A comparative study of dynamic structures of proteins by using normal mode analysis database.

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In this study we considered that a comparative study of normal mode analysis for wild-type and mutant lysozymes and for several proteins in the same superfamily could provide some valuable information about dynamic structures of proteins.1.In the study of lysozymes it was found that the changes in the dynamic structures (defined as changes in fluctuations of the amino acid residues here) of the mutant lysozymes from the wild-type one had little correlation with those in the static structures. In order to reveal the basic changes caused by amino acid substitutions we performed a principal component analysis of the fluctuations of amino acid residues with the various mutant lysozymes. As a result, it was found that the domain motions are essential to the fluctuations of the individual amino acid residues. Furthermore, it was found that the correlative movements of the specific atom pairs in the active site should be maintained for the activity of the mutant lysozymes.2.In the comparative … More study of homologous proteins, the proteins were structurally aligned and then the fluctuations of the amino acids were compared at the equivalent sites. Although their amino acid sequences considerably differed in some cases (but their folds were very similar), the fluctuations of the amino acid residues at the equivalent sites in the secondary structure regions agreed well not only qualitatively but also quantitatively with each other. On the other hand, in the loop regions, since the fluctuations were essentially larger and affected by the insertion and deletion of amino acid residues, the changes in the fluctuations differed quantitatively. Furthermore, the dynamic domains were compared. The common regions constructing the dynamic domains among the homologous proteins were detected by visually inspecting their structures best-fitted. Such regions are considered to form a nucleus in the dynamic structure of the superfamily. This kind of observation can be obtained only when several proteins derived from the database we constructed are compared. Less