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Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I

https://doi.org/10.1016/j.bbabio.2020.148240

Khaniya, Umesh; Gupta, Chitrak; Cai, Xiuhong; Mao, Junjun; Kaur, Divya; Zhang, Yingying; Singharoy, Abhishek; Gunner, M.R. (October 2020, Biochimica et Biophysica Acta (BBA) - Bioenergetics)
null (Ed.)
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Identifying the proton loading site cluster in the ba cytochrome c oxidase that loads and traps protons

https://doi.org/10.1016/j.bbabio.2020.148239

Cai, Xiuhong; Son, Chang Yun; Mao, Junjun; Kaur, Divya; Zhang, Yingying; Khaniya, Umesh; Cui, Qiang; Gunner, M.R. (October 2020, Biochimica et Biophysica Acta (BBA) - Bioenergetics)

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Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields

https://doi.org/10.1142/S2737416520420016

Zhang, Yingying; Haider, Kamran; Kaur, Divya; Ngo, Van A.; Cai, Xiuhong; Mao, Junjun; Khaniya, Umesh; Zhu, Xuyu; Noskov, Sergei; Lazaridis, Themis; et al (March 2021, Journal of Computational Biophysics and Chemistry)
null (Ed.)
• Water is the primary cellular solvent, yet is challenging to simulate computationally. Here we simulate water molecules in the Gramicidin A channel comparing Monte Carlo (MC) sampling with a continuum electrostatics and Molecular Dynamics (MD) calculations with the non-polarizable CHARMM36 and polarizable Drude force fields. • These give different water properties, with classical MD yielding well oriented water wires, while the Drude or continuum electrostatics force fields lead to more disordered water molecules, often changing orientation in the middle of the channel.
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Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

https://doi.org/10.1016/j.bbabio.2018.05.010

Cai, Xiuhong; Haider, Kamran; Lu, Jianxun; Radic, Slaven; Son, Chang Yun; Cui, Qiang; Gunner, M.R. (May 2018, Biochimica et Biophysica Acta (BBA) - Bioenergetics)

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