Chakravarty S, Varadarajan R
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Structure. 1999 Jul 15;7(7):723-32. doi: 10.1016/s0969-2126(99)80097-5.
Accessible surface area is a parameter that is widely used in analyses of protein structure and stability. Accessible surface area does not, however, distinguish between atoms just below the protein surface and those in the core of the protein. In order to differentiate between such buried residues we describe a computational procedure for calculating the depth of a residue from the protein surface.
Residue depth correlates significantly better than accessibility with effects of mutations on protein stability and on protein-protein interactions. The deepest residues in the native state invariably undergo hydrogen exchange by global unfolding of the protein and are often significantly protected in the corresponding molten-globule states.
Depth is often a more useful gage of residue burial than accessibility. This is probably related to the fact that the protein interior and surrounding solvent differ significantly in polarity and packing density. Hence, the strengths of van der Waals and electrostatic interactions between residues in a protein might be expected to depend on the distance of the residue(s) from the protein surface.
可及表面积是一个在蛋白质结构与稳定性分析中广泛应用的参数。然而，可及表面积无法区分蛋白质表面下方的原子与蛋白质核心部位的原子。为了区分这类埋藏残基，我们描述了一种计算程序，用于计算残基距蛋白质表面的深度。
与可及性相比，残基深度与突变对蛋白质稳定性及蛋白质-蛋白质相互作用的影响之间的相关性显著更好。天然状态下最深的残基在蛋白质整体展开时总是会发生氢交换，并且在相应的熔球态中通常受到显著保护。
深度通常是比可及性更有用的残基埋藏衡量指标。这可能与蛋白质内部和周围溶剂在极性和堆积密度上存在显著差异这一事实有关。因此，蛋白质中残基之间范德华力和静电相互作用的强度可能取决于残基距蛋白质表面的距离。
