Applications of rare event dynamics on the free energy calculations for membrane protein systems

• Published in: Canadian journal of chemistry Vol. 91; no. 9; pp. 769 - 774
• Main Authors: Wang, Yun-Kun, Wei, Dong-Qing, Gu, Ruo-Xu, Fan, Huai-Meng, Ulmschneider, Jakob
• Format: Journal Article
• Language: English
• Published: Ottawa NRC Research Press 01.09.2013; Canadian Science Publishing NRC Research Press
• Subjects: Binding sites; calculs d’énergie libre; dynamique des événements rares; Free energy; free energy calculations; Gibbs' free energy; Insertion; Membrane proteins; Membranes; Metabolism; Molecular dynamics; molecular dynamics simulations; Peptides; Properties; Proteins; protéines membranaires; rare event dynamics; Simulation; simulations de la dynamique moléculaire; Strings; Thermodynamics; umbrella sampling; échantillonnage « parapluie; China
• ISSN: 0008-4042; 1480-3291
• DOI: 10.1139/cjc-2012-0391

Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions.