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A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin

Nature Structural Biology volume 4, pages 202–208 (1997)Cite this article

Abstract

The distribution of carbon monoxide after photodissociation in the myoglobin haem pocket has been investigated using molecular dynamics simulations at 300 K. The results show that both intermediates (one close to the haem iron and one further away) observed in recent low temperature X-ray studies of photodissociated CO have a high probability of occurrence, even at ambient temperatures. The fact that the O of CO is oriented toward the haem iron in the closer intermediate provides an explanation for the slow rate of CO geminate rebinding. A refinement against X-ray data generated from the molecular dynamics simulations indicates that the CO has a broader distribution in the haem pocket than is apparent from the experimental electron density. This effect is likely to be general for systems containing highly mobile groups.

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Authors and Affiliations

  1. Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts, 02254, USA

    Dennis Vitkup & Gregory A. Petsko

  2. Department of Biology, Program in Biophysics, Brandeis University, Waltham, Massachusetts, 02254, USA

    Dennis Vitkup

  3. Departments of Chemistry and Biochemistry, Brandeis University, Waltham, Massachusetts, 02254, USA

    Gregory A. Petsko

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

    Dennis Vitkup & Martin Karplus

  5. Laboratoire de Chimie Biophysique, Institut le Bel, Université Louis Pasteur, 67000, Strasbourg, France

    Martin Karplus

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Vitkup, D., Petsko, G. & Karplus, M. A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin. Nat Struct Mol Biol 4, 202–208 (1997). https://doi.org/10.1038/nsb0397-202

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