pH replica-exchange method based on discrete protonation states.
pH replica-exchange method based on discrete protonation states.
复制标题
DOI：
10.1002/prot.23176
复制
发表时间：
2011-12
影响因子：
2.9
通讯作者：
Brooks, Bernard R.
中科院分区：
文献类型：
--
作者：
Itoh, Satoru G.;Damjanovic, Ana;Brooks, Bernard R.
提出了一种新的可电离残基质子滴定曲线的算法。该算法是pH复制交换法（PHREM），它是基于Mongan等人的恒定pH算法。在原始的副本交换方法中，在不同的温度下对不同的副本进行模拟，并且在副本之间交换温度。在我们的pH复制交换方法中，在不同的pH值下进行不同复制品的模拟，并且在复制品之间交换pH。PHREM被施加到一个封闭的氨基酸和两个蛋白质系统（蛇卵毒素和土耳其卵类粘蛋白第三域），结合广义玻恩隐式溶剂。将该算法与原有的恒pH法（PHMD）进行了性能和精度的比较。对于在不同pH下的单组模拟，使用PHREM产生更准确的可滴定残基的希尔系数。通过执行多组从不同初始状态开始的恒定pH值模拟，预测的pKa值和用PHREM和PHMD方法获得的希尔系数的准确度变得相当。然而，PHREM算法表现出更好的采样的质子化状态的可滴定的残基和更少的分散的滴定点，从而更好的精度测量的pKa值和希尔系数。此外，PHREM表现出更快的收敛速度比原来的恒定pH值算法的个人模拟。
We propose a new algorithm for obtaining proton titration curves of ionizable residues. The algorithm is a pH replica-exchange method (PHREM) which is based on the constant pH algorithm of Mongan et al.. In the original replica-exchange method, simulations of different replicas are performed at different temperature, and the temperatures are exchanged between the replicas. In our pH replica-exchange method, simulations of different replicas are performed at different pH values, and the pHs are exchanged between the replicas. The PHREM was applied to a blocked amino acid and to two protein systems (Snake Cardiotoxin and Turkey Ovomucoid Third Domain), in conjunction with a generalized Born implicit solvent. The performance and accuracy of this algorithm and the original constant pH method (PHMD) were compared. For a single set of simulations at different pHs, the use of PHREM yields more accurate Hill coefficients of titratable residues. By performing multiple sets of constant pH simulations started with different initial states the accuracy of predicted pKa values and Hill coefficients obtained with PHREM and PHMD methods becomes comparable. However, the PHREM algorithm exhibits better samplings of the protonation states of titratable residues and less scatter of the titration points and thus better precision of measured pKa values and Hill coefficients. In addition, PHREM exhibits faster convergence of individual simulations than the original constant pH algorithm.
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影响因子：
2.9
作者：
BASHFORD, D;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
2.9
作者：
Antosiewicz, J;McCammon, JA;Gilson, MK
通讯作者：
Gilson, MK
DOI：
10.1016/s0168-9002(97)00048-x
发表时间：
1997-04-11
影响因子：
1.4
作者：
Brun, R;Rademakers, F
通讯作者：
Rademakers, F
影响因子：
2.4
作者：
GRUBMULLER, H
通讯作者：
GRUBMULLER, H
影响因子：
4.4
作者：
Börjesson, U;Hünenberger, PH
通讯作者：
Hünenberger, PH