Department of Chemistry, Texas A&M University, P.O. Box 3012, College Station, Texas 77842, USA.
J Phys Chem B. 2010 Sep 16;114(36):11820-6. doi: 10.1021/jp103770y.
Following the studies of urea denaturation of β-hairpins using molecular dynamics, in this paper, molecular dynamics simulations of two peptides, a 35 residue three helix bundle villin headpiece protein HP-35 and its doubly norleucine-substituent mutant (Lys24Nle/Lys29Nle) HP-35 NleNle, were undertaken in urea solutions to understand the molecular mechanism of urea denaturation of α-helices. The mutant HP-35 NleNle was found to denature more easily than the wild type. During the expansion of the small hydrophobic core, water penetration occurs first, followed by that of urea molecules. It was also found that the initial hydration of the peptide backbone is achieved through water hydrogen bonding with the backbone CO groups during the denaturation of both polypeptides. The mutation of the two charged lysine residues to apolar norleucine enhances the accumulation of urea near the hydrophobic core and facilitates the denaturation process. Urea also interacts directly with the peptide backbone as well as side chains, thereby stabilizing nonnative conformations. The mechanism revealed here is consistent with the previous study on secondary structure of β-hairpin polypeptide, GB1, PEPTIDE 1, and TRPZIP4, suggesting that there is a general mechanism in the denaturation of protein backbone hydrogen bonds by urea.
在使用分子动力学研究 β-发夹的尿素变性之后，本文在尿素溶液中对两个肽进行了分子动力学模拟，一个是 35 个残基三螺旋束绒毛蛋白 HP-35 及其双正亮氨酸取代突变体（Lys24Nle/Lys29Nle）HP-35 NleNle，以了解 α-螺旋的尿素变性的分子机制。发现突变体 HP-35 NleNle 比野生型更容易变性。在小疏水核扩张过程中，首先发生水渗透，然后是尿素分子渗透。还发现，在两种多肽的变性过程中，肽主链的初始水合作用是通过与主链 CO 基团的水氢键实现的。将两个带电荷的赖氨酸残基突变为非极性正亮氨酸增强了疏水核附近脲的积累并促进了变性过程。尿素还与肽主链以及侧链直接相互作用，从而稳定非天然构象。这里揭示的机制与以前对β-发夹多肽、GB1、PEPTIDE1 和 TRPZIP4 的二级结构的研究一致，表明尿素使蛋白质主链氢键变性存在普遍机制。
