All publications link to either the KS Research Group repository or the journal's webpage. Please contact me if you cannot obtain access to any of the publications.

Link to my Google Scholar profile.

    - 2013 -

  1. Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion. James C. Gumbart, Ivan Teo, Benoit Roux, and Klaus Schulten. Journal of the American Chemical Society, 135:2291–2297, 2013.
  2. Standard binding free energies from computer simulations: What is the best strategy? James C. Gumbart, Benoit Roux, and Christophe Chipot. Journal of Chemical Theory and Computation, 9:794-802, 2013.

    3. - 2012 -

  3. A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism. Simon G. Broadley, James C. Gumbart, Brandon W. Weber, Mohlopheni J. Marakalala, Daniel J. Steenkamp, and Bryan T. Sewell. Acta Cryst. D, 68:1450-1459, 2012.
  4. Mechanisms of SecM-mediated stalling in the ribosome. James Gumbart , Eduard Schreiner, Daniel N. Wilson, Roland Beckmann, and Klaus Schulten. Biophysical Journal, 103:331-341, 2012.
  5. Structural basis for iron piracy by pathogenic Neisseria. Nicholas Noinaj, Nicole C. Easley, Muse Oke, Naoko Mizuno, James Gumbart, Evzen Boura, Ashley N. Steere, Olga Zak, Philip Aisen, Emad Tajkhorshid, Robert W. Evans, Andrew R. Gorringe, Anne B. Mason, Alasdair C. Steven, and Susan K. Buchanan. Nature, 483:53-58, 2012.
  6. Determination of membrane-insertion free energies by molecular dynamics simulations. James Gumbart and Benoit Roux. Biophysical Journal, 102:795-801, 2012.
  7. Constant electric field simulations of the membrane potential illustrated with simple systems. James Gumbart, Fatemeh Khalili-Araghi, Marcos Sotomayor, and Benoit Roux. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818:294-302, 2012.
  8. Molecular basis for activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter. Travis J. Barnard, James Gumbart, Janine H. Peterson, Nicholas Noinaj, Nicole C. Easley, Nathalie Dautin, Adam J. Kuszak, Emad Tajkhorshid, Harris D. Bernstein, and Susan K. Buchanan. Journal of Molecular Biology, 415:128-142, 2012.

    9. - 2011 -

  9. Symmetry-restrained flexible fitting for symmetric EM maps. Kwok-Yan Chan, James Gumbart, Ryan McGreevy, Jean M. Watermeyer, B. Trevor Sewell, and Klaus Schulten. Structure, 19:1211-1218, 2011.
  10. Free energy of nascent-chain folding in the translocon. James Gumbart, Christophe Chipot, and Klaus Schulten. Journal of the American Chemical Society, 133:7602-7607, 2011.
  11. Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Jens Frauenfeld, James Gumbart, Eli O. van der Sluis, Soledad Funes, Marco Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas Becker, Klaus Schulten, and Roland Beckmann. Nature Structural & Molecular Biology, 18:614-621, 2011.
  12. Free-energy cost for translocon-assisted insertion of membrane proteins. James Gumbart, Christophe Chipot, and Klaus Schulten. Proceedings of the National Academy of Sciences, USA, 108:3596-3601, 2011.
  13. Applications of the molecular dynamics flexible fitting method. Leonardo G. Trabuco, Eduard Schreiner, James Gumbart, Jen Hsin, Elizabeth Villa, and Klaus Schulten. Journal of Structural Biology, 173:420-427, 2011.

    14. - 2010 -

  14. Self-assembly of photosynthetic membranes. Jen Hsin, Danielle E. Chandler, James Gumbart, Christopher B. Harrison, Melih Sener, Johan Strumpfer, and Klaus Schulten. ChemPhysChem, 11:1154-1159, 2010.

    15. - 2009 -

  15. Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Thomas Becker, Shashi Bhushan, Alexander Jarasch, Jean-Paul Armache, Soledad Funes, Fabrice Jossinet, James Gumbart, Thorsten Mielke, Otto Berninghausen, Klaus Schulten, Eric Westhof, Reid Gilmore, Elisabet C. Mandon, and Roland Beckmann. Science, 326:1369-1373, 2009.
  16. Membrane curvature induced by aggregates of LH2s and monomeric LH1s. Danielle E. Chandler, James Gumbart, John D. Stack, Christophe Chipot, and Klaus Schulten. Biophysical Journal, 97:2978-2984, 2009.
  17. Regulation of the protein-conducting channel by a bound ribosome. James Gumbart, Leonardo G. Trabuco, Eduard Schreiner, Elizabeth Villa, and Klaus Schulten. Structure, 17:1453-1464, 2009.
  18. Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Journal of Molecular Biology, 393:1129-1142, 2009.
  19. Protein-induced membrane curvature investigated through molecular dynamics flexible fitting. Jen Hsin, James Gumbart, Leonardo G. Trabuco, Elizabeth Villa, Pu Qian, C. Neil Hunter, and Klaus Schulten. Biophysical Journal, 97:321-329, 2009.
  20. Molecular dynamics simulations of membrane channels and transporters. Fatemeh Khalili-Araghi, James Gumbart, Po-Chao Wen, Marcos Sotomayor, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 19:128-137, 2009.

    21. - 2008 -

  21. The roles of pore ring and plug in the SecY protein-conducting channel. James Gumbart and Klaus Schulten. Journal of General Physiology, 132:709-719, 2008.
  22. Intrinsic curvature properties of photosynthetic proteins in chromatophores. Danielle Chandler, Jen Hsin, Christopher B. Harrison, James Gumbart, and Klaus Schulten. Biophysical Journal, 95:2822-2836, 2008.

    23. - 2007 -

  23. Structural determinants of lateral gate opening in the protein translocon. James Gumbart and Klaus Schulten. Biochemistry, 46:11147-11157, 2007.
  24. Mechanics of force propagation in TonB-dependent outer membrane transport. James Gumbart, Michael C. Wiener, and Emad Tajkhorshid. Biophysical Journal, 93:496-504, 2007.
    Featured in Science Magazine’s Editors’ Choice: Science, 316:1101, 2007.

    - 2006 -

  25. Molecular dynamics studies of the archaeal translocon. James Gumbart and Klaus Schulten. Biophysical Journal, 90:2356-2367, 2006.

    26. - 2005 -

  26. Scalable molecular dynamics with NAMD. James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Journal of Computational Chemistry, 26:1781-1802, 2005.
  27. Molecular dynamics simulations of proteins in lipid bilayers. James Gumbart, Yi Wang, Alekseij Aksimentiev, Emad Tajkhorshid, and Klaus Schulten. Current Opinion in Structural Biology, 15:423-431, 2005.

Book chapters and conference proceedings

  1. Exploring substrate diffusion using biased molecular dynamics simulations. James Gumbart. In N. Vaidehi and J. Klein-Seetharaman, editors, Methods in Molecular Biology. 914:337-350. Springer, 2012.
  2. Viewing the mechanisms of translation through the computational microscope. James Gumbart, Eduard Schreiner, Leonardo G. Trabuco, Kwok-Yan Chan, and Klaus Schulten. In Joachim Frank, editor, Molecular Machine in Biology, chapter 8, pp. 142-157. Cambridge University Press, 2011.
  3. Molecular mechanisms of active transport across the cellular membrane. Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart, and Emad Tajkhorshid. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes: From Biophysics to Function, chapter 10, pp. 248-286. Royal Society of Chemistry, 2010.
  4. Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software. Kirby Vandivort, James C. Phillips, Elizabeth Villa, Peter L. Freddolino, James Gumbart, Leonardo G. Trabuco, Danielle E. Chandler, Jen Hsin, Christopher B. Harrison, Laxmikant Kale, and Klaus Schulten. Proceedings of the 2008 TeraGrid Conference, 2008.