Two-Phase Simulation of Nascent Protein Folding

A.W. Znamirowski and L. Znamirowski (Poland)


Conformations, molecular nanotechnology, nascent polypeptide, protein folding, and structure simulation


The translation process from the RNA description into the nascent polypeptide conformation performed in the ribosome, determines the initial spatial shape of created protein followed by conformation modifications proc esses. The formed, nascent conformation of protein deter mines initial condition for a future conformation modi fications and plays a crucial role in fixing the biological and chemical features of created protein. In the paper, the method for determining of the confor mation of nascent protein folding based on two-phase simulation approach is presented. In both phases the po tential energy of molecule under construction is mini mized, 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 the increased chain. The simulation of conformation process is illustra ted through the numerical example of nascent protein fol ding for a small protein.

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