Wilfred F. van Gunsteren

Bio: Wilfred F. van Gunsteren is an academic researcher from École Polytechnique Fédérale de Lausanne. The author has contributed to research in topics: Molecular dynamics & Thermodynamic integration. The author has an hindex of 86, co-authored 427 publications receiving 31426 citations. Previous affiliations of Wilfred F. van Gunsteren include University of Oxford & University of Groningen.

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6.

Abstract: Successive parameterizations of the GROMOS force field have been used successfully to simulate biomolecular systems over a long period of time. The continuing expansion of computational power with time makes it possible to compute ever more properties for an increasing variety of molecular systems with greater precision. This has led to recurrent parameterizations of the GROMOS force field all aimed at achieving better agreement with experimental data. Here we report the results of the latest, extensive reparameterization of the GROMOS force field. In contrast to the parameterization of other biomolecular force fields, this parameterization of the GROMOS force field is based primarily on reproducing the free enthalpies of hydration and apolar solvation for a range of compounds. This approach was chosen because the relative free enthalpy of solvation between polar and apolar environments is a key property in many biomolecular processes of interest, such as protein folding, biomolecular association, membrane formation, and transport over membranes. The newest parameter sets, 53A5 and 53A6, were optimized by first fitting to reproduce the thermodynamic properties of pure liquids of a range of small polar molecules and the solvation free enthalpies of amino acid analogs in cyclohexane (53A5). The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed.

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

Abstract: New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N-H, C=O repulsion, a new atom type for a charged -CH(3) in the choline moiety is added, the Na(+) and Cl(-) ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained.

Peptide Folding: When Simulation Meets Experiment

Abstract: Accurate reproduction of the mechanism of peptide folding in solution and conformational preferences as a function of amino acid sequence is possible with atomic level dynamics simulations. For example, the simulations correctly predict a left-handed 31-helical fold for the β-heptapeptide 1 (the molecular model is shown in the picture) and a right-handed helical fold for the β-hexapeptide 2, as was confirmed by NMR spectroscopy.

A generalized reaction field method for molecular dynamics simulations

Abstract: Molecular dynamics simulations of ionic systems require the inclusion of long‐range electrostatic forces. We propose an expression for the long‐range electrostatic forces based on an analytical solution of the Poisson–Boltzmann equation outside a spherical cutoff, which can easily be implemented in molecular simulation programs. An analytical solution of the linearized Poisson–Boltzmann (PB) equation valid in a spherical region is obtained. From this general solution special expressions are derived for evaluating the electrostatic potential and its derivative at the origin of the sphere. These expressions have been implemented for molecular dynamics (MD) simulations, such that the surface of the cutoff sphere around a charged particle is identified with the spherical boundary of the Poisson–Boltzmann problem. The analytical solution of the Poisson–Boltzmann equation is valid for the cutoff sphere and can be used for calculating the reaction field forces on the central charge, assuming a uniform continuum of given ionic strength beyond the cutoff. MD simulations are performed for a periodic system consisting of 2127 SPC water molecules with 40 NaCl ions (1 molar). We compare the structural and dynamical results obtained from MD simulations in which the long range electrostatic interactions are treated differently; using a cutoff radius, using a cutoff radius and a Poisson–Boltzmann generalized reaction field force, and using the Ewald summation. Application of the Poisson–Boltzmann generalized reaction field gives a dramatic improvement of the structure of the solution compared to a simple cutoff treatment, at no extra computational cost.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

A smooth particle mesh Ewald method

Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

Quantum mechanical continuum solvation models.

Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...