Beardsley D S, Kauzmann W J
Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06510, USA.
Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4448-53. doi: 10.1073/pnas.93.9.4448.
We have investigated the efficiency of packing by calculating intramolecular packing density above and below peptide planes of internal beta-pleated sheet residues in five globular proteins. The orientation of interest was chosen to allow study of regions that are approximately perpendicular to the faces of beta-pleated sheets. In these locations, nonbonded van der Waals packing interactions predominate over hydrogen bonding and solvent interactions. We observed considerable variability in packing densities within these regions, confirming that the interior packing of a protein does not result in uniform occupation of the available space. Patterns of fluctuation in packing density suggest that the regular backbone-to-backbone network of hydrogen bonds is not likely to be interrupted to maximize van der Waals interactions. However, high-density packing tends to occur toward the ends of beta-structure strands where hydrogen bonds are more likely to involve nonpolar side-chain groups or solvent molecules. These features result in internal protein folding with a central low-density core surrounded by a higher-density subsurface shell, consistent with our previous calculations regarding overall protein packing density.
我们通过计算五种球状蛋白质内部β-折叠片层残基肽平面上下的分子内堆积密度，研究了堆积效率。选择感兴趣的方向以便研究与β-折叠片层表面大致垂直的区域。在这些位置，非键合范德华堆积相互作用比氢键和溶剂相互作用更为突出。我们观察到这些区域内堆积密度存在相当大的变异性，证实蛋白质的内部堆积不会导致对可用空间的均匀占据。堆积密度的波动模式表明，规则的主链间氢键网络不太可能被打断以最大化范德华相互作用。然而，高密度堆积倾向于出现在β-结构链的末端，在那里氢键更可能涉及非极性侧链基团或溶剂分子。这些特征导致蛋白质内部折叠形成一个中心低密度核心，周围是一个较高密度的次表面壳层，这与我们之前关于整体蛋白质堆积密度的计算结果一致。
