New Advance in Computational Chemistry:  Full Quantum Mechanical ab Initio Computation of Streptavidin−Biotin Interaction Energy

Abstract

Benchmark full quantum mechanical Hartree-Fock calculation has been carried out to compute interaction energies for the streptavidin-biotin binding complex. In this report, the entire streptavidin-biotin interaction system with a total of 1775 atoms is treated by quantum mechanics. The full quantum energy calculation for this protein system is made possible by applying a recently developed MFCC approach in which the protein molecule is decomposed into amino-acid-based fragments that are properly capped. Ab initio calculations are performed at the Hartree-Fock level with a 3-21G basis set. The energies are computed for geometries of the binding complex near two configurations, corresponding to the crystal structure of the binding complex and a minimum energy geometry found from molecular force field, respectively. Comparisons are made of the computed ab initio energies with those from a force field. The present calculation shows that ab initio binding energies (at HF/3-21G level) are almost 30 kcal/mol larger than those given by a force field.