Marti Marcelo A, Capece Luciana, Bidon-Chanal Axel, Crespo Alejandro, Guallar Victor, Luque F Javier, Estrin Dario A
Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina.
Methods Enzymol. 2008;437:477-98. doi: 10.1016/S0076-6879(07)37024-9.
This chapter reviews the application of classical and quantum-mechanical atomistic simulation tools used in the investigation of several relevant issues in nitric oxide reactivity with globins and presents different simulation strategies based on classical force fields: standard molecular dynamics, essential dynamics, umbrella sampling, multiple steering molecular dynamics, and a novel technique for exploring the protein energy landscape. It also presents hybrid quantum-classical schemes as a tool to obtain relevant information regarding binding energies and chemical reactivity of globins. As illustrative examples, investigations of the structural flexibility, ligand migration profiles, oxygen affinity, and reactivity toward nitric oxide of truncated hemoglobin N of Mycobacterium tuberculosis are presented.
本章回顾了经典和量子力学原子模拟工具在研究一氧化氮与珠蛋白反应的几个相关问题中的应用，并介绍了基于经典力场的不同模拟策略：标准分子动力学、主成分动力学、伞形采样、多引导分子动力学，以及一种探索蛋白质能量景观的新技术。本章还介绍了混合量子-经典方案，作为获取有关珠蛋白结合能和化学反应性相关信息的工具。作为示例，展示了对结核分枝杆菌截短血红蛋白N的结构灵活性、配体迁移概况、氧亲和力和对一氧化氮的反应性的研究。
