Nielsen Jens Erik, McCammon J Andrew
Departments of Pharmacology, Chemistry, and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
Protein Sci. 2003 Sep;12(9):1894-901. doi: 10.1110/ps.03114903.
The ionization properties of the active-site residues in enzymes are of considerable interest in the study of the catalytic mechanisms of enzymes. Knowledge of these ionization constants (pKa values) often allows the researcher to identify the proton donor and the catalytic nucleophile in the reaction mechanism of the enzyme. Estimates of protein residue pKa values can be obtained by applying pKa calculation algorithms to protein X-ray structures. We show that pKa values accurate enough for identifying the proton donor in an enzyme active site can be calculated by considering in detail only the active-site residues and their immediate electrostatic interaction partners, thus allowing for a large decrease in calculation time. More specifically we omit the calculation of site-site interaction energies, and the calculation of desolvation and background interaction energies for a large number of pairs of titratable groups. The method presented here is well suited to be applied on a genomic scale, and can be implemented in most pKa calculation algorithms to give significant reductions in calculation time with little or no impact on the accuracy of the results. The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts.
酶活性位点残基的电离特性在酶催化机制的研究中备受关注。了解这些电离常数（pKa值）通常能使研究人员在酶的反应机制中确定质子供体和催化亲核试剂。通过将pKa计算算法应用于蛋白质X射线结构，可以获得蛋白质残基pKa值的估计值。我们表明，通过仅详细考虑活性位点残基及其直接的静电相互作用伙伴，就可以计算出足够准确的pKa值，以识别酶活性位点中的质子供体，从而大幅减少计算时间。更具体地说，我们省略了位点间相互作用能的计算，以及大量可滴定基团对的去溶剂化和背景相互作用能的计算。这里提出的方法非常适合在基因组规模上应用，并且可以在大多数pKa计算算法中实现，从而在对结果准确性影响很小或没有影响的情况下显著减少计算时间。这里展示的工作对于全面理解酶以及设计新型生物催化剂具有重要意义。
