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

The starting structure of ab initio protein structure prediction methods is problem- atic as the energy minimization procedure stops searching for an optimal structure of the func- tion'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 for- mation 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 modi- fied step by step as the role of the side chain interactions increases during the energy minimiza- tion procedure. Here, the method is applied to human hemoglobin chainsandto test the applicability of the method to proteins with a high content of helical forms and lacking disul- phide bonds.