Ekonomiuk Dariusz, Kielbasinski Marcin, Kolinski Andrzej
Faculty of Chemistry, Warsaw University, Warszawa, Poland.
Acta Biochim Pol. 2005;52(4):741-8. Epub 2005 May 31.
A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon beta-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the beta-sheet.
一种高分辨率的蛋白质简化模型被用于对一种小球状蛋白质——链球菌蛋白G的B1免疫球蛋白结合结构域折叠机制的蒙特卡罗动力学研究。结果表明，为了重现折叠转变的物理过程，基于联合原子的模型需要一组模仿短程构象倾向和类似蛋白质链刚性的基于知识的势、一个定向和协同氢键模型，以及经过适当设计的侧基之间长程相互作用的基于知识的势。该模型蛋白质的折叠是协同且非常快速的。在单个轨迹中，观察到了多个折叠/去折叠循环。通常，折叠过程由C端发夹的类似天然结构的组装启动。在下一阶段，其余的四链β-折叠片层折叠。该途径中最慢的步骤是在β-折叠片层支架上组装中央螺旋。
