The interactions among 20 types of amino acid residues are crucial to protein folding and structure stability.As a consequence, study of inter-residue potential energy functions is of great importance to protein structure prediction and folding simulation.This work presents the developments of potential energy models based on crystallized protein structures.First, the physical assumptions, intrinsic character and key factors are illustrated for the mean force energy functions.Then, the derivations of pair-residue and tri-residue energy functions are described in details.Finally, the applications of potential energy to structure prediction and decoy discrimination are discussed.The present paper suggests that protein structure stability is a balance state of residue potential energy, showing not only competition but also compromise between multi-interactions.Further research on residue cluster and network energy is a promising direction for multi-scale structure models, which provides energy estimations from atom level to whole protein level.Meanwhile, micro-scale mechanism is to be established for explaining macro-scale protein behaviors from the viewpoint of structure energy.%阐述了基于蛋白质晶体结构的残基势能函数的研究进展,从平均作用力场势能函数的基本物理假设、势能函数性质和影响势能函数准确性的因素3个方面出发,分析了导出残基相互作用势能的方法,给出了残基对之间和3个残基之间的平均作用力势能函数计算过程,并介绍了残基势能函数在蛋白质结构研究领域的应用.基于蛋白质晶体结构的残基相互作用势能研究表明,蛋白质结构稳定是多种作用力相互竞争、相互协调进而达到平衡状态的结果.未来对于残基团簇及其相互作用网络能量分布的研究,能够建立介于原子尺度和蛋白质整体结构尺度之间的作用力物理模型,为蛋白质结构宏观尺度研究提供重要的微观力学机理.
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