Smith-Brown M J, Kominos D, Levy R M
Department of Chemistry, Rutgers University, New Brunswick, NJ 08903.
Protein Eng. 1993 Aug;6(6):605-14. doi: 10.1093/protein/6.6.605.
A Monte Carlo method is presented which can obtain the correct tertiary fold of a protein given the secondary structure and as few as three interactions between each secondary structure unit. This method was used to fold hemerythrin, flavodoxin, bovine pancreatic trypsin inhibitor and a variable light domain from an immunoglobulin using the known secondary structures of these proteins. Each of the proteins was successfully folded to obtain a structure resembling the initial X-ray structure. Reasonable success was also achieved when using a secondary structure prediction algorithm to assign secondary structure. The r.m.s. deviations between the folded proteins and the crystal structures are in the order of 3-5 A for the backbone coordinates. Evaluation of the r.m.s. deviations between members of the globin family indicates that two equivalent overall folds may have r.m.s. deviations of this or even larger magnitude. The limiting number of constraints necessary to achieve the correct fold is discussed.
本文提出了一种蒙特卡罗方法，该方法在已知二级结构且每个二级结构单元之间仅有三个相互作用的情况下，能够获得蛋白质正确的三级折叠结构。利用这些蛋白质已知的二级结构，该方法被用于折叠蚯蚓血红蛋白、黄素氧还蛋白、牛胰蛋白酶抑制剂以及免疫球蛋白的可变轻链结构域。每种蛋白质都成功折叠，得到了与初始X射线结构相似的结构。当使用二级结构预测算法来确定二级结构时，也取得了一定的成功。对于主链坐标，折叠后的蛋白质与晶体结构之间的均方根偏差约为3 - 5埃。对球蛋白家族成员之间均方根偏差的评估表明，两个等效的整体折叠结构可能具有这种或更大程度的均方根偏差。文中还讨论了实现正确折叠所需的最少约束数量。
