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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Mechanisms and kinetics of beta-hairpin formation
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Mechanisms and kinetics of beta-hairpin formation

机译：β-发夹形成的机理和动力学

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Thermodynamics and kinetics of off lattice models with side chains for the beta-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except re folding time Th) there are no qualitetive differences between the full model and the Go version. The validity of the models is established by comparison of the calculated native structure with the Protein Data Bank coordi- nates and by reproducing the experimental results for the degree of cooperativity and TF. For the full model TF ≈ 2 μs at the folding temperature (experimental value is 6 μs): the Go model folds 50 times faster. Upon refolding, structural changes take place over three time scales. On the collapse time scale compact structures with intact hydrophobic duster form. Subsequently, hydrogen bonds form, pre- dominantly originating from the turn by a kinetic zipping mechanism. The assembly of the hairpin is complete when most of the interstrand cont8CtS (the rate-limiting step) is formed. The dominant transition State structure (located by using cluster analysis) is compact and structured. We predict that when hydrophobic cluster is moved to the loop w marginally increases, whereas moving the hydrophobic cluster closer to the termini results in significant decrease in tF relative to wild type. The mechanism of hairpin formation is predicted to depend on turn stiffness.
机译：报道了带有免疫球蛋白结合蛋白及其变体的β-发夹片段侧链的非晶格模型的热力学和动力学。对于所有属性（重新折叠时间Th除外），完整模型和Go版本之间没有本质上的区别。通过将计算出的天然结构与蛋白质数据库的坐标进行比较，并通过再现协同度和TF的实验结果，可以建立模型的有效性。对于折叠温度下的完整模型TF≈2μs（实验值为6μs）：Go模型的折叠速度快50倍。重新折叠后，结构会在三个时间范围内发生变化。在坍塌时间尺度上，具有完整的疏水性喷粉形式的紧凑结构。随后，形成氢键，主要通过动力学拉链机制起源于转弯。当大部分链间竞争蛋白（限速步骤）形成时，发夹的组装就完成了。主导的过渡状态结构（通过使用聚类分析进行定位）是紧凑且结构化的。我们预测，当疏水簇移动到环上时，w会略有增加，而将疏水簇移动到更靠近末端会导致tF相对于野生型显着下降。预计发夹形成的机理取决于转弯刚度。

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