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Efficient mapping of ligand migration channel networks in dynamic proteins
2011-11-04  【 】【打印】【关闭
Institute of Theoretical Physics
Chinese Academy of Sciences
学术报告
Title
题目
Efficient mapping of ligand migration channel networks in dynamic proteins
Speaker
报告人
Prof. Guang Song
Iowa State University (USA)
Date
日期
2011-11-04 AM 10:00 Friday
Venue
地点
Conference Hall 322, ITP/理论物理所322报告厅
Abstract
摘要

For many proteins such as myoglobin, the binding site lies in the interior, and there is no obvious route from the exterior to the binding site in the average structure. Although computer simulations for a limited number of proteins have found some transiently open channels, it is not clear if there exist more channels elsewhere or how the channels are regulated. A systematic approach that can map out the whole ligand migration channel network is lacking. In this work, we present a novel robotic motion planning inspired approach that can map the ligand migration channel network in a dynamic protein. The method combines an efficient spatial mapping of protein inner space with a temporal exploration of protein structural heterogeneity, which is represented by a structure ensemble. The spatial mapping of each conformation in the ensemble produces a partial map of protein inner cavities and their interconnectivity. These maps are then merged to form a super map that contains all the channels that open dynamically. Results on the pathways in myoglobin for gaseous ligands demonstrate the efficiency of our approach in mapping the ligand migration channel networks. The results, obtained in a significantly less amount of time than trajectory-based approaches, are in agreement with previous simulation results.

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