Noé Frank, Daidone Isabella, Smith Jeremy C, di Nola Alfredo, Amadei Andrea
DFG Research Center Matheon, Free University of Berlin, Arnimallee 6, 14159 Berlin, Germany.
J Phys Chem B. 2008 Sep 4;112(35):11155-63. doi: 10.1021/jp801391t. Epub 2008 Aug 12.
A quantitative understanding of the complex relationship between microscopic structure and the thermodynamics driving peptide and protein folding is a major goal of biophysical chemistry. Here, we present a methodology comprising the use of an extended quasi-Gaussian entropy theory parametrized using molecular dynamics simulation that provides a complete description of the thermodynamics of peptide conformational states. The strategy is applied to analyze the conformational thermodynamics of MR121-GSGSW, a peptide well characterized in experimental studies. The results demonstrate that the extended state of the peptide possesses the lowest partial molar entropy. The origin of this entropy decrease is found to be in the increase of the density and orientational order of the hydration water molecules around the peptide, induced by the "unfolding". While such a reduction of the configurational entropy is usually associated with the hydrophobic effect, it is here found to be mainly due to the interaction of the solute charges with the solvent, that is, electrostriction.
对微观结构与驱动肽和蛋白质折叠的热力学之间复杂关系进行定量理解是生物物理化学的一个主要目标。在此,我们提出一种方法,该方法包括使用通过分子动力学模拟参数化的扩展准高斯熵理论,它能完整描述肽构象状态的热力学。该策略被应用于分析MR121 - GSGSW的构象热力学,这是一种在实验研究中得到充分表征的肽。结果表明,该肽的伸展状态具有最低的偏摩尔熵。发现这种熵降低的起源在于肽周围水化水分子的密度和取向有序性的增加,这是由“展开”诱导的。虽然这种构型熵的降低通常与疏水效应相关,但在此发现主要是由于溶质电荷与溶剂的相互作用,即电致伸缩。