Brylinski Michal, Konieczny Leszek, Roterman Irena
Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland.
Biochimie. 2006 Sep;88(9):1229-39. doi: 10.1016/j.biochi.2006.03.008. Epub 2006 Apr 7.
Hydrophobic collapse is commonly considered as a process of significance for protein folding. Many models have been applied for description of this event. A model introducing an external force field mimicking the hydrophobic environment and simultaneously the driving force for the folding process is presented in this paper. Bovine pancreatic trypsin inhibitor (BPTI) was taken as a test protein. An early-stage folding (in silico) model presented elsewhere was used to create the starting structure for hydrophobic collapse. The resulting structure was energy-refined using molecular dynamics simulation in an explicit solvent. The similarity versus the crystal structure of BPTI is estimated using visual analysis, residue-residue contacts, phi, psi angle distributions, RMSD, accessible solvent area, radii of gyration and hydrodynamic radii. A program allowing creation of early-stage folding structural forms to be created for any protein is available from http://bioinformatics.cm-uj.krakow.pl/earlystage. The program for late-stage folding simulation is available on request.
疏水塌缩通常被认为是蛋白质折叠过程中的一个重要过程。许多模型已被用于描述这一事件。本文提出了一个引入外力场的模型，该外力场模拟疏水环境并同时作为折叠过程的驱动力。牛胰蛋白酶抑制剂（BPTI）被用作测试蛋白。使用在其他地方提出的早期折叠（计算机模拟）模型来创建疏水塌缩的起始结构。通过在显式溶剂中的分子动力学模拟对所得结构进行能量优化。使用可视化分析、残基-残基接触、φ、ψ角分布、均方根偏差（RMSD）、可及溶剂面积、回转半径和流体动力学半径来估计与BPTI晶体结构的相似性。可从http://bioinformatics.cm-uj.krakow.pl/earlystage获取一个允许为任何蛋白质创建早期折叠结构形式的程序。后期折叠模拟程序可根据要求提供。
