Haliloglu Turkan, Kolinski Andrzej, Skolnick Jeffrey
Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek 80815, Istanbul, Turkey.
Biopolymers. 2003 Dec;70(4):548-62. doi: 10.1002/bip.10511.
NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, are used as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints are applied using a recently developed SICHO (SIde-CHain-Only) lattice protein model that employs a replica exchange Monte Carlo (MC) algorithm to search conformational space. Using a small number of RDC restraints, the quality of the predicted structures is improved as reflected by lower RMSD/dRMSD (root mean square deviation/distance root mean square deviation) values from the corresponding native structures and by the higher correlation of the most cooperative mode of motion of each predicted structure with that of the native structure. The latter, in particular, has possible implications for the structure-based functional analysis of predicted structures.
核磁共振剩余偶极耦合（RDCs），以各原子核间键向量之间的投影角度形式，被用作六个蛋白质测试集从头结构预测中的结构约束。这些约束通过最近开发的SICHO（仅侧链）晶格蛋白质模型应用，该模型采用复制交换蒙特卡罗（MC）算法搜索构象空间。使用少量的RDC约束，预测结构的质量得到了改善，这体现在与相应天然结构相比更低的RMSD/dRMSD（均方根偏差/距离均方根偏差）值，以及每个预测结构最协同运动模式与天然结构的更高相关性上。特别是后者，对预测结构基于结构的功能分析可能具有重要意义。
