Residue depth: a novel parameter for the analysis of protein structure and stability
Residue depth: a novel parameter for the analysis of protein structure and stability
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DOI：
10.1016/s0969-2126(99)80097-5
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发表时间：
1999-07-15
期刊：
影响因子：
--
通讯作者：
Varadarajan, R
中科院分区：
文献类型：
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作者：
Chakravarty, S;Varadarajan, R
研究背景：可渗透表面积是一个广泛用于蛋白质结构和稳定性分析的参数。然而，可渗透表面积并不能区分蛋白质表面下的原子和蛋白质核心中的原子。为了区分这些埋藏的残基，我们描述了一个计算程序，用于计算残基从蛋白质表面的深度。残基深度与突变对蛋白质稳定性和蛋白质-蛋白质相互作用的影响的相关性显著优于可及性，天然石板中最深的残基总是通过蛋白质的整体展开进行氢交换，并且通常在蛋白质中受到显著保护。结论：深度往往是一个更有用的衡量残留物埋藏比可及性。这可能与蛋白质内部和周围溶剂在极性和堆积密度上显著不同的事实有关。因此，蛋白质中残基之间的货车范德华力和静电相互作用的强度可能取决于残基与蛋白质表面的距离。
Background: 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.Results: 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 slate invariably undergo hydrogen exchange by global unfolding of the protein and are often significantly protected in the corresponding molten-globule states.Conclusions: 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.