The determinants of pK(a)s in proteins
The determinants of pK(a)s in proteins
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DOI：
10.1021/bi9601565
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发表时间：
1996-06-18
期刊：
影响因子：
2.9
通讯作者：
Gilson, MK
中科院分区：
文献类型：
--
作者：
Antosiewicz, J;McCammon, JA;Gilson, MK
虽然验证研究表明，预测蛋白质中可电离基团pK（a）s的理论模型越来越准确，但仍存在一些重要问题：（1）哪些因素限制了当前模型的准确性？(2)如何才能最好地解释蛋白质的构象灵活性？(3)在计算中使用溶液结构，而不是晶体结构，是否会提高计算的pK（a）s的准确性？以及（4）为什么蛋白质pK（a）s的精确预测似乎要求蛋白质内部具有高介电常数？本文件讨论这些问题和相关问题。结果表明：（1）在NMR结构集上计算的pK（a）s平均值比基于单晶结构的pK（a）s平均值更精确;（2）当蛋白质介电常数较低时，采用优化的原子参数重现小分子的水化能，提高了与实验的一致性;（3）尽管使用了NMR结构和优化的原子参数，但用蛋白质介电常数为20计算的pK（a）s比用低蛋白质介电常数计算的pK（a）s更准确;（4）核糖核酸酶A中磷酸结合引起的pK（a）位移通过计算得到了合理的再现：（5）在火鸡卵类粘蛋白第三结构域中观察到的大量pK（a）位移主要是由电离基团之间的相互作用引起的;（6）实验数据和计算都表明，蛋白质有降低Asp侧链pK（a）s的趋势，但对其它可电离基团的pK（a）s总体影响不大。
Although validation studies show that theoretical models for predicting the pK(a)s of ionizable groups in proteins are increasingly accurate, a number of important questions remain: (1) What factors limit the accuracy of current models? (2) How can conformational flexibility of proteins best be accounted for? (3) Will use of solution structures in the calculations, rather than crystal structures, improve the accuracy of the computed pK(a)s? and (4) Why does accurate prediction of protein pK(a)s seem to require that a high dielectric constant be assigned to the protein interior? This paper addresses these and related issues. Among the conclusions are the following: (1) computed pK(a)s averaged over NMR structure sets are more accurate than those based upon single crystal structures; (2) use of atomic parameters optimized to reproduce hydration energies of small molecules improves agreement with experiment when a low protein dielectric constant is assumed; (3) despite use of NMR structures and optimized atomic parameters, pK(a)s computed with a protein dielectric constant of 20 are more accurate than those computed with a low protein dielectric constant; (4) the pK(a) shifts in ribonuclease A that result from phosphate binding are reproduced reasonably well by calculations; (5) the substantial pK(a) shifts observed in turkey ovomucoid third domain result largely from interactions among ionized groups; and (6) both experimental data and calculations indicate that proteins tend to lower the pK(a)s of Asp side chains but have little overall effect upon the pK(a)s of other ionizable groups.