Computational identification of slow conformational fluctuations in proteins.
Computational identification of slow conformational fluctuations in proteins.
复制标题
蛋白质缓慢构象波动的计算鉴定。
DOI：
10.1021/jp9077213
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Agarwal,PratulK
中科院分区：
文献类型：
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作者：
Ramanathan,Arvind;Agarwal,PratulK
蛋白质的构象灵活性与其指定的功能有关。特别是在微秒到毫秒时间尺度上发生的缓慢构象波动最近引起了人们对酶催化机制的极大兴趣。计算方法为蛋白质结构、灵活性和功能之间的联系提供了有价值的见解。在本报告中，我们基于准谐波分析（QHA）和正态模式分析（NMA）介绍了泛素微秒灵活性的识别和表征研究。结果表明，从 0.5 μs 分子动力学系综计算得出的最慢 10 个 QHA 模式贡献了所有运动的 78% 以上。所识别的缓慢运动与核磁共振系综中观察到的构象波动有超过 75% 的相似性，也与 X 射线结构组中的位移一致。最慢的模式在 β1−β2、α1−β3 和 β3−β4 环区域显示出高度灵活性，对结合其他蛋白质的机制具有功能影响。泛素结构的 NMA 无法重现长时间尺度的波动，因为它们被发现强烈依赖于参考结构。此外，基于沿反应途径采样的构象的 QHA，还鉴定并表征了与亲环蛋白 A (CypA) 酶催化的顺式/反式异构化反应耦合的构象波动，这些波动发生在微秒至毫秒的时间尺度。结果表明，QHA 覆盖了与实验观察到的 CypA 灵活性相同的构象景观。总的来说，泛素和 CypA 中发现的缓慢构象波动表明这些蛋白质的内在灵活性与其指定的功能密切相关。
Conformational flexibility of proteins has been linked to their designated functions. Slow conformational fluctuations occurring at the microsecond to millisecond time scale, in particular, have recently attracted considerable interest in connection to the mechanism of enzyme catalysis. Computational methods are providing valuable insights into the connection between protein structure, flexibility, and function. In this report, we present studies on identification and characterization of microsecond flexibility of ubiquitin, based on quasi-harmonic analysis (QHA) and normal-mode analysis (NMA). The results indicate that the slowest 10 QHA modes, computed from the 0.5 μs molecular dynamics ensemble, contribute over 78% of all motions. The identified slow movements show over 75% similarity with the conformational fluctuations observed in nuclear magnetic resonance ensemble and also agree with displacements in the set of X-ray structures. The slowest modes show high flexibility in the β1−β2, α1−β3, and β3−β4 loop regions, with functional implications in the mechanism of binding other proteins. NMA of ubiquitin structures was not able to reproduce the long time scale fluctuations, as they were found to strongly depend on the reference structures. Further, conformational fluctuations coupled to thecis/transisomerization reaction catalyzed by the enzyme cyclophilin A (CypA), occurring at the microsecond to millisecond time scale, have also been identified and characterized on the basis of QHA of conformations sampled along the reaction pathway. The results indicate that QHA covers the same conformational landscape as the experimentally observed CypA flexibility. Overall, the identified slow conformational fluctuations in ubiquitin and CypA indicate that the intrinsic flexibility of these proteins is closely linked to their designated functions.