Riccardi Demian, Yang Shuo, Cui Qiang
Department of Biochemistry, University of Wisconsin, Madison, Madison, WI 53706, USA.
Biochim Biophys Acta. 2010 Feb;1804(2):342-51. doi: 10.1016/j.bbapap.2009.07.026. Epub 2009 Aug 11.
Recent QM/MM analyses of proton transfer function of human carbonic anhydrase II (CAII) are briefly reviewed. The topics include a preliminary analysis of nuclear quadrupole coupling constant calculations for the zinc ion and more detailed analyses of microscopic pK(a) of the zinc-bound water and free energy profile for the proton transfer. From a methodological perspective, our results emphasize that performing sufficient sampling is essential to the calculation of all these quantities, which reflects the well solvated nature of CAII active site. From a mechanistic perspective, our analyses highlight the importance of electrostatics in shaping the energetics and kinetics of proton transfer in CAII for its function. We argue that once the pK(a) for the zinc-bound water is modulated to be in the proper range (approximately 7.0), proton transfer through a relatively well solvated cavity towards/from the protein surface (His64) does not require any major acceleration. Therefore, although structural details like the length of the water wire between the donor and acceptor groups still may make a non-negligible contribution, our computational results and the framework of analysis suggest that the significance of such "fine-tuning" is likely secondary to the modulation of pK(a) of the zinc-bound water. We encourage further experimental analysis with mutation of (charged) residues not in the immediate neighborhood of the zinc ion to quantitatively test this electrostatics based framework; in particular, Phi analysis based on these mutations may shed further light into the relative importance of the classical Grotthus mechanism and the "proton hole" pathway that we have proposed recently for CAII.
本文简要回顾了近期对人类碳酸酐酶II（CAII）质子转移功能的量子力学/分子力学（QM/MM）分析。主题包括对锌离子核四极耦合常数计算的初步分析，以及对锌结合水的微观pK(a)和质子转移自由能分布的更详细分析。从方法学角度来看，我们的结果强调进行充分采样对于所有这些量的计算至关重要，这反映了CAII活性位点良好的溶剂化性质。从机理角度来看，我们的分析突出了静电作用在塑造CAII中质子转移的能量学和动力学以实现其功能方面的重要性。我们认为，一旦锌结合水的pK(a)被调节到合适范围（约7.0），通过相对良好溶剂化的腔向/从蛋白质表面（His64）的质子转移不需要任何重大加速。因此，尽管供体和受体基团之间水线长度等结构细节仍可能有不可忽略的贡献，但我们的计算结果和分析框架表明，这种“微调”的重要性可能次于锌结合水pK(a)的调节。我们鼓励对不在锌离子紧邻区域的（带电）残基进行突变的进一步实验分析，以定量测试这个基于静电作用的框架；特别是，基于这些突变的Phi分析可能会进一步阐明我们最近为CAII提出的经典Grotthus机制和“质子孔”途径的相对重要性。
