Showing papers by "Wilfred F. van Gunsteren published in 2010"

A new force field for simulating phosphatidylcholine bilayers.

Abstract: A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid-crystalline, fluid phase at zero surface tension is presented. The structure of the bilayer with the area per lipid (0.629 nm(2); experiment 0.629-0.64 nm(2)), the volume per lipid (1.226 nm(3); experiment 1.229-1.232 nm(3)), and the ordering of the palmitoyl chains (order parameters) are all in very good agreement with experiment. Experimental electron density profiles are well reproduced in particular with regard to the penetration of water into the bilayer. The force field was further validated by simulating the spontaneous assembly of DPPC into a bilayer in water. Notably, the timescale on which membrane sealing was observed using this model appears closer to the timescales for membrane resealing suggested by electroporation experiments than previous simulations using existing models.

Comparing geometric and kinetic cluster algorithms for molecular simulation data.

Abstract: The identification of metastable states of a molecule plays an important role in the interpretation of molecular simulation data because the free-energy surface, the relative populations in this landscape, and ultimately also the dynamics of the molecule under study can be described in terms of these states. We compare the results of three different geometric cluster algorithms (neighbor algorithm, K-medoids algorithm, and common-nearest-neighbor algorithm) among each other and to the results of a kinetic cluster algorithm. First, we demonstrate the characteristics of each of the geometric cluster algorithms using five two-dimensional data sets. Second, we analyze the molecular dynamics data of a beta-heptapeptide in methanol--a molecule that exhibits a distinct folded state, a structurally diverse unfolded state, and a fast folding/unfolding equilibrium--using both geometric and kinetic cluster algorithms. We find that geometric clustering strongly depends on the algorithm used and that the density based common-nearest-neighbor algorithm is the most robust of the three geometric cluster algorithms with respect to variations in the input parameters and the distance metric. When comparing the geometric cluster results to the metastable states of the beta-heptapeptide as identified by kinetic clustering, we find that in most cases the folded state is identified correctly but the overlap of geometric clusters with further metastable states is often at best approximate.

Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex

Abstract: The mechanism of solvent effects on the stereoselectivity of glycosylation reactions is investigated using quantum-mechanical (QM) calculations and molecular dynamics (MD) simulations, considering a methyl-protected glucopyranoside triflate as a glycosyl donor equivalent and the solvents acetonitrile, ether, dioxane, or toluene, as well as gas-phase conditions (vacuum). The QM calculations on oxacarbenium-solvent complexes do not provide support to the usual solvent-coordination hypothesis, suggesting that an experimentally observed β-selectivity (α-selectivity) is caused by the preferential coordination of a solvent molecule to the reactive cation on the α-side (β-side) of the anomeric carbon. Instead, explicit-solvent MD simulations of the oxacarbenium-counterion (triflate ion) complex (along with corresponding QM calculations) are compatible with an alternative mechanism, termed here the conformer and counterion distribution hypothesis. This new hypothesis suggests that the stereoselectivity is dictated by two interrelated conformational properties of the reactive complex, namely, (1) the conformational preferences of the oxacarbenium pyranose ring, modulating the steric crowding and exposure of the anomeric carbon toward the α or β face, and (2) the preferential coordination of the counterion to the oxacarbenium cation on one side of the anomeric carbon, hindering a nucleophilic attack from this side. For example, in acetonitrile, the calculations suggest a dominant B2,5 ring conformation of the cation with preferential coordination of the counterion on the α side, both factors leading to the experimentally observed β selectivity. Conversely, in dioxane, they suggest a dominant (4)H3 ring conformation with preferential counterion coordination on the β side, both factors leading to the experimentally observed α selectivity.

Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1

Abstract: The C-terminal trigger sequence is essential in the coiled-coil formation of GCN4-p1; its conformational properties are thus of importance for understanding this process at the atomic level. A solution NMR model structure of a peptide, GCN4p16–31, encompassing the GCN4-p1 trigger sequence was proposed a few years ago. Derived using a standard single-structure refinement protocol based on 172 nuclear Overhauser effect (NOE) distance restraints, 14 hydrogen-bond and 11 ϕ torsional-angle restraints, the resulting set of 20 NMR model structures exhibits regular α-helical structure. However, the set slightly violates some measured NOE bounds and does not reproduce all 15 measured 3J(HN-HCα)-coupling constants, indicating that different conformers of GCN4p16–31 might be present in solution. With the aim to resolve structures compatible with all NOE upper distance bounds and 3J-coupling constants, we executed several structure refinement protocols employing unrestrained and restrained molecular dynamics (MD) simulations with two force fields. We find that only configurational ensembles obtained by applying simultaneously time-averaged NOE distance and 3J-coupling constant restraining with either force field reproduce all the experimental data. Additionally, analyses of the simulated ensembles show that the conformational variability of GCN4p16–31 in solution admitted by the available set of 187 measured NMR data is larger than represented by the set of the NMR model structures. The conformations of GCN4p16–31 in solution differ in the orientation not only of the side-chains but also of the backbone. The inconsistencies between the NMR model structures and the measured NMR data are due to the neglect of averaging effects and the inclusion of hydrogen-bond and torsional-angle restraints that have little basis in the primary, i.e. measured NMR data.

A GPU solvent–solvent interaction calculation accelerator for biomolecular simulations using the GROMOS software

Abstract: During the past few years, graphics processing units (GPUs) have become extremely popular in the high performance computing community. In this study, we present an implementation of an acceleration engine for the solvent–solvent interaction evaluation of molecular dynamics simulations. By careful optimization of the algorithm speed-ups up to a factor of 54 (single-precision GPU vs. double-precision CPU) could be achieved. The accuracy of the single-precision GPU implementation is carefully investigated and does not influence structural, thermodynamic, and dynamic quantities. Therefore, the implementation enables users of the GROMOS software for biomolecular simulation to run the solvent–solvent interaction evaluation on a GPU, and thus, to speed-up their simulations by a factor 6–9. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

Prediction of folding equilibria of differently substituted peptides using one-step perturbation.

Abstract: Computer simulation using long molecular dynamics (MD) can be used to simulate the folding equilibria of peptides and small proteins. However, a systematic investigation of the influence of the side-chain composition and position at the backbone on the folding equilibrium is computationally as well as experimentally too expensive because of the exponentially growing number of possible side-chain compositions and combinations along the peptide chain. Here, we show that application of the one-step perturbation technique may solve this problem, at least computationally; that is, one can predict many folding equilibria of a polypeptide with different side-chain substitutions from just one single MD simulation using an unphysical reference state. The methodology reduces the number of required separate simulations by an order of magnitude.

Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA.

Abstract: With the aim to gain a better understanding of the various driving forces that govern sequence specific DNA minor groove binding, we performed a thermodynamic analysis of netropsin binding to an AT-containing and to a set of six mixed AT/GC-containing binding sequences in the DNA minor groove. The relative binding free energies obtained using molecular dynamics simulations and free energy calculations show significant variations with the binding sequence. While the introduction of a GC base pair in the middle or close to the middle of the binding site is unfavorable for netropsin binding, a GC base pair at the end of the binding site appears to have no negative influence on the binding. The results of the structural and energetic analyses of the netropsin-DNA complexes reveal that the differences in the calculated binding affinities cannot be explained solely in terms of netropsin-DNA hydrogen-bonding or interaction energies. In addition, solvation effects and entropic contributions to the relative binding free energy provide a more complete picture of the various factors determining binding. Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively.

Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation.

Abstract: Proteins comprising each of the two plant nonspecific lipid transfer protein (LTP) families, LTP1s and LTP2s, share similar folds and biological functions and are stabilized by four native disulfide bonds. Disulfide-scrambling experiments suggested that rice LTP2 is more thermostable than rice LTP1 and identified multiple disulfide-scrambled isomers for LTP1 but only one for LTP2. According to the potential energy evaluated in two GROMOS force fields, however, rice LTP1 is more stable than either rice or wheat LTP2. Moreover, the published rice LTP2 NMR model structure is found to be highly unfavorable. The reasons for this are investigated, and it is found that the rice LTP2 sequence is in fact more compatible with the more ordered X-ray structure of wheat LTP2 than with the published rice LTP2 NMR model structure. The proposed disulfide bond shuffling of rice LTP1, rice LTP2, and, for comparative purposes, wheat LTP2 and a homology model combining the rice LTP2 sequence with the wheat LTP2 structure is ...

A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability.

Abstract: The right-handed α-helix is the dominant helical fold of α-peptides, whereas the left-handed 314-helix is the dominant helical fold of β-peptides. Using molecular dynamics simulations, the properties of α-helical α-peptides and 314-helical β-peptides with different C-terminal protonation states and in the solvents water and methanol are compared. The observed energetic and entropic differences can be traced to differences in the polarity of the solvent-accessible surface area and, in particular, the solute dipole moments, suggesting different reasons for their stability.

A one-site polarizable model for liquid chloroform: COS/C

Abstract: A one-site polarizable liquid chloroform model based on the charge-on-spring method is presented. It consists of five van der Waals sites and point charges, with one polarizable center on the carbon atom. The partial charges were adjusted to fit the gas-phase dipole moment of chloroform, and the Lennard–Jones parameters were varied to reproduce the density and the heat of vapourization of liquid chloroform. In this way, a simple polarizable model for liquid chloroform was obtained that correctly describes a variety of its thermodynamic, dynamic and dielectric properties, while the computational costs are only a factor of 2 higher than for a similar non-polarizable chloroform model. The model is simpler than two previously developed polarizable chloroform models, with four or five polarizable sites. The developed COS/C model is expected to show realistic behaviour of chloroform molecules in response to changes in electric field strength or the dielectric environment and should be applicable in simulations ...

What stabilizes the 314-helix in β3-peptides? A conformational analysis using molecular simulation

Abstract: Beta-peptides are analogs of natural alpha-peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side-chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. In order to unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a beta^3-substited peptide with an additional methyl group on the central C_alpha-atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the C_alpha- and C_beta-atoms of the central residue by alchemically changing them into dummy atoms, which have no non-bonded interactions. We find that the folded state of the beta^3-peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the psi-dihedral angles (enthalpic effect). The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides.

Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution.

Abstract: Computer simulation using molecular dynamics is increasingly used to simulate the folding equilibria of peptides and small proteins. Yet, the quality of the obtained results depends largely on the quality of the force field used. This comprises the solute as well as the solvent model and their energetic and entropic compatibility. It is, however, computational very expensive to perform test simulations for each combination of force-field parameters. Here, we use the one-step perturbation technique to predict the change of the free enthalpy of folding of a beta-peptide in methanol solution due to changing a variety of force-field parameters. The results show that changing the solute backbone partial charges affects the folding equilibrium, whereas this is relatively insensitive to changes in the force constants of the torsional energy terms of the force field. Extending the cut-off distance for nonbonded interactions beyond 1.4 nm does not affect the folding equilibrium. The same result is found for a change of the reaction-field permittivity for methanol from 17.7 to 30. The results are not sensitive to the criterion, e.g., atom-positional RMSD or number of hydrogen bonds, that is used to distinguish folded and unfolded conformations. Control simulations with perturbed Hamiltonians followed by backward one-step perturbation indicated that quite large perturbations still yield reliable results. Yet, perturbing all solvent molecules showed where the limitations of the one-step perturbation technique are met. The evaluated methodology constitutes an efficient tool in force-field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude.

Exploring the trigger sequence of the GCN4 coiled-coil: biased molecular dynamics resolves apparent inconsistencies in NMR measurements.

Abstract: Trigger sequences are indispensable elements for coiled-coil formation. The monomeric helical trigger sequence of the yeast transcriptional activator GCN4 has been investigated recently using several solution NMR observables including nuclear Overhauser enhancement (NOE) intensities and 3J(HN,HCα)-coupling constants, and a set of 20 model structures was proposed. Constrained to satisfy the NOE-derived distance bounds, the NMR model structures do not appear to reproduce all the measured 3J(HN-HCα)-coupling constant values, indicating that the α-helical propensity is not uniform along the GCN4 trigger sequence. A recent methodological study of unrestrained and restrained molecular dynamics (MD) simulations of the GCN4 trigger sequence in solution showed that only MD simulations incorporating time-averaged NOE distance restraints and instantaneous or local-elevation 3J-coupling restraints could satisfy the entire set of the experimental data. In this report, we assess by means of cluster analyses the model structures characteristic of the two simulations that are compatible with the measured data and compare them with the proposed 20 NMR model structures. Striking characteristics of the MD model structures are the variability of the simulated configurations and the indication of entropic stability mediated by the aromatic N-terminal residues 17Tyr and 18His, which are absent in the set of NMR model structures.

Structure Determination of a Flexible Cyclic Peptide Based on NMR and MD Simulation 3J‐Coupling

Abstract: Molecular dynamics (MD) simulations, in which experimental values such as nuclear Overhauser effects (NOEs), dipolar couplings, (3)J-coupling constants or crystallographic structure factors are used to bias the values of specific molecular properties towards experimental ones, are often carried out to study the structure refinement of peptides and proteins. However, (3)J-coupling constants are usually not employed because of the multiplicity of torsional angle values (phi) corresponding to each (3)J-coupling constant value. Here, we apply the method of adaptively enforced restraining using a local-elevation (LE) biasing potential energy function in which a memory function penalizes conformations in case both the average and the current (3)J-values deviate from the experimental target value. Then, the molecule is forced to sample other parts of the conformational space, thereby being able to cross high energy barriers and to bring the simulated average close to the measured value. Herein, we show the applicability of this method in structure refinement of a cyclo-beta-tetrapeptide by enforcing the (3)J-value restraining with LE on twelve backbone torsional angles. The resulting structural ensemble satisfies the experimental (3)J-coupling data better than the NMR model structure derived using conventional single-structure refinement based on these data. Thus, application of local-elevation search MD simulation in combination with biasing towards (3)J-coupling makes it possible to use (3)J-couplings quantitatively in structure determination of peptides.

Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides

Abstract: The one-step perturbation technique is used to predict the folding equilibria for 16 peptides with different stereochemical side-chain substitutions through one or two long-time simulations, one of an unphysical reference state and another of one of the 16 peptides for which many folding events can be sampled. The accuracy of the one-step perturbation results was investigated by comparing to results available from long-time MD simulations of particular peptides. Their folding free energies were reproduced within statistical accuracy. The one-step perturbation results show that an axial substitution at either the Cα or the Cβ position destabilizes the 314-helical conformation of the hepta-β-peptide, which is consistent with data inferred from experimental CD spectra. The methodology reduces the number of required separate simulations by an order of magnitude.

The thermal isomerization of the GFP chromophore: A computational study

Abstract: We present a density functional theory (B3LYP) study of the isomerization of 4-hydroxybenzylidene-1,2-dimethyl-imidazolinone (HOBDI), which is to mimic the green fluorescent protein (GFP) chromophore, in the ground state promoted by a nucleophile. Four solvents with different polarity, water, DMSO, methanol, and benzene, have been used to characterize the nucleophile assisted mechanism. The former three solvents have been used as nucleophile to participate in the reaction, while in benzene, we use n-propylamine as the nucleophile. When water, methanol and n-propylamine are used as nucleophile, the isomerization is characterized as a three-step process and the addition of the nucleophile is the rate-determining step. A proton transfer from the nucleophile to the oxygen of imidazolinone (O1) is observed during the addition step, which stabilizes the negative charge on O1 due to the reduction of the C1C2 double bond. The energy barrier to the reaction increases in the order of CH3OH ≤ water < n-propylamine, which is consistent with the experimental data. Whereas in DMSO, the calculations predict a one-step reaction for the isomerization starting from the zwitterionic state with a high barrier of 26.8 kcal mol−1, in accord with the slow reaction observed experimentally. Our study suggests that the ability of a nucleophile to assist the thermal isomerization of HOBDI mainly depends on its ability to give a proton upon the addition of the nucleophile to the substrate.

Molecular Dynamics Simulation of Ester‐Linked Hen Egg White Lysozyme Reveals the Effect of Missing Backbone Hydrogen Bond Donors on the Protein Structure

Abstract: The three-dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester-linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester-linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains.

Molecular dynamics computer simulation as a tool for the analysis of solvation: A study of dilute aqueous solutions of 1,4‐dioxane and 1,3‐dioxane

Abstract: It is shown how the computer simulation technique of molecular dynamics (MD) can be used to obtain a detailed picture of the static and dynamic properties of a solution at the atomic level. The method is applied to the solvation of a single molecule of 1,4-dioxane and 1,3-dioxane dissolved in 122 water molecules. The structure of the solvation shell was found to be clathrate-like although the dioxane oxygen atoms disturb this arrangement considerably. This is especially apparent for 1,3-dioxane as a result of its large dipole moment and the favorable position of its oxygen atoms for double hydrogen bonding. Generally, comparison of simulated properties with available experimental data shows good agreement. Consideration of both static and dynamic properties leads to the conclusion that there is a balance between structure-breaking and structure-making properties for 1,4-dioxane. By contrast, 1,3-dioxane is definitely structure-breaking. The hydration shell of 1,3-dioxane is clearly more labile than that of 1,4-dioxane.

The Propensity of α-Aminoisobutyric Acid (=2-Methylalanine; Aib) to Induce Helical Secondary Structure in an α-Heptapeptide: A Computational Study

Abstract: We present a molecular-dynamics simulation study of an α-heptapeptide containing an α-aminoisobutyric acid (=2-methylalanine; Aib) residue, Val1-Ala2-Leu3-Aib4-Ile5-Met6-Phe7, and a quantum-mechanical (QM) study of simplified models to investigate the propensity of the Aib residue to induce 310/α-helical conformation. For comparison, we have also performed simulations of three analogues of the peptide with the Aib residue being replaced by L-Ala, D-Ala, and Gly, respectively, which provide information on the subtitution effect at C(α) (two Me groups for Aib, one for L-Ala and D-Ala, and zero for Gly). Our simulations suggest that, in MeOH, the heptapeptide hardly folds into canonical helical conformations, but appears to populate multiple conformations, i.e., C7 and 310-helical ones, which is in agreement with results from the QM calculations and NMR experiments. The populations of these conformations depend on the polarity of the solvent. Our study confirms that a short peptide, though with the presence of an Aib residue in the middle of the chain, does not have to fold to an α-helical secondary structure. To generate a helical conformation for a linear peptide, several Aib residues should be present in the peptide, either sequentially or alternatively, to enhance the propensity of Aib-containing peptides towards the helical conformation. A correction of a few of the published NMR data is reported.

Cyclic β-Helical/β-Hairpin d,l-α-Peptide: Study of Its Folding Properties and Structure Refinement Using Molecular Dynamics

Abstract: A molecular dynamics (MD) simulation study of a cyclic 22 residue d,l-α-peptide is reported. The 154 experimental ROE distance bounds that determine a β-helical fold in chloroform are all satisfied...

α‐Cyclodextrin Host–Guest Binding: A Computational Study of the Different Driving Forces

Abstract: Free-energy differences govern the equilibrium between bound and unbound states of a host and its guest molecules. The understanding of the underlying entropic and enthalpic contributions, and their complex interplay are crucial for the design of new drugs and inhibitors. In this study, molecular dynamics (MD) simulations were performed with inclusion complexes of α-cyclodextrin (αCD) and three monosubstituted benzene derivatives to investigate host–guest binding. αCD Complexes are an ideal model system, which is experimentally and computationally well-known. Thermodynamic integration (TI) simulations were carried out under various conditions for the free ligands in solution and bound to αCD. The two possible orientations of the ligand inside the cavity were investigated. Agreement with experimental data was only found for the more stable orientation, where the substituent resides inside the cavity. The better stability of this conformation results from stronger Van der Waals interactions and a favorable antiparallel host–guest dipole–dipole alignment. To estimate the entropic contributions, simulations were performed at three different temperatures (250, 300, and 350 K) and using positional restraints for the host. The system was found to be insensitive to both factors, due to the large and symmetric cavity of αCD, and the nondirectional nature of the host–guest interactions.

The Effect of Fluoro Substitution upon the β‐Hairpin Fold of a β‐Tetrapeptide in Methanol

Abstract: The importance of β-peptides lies in their ability to mimic the conformational behavior of α-peptides, even with a much shorter chain length, and in their resistance to proteases. To investigate the effect of substitution of β-peptides on their dominant fold, we have carried out a molecular-dynamics (MD) simulation study of two tetrapeptides, Ac-(2R,3S)-β2,3hVal(αMe)-(2S)-β2hPhe-(R)-β3hLys-(2R,3S)-β2,3-Ala(αMe)-NH2, differing in the substitution at the Cα of Phe2 (pepF with F, and pepH with H). Three simulations, unrestrained (UNRES), using 3J-coupling biasing with local elevation in combination with either instantaneous (INS) or time-averaging (AVE) NOE distance restraining, were carried out for each peptide. In the unrestrained simulations, we find three (pepF) and two (pepH) NOE distance bound violations of maximally 0.22 nm that involve the terminal residues. The restrained simulations match both the NOE distance bounds and 3J-values derived from experiment. The fluorinated peptide shows a slightly larger conformational variability than the non-fluorinated one.