Quantifying the accessible surface area of protein residues in their local environment
Quantifying the accessible surface area of protein residues in their local environment
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DOI：
10.1093/protein/15.8.659
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发表时间：
2002-08-01
期刊：
影响因子：
--
通讯作者：
Chakrabarti, P
中科院分区：
文献类型：
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作者：
Samanta, U;Bahadur, RP;Chakrabarti, P
蛋白质中残基的堆积和配体与大分子的对接的定量对于理解蛋白质稳定性和药物设计是重要的。接触的原子数（在4.5埃的距离内）可以用来描述残留物的局部环境。随着该数目的增加，残基的可及表面积（阿萨）呈指数下降，并且该变化可以用y = a（1）exp（-x/a（2））形式的指数方程来描述，每个残基具有其自己的一组参数a（1）和a（2），这也取决于是考虑整个残基还是仅考虑侧链。疏水性和亲水性残基可以根据周围原子的平均数和阿萨的变化来区分。对于给定数目的伴侣原子，所观察到的阿萨与从方程获得的预期值的比较提供了一种评估蛋白质结构中残基包装的良好性或其在配体结合中的重要性的方法。该方程提供了一种方法来估计ASA的蛋白质分子和不同残基的平均相对accessories，后者与疏水性值呈负相关。
The quantification of the packing of residues in proteins and docking of ligands to macromolecules is important in understanding protein stability and drug design. The number of atoms in contact (within a distance of 4.5 Angstrom) can be used to describe the local environment of a residue. As this number increases, the accessible surface area (ASA) of the residue decreases exponentially and the variation can be described in terms of an exponential equation of the form y = a(1)exp(-x/a(2)), each residue having its own set of parameters a(1) and a(2), which also depend on whether the whole residue or just the side chain is considered. Hydrophobic and hydrophilic residues can be distinguished on the basis of both the average number of surrounding atoms and the variation of ASA. For a given number of partner atoms, a comparison of the observed ASA with the expected value obtained from the equation provides a method of assessing the goodness of packing of the residue in a protein structure or its importance in the binding of a ligand. The equation provides a method to estimate the ASA of a protein molecule and the average relative accessibilities of different residues, the latter being inversely correlated with hydrophobicity values.