pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.
pK(a) Calculations suggest storage of an excess proton in a hydrogen-bonded water network in bacteriorhodopsin.
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pK(a) 计算表明细菌视紫红质的氢键水网络中储存了过量的质子。
DOI：
10.1006/jmbi.2001.4902
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发表时间：
2001
期刊：
影响因子：
--
通讯作者：
Bashford,D
中科院分区：
文献类型：
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作者：
Spassov,VZ;Luecke,H;Gerwert,K;Bashford,D
利用最近获得的1.55 μ m分辨率的X射线晶体结构，计算了细菌视紫红质在静止状态下的质子化状态和可电离基团的pKa值。的计算是在合理的协议与现有的实验数据组或附近的离子传输链（视网膜席夫碱; Asp 85，96，115，212，和Arg 82）。与早期使用低分辨率结构数据的研究相反，这种一致性是在没有操纵晶体学确定的重原子位置或特别调整的固有pKa的席夫碱。因此，所使用的理论方法提供了更高的可靠性，因为输入的结构数据得到了改善。只有轻微的影响与实验的协议被发现与方法的变化，如单与多构象处理的氢原子的位置，或保留晶体学确定的内部水分子与处理它们作为高介电腔。在光循环的L-至-M过渡期间释放质子至膜的细胞外侧的基团的身份的长期存在的问题通过包括作为pH可滴定位点不仅Glu 204和Glu 194（已被提议作为释放基团的细胞外侧附近的残基）而且在附近腔中的H5 O2+分子来解决。后者代表了最近提出的存储在氢键水网络中的释放质子。在包括这种可能性的所有计算中，质子存储在H5 O2+中，而不是存储在谷氨酸中的任一个上，从而在细菌视紫红质中的释放质子存储在氢键合的水网络中的理论基础上建立可亲合性。这里使用的方法也可以适用于以这种方式储存质子的其他蛋白质，例如光合反应中心和细胞色素c氧化酶。
Calculations of protonation states and pKavalues for the ionizable groups in the resting state of bacteriorhodopsin have been carried out using the recently available 1.55 Å resolution X-ray crystallographic structure. The calculations are in reasonable agreement with the available experimental data for groups on or near the ion transport chain (the retinal Schiff base; Asp85, 96, 115, 212, and Arg82). In contrast to earlier studies using lower-resolution structural data, this agreement is achieved without manipulations of the crystallographically determined heavy-atom positions or ad hoc adjustments of the intrinsic pKaof the Schiff base. Thus, the theoretical methods used provide increased reliability as the input structural data are improved. Only minor effects on the agreement with experiment are found with respect to methodological variations, such as single versus multi-conformational treatment of hydrogen atom placements, or retaining the crystallographically determined internal water molecules versus treating them as high-dielectric cavities. The long-standing question of the identity of the group that releases a proton to the extracellular side of the membrane during the L-to-M transition of the photocycle is addressed by including as pH-titratable sites not only Glu204 and Glu194, residues near the extracellular side that have been proposed as the release group, but also an H5O2+molecule in a nearby cavity. The latter represents the recently proposed storage of the release proton in an hydrogen-bonded water network. In all calculations where this possibility is included, the proton is stored in the H5O2+rather than on either of the glutamic acids, thus establishing the plausibility on theoretical grounds of the storage of the release proton in bacteriorhodopsin in a hydrogen-bonded water network. The methods used here may also be applicable to other proteins that may store a proton in this way, such as the photosynthetic reaction center and cytochrome c oxidase.