Identification of proton-transfer pathways in human carbonic anhydrase II
Identification of proton-transfer pathways in human carbonic anhydrase II
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DOI：
10.1021/jp073499t
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发表时间：
2007-09-06
影响因子：
3.3
通讯作者：
Taraphder, Srabani
中科院分区：
文献类型：
--
作者：
Roy, Arijit;Taraphder, Srabani
我们研究了质子从人碳酸酐酶II的表面通过His-64进入活性位点空腔的可能途径，His-64被广泛认为是质子转移途径沿着的关键残基，静态晶体结构中氢键簇的递归分析表明，在其实验检测到的构象中，不存在通过His-64的完整路径。发现His-64从其向外构象朝向活性位点的侧链构象波动提供了完成与蛋白质结构和水合的局部重组相耦合的路径所需的关键动态连接。能量和自由能垒沿着检测到的途径已被估计，推导出的机制，His-64旋转向活性位点。我们还研究了一个动态的连接图，突出无序的水分子，可能会促进直接（可能是瞬态）访问的溶剂的活性位点的网络。我们的研究揭示了这种溶剂通道可能与His-64介导的假定质子穿梭有关。因此，确定的路径可以潜在地用作反应坐标的酶作用的分子机制的进一步研究。
We investigate the probable proton-transfer pathways from the surface of human carbonic anhydrase II into the active site cavity through His-64 that has been widely implicated as a key residue along the protontransfer path. A recursive analysis of hydrogen-bonded clusters in the static crystallographic structure shows that there is no complete path through His-64 in either of its experimentally detected conformations. Side chain conformational fluctuation of His-64 from its outward conformation toward the active site is found to provide a crucial dynamic connectivity needed to complete the path coupled to local reorganization of the protein structure and hydration. The energy and free energy barriers along the detected pathway have been estimated to derive the mechanism of His-64 rotation toward the active site. We also investigate a dynamical connectivity map that highlights networks of disordered water molecules that may promote a direct (and probably transient) access of the solvent to the active site. Our studies reveal how such solvent access channels may be related to the putative proton shuttle mediated by His-64. The paths thus identified can be potentially used as reaction coordinates for further studies on the molecular mechanism of enzyme action.