Delineation of a new structural motif involving NHN γ‐turn

Jesmita Dhar, R. Kishore, P. Chakrabarti
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引用次数: 3

Abstract

Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non‐redundant protein chains reveals the existence of a three‐residue, (i − 1) to (i + 1), structural motif, having two hydrogen‐bonded five‐membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side‐chain at (i‐1) and the main‐chain NH of (i + 1). The average backbone torsion angles of −76(±21)° and – 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ‐turn. Indeed, a search of three‐residue fragments with restriction on the terminal Cα···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ‐turn, distinct from the NHO γ‐turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main‐chain atoms. As in the latter, the newly identified γ‐turns are also of two types—classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.
描述一个涉及NHN γ - turn的新结构基序
大分子的特点是氢键的排列方式不同。不同的氢键模式产生了不同而稳定的结构基序。对4114条非冗余蛋白链的分析表明,存在一个三残基(i−1)至(i + 1)结构基序,具有两个氢键五元伪环(第一个是N - H···O C,涉及第一个残基,第二个是N - H∙∙∙N,涉及最后两个残基),由肽键分开。在(i‐1)的侧链和(i + 1)的主链NH之间可能有一个额外的氢键。在i处,骨架的平均扭转角为- 76(±21)°和- 12(±17)°,在多肽链上形成了一个紧密的转折,类似于γ‐转折。事实上,对末端Cα···Cα距离受限的三个残基片段和两侧两个伪环的存在进行了搜索,发现了14846个变体,称为NHN γ - turn,不同于传统上以NHO氢键连接末端主链原子为特征的NHO γ - turn(2032个)。与后者一样,新发现的γ‐匝数也有两种类型——经典匝数和逆匝数,比例为1:6。已经列举了这些旋回中残留物发生的倾向及其次级结构特征。对这些转变的理解将有助于结构预测和循环建模,并可以作为模型来表示蛋白质中的一些未折叠状态或无序区域。
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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