Kurochkina N, Lee B
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Protein Eng. 1995 May;8(5):437-42. doi: 10.1093/protein/8.5.437.
An approximate but rapid method for estimating hydrophobic energy is proposed. Aside from a scale factor, it is given by the pairwise sum of the surface area buried by each neighbor atom, but excluding those atoms in the same residue or in its sequence neighbor residues. This sum is found to be linearly related to the true buried area as calculated by the algorithm of Lee and Richards [1971, J. Mol. Biol., 55, 379-400], and to the contact potential of Miyazawa and Jernigan [1985, Macromolecules, 18, 534-552]. It correlates with experimental transfer free energies to approximately the same degree as that calculated using the true buried area. Furthermore, in a simple test of helix packing with ROP protein monomer, the new hydrophobic energy clearly discriminated one structure, with the lowest r.m.s. deviation from the crystal structure, against an exhaustive set of others.
提出了一种估算疏水能量的近似但快速的方法。除比例因子外，它由每个相邻原子掩埋的表面积的成对总和给出，但不包括同一残基或其序列相邻残基中的那些原子。发现该总和与通过Lee和Richards [1971，J. Mol. Biol.，55，379 - 400]算法计算的真实掩埋面积以及Miyazawa和Jernigan [1985，Macromolecules，18，534 - 552]的接触势呈线性相关。它与实验转移自由能的相关性与使用真实掩埋面积计算的相关性大致相同。此外，在对ROP蛋白单体进行螺旋堆积的简单测试中，新的疏水能量能够清楚地区分出一种结构，该结构与晶体结构的均方根偏差最小，与其他一系列详尽的结构形成对比。
