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The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces

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Molecular Modeling and Dynamics of Bioinorganic Systems

Part of the book series: NATO ASI Series ((ASHT,volume 41))

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Abstract

Living organisms store information in a compact and flexible manner in nucleic acids and use proteins to create both structural and catalytic molecules. A wealth of information about the atomic 3-dimensional structure of many proteins and some nucleic acids is available and stored in a readily accessible form in the Brookhaven Data Bank [1]. The challenge is to understand how the structure of these biomolecules enables them to carry out their function. Each molecule of protein is a linear polymer with identical backbone units. The same is true for the nucleic acids DNA and RNA. It is the specific sequence of amino acid side chains in a protein or bases in a nucleic acid that makes each unique. Thus, it is non-bonded interactions between the side chains that influence the backbone geometry, defining regions of α-helix or β-sheet as well as the overall fold in proteins, the propensity for A, B, Z DNA, or the structure of an RNA molecule. In addition, it is the non-bonded interactions that enable proteins and nucleic acids to bind reaction partners and participate in the appropriate reactions.

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  1. Department of Physics, City College of New York, 138th and Convent Avenue, New York, NY, 10031, USA

    Marilyn R. Gunner & Emil Alexov

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  1. Marilyn R. Gunner
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  2. Emil Alexov
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  1. Department of Chemistry, University of Florence, Florence, Italy

    Lucia Banci

  2. Anorganisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany

    Peter Comba

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Gunner, M.R., Alexov, E. (1997). The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces. In: Banci, L., Comba, P. (eds) Molecular Modeling and Dynamics of Bioinorganic Systems. NATO ASI Series, vol 41. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-5171-9_17

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