Mathematical Modeling of Linear Docking. I. Determination of Regions of Binding of Protein Molecules

Abstract

We report on the results of mathematical simulation of the interaction of various sequences of proteins Mdm2, P53, and Nap1 in accordance with the developed algorithms that were used for identifying the region of binding of various proteins during the formation of biological complexes P53–Mdm2, Mdm2–Mdm2, and Nap1–Nap1. The approach developed in this work will make it possible to determine active regions of binding of polypeptide chains of various proteins and to choose and synthesize highly selective peptides that will be bound in the active center of a protein and will lead to its activation or inhibition and blocking of its biological functions.