Non-gradient, Sequential Algorithm for Simulation of Nascent Polypeptide Folding

In the paper, the method for determining of the conformation of nascent protein folding based on two-phase, sequential simulation approach is presented. In both phases the potential energy of molecule under construction is minimized, however in the first phase the minimization is performed for the structure {new amino acid}/{existing amino acid chain} and in the second phase, the {new existing amino acid chain} conformation is “tuned” to reach the minimal potential energy of growing chain. The formed, nascent conformation of protein determines initial condition for a future conformation modifications and plays a crucial role in fixing the biological and chemical features of created protein. The simulation of conformation process is illustrated through the numerical example of nascent protein folding for a selected protein.