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1 TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

1 2004

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Limitation of conformational space for proteins -- early stage folding simulation of human alpha and beta hemoglobin chains

Bryliński M., Jurkowski W., Konieczny L., Roterman I.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2004

Vol. 8, No 3

413-422

The starting structure of ab initio protein structure prediction methods is problematic as the energy minimization procedure stops searching for an optimal structure of the function's local minimum. The method presented in the paper helps to find the starting structure. Although it is based on the known native protein structure, it seems to deliver a key to the formation of a common universal starting structure. The limited conformational sub-space, defined on the basis of a geometrical model of the polypeptide backbone with the side chain-side chain interaction excluded, seems to deliver the original structure of the polypeptide, which is modified step by step as the role of the side chain interactions increases during the energy minimization procedure. Here, the method is applied to human hemoglobin chains alpha and ß to test the applicability of the method to proteins with a high content of helical forms and lacking disulphide bonds.