Quantum study of HIV-1 protease-bridge water interaction
Quantum study of HIV-1 protease-bridge water interaction
复制标题
HIV-1 蛋白酶-桥水相互作用的量子研究
DOI：
10.1063/1.2770720
复制
发表时间：
2007-10-14
影响因子：
4.4
通讯作者：
Zhang, John Z. H.
中科院分区：
文献类型：
--
作者：
Duan, Li L.;Tong, Yan;Zhang, John Z. H.
我们提出了一个完整的量子力学计算之间的结合相互作用的HIV-1蛋白酶（PR）和水分子W301的蛋白酶与PR的抑制剂的瓣桥。量子计算是通过应用最近开发的分子分馏与共轭帽（MFCC）的方法，该方法将蛋白质分子分为加帽的氨基酸为基础的片段和它们的共轭帽。这些单独的片段被适当地处理以保留被切割的键的化学性质。采用从头算方法，在HF，B3 LYP和MP2水平上，采用固定基组6-31+G* 进行计算. MFCC计算产生代表PR和W301的各个残基之间的相互作用的量子力学相互作用“图”。这使得在量子力学水平上对W301与PR的特定残基的结合进行详细的定量分析成为可能。(C)2007年，美国物理学会。
We present a fully quantum mechanical calculation for binding interaction between HIV-1 protease (PR) and the water molecule W301 which bridges the flaps of the protease with the inhibitors of PR. The quantum calculation is made possible by applying a recently developed molecular fractionation with conjugate caps (MFCC) method which divides a protein molecule into capped amino acid-based fragments and their conjugate caps. These individual fragments are properly treated to preserve the chemical property of bonds that are cut. Ab initio methods at HF, B3LYP, and MP2 levels with a fixed basis set 6-31+G* have been employed in the present calculation. The MFCC calculation produces a quantum mechanical interaction "map" representing interactions between individual residues of PR and W301. This enables a detailed quantitative analysis on binding of W301 to specific residues of PR at quantum mechanical level. (C) 2007 American Institute of Physics.