Department of Chemistry, Stanford University, Stanford, California 94305, USA.
J Chem Phys. 2017 Sep 14;147(10):104107. doi: 10.1063/1.4993207.
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.
β发夹是蛋白质中发现的亚结构，可以深入了解更复杂的系统。此外，β发夹的折叠是实验和理论方法基准测试的一个有价值的案例。在这里，我们使用一系列最先进的蛋白质力场来模拟实验熔化温度下具有β发夹结构的 CLN025 小蛋白的折叠。我们构建了马尔可夫状态模型，以研究折叠的热力学、动力学、机制和速率决定步骤。从机制上讲，我们发现折叠过程受到转角区域氢键形成的限制，这发生在伸展变性蛋白的疏水塌陷之后。这些结果是在已建立的和矛盾的β发夹折叠过程理论的背景下提出的。此外，我们的分析表明，在该温度下，AMBER-FB15 力场最能描述完整实验 CLN025 构象总体的特征，而 AMBER ff99SB-ILDN 和 CHARMM22* 力场则显示出过度稳定天然状态的趋势。
