Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, T_m, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the “coordination shell volume,” also shows a direct correlation with T_m. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.

中文翻译：

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对亲环蛋白 40 的 TPR 结构域中的位点突变进行分子动力学模拟，识别具有不同动态和酶学特性的构象状态


亲环蛋白 40 (Cyp40) 是亲免蛋白家族的成员，充当肽基脯氨酰异构酶并与热休克蛋白 90 (Hsp90) 结合。其结构包含 N 端亲环蛋白结构域和 C 端四三肽 (TPR) 结构域。 Cyp40 在前列腺癌和某些 T 细胞淋巴瘤中过度表达。 TPR 结构域上用于 Hsp90 结合的凹槽包括残基 Lys227 和 Lys308，称为羧酸钳，对于 Cyp40-Hsp90 结合至关重要。在本研究中，通过在显式溶剂中进行总共 5.76 μs的全原子分子动力学 (MD) 模拟，研究了两种突变 K227A 和 K308A 及其组合突变体的影响。除 K308A 突变体外，所有模拟均采用由不同亲环蛋白-TPR 域间距离定义的两种不同（扩展或紧凑）构象异构体。 K308A突变体仅以在Cyp40 X射线结构中观察到的延伸形式被观察到。野生型、K227A 和组合突变体也显示出双峰分布。突变体的实验熔解温度T _m值与K308A延伸突变体的致密程度相关，K308A延伸突变体具有稍微较低的熔解温度。根据 MD 数据确定的另一种新颖的致密性测量方法“配位壳体积”也显示出与 T _{m 的}直接相关性。此外，MD 模拟显示，远程 TPR 结构域中的突变具有变构效应，对酶促亲环蛋白结构域的分子运动具有显着影响，这有助于合理化实验观察到的所有三种突变测量的酶活性增加。