Research Topics
| Gerhard HummerSummaryAffiliation: National Institutes of Health Country: USA Publications
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Publications
From transition paths to transition states and rate coefficientsGerhard Hummer
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
J Chem Phys 120:516-23. 2004..An algorithm is proposed to calculate rate coefficients from the transition-path and equilibrium ensembles by estimating the frequency of transitions between reactants and products...
Water pulls the strings in hydrophobic polymer collapseGerhard Hummer
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
Proc Natl Acad Sci U S A 104:14883-4. 2007- Free energy profiles from single-molecule pulling experimentsGerhard Hummer
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 107:21441-6. 2010..The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces... - Intrinsic rates and activation free energies from single-molecule pulling experimentsOlga K Dudko
Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
Phys Rev Lett 96:108101. 2006..We consider the uniqueness of the extracted kinetic information and suggest guidelines to avoid over-interpretation of experiments... - Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin bindingYoung C Kim
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
J Mol Biol 375:1416-33. 2008..We also find that the interactions between ubiquitin and Vps27 are highly dynamic, with conformational rearrangements enabling binding of Vps27 to diverse targets as part of the multivesicular-body protein-sorting pathway... - Peptide folding kinetics from replica exchange molecular dynamicsNicolae Viorel Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
Phys Rev E Stat Nonlin Soft Matter Phys 77:030902. 2008..We show that accurate rates in the approximately 1(100 ns) to approximately 1(1 ns) range can be obtained from REMD with exchange times of 5 ps , in excellent agreement with results from long equilibrium molecular dynamics... - Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scissionEvzen Boura
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Structure 20:874-86. 2012..The hybrid refinement used here is general and should be applicable to other dynamic multiprotein assmeblies... - Gating transition of pentameric ligand-gated ion channelsFangqiang Zhu
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
Biophys J 97:2456-63. 2009..In addition, helix M2 changes its bending state, which results in an early closure of the pore during the open-to-closed transition... - Kinetic gating of the proton pump in cytochrome c oxidaseYoung C Kim
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 106:13707-12. 2009..The fundamental mechanism identified here for the efficient conversion of chemical energy into an electrochemical potential should prove relevant also for other molecular machines and novel fuel-cell designs... - Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpinsOlga K Dudko
Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
Biophys J 92:4188-95. 2007..The problem of extracting unique and accurate kinetic parameters of a molecular transition is discussed in light of the apparent success of the microscopic theories in reproducing the experimental data... - Nucleic acid transport through carbon nanotube membranesIn-Chul Yeh
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
Proc Natl Acad Sci U S A 101:12177-82. 2004..Differences in RNA conformational flexibility and hydrophobicity result in sequence-dependent rates of translocation, a prerequisite for nanoscale separation devices... - Reactive flux and folding pathways in network models of coarse-grained protein dynamicsAlexander Berezhkovskii
Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
J Chem Phys 130:205102. 2009.... - Reaction coordinates and rates from transition pathsRobert B Best
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Room 132, Bethesda, MD 20892-0520, USA
Proc Natl Acad Sci U S A 102:6732-7. 2005..The resulting one-dimensional reaction coordinate captures the folding transition state, with formation and packing of helix 2 and 3 constituting the bottleneck for folding... - Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulationsEdina Rosta
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
J Am Chem Soc 133:8934-41. 2011..Proton-transfer reactions and changes in the metal ion coordination emerge as central factors in the RNA-cleavage reaction... - Effects of electric fields on proton transport through water chainsSergio A Hassan
Center for Molecular Modeling, DCB CIT, National Institutes of Health, U S DHHS, Bethesda, Maryland 20892, USA
J Chem Phys 124:204510. 2006..The implications of these observations on PT in biomolecular systems and its control by external perturbing fields are discussed... - Are current molecular dynamics force fields too helical?Robert B Best
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Biophys J 95:L07-9. 2008..We conclude that radical changes to the best current force fields are not necessary, based on the NMR data. Nevertheless, experiments on short peptides open the way toward the systematic improvement of current simulation models... - Binding-induced folding of a natively unstructured transcription factorAdrian Gustavo Turjanski
Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS Comput Biol 4:e1000060. 2008..The simulations are in general agreement with the results of a recently reported nuclear magnetic resonance study, and aid in the interpretation of the experimental binding kinetics... - Diffusive model of protein folding dynamics with Kramers turnover in rateRobert B Best
Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Phys Rev Lett 96:228104. 2006.... - Pore opening and closing of a pentameric ligand-gated ion channelFangqiang Zhu
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 107:19814-9. 2010..The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening... - Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopyEvzen Boura
Laboratory of Molecular Biology and Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 108:9437-42. 2011..These conformations provide reference points for the structural pathway by which ESCRT-I induces membrane buds... - Free energy surfaces from single-molecule force spectroscopyGerhard Hummer
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Acc Chem Res 38:504-13. 2005..We illustrate our rigorous free energy reconstruction procedure by applying it to force-induced RNA unfolding experiments... - Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulationsIn-Chul Yeh
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Biophys J 86:681-9. 2004..As a consequence, apparent diffusion coefficients measured by capillary zone electrophoresis can be significantly larger than the actual values at certain experimental conditions... - Slow conformational dynamics and unfolding of the calmodulin C-terminal domainYng-Gwei Chen
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
J Am Chem Soc 129:2414-5. 2007 - Replica exchange simulations of transient encounter complexes in protein-protein associationYoung C Kim
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 105:12855-60. 2008..Nonspecific complexes may not only accelerate the binding kinetics by enhancing the rate of success of random diffusional encounters but also play a role in protein function as alternative binding modes... - Hybrid structural model of the complete human ESCRT-0 complexXuefeng Ren
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
Structure 17:406-16. 2009..Coarse-grained Monte Carlo simulations constrained by experimental RH values for ESCRT-0 reveal a dynamic ensemble of conformations well suited for diverse functions... - Error and efficiency of replica exchange molecular dynamics simulationsEdina Rosta
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
J Chem Phys 131:165102. 2009.... - Dynamics of cholesterol exchange in the oxysterol binding protein familyBertram J Canagarajah
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U S Department of Health and Human Services, Bethesda, MD 20892, USA
J Mol Biol 378:737-48. 2008.... - How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM studyAdrian Gustavo Turjanski
Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, and Laboratory of Chemical Physics, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
J Am Chem Soc 131:6141-8. 2009..Taken together, our results provide a detailed description of the molecular events involved in the phosphorylation reaction catalyzed by MAPK and contribute to the general understanding of kinase activity... 
Protein folding kinetics under force from molecular simulationRobert B Best
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
J Am Chem Soc 130:3706-7. 2008..Our findings explain why refolding becomes very slow at even moderate pulling forces and suggest how it could be practically observed in experiments at higher forces...- Pulling direction as a reaction coordinate for the mechanical unfolding of single moleculesRobert B Best
Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
J Phys Chem B 112:5968-76. 2008..The apparent similarity between extrapolated and intrinsic rates in experiments, unexpected for different unfolding barriers, can be explained if the turnover occurs at low forces... - Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculationsChristine Peter
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
Biophys J 89:2222-34. 2005.... - Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrilsNicolae Viorel Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520
Biophys J 92:3032-9. 2007..The interior C-terminal beta-sheets in the hydrophobic core remain largely intact, indicating that their formation and stability is crucial to the dissociation/elongation and stability of Abeta fibrils... - Characterization of a dynamic string method for the construction of transition pathways in molecular reactionsMargaret E Johnson
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, United States
J Phys Chem B 116:8573-83. 2012..We derive a simple method for calculating the committor function along paths that follow the reactive flux. Lastly, we provide guidance for the practical implementation of the dynamic string method... - Protein conformational transitions explored by mixed elastic network modelsWenjun Zheng
Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
Proteins 69:43-57. 2007..The MENM formalism is computationally efficient and generally applicable even for large protein systems that undergo highly collective structural changes... - Atomistic insights into rhodopsin activation from a dynamic modelIrina G Tikhonova
Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
J Am Chem Soc 130:10141-9. 2008.... - Coarse master equations for peptide folding dynamicsNicolae Viorel Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
J Phys Chem B 112:6057-69. 2008..5 and 7 ns. The master equation models not only give access to the slow conformational dynamics but also shed light on the molecular mechanisms of the helix-coil transition... - Static and dynamic correlations in water at hydrophobic interfacesJeetain Mittal
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 105:20130-5. 2008..These fluctuations result in transitions between locally wet and dry regions that are slow on a molecular time scale... - Kinetics from nonequilibrium single-molecule pulling experimentsGerhard Hummer
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Biophys J 85:5-15. 2003..Our procedure to extract kinetic information from pulling experiments is simple to implement and should prove useful in the analysis of experiments on a variety of systems... - Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubesSubramanian Vaitheeswaran
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, MD 20892-0520, USA
J Chem Phys 121:7955-65. 2004..We also discuss implications for proton transfer reactions in biology... - Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase HEdina Rosta
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
J Comput Chem 30:1634-41. 2009..The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations... - Water clusters in nonpolar cavitiesSubramanian Vaitheeswaran
National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, MD 20892-0520, USA
Proc Natl Acad Sci U S A 101:17002-5. 2004..Water penetration into pores can thus be modulated by small changes in the polarity and structure of the cavity. Implications on water penetration into proteins are discussed... - Energetics of direct and water-mediated proton-coupled electron transferVille R I Kaila
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
J Am Chem Soc 133:19040-3. 2011..Our calculations suggest that the π-stacking of the tyrosine dimer in RNR results in strong electronic coupling and adiabatic PCET. Water participation in the PCET can be identified perturbatively in a Brønsted analysis... - Nonspecific binding limits the number of proteins in a cell and shapes their interaction networksMargaret E Johnson
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 108:603-8. 2011..We conclude that nonspecific binding adds to the evolutionary pressure to develop scale-free protein-protein interaction networks... - SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitionsBartosz Różycki
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Structure 19:109-16. 2011..The simulation-based ensemble refinement is general and effectively increases the resolution of SAXS beyond shape information to atomically detailed structures... - Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein"Robert B Best
Laboratory of Chemical Physics, National Institute of Diabetes andDigestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda MD 20892-0520, USA
Science 308:498; author reply 498. 2005 - Convergence and error estimation in free energy calculations using the weighted histogram analysis methodFangqiang Zhu
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
J Comput Chem 33:453-65. 2012..Together, the estimates of the statistical errors and the diagnostics of inconsistencies in the potentials of mean force provide a basis for the efficient allocation of computational resources in free energy simulations... - Osmotic water transport through carbon nanotube membranesAmrit Kalra
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
Proc Natl Acad Sci U S A 100:10175-80. 2003..Structural and thermodynamic aspects of confined water monolayers are studied... - Molecular dynamics simulations of Alzheimer's beta-amyloid protofilamentsNicolae-Viorel Buchete
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
J Mol Biol 353:804-21. 2005..Calculated X-ray fiber diffraction patterns show the characteristics of packed beta-sheets seen in experiments, and suggest new experiments that could discriminate between various fibril topologies... - Error and efficiency of simulated tempering simulationsEdina Rosta
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 5, Bethesda, Maryland 20892 0520, USA
J Chem Phys 132:034102. 2010..Based on the efficiency formula, we provide recommendations for the optimal choice of ST simulation parameters, in particular, the range and number of temperatures, and the frequency of attempted temperature changes... - Layering and position-dependent diffusive dynamics of confined fluidsJeetain Mittal
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Phys Rev Lett 100:145901. 2008..Parallel and average normal diffusivities are strongly coupled at high densities and deviate from bulk fluid behavior... - Kinetic models of redox-coupled proton pumpingYoung C Kim
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 104:2169-74. 2007..The general design principles are relevant also for other molecular machines and suggest future applications in biology-inspired fuel cells... - Biological proton pumping in an oscillating electric fieldYoung C Kim
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
Phys Rev Lett 103:268102. 2009..A spectral analysis reveals dominant reaction steps consistent with an electron-gated pumping mechanism... - The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sortingGali Prag
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U S Department of Health and Human Services, Bethesda, MD 20892, USA
Dev Cell 12:973-86. 2007..Coarse-grained Monte Carlo simulations of the Vps27/Hse1 complex on a membrane show how the complex binds cooperatively to lipids and ubiquitinated membrane proteins and acts as a scaffold for ubiquitination reactions... - Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallographyFriedrich Schotte
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Proc Natl Acad Sci U S A 109:19256-61. 2012.... - Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexesBartosz Różycki
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
PLoS Comput Biol 8:e1002736. 2012..Our membrane elasticity model thus sheds light on the energetics and possible mechanisms of ESCRT-induced membrane budding... - 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 SIVElena Gustchina
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
J Med Chem 48:3036-44. 2005..This result suggests that C34 from HIV-2 EHO may present a potentially useful therapeutic agent against diverse and/or resistant strains of HIV-1... - Crystal structure and allosteric activation of protein kinase C βIIThomas A Leonard
Laboratory of Molecular Biology, National Institutes of Health, Bethesda, MD 20892, USA
Cell 144:55-66. 2011..Together, these results show how PKCβII is allosterically regulated in two steps, with the second step defining a novel protein kinase regulatory mechanism... - Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solventIn-Chul Yeh
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
J Am Chem Soc 124:6563-8. 2002..However, end-to-end contacts form more rapidly, with characteristic times less than 10 ns. The contact formation rates for the two force fields are similar despite differences in the respective ensembles of peptide conformations... - Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressorRobert B Best
Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Structure 13:1755-63. 2005..Transient local unfolding is consistent with the low hydrogen exchange protection factors of the switch region. Also in agreement with experiment, the isomerization occurs independently of the global folding/dimerization transition... - Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channelsAlexander M Berezhkovskii
Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
Phys Rev Lett 97:020601. 2006..We show that the distributions of direct translocation times are identical for translocation in both directions, independent of any asymmetry in the potential across the channel and, hence, the translocation probabilities... - Energetics and dynamics of proton transfer reactions along short water wiresVille R I Kaila
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892 0520, USA
Phys Chem Chem Phys 13:13207-15. 2011..We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Brønsted slopes of one and zero, respectively... - Single-file water in nanoporesJürgen Köfinger
Laboratory of Chemical Physics, Bldg 5, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
Phys Chem Chem Phys 13:15403-17. 2011..In this Perspective, we revisit results for single-file water in apolar pores, and examine the similarities and the differences between these simple systems and water in more complex pores... - Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450camSrabani Taraphder
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
J Am Chem Soc 125:3931-40. 2003..Our observations emphasize the intrinsic dynamical nature of proton pathways where critical connections in the network may be transiently provided by mobile groups... - Single-file transport of water molecules through a carbon nanotubeAlexander Berezhkovskii
Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
Phys Rev Lett 89:064503. 2002..Theoretical predictions for different collective properties of the single-file transport agree with the simulation results... - Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulationsGerhard Hummer
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520, USA
Proc Natl Acad Sci U S A 101:15330-4. 2004..The simulations also suggest how picosecond protein motions modulate the functional dissociation of oxygen and suppress the geminate recombination of toxic carbon monoxide... - Water-gated mechanism of proton translocation by cytochrome c oxidaseMarten Wikstrom
Helsinki Bioenergetics Group, Institute of Biotechnology and Biocentrum Helsinki, University of Helsinki, PB 65 Viikinkaari 1, FI 00014 Helsinki, Finland
Biochim Biophys Acta 1604:61-5. 2003..This pumping mechanism explains the unique arrangement of the metal cofactors in the structure. It is consistent with the large body of biochemical data, and is shown to be plausible by molecular dynamics simulations... - Proton transport through water-filled carbon nanotubesChristoph Dellago
Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
Phys Rev Lett 90:105902. 2003..Excess protons interact with hydrogen-bonding defects through long-range electrostatics, resulting in coupled motion of protons and defects... - Water in nonpolar confinement: from nanotubes to proteins and beyondJayendran C Rasaiah
Department of Chemistry, University of Maine, Orono, Maine 04469, USA
Annu Rev Phys Chem 59:713-40. 2008..The unusual properties of water in nonpolar confinement are also relevant to the design of novel nanofluidic and molecular separation devices or fuel cells... - Dynamics of the glutamic acid 242 side chain in cytochrome c oxidaseAnne Tuukkanen
Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
Biochim Biophys Acta 1767:1102-6. 2007.... - Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachionHao Yin
Department of Chemistry, University of Maine, Orono, Maine 04469 5706, USA
J Am Chem Soc 129:7369-77. 2007..We suggest that the large hydrophobic cavities may act as binding sites for two proteases, possibly explaining the unusual thermostability of the resulting protease-stalk complexes (up to approximately 393 K, 120 degrees C)... - Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallographyMarcus D Collins
Department of Physics, Cornell University, Ithaca, NY 14853, USA
J Mol Biol 367:752-63. 2007..The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone... - Kinetics and mechanism of proton transport across membrane nanoporesChristoph Dellago
Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
Phys Rev Lett 97:245901. 2006..At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube... - Coarse master equation from Bayesian analysis of replica molecular dynamics simulationsSaravanapriyan Sriraman
Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
J Phys Chem B 109:6479-84. 2005..We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference... - Effect of flexibility on hydrophobic behavior of nanotube water channelsStefan Andreev
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
J Chem Phys 123:194502. 2005..We quantify the magnitude of the effect and show that it arises from the formation of energetically favorable low-dimensional water structures inside the nanotube such as one-dimensional wires and two-dimensional sheets... - Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulationMarcus D Collins
Department of Physics, Cornell University, Ithaca, NY 14853, USA
Proc Natl Acad Sci U S A 102:16668-71. 2005.... - Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubesSaravanapriyan Sriraman
Department of Chemical Engineering and PACM, Princeton University, Princeton, New Jersey 08544, USA
Phys Rev Lett 95:130603. 2005..The corresponding coarse-grained free-energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations... - Macroscopically ordered water in nanoporesJürgen Köfinger
Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
Proc Natl Acad Sci U S A 105:13218-22. 2008..g., in fuel cells. For water-filled nanotube bundles and membranes, we expect anti-ferroelectric behavior, resulting in a rich phase diagram similar to that of a 2D Coulomb gas... - Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidaseVille R I Kaila
Helsinki Bioenergetics Group, Structural Biology and Biophysics Program, Institute of Biotechnology, University of Helsinki, Viikinkaari 1, P O Box 65, 00014, Helsinki, Finland
Proc Natl Acad Sci U S A 105:6255-9. 2008..Suppression of proton leakage is particularly important in mitochondria under physiological conditions, where production of ATP takes place in the presence of a high electrochemical proton gradient... - Prevention of leak in the proton pump of cytochrome c oxidaseVille R I Kaila
Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, PB 65 Viikinkaari 1, 00014 University of Helsinki, Helsinki, Finland
Biochim Biophys Acta 1777:890-2. 2008.... - Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phasesMarkus Zweckstetter
Max Planck Institute for Biophysical Chemistry, Am Fassberg, Gottingen, Germany
Biophys J 86:3444-60. 2004..Inclusion of electrostatic interactions in addition to steric effects makes the extended model applicable to all liquid crystals used in biological NMR to date...