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Molecular dynamics simulations of biomolecules

Nature Structural Biology volume 9, pages 646–652 (2002)Cite this article

A Corrigendum to this article was published on 01 October 2002

Abstract

Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin and early uses of biomolecular simulations. It then outlines some recent studies that illustrate the utility of such simulations and closes with a discussion of their ever-increasing potential for contributing to biology.

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Figure 1: Conformational change in the functional cycle of GroEL obtained by simulation of a single subunit (see ref. 45).
Figure 2: Fluctuation of the width of the bottleneck in the main channel or 'gorge' of mouse acetylcholinesterase.
Figure 3: Folding simulations of a three-stranded β-sheet peptide.
Figure 4: The permeation of water through a model of aquaporin (blue) in a lipid bilayer membrane (head groups in yellow and hydrocarbon tails in green).

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Acknowledgements

Work in the Karplus group is supported in part by a grant from the NIH. Work in the McCammon group is supported in part by the NSF, NIH, the W.M. Keck Foundation, the National Biomedical Computation Resource and the HHMI. As is evident from the references, our co-workers have contributed much of the work summarized here. We apologize to the large number of scientists whose important contributions to molecular dynamics simulations could not be cited because of space limitations on this short review.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, 02138, Massachusetts, USA

    Martin Karplus

  2. Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, Strasbourg, 67000, France

    Martin Karplus

  3. Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, 92093-0365, California, USA

    J. Andrew McCammon

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Correspondence to Martin Karplus.

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Karplus, M., McCammon, J. Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9, 646–652 (2002). https://doi.org/10.1038/nsb0902-646

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