Lattman E E, Fiebig K M, Dill K A
Department of Biophysics and Biophysical Chemistry, Johns Hopkins Medical School, Baltimore, Maryland 21205-2185.
Biochemistry. 1994 May 24;33(20):6158-66. doi: 10.1021/bi00186a015.
We propose a model for the conformations of compact denatured states of globular proteins: that they are broad ensembles of chain backbone conformations that involve common localized hydrophobic clustering and helical contacts, depending on the amino acid sequence. We construct representative ensembles for chain lengths up to 136 monomers on three-dimensional cubic lattices using the "hydrophobic zippers" method (Fiebig & Dill, 1993). We find that model conformations with radii of gyration about 20% larger than native conformations commonly have bimodal distributions of P(r), of the pairwise interatomic distances, r, and Kratky plots in agreement with recent small-angle X-ray scattering (Sosnick & Trewhella, 1992; Flanagan et al., 1992; Kataoka et al., 1993; Flanagan et al., 1993) experiments on three different proteins. We also find that the lattice model of the Shortle 1-136 fragment of staphylococcal nuclease does not appear capable of forming a single hydrophobic core by hydrophobic zippering, consistent with experiments.
即它们是链骨架构象的宽泛集合，这些构象涉及常见的局部疏水簇集和螺旋接触，这取决于氨基酸序列。我们使用“疏水拉链”方法（Fiebig和Dill，1993年）在三维立方晶格上构建了链长高达136个单体的代表性集合。我们发现，回转半径比天然构象大约20%的模型构象通常具有成对原子间距离r的P(r)双峰分布以及与最近对三种不同蛋白质进行的小角X射线散射实验（Sosnick和Trewhella，1992年；Flanagan等人，1992年；Kataoka等人，1993年；Flanagan等人，1993年）一致的Kratky图。我们还发现，葡萄球菌核酸酶Shortle 1 - 136片段的晶格模型似乎无法通过疏水拉链形成单个疏水核心，这与实验结果一致。
