Umesh Khaniya Postdoc | Antibody Engineering | Computational Biology

Portfolio

Publications

Book chapters and journal articles spanning computational biophysics, proton transfer, and immunoglobulin-fold structural analysis.

Google Scholar

Book Chapter

  • Gupta, C., Khaniya, U., Vant, J., Shekhar, M., Mao, J., Gunner, M. R., Singharoy, A. Poor Person’s pH Simulation of Membrane Proteins Methods in Molecular Biology, Vol. 2315 (Computational Design of Membrane Proteins), 197-217, 2021.
  • Tawfeeq C., Song J., Khaniya, U., Madej T. et al. (2024) Towards a structural and functional analysis of the immunoglobulin-fold proteome. Vol. 138 (Advances in Protein Chemistry and Structural Biology), 135-178 (Book Chapter).

Papers

  • Wei, R.J., Khaniya, U., Mao, J. et al. (2022) Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers. Photosynth Res 156, 101-112.
  • Khaniya, U., Mao, J., Wei, R. J., and Gunner, M. R. (2022). Characterizing protein protonation microstates using monte carlo sampling. J. Phys. Chem. B. 126, 2476-2485.
  • Wei, R.J., Zhang Y., Mao J., Kaur D., Khaniya U., Gunner M.R. (2022). Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers, Photosynth. Res. 152, 153-165.
  • Kaur, D*., Khaniya, U.* Zhang, Y*., Gunner, M. Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient, Frontiers in Chemistry 9, 446 (2021).
  • Zhang, Y., Haider, K., Kaur, D., Ngo, V.A., Cai, X., Mao, J., Khaniya, U., et al. (2021). 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, J. Comput. Biophys. Chem. 20, 111-130.
  • Khaniya, U., Gupta, C., Cai, X., Mao, J., Kaur, D., Zhang, Y., et al. (2020). Hydrogen Bond Network Analysis Reveals the Pathway for the Proton Transfer in the E-Channel of T. thermophilus Complex I. Biochim. Biophys. Acta (Bba) - Bioenerg. 1861, 148240.
  • Cai, X., Son, C. Y., Mao, J., Kaur, D., Zhang, Y., Khaniya, U., et al. (2020). Identifying the Proton Loading Site Cluster in the Ba Cytochrome C Oxidase that Loads and Traps Protons. Biochim. Biophys. Acta (Bba) - Bioenerg. 1861, 148239.
  • Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., et al. (2020). Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. J. Am. Chem. Soc. 142, 9220-9230.
  • Kaur D., Szejgis, W., Mao, J., Amin, M., Reiss, K. M., Askerka, M., Cai, X., Khaniya, U., et al. Relative Stability of the S2 Isomers of the Oxygen Evolving Complex of Photosystem II, Photosynth. Res., 2019, 141(3), 331-341.
  • Kaur, D., Cai, X., Khaniya, U., Zhang, Y., Mao, J., Mandal, M., et al. (2019). Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome C Oxidase. Inorganics 7, 14.