Macdonald Bryanne, McCarley Shannon, Noeen Sundus, van Giessen Alan E
Department of Chemistry, Mount Holyoke College , 50 College Street, South Hadley, Massachusetts 01075, United States.
J Phys Chem B. 2015 Feb 19;119(7):2956-67. doi: 10.1021/jp512630s. Epub 2015 Jan 28.
The dense, heterogeneous cellular environment is known to affect protein stability through interactions with other biomacromolecules. The effect of excluded volume due to these biomolecules, also known as crowding agents, on a protein of interest, or test protein, has long been known to increase the stability of a test protein. Recently, it has been recognized that attractive protein-crowder interactions play an important role. These interactions affect protein stability and can destabilize the test protein. However, most computational work investigating the role of attractive interactions has used spherical crowding agents and has neglected the specific roles of crowding agent hydrophobicity and hydrogen bonding. Here we use multicanonical molecular dynamics and a coarse-grained protein model to study the folding thermodynamics of a small helical test protein in the presence of crowding agents that are themselves proteins. Our results show that the stability of the test protein depends on the hydrophobicity of the crowding agents. For low values of crowding agent hydrophobicity, the excluded volume effect is dominant, and the test protein is stabilized relative to the dilute solution. For intermediate values of the crowding agent hydrophobicity, the test protein is destabilized by favorable side chain-side chain interactions stabilizing the unfolded states. For high values of the crowding agent hydrophobicity, the native state is stabilized by the strong intermolecular attractions, causing the formation of a packed structure that increases the stability of the test protein through favorable side chain-side chain interactions. In addition, increasing crowding agent hydrophobicity increases the "foldability" of the test protein and alters the potential energy landscape by simultaneously deepening the basins corresponding to the folded and unfolded states and increasing the energy barrier between them.
众所周知，密集且异质的细胞环境会通过与其他生物大分子的相互作用影响蛋白质稳定性。这些生物分子（也称为拥挤剂）产生的排阻体积对目标蛋白质（即测试蛋白质）的影响，长期以来被认为会增加测试蛋白质的稳定性。最近，人们认识到蛋白质与拥挤剂之间的吸引相互作用起着重要作用。这些相互作用会影响蛋白质稳定性，并可能使测试蛋白质不稳定。然而，大多数研究吸引相互作用作用的计算工作都使用了球形拥挤剂，而忽略了拥挤剂疏水性和氢键的具体作用。在这里，我们使用多规范分子动力学和粗粒度蛋白质模型来研究一种小螺旋测试蛋白质在存在自身为蛋白质的拥挤剂时的折叠热力学。我们的结果表明，测试蛋白质的稳定性取决于拥挤剂的疏水性。对于低疏水性的拥挤剂，排阻体积效应占主导，测试蛋白质相对于稀溶液更稳定。对于中等疏水性的拥挤剂，测试蛋白质会因稳定未折叠状态的有利侧链 - 侧链相互作用而不稳定。对于高疏水性的拥挤剂，天然状态会因强烈的分子间吸引力而稳定，导致形成紧密堆积结构，通过有利的侧链 - 侧链相互作用增加测试蛋白质的稳定性。此外，增加拥挤剂疏水性会增加测试蛋白质的“可折叠性”，并通过同时加深对应折叠和未折叠状态的势阱以及增加它们之间的能垒来改变势能面。
