department head

Wechsler, Risa H.

289

Conformation and musculoskeletal problems in the racehorse  

Microsoft Academic Search

Conformation is the form (outline) or physical appearance of a horse from the arrangement of muscles, bones, and tissues. In Thoroughbreds long bone and segmental limb lengths are proportional and relationships exist between these measurements and withers height. Carpal conformation progressively changes from “back at the knee” to slightly “over at the knee” between the weanling and 3-year-old year and

C. Wayne McIlwraith; Tina M. Anderson; Elizabeth M. Sanschi

2003-01-01

290

NON-AUTONOMOUS CONFORMAL ITERATED FUNCTION SYSTEMS  

E-print Network

NON-AUTONOMOUS CONFORMAL ITERATED FUNCTION SYSTEMS AND MORAN-SET CONSTRUCTIONS LASSE REMPE-GILLEN AND MARIUSZ URBA´NSKI Abstract. We study non-autonomous conformal iterated function systems, with finite or countable infinite alphabet alike. These differ from the usual (autonomous) iterated function systems

Urbanski, Mariusz

291

Conformational readout of RNA by small ligands  

PubMed Central

RNA molecules have highly versatile structures that can fold into myriad conformations, providing many potential pockets for binding small molecules. The increasing number of available RNA structures, in complex with proteins, small ligands and in free form, enables the design of new therapeutically useful RNA-binding ligands. Here we studied RNA ligand complexes from 10 RNA groups extracted from the protein data bank (PDB), including adaptive and non-adaptive complexes. We analyzed the chemical, physical, structural and conformational properties of binding pockets around the ligand. Comparing the properties of ligand-binding pockets to the properties of computed pockets extracted from all available RNA structures and RNA-protein interfaces, revealed that ligand-binding pockets, mainly the adaptive pockets, are characterized by unique properties, specifically enriched in rare conformations of the nucleobase and the sugar pucker. Further, we demonstrate that nucleotides possessing the rare conformations are preferentially involved in direct interactions with the ligand. Overall, based on our comprehensive analysis of RNA-ligand complexes, we suggest that the unique conformations adopted by RNA nucleotides play an important role in RNA recognition by small ligands. We term the recognition of a binding site by a ligand via the unique RNA conformations “RNA conformational readout.” We propose that “conformational readout” is a general way by which RNA binding pockets are recognized and selected from an ensemble of different RNA states. PMID:23618839

Kligun, Efrat; Mandel-Gutfreund, Yael

2013-01-01

292

Black holes cannot support conformal scalar hair  

E-print Network

It is shown that the only static asymptotically flat non-extrema black hole solution of the Einstein-conformally invariant scalar field equations having the scalar field bounded on the horizon, is the Schwarzschild one. Thus black holes cannot be endowed with conformal scalar hair of finite length.

T. Zannias

1994-09-14

293

Conformal blocks for highly disparate scaling dimensions  

NASA Astrophysics Data System (ADS)

We show that conformal blocks simplify greatly when there is a large difference between two of the scaling dimensions for external operators. In particular the spacetime dimension only appears in an overall constant which we determine via recurrence relations. Connections to the conformal bootstrap program and the AdS / CFT correspondence are also discussed.

Behan, Connor

2014-09-01

294

Conformal invariance, supersymmetry and string theory  

Microsoft Academic Search

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

Daniel Friedan; Emil Martinec; Stephen Shenker

1986-01-01

295

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

NASA Technical Reports Server (NTRS)

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.

Hofer, Richard R. (Inventor)

2013-01-01

296

Conformal nets III: fusion of defects  

E-print Network

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.

Arthur Bartels; Christopher L. Douglas; André Henriques

2013-10-30

297

Protein biosynthesis with conformationally restricted amino acids  

SciTech Connect

The incorporation of conformationally constrained amino acids into peptides is a powerful approach for generating structurally defined peptides as conformational probes and bioactive agents. The ability to site-specifically introduce constrained amino acids into large polypeptide chains would provide a similar opportunity to probe the flexibility, conformation, folding and stability of proteins. To this end, we have examined the competence of the Escherichia coli protein biosynthetic machinery to incorporate a number of these unnatural amino acids into the 164 residue protein T4 lysozyme (T4L). Results clearly demonstrate that the protein biosynthetic machinery can accommodate a wide variety of conformationally constrained amino acids. The expansion of structural motifs that can be biosynthetically incorporated into proteins to include a large number of conformationally constrained amino acids significantly increases the power of mutagenesis methods as probes of protein structure and function and provides additional insights into the steric requirements of the translational machinery. 13 refs., 2 figs.

Mendel, D. (Univ. of California, Berkeley (United States) Lawrence Berkeley Lab., CA (United States)); Ellman, J.; Schultz, P.G. (Univ. of California, Berkeley (United States))

1993-05-19

298

Higher symmetries of the conformal powers of the Laplacian on conformally flat manifolds  

NASA Astrophysics Data System (ADS)

On locally conformally flat manifolds, we describe a construction which maps generalised conformal Killing tensors to differential operators which may act on any conformally weighted tensor bundle; the operators in the range have the property that they are symmetries of any natural conformally invariant differential operator between such bundles. These are used to construct all symmetries of the conformally invariant powers of the Laplacian (often called the GJMS operators) on manifolds of dimension at least 3. In particular, this yields all symmetries of the powers of the Laplacian ?k, kin {Z}>0, on Euclidean space {E}^n. The algebra formed by the symmetry operators is described explicitly.

Gover, A. Rod; Šilhan, Josef

2012-03-01

299

Circular dichroism spectrum of peptides in the poly(Pro)II conformation.  

PubMed

The poly(Pro)II (P(II)) conformation is increasingly recognized as an important element in peptide and protein conformation. Circular dichroism (CD) is one of the most useful methods for detecting and characterizing P(II). Although the standard exciton-based model for predicting peptide CD spectra works well for alpha-helices and beta-sheets, it fails to reproduce the P(II) CD spectrum because it does not account for mixing of the n pi* and pi pi* transitions with transitions in the deep UV, which is significant for the P(II) conformation. In this work, the exciton model is extended to include this mixing, using ab initio-derived bond polarizability tensors to calculate the contributions of the high-energy transitions. The strong negative 195-nm and weaker positive 220-nm CD bands of P(II) are reproduced for (Ala)(n) conformers in the P(II) region of the Ramachandran map. For the canonical P(II) conformation from fiber diffraction of poly(Pro)II (-77, +146), the results are poor, but conformations with less negative phi (approximately -60 degrees) and more positive psi (> or = 160 degrees) give spectra showing the P(II) characteristics. The CD of (Pro)(n) is not reproduced by the calculations, probably because variations in (phi,Psi), ring puckering, and cis-trans isomerism are not included in the model The extended model also gives improved results for alpha-helical polypeptides, leading to increased amplitude for the 205-nm band and decreased amplitude for a negative band predicted near 180 nm. PMID:19462996

Woody, Robert W

2009-06-17

300

CONFORMAL KILLING SPINORS AND THE HOLONOMY PROBLEM IN LORENTZIAN GEOMETRY  

E-print Network

. Conformal Killing spinors give rise to conformal Killing vector fields and conformal Killing formsCONFORMAL KILLING SPINORS AND THE HOLONOMY PROBLEM IN LORENTZIAN GEOMETRY ­ A SURVEY OF NEW RESULTS ­ HELGA BAUM Abstract. This paper is a survey of recent results about conformal Killing spinors

Baum, Helga

301

CONFORMAL KILLING SPINORS AND THE HOLONOMY PROBLEM IN LORENTZIAN GEOMETRY  

E-print Network

. Conformal Killing spinors give rise to conformal Killing vector fields and conformal Killing formsCONFORMAL KILLING SPINORS AND THE HOLONOMY PROBLEM IN LORENTZIAN GEOMETRY -- A SURVEY OF NEW RESULTS -- HELGA BAUM # Abstract. This paper is a survey of recent results about conformal Killing spinors

Baum, Helga

302

Miniaturization techniques benefit conformal arrays  

NASA Astrophysics Data System (ADS)

Crucial design tools for lightweight conformal arrays include low-loss, lightweight microstrip elements and substrates, the optimization of fabrication methods, and the design of the radome. It is noted that all these have demonstrated their effectiveness in the design of an S-band receive array. This new receive array comprises the radiation aperture, substrate, feed, and bonding skins. A circular microstrip patch is chosen as the lightweight radiation element owing to its small size and well-known performance characteristics. It is noted that honeycomb materials with bonding skins have proven to be excellent substrates for these elements. A honeycomb substrate material made up of a uniform lattice of circular cells extruded from a polycarbonate thermoplastic resin forms the element, which typically weighs less than 4 oz. per square foot. This honeycomb possesses good RF properties and affords very high resistance to rain and hail impact without sacrificing electrical performance. The design of the array grid is optimized by considering the effects of grating lobes, sidelobes, and the expected scanning performance.

Chuang, C. A.; Martin, D. J.; Moldovan, N.

1984-03-01

303

Cosmology in Conformally Flat Spacetime  

NASA Astrophysics Data System (ADS)

A possible solution to cosmological age and redshift-distance difficulties has recently been proposed by applying the appropriate conformally flat spacetime (CFS) coordinates to the standard solution of the field equations in a standard dust model closed universe. Here it is shown that CFS time correctly measures the true age of the universe, thus answering a major theoretical objection to the proposal. It is also shown that the CFS interpretation leads to a strong Copernican principle and is in all other respects wholly self-consistent. The deceleration parameter q0 is related to t0, the present age of the universe divided by L, the scale length of its curvature (an absolute constant). The values of q0 and L are approximately 5/6 and 9.2 × 109 yr, respectively. It is shown that the universe started everywhere simultaneously, with no recession velocity until the effects of its closed topology became significant. Conclusions to the contrary in standard theory (the big bang) stem from a different definition of recession velocity. The theoretical present cosmological mass density is quantified as 4.4 × 10-27 kg m-3 approximately, thus greatly reducing, in a closed universe, the observational requirement to find hidden mass. It is also shown that the prediction of standard theory, for a closed universe, of collapse toward a big crunch termination, will not in fact take place.

Endean, Geoffrey

1997-04-01

304

Molecular dynamics simulations reveal that apo-HisJ can sample a closed conformation.  

PubMed

The Escherichia coli histidine binding protein HisJ is a type II periplasmic binding protein (PBP) that preferentially binds histidine and interacts with its cytoplasmic membrane ABC transporter, HisQMP2 , to initiate histidine transport. HisJ is a bilobal protein where the larger Domain 1 is connected to the smaller Domain 2 via two linking strands. Type II PBPs are thought to undergo "Venus flytrap" movements where the protein is able to reversibly transition from an open to a closed conformation. To explore the accessibility of the closed conformation to the apo state of the protein, we performed a set of all-atom molecular dynamics simulations of HisJ starting from four different conformations: apo-open, apo-closed, apo-semiopen, and holo-closed. The simulations reveal that the closed conformation is less dynamic than the open one. HisJ experienced closing motions and explored semiopen conformations that reverted to closed forms resembling those found in the holo-closed state. Essential dynamics analysis of the simulations identified domain closing/opening and twisting as main motions. The formation of specific inter-hinge strand and interdomain polar interactions contributed to the adoption of the closed apo-conformations although they are up to 2.5-fold less prevalent compared with the holo-closed simulations. The overall sampling of the closed form by apo-HisJ provides a rationale for the binding of unliganded PBPs with their cytoplasmic membrane ABC transporters. PMID:23966221

Chu, B C H; Chan, D I; DeWolf, T; Periole, X; Vogel, H J

2014-03-01

305

Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin.  

PubMed

The equilibrium population of different conformational states of a polypeptide can in principle be obtained by a very long molecular dynamics simulation. The method of internal coordinate molecular dynamics earlier developed in this laboratory (A.K. Mazur and R.A. Abagyan J. Biomol. Struct. Dyn. 6,833 (1989)) allows one to use time steps much larger than usual for computing molecular trajectories. It is shown here that the sampling of the conformational space can be additionally enhanced by adding a random component to the set of forces applied to atoms. We describe the algorithms by which the random force is introduced and also a special method which excludes the fast rotation of polar hydrogens from equations of motion but keeps them movable. As a result the task stated in the title becomes realistic. Internal coordinate stochastic dynamics is applied for scanning the conformational space of the pentapeptide Met5-enkephalin which is a common test example widely used in theoretical studies. A large number of conformational transitions is observed during the 20 ns simulation starting from the global energy minimum thus allowing us to arrive at a nearly Boltzmann distribution of populations of conformational states. A few states are found which are distinguished by high apparent configurational entropy which turn out to correspond well to experimentally observed conformations of enkephalins. PMID:8216941

Dorofeyev, V E; Mazur, A K

1993-08-01

306

Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions.  

PubMed

The HIV-1 envelope (Env) mediates viral entry into host cells. To enable the direct imaging of conformational dynamics within Env, we introduced fluorophores into variable regions of the glycoprotein gp120 subunit and measured single-molecule fluorescence resonance energy transfer within the context of native trimers on the surface of HIV-1 virions. Our observations revealed unliganded HIV-1 Env to be intrinsically dynamic, transitioning between three distinct prefusion conformations, whose relative occupancies were remodeled by receptor CD4 and antibody binding. The distinct properties of neutralization-sensitive and neutralization-resistant HIV-1 isolates support a dynamics-based mechanism of immune evasion and ligand recognition. PMID:25298114

Munro, James B; Gorman, Jason; Ma, Xiaochu; Zhou, Zhou; Arthos, James; Burton, Dennis R; Koff, Wayne C; Courter, Joel R; Smith, Amos B; Kwong, Peter D; Blanchard, Scott C; Mothes, Walther

2014-11-01

307

Global structure of conformal theories in the SU(3) gauge theory  

NASA Astrophysics Data System (ADS)

We investigate SU(3) gauge theories in four dimensions with Nf fundamental fermions on a lattice using the Wilson fermion. Clarifying the vacuum structure in terms of Polyakov loops in spatial directions and properties of temporal propagators using a new method that we call "local analysis," we conjecture that the "conformal region" exists together with the confining region and the deconfining region in the phase structure parametrized by ? and K, both in the cases of the large Nf QCD within the conformal window (referred as conformal QCD) with an IR cutoff and small Nf QCD at T/Tc>1 with Tc being the chiral transition temperature (referred to as high-temperature QCD). Our numerical simulation on a lattice of the size 163×64 shows the following evidence of the conjecture. In the conformal region, we find that the vacuum is the nontrivial Z(3) twisted vacuum modified by nonperturbative effects and that temporal propagators of mesons behave at large t as a power-law-corrected Yukawa-type decaying form. The transition from the conformal region to the deconfining region or the confining region is a sharp transition between different vacua, and therefore, it suggests a first-order transition both in conformal QCD and high-temperature QCD. To confirm the conjecture and distinguish it from the possibility of crossover phenomena, we need to take the continuum/thermodynamic limit, which we do not attempt in this work. Within our fixed-lattice simulation, we find that there is a precise correspondence between conformal QCD and high-temperature QCD in the temporal propagators under the change of the parameters Nf and T/Tc, respectively: one boundary is close to meson states, and the other is close to free quark states. In particular, conformal QCD with Nf=7 corresponds to high-temperature QCD with Nf=2 at T˜2Tc, both of which are in close relation to a meson unparticle model. From this, we estimate the anomalous mass dimension ?*=1.2(1) for Nf=7. We also show that the asymptotic state in the limit T/Tc?? is a free quark state in the Z(3) twisted vacuum. The approach to a free quark state is very slow; even at T/Tc˜105, the state is affected by nonperturbative effects. This is possibly connected with the slow approach of the free energy to the Stefan-Boltzmann ideal gas limit.

Ishikawa, K.-I.; Iwasaki, Y.; Nakayama, Yu; Yoshie, T.

2014-06-01

308

Transitional Care  

ERIC Educational Resources Information Center

Transitional care encompasses a broad range of services and environments designed to promote the safe and timely passage of patients between levels of health care and across care settings. High-quality transitional care is especially important for older adults with multiple chronic conditions and complex therapeutic regimens, as well as for their…

Naylor, Mary; Keating, Stacen A.

2008-01-01

309

Feature space resampling for protein conformational search.  

PubMed

De novo protein structure prediction requires location of the lowest energy state of the polypeptide chain among a vast set of possible conformations. Powerful approaches include conformational space annealing, in which search progressively focuses on the most promising regions of conformational space, and genetic algorithms, in which features of the best conformations thus far identified are recombined. We describe a new approach that combines the strengths of these two approaches. Protein conformations are projected onto a discrete feature space which includes backbone torsion angles, secondary structure, and beta pairings. For each of these there is one "native" value: the one found in the native structure. We begin with a large number of conformations generated in independent Monte Carlo structure prediction trajectories from Rosetta. Native values for each feature are predicted from the frequencies of feature value occurrences and the energy distribution in conformations containing them. A second round of structure prediction trajectories are then guided by the predicted native feature distributions. We show that native features can be predicted at much higher than background rates, and that using the predicted feature distributions improves structure prediction in a benchmark of 28 proteins. The advantages of our approach are that features from many different input structures can be combined simultaneously without producing atomic clashes or otherwise physically inviable models, and that the features being recombined have a relatively high chance of being correct. PMID:20131376

Blum, Ben; Jordan, Michael I; Baker, David

2010-05-01

310

Conformation-dependent DNA attraction  

NASA Astrophysics Data System (ADS)

Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription.Understanding how DNA molecules interact with other biomolecules is related to how they utilize their functions and is therefore critical for understanding their structure-function relationships. For a long time, the existence of Z-form DNA (a left-handed double helical version of DNA, instead of the common right-handed B-form) has puzzled the scientists, and the definitive biological significance of Z-DNA has not yet been clarified. In this study, the effects of DNA conformation in DNA-DNA interactions are explored by molecular dynamics simulations. Using umbrella sampling, we find that for both B- and Z-form DNA, surrounding Mg2+ ions always exert themselves to screen the Coulomb repulsion between DNA phosphates, resulting in very weak attractive force. On the contrary, a tight and stable bound state is discovered for Z-DNA in the presence of Mg2+ or Na+, benefiting from their hydrophobic nature. Based on the contact surface and a dewetting process analysis, a two-stage binding process of Z-DNA is outlined: two Z-DNA first attract each other through charge screening and Mg2+ bridges to phosphate groups in the same way as that of B-DNA, after which hydrophobic contacts of the deoxyribose groups are formed via a dewetting effect, resulting in stable attraction between two Z-DNA molecules. The highlighted hydrophobic nature of Z-DNA interaction from the current study may help to understand the biological functions of Z-DNA in gene transcription. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr03235c

Li, Weifeng; Nordenskiöld, Lars; Zhou, Ruhong; Mu, Yuguang

2014-05-01

311

Conformal dynamical equivalence and applications  

NASA Astrophysics Data System (ADS)

The "Conformal Dynamical Equivalence" (CDE) approach is briefly reviewed, and some of its applications, at various astrophysical levels (Sun, Solar System, Stars, Galaxies, Clusters of Galaxies, Universe as a whole), are presented. According to the CDE approach, in both the Newtonian and general-relativistic theories of gravity, the isentropic hydrodynamic flows in the interior of a bounded gravitating perfect-fluid source are dynamically equivalent to geodesic motions in a virtual, fully defined fluid source. Equivalently, the equations of hydrodynamic motion in the former source are functionally similar to those of the geodesic motions in the latter, physically, fully defined source. The CDE approach is followed for the dynamical description of the motions in the fluid source. After an observational introduction, taking into account all the internal physical characteristics of the corresponding perfect-fluid source, and based on the property of the isentropic hydrodynamic flows (quite reasonable for an isolated physical system), we examine a number of issues, namely, (i) the classical Newtonian explanation of the celebrated Pioneer-Anomaly effect in the Solar System, (ii) the possibility of both the attractive gravity and the repulsive gravity in a non-quantum Newtonian framework, (iii) the evaluation of the masses - theoretical, dynamical, and missing - and of the linear dimensions of non-magnetized and magnetized large-scale cosmological structures, (iv) the explanation of the flat-rotation curves of disc galaxies, (v) possible formation mechanisms of winds and jets, and (vi) a brief presentation of a conventional approach - toy model to the dynamics of the Universe, characterized by the dominant collisional dark matter (with its subdominant luminous baryonic "contamination"), correctly interpreting the cosmological observational data without the need of the notions dark energy, cosmological constant, and universal accelerating expansion.

Spyrou, N. K.

2011-02-01

312

47 CFR 2.1072 - Limitation on Declaration of Conformity.  

Code of Federal Regulations, 2010 CFR

... false Limitation on Declaration of Conformity. 2.1072 Section 2.1072 Telecommunication...Authorization Procedures Declaration of Conformity § 2.1072 Limitation on Declaration of Conformity. (a) The Declaration...

2010-10-01

313

47 CFR 2.906 - Declaration of Conformity.  

Code of Federal Regulations, 2010 CFR

... 2010-10-01 false Declaration of Conformity. 2.906 Section 2.906 Telecommunication...General Provisions § 2.906 Declaration of Conformity. (a) A Declaration of Conformity is a procedure where the...

2010-10-01

314

40 CFR 93.104 - Frequency of conformity determinations.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Frequency of conformity determinations. 93.104 Section...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR FEDERAL IMPLEMENTATION PLANS Conformity to State or Federal...

2010-07-01

315

40 CFR 51.857 - Frequency of conformity determinations.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Frequency of conformity determinations. 51.857 Section...OF IMPLEMENTATION PLANS Determining Conformity of General Federal Actions to State...Implementation Plans § 51.857 Frequency of conformity determinations. Link to an...

2010-07-01

316

47 CFR 68.324 - Supplier's Declaration of Conformity requirements.  

Code of Federal Regulations, 2010 CFR

... false Supplier's Declaration of Conformity requirements. 68.324 Section...324 Supplier's Declaration of Conformity requirements. (a) Each responsible...include in the Supplier's Declaration of Conformity, the following information:...

2010-10-01

317

20 CFR 604.6 - Conformity and substantial compliance.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 2010-04-01 false Conformity and substantial compliance. 604...UNEMPLOYMENT COMPENSATION § 604.6 Conformity and substantial compliance. (a...program. (b) Resolving Issues of Conformity and Substantial Compliance. For...

2010-04-01

318

45 CFR 1355.34 - Criteria for determining substantial conformity.  

Code of Federal Regulations, 2010 CFR

...Criteria for determining substantial conformity. 1355.34 Section 1355.34 ...Criteria for determining substantial conformity. (a) Criteria to be satisfied...will determine a State's substantial conformity with title IV-B and title...

2010-10-01

319

40 CFR 93.157 - Frequency of conformity determinations.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Frequency of conformity determinations. 93.157 ...PROGRAMS (CONTINUED) DETERMINING CONFORMITY OF FEDERAL ACTIONS TO STATE OR...IMPLEMENTATION PLANS Determining Conformity of General Federal Actions...

2010-07-01

320

47 CFR 68.320 - Supplier's Declaration of Conformity.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 false Supplier's Declaration of Conformity. 68.320 Section 68.320 Telecommunication...68.320 Supplier's Declaration of Conformity. (a) Supplier's Declaration of Conformity is a procedure where the...

2010-10-01

321

21 CFR 26.69 - Monitoring of conformity assessment bodies.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 false Monitoring of conformity assessment bodies. 26.69 Section...Provisions § 26.69 Monitoring of conformity assessment bodies. The following shall apply with regard to the monitoring of conformity assessment bodies (CAB's)...

2010-04-01

322

40 CFR 89.121 - Certificate of conformity effective dates.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Certificate of conformity effective dates. 89.121 Section...Provisions § 89.121 Certificate of conformity effective dates. The certificate of conformity is valid from the date of issuance...

2010-07-01

323

21 CFR 26.70 - Conformity assessment bodies.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 2010-04-01 false Conformity assessment bodies. 26.70 Section...âFrameworkâ Provisions § 26.70 Conformity assessment bodies. Each party recognizes that the conformity assessment bodies (CAB's)...

2010-04-01

324

Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes  

NASA Technical Reports Server (NTRS)

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.

Egli, M.; Usman, N.; Rich, A.

1993-01-01

325

Conformational and Vibrational Studies of Triclosan  

NASA Astrophysics Data System (ADS)

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.

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

2010-01-01

326

On Conformal Conic Mappings of Spherical Domains  

PubMed Central

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

Bourchtein, Ludmila

2014-01-01

327

On conformal conic mappings of spherical domains.  

PubMed

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

Bourchtein, Andrei; Bourchtein, Ludmila

2014-01-01

328

Modeling of the conformational behavior of polyvinylchloride  

Microsoft Academic Search

The conformational behavior of polyvinylchloride was modeled by calculations of different conformers, rotational barriers, and rotation-energy profile diagrams of some model compounds, such as 1,3-dichloropropane, 1,3,5-trichloropentane, 1,3,5,7-tetrachloroheptane, 2,4-dichloropentane and 2,4,6-trichloropentane using the PCILO-and MM2-methods. These calculations allow some assertions about the conformational behavior of PVC. It was found that already a simple increment system derived from the model molecules is

M. Bölke; M. Möllhoff; P. Hallpap; J. R. Lochmann

1991-01-01

329

Matching univalent functions and conformal welding  

E-print Network

Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

Erlend Grong; Pavel Gumenyuk; Alexander Vasil'ev

2008-06-05

330

Matching univalent functions and conformal welding  

E-print Network

Given a conformal mapping $f$ of the unit disk $\\mathbb D$ onto a simply connected domain $D$ in the complex plane bounded by a closed Jordan curve, we consider the problem of constructing a matching conformal mapping, i.e., the mapping of the exterior of the unit disk $\\mathbb D^*$ onto the exterior domain $D^*$ regarding to $D$. The answer is expressed in terms of a linear differential equation with a driving term given as the kernel of an operator dependent on the original mapping $f$. Examples are provided. This study is related to the problem of conformal welding and to representation of the Virasoro algebra in the space of univalent functions.

Grong, Erlend; Vasil'ev, Alexander

2008-01-01

331

Structure, Intent and Conformance Monitoring in ATC  

NASA Technical Reports Server (NTRS)

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.

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

2004-01-01

332

The conformal anomaly of M5-branes  

NASA Astrophysics Data System (ADS)

We show that the conformal anomaly for N M5-branes grows like N 3. The method we employ relates Coulomb branch interactions in six dimensions to interactions in four dimensions using supersymmetry. This leads to a relation between the six-dimensional conformal anomaly and the conformal anomaly of N = 4 Yang-Mills. Along the way, we determine the structure of the four derivative interactions for the toroidally compactified (2, 0) theory, while encountering interesting novelties in the structure of the six derivative interactions.

Maxfield, Travis; Sethi, Savdeep

2012-06-01

333

How Many Conformations Can a Protein Remember?  

NASA Astrophysics Data System (ADS)

We show that a protein can be trained to recognize multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield network, the number of conformations which can be remembered by a protein sequence depends on the size of the amino acid alphabet as lnA, independent of protein length. This admits the possibility of certain proteins, such as prions, evolving to fold to independent stable conformations, as well as novel possibilities for protein and heteropolymer design.

Fink, Thomas M.; Ball, Robin C.

2001-11-01

334

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis.  

PubMed

We describe automated procedures for the first stages of a systematic computational investigation of reaction mechanisms. They include (i) selection of computational method and basis set based on statistical analysis of structural and energy data relating to experimental values, (ii) determination of all distinct conformations of transition states with large conformational freedom, and (iii) generation of unknown geometry of the transition states, based on pre-defined connectivity of the atoms involved in the reaction. For the conformational search we employed an efficient procedure for exploration of various possible conformations of the transition states and elimination of the equivalent structures in several steps using molecular-mechanical and quantum-mechanical methods. The procedure was applied to the determination of the structures of transition states and intermediates in the ammonolysis of monoformylated 1,2-ethanediol, which were subsequently used for identification of the lowest energy reaction paths. For the same reaction system we also used the approach for generation of the initial structures of transition states with unknown geometry. The reported procedures are implemented in the MolRan program suite. PMID:20727802

Rangelov, Miroslav A; Petrova, Galina P; Yomtova, Vihra M; Vayssilov, Georgi N

2010-09-01

335

Hidden conformal symmetry of extremal black holes  

SciTech Connect

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.

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

336

3D face recognition via conformal representation  

NASA Astrophysics Data System (ADS)

In this paper, we propose a 3D face recognition approach based on the conformal representation of facial surfaces. Firstly, facial surfaces are mapped onto the 2D unit disk by Riemann mapping. Their conformal representation (i.e. the pair of mean curvature (MC) and conformal factor (CF) ) are then computed and encoded to Mean Curvature Images (MCIs) and Conformal Factor Images (CFIs). Considering that different regions of face deform unequally due to expression variation, MCIs and CFIs are divided into five parts. LDA is applied to each part to obtain the feature vector. At last, five parts are fused on the distance level for recognition. Extensive experiments carried out on the BU-3DFE database demonstrate the effectiveness of the proposed approach.

Han, Junhui; Fang, Chi; Ding, Xiaoqing; Sun, Jian; Gu, Xianfeng D.

2014-03-01

337

Conformable apparatus in a drill string  

DOEpatents

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.

Hall, David R. (Provo, UT); Hall, Jr., H. Tracy (Provo, UT); Pixton, David S. (Lehi, UT); Fox, Joe (Spanish Fork, UT)

2007-08-28

338

21 CFR 886.3130 - Ophthalmic conformer.  

... An ophthalmic conformer is a device usually made of molded plastic intended to be inserted temporarily between the eyeball...prevent closure or adhesions during the healing process following surgery. ] (b) Classification. Class II (special...

2014-04-01

339

Supersymmetric Dualities beyond the Conformal Window  

SciTech Connect

Using the superconformal (SC) indices techniques, we construct Seiberg type dualities for N=1 supersymmetric field theories outside the conformal windows. These theories are physically distinguished by the presence of chiral superfields with small or negative R charges.

Spiridonov, V. P. [Bogoliubov Laboratory of Theoretical Physics, JINR, Dubna, Moscow Region 141980 (Russian Federation); Vartanov, G. S. [Max-Planck-Institut fuer Gravitationsphysik, Albert-Einstein-Institut 14476 Golm (Germany)

2010-08-06

340

On Functional Representations of the Conformal Algebra  

E-print Network

Starting with conformally covariant correlation functions, a sequence of functional representations of the conformal algebra is constructed. A key step is the introduction of representations which involve an auxiliary functional. It is observed that these functionals are not arbitrary but rather must satisfy a pair of consistency equations; one such is identified, in a particular representation, as an Exact Renormalization Group equation specialized to a fixed-point. Therefore, the associated functional is identified with the Wilsonian Effective Action and this creates a concrete link between action-free formulations of Conformal Field Theory and the cutoff-regularized path integral approach. Following this, the energy-momentum tensor is investigated, from which it becomes apparent that the conformal Ward Identities serve to define a particular representation of the energy-momentum tensor. It follows, essentially trivially, that if the Schwinger functional exists and is non-vanishing then theories exhibiting ...

Rosten, Oliver J

2014-01-01

341

Excision boundary conditions for the conformal metric  

SciTech Connect

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.

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

342

Certificate of Conformance Program for Financial Reporting  

ERIC Educational Resources Information Center

A request is made that once a school district has been awarded the "Certificate for Conformance" for compliance with accounting standards, the Certificate should remain with the district and be revoked only for cause. (Author/MLF)

Lewandowski, Raymond J.

1977-01-01

343

Ward identities for Lagrangian conformal models.  

National Technical Information Service (NTIS)

Some aspects of conformal theories with Lagrangian representation, are discussed. The study is carried out in the framework of formal perturbative series. The development of the concepts and the problems raised, are illustrated by the free bosonic string....

S. Lazzarini, R. Stora

1989-01-01

344

Conformal Field Theories in Fractional Dimensions  

NASA Astrophysics Data System (ADS)

We study the conformal bootstrap in fractional space-time dimensions, obtaining rigorous bounds on operator dimensions. Our results show strong evidence that there is a family of unitary conformal field theories connecting the 2D Ising model, the 3D Ising model, and the free scalar theory in 4D. We give numerical predictions for the leading operator dimensions and central charge in this family at different values of D and compare these to calculations of ?4 theory in the ? expansion.

El-Showk, Sheer; Paulos, Miguel; Poland, David; Rychkov, Slava; Simmons-Duffin, David; Vichi, Alessandro

2014-04-01

345

Condensate mechanism of conformal symmetry breaking  

E-print Network

The low energy Gell-Mann-Oakes-Renner relation, Higgs particle mass value, and the new observational cosmological data are considered as evidence of the condensate mechanism of conformal symmetry breaking at the quantum level. The condensate mechanism occurs by means of normal ordering of field operators in QCD, Minimal Standard Model of electroweak interactions without the Higgs potential, and the Dirac conformal General Relativity with long range forces.

V. Pervushin; A. Arbuzov; B. Barbashov; A. Cherny; A. Dorokhov; A. Borowiec; R. Nazmitdinov; A. Pavlov; V. Shilin; A. Zakharov

2012-11-19

346

Difierential equations and conformal fleld theories  

Microsoft Academic Search

We discuss the recent results of the author on the existence of systems of difierential equations for chiral genus-zero and genus-one correlation functions in conformal fleld theories. Two-dimensional conformal fleld theories form a particular class of nontopolog- ical quantum fleld theories which have now been formulated and studied rigor- ously using various methods from difierent branches of mathematics. In physics,

Yi-Zhi Huang

347

Transit Math  

NSDL National Science Digital Library

This is a collection of mathematical problems about transits in the solar system. Learners can work problems created to be authentic glimpses of modern science and engineering issues, often involving actual research data.

348

Transitional determinacies.  

PubMed

In classic generative grammar a distinction is drawn between linguistic 'competence' and linguistic 'performance', the former referring to linguistic knowledge, the latter to how linguistic knowledge is used. However, this controversial differentiation obscures the additional dichotomy between linguistic knowledge for production and linguistic knowledge for recognition. In this article it is shown that production and recognition differ, that recognition is not simply the inverse of production, and that the derivation of production from recognition and recognition from production require a small set of generalizable 'transitional determinacies'. Secondly, it is shown that transitional determinacies explain the difference between 'overt' and 'covert' recognition recently observed in prosopagnosics, patients unable to recognize familiar faces. Prosopagnosics and normals are found to differ in their transitional determinacies, such that prosopagnosics require more binders (precisors) for covert recognition than normals. In general, it is concluded that transitional determinacies are as necessary to the theory of grammar as determinacies themselves. PMID:1286840

Luelsdorff, P A

1992-01-01

349

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

PubMed

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

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

2013-04-14

350

Autophosphorylation Activity of a Soluble Hexameric Histidine Kinase Correlates with the Shift in Protein Conformational Equilibrium  

PubMed Central

Summary In a commonly accepted model, in response to stimuli, bacterial histidine kinases undergo a conformational transition between an active and inactive form. Structural information on histidine kinases is limited. By using ion mobility-mass spectrometry (IM-MS), we demonstrate an exchange between two conformational populations of histidine kinase ExsG that are linked to different levels of kinase activity. ExsG is an atypical signaling protein that incorporates an uncommon histidine kinase catalytic core at the C terminus preceded by an N-terminal “receiver domain” that is normally associated with the response regulator proteins in two-component signal transduction systems. IM-MS analysis and enzymatic assays indicate that phosphorylation of the ExsG receiver domain stabilizes the “compact” form of the protein and inhibits kinase core activity; in contrast, nucleotide binding required for kinase activity is associated with the more open conformation of ExsG. PMID:24210218

Wojnowska, Marta; Yan, Jun; Sivalingam, Ganesh N.; Cryar, Adam; Gor, Jayesh; Thalassinos, Konstantinos; Djordjevic, Snezana

2013-01-01

351

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

PubMed Central

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

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

2013-01-01

352

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

PubMed

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

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

2013-05-29

353

Health care for gender variant or gender non-conforming children.  

PubMed

Most children explore various aspects of gender and sexuality as children. Youth with consistent, persistent, and insistent gender non-conformity or gender dysphoria are important to identify in the pre- and early-pubertal years as early intervention and support may be lifesaving. Those whose gender non-conformity persists into puberty and adolescence are most likely to identify as transgender. Blocking pubertal development at Tanner stage 2 for pre-pubertal, gender non-conforming children is a relatively new but reversible and highly beneficial strategy to delay puberty, giving patients and families time to come up with a transition plan. Early identification, collaborative support from healthcare providers and mental health clinicians, and supportive interventions for both children and families grappling with gender variance may improve social and mental health outcomes for what has traditionally been considered a high-risk, vulnerable population. PMID:23641446

Forcier, Michelle M; Haddad, Emily

2013-04-01

354

Structural Basis and Kinetics of Force-Induced Conformational Changes of an ?A Domain-Containing Integrin  

PubMed Central

Background Integrin ?L?2 (lymphocyte function-associated antigen, LFA-1) bears force upon binding to its ligand intercellular adhesion molecule 1 (ICAM-1) when a leukocyte adheres to vascular endothelium or an antigen presenting cell (APC) during immune responses. The ligand binding propensity of LFA-1 is related to its conformations, which can be regulated by force. Three conformations of the LFA-1 ?A domain, determined by the position of its ?7-helix, have been suggested to correspond to three different affinity states for ligand binding. Methodology/Principal Findings The kinetics of the force-driven transitions between these conformations has not been defined and dynamically coupled to the force-dependent dissociation from ligand. Here we show, by steered molecular dynamics (SMD) simulations, that the ?A domain was successively transitioned through three distinct conformations upon pulling the C-terminus of its ?7-helix. Based on these sequential transitions, we have constructed a mathematical model to describe the coupling between the ?A domain conformational changes of LFA-1 and its dissociation from ICAM-1 under force. Using this model to analyze the published data on the force-induced dissociation of single LFA-1/ICAM-1 bonds, we estimated the force-dependent kinetic rates of interstate transition from the short-lived to intermediate-lived and from intermediate-lived to long-lived states. Interestingly, force increased these transition rates; hence activation of LFA-1 was accelerated by pulling it via an engaged ICAM-1. Conclusions/Significance Our study defines the structural basis for mechanical regulation of the kinetics of LFA-1 ?A domain conformational changes and relates these simulation results to experimental data of force-induced dissociation of single LFA-1/ICAM-1 bonds by a new mathematical model, thus provided detailed structural and kinetic characterizations for force-stabilization of LFA-1/ICAM-1 interaction. PMID:22140490

Li, Tian; Chen, Wei; Lou, Jizhong; Zhu, Cheng

2011-01-01

355

Microwave spectrum, structure, tautomeric, and conformational composition of 4-vinylimidazole  

NASA Astrophysics Data System (ADS)

The microwave spectra of the two conformers each, of the 1H and 3H tautomers of 4-vinylimidazole, have been measured in the 48-72 GHz spectral region. The 4-vinylimidazole was generated in situ by the facile decarboxylation of urocanic acid at its vaporization temperature of 220 °C. The recognition of this reaction casts doubt on the reliability of a previous published spectroscopic study apparently mistakenly thought to be of uncontaminated vaporized urocanic acid, a natural product of great interest in skin cancer etiology. Quantum chemical theoretical predictions of the structures of each of ten possible conformers/tautomers of urocanic acid and four of 4-vinylimidazole were performed at the ab initio MP2/cc-pVTZ level, with vibrational predictions at the B3LYP/cc-pVTZ and M062X/cc-pVTZ levels. The predicted values of rotational constants for all the urocanic acid species were found to be quite inconsistent with those of the four observed spectra. For the 4-vinylimidazole isomers, the calculated relative energies suggested that all four species would have substantial equilibrium mole fractions at 220 °C. The isomers were identified by matching the observed and calculated rotational constants. The resulting assignment was found to be consistent with the predicted and observed 14N nuclear quadrupole hyperfine multiplet patterns for a suitable rotational transition, and with the observed versus empirically calculated inertial defects. With one exception, the predicted structures were found to be planar. Resembling the case of 1-vinylimidazole, where one conformer is nonplanar, one isomer of 4-vinylimidazole was found to be quasiplanar. This seems to belong to a class of spontaneous symmetry-breaking observed in the molecular structure of some otherwise planar vinyl aromatic compounds.

Godfrey, Peter D.; Robertson, Evan G.

2012-08-01

356

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover  

PubMed Central

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. PMID:23332074

McGowan, Lauren C.; Hamelberg, Donald

2013-01-01

357

Chemistry and conformation of vitamin D molecules.  

PubMed

1 alpha,25-Dihydroxyvitamin D3 (1,25) is a structurally unique steroid hormone because it not only possesses the complete 25-hydroxycholesterol side chain, but most notably, it possesses a seco-B triene structure (it lacks a B-ring and is usually depicted in a non-steroidal, extended conformation). In contrast, the classical steroid hormones possess a truncated side chain (progesterone, cortisol, and aldosterone) or no side chain (estradiol and testosterone) and they all possess the fully intact ABCD steroid rings. These structural differences render the seco-B-steroid 1,25 considerably more conformationally flexible. Since 1,25 is now known to target a myriad of tissues where specific interactions occur to produce an array of biological responses, it is of interest to determine whether different topologies of 1,25 (resulting from different conformational orientations of 1,25) are necessary to interact effectively at the different target sites. The array of biological responses include both non-genomic and genomic effects and there is considerable promise for the efficacy of 1,25 analogs as chemotherapeutic agents in a variety of human disease states. For the non-genomic calcium transport response of transcaltachia, the finding that two 6-s-cis locked analogs, 1 alpha,25-dihydroxyprevitamin D3 (pre-1,25) and 1 alpha,25-dihydroxylumisterol3 (1,25-Lumi), are equipotent to 1,25, points strongly to the involvement of the 6-s-cis conformer of 1,25 as the biologically active conformer. Since there is a continuum of easily interconvertible 6,7-single bond conformers of the seco-B ring available to 1,25, conformational minima (either local or global) may have little to do with the manner in which 1,25 is bound to receptor. For the genomic calcium transport response, and for other genomic (or non-genomic) effects, there is no clear evidence whether the steroidal (s-cis) or non-steroidal (s-trans) conformer of 1,25 is involved. In order to address this matter further, efforts are underway to evaluate other conformationally locked analogs of 1,25 which might mimic either the planar 6-s-trans-1,25 or some intermediate conformer between it and the planar-6-s-cis form. PMID:7626517

Okamura, W H; Midland, M M; Hammond, M W; Abd Rahman, N; Dormanen, M C; Nemere, I; Norman, A W

1995-06-01

358

Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases  

NASA Astrophysics Data System (ADS)

Nucleic acid bases (NABs) have been considered for many years to be planar and conformationally rigid. However, recently, two possible sources of nucleobases nonplanarity have been found. Ab initio quantum-chemical calculations using large basis sets augmented by inclusion of electron correlation and recent experimental studies revealed that amino groups in isolated cytosine, guanine, and adenine adopt a nonplanar trigonal-pyramidal configuration. Since the values of amino group inversion barriers do not exceed approximately 1 kcal mol-1, this group possesses rather flexible geometry. A different source of nonplanarity of nucleobases originates from the high deformability of the pyrimidine ring. Transition of such a ring in uracil, thymine, cytosine, and guanine molecules from a planar equilibrium conformation to a sofa configuration characterized by a relevant torsion angle of ±20° entails an increase of energy by less than 1.5 kcal mol-1. Therefore, at room temperature, certain fraction of isolated DNA bases should possess nonplanar structure of the heterocyclic ring. This review summarizes recent theoretical studies on the flexibility of the NABs.

Shishkin, Oleg V.; Gorb, Leonid; Leszczynski, Jerzy

359

Conformal mechanics on rotating Bertotti-Robinson spacetime  

NASA Astrophysics Data System (ADS)

We investigate conformal mechanics associated with the rotating Bertotti-Robinson (RBR) geometry found recently as the near-horizon limit of the extremal rotating Einstein-Maxwell dilaton-axion black holes. The solution breaks the SL(2, R)× SO(3) symmetry of Bertotti-Robinson (BR) spacetime to SL(2, R)× U(1) and breaks supersymmetry in the sence of N=4, d=4 supergravity as well. However, it shares with BR such properties as confinement of timelike geodesics and discreteness of the energy of test fields on the geodesically complete manifold. Conformal mechanics governing the radial geodesic motion coincides with that for a charged particle in the BR background (a relativistic version of the de Alfaro-Fubini-Furlan model), with the azimuthal momentum playing the role of a charge. Similarly to the BR case, the transition from Poincaré to global coordinates leads to a redefinition of the Hamiltonian making the energy spectrum discrete. Although the metric does not split into a product space even asymptotically, it still admits an infinite-dimensional extension of SL(2, R) as asymptotic symmetry. The latter is shown to be given by the product of one copy of the Virasoro algebra and U(1), the same being valid for the extremal Kerr throat.

Clément, Gérard; Gal'tsov, Dmitri

2001-12-01

360

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

PubMed Central

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

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

2013-01-01

361

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

E-print Network

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

Clore, G. Marius

362

Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase.  

PubMed

Molecular plasticity controls enzymatic activity: the native fold of a protein in a given environment is normally unique and at a global free-energy minimum. Some proteins, however, spontaneously undergo substantial fold switching to reversibly transit between defined conformers, the "metamorphic" proteins. Here, we present a minimal metamorphic, selective, and specific caseinolytic metallopeptidase, selecase, which reversibly transits between several different states of defined three-dimensional structure, which are associated with loss of enzymatic activity due to autoinhibition. The latter is triggered by sequestering the competent conformation in incompetent but structured dimers, tetramers, and octamers. This system, which is compatible with a discrete multifunnel energy landscape, affords a switch that provides a reversible mechanism of control of catalytic activity unique in nature. PMID:25159620

López-Pelegrín, Mar; Cerdà-Costa, Núria; Cintas-Pedrola, Anna; Herranz-Trillo, Fátima; Bernadó, Pau; Peinado, Juan R; Arolas, Joan L; Gomis-Rüth, F Xavier

2014-09-26

363

A Kinesin Motor In A Force-producing Conformation  

SciTech Connect

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.

Heuston, E.; Bronner, C; Kull, F; Endow, S

2010-01-01

364

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

E-print Network

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. ...

Smith, Adam Wilcox, 1977-

2008-01-01

365

PH-gated porosity and reversible swelling transitions in polyelectrolyte multilayers  

E-print Network

This thesis explores the design of novel pH-responsive polyelectrolyte multilayer (PEM) films. The discoveries of discontinuous pH-induced swelling transitions and concomitant conformational memory effects as well as ...

Hiller, Jeri' Ann, 1976-

2003-01-01

366

Electronic spectra of jet-cooled isoindoline: Spectroscopic determination of energy difference between conformational isomers  

NASA Astrophysics Data System (ADS)

The electronic spectra of jet-cooled isoindoline between the electronic ground (S0) state and the ??* lowest-excited singlet state (S1) were observed by the fluorescence excitation and single-vibronic-level dispersed fluorescence methods. The low-frequency progression due to the puckering vibration appeared in both spectra. Analysis of dispersed spectra together with geometry optimization at the level of B3LYP/6-311+G(d) indicated the presence of conformational isomers possessing axial and equatorial N-H bonds with respect to the molecular plane. The 0-0 bands of the axial and equatorial conformers were measured at 37 022 and 36 761 cm-1, respectively. Three common levels in the S1 state accessible from the respective S0-state zero levels were observed. From their transition frequencies, the S0-state energy difference between the isomers was determined to be 47.7+/-0.2 cm-1, where the axial conformer was more stable. In the S1 state, the energy difference was 213.7+/-0.2 cm-1, and the equatorial conformer was more stable. The cause of switching from a stable conformation upon excitation is discussed in terms of the electron conjugation between the ?* orbital in benzene and the lone pair orbital of nitrogen.

Tanaka, Sei'ichi; Okuyama, Katsuhiko

2010-04-01

367

Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR  

PubMed Central

RNA aptamers are in vitro–selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 2?-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding. PMID:21097555

Wunnicke, Dorith; Strohbach, Denise; Weigand, Julia E.; Appel, Bettina; Feresin, Emiliano; Suess, Beatrix; Muller, Sabine; Steinhoff, Heinz-Jurgen

2011-01-01

368

Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR.  

PubMed

RNA aptamers are in vitro-selected binding domains that recognize their respective ligand with high affinity and specificity. They are characterized by complex three-dimensional conformations providing preformed binding pockets that undergo conformational changes upon ligand binding. Small molecule-binding aptamers have been exploited as synthetic riboswitches for conditional gene expression in various organisms. In the present study, double electron-electron resonance (DEER) spectroscopy combined with site-directed spin labeling was used to elucidate the conformational transition of a tetracycline aptamer upon ligand binding. Different sites were selected for post-synthetic introduction of either the (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate by reaction with a 4-thiouridine modified RNA or of 4-isocyanato-2,6-tetramethylpiperidyl-N-oxid spin label by reaction with 2'-aminouridine modified RNA. The results of the DEER experiments indicate the presence of a thermodynamic equilibrium between two aptamer conformations in the free state and capture of one conformation upon tetracycline binding. PMID:21097555

Wunnicke, Dorith; Strohbach, Denise; Weigand, Julia E; Appel, Bettina; Feresin, Emiliano; Suess, Beatrix; Müller, Sabine; Steinhoff, Heinz-Jürgen

2011-01-01

369

Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics.  

PubMed

Single-molecule Förster resonance energy transfer (smFRET) is a powerful method for studying the conformational dynamics of a biomolecule in real-time. However, studying how interacting ligands correlate with and regulate the conformational dynamics of the biomolecule is extremely challenging because of the availability of a limited number of fluorescent dyes with both high quantum yield and minimal spectral overlap. Here we report the use of a nonfluorescent quencher (Black Hole Quencher, BHQ) as an acceptor for smFRET. Using a Cy3/BHQ pair, we can accurately follow conformational changes of the ribosome during elongation in real time. We demonstrate the application of single-color FRET to correlate the conformational dynamics of the ribosome with the compositional dynamics of tRNA. We use the normal Cy5 FRET acceptor to observe arrival of a fluorescently labeled tRNA with a concomitant transition of the ribosome from the locked to the unlocked conformation. Our results illustrate the potential of nonfluorescent quenchers in single-molecule correlation studies. PMID:22428667

Chen, Jin; Tsai, Albert; Petrov, Alexey; Puglisi, Joseph D

2012-04-01

370

Entropy reduction in unfolded peptides (and proteins) due to conformational preferences of amino acid residues.  

PubMed

As established by several groups over the last 20 years, amino acid residues in unfolded peptides and proteins do not exhibit the unspecific random distribution as assumed by the classical random coil model. Individual amino acid residues in small peptides were found to exhibit different conformational preferences. Here, we utilize recently obtained conformational distributions of guest amino acid residues in GxG peptides to estimate their conformational entropy, which we find to be significantly lower than the entropy of an assumed random coil like distribution. Only at high temperature do backbone entropies approach random coil like values. We utilized the obtained backbone entropies of the investigated amino acid residues to estimate the loss of conformational entropy caused by a coil ? helix transition and identified two subsets of amino acid residues for which the thus calculated entropy losses correlate well with the respective Gibbs energy of helix formation obtained for alanine based host-guest systems. Calculated and experimentally derived entropic losses were found to be in good agreement. For most of the amino acid residues investigated entropic losses derived from our GxG distributions correlate very well with corresponding values recently obtained from MD simulations biased by conformational propensities derived from truncated coil libraries. Both, conformational entropy and the entropy of solvation exhibit a strong, residue specific temperature dependence, which can be expected to substantially affect the stability of unfolded states. Altogether, our results provide strong evidence for the notion that conformational preferences of amino acid residues matter with regard to the thermodynamics of peptide and protein folding. PMID:25227444

Schweitzer-Stenner, Reinhard; Toal, Siobhan E

2014-11-01

371

ATP Induced Conformational Changes in Hsp70: Molecular Dynamics and Experimental Validation of an In Silico Predicted Conformation  

PubMed Central

The 70-kD heat shock proteins (Hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling ATP binding and hydrolysis to protein substrate release and binding, respectively. ATP binding is believed to induce closing of the Hsp70 nucleotide binding domain (NBD) around the nucleotide. We report here a combined computational/experimental study of this open-closed transition. All-atom molecular dynamics simulations were performed for isolated open state NBDs with and without bound ATP. The nucleotide-free NBD samples a wide range of open configurations exhibiting flexible rearrangements of its four subdomains (IA-IIB). In contrast, the ATP-bound Hsp70 NBD closes to a range of configurations that is substantially more closed than the conformation observed in crystals of ATP-complexed NBDs. The close approach of subdomains IB and IIB observed in the simulations results in a strong coordination of the fluorescence probe Trp90 of IB with Arg261 of IIB, a feature not seen in the crystal structures. To determine if this computationally observed conformation occurs in solution, we constructed an R261A mutant. The mutation was found to increase the Km and kcat for ATP and to significantly reduce the extent of the fluorescence quench observed upon ATP binding. Our results thus account for the previously unexplained ATP-driven change in Trp90 fluorescence seen in the isolated NBD. PMID:19883127

Woo, Hyung-June; Jiang, Jianwen; Lafer, Eileen M.; Sousa, Rui

2009-01-01

372

The Relationship between Creativity and Conformity among Preschool Children.  

ERIC Educational Resources Information Center

This study investigated the relationship between creativity and conformity (social conformity and impersonal conformity) with 45 preschool children. Findings support the hypothesis that highly conforming and highly nonconforming children do not score as highly on creativity measurements as children in the freedom of expression group (i.e., not…

Van Hook, Cheryl W.; Tegano, Deborah W.

2002-01-01

373

LETTER: Conformal Ricci Collineations of Space-Times  

Microsoft Academic Search

We study conformal vector fields on space-times which in addition are compatible with the Ricci tensor (so-called conformal Ricci collineations). In the case of Einstein metrics any conformal vector field is automatically a Ricci collineation as well. For Riemannian manifolds, conformal Ricci collineation were called concircular vector fields and studied in the relationship with the geometry of geodesic circles. Here

W. Kühnel; H.-B. Rademacher

2001-01-01

374

Hierarchical Docking of Databases of Multiple Ligand Conformations  

Microsoft Academic Search

Ligand flexibility is an important problem in molecular docking and virtual screening. To address this challenge, we investigate a hierarchical pre-organization of multiple conformations of small molecules. Such organization of pre-calculated conformations removes the exploration of ligand conformational space from the docking calculation and allows for concise representation of what can be thousands of conformations. The hierarchy also recognizes and

David M. Lorbera; Brian K. Shoichet

2005-01-01

375

Quantum critical spin liquids and conformal field theory in 2+1 dimensions  

E-print Network

We describe new conformal field theories based on symplectic fermions that can be extrapolated between 2 and 4 dimensions. The critical exponents depend continuously on the number of components N of the fermions and the dimension D. In the context of anti-ferromagnetism, the N=2 theory is proposed to describe a deconfined quantum critical spin liquid corresponding to a transition between a Neel ordered phase and a VBS-like phase.

André LeClair

2006-10-23

376

UV Resonance Raman Elucidation of the Terminal and Internal Peptide Bond Conformations of Crystalline and Solution Oligoglycines  

PubMed Central

Spectroscopic investigations of macromolecules generally attempt to interpret the measured spectra in terms of the summed contributions of the different molecular fragments. This is the basis of the local mode approximation in vibrational spectroscopy. In the case of resonance Raman spectroscopy independent contributions of molecular fragments require both a local mode-like behavior and the uncoupled electronic transitions. Here we show that the deep UV resonance Raman spectra of aqueous solution phase oligoglycines show independent peptide bond molecular fragment contributions indicating that peptide bonds electronic transitions and vibrational modes are uncoupled. We utilize this result to separately determine the conformational distributions of the internal and penultimate peptide bonds of oligoglycines. Our data indicate that in aqueous solution the oligoglycine terminal residues populate conformations similar to those found in crystals (31-helices and ?-strands), but with a broader distribution, while the internal peptide bond conformations are centered around the 31-helix Ramachandran angles. PMID:20657703

Bykov, Sergei V.; Asher, Sanford A.

2010-01-01

377

Global attractors of complete conformal foliations  

SciTech Connect

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.

Zhukova, Nina I [N.I. Lobachevsky Nizhni Novgorod State University, Nizhnii Novgorod (Russian Federation)

2012-03-31

378

Conformational phases of membrane bound cytoskeletal filaments  

NASA Astrophysics Data System (ADS)

Membrane bound cytoskeletal filaments found in living cells are employed to carry out many types of activities including cellular division, rigidity and transport. When these biopolymers are bound to a membrane surface they may take on highly non-trivial conformations as compared to when they are not bound. This leads to the natural question; What are the important interactions which drive these polymers to particular conformations when they are bound to a surface? Assuming that there are binding domains along the polymer which follow a periodic helical structure set by the natural monomeric handedness, these bound conformations must arise from the interplay of the intrinsic monomeric helicity and membrane binding. To probe this question, we study a continuous model of an elastic filament with intrinsic helicity and map out the conformational phases of this filament for various mechanical and structural parameters in our model, such as elastic stiffness and intrinsic twist of the filament. Our model allows us to gain insight into the possible mechanisms which drive real biopolymers such as actin and tubulin in eukaryotes and their prokaryotic cousins MreB and FtsZ to take on their functional conformations within living cells.

Quint, David A.; Grason, Gregory; Gopinathan, Ajay

2013-03-01

379

Conformal anomaly and the production of massless particles by a conformally flat metric  

Microsoft Academic Search

It is shown that a conformally flat gravitational field can produce gauge bosons through the anomaly in the trace of the energy--momentum tensor. An equation is obtained for the single-particle wave function of a photon with allowance for the electromagnetic corrections in an arbitrary conformally flat gravitational field. The solution of this equation determines the amplitude for photon production by

Dolgov

1981-01-01

380

Intermolecularly-induced conformational disorder in ferrocene, 1-bromoferrocene and 1,1?-dibromoferrocene  

NASA Astrophysics Data System (ADS)

Conformational preferences for isolated molecules of ferrocene, 1-bromoferrocene and 1,1?-dibromoferrocene were obtained by combined use of matrix-isolation infrared spectroscopy and quantum chemical calculations. Monomeric ferrocene and 1-dibromoferrocene were found to exist in a low temperature argon matrix (T = 15 K) exclusively in the eclipsed configuration, which corresponds to their most stable conformation in gas phase. On the other hand, for the neat compounds in crystalline phase, intermolecular interactions induce conformational disorder, leading to presence in the room temperature polymorphic forms of monomeric units with the staggered (or nearly staggered) conformation. 1,1?-Dibromoferrocene exists in both gas phase and low temperature argon matrix in two conformers of C2 symmetry (C2-I and C2-II), with eclipsed cyclopentadienyl moieties and Br atoms opposed to H atoms. The populations of the two conformers trapped in the as-deposited matrix were found to correspond to those estimated from theory for the room temperature equilibrium gas phase. By increasing the temperature of the matrix (up to 35 K), the gas phase lower energy form (C2-I) converted to the C2-II form. Besides allowing the precise structural and spectroscopic characterization of the two forms, these studies also revealed that the C2-II conformer (having a largest dipole moment) is stabilized in the matrix media, thus becoming more stable than the C2-I form under these conditions. Very interestingly, the room temperature stable polymorph of the compound (Tfus = 325.4 ± 0.1 K) is composed by 1,1?-dibromoferrocene units exhibiting the C2v symmetry eclipsed conformation with opposed bromine atoms, which for the isolated molecule corresponds to the highest energy conformation along the ring torsional coordinate and is the transition state structure between the two symmetry equivalent C2-II minima. Differential scanning calorimetry, polarized light thermomicroscopy and infrared measurements on 1,1?-dibromoferrocene allowed to identify a new polymorph of the compound, with Tfus = 320.2 ± 0.1 K. On the whole, the results presented in this article represent illuminating examples of intermolecularly-induced conformational disorder in solid phase and of its relevance to polymorphism.

Silva, Patrícia A.; Maria, Teresa M. R.; Nunes, Cláudio M.; Eusébio, Maria Ermelinda S.; Fausto, Rui

2014-12-01

381

Metric transition  

NASA Astrophysics Data System (ADS)

This report describes NASA's metric transition in terms of seven major program elements. Six are technical areas involving research, technology development, and operations; they are managed by specific Program Offices at NASA Headquarters. The final program element, Institutional Management, covers both NASA-wide functional management under control of NASA Headquarters and metric capability development at the individual NASA Field Installations. This area addresses issues common to all NASA program elements, including: Federal, state, and local coordination; standards; private industry initiatives; public-awareness initiatives; and employee training. The concluding section identifies current barriers and impediments to metric transition; NASA has no specific recommendations for consideration by the Congress.

1992-06-01

382

Metric transition  

NASA Technical Reports Server (NTRS)

This report describes NASA's metric transition in terms of seven major program elements. Six are technical areas involving research, technology development, and operations; they are managed by specific Program Offices at NASA Headquarters. The final program element, Institutional Management, covers both NASA-wide functional management under control of NASA Headquarters and metric capability development at the individual NASA Field Installations. This area addresses issues common to all NASA program elements, including: Federal, state, and local coordination; standards; private industry initiatives; public-awareness initiatives; and employee training. The concluding section identifies current barriers and impediments to metric transition; NASA has no specific recommendations for consideration by the Congress.

1992-01-01

383

Human Meibum Lipid Conformation and Thermodynamic Changes with Meibomian-Gland Dysfunction  

PubMed Central

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

Borchman, Douglas; Yappert, Marta C.; Bell, James; Wells, Emily; Neravetla, Shantanu; Greenstone, Victoria

2011-01-01

384

Design of an Optical Switch for Studying Conformational Dynamics in Individual Molecules of GroEL  

PubMed Central

We describe the design of an optical switch in the chaperonin GroEL that is opened and closed by its ATP- and cochaperonin GroES-driven conformational changes. The switch, based on a fluorophore and a quencher, is engineered into the single-ring variant of the chaperone, and shows dramatic modulation of its fluorescent intensity in response to the transition of the protein between its allosteric states. It, therefore, forms a sensitive probe for the dynamics of the allosteric transitions of this machine, both in the bulk and in single molecules. PMID:18572960

Frank, Gabriel A.; Kipnis, Yakov; Smolensky, Elena; Daube, Shirley S.; Horovitz, Amnon; Haran, Gilad

2008-01-01

385

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

Federal Register 2010, 2011, 2012, 2013

...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...

2010-05-26

386

Necleoside conformations. 19. Temperature and pH effects on the conformation of guanosine phosphates.  

PubMed Central

Proton magnetic resonance spectra at 250 MHz were measured as a function of temperature and pH of the three guanosine phosphates. From these data and previously published work the conformational parameters of these compounds were determinated. The phosphate group of Guo-5'-P changes its conformation around the C-O bond and its rotation is relatively slow at 20 degrees. At neutral pD the S conformation is favoured and the N form at acid pD. This conformational change is paralleled by a change in exocyclic rotamer distribution and takes place at the pK of the protonation of the base on N-7. Although correlation appears to exist between the various conformations, notable exceptions exist. PMID:238183

Son, T D; Guschlbauer, W

1975-01-01

387

Enkephalin: Conformational Analysis by means of Empirical Energy Calculations  

Microsoft Academic Search

Low-energy conformations of methionine-enkephalin were generated by means of an empirical method of computation. Many compact conformations, including those containing various standard bends, were of comparable energy. However, one conformation was found to have a potential energy about 5 kcal\\/mol (21 × 103 J\\/mol) below that of the large group of compact conformations. In this conformation, the 3-glycyl and 4-phenylalanyl

Yoshinori Isogai; George Nemethy; Harold A. Scheraga

1977-01-01

388

Discriminative learning for protein conformation sampling  

PubMed Central

Protein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Conditional Random Fields (CRFs). Using a discriminative learning method, CRFSampler can automatically learn more than ten thousand parameters quantifying the relationship among primary sequence, secondary structure, and (pseudo) backbone angles. Using only compactness and self-avoiding constraints, CRFSampler can efficiently generate protein-like conformations from primary sequence and predicted secondary structure. CRFSampler is also very flexible in that a variety of model topologies and feature sets can be defined to model the sequence-structure relationship without worrying about parameter estimation. Our experimental results demonstrate that using a simple set of features, CRFSampler can generate decoys with much higher quality than the most recent HMM model. PMID:18412258

Zhao, Feng; Li, Shuaicheng; Sterner, Beckett W.; Xu, Jinbo

2010-01-01

389

Supersymmetric extension of Galilean conformal algebras  

SciTech Connect

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.

Bagchi, Arjun; Mandal, Ipsita [Harish-Chandra Research Institute, Chhatnag Road, Jhusi, Allahabad 211019 (India)

2009-10-15

390

Conformal Symmetry for General Black Holes  

E-print Network

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.

Mirjam Cveti?; Finn Larsen

2011-06-16

391

Conformal Higgs model: predicted dark energy density  

E-print Network

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.

R. K. Nesbet

2010-04-28

392

QCD evolution equations from conformal symmetry  

E-print Network

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.

V. M. Braun; A. N. Manashov

2014-08-28

393

Automatic field shaping for conformal radiation therapy.  

PubMed

A computer method has been developed to shape the radiation field to conform to the shape of the target as visualized through the beam's eye view (BEV) perspective for conformal radiation therapy. Initially, a series of 2D target contours to define the target size are input into the computer. These target contour data are mapped onto a 3D surface and thereafter projected onto a BEV plane. The projection's outer boundary of the target is auto-contoured. After auto-contouring, a margin is automatically added to define the radiation beam cross section. Since the BEV plane is arbitrarily oriented about the target, the beam orientation can be non-coplanar to the plane of the target contours. For a chosen beam orientation, the conformal treatment beam cross section can be generated automatically using this computer technique and output to either a laser printer, a plotter or stored on files for transfer to the linear accelerator computer system. PMID:7924269

Ayyangar, K

1994-04-01

394

Logarithm conformal mapping brings the cloaking effect.  

PubMed

Over the past years, invisibility cloaks have been extensively discussed since transformation optics emerges. Generally, the electromagnetic parameters of invisibility cloaks are complicated tensors, yet difficult to realize. As a special method of transformation optics, conformal mapping helps us design invisibility cloak with isotropic materials of a refractive index distribution. However, for all proposed isotropic cloaks, the refractive index range is at such a breadth that challenges current experimental fabrication. In this work, we propose two new kinds of logarithm conformal mappings for invisible device designs. For one of the mappings, the refractive index distribution of conformal cloak varies from 0 to 9.839, which is more feasible for future implementation. Numerical simulations by using finite element method are performed to confirm the theoretical analysis. PMID:25359138

Xu, Lin; Chen, Huanyang

2014-01-01

395

Conformal coatings : challenging environments lead to growth.  

SciTech Connect

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.

Challener, Cynthia A.

2005-08-01

396

Logarithm conformal mapping brings the cloaking effect  

PubMed Central

Over the past years, invisibility cloaks have been extensively discussed since transformation optics emerges. Generally, the electromagnetic parameters of invisibility cloaks are complicated tensors, yet difficult to realize. As a special method of transformation optics, conformal mapping helps us design invisibility cloak with isotropic materials of a refractive index distribution. However, for all proposed isotropic cloaks, the refractive index range is at such a breadth that challenges current experimental fabrication. In this work, we propose two new kinds of logarithm conformal mappings for invisible device designs. For one of the mappings, the refractive index distribution of conformal cloak varies from 0 to 9.839, which is more feasible for future implementation. Numerical simulations by using finite element method are performed to confirm the theoretical analysis. PMID:25359138

Xu, Lin; Chen, Huanyang

2014-01-01

397

Understanding Modern Magnets through Conformal Mapping  

SciTech Connect

When I had to choose, within some narrow range, the topic of this paper, I received great help from a colleague in Berkeley and from Prof. Little when it was suggested that I should pick among the possible subjects of my talk the subject that Prof. Bloch would have enjoyed most. Since Prof. Bloch would prefer a scalpel over a sword every time, I hope and think that most people will approve my choice. When one intends to talk about a subject that is as old as conformal mapping and one does not want to lose the audience in a very short time, it is advisable to start by explaining both the motivation for the talk as well as the goals one has in mind when giving the talk. This particular talk has been motivated by the increasing frequency with which one hears, from people that ought to know better, statements like: 'Conformal mapping is really a thing of the past because of all the marvelous computer programs that we now have'. Even though, or more likely because, I have been intimately involved in the development of some large and widely used computer codes, I am deeply disturbed by such statements since they indicate a severe lack of understanding of the purpose of conformal mapping techniques, computers, and computer codes. In my view, conformal mapping can be an extremely powerful computational technique, and the easy availability of computers has made that aspect even more important now than it has been in the past. Additionally, and more importantly, conformal mapping can give very deep and unique insight into problems, giving often solutions to problems that can not be obtained with any other method, in particular not with computers. Wanting to demonstrate in particular the latter part, I set myself two goals for this talk: (1) 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 H.Kober's Dictionary of Conformal Representations (ref. 1). 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: (2) 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. This is followed by a brief summary of the most important properties of functions of a complex variable. When reading this introduction into the relevant mathematics, the reader needs to keep in mind that this is not a mathematics essay, but a demonstration how beautiful and powerful, but not always appreciated, mathematics can be if used by a physicist or engineer to solve some real life problems.

Halbach, K.

1989-10-27

398

Conformational changes and catalysis by alcohol dehydrogenase.  

PubMed

As shown by X-ray crystallography, horse liver alcohol dehydrogenase undergoes a global conformational change upon binding of NAD(+) or NADH, involving a rotation of the catalytic domain relative to the coenzyme binding domain and the closing up of the active site to produce a catalytically efficient enzyme. The conformational change requires a complete coenzyme and is affected by various chemical or mutational substitutions that can increase the catalytic turnover by altering the kinetics of the isomerization and rate of dissociation of coenzymes. The binding of NAD(+) is kinetically limited by a unimolecular isomerization (corresponding to the conformational change) that is controlled by deprotonation of the catalytic zinc-water to produce a negatively-charged zinc-hydroxide, which can attract the positively-charged nicotinamide ring. The deprotonation is facilitated by His-51 acting through a hydrogen-bonded network to relay the proton to solvent. Binding of NADH also involves a conformational change, but the rate is very fast. After the enzyme binds NAD(+) and closes up, the substrate displaces the hydroxide bound to the catalytic zinc; this exchange may involve a double displacement reaction where the carboxylate group of a glutamate residue first displaces the hydroxide (inverting the tetrahedral coordination of the zinc), and then the exogenous ligand displaces the glutamate. The resulting enzyme-NAD(+)-alcoholate complex is poised for hydrogen transfer, and small conformational fluctuations may bring the reactants together so that the hydride ion is transferred by quantum mechanical tunneling. In the process, the nicotinamide ring may become puckered, as seen in structures of complexes of the enzyme with NADH. The conformational changes of alcohol dehydrogenase demonstrate the importance of protein dynamics in catalysis. PMID:19583966

Plapp, Bryce V

2010-01-01

399

Conformational Changes and Catalysis by Alcohol Dehydrogenase§  

PubMed Central

As shown by X-ray crystallography, horse liver alcohol dehydrogenase undergoes a global conformational change upon binding of NAD+ or NADH, involving a rotation of the catalytic domain relative to the coenzyme binding domain and the closing up of the active site to produce a catalytically efficient enzyme. The conformational change requires a complete coenzyme and is affected by various chemical or mutational substitutions that can increase the catalytic turnover by altering the kinetics of the isomerization and rate of dissociation of coenzymes. The binding of NAD+ is kinetically limited by a unimolecular isomerization (corresponding to the conformational change) that is controlled by deprotonation of the catalytic zinc-water to produce a negatively-charged zinc-hydroxide, which can attract the positively-charged nicotinamide ring. The deprotonation is facilitated by His-51 acting through a hydrogen-bonded network to relay the proton to solvent. Binding of NADH also involves a conformational change, but the rate is very fast. After the enzyme binds NAD+ and closes up, the substrate displaces the hydroxide bound to the catalytic zinc; this exchange may involve a double displacement reaction where the carboxylate group of a glutamate residue first displaces the hydroxide (inverting the tetrahedral coordination of the zinc), and then the exogenous ligand displaces the glutamate. The resulting enzyme-NAD+-alcoholate complex is poised for hydrogen transfer, and small conformational fluctuations may bring the reactants together so that the hydride ion is transferred by quantum mechanical tunneling. In the process, the nicotinamide ring may become puckered, as seen in structures of complexes of the enzyme with NADH. The conformational changes of alcohol dehydrogenase demonstrate the importance of protein dynamics in catalysis. PMID:19583966

Plapp, Bryce V.

2009-01-01

400

Cation-specific conformational behavior of polyelectrolyte brushes: from aqueous to nonaqueous solvent.  

PubMed

We have investigated changes in the cation-specific conformational behavior of poly(sodium styrenesulfonate) (PSS) brushes as the solvent changes from water to methanol using a quartz crystal microbalance with dissipation (QCM-D). A solvation to desolvation transition of the grafted chains accompanied by swelling to the collapse transition of the brushes is observed for Na(+). In the case of Cs(+), the brushes undergo solvation to desolvation to resolvation accompanied by swelling to collapse to reswelling transitions. The resolvation and reswelling transitions for Cs(+) are induced by the charge inversion of the brushes via van der Waals interactions between Cs(+) and the brushes. All of the transitions for monovalent cations become less obvious as the methanol content increases. For divalent Ca(2+) and trivalent La(3+), a solvation to desolvation to resolvation transition of the grafted chains accompanied by a swelling to collapse to reswelling transition of the brushes can be observed. The resolvation and reswelling of the brushes for the multivalent cations are induced by the charge inversion of the brushes via charge-image charge interactions. The extent of the transitions for the PSS brushes in the presence of multivalent cations is only slightly influenced by the methanol content. PMID:25300430

Wang, Tao; Long, Yunchao; Liu, Lvdan; Wang, Xiaowen; Craig, Vincent S J; Zhang, Guangzhao; Liu, Guangming

2014-11-01

401

Modeling the solid-liquid phase transition in saturated triglycerides  

NASA Astrophysics Data System (ADS)

We investigated theoretically two competing published scenarios for the melting transition of the triglyceride trilaurin (TL): those of (1) Corkery et al. [Langmuir 23, 7241 (2007)], in which the average state of each TL molecule in the liquid phase is a discotic ``Y'' conformer whose three chains are dynamically twisted, with an average angle of ~120° between them, and those of (2) Cebula et al. [J. Am. Oil Chem. Soc. 69, 130 (1992)], in which the liquid-state conformation of the TL molecule in the liquid phase is a nematic h*-conformer whose three chains are in a modified ``chair'' conformation. We developed two competing models for the two scenarios, in which TL molecules are in a nematic compact-chair (or ``h'') conformation, with extended, possibly all-trans, chains at low-temperatures, and in either a Y conformation or an h* conformation in the liquid state at temperatures higher than the phase-transition temperature, T*=319 K. We defined an h-Y model as a realization of the proposal of Corkery et al. [Langmuir 23, 7241 (2007)], and explored its predictions by mapping it onto an Ising model in a temperature-dependent field, performing a mean-field approximation, and calculating the transition enthalpy ?H. We found that the most plausible realization of the h-Y model, as applied to the solid-liquid phase transition in TL, and likely to all saturated triglycerides, gave a value of ?H in reasonable agreement with the experiment. We then defined an alternative h-h* model as a realization of the proposal of Cebula et al. [J. Am. Oil Chem. Soc. 69, 130 (1992)], in which the liquid phase exhibits an average symmetry breaking similar to an h conformation, but with twisted chains, to see whether it could describe the TL phase transition. The h-h* model gave a value of ?H that was too small by a factor of ~3-4. We also predicted the temperature dependence of the 1132 cm-1 Raman band for both models, and performed measurements of the ratios of three TL Raman bands in the temperature range of -20 °C<=T<=90 °C. The experimental results were in accord with the predictions of the h-Y model and support the proposal of Corkery et al. [Langmuir 23, 7241 (2007)] that the liquid state is made up of molecules that are each, on average, in a Y conformation. Finally, we carried out computer simulations of minimal-model TLs in the liquid phase, and concluded that although the individual TL molecules are, on average, Y conformers, long-range discotic order is unlikely to exist.

Pink, David A.; Hanna, Charles B.; Sandt, Christophe; MacDonald, Adam J.; MacEachern, Ronald; Corkery, Robert; Rousseau, Dérick

2010-02-01

402

Conformal pure radiation with parallel rays  

NASA Astrophysics Data System (ADS)

We define pure radiation metrics with parallel rays to be n-dimensional pseudo-Riemannian metrics that admit a parallel null line bundle K and whose Ricci tensor vanishes on vectors that are orthogonal to K. We give necessary conditions in terms of the Weyl, Cotton and Bach tensors for a pseudo-Riemannian metric to be conformal to a pure radiation metric with parallel rays. Then, we derive conditions in terms of the tractor calculus that are equivalent to the existence of a pure radiation metric with parallel rays in a conformal class. We also give analogous results for n-dimensional pseudo-Riemannian pp-waves.

Leistner, Thomas; Nurowski, Pawe?

2012-03-01

403

Simulating Massive Conformation Changes within Polypeptide Systems  

NASA Astrophysics Data System (ADS)

In this dissertation I employ all-atom structure based models with stable energy basins to several existing and novel polypeptide systems (postulated conformation changes of the mammalian prion protein and structurally dual proteins). The common themes are finding unfolding and refolding pathways between highly dissimilar protein structures as a means of understanding exactly how and why a protein may misfold. The modeling is based on the energy funnel landscape theory of protein conformation space. The principle of minimal frustration is considered as the model includes parameters which vary the roughness of the landscape and give rise to off-pathway misfoldings. The dual basin model is applied to the C-terminal (residues 166-226) of the mammalian prion protein. One basin represents the known alpha-helical (aH) structure while the other represents the same residues in a lefthanded beta-helical (LHBH) conformation. The LHBH structure has been proposed to help describe one class of in vitro grown fibrils, as well as possibly self-templating the conversion of normal cellular prion protein to the infectious form. Yet, it is unclear how the protein may make this global rearrangement. Our results demonstrate that the conformation changes are not strongly limited by large-scale geometry modification and that there may exist an overall preference for the LHBH conformation. Furthermore, our model presents novel intermediate trapping conformations with twisted LHBH structure. Polypeptides that display structural duality have primary structures that can give rise to different potential native conformations. We apply the structure-based all-atom model to a leucine zipper protein template with a stable aH structure that has been shown in experiment to switch to a ? hairpin structure when exposed to a low-pH environment. We show that the model can be used to perform large-scale temperature-dependent conformational switching by simulating this switching behavior. We augmented the switching by modifying the proteins in two different ways: first, by mutating the Gln residues in the protein to Thr and second, by binding the cysteine residues at the protein termini.

Singh, Jaspinder Paul

404

Rigid supersymmetry, conformal coupling and twistor spinors  

E-print Network

We investigate the relationship between conformal and spin structure on lorentzian manifolds and see how their compatibility influences the formulation of rigid supersymmetric field theories. In dimensions three, four, six and ten, we show that if the Dirac current associated with a generic spinor defines a null conformal Killing vector then the spinor must obey a twistor equation with respect to a certain connection with torsion. Of the theories we consider, those with classical superconformal symmetry in Minkowski space can be reformulated as rigid supersymmetric theories on any lorentzian manifold admitting twistor spinors. In dimensions six and ten, we also describe rigid supersymmetric gauge theories on bosonic minimally supersymmetric supergravity backgrounds.

de Medeiros, Paul

2012-01-01

405

Rigid supersymmetry, conformal coupling and twistor spinors  

E-print Network

We investigate the relationship between conformal and spin structure on lorentzian manifolds and see how their compatibility influences the formulation of rigid supersymmetric field theories. In dimensions three, four, six and ten, we show that if the Dirac current associated with a generic spinor defines a null conformal Killing vector then the spinor must obey a twistor equation with respect to a certain connection with torsion. Of the theories we consider, those with classical superconformal symmetry in Minkowski space can be reformulated as rigid supersymmetric theories on any lorentzian manifold admitting twistor spinors. In dimensions six and ten, we also describe rigid supersymmetric gauge theories on bosonic minimally supersymmetric supergravity backgrounds.

Paul de Medeiros

2012-09-18

406

Classical conformal blocks and Painlevé VI  

NASA Astrophysics Data System (ADS)

We study the classical c ? ? limit of the Virasoro conformal blocks. We point out that the classical limit of the simplest nontrivial null-vector decoupling equation on a sphere leads to the Painlevé VI equation. This gives the explicit representation of generic four-point classical conformal block in terms of the regularized action evaluated on certain solution of the Painlevé VI equation. As a simple consequence, the monodromy problem of the Heun equation is related to the connection problem for the Painlevé VI.

Litvinov, Alexey; Lukyanov, Sergei; Nekrasov, Nikita; Zamolodchikov, Alexander

2014-07-01

407

Static wormholes in vacuum for conformal gravity  

E-print Network

A static spherically symmetric wormhole solution for conformal gravity in vacuum is found. The solution possesses a single integration constant which determines the size of the neck connecting two static homogeneous universes of constant spatial curvature. Time runs at different rates on each side of the neck, and depending on the value of the parameter, the wormhole can develop a cosmological horizon only at one side. It is shown that the wormholes correspond to the matching of different Einstein spacetimes by means of improper conformal transformations.

Julio Oliva; David Tempo; Ricardo Troncoso

2009-07-07

408

Static cylindrical symmetry and conformal flatness  

E-print Network

We present the whole set of equations with regularity and matching conditions required for the description of physically meaningful static cylindrically symmmetric distributions of matter, smoothly matched to Levi-Civita vacuum spacetime. It is shown that the conformally flat solution with equal principal stresses represents an incompressible fluid. It is also proved that any conformally flat cylindrically symmetric static source cannot be matched through Darmois conditions to the Levi-Civita spacetime. Further evidence is given that when the Newtonian mass per unit length reaches 1/2 the spacetime has plane symmetry.

L. Herrera; G. Le Denmat; G. Marcilhacy; N. O. Santos

2004-11-23

409

Collisions of Einstein-Conformal Scalar Waves  

E-print Network

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.

C. Klim?{\\'?}k; P. Koln{\\'?}k

1992-12-18

410

N=2 Conformal Superspace in Four Dimensions  

E-print Network

We develop the geometry of four dimensional N=2 superspace where the entire conformal algebra of SU(2,2|2) is realized linearly in the structure group rather than just the SL(2,C) x U(2)_R subgroup of Lorentz and R-symmetries, extending to N=2 our prior result for N=1 superspace. This formulation explicitly lifts to superspace the existing methods of the N=2 superconformal tensor calculus; at the same time the geometry, when degauged to SL(2,C) x U(2)_R, reproduces the existing formulation of N=2 conformal supergravity constructed by Howe.

Butter, Daniel

2011-01-01

411

N=2 Conformal Superspace in Four Dimensions  

E-print Network

We develop the geometry of four dimensional N=2 superspace where the entire conformal algebra of SU(2,2|2) is realized linearly in the structure group rather than just the SL(2,C) x U(2)_R subgroup of Lorentz and R-symmetries, extending to N=2 our prior result for N=1 superspace. This formulation explicitly lifts to superspace the existing methods of the N=2 superconformal tensor calculus; at the same time the geometry, when degauged to SL(2,C) x U(2)_R, reproduces the existing formulation of N=2 conformal supergravity constructed by Howe.

Daniel Butter

2011-03-30

412

Conformal metamaterial absorber for curved surface.  

PubMed

In this paper, three different unit cells are designed on the basis split-ring-cross resonators, and each unit cell has an absorption rate greater than 90% at incident angles of 0°, 30°, and 45°, respectively. They are non-periodically placed in three different zones on the curved surface. Therefore, the proposed conformal metamaterial absorber can achieve a high absorption rate. The performance of the proposed absorber is compared with that of a metallic curved surface and a conformal metamaterial absorber with the same unit cells. PMID:24104326

Jang, Youngsoo; Yoo, Minyeong; Lim, Sungjoon

2013-10-01

413

On conformal higher spin wave operators  

E-print Network

We analyze free conformal higher spin actions and the corresponding wave operators in arbitrary even dimensions and backgrounds. We show that the wave operators do not factorize in general, and identify the Weyl tensor and its derivatives as the obstruction to factorization. We give a manifestly factorized form for them on (A)dS backgrounds for arbitrary spin and on Einstein backgrounds for spin 2. We are also able to fix the conformal wave operator in d=4 for s=3 up to linear order in the Riemann tensor on generic Bach-flat backgrounds.

Teake Nutma; Massimo Taronna

2014-04-29

414

Transition paths, diffusive processes, and preequilibria of protein folding  

PubMed Central

Fundamental relationships between the thermodynamics and kinetics of protein folding were investigated using chain models of natural proteins with diverse folding rates by extensive comparisons between the distribution of conformations in thermodynamic equilibrium and the distribution of conformations sampled along folding trajectories. Consistent with theory and single-molecule experiment, duration of the folding transition paths exhibits only a weak correlation with overall folding time. Conformational distributions of folding trajectories near the overall thermodynamic folding/unfolding barrier show significant deviations from preequilibrium. These deviations, the distribution of transition path times, and the variation of mean transition path time for different proteins can all be rationalized by a diffusive process that we modeled using simple Monte Carlo algorithms with an effective coordinate-independent diffusion coefficient. Conformations in the initial stages of transition paths tend to form more nonlocal contacts than typical conformations with the same number of native contacts. This statistical bias, which is indicative of preferred folding pathways, should be amenable to future single-molecule measurements. We found that the preexponential factor defined in the transition state theory of folding varies from protein to protein and that this variation can be rationalized by our Monte Carlo diffusion model. Thus, protein folding physics is different in certain fundamental respects from the physics envisioned by a simple transition-state picture. Nonetheless, transition state theory can be a useful approximate predictor of cooperative folding speed, because the height of the overall folding barrier is apparently a proxy for related rate-determining physical properties. PMID:23213246

Zhang, Zhuqing; Chan, Hue Sun

2012-01-01

415

Conformational changes in tertiary structure near the ligand binding site of an integrin I domain.  

PubMed

For efficient ligand binding, integrins must be activated. Specifically, a conformational change has been proposed in a ligand binding domain present within some integrins, the inserted (I) domain [Lee, J., Bankston, L., Arnaout, M. & Liddington, R. C. (1995) Structure (London) 3, 1333-1340]. This proposal remains controversial, however, despite extensive crystal structure studies on the I domain [Lee, J., Bankston, L., Arnaout, M. & Liddington, R. C. (1995) Structure (London) 3, 1333-1340; Liddington, R. & Bankston, L. (1998) Structure (London) 6, 937-938; Qu, A. & Leahy, D. J. (1996) Structure (London) 4, 931-942; and Baldwin, E. T., Sarver, R. W., Bryant, G. L., Jr., Curry, K. A., Fairbanks, M. B., Finzel, B. C. , Garlick, R. L., Heinrikson, R. L., Horton, N. C. & Kelly, L. L. (1998) Structure (London) 6, 923-935]. By defining the residues present in the epitope of a mAb against the human Mac-1 integrin (alphaMbeta2, CD11b/CD18) that binds only the active receptor, we provide biochemical evidence that the I domain itself undergoes a conformational change with activation. This mAb, CBRM1/5, binds the I domain very close to the ligand binding site in a region that is widely exposed regardless of activation as judged by reactivity with other antibodies. The conformation of the epitope differs in two crystal forms of the I domain, previously suggested to represent active and inactive receptor. Our data suggests that conformational differences in the I domain are physiologically relevant and not merely a consequence of different crystal lattice interactions. We also demonstrate that the transition between the two conformational states depends on species-specific residues at the bottom of the I domain, which are proposed to be in an interface with another integrin domain, and that this transition correlates with functional activity. PMID:10051621

Oxvig, C; Lu, C; Springer, T A

1999-03-01

416

STEM Transitions  

NSDL National Science Digital Library

Under the direction of the Center for Occupational Research and Development (CORD), the STEM Transitions initiative has worked with 40 community college faculty to create integrated curriculum projects for use in math, science, and technical courses in the six STEM-related clusters. Much of this work has been funded by the U.S. Department of Education's Office of Vocational and Adult Education. First-time visitors can get an overview in the "Using This Site" area and then visit the "Integrated Projects" area. After signing up for a free account, they can take advantage of over 60 lesson plans and activities such as "The Secret Ingredient: Nutrient Analysis of Selected Food Items" and "Good Dirty, Bad Dirty: Soil Types and Erosion Potential." The site also provides information about upcoming webinars and workshops sponsored by the STEM Transitions, along with information about their faculty affiliates.

417

Conformation-dependent ionization of ?-phenylalanine: structures and energetics of cationic conformers  

NASA Astrophysics Data System (ADS)

The vertical ionization energy of L-phenylalanine was found to depend uniquely on the type of intramolecular hydrogen bonding in the neutral conformers. Between the two known subgroups of conformers, the ionization energy of those with a large backbone-residue interaction through a ?-hydrogen bond was considerably higher than the others because of the repulsion between the backbone and the residue in the cation. It was strongly noted from this study and others in the past that the neutral conformation uniquely determines such disparate properties as the cationic structure, the magnitude of the ionization energy, and the propensity toward hydration.

Lee, Kang Taek; Sung, Jiha; Lee, Kwang Jun; Kim, Seong Keun; Park, Young Dong

2003-01-01

418

Logarithmic correlators in nonrelativistic conformal field theory  

SciTech Connect

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.

Hosseiny, Ali; Rouhani, Shahin [Department of Physics, Sharif University of Technology, Tehran 11165-9161 (Iran, Islamic Republic of)

2010-10-15

419

Brain Surface Conformal Parameterization with Algebraic Functions  

E-print Network

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

Wang, Yalin

420

Conformity Behavior and Self-Consciousness.  

ERIC Educational Resources Information Center

Compliance, conforming behavior as a response to social influences, is affected by a variety of factors within the self. Some of these factors pertain to one's perceived place in the social context; others pertain to the salience of one's immediate affective and perceptual experience. The self-aspect chosen as the object of one's attention can…

Froming, William J.

421

Change of angles in conformal welding  

Microsoft Academic Search

Let be a given bijective analytic mapping of the circumference C of the unit circle onto itself. By the uniformization theorem, there exists an analytic Jordan curve ? with the following property: there are two bijective conformal mappings F (interior of C? interior of ?) and G (exterior of C ? exterior of ?) such that for all . We

Alfred Huber

1986-01-01

422

Lobachevsky geometry of (super)conformal mechanics  

E-print Network

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.

Tigran Hakobyan; Armen Nersessian

2008-03-09

423

Conformal anomaly actions for dilaton interactions  

E-print Network

We discuss, in conformally invariant field theories such as QCD with massless fermions, a possible link between the perturbative signature of the conformal anomaly, in the form of anomaly poles of the 1-particle irreducible effective action, and its description in terms of Wess-Zumino actions with a dilaton. The two descriptions are expected to capture the UV and IR behaviour of the conformal anomaly, in terms of fundamental and effective degrees of freedom respectively, with the dilaton effective state appearing in a nonlinear realization. As in the chiral case, conformal anomalies seem to be related to the appearance of these effective interactions in the 1PI action in all the gauge-invariant sectors of the Standard Model. We show that, as a consequence of the underlying anomalous symmetry, the infinite hierarchy of recurrence relations involving self-interactions of the dilaton is entirely determined only by the first four of them. This relation can be generalized to any even space-time dimension.

Rose, Luigi Delle; Serino, Mirko

2014-01-01

424

Conformally flat polytropes for anisotropic matter  

E-print Network

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.

Herrera, L; Barreto, W; Ospino, J

2014-01-01

425

Conformally flat polytropes for anisotropic matter  

E-print Network

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.

L. Herrera; A. Di Prisco; W. Barreto; J. Ospino

2014-10-24

426

Influence of stabilizers cosolutes on catalase conformation  

Microsoft Academic Search

The effects of sucrose, mannitol and betaine on the thermodynamic stability and the conformational state of the catalase enzyme were analyzed in order to understand the molecular mechanism whereby the solutes stabilized the enzyme. Catalase was selected as the model enzyme because it is used in several biotechnological processes. In the presence of each cosolute, our data have shown that

Soledad Belluzo; Valeria Boeris; Beatriz Farruggia; Guillermo Picó

2011-01-01

427

Macromolecular conformational dynamics in torsional angle space  

NASA Astrophysics Data System (ADS)

A Brownian dynamics treatment in torsional angle space is presented for the simulation of conformational dynamics of macromolecules with fixed bond lengths and bond angles and with an arbitrary intramolecular potential energy function. The advantages of the torsional angle space treatment over similar treatments (Brownian dynamics or molecular dynamics) in atomic coordinate space are that, first, the number of variables is reduced by roughly a factor of 10 and, second, the integration time step size is increased by 3 to 4 orders of magnitude (because, by confining the treatment to the torsional angle space, the time step size is not limited by the fast oscillation modes of covalent bonds but rather by the slow motion of macromolecular segments whose time scale is roughly 3 to 4 orders of magnitude larger than that of bond oscillations). Consequently, the exploration of global conformational relaxation processes becomes computationally possible. The treatment is tested by studying the folding kinetics of off-lattice chains with fixed bond lengths and bond angles and with prescribed sequences. The present treatment is a general purpose one applicable to all macromolecular conformational relaxation processes (e.g., protein folding kinetics, drug/ligand docking on to target proteins, conformational multiple-minima problems, etc.). It serves as a complement to the molecular dynamics or Brownian dynamics treatments in atomic coordinate space.

He, Siqian; Scheraga, Harold A.

1998-01-01

428

Role Conflict and Conformity in Dress.  

ERIC Educational Resources Information Center

Examined conflict regarding what form of dress is appropriate for Roman Catholic priest. Data from 5,475 American Catholic priests revealed that priests who conformed to church regulations regarding dress differed from nonconformists in beliefs about their roles as priests and in their opinions of church reform, commitment to the priesthood,…

Jasper, Cynthia R.; Roach-Higgins, Mary Ellen

1988-01-01

429

Reproducing Kernel Element Interpolation: Globally Conforming Im  

E-print Network

Reproducing Kernel Element Interpolation: Globally Conforming Im /Cn /P k Hierarchies Shaofan Li1 hierarchies are constructed in the framework of reproducing kernel element method (RKEM) for multi in multiple dimension was the challenge in the early development of finite element methods. It attracted

Li, Shaofan

430

Initiation of multileaf collimator conformal radiation therapy  

Microsoft Academic Search

Clinical studies have been initiated in conformal radiotherapy using computer controlled multileaf collimator. Quantitative dosimetry and treatment planning studies comparing field shaping by lead alloy blocks and the multileaf collimator demonstrate the clinical acceptability of the multileaf collimator. Sixteen patients with tumors in multiple sites have received some part of their treatments with both blocking systems. Studies of dosimetry and

William D. Powlis; Alfred R. Smith; Elizabeth Cheng; James M. Galvin; Frank Villari; Peter Bloch; Morton M. Kligerman

1993-01-01

431

On Hydrophobicity and Conformational Specificity in Proteins  

E-print Network

On Hydrophobicity and Conformational Specificity in Proteins Erik Sandelin1 2 Stockholm of monomeric globular single domain proteins. We find that the total fraction of hydrophobic residues is roughly constant and has no discernible dependence on protein size. This results in a decrease

Sandelin, Erik

432

Surveillance and conformity in competitive youth swimming  

Microsoft Academic Search

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

Melanie Lang

2010-01-01

433

Conformal symmetry of brane world effective actions  

SciTech Connect

A simple derivation of the low-energy effective action for brane worlds is given, highlighting the role of conformal invariance. We show how to improve the effective action for a positive- and negative-tension brane pair using the AdS/CFT correspondence.

McFadden, Paul L.; Turok, Neil [DAMTP, CMS, Wilberforce Road, Cambridge, CB3 0WA (United Kingdom); African Institute for Mathematical Sciences, 6 Melrose Road, Muizenberg, Cape Town 7945 (South Africa)

2005-01-15

434

Eliminating Transitions  

ERIC Educational Resources Information Center

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…

Gallick, Barb; Lee, Lisa

2010-01-01

435

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection  

SciTech Connect

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics and catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.

Sullivan, Sarah M.; Holyoak, Todd (Kansas)

2008-09-17

436

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection  

SciTech Connect

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics and catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.

Sullivan, S.M.; Holyoak, T.

2009-05-26

437

Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS)  

PubMed Central

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

Widom, Julia R.; Johnson, Neil P.; von Hippel, Peter H.; Marcus, Andrew H.

2013-01-01

438

Modeling the liquid-solid transition in saturated triglycerides  

NASA Astrophysics Data System (ADS)

Corkery et al. have proposed that the high-temperature state of the triglyceride trilaurin (TL) is a Y-conformer, in which the three hydrocarbon chains are dynamically twisted with an average angle of ˜120 between them. Using computer simulations, we first show that the high-temperature state is indeed the Y conformation. We then develop a theory of the liquid-solid transition of this system, in which TL molecules are in a chair (h) conformation, with extended, possibly all-trans, chains at low-temperatures, and are in a Y conformation in the liquid phase at temperatures higher than the transition temperature, T* 319K. We map this ``h-Y model'' onto an Ising model in a temperature-dependent field, perform a mean-field approximation, and calculate the transition enthalpy, which is in good agreement with experiment. We also predict the temperature-dependence of the 1132 cm-1 Raman band. Our results support the proposal that the liquid state is made up of molecules in the Y conformation.

Hanna, C. B.; Pink, D. A.; MacDonald, A. J.; Thillainadarajah, K.; Corkery, R.; Rousseau, D.

2007-03-01

439

Submaximal conformal symmetry superalgebras for Lorentzian manifolds of low dimension  

E-print Network

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.

Paul de Medeiros

2014-06-19

440

Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation  

NASA Astrophysics Data System (ADS)

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.

Ruan, Qing-Xia; Zhou, Ping

2008-07-01