Gerhard Hummer

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint From transition paths to transition states and rate coefficients
    Gerhard 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
  2. pmc Free energy profiles from single-molecule pulling experiments
    Gerhard 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
  3. pmc Water pulls the strings in hydrophobic polymer collapse
    Gerhard 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
  4. ncbi request reprint Intrinsic rates and activation free energies from single-molecule pulling experiments
    Olga 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
  5. pmc Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding
    Young 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
  6. ncbi request reprint Peptide folding kinetics from replica exchange molecular dynamics
    Nicolae 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
  7. pmc Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission
    Evzen 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
  8. pmc Gating transition of pentameric ligand-gated ion channels
    Fangqiang 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
  9. pmc Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins
    Olga 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
  10. pmc Kinetic gating of the proton pump in cytochrome c oxidase
    Young 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

Collaborators

Detail Information

Publications82

  1. ncbi request reprint From transition paths to transition states and rate coefficients
    Gerhard 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...
  2. pmc Free energy profiles from single-molecule pulling experiments
    Gerhard 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...
  3. pmc Water pulls the strings in hydrophobic polymer collapse
    Gerhard 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
  4. ncbi request reprint Intrinsic rates and activation free energies from single-molecule pulling experiments
    Olga 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...
  5. pmc Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding
    Young 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...
  6. ncbi request reprint Peptide folding kinetics from replica exchange molecular dynamics
    Nicolae 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...
  7. pmc Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission
    Evzen 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...
  8. pmc Gating transition of pentameric ligand-gated ion channels
    Fangqiang 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...
  9. pmc Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins
    Olga 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...
  10. pmc Kinetic gating of the proton pump in cytochrome c oxidase
    Young 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...
  11. pmc Reactive flux and folding pathways in network models of coarse-grained protein dynamics
    Alexander 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
    ....
  12. pmc Reaction coordinates and rates from transition paths
    Robert 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...
  13. pmc Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations
    Edina 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...
  14. pmc Effects of electric fields on proton transport through water chains
    Sergio 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...
  15. pmc Nucleic acid transport through carbon nanotube membranes
    In 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...
  16. pmc 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...
  17. ncbi request reprint Diffusive model of protein folding dynamics with Kramers turnover in rate
    Robert B Best
    Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892 0520, USA
    Phys Rev Lett 96:228104. 2006
    ....
  18. pmc Pore opening and closing of a pentameric ligand-gated ion channel
    Fangqiang 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...
  19. pmc Binding-induced folding of a natively unstructured transcription factor
    Adrian 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...
  20. pmc Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy
    Evzen 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...
  21. ncbi request reprint Slow conformational dynamics and unfolding of the calmodulin C-terminal domain
    Yng 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
  22. pmc Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils
    Nicolae 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...
  23. pmc Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations
    In 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...
  24. pmc How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study
    Adrian 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...
  25. pmc Hybrid structural model of the complete human ESCRT-0 complex
    Xuefeng 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...
  26. doi request reprint Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules
    Robert 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...
  27. doi request reprint Protein folding kinetics under force from molecular simulation
    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
    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...
  28. pmc Dynamics of cholesterol exchange in the oxysterol binding protein family
    Bertram 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
    ....
  29. pmc Replica exchange simulations of transient encounter complexes in protein-protein association
    Young 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...
  30. ncbi request reprint Free energy surfaces from single-molecule force spectroscopy
    Gerhard 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...
  31. pmc Error and efficiency of replica exchange molecular dynamics simulations
    Edina 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
    ....
  32. pmc Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations
    Christine 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
    ....
  33. pmc Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes
    Bartosz 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...
  34. pmc Characterization of a dynamic string method for the construction of transition pathways in molecular reactions
    Margaret 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...
  35. pmc Static and dynamic correlations in water at hydrophobic interfaces
    Jeetain 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...
  36. pmc Water clusters in nonpolar cavities
    Subramanian 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...
  37. pmc Kinetics from nonequilibrium single-molecule pulling experiments
    Gerhard 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...
  38. ncbi request reprint Protein conformational transitions explored by mixed elastic network models
    Wenjun 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...
  39. pmc Atomistic insights into rhodopsin activation from a dynamic model
    Irina 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
    ....
  40. pmc Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H
    Edina 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...
  41. ncbi request reprint Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes
    Subramanian 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...
  42. doi request reprint Coarse master equations for peptide folding dynamics
    Nicolae 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...
  43. doi request reprint Energetics of direct and water-mediated proton-coupled electron transfer
    Ville 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...
  44. ncbi request reprint 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
  45. pmc SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions
    Bartosz 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...
  46. pmc Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks
    Margaret 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...
  47. ncbi request reprint Atomic-resolution structural information from scattering experiments on macromolecules in solution
    Jürgen 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 Rev E Stat Nonlin Soft Matter Phys 87:052712. 2013
    ..Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold...
  48. pmc Native contacts determine protein folding mechanisms in atomistic simulations
    Robert B Best
    Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 0520
    Proc Natl Acad Sci U S A 110:17874-9. 2013
    ..More remarkably, however, we found that for almost all the proteins, with the designed protein α3D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms. ..
  49. pmc Convergence and error estimation in free energy calculations using the weighted histogram analysis method
    Fangqiang 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...
  50. ncbi request reprint Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments
    Nicolae 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...
  51. pmc Biological proton pumping in an oscillating electric field
    Young 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...
  52. pmc Error and efficiency of simulated tempering simulations
    Edina 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...
  53. pmc Kinetic models of redox-coupled proton pumping
    Young 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...
  54. pmc Osmotic water transport through carbon nanotube membranes
    Amrit 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...
  55. ncbi request reprint Layering and position-dependent diffusive dynamics of confined fluids
    Jeetain 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...
  56. pmc The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
    Gali 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...
  57. pmc Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography
    Friedrich 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
    ....
  58. pmc Energetics and dynamics of proton transfer reactions along short water wires
    Ville 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...
  59. ncbi request reprint Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor
    Robert 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...
  60. ncbi request reprint 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
    Elena 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...
  61. pmc Crystal structure and allosteric activation of protein kinase C βII
    Thomas 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...
  62. ncbi request reprint Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels
    Alexander 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...
  63. ncbi request reprint Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
    In 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...
  64. pmc Single-file water in nanopores
    Jürgen 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...
  65. pmc Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations
    Gerhard 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...
  66. ncbi request reprint Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam
    Srabani 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...
  67. ncbi request reprint Single-file transport of water molecules through a carbon nanotube
    Alexander 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...
  68. ncbi request reprint Water-gated mechanism of proton translocation by cytochrome c oxidase
    Marten 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...
  69. ncbi request reprint Proton transport through water-filled carbon nanotubes
    Christoph 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...
  70. ncbi request reprint Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes
    Saravanapriyan 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...
  71. pmc Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
    Marcus D Collins
    Department of Physics, Cornell University, Ithaca, NY 14853, USA
    Proc Natl Acad Sci U S A 102:16668-71. 2005
    ....
  72. ncbi request reprint Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase
    Anne Tuukkanen
    Helsinki Bioenergetics Group, Structural Biology and Biophysics Programme, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Biochim Biophys Acta 1767:1102-6. 2007
    ....
  73. ncbi request reprint Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion
    Hao 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)...
  74. pmc Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography
    Marcus 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...
  75. ncbi request reprint Kinetics and mechanism of proton transport across membrane nanopores
    Christoph 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...
  76. ncbi request reprint Coarse master equation from Bayesian analysis of replica molecular dynamics simulations
    Saravanapriyan 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...
  77. ncbi request reprint Effect of flexibility on hydrophobic behavior of nanotube water channels
    Stefan 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...
  78. ncbi request reprint Water in nonpolar confinement: from nanotubes to proteins and beyond
    Jayendran 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...
  79. pmc Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases
    Markus 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...
  80. doi request reprint Prevention of leak in the proton pump of cytochrome c oxidase
    Ville 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
    ....
  81. pmc Macroscopically ordered water in nanopores
    Jürgen 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...
  82. pmc Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
    Ville 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...