Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics

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• 作者：Alessio Atzori ; Neil J. Bruce ; Kepa K. Burusco ; Berthold Wroblowski ; Pascal Bonnet ; Richard A. Bryce
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2014
• 出版时间：October 27, 2014
• 年：2014
• 卷：54
• 期：10
• 页码：2764-2775
• 全文大小：773K
• ISSN：1549-960X

文摘

Protein plasticity, while often linked to biological function, also provides opportunities for rational design of selective and potent inhibitors of their function. The application of computational methods to the prediction of concealed protein concavities is challenging, as the motions involved can be significant and occur over long time scales. Here we introduce the swarm-enhanced sampling molecular dynamics (sesMD) method as a tool to improve sampling of conformational landscapes. In this approach, a swarm of replica simulations interact cooperatively via a set of pairwise potentials incorporating attractive and repulsive components. We apply the sesMD approach to explore the conformations of the DFG motif in the protein p38伪 mitogen-activated protein kinase. In contrast to multiple MD simulations, sesMD trajectories sample a range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between the DFG-in and DFG-out conformations are predicted to have druggable pockets of interest for structure-based ligand design.