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力学进展 ›› 2009, Vol. 39 ›› Issue (2): 129-153.doi: 10.6052/1000-0992-2009-2-J2008-045

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蛋白质结构动力学研究进展

孙卫涛   

  1. 清华大学周培源应用数学研究中心
  • 收稿日期:2008-04-07 修回日期:2008-07-31 出版日期:2009-03-25 发布日期:2009-03-25

RESEARCH ADVANCES IN PROTEIN STRUCTURE DYNAMICS

  • Received:2008-04-07 Revised:2008-07-31 Online:2009-03-25 Published:2009-03-25

摘要: 蛋白质是生物体赖以存在和生长的重要大分子有机化合物,由20种不同的氨基酸通过肽键连接成线性高分子链,具有特殊的三维空间结构. 蛋白质生物功能与结构动力学特征紧密相关,不同结构运动模式决定了蛋白质在生化过程中的不同生物功能.给定一种蛋白质的空间结构, 通过建立结构动力学模型,进而得到蛋白质结构的运动轨迹,或者将结构整体运动分解为不同频率振动模态的叠加,能够帮助进一步理解蛋白质生物活性点在配体结合、催化过程中的运动特征.阐述了蛋白质结构动力学研究的最新进展,分析了3种蛋白质结构动力学的物理模型和求解方法,详细讨论了谐波模型中的原子模态分析、弹性网络模型等动力学方法,并介绍了蛋白质结构动力学在生物研究领域的应用.蛋白质结构动力学方法的研究和发展表明,从物理原理和简化模型出发的理论分析方法,能够为生物学前沿研究提供有力帮助, 是蛋白质折叠和结构预测中的一个重要研究方向.

关键词: 蛋白质, 结构动力学,分子动力学, 谐波动力学, 随机动力学

Abstract: Protein is an important macro molecular organic compound that body need to maintain itself and grow. Proteins are linear polymers made of 20 kinds of amino acids linked by peptide bonds, which fold into unique 3-dimensional structures. Biological functions are closely related to protein structure dynamics, and different protein structures generate accordingly different biological functions in biochemistry process. For a protein structure, structure dynamics models can produce protein movement trajectories, or decompose collective motions into a combination of independent harmonic oscillators with different frequencies. In this way, many of those functional motions of active sites can be analyzed in detail and understood that occur in numerous biological phenomena, such as ligand binding and catalytic activity of enzymes. This study elucidates the latest advances in protein structure harmonic dynamics. Three important physical models are analyzed, and computation methods are discussed for protein dynamics. Detailed formulations are given for harmonic dynamics model, including atomic normal modes analysis (NMA), elastic network model (ENM) and other dynamics methods. Some applications of structure dynamics methods are presented with respect to biological research. Highlighted by recent advances in protein structure dynamics, it is clear that theoretical methods based on physical principle and simplified models can lend important supports to frontier research in biology, and protein structure dynamics becomes now an important research direction in protein folding and protein structure prediction.

Key words: protein, structure dynamics,