S.H. Heater, E.D. Zukowska (USA), and L. Znamirowski (Poland)
Conformations, Covalent Modifications, Medical andBioengineering, Parallel Computations, Protein Folding.
The paradigm for simulation of conformation switching process of the polypeptide chain in an aspect of changes of the protein torsion angles is discussed. The polypeptide synthesized in the ribosome is modeled using torsion an gles as a degrees of freedom. In the paper, the conforma tion switching by selected group of chemical modification is presented. When the chemical stimulation takes place, we can observe in many important protein, fast changes of conformation. Chemical modification through the protein conformation forcing, is highly effective means of switching the activity (e.g. biological) of target proteins. To find the set of protein torsion angles and (deter mining the spatial shape of protein) in an amino-acid sequence, as usual, we will exploit a tendency of the sys tem chain of polypeptide to get minimum total free energy. To determine the conformation of backbone of the poly peptide chain before and after switching, the Dynamic Programming method is used. The simulation of confor mation switching processes is illustrated through the ex amples for small protein cleavage and pH step changes in the polypeptide environment.
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