Vieth M, Kolinski A, Brooks C L, Skolnick J
Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037.
J Mol Biol. 1994 Apr 8;237(4):361-7. doi: 10.1006/jmbi.1994.1239.
A hierarchical approach is described for the prediction of the three-dimensional structure and folding pathway of the GCN4 leucine zipper. Dimer assembly is simulated by Monte Carlo dynamics. The resulting lowest energy structures undergo cooperative rearrangement of their hydrophobic core leading to side-chain fixation. The coarse-grained structures are further refined using a molecular dynamics annealing protocol. This produces full atom models with a backbone root-mean-square deviation from the crystal structure of 0.81 A. Thus, we demonstrate the predictive ability of our approach to yield high resolution structures of small coiled coils from their sequence.
本文描述了一种用于预测GCN4亮氨酸拉链三维结构和折叠途径的分层方法。通过蒙特卡罗动力学模拟二聚体组装。由此产生的最低能量结构经历其疏水核心的协同重排，导致侧链固定。使用分子动力学退火协议进一步细化粗粒度结构。这产生了与晶体结构的主链均方根偏差为0.81 Å的全原子模型。因此，我们证明了我们的方法从序列中产生小卷曲螺旋高分辨率结构的预测能力。
