B. J. Berne

Reversible multiple time scale molecular dynamics

The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators. This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces. The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods. These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods. It is shown how the new RESPA methods are related to predictor–corrector integrators. Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats.

Modification of the overlap potential to mimic a linear site–site potential

A modification of the overlap potential of Berne and Pechukas is proposed. The overlap strength and range parameters are used in a new functional form resulting in a single‐site potential which closely resembles a linear site–site potential.

Dynamical fluctuating charge force fields: Application to liquid water

A new molecular dynamics model in which the point charges on atomic sites are allowed to fluctuate in response to the environment is developed and applied to water. The idea for treating charges as variables is based on the concept of electronegativity equalization according to which: (a) the electronegativity of an atomic site is dependent on the atom’s type and charge and is perturbed by the electrostatic potential it experiences from its neighbors and (b) charge is transferred between atomic sites in such a way that electronegativities are equalized. The charges are treated as dynamical variables using an extended Lagrangian method in which the charges are given a fictitious mass, velocities, and kinetic energy and then propagated according to Newtonian mechanics along with the atomic degrees of freedom. Models for water with fluctuating charges are developed using the geometries of two common fixed‐charge water potentials: the simple point charge (SPC) and the four‐point transferable intermolecular po...

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high‐throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.

The free energy landscape for β hairpin folding in explicit water

The folding free energy landscape of the C-terminal β hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and oplsaa force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the β strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding

The thermodynamic properties and phase behavior of water in confined regions can vary significantly from that observed in the bulk. This is particularly true for systems in which the confinement is on the molecular-length scale. In this study, we use molecular dynamics simulations and a powerful solvent analysis technique based on inhomogenous solvation theory to investigate the properties of water molecules that solvate the confined regions of protein active sites. Our simulations and analysis indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein–ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our analysis elucidates several challenging cases, including the super affinity of the streptavidin–biotin system.

Gaussian Model Potentials for Molecular Interactions

Simple analytical forms for the orientation dependence of the potential between two molecules are derived from a Gaussian overlap model. Orientation‐dependent range and energy parameters are determined, which can be used with any two‐parameter atomic potential to give simple and reasonable polyatomic potentials.

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

Understanding the underlying physics of the binding of small-molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying molecular physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small molecule and its associated receptor that captures the effects of the ligand displacing the solvent from the protein active site with atomic detail. This descriptor quantitatively predicts (R(2) = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates physical properties of the active-site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.

Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding

The mechanism of denaturation of proteins by urea is explored by using all-atom microseconds molecular dynamics simulations of hen lysozyme generated on BlueGene/L. Accumulation of urea around lysozyme shows that water molecules are expelled from the first hydration shell of the protein. We observe a 2-stage penetration of the protein, with urea penetrating the hydrophobic core before water, forming a “dry globule.” The direct dispersion interaction between urea and the protein backbone and side chains is stronger than for water, which gives rise to the intrusion of urea into the protein interior and to ureas preferential binding to all regions of the protein. This is augmented by preferential hydrogen bond formation between the urea carbonyl and the backbone amides that contributes to the breaking of intrabackbone hydrogen bonds. Our study supports the “direct interaction mechanism” whereby urea has a stronger dispersion interaction with protein than water.

Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals

New path integral molecular dynamics (PIMD) and path integral hybrid Monte Carlo (PIHMC) algorithms are developed. It is shown that the use of a simple noncanonical change of variables that naturally divides the quadratic part of the action into long and short wavelength modes and multiple time scale integration techniques results in very efficient algorithms. The PIMD method also employs a constant temperature MD technique that has been shown to give canonical averages even for stiff systems. The new methods are applied to the simple quantum mechanical harmonic oscillator and to electron solvation in fluid helium and xenon. Comparisons are made with PIMC and the more basic PIMD and PIHMC methods.