Computational active site analysis of molecular pathways to improve functional classification of enzymes

    Authors

    A. S. Ozyurt;T. L. Selby

    Comments

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    Abbreviated Journal Title

    Proteins

    Keywords

    active site analysis; computational docking; protein evolution; structural biology; enzyme substrate interactions; PEDANT GENOME DATABASE; THERMOTOGA-MARITIMA PROTEOME; MU-CRYSTALLIN; ORNITHINE CYCLODEAMINASE; STRUCTURAL GENOMICS; PHOSPHOLIPASE-C; DOMAIN-STRUCTURE; SEQUENCE; ANNOTATION; FOLD; Biochemistry & Molecular Biology; Biophysics

    Abstract

    This study describes a method to computationally assess the function of homologous enzymes through small molecule binding interaction energy. Three experimentally determined Xray structures and four enzyme models from ornithine cyclo-deaminase, alanine dehydrogenase, and mu-crystallin were used in combination with nine small molecules to derive a function score (FS) for each enzyme-model combination. While energy values varied for a single molecule-enzyme combination due to differences in the active sites, we observe that the binding energies for the entire pathway were proportional for each set of small molecules investigated. This proportionality of energies for a reaction pathway appears to be dependent on the amino acids in the active site and their direct interactions with the small molecules, which allows a function score (FS) to be calculated to assess the specificity of each enzyme. Potential of mean force (PMF) calculations were used to obtain the energies, and the resulting FS values demonstrate that a measurement of function may be obtained using differences between these PMF values. Additionally, limitations of this method are discussed based on: (a) larger substrates with significant conformational flexibility, (b) low homology enzymes, and (c) open active sites. This method should be useful in accurately predicting specificity for single enzymes that have multiple steps in their reactions and in high throughput computational methods to accurately annotate uncharacterized proteins based on active site interaction analysis.

    Journal Title

    Proteins-Structure Function and Bioinformatics

    Volume

    72

    Issue/Number

    1

    Publication Date

    1-1-2008

    Document Type

    Article

    Language

    English

    First Page

    184

    Last Page

    196

    WOS Identifier

    WOS:000256609800015

    ISSN

    0887-3585

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