Characterization of a linear pentapeptide containing two consecutive beta-turns.

Peptide research Pub Date : 1994-09-01
K Ramnarayan, V N Balaji, K I Varughese
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Abstract

The contiguous occurrence of two beta-turns is examined using molecular mechanics calculations. A tripeptide can take up special conformations known as beta-turns resulting in the reversal of the chain. There are two major classes of beta-turns, called type I beta-turn and type II beta-turn. In the specific case described here, the third peptide unit forms a part of a second turn resulting in the formation of a two-turn motif. In the case of dihydropteridine reductase, this motif is involved in cofactor binding. This study examines the energetic and conformational preferences for chain-reversed motifs. Energy minimizations were carried out on models of pentapeptides with four different sequences for residues 2 through 5: (i) GGGG, (ii) AGGA, (iii) AGAG and (iv) AAAA. For each of the above sequences, all four possible combinations of type I and type II beta-turns were considered. Out of the four possible combinations, the (II, II) combination is the most planar one. The (I, I) combination is the least planar. For the all-Gly model and the all-Ala model, the most favored conformation energetically is a type I-type I combination. On the other hand, the sequence AGGA favors a type II-type I combination, and the sequence AGAG prefers a type II-type II combination. A computer search for double-turn motifs at the Brook-haven Protein Data Bank revealed that the (I, I) combination occurs with the highest frequency, and the (I, II) combination has the next highest frequency.(ABSTRACT TRUNCATED AT 250 WORDS)

一个线性五肽的特性,包含两个连续的-转。
使用分子力学计算检查了连续出现的两个β匝。三肽可以形成一种特殊的构象,称为-旋,从而导致链的反转。有两种主要类型的转体,称为I型转体和II型转体。在这里描述的特定情况下,第三个肽单元形成第二回合的一部分,从而形成双回合基序。在二氢蝶啶还原酶的情况下,该基序参与辅因子结合。本研究考察了链反转基序的能量和构象偏好。对残基2 ~ 5的四种不同序列的五肽模型进行能量最小化:(i) GGGG, (ii) AGGA, (iii) AGAG和(iv) AAAA。对于上述每个序列,考虑了I型和II型β -turn的所有四种可能组合。在四种可能的组合中,(II, II)组合是最平面的组合。(I, I)组合是最小平面。对于全gly模型和全ala模型,能量上最有利的构象是I型- I型组合。另一方面,序列AGGA倾向于II型- I型组合,序列AGAG倾向于II型- II型组合。在Brook-haven蛋白质数据库中对双转基序的计算机搜索显示,(I, I)组合出现的频率最高,(I, II)组合出现的频率次之。(摘要删节250字)
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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