Molecular dynamics simulations in biology

  title={Molecular dynamics simulations in biology},
  author={Martin Karplus and Gregory A. Petsko},
Molecular dynamics—the science of simulating the motions of a system of particles—applied to biological macromolecules gives the fluctuations in the relative positions of the atoms in a protein or in DNA as a function of time. Knowledge of these motions provides insights into biological phenomena such as the role of flexibility in ligand binding and the rapid solvation of the electron transfer state in photosynthesis. Molecular dynamics is also being used to determine protein structures from… 


Molecular simulations can help to understand biological complexity at the atomic and molecular levels and give promising insights into the thermodynamic and functional/mechanistic behavior of biological processes.

Molecular Dynamics Computer Modelling and Protein Engineering

Modelling of collective motion in proteins’ secondary structural elements, thermal stability of protein structures, differential stability in protein folds and surface plasticity properties of proteins, and the perspective of computer simulation as a tool in molecular engineering is explored.

Protein dynamics: comparison of simulations with inelastic neutron scattering experiments

  • J. Smith
  • Physics
    Quarterly Reviews of Biophysics
  • 1991
To deepen our understanding of the principles determining the folding and functioning of globular proteins the determination of their three-dimensional structures must be supplemented with the

Molecular dynamics analysis of biomolecular systems including nucleic acids

In this review, the current situation and future directions of the field are described, hopefully as a guide to collaboration between experiment and computation.

Characterizing semilocal motions in proteins by NMR relaxation studies.

This work proposes to measure the relaxation of additional nuclei on each peptide plane allowing for the observation of anisotropic local motions in proteins, allowing the nature of local motions to be characterized in proteins.

Molecular Dynamics of Water at the Protein-Solvent Interface

The use of molecular dynamics simulation to investigate the properties of hydration water around proteins is outlined. A variety of structural and dynamical properties of the protein hydration water

Molecular dynamics simulation in virus research

The recent advances in MD simulations in the study of virus–host interactions and evolution are summarized, future perspectives on this technique are presented, and MD simulation is quickly extending the range of applications in biology.

The Global Minimum Problem in Molecular Mechanics: Simulated Annealing and Related Techniques

Three of the greatest challenges facing computational chemistry in the field of biomolecular modelling are: macromolecular solution structure determination from NMR experiments;1 the calculation of



Hidden thermodynamics of mutant proteins: a molecular dynamics analysis.

By exposing the individual contributions, the free energy simulation provides new insights into the origin of thermodynamic changes in mutant proteins and demonstrates the role of effects beyond those usually considered in structural analyses.

Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

A molecular dynamics simulation of myoglobin provides the first direct demonstration that the potential energy surface of a protein is characterized by a large number of thermally accessible minima

Improved simulation of liquid water by molecular dynamics

Molecular dynamics calculations on a classical model for liquid water have been carried out at mass density 1 g/cm3 and at four temperatures. The effective pair potential employed is based on a

Dynamics of folded proteins

The dynamics of a folded globular protein have been studied by solving the equations of motion for the atoms with an empirical potential energy function and suggest that the protein interior is fluid-like in that the local atom motions have a diffusional character.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build

Vicinal coupling constants and protein dynamics.

It is concluded that for the main chain, motional effects do not introduce significant errors where vicinal coupling constants are used in structure determinations; however, for side chains, the motional average can alter deductions about the structure.

Three-dimensional structure of proteins determined by molecular dynamics with interproton distance restraints: application to crambin.

Model calculations are performed to evaluate the utility of molecular dynamics with NMR interproton distance restraints for determining the three-dimensional structure of proteins and it is shown that a restrained dynamics structure with significantly larger deviations can be characterized as incorrect, independent of a knowledge of the crystal structure.

Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics

Potential Functions. Dynamical Simulation Methods. Thermodynamic Methods. Atom and Sidechain Motions. Rigid-Body Motions. Larger-Scale Motions. Solvent Influence on Protein Dynamics. Thermodynamic

Dynamics of ligand binding to heme proteins.