Search PubMed⌕ Search

Biomedical subjects

W F van Gunsteren

Publications and source records attributed to W F van Gunsteren.

At least 19 recordsLinked to original sources
PubMed2001

Free energy barrier estimation of unfolding the alpha-helical surfactant-associated polypeptide C.

Molecular dynamics simulations were conducted to estimate the free energy barrier of unfolding surfactant-associated polypeptide C (SP-C) from an alpha-helical conformation. Experimental studies indicate that while the helical fold of SP-C is thermodynamically stable in phospholipid micelles, it is metastable in a mixed organic solvent of CHCl3/CH3OH/0.1 M HCl at 32:64:5 (v/v/v), in which it undergoes an irreversible transformation to an insoluble aggregate that contains beta-sheet. On the basis of experimental observations, the free energy barrier was estimated to be approximately 100 kJ/mole by applying Eyring's transition state theory to the experimental rate of unfolding [Protein Sci 1998;7:2533-2540]. These studies prompted us to carry out simulations to investigate the unwinding process of two helical turns encompassing residues 25-32 in water and in methanol. The results give an upper bound estimation for the free energy barrier of unfolding of SP-C of approximately 20 kJ/mole. The results suggest a need to reconsider the applicability of a single-mode activated process theory to protein unfolding.

Amino Acid Sequence↗
PubMed2001

Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal.

Eight molecular dynamics simulations of a ubiquitin crystal unit cell were performed to investigate the effect of different schemes to treat the long-range electrostatic interactions as well as the need to include counter ions. A crystal system was chosen as the test system, because the higher charge density compared with a protein in solution makes it more sensitive to the way of treating the electrostatic interactions. Three different schemes of treating the long-range interactions were compared: straight cutoff, reaction-field approximation, and a lattice-sum method (P3M). For each of these schemes, two simulations were performed, one with and one without the counter ions. Two additional simulations with a reaction-field force and different initial placements of the counter ions were performed to examine the effect of the initial positions of the ions. The inclusion of long-range electrostatic interactions using either a reaction-field or a lattice-sum method proved to be necessary for the simulation of crystals. These two schemes did not differ much in their ability to reproduce the crystallographic structure. The inclusion of counter ions, on the other hand, seems not necessary for obtaining a stable simulation. The initial positions of the ions have a visible but small effect on the simulation.

Amino Acid Sequence↗
PubMed2001

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

The configurational entropy of a beta-heptapeptide in solution at four different temperatures is calculated. The contributions of the backbone and of the side-chain atoms to the total peptide entropy are analyzed separately and the effective contribution to the entropy arising from correlations between these terms determined. The correlation between the backbone and side-chain atoms amounts to about 17% and is rather insensitive to the temperature. The correlation of motion within the backbone and within side-chains is much larger and decreases with temperature. As the peptide reversibly folds at higher temperatures, its change in entropy and enthalpy upon folding is analyzed. The change in entropy and enthalpy upon folding of the peptide alone cannot account for the observed change in free energy on folding of the peptide in solution. Enthalpic and entropic contributions of the solvent thus also play a key role. Proteins 2001;43:45-56.

Entropy↗
PubMed2001

The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation.

The structural and thermodynamic properties of a 6-residue beta-peptide that was designed to form a hairpin conformation have been studied by NMR spectroscopy and MD simulation in methanol solution. The predicted hairpin would be characterized by a 10-membered hydrogen-bonded turn involving residues 3 and 4, and two extended antiparallel strands. The interproton distances and backbone torsional dihedral angles derived from the NMR experiments at room temperature are in general terms compatible with the hairpin conformation. Two trajectories of system configurations from 100-ns molecular-dynamics simulations of the peptide in solution at 298 and 340 K have been analyzed. In both simulations reversible folding to the hairpin conformation is observed. Interestingly, there is a significant conformational overlap between the unfolded state of the peptide at each of the temperatures. As already observed in previous studies of peptide folding, the unfolded state is composed of a (relatively) small number of predominant conformers and in this case lacks any type of secondary-structure element. The trajectories provide an excellent ground for the interpretation of the NMR-derived data in terms of ensemble averages and distributions as opposed to single-conformation interpretations. From this perspective, a relative population of the hairpin conformation of 20% to 30% would suffice to explain the NMR-derived data. Surprisingly, however, the ensemble of structures from the simulation at 340 K reproduces more accurately the NMR-derived data than the ensemble from the simulation at 298 K, a question that needs further investigation.

Magnetic Resonance Spectroscopy↗
PubMed2001

Viscosity dependence of protein dynamics.

The influence of solvent viscosity on protein dynamics was investigated with molecular dynamics simulations of factor Xa in two solvents differing only in viscosity, by a factor of 10. We obtained this viscosity change by changing the masses of the solvent atoms by a factor of 100. Equilibrium properties of the protein, that is, the average structure, its fluctuations, and the secondary structure, show no significant dependence on the solvent viscosity. The dynamic properties of the protein, that is, the atom-positional correlation times and torsional angle transitions, however, depend on the solvent viscosity. The protein appears to be much more mobile in the solvent of lower viscosity. It feels the influence of the solvent not only on the surface but even in its core. With increasing solvent viscosity, the positional relaxation times of atoms in the protein core increase as much as those of atoms on the protein surface, and the relative increase in the core is even larger than on the surface.

Computational Biology↗
PubMed2001

Molecular dynamics simulation of n-dodecyl phosphate aggregate structures.

Aggregates of n-dodecyl phosphate present an attractive model system of simple phospholipid amphiphile supramolecular structures for study by molecular dynamics simulation, since these systems have previously been studied experimentally under various conditions. A detailed molecular dynamics description of the properties of planar bilayer membranes (as a model for unilamellar vesicular membranes) and spherical micelles under various simulated conditions is presented. It is shown that the united-atom model of GROMOS96 applying the force-field parameter set 43A2 for biomolecular systems yields properties in agreement with experimental ones in most cases. Hydrogen bonding plays a role in stabilizing the bilayer aggregates at low pH, but not for the micelles, which are energetically favoured at high pH. NMR -S(CD) order parameters for a lipid bilayer system, the diffusion of amphiphiles within aggregates and of counterions, and lifetimes of hydrogen bonds between amphiphiles and to water are estimated from the MD simulations.

Hydrogen Bonding↗
PubMed2001

Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature.

We have used a standard Fröhlich-Kirkwood dipole moment fluctuation model to calculate the static dielectric permittivity, epsilon(0), for four different proteins, each of which was simulated under at least two different conditions of pH, temperature, solvation, or ligand binding. For the range of proteins and conditions studied, we calculate values for epsilon(0) between 15 and 40. Our results show, in agreement with prior work, that the behavior of charged residues is the primary determinant of the effective permittivity. Furthermore, only environmental changes that alter the properties of charged residues exert a significant effect on epsilon. In contrast, buried water molecules or ligands have little or no effect on protein dielectric properties.

Animals↗
PubMed2001

Fibrillation power, an alternative method of ECG spectral analysis for prediction of countershock success in a porcine model of ventricular fibrillation.

BACKGROUND: Noninvasive prediction of defibrillation success after cardiac arrest and cardiopulmonary resuscitation (CPR) may help in determining the optimal time for a countershock, and thus increase the chance for survival. METHODS: In a porcine model (n=25) of prolonged cardiac arrest, advanced cardiac life support was provided by administration of two or three doses of either vasopressin or epinephrine after 3 or 8 min of basic life support. After 4 min of ventricular fibrillation and 18 min of life support, defibrillation was attempted. The denoised power spectral density of 10 s intervals of the ventricular fibrillation electrocardiogram (ECG) was estimated from averaged and smoothed Fourier transforms. We have eliminated the spectral contribution of artifacts from manual chest compressions and provide a definition for the contribution of ventricular fibrillation to the power spectral density. This contribution is quantified and termed "fibrillation power". RESULTS: We tested fibrillation power and two established methods in their discrimination of survivors (n=16) vs. non-survivors (n=9) in the last minute before the countershock. A fibrillation power > or =79 dB predicted successful defibrillation with sensitivity, specificity, positive predictive value and negative predictive value of 98%, 98%, 99% and 97% while a mean fibrillation frequency > or =7.7 Hz was predictive with 85%, 83%, 90% and 77% and a mean amplitude > or =0.49 mV was predictive with 95%, 90%, 94% and 91%. CONCLUSIONS: We suggest that fibrillation power is an alternative source of information on the status of a fibrillating heart and that it may match the established mean frequency and amplitude analysis of ECG in predicting successful countershock during CPR.

Animals↗
PubMed2001

Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations.

Comparatively small molecules such as peptides can show a high internal mobility with transitions between several conformational minima and sometimes coupling between rotational and internal degrees of freedom. In those cases the interpretation of NMR relaxation data is difficult and the use of standard methods for structure determination is questionable. On the other hand, in the case of those system sizes, the timescale of both rotational and internal motions is accessible by molecular dynamics (MD) simulations using explicit solvent. Thus a comparison of distance averages ([r(-6)](-1/6) or [r(-3)](1/3)) over the MD trajectory with NOE (or ROE) derived distances is no longer necessary, the (back)calculation of the complete spectra becomes possible. In the present study we use two 200 ns trajectories of a heptapeptide of beta-amino acids in methanol at two different temperatures to obtain theoretical ROESY spectra by calculating the exact spectral densities for the interproton vectors and the full relaxation matrix. Those data are then compared with the experimental ones. This analysis permits to test some of the assumptions and approximations that generally have to be made to interpret NMR spectra, and to make a more reliable prediction of the conformational equilibrium that leads to the experimental spectrum.

Computer Simulation↗
PubMed2001

Assessing the effect of conformational averaging on the measured values of observables.

Experiment and computer simulation are two complementary tools to understand the dynamics and behavior of biopolymers in solution. One particular area of interest is the ensemble of conformations populated by a particular molecule in solution. For example, what fraction of a protein sample exists in its folded conformation? How often does a particular peptide form an alpha helix versus a beta hairpin? To address these questions, it is important to determine the sensitivity of a particular experiment to changes in the distribution of molecular conformations. Consequently, a general analytic formalism is proposed to determine the sensitivity of a spectroscopic observable to the underlying distribution of conformations. A particular strength of the approach is that it provides an expression for a weighted average across conformational substates that is independent of the averaging function used. The formalism is described and applied to experimental and simulated nuclear Overhauser enhancement (NOE) and 3J-coupling data on peptides in solution.

Computer Simulation↗
PubMed2000

Molecular-dynamics simulation of the beta domain of metallothionein with a semi-empirical treatment of the metal core.

The three-metal-containing beta domain of rat liver metallothionein-2 in aqueous solution was simulated with different metal contents. The Cd(3), the CdZn(2), and the Zn(3) variant were investigated using a conventional molecular dynamics simulation, as well as a simulation with a semi-empirical quantum-chemical description (MNDO and MNDO/d) of the metal core embedded in a classical environment. For the purely classical simulations, the standard GROMOS96 force-field parameters were used, and parameters were estimated for cadmium. The results of both kinds of simulations were compared to each other and to the corresponding experimental X-ray crystallographic and NMR solution data. The purely classical simulations were found to produce a too compact metal cluster with partially incorrect geometries, which affected the enfolding protein backbone structure. The inclusion of MNDO/d for the treatment of the metal cluster improved the results to give correct cluster geometries and an overall protein structure in agreement with the experiment. The metal cluster and the cysteine residues bound to it are structurally stable, while the irregular polypeptide backbone loops between the cysteines exhibit a considerable flexibility. MNDO without extension to d orbitals failed to maintain the structure of the metal core.

Animals↗
PubMed2000

Molecular dynamics simulations highlight mobile regions in proteins: A novel suggestion for converting a murine V(H) domain into a more tractable species.

The V(H) region of the murine antibody 1F7 has been identified as a single-domain chorismate mutase, but a tendency to denature and aggregate has hampered its biochemical characterization. Standard mutagenesis approaches targeting antibody chain dimerization areas have been exhausted. We describe a new approach to the problem, where we use molecular dynamics (MD) simulations to find the differences between the untractable protein and the known soluble V(H) domain from a llama antibody. MD simulations of proteins yield information on the relative stability and fluctuations of parts of the proteins. By comparing simulation results of two related proteins their differences in stability and fluctuations can be analyzed and may suggest mutations aimed at (de)stabilization of one of the two proteins. For the mouse versus llama simulations, this approach highlights an untried area in the protein which shows increased fluctuations. The replacement of this eight-residue segment with the corresponding llama sequence gave a chimeric mutant which shows significantly decreased fluctuations. We see this as a general scheme to generate suggestions for mutagenesis experiments, not only obviously generalizable to other immunoglobulin domains, but to other protein systems as well.

Amino Acid Sequence↗
PubMed2000

Molecular dynamics simulation of hen egg white lysozyme: a test of the GROMOS96 force field against nuclear magnetic resonance data.

Biomolecular force fields for use in molecular dynamics (MD) simulations of proteins, DNA, or membranes are generally parametrized against ab initio quantum-chemical and experimental data for small molecules. The application of a force field in a simulation of a biomolecular system, such as a protein in solution, may then serve as a test of the quality and transferability of the force field. Here, we compare various properties obtained from two MD simulations of the protein hen egg white lysozyme (HEWL) in aqueous solution using the latest version, GROMOS96, of the GROMOS force field and an earlier version, GROMOS87+, with data derived from nuclear magnetic resonance (NMR) experiments: NOE atom-atom distance bounds, (3)J(HNalpha)-coupling constants, and backbone and side-chain order parameters. The convergence of these quantities over a 2-ns period is considered, and converged values are compared to experimental ones. The GROMOS96 simulation shows better agreement with the NMR data and also with the X-ray crystal structure of HEWL than the GROMOS87+ simulation, which was based on an earlier version of the GROMOS force field.

Animals↗
PubMed2000

beta-hairpin stability and folding: molecular dynamics studies of the first beta-hairpin of tendamistat.

The stability and (un)folding of the 19-residue peptide, SCVTLYQSWRYSQADNGCA, corresponding to the first beta-hairpin (residues 10 to 28) of the alpha-amylase inhibitor tendamistat (PDB entry 3AIT) has been studied by molecular dynamics simulations in explicit water under periodic boundary conditions at several temperatures (300 K, 360 K and 400 K), starting from various conformations for simulation lengths, ranging from 10 to 30 ns. Comparison of trajectories of the reduced and oxidized native peptides reveals the importance of the disulphide bridge closing the beta-hairpin in maintaining a proper turn conformation, thereby insuring a proper side-chain arrangement of the conserved turn residues. This allows rationalization of the conservation of those cysteine residues among the family of alpha-amylase inhibitors. High temperature simulations starting from widely different initial configurations (native beta-hairpin, alpha and left-handed helical and extended conformations) begin sampling similar regions of the conformational space within tens of nanoseconds, and both native and non-native beta-hairpin conformations are recovered. Transitions between conformational clusters are accompanied by an increase in energy fluctuations, which is consistent with the increase in heat capacity measured experimentally upon protein folding. The folding events observed in the various simulations support a model for beta-hairpin formation in which the turn is formed first, followed by hydrogen bond formation closing the hairpin, and subsequent stabilization by side-chain hydrophobic interactions.

Amino Acid Sequence↗
PubMed2000

On the temperature and pressure dependence of a range of properties of a type of water model commonly used in high-temperature protein unfolding simulations.

Molecular dynamics simulations of protein folding and unfolding are often carried out at temperatures (400-600 K) that are much higher than physiological or room temperature to speed up the (un)folding process. Use of such high temperatures changes both the protein and solvent properties considerably, compared to physiological or room temperature. Water models designed for use in conjunction with biomolecules, such as the simple point charge (SPC) model, have generally been calibrated at room temperature and pressure. To determine the distortive effect of high simulation temperatures on the behavior of such "room temperature" water models, the structural, dynamic, and thermodynamic properties of the much-used SPC water model are investigated in the temperature range from 300 to 500 K. Both constant pressure and constant volume conditions, as used in protein simulations, were analyzed. We found that all properties analyzed change markedly with increasing temperature, but no phase transition in this temperature range was observed.

Calibration↗
PubMed2000

Factor Xa: simulation studies with an eye to inhibitor design.

Factor Xa is a serine protease which activates thrombin and plays a key regulatory role in the blood-coagulation cascade. Factor Xa is at the crossroads of the extrinsic and intrinsic pathways of coagulation and, hence, has become an important target for the design of anti-thrombotics (inhibitors). It is not known to be involved in other processes than hemostasis and its binding site is different to that of other serine proteases, thus facilitating selective inhibition. The design of high-affinity selective inhibitors of factor Xa requires knowledge of the structural and dynamical characteristics of its active site. The three-dimensional structure of factor Xa was resolved by X-ray crystallography and refined at 2.2 A resolution by Padmanabhan and collaborators. In this article we present results from molecular dynamics simulations of the catalytic domain of factor Xa in aqueous solution. The simulations were performed to characterise the mobility and flexibility of the residues delimiting the unoccupied binding site of the enzyme, and to determine hydrogen bonding propensities (with protein and with solvent atoms) of those residues in the active site that could interact with a substrate or a potential inhibitor. The simulation data is aimed at facilitating the design of high-affinity selective inhibitors of factor Xa.

Amino Acid Sequence↗
PubMed2000

On the similarity of properties in solution or in the crystalline state: a molecular dynamics study of hen lysozyme.

As protein crystals generally possess a high water content, it is assumed that the behaviour of a protein in solution and in crystal environment is very similar. This assumption can be investigated by molecular dynamics (MD) simulation of proteins in the different environments. Two 2ns simulations of hen egg white lysozyme (HEWL) in crystal and solution environment are compared to one another and to experimental data derived from both X-ray and NMR experiments, such as crystallographic B-factors, NOE atom-atom distance bounds, 3J(H N alpha)-coupling constants, and 1H-15N bond vector order parameters. Both MD simulations give very similar results. The crystal simulation reproduces X-ray and NMR data slightly better than the solution simulation.

Animals↗