BACKGROUND Determination of proton uptake pathways in Cytochrome c Oxidase is difficult due to the complexity of the system. The transition networks approach allows sampling of proton transfer pathways without predefined reaction coordinate. METHODS Computation of the proton transfer pathways in a model of the D-channel of cytochrome c oxidase has been performed by a transition network approach that combines discrete, optimisation based and molecular dynamics based sampling. RESULTS The optimal pathway involves an opening of the so-called asparagine gate, hydration of the asparagine region, the formation of a hydrogen-bonded chain, and finally concerted proton hole transport along this chain. The optimal pathway finds the protonation of residue H26 close to the channel entrance favourable for lowering the transition energies of subsequent steps, in particular, opening of the Asn gate and formation of a hydrogen-bonded chain. Residue Y33 plays an important role in shuttling the transferred proton hole. CONCLUSIONS The optimal pathway found by the transition network approach shows the same important characteristics as pathways determined earlier by other methods. The computed barrier and reaction energies are also in good agreement with previous studies. The transition network approach provides an alternative to explore pathways in complex systems. GENERAL SIGNIFICANCE The correct function of the enzyme as oxidase and proton pump depends on the interplay of several redox and proton transport steps. Understanding the proton transport mechanism is therefore key to understanding the protein's function. The complex nature of long- distances proton transfer through a protein requires a non-trivial simulation strategy.

中文翻译：

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通过过渡网络方法模拟细胞色素C氧化酶D通道中的质子转移。

背景技术由于系统的复杂性，难以确定细胞色素c氧化酶中的质子吸收途径。过渡网络方法允许在没有预定义的反应坐标的情况下对质子转移路径进行采样。方法已通过结合结合离散，基于优化和基于分子动力学的采样的过渡网络方法，对细胞色素C氧化酶D通道模型中的质子转移途径进行了计算。结果最佳途径包括打开所谓的天冬酰胺门，天冬酰胺区域水化，氢键链的形成，以及最终沿着该链的一致的质子空穴传输。最佳途径发现靠近通道入口的残基H26的质子化有利于降低后续步骤的跃迁能，特别地，打开Asn门并形成氢键链。残留物Y33在穿梭转移的质子孔中起着重要作用。结论过渡网络方法发现的最佳途径与其他方法先前确定的途径具有相同的重要特征。计算得到的势垒和反应能也与以前的研究非常吻合。过渡网络方法为探索复杂系统中的路径提供了一种替代方法。一般意义该酶作为氧化酶和质子泵的正确功能取决于几个氧化还原和质子传输步骤之间的相互作用。因此，了解质子转运机制是了解蛋白质功能的关键。