Zhang Da W, Xiang Yun, Zhang John Z H
Department of Chemistry, New York University, New York, New York 10003.
J Phys Chem B. 2003 Nov 6;107(44):12039-41. doi: 10.1021/jp0359081.
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.
已进行基准全量子力学哈特里-福克计算，以计算链霉亲和素-生物素结合复合物的相互作用能。在本报告中，采用量子力学处理了总共包含1775个原子的完整链霉亲和素-生物素相互作用系统。通过应用最近开发的MFCC方法，使得对该蛋白质系统进行全量子能量计算成为可能，在该方法中，蛋白质分子被分解为经过适当封端的基于氨基酸的片段。在哈特里-福克水平上使用3-21G基组进行从头计算。分别针对结合复合物接近两种构型的几何结构计算能量，这两种构型分别对应于结合复合物的晶体结构和从分子力场中找到的最低能量几何结构。将计算得到的从头算能量与来自力场的能量进行比较。目前的计算表明，从头算结合能（在HF/3-21G水平）比力场给出的结合能大近30千卡/摩尔。
