Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials.
Beta-and gamma-turns in proteins revisited: a new set of amino acid turn-type dependent positional preferences and potentials.
复制标题
重新审视蛋白质中的β-和γ-转角：一组新的氨基酸转角类型依赖的位置偏好和潜力。
作者：
K. Guruprasad;S. Rajkumar
从最近的蛋白质数据库中选择的426种蛋白质三维晶体结构的代表性集合中的β-转角的数量几乎翻了一番，并且自上次分析以来，320种蛋白质的代表性集合中的γ-转角的数量增加了七倍以上。从这些蛋白质中提取的β-转角（7153）和γ-转角（911）用于推导一组经修订的类型依赖性氨基酸位置偏好和电位。与以前的结果相比，对于β-转角，对脯氨酸、甲硫氨酸和色氨酸的偏好增加，而对谷氨酰胺、缬氨酸、谷氨酸和丙氨酸的偏好降低。某些新的氨基酸的偏好，观察两个转角类型和个别氨基酸显示转角类型依赖的位置偏好。新的氨基酸偏好的理由进行了讨论，在光的氢键和其他相互作用涉及的转折。其中对于一些β-转角没有观察到NH（i + 3）-> CO（i）类型的主链氢键，观察到可能稳定这种β-转角的其它主链氢键或溶剂相互作用。还观察到许多在i + 2位置处具有脯氨酸的意想不到的孤立的β-转角。几乎所有的γ-转角都存在NH（i + 2）--> CO（i）氢键。近20%的经典伽马匝和43%的逆伽马匝是孤立匝。
The number of beta-turns in a representative set of 426 protein three-dimensional crystal structures selected from the recent Protein Data Bank has nearly doubled and the number of gamma-turns in a representative set of 320 proteins has increased over seven times since the previous analysis. Beta-turns (7153) and gamma-turns (911) extracted from these proteins were used to derive a revised set of type-dependent amino acid positional preferences and potentials. Compared with previous results, the preference for proline, methionine and tryptophan has increased and the preference for glutamine, valine, glutamic acid and alanine has decreased for beta-turns. Certain new amino acid preferences were observed for both turn types and individual amino acids showed turn-type dependent positional preferences. The rationale for new amino acid preferences are discussed in the light of hydrogen bonds and other interactions involving the turns. Where main-chain hydrogen bonds of the type NH(i + 3) --> CO(i) were not observed for some beta-turns, other main-chain hydrogen bonds or solvent interactions were observed that possibly stabilize such beta-turns. A number of unexpected isolated beta-turns with proline at i + 2 position were also observed. The NH(i + 2) --> CO(i) hydrogen bond was observed for almost all gamma-turns. Nearly 20% classic gamma-turns and 43% inverse gamma-turns are isolated turns.