Google Scholar profile

*denotes co-first authors.
†denotes co-corresponding authors.

• 148) Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA.
  C.O. Cottom, R. Stephenson, D. Ricci, Li. Yang, J.C. Gumbart, and N. Noinaj. Structure. 32:2038-2048.e3, 2024.
• 147) Molecular dynamics reveals altered interactions between belzutifan and HIF-2 with natural variant G323E or proximal phosphorylation at T324.
  V. Natarajan, V. Satalkar†, J.C. Gumbart, and M. Torres†. ACS Omega. 9:37843–37855, 2024.
• 146) Allosteric coupling of substrate binding and proton translocation in MmpL3 transporter from Mycobacterium tuberculosis.
  S. Babii, Wei Li, Li. Yang, A. Grzegorzewicz, M. Jackson, J.C. Gumbart, and H. Zgurskaya. mBio. 15:e02183-24, 2024.
• 145) Broadening access to small-molecule parameterization with the Force Field Toolkit.
  Y. Zeng*, A. Pavlova*, P.M. Nelson, Z.L. Glick, La. Yang, Y.T. Pang, M. Spivak, G. Licari, E. Tajkhorshid†, C.D. Sherrill†, and J.C. Gumbart†. J. Chemical Physics. 160:242501, 2024.
  FFTK update to install in your local VMD installation plugins directory: fftk-July-2024.zip
• 144) SANS reveals lipid-dependent oligomerization of an intramembrane aspartyl protease from H. volcanii.
  G.M. Thomas*, Y. Wu*, W. Leite*, S.V. Pingali, K.L. Weiss, A.J. Grant, M.W. Diggs, I. Schmidt-Krey, G. Gutishvili, J.C. Gumbart, V.S. Urban†, and R.L. Lieberman†. Biophysical Journal. 123:1846-1856, 2024.
• 143) Thicket-and-Mesh: How the Outer Membrane Can Resist Tension Imposed by the Cell Wall.
  D. Ryoo, H. Hwang, and J.C. Gumbart. J. Physical Chemistry B. 128:5371-5377, 2024.
• 142) Enhanced surface accessibility of SARS-CoV-2 Omicron spike protein due to an altered glycosylation profile.
  D. Wang*†, Z. Zhang*, J. Baudys, C. Haynes, S.H. Osman, B. Zhou, J.R. Barr, and J.C. Gumbart†. ACS Infectious Diseases. 10:2032-2046, 2024.
• 141) Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations.
  G. Gutishvili, Li. Yang, and J.C. Gumbart. Current Opinion in Structural Biology. 87:102828, 2024.
• 140) Biophysics-guided lead discovery of HBV capsid assembly modifiers.
  Z. Fan, A. Pavlova, M.C. Jenkins, L. Bassit, M. Salman, D.L. Lynch, D. Patel, M. Korablyov, M.G. Finn, R.F. Schinazi, and J.C. Gumbart. ACS Infectious Diseases. 10:1162–1173, 2024.
• 139) Substrate recognition mechanism of the endoplasmic reticulum-associated ubiquitin ligase Doa10.
  K. Wu*, S. Itskanov*, D.L. Lynch, Y. Chen, A. Turner, J.C. Gumbart, and E. Park. Nature Communications. 15:2182, 2024.
• 138) Generative β-hairpin design using a residue-based physicochemical property landscape.
  V. Satalkar, G.D. Degaga, W. Li, Y.T. Pang, A.C. McShan, J.C. Gumbart, J.C. Mitchell, and M.P. Torres. Biophysical Journal. 123:2790-2806, 2024.
• 137) From simple to complex: reconstructing all-atom structures from CG models using cg2all.
  Y.T. Pang, Li. Yang, and J.C. Gumbart. Structure. 32:5-7, 2024.
• 136) Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller.
  E.G. Saccuzzo*, M.D. Mebrat*, H.F. Scelsi, M. Kim, M.T. Ma, X. Su, S.E. Hill, E. Rheaume, R. Li, M.P. Torres, J.C. Gumbart, W.D. Van Horn, and R.L. Lieberman. Nature Communications. 15:155, 2024.
• 135) A partial human LCK defect causes a T-cell immunodeficiency with intestinal inflammation.
  V.G. Lui*, M. Hoenig*, B. Cabrera-Martinez, R.M. Baxter, J.E. Garcia-Perez, A. Acharya, K. Lundquist, J. Capera, P. Matusewicz, F.A. Hartl, M. D’Abramo, J. Alba, E.-M. Jacobsen, D. Niewolik, M. Lorenz, U. Pannicke, A.S. Schulz, K.-M. Debatin, W.W. Schamel, S. Minguet, J.C. Gumbart, M. Dustin, J.C. Cambier, K. Schwarz, and E.W.Y. Hsieh. J. Experimental Medicine. 221:e20230927, 2024.

• 134) A rigorous framework for calculating protein-protein binding affinities in membranes.
  M. Blazhynska, J.C. Gumbart, H. Chen, E. Tajkhorshid, B. Roux, and C. Chipot. J. Chemical Theory and Computation. 19: 9077-9092, 2023.
• 133) Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.
  D.J.E. Huard*, A.M. Johnson*, Z. Fan, L.G. Kenney, M. Xu, R. Drori, J.C. Gumbart, S. Dai, R.L. Lieberman, and J.B. Glass. PNAS Nexus. 2:pgad268, 2023.
• 132) Drug binding to BamA targets its lateral gate.
  K.M. Kuo, J. Liu, A. Pavlova, and J.C. Gumbart. J. Physical Chemistry B. 127:7509–7517, 2023.
• 131) N-terminal intrinsic disorder is an ancestral feature of Gγ subunits that influences the balance between different Gβγ signaling axes in yeast.
  X. Su, Y.T. Pang, W. Li, J.C. Gumbart, J. Kelley, and M. Torres. J. Biological Chemistry. 299:104947, 2023.
• 130) Conformational restriction shapes the inhibition of a multidrug efflux adaptor protein.
  B.R. Lewis, M.R. Uddin, M. Moniruzzaman, K.M. Kuo, A. Higgins, L.M.N. Shah, F. Sobott, J.M. Parks, D. Hammerschmid, J.C. Gumbart†, H.I. Zgurskaya†, and E. Reading†. Nature Communications. 14:3900, 2023.
• 129) Structural basis of mitochondrial protein import by the TIM23 complex.
  S.I. Sim*, Y. Chen*, D.L. Lynch, J.C. Gumbart, and E. Park. Nature. 621:620–626, 2023.
• 128) Understanding virus structure and dynamics through molecular simulations.
  D.L. Lynch, A. Pavlova, Z. Fan, and J.C. Gumbart. J. Chemical Theory and Computation. 19:3025–3036, 2023.
• 127) Toward a 3D physical model of diffusive polymer chains.
  A. Karsai, G.J. Cassidy, A.P. Rajanala, Li. Yang, D. Kerimoglu, J.C. Gumbart, H.D. Kim, and D.I. Goldman. Frontiers in Physics. 11:1142004, 2023.
• 126) Uncovering the folding mechanism of pertactin: A comparative study of isolated and vectorial folding.
  Y.T. Pang*, A.J. Hazel*, and J.C. Gumbart. Biophysical Journal. 122:2988-2995, 2023.
• 125) Insights into substrate transport and water permeation in the mycobacterial transporter MmpL3.
  Y. Li*, A. Acharya*, Li. Yang, J. Liu, E. Tajkhorshid, H.I. Zgurskaya, M. Jackson, and J.C. Gumbart. Biophysical Journal. 122:2342-2352, 2023.
• 124) Weak tension accelerates hybridization and dehybridization of short oligonucleotides.
  D.J. Hart, J. Jeong, J.C. Gumbart, and H.D. Kim. Nucleic Acids Research. 51:3030–3040, 2023.
• 123) Species-agnostic polymeric formulations for inhalable messenger RNA delivery to the lung.
  L. Rotolo*, D. Vanover*, N.C. Bruno*, H.E. Peck, C. Zurla, J. Murray, R.K. Noel, L. O’Farrell, M. Araínga, N. Orr-Burks, J.Y. Joo, L.C.S. Chaves, Y. Jung, J. Beyersdorf, S. Gumber, R. Guerrero-Ferreira, S. Cornejo, M. Thoresen, A.K. Olivier, K.M. Kuo, J.C. Gumbart, A.R. Woolums, F. Villinger, E.R. Lafontaine, R.J. Hogan, M.G. Finn, and P.J. Santangelo. Nature Materials. 22:369–379, 2023.
• 122) Structural Determinants of Indole-2-carboxamides: Identification of Lead Acetamides with Pan Antimycobacterial Activity.
  P. Bhattarai, P. Hegde, W. Li, P.K. Prathipati, C. Stevens, Li. Yang, H. Zhou, A. Pandya, K. Cunningham, J. Grissom, M.R. Sotelo, M. Sowards, L. Calisto, C.J. Destache, S. Rocha-Sanchez, J.C. Gumbart, H. Zgurskaya, M. Jackson, and E.J. North. J. Medicinal Chemistry. 66:170–187, 2023.

• 121) SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact.
  Y.T. Pang*, A. Acharya*, D.L. Lynch, A. Pavlova, and J.C. Gumbart. Communications Biology. 5:1170, 2022.
• 120) Point mutations in TbpA abrogate human transferrin binding in Neisseria gonorrhoeae.
  A.N. Greenawalt, J. Stoudenmire, K. Lundquist, N. Noinaj, J.C. Gumbart, and C.N. Cornelissen. Infection and Immunity. 90:e00414-22, 2022.
• 119) Extraction of dielectric permittivity from atomistic molecular dynamics simulations and microwave measurements.
  A. Saad-Falcon*, Z. Zhang*, D. Ryoo, J. Dee, R. Westafer, and J.C. Gumbart. J. Physical Chemistry B. 126:8021–8029, 2022.
• 118) When the dust has settled: Calculation of binding affinities from first principles for SARS-CoV-2 variants with quantitative accuracy.
  E. Goulard Coderc de Lacam*, M. Blazhynska*, H. Chen, J.C. Gumbart†, and C. Chipot†. J. Chemical Theory and Computation. 18:5890–5900, 2022.
• 117) Antimicrobial peptide mechanism studied by scattering-guided molecular dynamics simulation.
  R. Allsopp, A. Pavlova, T. Cline, A.M. Salyapongse, R.E. Gillilan, Y.P. Di, B. Deslouches, J.B. Klauda†, J.C. Gumbart†, and S. Tristram-Nagle†. J. Physical Chemistry B. 126:6922–6935, 2022.
• 116) Modeling intermediates of BamA folding an outer membrane protein.
  K.M. Kuo, D. Ryoo, K. Lundquist, and J.C. Gumbart. Biophysical Journal. 121:3242-3252, 2022.
• 115) Restoring and enhancing the potency of existing antibiotics against drug-resistant Gram-negative bacteria through the development of potent small-molecule adjuvants.
  B. Yu, M.R. Choudhury, X. Yang, S.L. Benoit, E. Womack, K.v.M. Lyles, A. Acharya, A. Kumar, C. Yang, A. Pavlova, M. Zhu, Z. Yuan, J.C. Gumbart, D.W. Boykin, R.J. Maier, Z. Eichenbaum, and B. Wang. ACS Infectious Diseases. 8:1491–1508, 2022.
• 114) Proton transfer activity of the reconstituted Mycobacterium tuberculosis MmpL3 is modulated by substrate mimics and inhibitors.
  C. Stevens, S. Babii, A.N. Pandya, W. Li, Y. Li, J. Mehla, R. Scott, P. Hegde, P.K. Prathipati, A. Acharya, J. Liu, J.C. Gumbart, J. North, M. Jackson, and H.I. Zgurskaya. Proceedings of the National Academy of Sciences, USA. 119:e2113963119, 2022.
• 113) The role of extracellular loops in the folding of outer membrane protein X (OmpX) of Escherichia coli.
  S. Hermansen, D. Ryoo, M. Orwick-Rydmark, A. Saragliadis, J.C. Gumbart, and D. Linke. Frontiers in Molecular Biosciences. 9:918480, 2022.
• 112) Mechanism of action of HBV capsid assembly modulators can be predicted from binding to early assembly intermediates.
  A. Pavlova, L. Bassit, B.D. Cox, M. Korablyov, C. Chipot, D. Patel, D.L. Lynch, F. Amblard, R.F. Schinazi, and J.C. Gumbart. J. Medicinal Chemistry. 65:4854–4864, 2022.
• 111) Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations.
  H. Fu, H. Chen, M. Blazhynska, E. Goulard Coderc de Lacam, F. Szczepaniak, A. Pavlova, X. Shao, J.C. Gumbart, F. Dehez, B. Roux, W. Cai, and C. Chipot. Nature Protocols. 17:1114–1141, 2022.
• 110) Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor.
  D.W. Kneller, O. Gerlits, L.L. Daemen, A. Pavlova, J.C. Gumbart, Y. Cheng, and A. Kovalevsky. Physical Chemistry Chemical Physics. 24:3586-3597, 2022.
• 109) Adaptation of the periplasm to maintain spatial constraints essential for cell envelope processes and cell viability.
  E. Mandela*, C.J. Stubenrauch*, D. Ryoo, H. Hwang, E.J. Cohen, V.L. Torres, P. Deo, C.T. Webb, C. Huang, R.B. Schittenhelm, M. Beeby, J.C. Gumbart†, T. Lithgow†, and I.D. Hay†. eLife. 11:e73516, 2022.
• 108) Resolving the hydride transfer pathway in oxidative conversion of proline to pyrrole.
  A. Acharya, D. Yi, A. Pavlova, V. Agarwal†, and J.C. Gumbart†. Biochemistry. 61:206-215, 2022.
• 107) Comprehensive structure and functional adaptations of the yeast nuclear pore complex.
  C.W. Akey*†, D. Singh*, C. Ouch*, I. Echeverria*, I. Nudelman, J.M. Varberg, Z. Yu, F. Fang, Y. Shi, J. Wang, D. Salzberg, K. Song, C. Xu, J.C. Gumbart, S. Suslov, J. Unruh, S.L. Jaspersen, B.T. Chait, A. Sali, J. Fernandez-Martinez†, S.J. Ludtke†, E. Villa†, and M.P. Rout†. Cell. 185:361-378, 2022.

• 106) Plasticity within the barrel domain of BamA mediates a hybrid-barrel mechanism by BAM.
  R. Wu*, J.W. Bakelar*, K. Lundquist*, Z. Zhang, K.M. Kuo, D. Ryoo, Y.T. Pang, C. Sun, T. White, T. Klose, W. Jiang, J.C. Gumbart†, and N. Noinaj†. Nature Communications. 12:7131, 2021.
• 105) Folding and insertion of transmembrane helices at the ER.
  P. Whitley, B. Grau, J.C. Gumbart, L. Martínez-Gil, and I. Mingarro. International Journal of Molecular Sciences. 22:12778, 2021.
• 104) Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump.
  J.C. Gumbart†, J.L. Ferreira, H. Hwang, A.J. Hazel, C.J. Cooper, J.M. Parks, J.C. Smith, H.I. Zgurskaya, and M. Beeby. Biophysical Journal. 120:3973-3982, 2021.
• 103) Quantifying Arrhythmic Long-QT Effects of Hydroxychloroquine and Azithromycin with Whole Heart Optical Mapping and Simulations.
  I. Uzelac, A. Kaboudian, S. Iravanian, J.G. Siles-Paredes, J.C. Gumbart, H. Ashikaga, N. Bhatia, R.F. Gilmour Jr., E.M. Cherry, F.H. Fenton. Heart Rhythm O2. 2:394-404, 2021.
• 102) Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2.
  A. Pavlova*, Z. Zhang*, A. Acharya, D.L. Lynch, Y.T. Pang, Z. Mou, J.M. Parks, C. Chipot*, and J.C. Gumbart*. J. Physical Chemistry Letters. 12:5494–5502, 2021.
• 101) Combinatorial phosphorylation modulates the structure and function of the G protein γ subunit in yeast.
  Z.N. Toosi, X. Su, R. Austin, S. Choudhury, W. Li, Y.T. Pang, J.C. Gumbart, and M.P. Torres. Science Signaling. 14:eabd2464, 2021.
• 100) Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.
  Z. Zhang, D. Ryoo, C. Balusek, A. Acharya, M. Orwick Rydmark, D. Linke, and J.C. Gumbart. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1863:183662, 2021.
• 99) ACE2 glycans preferentially interact with SARS-CoV-2 over SARS-CoV.
  A. Acharya†, D.L. Lynch, A. Pavlova, Y.T. Pang, and J.C. Gumbart†. Chemical Communications. 57:5949-5952, 2021.
• 98) Gatekeeping ketosynthases dictate initiation of assembly line biosynthesis of pyrrolic polyketides.
  D. Yi, A. Acharya, J.C. Gumbart, W. Gutekunst, and V. Agarwal. J. American Chemical Society. 143:7617–7622, 2021.
• 97) Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design.
  L. Zanetti-Polzi, M.D. Smith, C. Chipot, J.C. Gumbart, D.L. Lynch, A. Pavlova, J.C. Smith, and I. Daidone. J. Physical Chemistry Letters. 12:4195-4202, 2021.
• 96) Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding.
  N.M. Gravina, J.C. Gumbart, and H.D. Kim. J. Physical Chemistry B. 125:4016–4024, 2021.
• 95) Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.
  S. Itskanov, K.M. Kuo, J.C. Gumbart, and E. Park. Nature Structural & Molecular Biology. 28:162–172, 2021.
• 94) Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease.
  A. Pavlova, D.L. Lynch, I. Daidone, L. Zanetti-Polzi, M.D. Smith, C. Chipot, D.W. Kneller, A. Kovalevsky, L. Coates, A.A. Golosov, C.J. Dickson, C. Velez-Vega, J.S. Duca, J.V. Vermaas, Y.T. Pang, A. Acharya, J.M. Parks, J.C. Smith, and J.C. Gumbart. Chemical Science. 12:1513-1527, 2021.
• 93) Molecular Machinery Responsible for Graphene Oxide’s Distinct Inhibitory Effects towards Pseudomonas aeruginosa and Staphylococcus aureus Pathogens.
  N.A. Astani, F. Najafi, A. Maghsoumi, K. Huma, L. Azimi, A. Karimi, M.R. Ejtehadi, J.C. Gumbart, and N. Naseri. ACS Applied Bio Materials. 4:660–668, 2021.
• 92) Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle-Antibodies (SNAbs) for Selective Depletion of Target Cells.
  J. Liu, R. Toy, C. Vantucci, P. Pradhan, Z. Zhang, K.M. Kuo, K.P. Kubelick, D. Huo, J. Wen, J. Kim, Z. Lyu, S. Dhal, A. Atalis, S.K. Ghosh-Choudhary, E.J. Devereaux, J. C. Gumbart, Y. Xia, S.Y. Emelianov, N.J. Willett, and K. Roy. Nano Letters. 21:875–886, 2021.
• 91) A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels.
  J.C. Gumbart. Biophysical Journal. 120:185-186, 2021.
• 90) β-Barrel Proteins Tether the Outer Membrane in Many Gram-Negative Bacteria.
  K.M. Sandoz, R.A. Moore, P.A. Beare, A.V. Patel, R.E. Smith, M. Bern, H. Hwang, C.J. Cooper, S.A. Priola, J.M. Parks, J.C. Gumbart, S. Mesnage, and R.A. Heinzen. Nature Microbiology. 6:19-26, 2021.

• 89) Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
  A. Acharya, R. Agarwal, M. Baker, J. Baudry, D. Bhowmik, S. Boehm, K. Byler, L. Coates, S.Y.-C. Chen, C.J. Cooper, O. Demerdash, I. Daidone, J. Eblen, S.R. Ellingson, S. Forli, J. Glaser, J.C. Gumbart, J. Gunnels, O. Hernandez, S. Irle, J. Larkin, T.J. Lawrence, S. LeGrand, S.-H. Liu, J.C. Mitchell, G. Park, J.M. Parks, A. Pavlova, L. Petridis, D. Poole, L. Pouchard, A. Ramanathan, D. Rogers, D. Santos-Martins, A. Scheinberg, A. Sedova, S. Shen, J.C. Smith, M.D. Smith, C. Soto, A. Tsaris, M. Thavappiragasam, A.F. Tillack, J.V. Vermaas, V.Q. Vuong, J. Yin, S. Yoo, M. Zahran, L. Zanetti-Polzi. J. Chemical Information and Modeling. 60:5832–5852, 2020.
• 88) Membrane thinning and lateral gating are consistent features of BamA across multiple species.
  J. Liu and J.C. Gumbart. PLoS Computational Biology. 16:e1008355, 2020.
• 87) Structural insight into toxin secretion by contact dependent growth inhibition transporters.
  J. Guerin, I. Botos, Z. Zhang, K. Lundquist, J.C. Gumbart, and S.K. Buchanan. eLife. 9:e58100, 2020.
• 86) Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing and comparison.
  Y.T. Pang, A. Pavlova, E. Tajkhorshid, and J.C. Gumbart. J. Chemical Physics. 153:164104, 2020.
• 85) Fatal arrhythmias: Another reason why doctors remain cautious about chloroquine/hydroxychloroquine for treating COVID-19.
  I. Uzelac, S. Iravanian, H. Ashikaga, N.K. Bhatia, C. Herndon, A. Kaboudian, J.C. Gumbart, E.M. Cherry, and F.H. Fenton. Heart Rhythm. 17:1445–1451, 2020.
• 84) The Effect of (−)-epigallocatechin-3-gallate on the Amyloid-β Secondary Structure.
  A. Acharya, J. Stockmann, L. Beyer, T. Rudack, A. Nabers, J.C. Gumbart, K. Gerwert, and V.S. Batista. Biophysical Journal. 119:349–359, 2020.
• 83) Synergistic biophysical techniques reveal structural mechanisms of engineered cationic antimicrobial peptides in lipid model membranes.
  F. Heinrich, A. Salyapongse, A. Kumagai, F.G. Dupuy, K. Shukla, A. Penk, D. Huster, R.K. Ernst, A. Pavlova, J.C. Gumbart, B. Deslouches, Y.P. Di, and S. Tristram-Nagle. Chemistry: A European Journal. 26:6247–6256, 2020.
• 82) BamA is required for autotransporter secretion.
  D. Ryoo, M. Orwick Rydmark, Y.T. Pang, K. Lundquist, D. Linke, and J.C. Gumbart. Biochimica et Biophysica Acta (BBA) – General Subjects. 1864:129581, 2020.
• 81) Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface.
  C. Domínguez-Medina, M. Pérez-Toledo, A. Schager, J. Marshall, C. Cook, S. Bobat, H. Hwang, B. Chun, E. Logan, J. Bryant, W. Channell, F. Morris, S. Jossi, A. Alshayea, A. Rossiter, P. Barrow, W. Horsnell, C. MacLennan, I. Henderson, J. Lakey, J.C. Gumbart, C. López-Macías, V. Bavro, and A. Cunningham. Nature Communications. 11:851, 2020.
• 80) A minimal membrane metal transport system: Dynamics and energetics of mer proteins.
  H. Hwang, A. Hazel, P. Lian, J.C. Smith, J.C. Gumbart†, and J.M. Parks†. J. Computational Chemistry. 41:528–537, 2020.
• 79) Presence of substrate aids lateral gate separation in LptD.
  K.P. Lundquist and J.C. Gumbart. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1862:183025, 2020.

• 78) Non-detergent isolation of a cyanobacterial photosystem I using styrene maleic acid alternating copolymers.
  N.G. Brady, M. Li, Y. Ma, J.C. Gumbart, and B.D. Bruce. RSC Advances. 9:31781–31796, 2019.
• 77) Conformational dynamics of AcrA govern multidrug efflux pump assembly.
  A.J. Hazel, N. Abdali, I.V. Leus, J.M. Parks, J.C. Smith, H.I. Zgurskaya†, and J.C. Gumbart†. ACS Infectious Diseases. 5:1926–1935, 2019.
• 76) Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette.
  T.G. McCaslin, C.V. Pagba, H. Hwang, J.C. Gumbart, S.-H. Chi, J.W. Perry, and B.A. Barry. Chemical Communications. 55:9399–9402, 2019.
• 75) Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations.
  S.E. Hill, M.S. Kwon, M.D. Martin, A. Suntharalingam, A. Hazel, C.A. Dickey, J.C. Gumbart, and R.L. Lieberman. J. Biological Chemistry. 294:12717–12728, 2019.
• 74) Accelerating membrane simulations with Hydrogen Mass Repartitioning.
  C. Balusek*, H. Hwang*, C.H. Lau, K. Lundquist, A. Hazel, A. Pavlova, D.L. Lynch, P.H. Reggio, Y. Wang†, and J.C. Gumbart†. J. Chemical Theory and Computation. 15:4673–4686, 2019.
• 73) A novel human IL2RB mutation results in T and NK cell-driven immune dysregulation.
  I.Z. Fernandez, R.M. Baxter, J.E. Garcia-Perez, E. Vendrame, T. Ranganath, D.S. Kong, K. Lundquist, T. Nguyen, S. Ogolla, J. Black, C. Galambos, J.C. Gumbart, N. Dawany, J.R. Kelsen, E.F. De Zoeten, R. Quinones, H. Eissa, M. Verneris, K.E. Sullivan, R. Rochford, C.A. Blish, R.M. Kedl, C.M. Dutmer, and E.W.Y. Hsieh. J. Experimental Medicine. 216:1255–1267, 2019.
• 72) ATP-dependent signaling in simulations of a revised model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR).
  K.M. Strickland*, G. Stock*, G. Cui*, H. Hwang, D.T. Infield, I. Schmidt-Krey, N.A. McCarty†, and J.C. Gumbart†. J. Physical Chemistry B. 123:3177–3188, 2019.
• 71) Structure and function of tryptophan-tyrosine dyads in biomimetic β hairpins.
  T.G. McCaslin, C.V. Pagba, S.-H. Chi, H.J. Hwang, J.C. Gumbart, J.W. Perry, C. Olivieri, F. Porcelli, G. Veglia, Z. Guo, M. McDaniel, and B.A. Barry. J. Physical Chemistry B. 123:2780–2791, 2019.
• 70) Identification of binding sites for efflux pump inhibitors of the Escherichia coli AcrAB-TolC component AcrA.
  Z.M. Darzynkiewicz, A.T. Green, N. Abdali, A. Hazel, R.L. Fulton, J. Kimball, Z. Gryczynski, J.C. Gumbart, J.M. Parks, J.C. Smith, H.I. Zgurskaya. Biophysical Journal. 116:648–658, 2019.

• 69) Transmembrane but not soluble helices fold inside the ribosome tunnel.
  M. Bañó-Polo*, C. Baeza-Delgado*, S. Tamborero*, A. Hazel*, B. Grau*, I. Nilsson, P. Whitley, J.C. Gumbart, G. von Heijne, and I Mingarro. Nature Communications. 9:5246, 2018.
• 68) Distribution of mechanical stress in the Escherichia coli cell envelope.
  H. Hwang*, N. Paracini*, J.M. Parks, J.H. Lakey†, and J.C. Gumbart†. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1860:2566–2575, 2018.
• 67) Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships.
  Y. Wang, J. Comer†, Z. Chen, J. Chen†, and J.C. Gumbart†. Environmental Science: Nano. 5:2117–2128, 2018.
• 66) C-terminal kink formation is required for lateral gating in BamA.
  K. Lundquist, J. Bakelar, N. Noinaj, and J.C. Gumbart. Proceedings of the National Academy of Sciences, USA. 115:E7942–E7949, 2018.
• 65) Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields.
  A. Hazel, E. Walters, C. Rowley, and J.C. Gumbart. J. Chemical Physics. 149:072317, 2018.
• 64) Computed free energies of peptide insertion into bilayers are independent of computational method.
  J.C. Gumbart†, M.B. Ulmschneider, A. Hazel, S.H. White, and J.P. Ulmschneider†. J. Membrane Biology. 251:345–356, 2018.
• 63) BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-energy Calculations.
  H. Fu, J.C. Gumbart, H. Chen, X. Shao, W. Cai, and C. Chipot. J. Chemical Information and Modeling. 58:556–560, 2018.
• 62) Development of CHARMM-compatible force-field parameters for cobalamin and related cofactors from quantum mechanical calculations.
  A. Pavlova, J.M. Parks†, and J.C. Gumbart†. J. Chemical Theory and Computation. 14:784–798, 2018.

• 61) Producing membrane proteins one simulation at a time.
  J.C. Gumbart. J. Biological Chemistry. 292:19546–19547, 2017.
• 60) Structure and misfolding of the flexible tripartite coiled coil domain of glaucoma-associated myocilin.
  S.E. Hill, E. Nguyen, R.K. Donegan, A.C. Patterson-Orazem, A. Hazel, J.C. Gumbart, and R.L. Lieberman. Structure. 25:1697–1707, 2017.
• 59) Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery.
  R.S. Bamert*, K. Lundquist*, H. Hwang*, C.T. Webb, T. Shiota, C.J. Stubenrauch, M.J. Belousoff, R.J.A. Goode, R.B. Schittenhelm, R. Zimmerman, M. Jung, J.C. Gumbart†, and T. Lithgow†. Mol. Microbiology. 106:142–156, 2017.
• 58) Toward the rational design of macrolide antibiotics to combat resistance.
  A. Pavlova, J.M. Parks, A.K. Oyelere, and J.C. Gumbart. Chemical Biology & Drug Design. 90:641–652, 2017.
• 57) Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation.
  H. Hwang, T. McCaslin, A. Hazel, C. Pagba, C. Nevin, A. Pavlova, B. Barry, and J.C. Gumbart. J. Physical Chemistry B. 121:3536–3545, 2017.
• 56) The β-barrel assembly machinery in motion.
  N. Noinaj, J.C. Gumbart, and S.K. Buchanan. Nature Reviews Microbiology. 15:197–204, 2017.

• 55) Role of the Native Outer-Membrane Environment on the Transporter BtuB.
  C. Balusek and J.C. Gumbart. Biophysical Journal. 111:1409–1417, 2016.
• 54) Dynamic Behavior of Trigger Factor on the Ribosome.
  J. Deeng, K.Y. Chan, E.O. van der Sluis, O. Berninghausen, W. Han, J. Gumbart, K. Schulten, B. Beatrix, and R. Beckmann. J. Molecular Biology. 428:3588–3602, 2016.
• 53) Transitions of Double-Stranded DNA Between the A- and B-Forms.
  J.T. Waters, X.-J. Lu, R. Galindo-Murillo, J.C. Gumbart, H.D. Kim, T.E. Cheatham III, and S.C. Harvey. J. Physical Chemistry B. 120:8449–8456, 2016.
• 52) DNA Scrunching in the Packaging of Viral Genomes.
  J.T. Waters, H.D. Kim, J.C. Gumbart, X.-J. Lu, and S.C. Harvey. J. Physical Chemistry B. 120:6200–6207, 2016.
• 51) 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. 56:721–733, 2016.
• 50) Structural and Functional Characterization of the LPS Transporter LptDE from Gram-negative Pathogens.
  I. Botos, N. Majdalani, S.J. Mayclin, J. G. McCarthy, K. Lundquist, D. Wojtowicz, T.J. Barnard, J.C. Gumbart, and S.K. Buchanan. Structure. 24:965–976, 2016.
• 49) Membrane proteins: Where theory meets experiment.
  J.C. Gumbart and S. Noskov. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1858:1553–1555, 2016.
• 48) Decrypting protein insertion through the translocon with free-energy calculations.
  J.C. Gumbart and C. Chipot. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1858:1663–1671, 2016.
• 47) Living on the edge: Simulations of bacterial outer-membrane proteins.
  A. Pavlova, H. Hwang, K. Lundquist, C. Balusek, and J.C. Gumbart. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1858:1753–1759, 2016.
• 46) Accelerating the use of molecular modeling in the high school classroom with VMD lite.
  K. Lundquist, C. Herndon, T.H. Harty, and J.C. Gumbart. Biochemistry and Molecular Biology Education. 44:124–129, 2016.

• 45) Parametrization of macrolide antibiotics using the force field toolkit.
  A. Pavlova and J.C. Gumbart. J. Computational Chemistry. 36:2052–2063, 2015.
• 44) Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape.
  L.T. Nguyen, J.C. Gumbart, M. Beeby, and G.J. Jensen. Proceedings of the National Academy of Sciences, USA. 112:E3689–E3698, 2015.
• 43) Conformational changes of the clamp of the protein translocation ATPase SecA.
  Y. Chen, B.W. Bauer, T.A. Rapoport, and J.C. Gumbart. J. Molecular Biology. 427:2348–2359, 2015.
• 42) Structural and biophysical characterization of epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.
  J.L. Johnson, K.C. Entzminger, J. Hyun, S. Kalyoncu, D.P. Heaner, I.A. Morales, A. Sheppard, J.C. Gumbart, J.A. Maynard and R.L. Lieberman. Acta Cryst. D. 71:896–906, 2015.
• 41) 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.

• 40) 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.
• 39) Thermodynamics of deca-alanine folding in water.
  A. Hazel, C. Chipot, and J.C. Gumbart. J. Chemical Theory and Computation. 10:2836–2844, 2014.
• 38) Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations.
  J.C. Gumbart, M. Beeby, G. Jensen, and B. Roux. PLoS Computational Biology. 10:e1003475, 2014.
• 37) Structure of the SecY channel during initiation of protein translocation.
  E. Park, J.-F. Ménétret, J.C. Gumbart, S.J. Ludtke, W. Li, A. Whynot, T.A. Rapoport and C.W. Akey. Nature. 506:102–106, 2014.
• 36) Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
  W. Jiang, J.C. Phillips, L. Huang, M. Fajer, Y. Meng, J.C. Gumbart, Yun Luo, K. Schulten, and B. Roux. Computer Physics Communications. 185:908–916, 2014.

• 35) Structural insight into the biogenesis of β-barrel membrane proteins.
  N. Noinaj, A.J. Kuszak, J.C. Gumbart, P. Lukacik, H. Chang, N.C. Easley, T. Lithgow, and S.K. Buchanan. Nature. 501:385–390, 2013.
• 34) Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.
  F. Khalili-Araghi, B. Ziervogel, J.C. Gumbart, and B. Roux. J. General Physiology. 142:465–475, 2013.
• 33) 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.
• 32) 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, and B.T. Sewell. J. Biological Chemistry. 288:28514–28523, 2013.
• 31) The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state.
  A. Briegel, P. Ames, J.C. Gumbart, C.M. Oikonomou, J.S. Parkinson, and G. Jensen. Mol. Microbiology. 89:831–841, 2013.
• 30) Efficient determination of protein-protein standard binding free energies from first principles.
  J.C. Gumbart, B. Roux, and C. Chipot. J. Chemical Theory and Computation. 9:3789–3798, 2013.
• 29) IcmQ in the Type 4b secretion system contains an NAD⁺ binding domain.
  J.D. Farelli, J.C. Gumbart, I.V. Akey, A. Hempstead, W. Amyot, J.F. Head, C.J. McKnight, R.R. Isberg, and C.W. Akey. Structure. 21:1361–1373, 2013.
• 28) Architecture and assembly of the Gram-positive cell wall.
  M. Beeby, J.C. Gumbart, B. Roux, and G. Jensen. Mol. Microbiology. 88:664–672, 2013.
• 27) Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion.
  J.C. Gumbart, I. Teo, B. Roux, and K. Schulten. J. American Chemical Society, 135:2291–2297, 2013.
• 26) Standard binding free energies from computer simulations: What is the best strategy?
  J.C. Gumbart, B. Roux, and C. Chipot. J. Chemical Theory and Computation. 9:794–802, 2013.

Start at Georgia Tech in Jan. 2013

• 25) A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism.
  S.G. Broadley, J.C. Gumbart, B.W. Weber, M.J. Marakalala, D.J. Steenkamp, and B.T. Sewell. Acta Cryst. D. 68:1450–1459, 2012.
• 24) Mechanisms of SecM-mediated stalling in the ribosome.
  J. Gumbart , E. Schreiner, D.N. Wilson, R. Beckmann, and K. Schulten. Biophysical Journal. 103:331–341, 2012.
• 23) Structural basis for iron piracy by pathogenic Neisseria.
  N. Noinaj, N.C. Easley, M. Oke, N. Mizuno, J. Gumbart, E. Boura, A.N. Steere, O. Zak, P. Aisen, E. Tajkhorshid, R.W. Evans, A.R. Gorringe, A.B. Mason, A.C. Steven, and S.K. Buchanan. Nature. 483:53–58, 2012.
• 22) Determination of membrane-insertion free energies by molecular dynamics simulations.
  J. Gumbart† and B. Roux. Biophysical Journal. 102:795–801, 2012.
  Featured in Biophysical Journal’s “Best of 2012”.
• 21) Constant electric field simulations of the membrane potential illustrated with simple systems.
  J. Gumbart, F. Khalili-Araghi, M. Sotomayor, and B. Roux. Biochimica et Biophysica Acta (BBA) – Biomembranes. 1818:294–302, 2012.
• 20) Molecular basis for activation of a catalytic asparagine residue in a self-cleaving bacterial autotransporter.
  T.J. Barnard, J. Gumbart, J.H. Peterson, N. Noinaj, N.C. Easley, N. Dautin, A.J. Kuszak, E. Tajkhorshid, H.D. Bernstein, and S.K. Buchanan. J. Molecular Biology. 415:128–142, 2012.

• 19) Symmetry-restrained flexible fitting for symmetric EM maps.
  K.-Y. Chan, J. Gumbart, R. McGreevy, J.M. Watermeyer, B.T. Sewell, and K. Schulten. Structure. 19:1211–1218, 2011.
• 18) Free energy of nascent-chain folding in the translocon.
  J. Gumbart, C. Chipot, and K. Schulten. J. American Chemical Society. 133:7602–7607, 2011.
• 17) Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
  J. Frauenfeld, J. Gumbart, E.O. van der Sluis, S. Funes, M. Gartmann, B. Beatrix, T. Mielke, O. Berninghausen, T. Becker, K. Schulten, and R. Beckmann. Nature Structural & Molecular Biology. 18:614–621, 2011.
• 16) Free-energy cost for translocon-assisted insertion of membrane proteins.
  J. Gumbart, C. Chipot, and K. Schulten. Proceedings of the National Academy of Sciences, USA. 108:3596–3601, 2011.
• 15) Applications of the molecular dynamics flexible fitting method.
  L.G. Trabuco, E. Schreiner, J. Gumbart, J. Hsin, E. Villa, and K. Schulten. J. Structural Biology. 173:420–427, 2011.

• 14) Self-assembly of photosynthetic membranes.
  J. Hsin, D.E. Chandler, J. Gumbart, C.B. Harrison, M. Sener, J. Strumpfer, and K. Schulten. ChemPhysChem. 11:1154–1159, 2010.

• 13) Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
  T. Becker, S. Bhushan, A. Jarasch, J.-P. Armache, S. Funes, F. Jossinet, J. Gumbart, T. Mielke, O. Berninghausen, K. Schulten, E. Westhof, R. Gilmore, E.C. Mandon, and R. Beckmann. Science. 326:1369–1373, 2009.
• 12) Membrane curvature induced by aggregates of LH2s and monomeric LH1s.
  D.E. Chandler, J. Gumbart, J.D. Stack, C. Chipot, and K. Schulten. Biophysical Journal. 97:2978–2984, 2009.
• 11) Regulation of the protein-conducting channel by a bound ribosome.
  J. Gumbart, L.G. Trabuco, E. Schreiner, E. Villa, and K. Schulten. Structure. 17:1453–1464, 2009.
• 10) Coupling of calcium and substrate binding through loop alignment in the outer membrane transporter BtuB.
  J. Gumbart, M.C. Wiener, and E. Tajkhorshid. J. Molecular Biology. 393:1129–1142, 2009.
• 9) Protein-induced membrane curvature investigated through molecular dynamics flexible fitting.
  J. Hsin, J. Gumbart, L.G. Trabuco, E. Villa, P. Qian, C.N. Hunter, and K. Schulten. Biophysical Journal. 97:321–329, 2009.
• 8) Molecular dynamics simulations of membrane channels and transporters.
  F. Khalili-Araghi, J. Gumbart, P.-C. Wen, M. Sotomayor, E. Tajkhorshid, and K. Schulten. Current Opinion in Structural Biology. 19:128–137, 2009.

• 7) The roles of pore ring and plug in the SecY protein-conducting channel.
  J. Gumbart and K. Schulten. J. General Physiology. 132:709–719, 2008.
• 6) Intrinsic curvature properties of photosynthetic proteins in chromatophores.
  D. Chandler*, J. Hsin*, C.B. Harrison*, J. Gumbart*, and K. Schulten. Biophysical Journal. 95:2822–2836, 2008.

• 5) Structural determinants of lateral gate opening in the protein translocon.
  J. Gumbart and K. Schulten. Biochemistry. 46:11147–11157, 2007.
• 4) Mechanics of force propagation in TonB-dependent outer membrane transport.
  J. Gumbart, M.C. Wiener, and E. Tajkhorshid. Biophysical Journal. 93:496–504, 2007.
  Featured in Science Magazine’s Editors’ Choice: Science, 316:1101, 2007.

• 3) Molecular dynamics studies of the archaeal translocon.
  J. Gumbart and K. Schulten. Biophysical Journal. 90:2356–2367, 2006.

• 2) Scalable molecular dynamics with NAMD.
  J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, and K. Schulten. J. Computational Chemistry. 26:1781–1802, 2005.
• 1) Molecular dynamics simulations of proteins in lipid bilayers.
  J. Gumbart, Y. Wang, A. Aksimentiev, E. Tajkhorshid, and K. Schulten. Current Opinion in Structural Biology. 15:423–431, 2005.

 

• Preparing membrane proteins for simulation using CHARMM-GUI. Y. Li, J. Liu, and J.C. Gumbart. In I. Schmidt-Krey and J.C. Gumbart, editors, Structure and Function of Membrane Proteins. Springer. pp. 237-251. 2021.
• Diverse protein-folding pathways and functions of β-hairpins and β-sheets.
  C. Balusek, H. Hwang, A. Hazel, K. Lundquist, A. Pavlova, and J.C. Gumbart. In L. Olivares-Quiroz, O. Guzman-Lopez, H.E. Jardon-Valadez, editors, Quantitative Models for Microscopic to Macroscopic Biological Macromolecules and Tissues. Springer. pp. 1–20. 2018.
• Coarse-grained molecular dynamics simulations of the bacterial cell wall. L.T. Nguyen, J.C. Gumbart, and G.J. Jensen. In H-J. Hong, editor, Methods in Molecular Biology. 1440:247–270. Springer, 2016.
• Exploring substrate diffusion using biased molecular dynamics simulations. J. Gumbart. In N. Vaidehi and J. Klein-Seetharaman, editors, Methods in Molecular Biology. 914:337–350. Springer, 2012.
• Viewing the mechanisms of translation through the computational microscope.
  J. Gumbart, E. Schreiner, L.G. Trabuco, K.-Y. Chan, and K. Schulten. In Joachim Frank, editor, Molecular Machine in Biology, chapter 8, pp. 142–157. Cambridge University Press, 2011.
• Molecular mechanisms of active transport across the cellular membrane.
  P.-C. Wen, Z. Huang, G. Enkavi, Y. Wang, J. Gumbart, and E. 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.
• Long time and large size molecular dynamics simulations made feasible through new TeraGrid hardware and software.
  K. Vandivort, J.C. Phillips, E. Villa, P.L. Freddolino, J. Gumbart, L.G. Trabuco, D.E. Chandler, J. Hsin, C.B. Harrison, L. Kale, and K. Schulten. Proceedings of the 2008 TeraGrid Conference, 2008.