Floriano Wely B, Domont Gilberto B, Nascimento Marco A C
Biological Sciences Department, California State Polytechnic University Pomona, 3801 W Temple Ave, Pomona, California 91768, USA.
J Phys Chem B. 2007 Feb 22;111(7):1893-9. doi: 10.1021/jp066978l. Epub 2007 Jan 30.
We analyzed the correlations between molecular volume, solvent-accessible surface, and folding state (secondary structure content) for unfolded conformers of alpha (holo- and apomyoglobin) and beta (retinal-binding protein) proteins and a small water-soluble alanine-rich alpha-helical peptide. Conformers with different degrees of folding were obtained using molecular dynamics at constant temperature and pressure with implicit solvent (dielectric constant adjustment) for all four systems and with explicit solvent for the single helix peptide. Our results support the view that unfolded conformations are not necessary extended, that volume variation is not a good indication of folding state and that the simple model of water penetrating the interior of the protein does not explain the increase in volume upon unfolding.
我们分析了α（全肌红蛋白和脱辅基肌红蛋白）和β（视网膜结合蛋白）蛋白以及一种富含丙氨酸的水溶性小α螺旋肽的未折叠构象的分子体积、溶剂可及表面积与折叠状态（二级结构含量）之间的相关性。对于所有四个系统，使用恒温恒压下的分子动力学结合隐式溶剂（介电常数调整），对于单螺旋肽则使用显式溶剂，从而获得了不同折叠程度的构象。我们的结果支持以下观点：未折叠构象不一定是伸展的，体积变化不是折叠状态的良好指标，并且水渗透到蛋白质内部的简单模型无法解释未折叠时体积的增加。
