Liwo A, Lee J, Ripoll D R, Pillardy J, Scheraga H A
Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
Proc Natl Acad Sci U S A. 1999 May 11;96(10):5482-5. doi: 10.1073/pnas.96.10.5482.
An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predictions were made, shows that large fragments (61 residues) of both proteins were predicted with rms deviations of 4.2 and 6.0 A for the Calpha atoms, for HDEA and MarA, respectively. This represents 80% and 53% of the observed structures of HDEA and MarA, respectively. Similar rms deviations were obtained for approximately 60-residue fragments of the other three proteins. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence.
一种仅基于寻找合适势能函数全局最小值的方法，已被用于预测五种球状蛋白质的未知结构，这些蛋白质的大小范围为89至140个氨基酸残基。在预测完成后，将其中两种蛋白质（HDEA和MarA）计算得到的最低能量结构与蛋白质数据库发布的晶体结构进行比较，结果表明，对于HDEA和MarA，两种蛋白质的大片段（61个残基）的预测结果中，Cα原子的均方根偏差分别为4.2 Å和6.0 Å。这分别占HDEA和MarA观察到的结构的80%和53%。对于其他三种蛋白质约60个残基的片段，也获得了类似的均方根偏差。这些结果代表了仅基于对给定氨基酸序列的势能函数进行全局优化来预测蛋白质结构的重要一步。
