PREDICTION OF PH-DEPENDENT PROPERTIES OF PROTEINS
PREDICTION OF PH-DEPENDENT PROPERTIES OF PROTEINS
复制标题
DOI：
10.1006/jmbi.1994.1301
复制
发表时间：
1994-05-06
影响因子：
5.6
通讯作者：
GILSON, MK
中科院分区：
文献类型：
--
作者：
ANTOSIEWICZ, J;MCCAMMON, JA;GILSON, MK
我们描述了什么可能是最准确的方法，目前可用于计算蛋白质中的电离基团的pKas。通过比较计算的pKas与总共7种蛋白质中60个测量的pKas来评估准确度。总均方根误差为0·89 pKa单位。线性回归分析的计算与测量pKas产生的斜率为0·95，y轴截距？0.02，相关系数为0.96。所提出的方法还挑选出许多移动的PKAs的基团在酶活性位点和特殊的盐桥。然而，它确实产生了几个过度偏移的pKa，并且倾向于低估由去溶剂化效应引起的pKa偏移。我们研究的能力，新的方法来重现蛋白质的稳定性依赖于pH值，使用电离多项式形式主义。稳定性曲线的总体特征被再现，但定量一致性不是特别好。产生分歧的原因可能与理论的准确性不足和蛋白质未折叠状态的性质的不确定性有关。这里描述的方法是基于有限差分解决方案的泊松？玻尔兹曼方程它的成功取决于使用相当高的蛋白质介电常数20。然而，理论上的考虑和由于去溶剂化而导致的pKa位移在这里被低估的事实意味着蛋白质内部的介电常数实际上低于20。我们建议，高蛋白质介电常数提高了与实验的总体一致性，因为它占了大约的现象，往往会减轻pKa的变化，并没有具体包括在模型中。这些包括构象弛豫和特异性离子结合。未来的模型基于低蛋白质介电常数，并明确处理这种现象，可能会产生更好的协议与实验。
We describe what may be the most accurate approach currently available for the calculation of the pKas of ionizable groups in proteins. The accuracy is assessed by comparison of computed pKas with 60 measured pKas in a total of seven proteins. The overall root-mean-square error is 0·89 pKa units. Linear regression analysis of computedversusmeasured pKas yields a slope of 0·95,y-intercept of ?0·02 and a correlation coefficient of 0·96. The proposed approach also picks out many of the shifted pKas of groups in enzyme active sites and special salt bridges. However, it does yield several over-shifted pKas and tends to underestimate pKa shifts which result from desolvation effects. We examine the ability of the new approach to reproduce the dependence of protein stability upon Ph, using the ionization polynomial formalism. Overall features of the stability curves are reproduced, but the quantitative agreement is not particularly good. The reasons for the disagreement may have to do both with insufficient accuracy in the theory and with uncertainty in the nature of the unfolded state of proteins. The methodology described here is based upon finite difference solutions of the Poisson?Boltzmann equation. Its success depend upon the use of the rather high protein dielectric constant of 20. However, theoretical considerations and the fact that pKa shifts which result from desolvation are underestimated here imply that the dielectric constant of the protein interior actually is lower than 20. We suggest that the high protein dielectric constant improves the overall agreement with experiment because it accounts approximately for phenomena which tend to mitigate pKa shifts and which are not specifically included in the model. These include conformational relaxation and specific ion-binding. Future models based upon a low protein dielectric constant and treating such phenomena explicitly might yield improved agreement with experiment.