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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Energy-based de novo protein folding by conformational space annealing and an off lattice united-residlle force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K
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Energy-based de novo protein folding by conformational space annealing and an off lattice united-residlle force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K

机译：构象空间退火和离格联合残余力场基于能量的从头蛋白质折叠：在葡萄球菌蛋白A的10-55片段和载脂蛋白calbindin D9K中的应用

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摘要

The conformational space annealing (CSA) method for global optimization has been applied to thc 10-55 fragment of the B-domain of staphylococcal protein A (protein A) and to a 75-residue protein, apo calbindin D9K (PDB ID code 1CLB), by using the UNRES off lattice united-residue force field. Although the potential was not calibrated with these two proteins, the native-like structures were found among the low-energy conformations, without the use of threading or secondary-structure predictiolls. This is because the CSA method can find many distinct families of low-energy conformations. Starting from random conformations, the CSA method found that there are two families of low-energy conformations for each of the two proteins, the native-like fold and its mirror image. Thc CSA method converged to the same low-energy folds in all cases studied, as opposed to other optimization methods. 1t appears that the CSA method with the UNRES force field, which is based on the thermodynamic hypothesis, can be used in prediction of protein structures in real time.
机译：全局优化的构象空间退火（CSA）方法已应用于葡萄球菌蛋白A（蛋白A）B结构域的10-55片段和75残基蛋白载脂蛋白Calbindin D9K（PDB ID码1CLB） ，通过使用UNRES离格联合残余力场。尽管未用这两种蛋白校准其潜力，但在低能构象中发现了天然样结构，而不使用穿线或二级结构预测。这是因为CSA方法可以找到许多不同的低能构象族。从随机构象开始，CSA方法发现两种蛋白质中的每一种都有两个低能构象家族，即天然折叠和其镜像。与其他优化方法相反，在所有研究的情况下，CSA方法都收敛到相同的低能倍数。从图1t可以看出，基于热力学假设的具有UNRES力场的CSA方法可用于实时预测蛋白质结构。

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