Beta-hairpins are substructures found in proteins that can lend insight into more complex systems. Furthermore, the folding of beta-hairpins is a valuable test case for benchmarking experimental and theoretical methods. Here, we simulate the folding of CLN025, a miniprotein with a beta-hairpin structure, at its experimental melting temperature using a range of state-of-the-art protein force fields. We construct Markov state models in order to examine the thermodynamics, kinetics, mechanism, and rate-determining step of folding. Mechanistically, we find the folding process is rate-limited by the formation of the turn region hydrogen bonds, which occurs following the downhill hydrophobic collapse of the extended denatured protein. These results are presented in the context of established and contradictory theories of the beta-hairpin folding process. Furthermore, our analysis suggests that the AMBER-FB15 force field, at this temperature, best describes the characteristics of the full experimental CLN025 conformational ensemble, while the AMBER ff99SB-ILDN and CHARMM22* force fields display a tendency to overstabilize the native state.

中文翻译：

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CLN025 β-发夹形成机制的建模

β-发夹是蛋白质中发现的子结构，可以帮助我们深入了解更复杂的系统。此外，β-发夹的折叠对于基准实验和理论方法来说是一个有价值的测试用例。在这里，我们使用一系列最先进的蛋白质力场模拟了 CLN025（一种具有 β 发夹结构的微型蛋白）在其实验熔解温度下的折叠。我们构建马尔可夫状态模型来研究折叠的热力学、动力学、机制和速率决定步骤。从机制上讲，我们发现折叠过程的速率受到转向区氢键形成的限制，这种氢键是在延伸的变性蛋白质的下坡疏水性塌陷之后发生的。这些结果是在 β-发夹折叠过程的既定且相互矛盾的理论背景下提出的。此外，我们的分析表明，在此温度下，AMBER-FB15 力场最能描述完整实验 CLN025 构象系综的特征，而 AMBER ff99SB-ILDN 和 CHARMM22* 力场显示出过度稳定自然状态的趋势。