Liu Yanxin, Chapagain Prem P, Parra Jose L, Gerstman Bernard S
Department of Physics, Florida International University, University Park, Miami, Florida 33199, USA.
J Chem Phys. 2008 Jan 28;128(4):045106. doi: 10.1063/1.2831513.
The highest level in the hierarchy of protein structure and folding is the formation of protein complexes through protein-protein interactions. We have made modifications to a well established computer lattice model to expand its applicability to two-protein dimerization and aggregation. Based on Brownian dynamics, we implement translation and rotation moves of two peptide chains relative to each other, in addition to the intrachain motions already present in the model. We use this two-chain model to study the folding dynamics of the yeast transcription factor GCN4 leucine zipper. The calculated heat capacity curves agree well with experimental measurements. Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process.
蛋白质结构和折叠层次体系中的最高级别是通过蛋白质-蛋白质相互作用形成蛋白质复合物。我们对一个成熟的计算机晶格模型进行了修改，以扩大其在双蛋白二聚化和聚集方面的适用性。基于布朗动力学，除了模型中已有的链内运动外，我们还实现了两条肽链相对于彼此的平移和旋转运动。我们使用这个双链模型来研究酵母转录因子GCN4亮氨酸拉链的折叠动力学。计算得到的热容曲线与实验测量结果吻合良好。计算了折叠过程的自由能景观和平均首次通过时间，并阐明了实验测量的特征，如二聚化过程的多态性质。
