Understanding the avidin–biotin binding based on polarized protein-specific charge

Abstract

In this study, charge updating schemes based on the local polarized protein-specific charge (LPPC) were introduced to vary the atomic charges of the biotin molecule and the residues in close contact during the simulation of the avidin–biotin complexes. The need of the charge variation of the ligand in response to changes in its surroundings was thoroughly studied. The results show that the calculated binding energy difference between biotin (BTN1) and 2′-iminobiotin (BTN2) and avidin is in excellent agreement with the experimental value, thus verifying the feasibility of updating the atomic charges of ligands during the simulation.