Machuqueiro Miguel, Baptista António M
Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, Portugal.
Proteins. 2008 Jul;72(1):289-98. doi: 10.1002/prot.21923.
In this work, we present the first application to a protein of the stochastic constant-pH molecular dynamics (MD) method with the inclusion of proton tautomerism. The acidic titration of HEWL was performed under different conditions. Both generalized reaction field (GRF) and particle mesh Ewald (PME) methods were used in the treatment of the long range electrostatics and, even though the PME simulations revealed to be more stable, the better results were obtained using GRF (pK(a) RMSD of 0.82 for GRF and 1.13 for PME). The results using PME at different dielectric constants (2, 4, and 8) also revealed that there was no significant improvement in pK(a)'s prediction upon increasing the dielectric constant. The secondary structure analysis of HEWL revealed a remarkably stable protein in the acidic pH range. The beta-sheet strands (unlike the alpha-helices) seem to be destabilized upon pH decrease, suggesting that the beta-domain is less stable than the alpha-domain. The four principal alpha-helices were also ordered according to their stability in the acidic pH range and the results (4 < 1 < 2 approximately = 3) were consistent with the ones obtained in thermal denaturation studies.
在这项工作中，我们首次将包含质子互变异构的随机恒定pH分子动力学（MD）方法应用于一种蛋白质。在不同条件下对溶菌酶（HEWL）进行了酸性滴定。广义反应场（GRF）和粒子网格埃瓦尔德（PME）方法都用于处理长程静电作用，尽管PME模拟显示更稳定，但使用GRF获得了更好的结果（GRF的pK(a)均方根偏差为0.82，PME为1.13）。在不同介电常数（2、4和8）下使用PME的结果还表明，增加介电常数时，pK(a)预测没有显著改善。溶菌酶的二级结构分析表明，该蛋白质在酸性pH范围内非常稳定。β-折叠链（与α-螺旋不同）似乎在pH降低时不稳定，这表明β结构域比α结构域稳定性更低。四个主要的α-螺旋也根据它们在酸性pH范围内的稳定性进行了排序，结果（4 < 1 < 2 ≈ 3）与热变性研究中获得的结果一致。
