The role of hydrophobic microenvironments in modulating pKa shifts in proteins
The role of hydrophobic microenvironments in modulating pKa shifts in proteins
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DOI：
10.1002/prot.10153
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发表时间：
2002-08-01
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影响因子：
--
通讯作者：
Garcia-Moreno, EB
中科院分区：
文献类型：
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作者：
Mehler, EL;Fuxreiter, M;Garcia-Moreno, EB
基于Rekker提出的疏水片段常数，结合对可滴定基团周围微环境的定量描述，应用屏蔽库仑势（SCP）方法计算了蛋白质中嵌入在极疏水微环境中的基团的pK（a）值。这种类型的微环境并不常见，但构成了一个小类，其中蛋白质的结构已经进化为嵌入的残基提供了特殊的性质。它们是重要的兴趣，因为它们在催化和质子和电子转移反应中经常是重要的。在SCP处理中，这些特殊情况被局部处理，因此不会影响在疏水性较低的环境中计算的其他残基的pK（a）值的准确度。在这里，该算法的校准扩展与早期的结果从溶菌酶和葡萄球菌核酸酶（SNase）的三个突变体的帮助下，专门设计用于测量的可滴定基团的电离能量埋在极端疏水的微环境。校准的算法随后被应用到SNase的第四突变体，然后到一个非常大的二聚胺氧化酶的1284个残基，其中334是可滴定的。所观察到的pK（a）移位的掩埋残基是大的（高达4.7 pK单位），所有的情况下都很好地再现了计算的均方根误差为0.22。这些结果支持的假设，蛋白质静电只能正确地描述和自我一致，如果这些系统的固有异质性是适当的。(C)2002 Wiley-Liss，Inc.
The screened Coulomb potential (SCP) method, combined with a quantitative description of the microenvironments around titratable groups, based on the Hydrophobic Fragmental Constants developed by Rekker, has been applied to calculate the pK(a) values of groups embedded in extremely hydrophobic microenvironments in proteins. This type of microenvironment is not common; but constitutes a small class, where the protein's architecture has evolved to lend special properties to the embedded residue. They are of significant interest because they are frequently important in catalysis and in proton and electron transfer reactions. In the SCP treatment these special cases are treated locally and therefore do not affect the accuracy of the pK(a) values calculated for other residues in less hydrophobic environments. Here the calibration of the algorithm is extended with the help of earlier results from lysozyme and of three mutants of staphylococcal nuclease (SNase) that were specially designed to measure the energetics of ionization of titratable groups buried in extremely hydrophobic microenvironments. The calibrated algorithm was subsequently applied to a fourth mutant of SNase and then to a very large dimeric amine oxidase of 1284 residues, where 334 are titratable. The observed pK(a) shifts of the buried residues are large (up to 4.7 pK units), and all cases are well reproduced by the calculations with a root mean square error of 0.22. These results support the hypothesis that protein electrostatics can only be described correctly and self-consistently if the inherent heterogeneity of these systems is properly accounted for. (C) 2002 Wiley-Liss, Inc.