engleski

New methods of finding flexibility in proteins

Proteins are complex macromolecular chemical structures made of amino acid residues. Function of a protein is determined by its composition, i.e. the amino acid sequence, and by its shape, a three dimensional structure known as protein conformation. For the purpose of analyzing protein flexibility and shape, it is important to define rigid and flexible protein domains. A protein may contain one or more rigid regions that are generally connected with flexible parts called hinges (usually, but not necessarily, few amino acids long). For the purpose of calculating protein flexibility we have used two approaches, the apriori flexibility procedure – flexibility calculation based only on a single protein conformation and the aposteriori flexibility procedure – flexibility calculation based on comparison of two or more conformations of the same protein. We argue not only that the aposteriotri procedure is currently the most accurate procedure for finding rigid and flexible domains within a protein, but also it is the only way to correctly determine test cases for assessing apriori protein flexibility. As a part of our research we developed a new aposteriori procedure for flexibility calculations. The core of the procedure uses techniques such as BLAST (Basic Local Alignment Search Tool), RMSD (Root Mean Square Deviation), SVD (Singular Value Decomposition), rotation matrices and sliding windows. The procedure has been applied on a test set containing nearly seventy entries. In this research using our procedure we are trying to establish a correlation between flexibility and protein parameters such as psi, phi, omega angles, polar, non-polar, backbone, side chain ASA (Accessible Surface Area), EIIP (Electron Ion Interaction Potential), ß-factor. This procedure is the first step in our research that we believe will result in finding a high accurate apriori procedure for predicting flexible and rigid protein domains.

protein; flexibility; correlation; conformational parameters

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