Measures of residue density in protein structures
Measures of residue density in protein structures
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DOI：
10.1073/pnas.96.22.12494
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发表时间：
1999-10-26
影响因子：
11.1
通讯作者：
Karlin, S
中科院分区：
文献类型：
--
作者：
Baud, F;Karlin, S
的层次结构的残留物密度评估和蛋白质结构中的包装性能进行了对比，包括常规密度，各种电荷密度，疏水密度，极性密度，和芳香密度。这些密度的调查替代的距离措施，也在多单元结构的界面。氨基酸根据三种二级结构状态和三种溶剂可及性水平分为九种结构类别。考虑到蛋白质结构中氨基酸丰度的差异，我们通过定义密度指数的预期密度将观察到的密度归一化。溶剂可及性水平在常规残基密度的测定中发挥主要影响。解释性地，规则密度值相对于溶剂可及性水平近似线性地变化，线性参数取决于氨基酸。电荷指数揭示了赖氨酸和精氨酸与酸性残基相互作用的显着不平等。所有结构类别中的芳香族密度计算与常规密度计算平行，表明芳香族残基作为所有残基的随机样本分布。此外，发现芳香族残基在所有氨基酸的邻近区域中过度存在。这一结果可能归因于成核位点和蛋白质稳定性基本上与芳香残基相关。
A hierarchy of residue density assessments and packing properties in protein structures are contrasted, including a regular density, a variety of charge densities, a hydrophobic density, a polar density, and an aromatic density. These densities are investigated by alternative distance measures and also at the interface of multiunit structures. Amino acids are divided into nine structural categories according to three secondary structure states and three solvent accessibility levels. To take account of amino acid abundance differences across protein structures, we normalize the observed density by the expected density defining a density index Solvent accessibility levels exert the predominant influence in determinations of the regular residue density. Explicitly, the regular density values vary approximately linearly with respect to solvent accessibility levels, the linearity parameters depending on the amino acid. The charge index reveals pronounced inequalities between lysine and arginine in their interactions with acidic residues. The aromatic density calculations in all structural categories parallel the regular density calculations, indicating that the aromatic residues are distributed as a random sample of all residues. Moreover, aromatic residues are found to be over-represented in the neighborhood of all amino acids. This result might be attributed to nucleation sites and protein stability being substantially associated with aromatic residues.