Forschungsprofil Prof. Dr. Gerhard Hummer

Prof. Dr. Gerhard Hummer
  • Dr. rer. nat., Physics, University of Vienna, Austria, and Max Planck Institute of Biophysical Chemistry, Göttingen, Germany, 1992
  • Postdoc, Los Alamos National Laboratory, USA, 1993-1996
  • Group leader, Los Alamos National Laboratory, USA, 1996-1999
  • Group leader, National Institutes of Health, USA, 1999-2013
  • Director, Department of Theoretical Biophysics, since 2013

    Prizes and Awards
    (Selection):
  • 2010 Raymond and Beverly Sackler International Prize in Biophysics
  • 2010 Nancy Nossal Scientific Mentorship Award, National Institutes of Health
  • 2005 Fellow, American Physical Society

Gerhard Hummer - Publication list

SELECTED PUBLICATIONS

A. H. Bahrami, M. G. Lin, X. Ren, J. H. Hurley, G. Hummer, “Scaffolding the cup-shaped double membrane in autophagy,” PLoS Comput Biol13(10): e1005817 (2017). [https://doi.org/10.1371/journal.pcbi.1005817]

C. T. Leahy, A. Kells, G. Hummer, E. Rosta, N.V. Buchete, “Peptide dimerization-dissociation rates from replica exchange molecular dynamics,” J. Chem. Phys. 147, 152725 (2017). [https://doi.org/10.1063/1.5004774

A. H. Bahrami, G. Hummer, “Formation and stability of lipid membrane nanotubes,” ACS Nano, 11, 9558-9565 (2017). [https://doi.org/10.1021/acsnano.7b05542]

L. Stelzl, G. Hummer, “Kinetics from replica exchange molecular dynamics simulations,” J. Chem. Theory. Comput. 13, 3927-3935 (2017). [https://doi.org/10.1021/acs.jctc.7b00372]

L. Stelzl, N. Erlenbach, M. Heinz, T. Prisner, G. Hummer, “Resolving the conformational dynamics of dna with Ångstrom resolution by PELDOR and molecular dynamics,” J. Am. Chem. Soc. [Communication] 139, 11674-11677 (2017). [https://doi.org/10.1021/jacs.7b05363]

L. Martini, A. Kells, R. Covino, G. Hummer, N.V. Buchete, E. Rosta, “Variational identification of Markovian transition states,” Phys. Rev. X 7, 031060 (2017). [https://doi.org/10.1103/PhysRevX.7.031060]

H. Jung, K.-i. Okazaki, G. Hummer, “Transition path sampling of rare events by shooting from the top,” J. Chem. Phys. 147, 152716 (2017). [https://doi.org/10.1063/1.4997378]

K. Halbleib, K. Pesek, R. Covino, H. F. Hofbauer, D. Wunnicke, I. Hänelt, G. Hummer, R. Ernst, “Activation of the unfolded protein response by lipid bilayer stress,” Mol. Cell 67, 63-684 (2017). [https://doi.org/10.1016/j.molcel.2017.06.012]

E. Chiavazzo, R.R. Coifman, R. Covino, C.W. Gear, A.S. Georgiou, G. Hummer, I.G. Kevrekidis, “Intrinsic Map Dynamics exploration for uncharted effective free energy landscapes,” Proc. Natl. Acad. Sci. U.S.A. 114, E5494–E5503 (2017). [https://doi.org/10.1073/pnas.1621481114]

M. Diskowski, A.R. Mehdipour, D. Wunnicke, D. J. Mills, V. Mikusevic, N. Bärland, J. Hoffmann, N. Morgner, H.J. Steinhoff, G . Hummer, J. Vonck, I. Hänelt, “Helical jackknives control the gates of the double pore K+ uptake system KtrAB”, eLife 6, e24303 (2017). [https://doi.org/10.7554/eLife.24303]

D. Malinverni, A. Jost Lopez, P. De Los Rios, G. Hummer, A. Barducci, “Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis,” eLife, 6, e23471 (2017). [https://doi.org/10.7554/eLife.23471]

A. Ghysels, R. Venable, R. Pastor, G. Hummer, “Position-dependent diffusion tensors in anisotropic media from simulation: oxygen transport in and through membranes,” J. Chem. Theor. Comput., 13, 2962-2976 (2017). [https://doi.org/10.1021/acs.jctc.7b00039]

C. Karathansis, G. Hummer, M. Heilemann, “Molecule counts in localization microscopy with organic fluorophores,” ChemPhysChem 18, 942-948 (2017). [https://doi.org/10.1002/cphc.201601425 ]

R. M. Bhaskara, S. Linker, M. Vögele, J. Köfinger, G. Hummer, “Carbon nanotubes mediate fusion of lipid vesicles,” ACS Nano 12, 1273-1280 (2017). [https://doi.org/10.1021/acsnano.6b05434]

A. Nöll, C. Thomas, V. Herbring, T. Zollmann, K. Barth, A. R. Mehdipour, T. M. Tomasiak, S. Brüchert, B. Joseph, R. Abele, V. Oliéric, M. Wang, K. Diederichs, G. Hummer, R. M. Stroud, K. M. Pos, R. Tampé, “Structure and mechanistic basis of a functional homolog of the antigen transporter TAP,” Proc. Natl. Acad. Sci. U.S.A. 114, E438–E447 (2017).[https://doi.org/10.1073/pnas.1620009114 ]

K. Reichel, O. Fisette, T. Braun, O.F. Lange, G. Hummer, and L.V. Schäfer, “Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints,”Proteins Struct. Funct. Bioinf. 85, 812-826 (2017). [https://doi.org/10.1002/prot.25224]

M. Simonson, G. Hummer, B. Roux, “On the equivalence of M- and P-summation in calculations of ionic solvation free energies,”J. Phys. Chem. A 121, 1525-1530 (2017). [https://doi.org/ 10.1021/acs.jpca.6b12691]

G. Hummer , A. Szabo, “Dynamics of the orientational factor in fluorescence resonance energy transfer,” J. Phys. Chem. B 121, 3331-3339 (2017) [Klaus Schulten Festschrift] [https://doi.org/10.1021/acs.jpcb.6b08345]

P. Cossio, D. Rohr, F. Baruffa, M. Rampp, V. Lindenstruth, G. Hummer, “BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images,” Computer Phys. Commun. 210, 163-171 (2017). [https://doi.org/10.1016/j.cpc.2016.09.014]

G. Hummer, F. Fricke, M. Heilemann, “Model-independent counting of molecules in single-molecule localization microscopy,” Mol. Biol. Cell 27 (22) 3637-3644 (2016). [https://doi.org/10.1091/mbc.E16-07-0525]

E. Lehnert, J. Mao, A. Mehdipour, G. Hummer, R. Abele, C. Glaubitz, R. Tampé, “Antigenic peptide recognition on the human ABC transporter TAP resolved by DNP-enhanced solid-state NMR spectroscopy,” J. Am. Chem. Soc. 138, 13967-13974 (2016). [https://doi.org/10.1021/jacs.6b07426]

R. Covino, S. Ballweg, C. Stordeur, J. B. Michaelis, K. Puth, F. Wernig, A. Bahrami, A. M. Ernst, G. Hummer, Robert Ernst, “A eukaryotic sensor for membrane lipid saturation,” Mol. Cell 63, 49-59 (2016). [https://doi.org/10.1016/j.molcel.2016.05.015].

P. Cossio, G. Hummer, A. Szabo, “Kinetic ductility and force-spike resistance of proteins from single-molecule force spectroscopy,” Biophys. J. 111, 832-840 (2016). [authors.elsevier.com/a/1TbSb1SPSgVDB]

A. R. Mehdipour, G. Hummer, “Cardiolipin puts the seal on ATP synthase,” Proc. Natl. Acad. Sci. U.S.A. 113, 8568-8570 (2016). [https://doi.org/10.1073/pnas.1609806113]

M. Vögele, G. Hummer, “Divergent diffusion coefficients in simulations of fluids and lipid membranes” J. Phys. Chem. B 120, 8722-8732 (2016). [https://doi.org/10.1021/acs.jpcb.6b05102]

C. T. Leahy, R. D. Murphy, G. Hummer, E. Rosta, and N.-V. Buchete, “Coarse master equations for binding kinetics of amyloid peptide dimers,” J. Phys. Chem. Lett. 7, 2676-2682 (2016). [https://doi.org/10.1021/acs.jpclett.6b00518]

R. B. Best, G. Hummer, “Microscopic interpretation of folding φ-values using the transition-path ensemble,” Proc. Natl. Acad. Sci. U.S.A. 113, 3263-3268 (2016). [https://doi.org/10.1073/pnas.1520864113]

G. Hummer, M. Wikström, “Molecular simulation and modeling of complex I,” Biochim. Biophys. Acta-Bioenergetics 1857, 915-921 (2016). [https://doi.org/10.1016/j.bbabio.2016.01.005]

M. Sugawa, K.-I. Okazaki, M. Kobayashi, T. Matsui, G. Hummer, T. Masaike, T. Nishizaka, “F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements,” Proc. Natl. Acad. Sci. U.S.A. 113, E2916-E2924 (2016) [https://doi.org/10.1073/pnas.1524720113]

A. Blees, K. Reichel, S. Trowitzsch, O. Fisette, C. Bock, R. Abele, G. Hummer, L. Schäfer, R. Tampé, “Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch,” Scientific Reports 5, 17341 (2015). [https://doi.org/10.1038/srep17341]

G. Hummer, J. Köfinger, “Bayesian ensemble refinement by replica simulations and reweighting,” J. Chem. Phys. 143, 243150 (2015). [https://doi.org/10.1063/1.4937786]

P. Cossio, G. Hummer, and A. Szabo. On artifacts in single-molecule force spectroscopy. Proc Natl Acad Sci, USA. Vol. 112, Issue 46, 14248-53 (2015). [https://doi.org/10.1073/pnas.1519633112]

T.R.M. Barends, L. Foucar, A. Ardevol, K. Nass, A. Aquila, S. Botha, R.B. Doak, K. Falahati, E. Hartmann, M. Hilpert, M. Heinz, M.C. Hoffmann, Köfinger J, J.E. Koglin, G. Kovacsova, M. Liang, D. Milathianaki, H. Lemke, J. Reinstein, C.M. Roome, R.L. Shoeman, G.J. Williams, I. Burghardt, G. Hummer, S. Boutet, I. Schlichting, “Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation,” Science 350, 445-450 (2015). [https://doi.org/10.1126/science.aac5492]

K.-I. Okazaki, G. Hummer, “Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase,” Proc. Natl. Acad. Sci. U.S.A. 112, 10720-10725 (2015). [https://doi.org/10.1073/pnas.1500691112]

V. Sharma, G. Belevich, A.P. Gamiz-Hernandez, T. Róga, I. Vattulainen,  M. Verkhovskaya, M. Wikström, G. Hummer, V.R.I. Kaila, “Redox-induced activation of the proton pump in the respiratory complex I”, Proc. Natl. Acad. Sci. U.S.A., 112, 11571-6 (2015) [https://doi.org/10.1073/pnas.1500691112]

A.B. Mantsyzov, A.Y. Shen, J.-H. Lee, G. Hummer, A. Bax, “MERA: A webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data,” J. Biomol. NMR, 63, 85-95 (2015) [https://doi.org/10.1007/s10858-015-9971-2]

J. Köfinger, M. J. Ragusa, I.-H. Lee, G. Hummer, J. H. Hurley, “Solution structure of the Atg1 complex: Implications for the architecture of the phagophore assembly site,” Structure 23, 809-818 (2015).

A. Sali, H.M. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S.K. Burley, J. Markley, H. Nakamura, P. Adams, A.M. Bonvin, W. Chiu, M.D. Peraro, M. Diaio F, T.E. Ferrin, K. Grünewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C.L. Lawson, J. Meiler, Marti-M.A. Renom, G.T. Montelione, M. Nilges, Nussinov R, A. Patwardhan, J. Rappsilber, R.J. Read, H. Saibil, Schröder G.F, C.D. Schwieters, C.A. Seidel, D. Svergun, M. Topf, E.L. Ulrich, S. Velankar, J.D. Westbrook, “Outcome of the first wwPDB hybrid/integrative methods task force workshop,” Structure 23, 1156-1167 (2015).

K. Kmita, C. Wirth, J. Warnau, S. Guerrero-Castillo, C. Hunte, G. Hummer, V.R.I. Kaila, K. Zwicker, U. Brandt, V. Zickermann, “Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I,” Proc. Natl. Acad. Sci. U.S.A. 112, 5685-5690 (2015).

M. Wikström,V. Sharma, V.R.I. Kaila, J. Hosler, G. Hummer, “New perspectives on proton pumping in cellular respiration,” Chemical Reviews, 115, 2196-2221 (2015). [https://doi.org/10.1021/cr500448t]

G. Hummer, A. Szabo, “Optimal dimensionality reduction of multistate kinetic and Markov-state models,” J. Phys. Chem. B, 119, 9029-9037 (2015).
[https://doi.org/10.1021/jp508375q]

A. P. Gamiz-Hernandez, A. Magomedov, G. Hummer, V. R. Kaila, “Linear energy relationships in ground state proton transfer and excited state proton-coupled electron transfer,” J. Phys. Chem. B 119, 2611–2619, (2015). [https://doi.org/10.1021/jp508790n]

E. Rosta, G. Hummer, “Free energies from dynamic weighted histogram analysis using unbiased Markov state model,” J. Chem. Theory Comput. 11, 276-285 (2015). [https://doi.org/10.1021/ct500719p]

A. Tokmakoff, G. Hummer, “Preface: Special topic on biological water,” J. Chem. Phys. 141, 22D101 (2014).

G. Hummer, “Potassium ions line up. Do K+ ions move in single file through potassium channels?” Science 346, 303 (2014). Summary - Reprint - Full text

M. E. Johnson, G. Hummer, “Free-propagator reweighting integrator for single-particle dynamics in reaction-diffusion models of heterogeneous protein-protein interaction systems,” Phys. Rev. X 4, 031037 (2014).

L. V. Nedialkova, Miguel A. Amat, I. G. Kevrekidis, G. Hummer, “Diffusion maps, clustering and fuzzy markov modeling in peptide folding transitions,” J. Chem. Phys. 141, 114102 (2014).

A. B. Mantsyzov, A. S. Maltsev, J. Ying, Y. Shen, G. Hummer, A. Bax, “A maximum entropy approach to the study of residue-specific backbone angle distributions in a-synuclein, an intrinsically disordered protein,” Protein Sci. 23, 1275-1290 (2014).

V. R. I. Kaila, M. Wikström, G. Hummer, “Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I,” Proc. Natl. Acad. Sci. USA 111, 6988–6993 (2014).

E. Rosta, W. Yang, G. Hummer, “Calcium inhibition of ribonuclease H1 two-metal ion catalysis,” J. Am. Chem. Soc. 136, 3137-3144 (2014).

V. R. I. Kaila, F. Schotte, H.-S. Cho, G. Hummer, P. A. Anfinrud, “Reconciling contradictions in time-resolved x-ray structures of early intermediates in the photocycle of photoactive yellow protein,” Nature Chemistry 6, 258-259 (2014).

Dellago C, Hummer G, “Computing equilibrium free energies using non-equilibrium molecular dynamics,” Entropy 16, 41-61 (2014).

Hummer G, “Nobel 2013 – Methods for computational chemistry. Computer experiments,” Nature 504, 96-97 (2013). [News & Views] [PMID: 24305156]

Best R.B, Hummer G, Eaton W.A, “Native contacts determine protein folding mechanisms in atomistic simulations,” Proc. Natl. Acad. Sci. USA 110, 17874-17879 (2013). [PMID: 24128758]

Cossio P, Hummer G, “Bayesian analysis of individual electron microscopy images: Towards structures of dynamic and heterogeneous biomolecular assemblies”, J. Struct. Biol. 184, 427-437 (2013). [PMID: 24161733]

Okazaki KI, Hummer G, Phosphate release coupled to rotary motion of F1-ATPase, Proc. Natl. Acad. Sci. USA (41):16468-73, 2013. [PMID: 24062450]

Johnson ME, Hummer G, Evolutionary pressure on the topology of protein interface interaction networks, J Phys Chem B, in press, 2013. [PMID: 23701316]

Johnson ME, Hummer G, Interface-resolved network of protein-protein interactions, PLoS Comp Biol (9):e1003065, 2013. [PMID: 23696724]

Köfinger J, Hummer G, Atomic-resolution structural information from scattering experiments on macromolecules in solution, Phys Rev E (87):052712, 2013. [PMID: 23767571]

Grigoriu S, Bond R, Cossio P, Chen JA, Ly N, Hummer G, Page R, Cyert MS, Peti W, The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin, PLoS Biol (11):e1001492, 2013. [PMID: 23468591]

Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À, Theoretical study of the mechanism of the hydride transfer between Ferredoxin NADP+ reductase and NADP+. The role of Tyr303, J Am Chem Soc (134):20544-20553, 2012. [PMID: 23181670]

Schotte F, Cho HS, Kaila VRI, Kamikubo H, Dashdorj N, Henry E, Graber T, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA, Picosecond photobiology: Watching a signaling protein function in real time via time-resolved Laue crystallography, Proc Natl Acad Sci USA (109):19256-19261, 2012. [PMID: 23132943]

Rozycki B, Boura E, Hurley JH, Hummer G, Membrane-elasticity model of coatless vesicle budding induced by ESCRT complexes, PLoS Comp Biol (10):e1002736, 2012. [PMID: 23093927]

Zhu F, Hummer G, Theory and simulation of ion conduction in the pentameric GLIC channel, J. Chem. Theory Comput. (8):3759-3768, 2012. [PMID: 22853899]

Zhu F, Hummer G, Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophys J (103):219-27, 2012. [PMID: 22853899]

Johnson ME, Hummer G, Characterization of a dynamic string method for the construction of transition pathways in molecular reactions. J Phys Chem B (116):8573-83, 2012. [PMID: 22616575]

Hummer G, Eaton WA, Viewpoint: Transition path times for DNA and RNA folding from force spectroscopy. Physics (5):87, 2012. [Full text/Abstract]

Mittal J, Hummer G, Pair diffusion, hydrodynamic interactions, and available volume in dense fluids. J Chem Phys (137):034110, 2012. [PMID: 22830686]

Waghe A, Rasaiah JC, Hummer G, Entropy of single-file water in (6, 6) carbon nanotubes. J Chem Phys (137):044709, 2012. [PMID: 22852646]

Wikström M, Hummer G, Stoichiometry of proton translocation by respiratory Complex I and its mechanistic implications. Proc Natl Acad Sci USA (109):4431-6, 2012. [PMID: 22392981]

Boura E, Rozycki B, Chung HS, Herrick DZ, Canagarajah B, Cafiso D, Eaton WA, Hummer G, Hurley JH, Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure (20):874-86, 2012. [PMID: 22579254]

Kim YC, Hummer G, Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach. Biochim Biophys Acta-Bioenergetics (1817):526-36, 2012. [PMID: 21946020]

Zhu F, Hummer G, Convergence and error estimation in free energy calculations using the weighted histogram analysis method. J Comp Chem (33):453-65, 2012. [PMID: 22109354]

Francis DM, Rozycki B, Koveal D, Hummer G, Page R, Peti W, Structural basis of p38α regulation and specificity by hematopoietic tyrosine phosphatase. Nature Chem Biol (7):916-24, 2011. [PMID: 22057126]

Francis DM, Rozycki B, Tortajada A, Hummer G, Peti W, Page R, Resting and Active States of the ERK2:HePTP Complex. J Am Chem Soc (133):17138–41, 2011. [PMID: 21985012] [Full text/Abstract]

Kaila VRI, Hummer G, Energetics of direct and water-mediated proton-coupled electron transfer. J Am Chem Soc (133):19040–3, 2011. [PMID: 21988482]

Best RB, Hummer G, Diffusion models of protein folding. Phys Chem Chem Phys (13):1690-11, 2011. [PMID: 21842082]

Köfinger J, Hummer G, Dellago C, Single-file water in nanopores. Phys Chem Chem Phys (13):15403-17, 2011. [PMID: 21779552]

Kaila VRI, Hummer G, Energetics and dynamics of proton transfer reactions along short water wires. Phys Chem Chem Phys 13, 13207-15, 2011. [PMID: 21701719]

Rosta E, Nowotny M, Yang W, Hummer G, Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc 133, 8934-41, 2011. [PMID: 21539371]

Boura E, Rozycki B, Herrick DZ, Chung HS, Vecer J, Eaton WA, Cafiso D, Hummer G, Hurley JH, Solution structure of the ESCRT-I complex by small angle x-ray scattering, EPR, and FRET spectroscopy. Proc Natl Acad Sci USA 108, 9437-42, 2011. [PMID: 21596998] [Full text/Abstract]

Johnson ME, Hummer G, Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci USA(108):603-8, 2011. [PMID: 21187424] [Full text/Abstract]

Rozycki B, Kim YC, Hummer G, SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure (19):109-16, 2011. [PMID: 21220121] [Full text/Abstract]

Leonard TA, Rozycki B, Saidi LF, Hummer G, Hurley JH Crystal structure and allosteric activation of protein kinase C bII. Cell (144):55-66, 2011. [PMID: 21215369] [Full text/Abstract]

Hummer G, Szabo A Free energy profiles from single-molecule pulling experiments. Proc Natl Acad Sci USA (107):21441-6, 2010. [PMID: 21098304] [Full text/Abstract]

Zhu F, Hummer G, Pore opening and closing of a pentameric ligand-gated ion channel. Proc Natl Acad Sci USA (107):19814-9, 2010. [PMID: 21041674] [Full text/Abstract]

Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC Water in the polar and nonpolar cavities of the protein interleukin-1β. J Phys Chem B (114):16290-7, 2010. [PMID: 21047091] [Full text/Abstract] 

Kalra A, Garde S, Hummer G, Lubrication by molecularly thin water films confined between nanostructured membranes. Eur Phys J (189):147-54, 2010. [Full text/Abstract] 

Hummer G, Molecular binding: under water’s influence. Nature Chemistry (2):906-7, 2010. [PMID: 20966940] [Full text/Abstract] 

Mittal J, Hummer G, Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discuss (146):341-52, 2010. [PMID: 21043431] [Full text/Abstract] 

Best RB, Hummer G, Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci USA (107):1088-93, 2010. [PMCID: PMC2824289] [Full text/Abstract]

Rosta E, Hummer G, Error and efficiency of simulated tempering simulations. J Chem Phys (132):034102, 2010. [PMID: 19894977] [Full text/Abstract]

Hummer G, Catching a protein in the act. Proc Natl Acad Sci USA (107):2381-2, 2010 [PMCID: PMC2823913] [Full text/Abstract]

Kim YC, Furchtgott L, Hummer G, Biological proton pumping in an oscillating electric field. Phys Rev Lett (103):268102, 2009. [PMID: 20366348] [Full text/Abstract]

Zhu FQ, Hummer G, Gating Transition of Pentameric Ligand-Gated Ion Channels. Biophysical Journal (97):2456-63, 2009. [Full text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Rosta E, Hummer G, Error and efficiency of replica exchange molecular dynamics simulations. Journal of Chemical Physics (131):165102, 2009. [Full text http://www2.niddk.nih.gov/Footer/Disclaimer.htm /Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Frewen TA, Hummer G, Kevrekidis IG Exploration of effective potential landscapes using coarse reverse integration. Journal of Chemical Physics (131):134104, 2009. [Full text http://www2.niddk.nih.gov/Footer/Disclaimer.htm /Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Kim YC, Wikström M, Hummer G, Kinetic gating of the proton pump in cytochrome c oxidase. Proceedings of the National Academy of Sciences USA (106):13707-12, 2009. [Full text http://www2.niddk.nih.gov/Footer/Disclaimer.htm/Abstract http://www2.niddk.nih.gov/Footer/Disclaimer.htm]

Kaila VRI, Verkhovsky MI, Hummer G, Wikström M Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochimica et Biophysica Acta-Bioenergetics (1787):1205-14, 2009. [Full text http://www2.niddk.nih.gov/Footer/Disclaimer.htm/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Best RB, Hummer G, Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides. Journal of Physical Chemistry B (113):9004-15, 2009. [Full texthttp://www2.niddk.nih.gov/Footer/Disclaimer.htm /Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial Reaction Coordinate Tunneling in Free-Energy Calculations: The Catalytic Reaction of RNase H. Journal of Computational Chemistry (30):1634-41, 2009. [Full text /Abstract]

Berezhkovskii A, Hummer G, Szabo A Reactive flux and folding pathways in network models of coarse-grained protein dynamics. Journal of Chemical Physics(130):205102, 2009. [Full text http://www2.niddk.nih.gov/Footer/Disclaimer.htm/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Turjanski AG, Hummer G, Gutkind JS How Mitogen-Activated Protein Kinases Recognize and Phosphorylate Their Targets: A QM/MM Study. Journal Of The American Chemical Society(131): 6141-8, 2009. [Full text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Rosta E, Buchete NV, Hummer G, Thermostat Artifacts in Replica Exchange Molecular Dynamics Simulations. Journal of Chemical Theory and Computation (5):1393-9, 2009. [Full text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Köfinger J, Hummer G, Dellago, C A one-dimensional dipole lattice model for water in narrow nanopores. Journal of Chemical Physics(130):154110, 2009. [Full texthttp://www2.niddk.nih.gov/Footer/Disclaimer.htm/Abstract]http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Ren XF, Kloer DP, Kim YC, Ghirlando R, Saidi LF, Hummer G, Hurley JH Hybrid Structural Model of the Complete Human ESCRT-0 Complex. Structure (17):406-16, 2009. [Full texthttp://www2.niddk.nih.gov/Footer/Disclaimer.htm/Abstract]http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Best RB, Hummer G, Unfolding the secrets of calmodulin. Science(323):593-4, 2009 [Summary ; Full Text ] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Mittal J, Hummer G, Static and dynamic correlations in water at hydrophobic interfaces. Proc Natl Acad Sci U S A(105):20130-5. 2008.

Best RB, Buchete NV, Hummer G, Are current molecular dynamics force fields too helical? Biophys J(95): L07-9, 2008. [Full Text/Abstract]

Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc(130): 10141-9, 2008. [Full Text/Abstract]

Turjanski AG, Gutkind JS, Best RB, Hummer G, Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol(4): e1000060, 2008. [Full Text/Abstract]

Buchete NV, Hummer G, Coarse Master Equations for Peptide Folding Dynamics. J Phys Chem B: 112(19):6057-69, 2008. [Full Text/Abstract]

Kim YC, Hummer G, Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol(375): 1416-33, 2008. [Full Text/Abstract]

Canagarajah BJ, Hummer G, Prinz WA, Hurley JH Dynamics of Cholesterol Exchange in the Oxysterol Binding Protein Family. J Mol Biol: 378(3):737-48, 2008. [Full Text/Abstract]

Kaila VR, Verkhovsky MI, Hummer G, Wikstrom M Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci U S A(105): 6255-9, 2008. [Full Text/Abstract]

Mittal J, Truskett TM, Errington JR, Hummer G, Layering and position-dependent diffusive dynamics of confined fluids. Phys Rev Lett(100): 145901, 2008. [Full Text/Abstract]

Kofinger J, Hummer G, Dellago C Macroscopically ordered water in nanopores. Proc Natl Acad Sci U S A(105): 13218-22, 2008. [Full Text/Abstract]

Buchete NV, Hummer G, Peptide folding kinetics from replica exchange molecular dynamics Physical Review E(77): 030902, 2008. [Full Text/Abstract]

Kaila VR, Verkhovsky M, Hummer G, Wikstrom M Prevention of leak in the proton pump of cytochrome c oxidase. Biochim Biophys Acta(1777): 890-2, 2008. [Full Text/Abstract]

Best RB, Hummer G, Protein folding kinetics under force from molecular simulation. J Am Chem Soc(130): 3706-7, 2008. [Full Text/Abstract]

Best RB, Paci E, Hummer G, Dudko OK Pulling Direction as a Reaction Coordinate for the Mechanical Unfolding of Single Molecules. J Phys Chem B: 112(19):5968-76, 2008. [Full Text/Abstract]

Kim YC, Tang C, Clore GM, Hummer G, Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci U S A(105): 12855-60, 2008. [Full Text/Abstract]

Dudko OK, Hummer G, Szabo A Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci U S A(105): 15755-60, 2008. [Full Text/Abstract]

Rasaiah JC, Garde S, Hummer G, Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond. Annu Rev Phys Chem: 59:713-40, 2008. [Full Text/Abstract]

Tuukkanen A, Kaila VR, Laakkonen L, Hummer G, Wikstrom M Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase. Biochim Biophys Acta, 2007. [Full Text/Abstract]

Dudko OK, Mathe J, Szabo A, Meller A, Hummer G, Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins. Biophys J(92): 4188-4195, 2007. [Full Text/Abstract]

Kim YC, Wikstrom M, Hummer G, Kinetic models of redox-coupled proton pumping. Proc Natl Acad Sci U S A (104): 2169-74, 2007. [Full Text/Abstract]

Yin H, Hummer G, Rasaiah JC Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc(129): 7369-77, 2007. [Full Text/Abstract]

Zheng W, Brooks BR, Hummer G, Protein conformational transitions explored by mixed elastic network models. Proteins(69): 43-57, 2007. [Full Text/Abstract]

Chen YG, Hummer G, Slow Conformational Dynamics and Unfolding of the Calmodulin C-Terminal Domain. J Am Chem Soc(129): 2414 -2415, 2007. [Full Text/Abstract]

Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography J Mol Biol(367): 752-763, 2007. [Full Text/Abstract]

Buchete NV, Hummer G, Structure and Dynamics of Parallel beta-Sheets, Hydrophobic Core, and Loops in Alzheimer's A-beta Fibrils. Biophys J(92): 3032-9, 2007. [Full Text/Abstract]

Milac AL, Buchete NV, Fritz TA, Hummer G, Tabak LA Substrate-induced Conformational Changes and Dynamics of UDP-N-Acetylgalactosamine:Polypeptide N-Acetylgalactosaminyltransferase-2. J Mol Biol, 2007. [Full Text/Abstract]

Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH The Vps27/Hse1 Complex Is a GAT Domain-Based Scaffold for Ubiquitin-Dependent Sorting. Dev Cell(12): 973-86, 2007. [Full Text/Abstract]

Hummer G, Water pulls the strings in hydrophobic polymer collapse. Proc Natl Acad Sci U S A(104): 14883-4, 2007. [Full Text/Abstract]

Hummer G, Water, proton, and ion transport: from nanotubes to proteins Molec. Phys.(105): 201-207, 2007. [Full Text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Best RB, Hummer G, Diffusive model of protein folding dynamics with kramers turnover in rate. Phys Rev Lett (96): 228104, 2006. [Full Text/Abstract]

Hassan SA, Hummer G, Lee YS Effects of electric fields on proton transport through water chains. J Chem Phys (124): 204510, 2006. [Full Text/Abstract]

Berezhkovskii AM, Hummer G, Bezrukov SM Identity of Distributions of Direct Uphill and Downhill Translocation Times for Particles Traversing Membrane Channels Phys Rev Lett(97): 020601, 2006. [Full Text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Dudko OK, Hummer G, Szabo A Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett (96): 108101, 2006. [Full Text/Abstract]

Dellago C, Hummer G, Kinetics and mechanism of proton transport across membrane nanopores. Phys Rev Lett (97): 245901, 2006. [Full Text/Abstract]

Sriraman S, Kevrekidis IG, Hummer G, Coarse master equation from Bayesian analysis of replica molecular dynamics simulations J. Phys. Chem. B(109): 6479-6484, 2005. [Full Text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Sriraman S, Kevrekidis IG, Hummer G, Coarse Nonlinear Dynamics and Metastability of Filling-Emptying Transitions: Water in Carbon Nanotubes Phys. Rev. Lett.(95): 130603, 2005. [Full Text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Best RB, Hummer G, Comment on Force-clamp spectroscopy monitors the folding trajectory of a single protein Science(308): 498, 2005. [Full Text/Abstract]

Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci U S A (102): 16668-16671, 2005. [Full Text/Abstract]

Gustchina E, Hummer G, Bewley CA, Clore GM Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV. J Med Chem (48): 3036-44, 2005. [Full Text/Abstract]

Andreev S, Reichman D, Hummer G, Effect of flexibility on hydrophobic behavior of nanotube water channels. J Chem Phys (123): 194502, 2005. [Full Text/Abstract]

Hummer G, Szabo A Free energy surfaces from single-molecule force spectroscopy. Acc Chem Res (38): 504-13, 2005. [Full Text/Abstract]

Peter C, Hummer G, Ion Transport through Membrane-Spanning Nanopores Studied by Molecular Dynamics Simulations and Continuum Electrostatics Calculations. Biophys J (89): 2222-34, 2005. [Full Text/Abstract]

Buchete NV, Tycko R, Hummer G, Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. J Mol Biol(353): 804-21, 2005. [Full Text/Abstract]

Hummer G, Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations New Journal of Physics(7): 34, 2005. [Full Text/Abstract] http://www2.niddk.nih.gov/Footer/Disclaimer.htm

Best RB, Hummer G, Reaction coordinates and rates from transition paths. Proc Natl Acad Sci U S A(102): 6732-6737, 2005. [Full Text/Abstract]

Best RB, Chen YG, Hummer G, Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure (Camb) (13): 1755-63, 2005. [Full Text/Abstract]

Yeh IC, Hummer G, Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys J (86): 681-9, 2004. [Full Text/Abstract]

Vaitheeswaran S, Rasaiah JC, Hummer G, Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. J Chem Phys (121): 7955-65, 2004. [Full Text/Abstract]

Kevrekidis IG, Gear CW, Hummer G, Equation-free: The computer-aided analysis of complex multiscale systems AIChE J.(50): 1346-55, 2004.

Hummer G, From transition paths to transition states and rate coefficients. J Chem Phys (120): 516-23, 2004. [Full Text/Abstract]

Kalra A, Garde S, Hummer G, Methane partitioning and transport in hydrated carbon nanotubes J. Phys. Chem. B(108): 544-9, 2004.

Kontaktinformationen:

Max-Planck-Institut für Biophysik

Prof. Dr. Gerhard Hummer, Direktor
Abteilung Theoretische Biophysik

Tel.: +49 (0) 69 6303-2500
Fax: +49 (0) 69 6303-2502
E-Mail: gerhard.hummer(at)biophys.mpg.de

Sekretariat: Christina Brandt
E-mail: office-hummer(at)biophys.mpg.de

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