Conformational Entropy as Collective Variable for Proteins,The Journal of Physical Chemistry Letters

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Conformational Entropy as Collective Variable for Proteins
The Journal of Physical Chemistry Letters ( IF 4.8 ) Pub Date : 2017-09-18 00:00:00 , DOI: 10.1021/acs.jpclett.7b01770
Ferruccio Palazzesi _{1,

2} , Omar Valsson _{1,

2,

3} , Michele Parrinello _{1,

2,

3}

Affiliation

Many enhanced sampling methods rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate descriptors has proven challenging. Here we suggest that the NMR S² order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between S² and conformational entropy. Using the S² order parameter and a surrogate for the protein enthalpy in conjunction with metadynamics or variationally enhanced sampling, we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. We also use S² in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.

中文翻译：

构象熵作为蛋白质的集体变量

许多增强的采样方法依赖于适当的集体变量的标识。对于蛋白质，即使是很小的蛋白质，找到合适的描述子也被证明具有挑战性。在这里，我们建议可以将NMR S ²阶参数用于此效果。我们将此陈述的有效性追溯到S ²与构象熵之间的建议关系。使用S ²阶参数和蛋白质焓的替代物，并结合代谢动力学或变分增强的采样，我们能够可逆地折叠和展开小蛋白质，并以无偏模拟所需时间的一小部分来吸收其自由能。我们也用S ²结合自由能驱油法来计算该肽的解折叠速率。我们在不同温度下重复此计算以获得展开的活化能。

更新日期：2017-09-18

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