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At least 1,099 records · Page 61Linked to original sources
PubMed2006

Accessibility of tobacco lipid transfer protein cavity revealed by 15N NMR relaxation studies and molecular dynamics simulations.

Plant LTP1 are small helical proteins stabilized by four disulfide bridges and are characterized by the presence of an internal cavity, in which various hydrophobic ligands can be inserted. Recently, we have determined the solution structure of the recombinant tobacco LTP1_1. Unexpectedly, despite a global fold very similar to the structures already known for cereal seed LTP1, its binding properties are different: Tobacco LTP1_1 is able to bind only one monoacylated lipid, whereas cereal LTP1 can bind either one or two. The 3D structure of tobacco LTP1_1 revealed the presence of a hydrophobic cluster, not observed on cereal LTP1 structures, which may hinder one of the two entrances of the cavity defined for wheat LTP1. To better understand the mechanism of lipid entrance for tobacco LTP1_1 and to define the regions of the protein monitoring the accessibility of the cavity, we have complemented our structural data by the study of the internal dynamics of tobacco LTP1_1, using (15)N magnetic relaxation rate data and MD simulations at room and high temperatures. This work allowed us to define two regions of the protein experiencing the largest motions. These two regions delineate a portal that opens up during the simulation constituting a unique entrance of the hydrophobic cavity, in contrast with wheat LTP1 where two routes were detected. The hydrophobic interactions resulting from a few point mutations are strong enough to completely block the second portal so that the accessibility of the cavity is restricted to one entrance, explaining why this particular LTP1 binds only one lipid molecule.

Amino Acid Sequence↗
PubMed1994

Calculation of the circular dichroism spectrum of cyclo-(L-tyr-L-tyr) based on a molecular dynamics simulation.

Theoretical calculations of CD spectra have generally assumed a single conformation, or a small number of conformers with Boltzmann averaging. Solvent effects on both the conformation and the CD have been neglected. In this work, we have calculated the CD spectrum of cyclo(L-Tyr-L-Tyr) in aqueous solution, taking dynamics and solvation into account. Starting geometries with chi 1 approximately 300 degrees or 60 degrees for both Tyr side chains were derived from MNDO/MOPAC, followed by energy minimization using GROMOS. After addition of 368 water molecules, the system was simulated for 1000 ps at 300 K using GROMOS. In addition to the starting conformer, two other conformers were observed during each simulation. However, each trajectory gave a distinct set of conformers. Rotational strengths were calculated for the cyclic dipeptide at each ps along the trajectories, using the matrix method. The CD spectra calculated from these rotational strengths were averaged over the trajectories. Agreement is very good for the strong negative band near 200 nm, while for the lower energy bands (near 230 and 280 nm), the signs are correct, but the magnitudes are too low. The spectrum calculated from a Boltzmann-weighted average over the in vacuo MNDO/MOPAC conformers was in poor agreement with experiment. Although the solvent did not significantly affect the rotational strength calculated for a given conformer, it is essential to include the solvent in the MD simulations because it affects the relative energies of the conformers and promotes transitions among them.

Chemical Phenomena↗
PubMed2000

Inversion of the roles of the nucleophile and acid/base catalysts in the covalent binding of epoxyalkyl xyloside inhibitor to the catalytic glutamates of endo-1,4-beta-xylanase (XYNII): a molecular dynamics study.

X-Ray crystal structures have revealed that 2, 3-epoxypropyl-beta-D-xyloside reacts with endo-1,4-beta-xylanase (XYNII) by forming a covalent bond with Glu86. In contrast, 3, 4-epoxybutyl-beta-D-xyloside forms a covalent bond with Glu177. In the normal enzyme reaction Glu86 acts as the catalytic nucleophile and Glu177 as the acid/base catalyst. To rationalize the observed reactivity of the two mechanism-based inhibitors, we carried out eight 300 ps molecular dynamics simulations for different enzyme-inhibitor complexes. Simulations were done for both stereo isomers (R and S) of the inhibitors and for enzyme in which the protonation state of the nucleophile and acid/base catalyst was normal (Glu86 charged, Glu177 neutral) and in which the roles of the catalytic residues were reversed (Glu86 neutral, Glu177 charged). The number of reactive conformations found in each simulation was used to predict the reactivity of epoxy inhibitors. The conformation was considered to be a reactive one when at the same time (i) the proton of the catalytic acid was close (<2.9/3.4/3.9 A) to the oxirane oxygen of the inhibitor, (ii) the nucleophile was close to the terminal carbon of the oxirane group (<3.4/3.9/4.4 A) and (iii) the nucleophile approached the terminal carbon from a reactive angle (<30/45/60 degrees from an ideal attack angle). On the basis of the number of reactive conformations, 2,3-epoxypropyl-beta-D-xyloside was predicted to form a covalent bond with Glu86 and 3, 4-epoxybutyl-beta-D-xyloside with Glu177, both in agreement with the experiment. Thus, the MD simulations and the X-ray structures indicate that in the covalent binding of 3, 4-epoxybutyl-beta-D-xyloside the roles of the catalytic glutamates of XYNII are reversed from that of the normal enzyme reaction.

Acids↗
PubMed2003

Optimization of tether length in nonglycosidically linked bivalent ligands that target sites 2 and 1 of a Shiga-like toxin.

A series of bivalent ligands for a Shiga-like toxin have been synthesized, their experimentally determined inhibitory activities were compared with a simplified thermodynamic model, and computer simulations were used to predict the optimal tether length in bivalent ligands. The design of the inhibitors exploits the proximity of the C-2' hydroxyl groups of two P(k)-trisaccharides when bound to two different, neighboring carbohydrate recognizing binding sites located on the surface of Shiga-like toxin. NMR studies of the complex between the toxin and bivalent ligands show that site 2 and site 1 of a single B subunit are simultaneously occupied by a tethered P(k)-trisaccharide dimer. A simplified thermodynamic treatment provides the intrinsic affinities and binding energies for the intermolecular and intramolecular association events and permits the deconvolution of the contributions to the relative binding energies for the set of bivalent ligands. Conformational analysis based on MD simulations for bivalent galabioside dimers containing different tethers demonstrated that the calculated local concentrations of the pendant ligand at the second binding site correlate with the experimentally determined relative affinity values of the respective bivalent ligands, thereby providing a predictive method to optimize tether length.

Cross-Linking Reagents↗
PubMed2006

Diffusion constant of K+ inside Gramicidin A: a comparative study of four computational methods.

The local diffusion constant of K(+) inside the Gramicidin A (GA) channel has been calculated using four computational methods based on molecular dynamics (MD) simulations, specifically: Mean Square Displacement (MSD), Velocity Autocorrelation Function (VACF), Second Fluctuation Dissipation Theorem (SFDT) and analysis of the Generalized Langevin Equation for a Harmonic Oscillator (GLE-HO). All methods were first tested and compared for K(+) in bulk water--all predicted the correct diffusion constant. Inside GA, MSD and VACF methods were found to be unreliable because they are biased by the systematic force exerted by the membrane-channel system on the ion. SFDT and GLE-HO techniques properly unbias the influence of the systematic force on the diffusion properties and predicted a similar diffusion constant of K(+) inside GA, namely, ca. 10 times smaller than in the bulk. It was found that both SFDT and GLE-HO methods require extensive MD sampling on the order of tens of nanoseconds to predict a reliable diffusion constant of K(+) inside GA.

Cations, Monovalent↗
PubMed2004

Differential recognition of resveratrol isomers by the human estrogen receptor-alpha: molecular dynamics evidence for stereoselective ligand binding.

Resveratrol (RSVL) is a phytoestrogen that occurs naturally in two forms (trans- (E) and cis- (Z)). We have conducted molecular dynamics (MD) studies to differentially characterize the estrogen receptor-alpha (ER-alpha) binding profiles of RSVL stereoisomers. Favorable orientations for RSVL isomers at the ER-alpha pocket were first inferred from (1) alignment with pharmacophoric elements of the pure ER-alpha agonists estradiol (E2) and (2) assessment of ligand recognition by the ER-alpha binding domain. Subsequently, these orientations for RSVL isomers were subjected to MD analyses versus E2. A 100-picosecond MD simulation revealed that E2 contributed four stable hydrogen bonds with the key ER-alpha pocket residue: Arg394, Glu353, His524, and Leu525. Further, E2 displayed favorable binding energy, conformational energy change (DeltaE), and movement of the binding pocket residues (RMSd). Compared to E2, (E)-RSVL lacked a hydrogen bond (HB) with His524 but formed three additional bonds with Gly521, Phe404, and Met343 of the ER-alpha pocket. Further, (E)-RSVL conferred more favorable energy of interaction, less favorable DeltaE, but comparable RMSd values. In contrast, (Z)-RSVL orientations missed hydrogen bonding (HB) with His524 and Leu525, two essential ligand binding residues, and/or produced considerably less favorable-binding energy, -DeltaE, and -RMSd values than did (E)-RSVL. In conclusion, the present study demonstrates the utility of this MD model in distinguishing between RSVL stereoisomers. The weak binding of (Z)-RSVL by the human ER-alpha binding is congruent with its inferior ligand profiles in ER-endowed biological systems. Further, evidence is provided for a considerable variation in the mode of recognition of the mixed agonist/antagonist (E)-RSVL, and the pure agonist E2.

Binding Sites↗
PubMed2002

Hydrogen and higher shell contributions in Zn2+, Ni2+, and Co2+ aqueous solutions: an X-ray absorption fine structure and molecular dynamics study.

A detailed investigation of the hydration structure of Zn2+, Ni2+, and Co2+ in water solutions has been carried out combining X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. The first quantitative analysis of EXAFS from hydrogen atoms in 3d transition metal ions in aqueous solutions has been carried out and the ion-hydrogen interactions have been found to provide a detectable contribution to the EXAFS spectra. An accurate determination of the structural parameters associated with the first hydration shell has been performed and compared with previous experimental results. No evidence of significant contributions from the second hydration shell to the EXAFS signal has been found for these solutions, while the inclusion of the hydrogen signal has been found to be important in performing a quantitative analysis of the experimental data. The high-frequency contribution present in the EXAFS spectra has been found to be due to multiple scattering (MS) effects inside the ion-oxygen first coordination shell. MD has been used to generate three-body distribution functions from which a reliable analysis of the MS contributions to the EXAFS spectra of these systems has been carried out.

Journal Article↗
PubMed2004

Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C.

The benzetheno exocyclic adduct of the cytosine (C) base (pBQ-C) is a product of reaction between DNA and a stable metabolite of the human carcinogen benzene, p-benzoquinone (pBQ). We reported previously that the pBQ-C-containing duplex is a substrate for the human AP endonuclease (APE1), an enzyme that cleaves an apurinic/apyrimidinic (AP) site from double stranded DNA. In this work, using molecular dynamics simulation (MD), we provided a structural explanation for the recognition of the pBQ-C adduct by APE1. Molecular modeling of the DNA duplex containing pBQ-C revealed significant displacement of this adduct toward the major groove with pronounced kinking of the DNA at the lesion site, which could serve as a structural element recognized by the APE1 enzyme. Using 3 ns MD it was shown that the position of the pBQ-C adduct is stabilized by two hydrogen bonds formed between the adduct and the active site amino acids Asp 189 and Ala 175. The pBQ-C/APE1 complex, generated by MD, has a similar hydrogen bond network between target phosphodiester bond at the pBQ-C site and key amino acids at the active site, as in the crystallographically determined APE1 complexed with an AP site-containing DNA duplex. The position of the adduct at the enzyme active site, together with the hydrogen bond network, suggests a similar reaction mechanism for phosphodiester bond cleavage of oligonucleotide containing pBQ-C as reported for the AP site.

Base Sequence↗
PubMed2007

Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential.

During replica exchange molecular dynamics (RexMD) simulations, several replicas of a system are simulated at different temperatures in parallel allowing for exchange between replicas at frequent intervals. This technique allows significantly improved sampling of conformational space and is increasingly being used for structure prediction of peptides and proteins. A drawback of the standard temperature RexMD is the rapid increase of the replica number with increasing system size to cover a desired temperature range. In an effort to limit the number of replicas, a new Hamiltonian-RexMD method has been developed that is specifically designed to enhance the sampling of peptide and protein conformations by applying various levels of a backbone biasing potential for each replica run. The biasing potential lowers the barrier for backbone dihedral transitions and promotes enhanced peptide backbone transitions along the replica coordinate. The application on several peptide cases including in all cases explicit solvent indicates significantly improved conformational sampling when compared with standard MD simulations. This was achieved with a very modest number of 5-7 replicas for each simulation system making it ideally suited for peptide and protein folding simulations as well as refinement of protein model structures in the presence of explicit solvent.

Alanine↗
PubMed2001

Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA.

In this work, a new ansatz is presented that combines molecular dynamics simulations with MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) to rank the binding affinities of 12 TIBO-like HIV-1 RT inhibitors. Encouraging results have been obtained not only for the relative binding free energies, but also for the absolute ones, which have a root-mean-square deviation of 1.0 kcal/mol (the maximum error is 1.89 kcal/mol). Since the root-mean-square error is rather small, this approach can be reliably applied in ranking the ligands from the databases for this important target. Encouraged by the results, we decided to apply MM-PBSA combined with molecular docking to determine the binding mode of efavirenz SUSTIVA(TM) another promising HIV-1 RT inhibitor for which no ligand-protein crystal structure had been published at the time of this work. To proceed, we define the following ansatz: Five hundred picosecond molecular dynamics simulations were first performed for the five binding modes suggested by DOCK 4.0, and then MM-PBSA was carried out for the collected snapshots. MM-PBSA successfully identified the correct binding mode, which has a binding free energy about 7 kcal/mol more favorable than the second best mode. Moreover, the calculated binding free energy (-13.2 kcal/mol) is in reasonable agreement with experiment (-11.6 kcal/mol). In addition, this procedure was also quite successful in modeling the complex and the structure of the last snapshot was quite close to that of the measured 2,3 A resolution crystal (structure the root-mean-square deviation of the 54 C(alpha) around the binding site and the inhibitor is 1.1 A). We want to point out that this result was achieved without prior knowledge of the structure of the efavirenz/RT complex. Therefore, molecular docking combined with MD simulations followed by MM-PBSA analysis is an attractive approach for modeling protein complexes a priori.

Alkynes↗
PubMed2002

Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease.

The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.

Binding Sites↗
PubMed2005

A facile and improved synthesis of sildenafil (Viagra) analogs through solid support microwave irradiation possessing tyrosinase inhibitory potential, their conformational analysis and molecular dynamics simulation studies.

Herein, the synthesis of some analogs of sildenafil (Viagra) (21) is described, employing MW irradiations in key steps such as, SNAr reaction on important precursor bromopyrazole (7). Compound 7 was synthesized by the bromination followed by the amidation of readily available 1-methyl-3-propyl-1H-pyrazole-5-carboxylic acid (5). Compounds 9 and 10 were obtained as SNAr reaction products, apparently through the proposed dipolar high-energy transition states TS-1 and TS-2 under MW irradiation, respectively. In contrast, conventional heating failed to produce similar results, even after prolonged heating. Compound 10, upon chlorosulfonation followed by the coupling of various nucleophiles, yielded a series of compounds 12-20 as analogs of sildenafil (21). Compounds 12-21 were subjected to tyrosinase inhibition studies and SAR studies were carried out. This study reflected that the inhibition was enhanced with increase of carbon chain. In case of the compound 17, the -OH group was replaced with -CH2-CH2-OH with a resulting increase in inhibition against tyrosinase. Compound 17 was found to be more potent than the potent reference inhibitor LM and KA. The 2D and 3D hydrogen bonding descriptors that help to study QSPR were also calculated. Energetically most stable conformations of these compounds were analyzed. Their kinetic, potential and total energies were also calculated through MD simulation.

Indicators and Reagents↗
PubMed2005

Structural characterization of cyclic kallidin analogues in DMSO by nuclear magnetic resonance and molecular dynamics.

The conformational properties in DMSO of two head-to-tail cyclic analogues of kallidin ([Lys(0)]-bradykinin, KL) as well as those of the corresponding linear peptides were studied by NMR and molecular dynamics (MD) simulations. The modifications in the sequence were introduced at position 6, resulting in the four peptides, [Tyr(6)]-KL (YKL), [Trp(6)]-KL (WKL), cyclo-([Tyr(6)]-KL) (YCKL) and cyclo-([Trp(6)]-KL) (WCKL). The linear WKL analogue was significantly more potent than kallidin on rat duodenum preparations, whereas YKL was significantly less potent. Both cyclic peptides, YCKL and WCKL displayed similar activity, lower than that of the linear analogues and also of cyclo-KL. The two linear analogues display high conformational flexibility in DMSO. In the predominant conformer, for both peptides, all three X-Pro bonds adopt a trans configuration. Three out of four conformers present in YCKL and WCKL were completely assigned. The configurations at the X-Pro bonds are the same for the two analogues. All cyclic conformers show a cis configuration in at least one X-Pro bond and always opposite configuration for the two consecutive X-Pro bonds. The NOE-restrained MD calculations resulted in the detection of several elements of secondary structure in each of the conformers. Such elements are described and their possible relevance to biological activity is discussed.

Dimethyl Sulfoxide↗
PubMed2003

Solvent reorganization in electron and ion transfer reactions near a smooth electrified surface: a molecular dynamics study.

Molecular dynamics simulations of electron and ion transfer reactions near a smooth surface are presented, analyzing the effect of the geometrical constraint of the surface and the interfacial electric field on the relevant solvation properties of both a monovalent negative ion and a neutral atom. The simulations show that, from the solvation point of view, ion adsorption is an uphill process due to the need to shed off the ion's solvation shell and displace water from the surface. Atom adsorption, on the other hand, has only a small barrier, related to the molecularity of the solvent. Both the electrostatic interaction of the ion with the solvent and the ion's solvent reorganization energy (the relevant parameter in the Marcus electron transfer theory) decrease as the surface is approached, whereas these parameters are not sensitive to the distance from the surface for the atom. This is a consequence of the importance of long-range electrostatic interactions for ion solvation and the importance of short-range interactions for atom solvation. The electric field either attracts or repels an ion to or from the surface, but the field has no influence on the solvent reorganization energy. By including the quantum-mechanical electron transfer between the metal surface and the ion/atom in solution in the MD simulation by using a model Hamiltonian, we calculated two-dimensional free energy surfaces for ion adsorption allowing for partial charge transfer, based on a fully molecular picture of ion solvation near the surface.

Journal Article↗
PubMed2001

Electronic structure effects from hydrogen bonding in the liquid phase and in chemisorption: an integrated theory and experimental effort.

A closely integrated theoretical and experimental effort to understand chemical bonding using X-ray spectroscopic probes is presented. Theoretical techniques to simulate XAS (X-ray absorption spectroscopy), XES (X-ray emission spectroscopy), RIXS (resonant inelastic X-ray scattering) and XPS (X-ray photoelectron spectroscopy) spectra have been developed and implemented within a density functional theory (DFT) framework. In combination with new experimental techniques, such as high-resolution XAS on liquid water under ambient conditions and XES on complicated surface adsorbates, new insight into e.g. hydrogen-bonded systems is obtained. For the (3x2) overlayer structure of glycine/Cu(110), earlier work has been extended to include adsorbate-adsorbate interactions. Structures are optimized for large cluster models and for periodic boundary conditions. It is found that specific features in the spectra arise from hydrogen-bonding interactions, which thus have important effects at the molecular-orbital level. XAS on liquid water shows a pronounced pre-edge feature with significant intensity, while the spectrum of ice shows only little intensity in this region. Theoretical spectrum calculations, based on instantaneous structures obtained from molecular-dynamics (MD) simulations, show that the pre-edge feature in the liquid is caused by water molecules with unsaturated hydrogen bonding. Some aspects of the theoretical simulations will be briefly discussed.

Journal Article↗
PubMed2004

Ion adsorption at the rutile-water interface: linking molecular and macroscopic properties.

A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (alpha-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy-Chapman-Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affinities calculated using ab initio bond lengths and partial charges. These results allow a direct correlation of the three-dimensional, crystallographically controlled arrangements of various species (H2O, Na+, Rb+, Ca2+, Sr2+, Zn2+, Y3+, Nd3+) with macroscopic observables (H+ release, metal uptake, zeta potential) and thermodynamic/electrostatic constraints. All cations are found to be adsorbed as "inner sphere" species bonded directly to surface oxygen atoms, while the specific binding geometries and reaction stoichiometries are dependent on ionic radius. Ternary surface complexes of sorbed cations with electrolyte anions are not observed. Finally, surface oxygen proton affinities computed using the MUSIC model are improved by incorporation of ab initio bond lengths and hydrogen bonding information derived from MD simulations. This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties (structure, diffusivity, dielectric constant), surface protonation and hydrolysis, and the effect of solution ionic strength.

Journal Article↗
PubMed2001

Computational analysis of binding of P1 variants to trypsin.

The binding of P1 variants of bovine pancreatic trypsin inhibitor (BPTI) to trypsin has been investigated by means of molecular dynamics simulations. The specific interaction formed between the amino acid at the primary binding (P1) position of the binding loop of BPTI and the specificity pocket of trypsin was estimated by use of the linear interaction energy (LIE) method. Calculations for 13 of the naturally occurring amino acids at the P1 position were carried out, and the results obtained were found to correlate well with the experimental binding free energies. The LIE calculations rank the majority of the 13 variants correctly according to the experimental association energies and the mean error between calculated and experimental binding free energies is only 0.38 kcal/mole, excluding the Glu and Asp variants, which are associated with some uncertainties regarding protonation and the possible presence of counter-ions. The three-dimensional structures of the complex with three of the P1 variants (Asn, Tyr, and Ser) included in this study have not at present been solved by any experimental techniques and, therefore, were modeled on the basis of experimental data from P1 variants of similar size. Average structures were calculated from the MD simulations, from which specific interactions explaining the broad variation in association energies were identified. The present study also shows that explicit treatment of the complex water-mediated hydrogen bonding network at the protein-protein interface is of crucial importance for obtaining reliable binding free energies. The successful reproduction of relative binding energies shows that this type of methodology can be very useful as an aid in rational design and redesign of biologically active macromolecules.

Animals↗
PubMed2003

Dynamic effects on j-couplings across hydrogen bonds in proteins.

We combine molecular dynamics simulation (MD) with density functional theory (DFT)/finite perturbation theory (FPT) to obtain the Fermi contact contributions to the 3hJNC' couplings in the SMN Tudor domain. Our results show that the effect of conformational motion needs to be considered for the accurate prediction of these scalar couplings. For hydrogen bonds in the beta-sheet regions, the calculated cumulative J-coupling averages remain constant after the first 200 ps. In the more flexible regions at the edges of the beta-sheets, the cumulative J-coupling averages vary over the 500-ps trajectory, providing a qualitative insight into the degree of conformational motion in different regions of the protein.

Computer Simulation↗