Jurkowski W, Brylinski M, Konieczny L, Roterman I
Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland.
J Biomol Struct Dyn. 2004 Oct;22(2):149-58. doi: 10.1080/07391102.2004.10506991.
The conformational sub-space oriented on early-stage protein folding is applied to lysozyme folding. The part of the Ramachandran map distinguished on the basis of a geometrical model of the polypeptide chain limited to the mutual orientation of the peptide bond planes is shown to deliver the initial structure of the polypeptide for the energy minimization procedure in the ab initio model of protein folding prediction. Two forms of energy minimization and molecular dynamics simulation procedures were applied to the assumed early-stage protein folding of lysozyme. One of them included the disulphide bond system and the other excluded it. The post-energy-minimization and post-dynamics structures were compared using RMS-D and non-bonding contact maps to estimate the degree of approach to the native, target structure of the protein molecule obtained using the limited conformational sub-space for the early stage of folding.
将早期蛋白质折叠所定向的构象子空间应用于溶菌酶折叠。基于多肽链的几何模型（限于肽键平面的相互取向）所区分的拉氏图部分，被证明可为蛋白质折叠预测的从头算模型中的能量最小化过程提供多肽的初始结构。两种形式的能量最小化和分子动力学模拟程序被应用于假定的溶菌酶早期蛋白质折叠。其中一种包括二硫键系统，另一种则排除了二硫键系统。使用均方根偏差（RMS-D）和非键接触图比较能量最小化后和动力学后的结构，以估计使用折叠早期有限构象子空间获得的蛋白质分子与天然目标结构的接近程度。
