Gumbart Lab

PI: JC Gumbart

 

Papers

In Press
  • Living on the edge: Simulations of bacterial outer-membrane proteins.  A. Pavlova, H. Hwang, K. Lundquist, C. Balusek, and J.C. Gumbart*.  BBA – Biomembranes. In press.
  • Decrypting protein insertion through the translocon with free-energy calculations. J.C. Gumbart* and C. Chipot. BBA – Biomembranes. In press
  • Structural and Functional Characterization of the LPS Transporter LptDE from Gram-negative Pathogens. S. J. Mayclin, J. G. McCarthy, I. Botos, K. Lundquist, N. Majdalani, D. Wojtowicz, T. J. Barnard, J. C. Gumbart, and S. K. Buchanan. Structure. In press.
  • Simulation-based approaches for determining membrane permeability of small compounds. C. Lee, J. Comer, C. Herndon, N. Leung, A. Pavlova, R. Swift, C. Tung, C. Rowley, R. Amaro, C. Chipot, Y. Wang, and *J. C. Gumbart. J. Chemical Information and Modeling. In press.
2015
  • The Adaptive Biasing Force method: Everything you always wanted to know, but were afraid to ask. J. Comer, J.C. Gumbart, J. Hénin, T. Lelièvre, A. Pohorille, and C. Chipot. J. Physical Chemistry B. 119:1129-1151. 2015.
  • The Adaptive Biasing Force method: Everything you always wanted to know, but were afraid to ask. J. Comer, J.C. Gumbart, J. Hénin, T. Lelièvre, A. Pohorille, and C. Chipot. J. Physical Chemistry B. 119:1129-1151. 2015.
2014
  • Structure of the SecY channel during initiation of protein translocation. E. Park, J.F. Menetret, J.C. Gumbart, S.J. Ludtke, W. Li, A. Whynot, T.A. Rapoport, and C.W. Akey. Nature. 506:102-106, 2014.
  • Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. J.C. Gumbart*, M. Beeby, G.J. Jensen, and B. Roux. PLoS Computational Biology.  10:e1003475, 2014.
  • Thermodynamics of deca-alanine folding in water. A. Hazel, C. Chipot, and J.C. Gumbart*. J. Chemical Theory and Computation. 10:2836-2844, 2014.
  • Lateral opening and exit pore formation are required for BamA function. N. Noinaj, A. J. Kuszak, C. Balusek, J.C. Gumbart, and S. K. Buchanan. Structure. 22:1055-1062, 2014.
  • Structure of the SecY channel during initiation of protein translocation. E. Park, J.F. Menetret, J.C. Gumbart, S.J. Ludtke, W. Li, A. Whynot, T.A. Rapoport, and C.W. Akey. Nature. 506:102-106, 2014.
  • Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations. J.C. Gumbart*, M. Beeby, G.J. Jensen, and B. Roux. PLoS Computational Biology.  10:e1003475, 2014.
  • Thermodynamics of deca-alanine folding in water. A. Hazel, C. Chipot, and J.C. Gumbart*. J. Chemical Theory and Computation. 10:2836-2844, 2014.
  • Lateral opening and exit pore formation are required for BamA function. N. Noinaj, A. J. Kuszak, C. Balusek, J.C. Gumbart, and S. K. Buchanan. Structure. 22:1055-1062, 2014.
2013
  • Structural insight into the biogenesis of β-barrel membrane proteins. N. Noinaj, A. J. Kuszak, J.C. Gumbart, P. Lukacik, H. Chang, N. Easley, T. Lithgow, and S. K. Buchanan. Nature. 501:385-390, 2013.
  • Rapid parameterization of small molecules using the Force Field Toolkit. C. G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, and J.C. Gumbart*. J. Computational Chemistry. 34:2757-2770, 2013.
  • The mechanism of the amidases: Mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning. B.W. Weber, S.W. Kimani, A. Varsani, D.A. Cowan, R. Hunter, G.A. Venter, J.C. Gumbart, B.T. Sewell. J. Biological Chemistry. 288:28514-28523, 2013.
  • Structural insight into the biogenesis of β-barrel membrane proteins. N. Noinaj, A. J. Kuszak, J.C. Gumbart, P. Lukacik, H. Chang, N. Easley, T. Lithgow, and S. K. Buchanan. Nature. 501:385-390, 2013.
  • Rapid parameterization of small molecules using the Force Field Toolkit. C. G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, and J.C. Gumbart*. J. Computational Chemistry. 34:2757-2770, 2013.
  • The mechanism of the amidases: Mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning. B.W. Weber, S.W. Kimani, A. Varsani, D.A. Cowan, R. Hunter, G.A. Venter, J.C. Gumbart, B.T. Sewell. J. Biological Chemistry. 288:28514-28523, 2013.

 

Awards

  • Roger M. Wartell, Ph.D., and Stephen E. Brossette, M.D., Ph.D., Award for Multidisciplinary Studies in Biology, Physics, and Mathematics (2016, Alex Covington)
  • Petit Undergraduate Research Scholar (2014, Conner Herndon)

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