Chen Yantao, Ding Jiandong
a State Key Laboratory of Molecular Engineering of Polymers, Shenzhen Key Laboratory of Functional Polymer , College of Chemistry and Chemical Engineering, Shenzhen University , Shenzhen , 518060 , China .
J Biomol Struct Dyn. 2014;32(5):792-803. doi: 10.1080/07391102.2013.791645. Epub 2013 Jun 8.
In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56 Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.
在蛋白质建模中，空间分辨率和计算效率始终相互矛盾。作为一种折衷方案，本研究构建了一种中等分辨率的晶格模型。每个残基被分解为四个基本单元，即α-碳基团、羧基、亚氨基和侧链基团，每个基本粗粒度单元由一个具有八个晶格位点的最小立方盒表示。晶格间距约为0.56 Å，是目前晶格蛋白质模型中最高的空间分辨率。作为该新模型的首次报道，通过动态蒙特卡罗模拟研究了聚丙氨酸链的螺旋-卷曲转变。形成的α-螺旋周期约为3.68个残基，接近天然α-螺旋的周期。结果发现，所得主链运动位于拉氏图中构象空间的实际区域内。通过动态氢键过程和扭转角变化进一步确定了螺旋传播常数和成核常数，并基于钱-谢尔曼关系将结果用于经典齐姆-布拉格理论和利夫森-罗伊格理论之间的比较。模拟结果证实，我们的晶格模型能够重现多肽的螺旋-卷曲转变，并构建适度精细的α-螺旋构象，而不会显著削弱晶格模型在效率方面的优势。
