ENERGY PARAMETERS IN POLYPEPTIDES .10. IMPROVED GEOMETRICAL PARAMETERS AND NONBONDED INTERACTIONS FOR USE IN THE ECEPP/3 ALGORITHM, WITH APPLICATION TO PROLINE-CONTAINING PEPTIDES
ENERGY PARAMETERS IN POLYPEPTIDES .10. IMPROVED GEOMETRICAL PARAMETERS AND NONBONDED INTERACTIONS FOR USE IN THE ECEPP/3 ALGORITHM, WITH APPLICATION TO PROLINE-CONTAINING PEPTIDES
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DOI：
10.1021/j100194a068
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发表时间：
1992-07-23
影响因子：
--
通讯作者：
SCHERAGA, HA
中科院分区：
文献类型：
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作者：
NEMETHY, G;GIBSON, KD;SCHERAGA, HA
在计算机程序ECEPP（肽的经验构象能程序）中用于描述氨基酸残基的几何形状和相互作用的势能的一些参数已经更新。这些变化是基于最近可用的实验信息。最显着的变化改善的几何形状和脯氨酰和羟基脯氨酰残基的相互作用，晶体结构数据的基础上。吡咯烷环的结构已被修改，以对应于实验确定的五元环的面外起皱的程度。Pro残基之前的肽基团的几何形状也被改变。涉及C（δ）和H（δ）原子的Pro和Hyp的非键相互作用的参数进行了修改。使用修订后的参数提供了改进的计算的最小能量构象的肽含有Pro-Pro和Ala-Pro序列。特别是，它表明，一个α-螺旋状构象的残基前Pro现在只有适度高的能量，因此它是一个可访问的状态。这一结果证实了在球状蛋白质中扭结的α-螺旋中观察到的Pro残基的存在。聚（Gly-Pro-Pro）三螺旋的结构，胶原蛋白结构的计算模型，已被重新计算。这种模型结构的有效性以前的计算已经得到证实。计算的相互作用的细化提供了一个新的通用模型结构，用于未来的计算胶原蛋白样多肽。
Some of the parameters that are used in the computer program ECEPP (Empirical Conformational Energy Program for Peptides) to describe the geometry of amino acid residues and the potential energy of interactions have been updated. The changes are based on recently available experimental information. The most significant changes improve the geometry and the interactions of prolyl and hydroxyprolyl residues, on the basis of crystallographic structural data. The structure of the pyrrolidine ring has been revised to correspond to the experimentally determined extent of out-of-plane puckering of the five-membered ring. The geometry of the peptide group preceding a Pro residue has also been altered. The parameters for nonbonded interactions involving the C(delta) and H(delta) atoms of Pro and Hyp have been modified. Use of the revised parameters provides improvements in the computed minimum-energy conformations of peptides containing the Pro-Pro and Ala-Pro sequences. In particular, it is demonstrated that an alpha-helix-like conformation of a residue preceding Pro is now only of moderately high energy, and thus it is an accessible state. This result corroborates the observed occurrence of Pro residues in kinked alpha-helices in globular proteins. The structure of the poly(Gly-Pro-Pro) triple helix, a computational model for collagen structure, has been recomputed. The validity of previous computations for this model structure has been confirmed. The refinement of the computed interactions has provided a new general model structure to be used for future computations on collagen-like polypeptides.