Wilfred F van Gunsteren

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. ncbi request reprint Biomolecular structure refinement based on adaptive restraints using local-elevation simulation
    Markus Christen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zurich, 8093 Zurich, Switzerland
    J Biomol NMR 39:265-73. 2007
  2. pmc Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
    Jozica Dolenc
    Faculty of Chemistry and Chemical Technology, University of Ljubljana Askerceva 5, SI 1000 Ljubljana, Slovenia
    Nucleic Acids Res 33:725-33. 2005
  3. ncbi request reprint On developing coarse-grained models for biomolecular simulation: a review
    Sereina Riniker
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Phys Chem Chem Phys 14:12423-30. 2012
  4. ncbi request reprint Validation of the 53A6 GROMOS force field
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    Eur Biophys J 34:273-84. 2005
  5. ncbi request reprint The thermal isomerization of the GFP chromophore: A computational study
    Dongqi Wang
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093, Zurich, Switzerland
    Phys Chem Chem Phys 12:11051-61. 2010
  6. doi request reprint Molecular simulation as an aid to experimentalists
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    Curr Opin Struct Biol 18:149-53. 2008
  7. ncbi request reprint Biomolecular modeling: Goals, problems, perspectives
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Angew Chem Int Ed Engl 45:4064-92. 2006
  8. ncbi request reprint Biomolecular simulation: historical picture and future perspectives
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Biochem Soc Trans 36:11-5. 2008
  9. ncbi request reprint Terminal-group effects on the folding behavior of selected beta-peptides
    Peter J Gee
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
    Proteins 63:136-43. 2006
  10. doi request reprint Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol
    Bruno A C Horta
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    J Comput Chem 33:1907-17. 2012

Collaborators

Detail Information

Publications104 found, 100 shown here

  1. ncbi request reprint Biomolecular structure refinement based on adaptive restraints using local-elevation simulation
    Markus Christen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zurich, 8093 Zurich, Switzerland
    J Biomol NMR 39:265-73. 2007
    ..Afterwards the torsional angles varphi are kept restrained by the built-up local-elevation potential energies...
  2. pmc Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
    Jozica Dolenc
    Faculty of Chemistry and Chemical Technology, University of Ljubljana Askerceva 5, SI 1000 Ljubljana, Slovenia
    Nucleic Acids Res 33:725-33. 2005
    ..The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding...
  3. ncbi request reprint On developing coarse-grained models for biomolecular simulation: a review
    Sereina Riniker
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Phys Chem Chem Phys 14:12423-30. 2012
    ..e. whether it reflects the underlying physical mechanisms or merely provides a set of pretty pictures of the process or substances of interest...
  4. ncbi request reprint Validation of the 53A6 GROMOS force field
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    Eur Biophys J 34:273-84. 2005
    ..The latter is a property that is directly associated with the free enthalpy of hydration, to which the 53A6 parameter set was parameterized...
  5. ncbi request reprint The thermal isomerization of the GFP chromophore: A computational study
    Dongqi Wang
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093, Zurich, Switzerland
    Phys Chem Chem Phys 12:11051-61. 2010
    ..Our study suggests that the ability of a nucleophile to assist the thermal isomerization of HOBDI mainly depends on its ability to give a proton upon the addition of the nucleophile to the substrate...
  6. doi request reprint Molecular simulation as an aid to experimentalists
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    Curr Opin Struct Biol 18:149-53. 2008
    ..A critical analysis of the various factors that may influence the apparent degree of agreement between the results of simulations and experimentally measured quantities is presented and illustrated using examples from recent literature...
  7. ncbi request reprint Biomolecular modeling: Goals, problems, perspectives
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Angew Chem Int Ed Engl 45:4064-92. 2006
    ..These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling...
  8. ncbi request reprint Biomolecular simulation: historical picture and future perspectives
    Wilfred F van Gunsteren
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    Biochem Soc Trans 36:11-5. 2008
    ..Progress over the last 30 years is sketched and perspectives are outlined for the future...
  9. ncbi request reprint Terminal-group effects on the folding behavior of selected beta-peptides
    Peter J Gee
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
    Proteins 63:136-43. 2006
    ..The simulated motions bear out empirical observations as to the effect of chemical protection of terminal groups on the stability of beta-peptide helical folds and they support the hypothesis of charge-dipole stabilization...
  10. doi request reprint Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: influence on the folding properties of two beta-peptides in methanol
    Bruno A C Horta
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    J Comput Chem 33:1907-17. 2012
    ....
  11. ncbi request reprint Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?
    Bojan Zagrovic
    Department of Chemistry and Applied Biosciences, ETH Honggerberg, Zurich, Switzerland
    Proteins 63:210-8. 2006
    ..In light of the examples given, we conclude that comparing experimental NOE distance restraints with large simulated ensembles provides just by itself only limited information about the quality of simulation...
  12. pmc Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding
    Jozica Dolenc
    Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
    Biophys J 91:1460-70. 2006
    ....
  13. doi request reprint Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
    Jozica Dolenc
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
    J Comput Aided Mol Des 25:709-16. 2011
    ..The differences in the free enthalpy of binding do not arise only from the changes in ligand-DNA interactions but also from changes in ligand-solvent interactions as well as from the loss of DNA configurational entropy upon restraining...
  14. ncbi request reprint An improved nucleic acid parameter set for the GROMOS force field
    Thereza A Soares
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    J Comput Chem 26:725-37. 2005
    ..The deviation between simulated and experimental observables is now of the same order of magnitude as the uncertainty in the experimental values themselves...
  15. pmc Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics
    David B Kony
    Laboratory of Physical Chemistry, ETH Zurich, CH 8093 Zurich, Switzerland
    Protein Sci 16:1101-18. 2007
    ....
  16. pmc Free energies of ligand binding for structurally diverse compounds
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Eidgenossische Technische Hochschule Honggerberg, CH 8093 Zurich, Switzerland
    Proc Natl Acad Sci U S A 102:6750-4. 2005
    ..The free-energy calculations can be straightforwardly parallelized, allowing for an efficient means to understand and predict relative binding free energies...
  17. ncbi request reprint A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer
    Alice Glättli
    Laboratorium fur Physikalische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg HCI, 8093 Zurich, Switzerland
    Eur Biophys J 35:255-67. 2006
    ..In addition, peptide-lipid interactions were investigated showing that the C-terminus of the peptide provides an anchor to the lipid bilayer by forming hydrogen bonds with the lipid head groups...
  18. ncbi request reprint The GROMOS software for biomolecular simulation: GROMOS05
    Markus Christen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Comput Chem 26:1719-51. 2005
    ..The organization of the program package is outlined and the included analysis package GROMOS++ is described. Finally, some applications illustrating the various available functionalities are presented...
  19. doi request reprint Folding and unfolding of two mixed alpha/beta peptides
    Dongqi Wang
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich Switzerland
    Chembiochem 10:2032-41. 2009
    ..We conclude that our simulations are complementary to the experiments by providing detailed information on the conformational distributions...
  20. ncbi request reprint Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation
    Iris Antes
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zentrum, 8092 Zurich, Switzerland
    Eur Biophys J 31:504-20. 2002
    ..These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant...
  21. ncbi request reprint Comparison of properties of Aib-rich peptides in crystal and solution: a molecular dynamics study
    Haibo Yu
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, 8093 Zurich, Switzerland
    Chemphyschem 5:633-41. 2004
    ....
  22. doi request reprint Biomolecular structure refinement using the GROMOS simulation software
    Nathan Schmid
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    J Biomol NMR 51:265-81. 2011
    ....
  23. doi request reprint Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software
    Sereina Riniker
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    J Phys Chem B 115:13570-7. 2011
    ..Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given...
  24. ncbi request reprint Simulation of beta-depsipeptides: the effect of missing hydrogen-bond donors on their folding equilibria
    Zrinka Gattin
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    Biopolymers 85:318-32. 2007
    ..The simulations are complementary to the experimental data by providing detailed insight into the conformational distributions that are compatible with the experimentally measured average values of observables...
  25. ncbi request reprint Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters
    Daan P Geerke
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
    J Phys Chem B 111:6425-36. 2007
    ....
  26. pmc Conformational and dynamical properties of disaccharides in water: a molecular dynamics study
    Cristina S Pereira
    Laboratory of Physical Chemistry, ETH Honggerberg, Zurich, Switzerland
    Biophys J 90:4337-44. 2006
    ....
  27. ncbi request reprint Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins
    Haibo Yu
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, Zurich, Switzerland
    Proteins 65:285-95. 2006
    ..The simulation trajectories suggest that the stability of the designed AR proteins can be increased by optimizing the electrostatic interactions within and between the different repeats...
  28. ncbi request reprint Protein under pressure: molecular dynamics simulation of the arc repressor
    Daniel Trzesniak
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
    Proteins 65:136-44. 2006
    ..Also, the onset of denaturation of the separated chains was observed...
  29. ncbi request reprint Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models
    Riccardo Baron
    Laboratorium fur Physikalische Chemie, ETH, Swiss Federal Institute of Technology Zurich, 8093 Zurich, Switzerland
    Chemphyschem 8:452-61. 2007
    ..However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties...
  30. ncbi request reprint Circular dichroism spectra of beta-peptides: sensitivity to molecular structure and effects of motional averaging
    Xavier Daura
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, 8093 Zurich, Switzerland
    Eur Biophys J 32:661-70. 2003
    ..This indicates that the CD spectra of these peptides are very sensitive to small local structural differences...
  31. ncbi request reprint A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    J Comput Chem 25:1656-76. 2004
    ..The partial charges were then adjusted to reproduce the hydration free enthalpies in water (53A6). Both parameter sets are fully documented, and the differences between these and previous parameter sets are discussed...
  32. doi request reprint Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers
    Dongqi Wang
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH 8093, Zurich, Switzerland
    Eur Biophys J 42:521-37. 2013
    ..In other words, for these compounds, solvent-exposed H-bonding appears to represent a minor (possibly adverse) conformational driving as well as steering force...
  33. pmc Exploration of swapping enzymatic function between two proteins: a simulation study of chorismate mutase and isochorismate pyruvate lyase
    Alexandra Choutko
    Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
    Protein Sci 22:809-22. 2013
    ..These observations might explain the difficulty of engineering isochorismate pyruvate lyase activity in EcCM by solely mutating active site residues...
  34. ncbi request reprint On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study
    Alice Glättli
    Laboratorium fur Physikalische Chemie, Swiss Federal Institute of Technology, ETH Honggerberg, HCI, 8093 Zurich, Switzerland
    Chemistry 11:7276-93. 2005
    ..In water, where the solvent competes with the solute-solute polar interactions, the folding process to the 3(14)-helix is faster in the simulations...
  35. doi request reprint Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution
    Niels Hansen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zurich CH 8093, Switzerland
    J Comput Chem 33:640-51. 2012
    ....
  36. ncbi request reprint Simulation of an all-beta 3-icosapeptide containing the 20 proteinogenic side chains: effect of temperature, pH, counterions, solvent, and force field on helix stability
    Daniel Trzesniak
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
    Biopolymers 83:636-45. 2006
    ..We further investigate the reasons for the 3(14)-helix stability/instability in methanol/water. Of all factors studied, the presence of counterions seems to be the one inducing most significant effects in the simulations...
  37. ncbi request reprint Numerical simulation of the effect of solvent viscosity on the motions of a beta-peptide heptamer
    Peter J Gee
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
    Chemistry 12:72-5. 2005
    ....
  38. doi request reprint Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study
    Jozica Dolenc
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
    Chembiochem 9:1749-56. 2008
    ..Together, our study contributes to understanding the principles of three-stranded coiled-coil formation...
  39. ncbi request reprint QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians
    Daan P Geerke
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, Zurich, Switzerland
    Phys Chem Chem Phys 10:297-302. 2008
    ..In addition, the compatibility of OM3 with the classical Hamiltonian improves upon explicitly including electronic polarization in the MM subsystem...
  40. ncbi request reprint Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations
    Riccardo Baron
    Laboratorium fur Physikalische Chemie, Eidgenossische Technische Hochschule Zurich, CH 8093 Zurich, Switzerland
    J Phys Chem B 110:15602-14. 2006
    ..For the AL model, the correction due to mode anharmonicities is small, but the correction due to pairwise (supralinear) mode correlations is sizable...
  41. doi request reprint Free enthalpies of replacing water molecules in protein binding pockets
    Sereina Riniker
    Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
    J Comput Aided Mol Des 26:1293-309. 2012
    ..Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design...
  42. doi request reprint On the calculation of ³Jαβ-coupling constants for side chains in proteins
    Denise Steiner
    Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
    J Biomol NMR 53:223-46. 2012
    ..The results show that the widely used Karplus relations are only a rough estimate for the relation between (3) J (αβ)-couplings and the corresponding χ(1)-angle in proteins...
  43. ncbi request reprint Interpreting NMR data for beta-peptides using molecular dynamics simulations
    Daniel Trzesniak
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Am Chem Soc 127:14320-9. 2005
    ..The MD conformational ensembles allowed for a detailed and consistent interpretation of the experimental data and showed the small but specific conformational differences between the protected and unprotected forms of the peptide...
  44. doi request reprint New functionalities in the GROMOS biomolecular simulation software
    Anna Pitschna E Kunz
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    J Comput Chem 33:340-53. 2012
    ..Examples that illustrate the use of these functionalities are given...
  45. doi request reprint Preferential affinity of the components of liquid mixtures at a rigid non-polar surface: enthalpic and entropic driving forces
    Alexandra Choutko
    Physical Chemistry, Swiss Federal Institute of Technology, ETH Honggerberg, 8093 Zurich, Switzerland
    Chemphyschem 12:3214-23. 2011
    ..Note that the latter effect is a generic concept and may in principle involve both a solvent release and an interaction component, depending on the solute considered...
  46. doi request reprint Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold
    Andreas P Eichenberger
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
    FEBS J 279:299-315. 2012
    ..Upon esterification, the backbone-side chain and side chain-side chain hydrogen-bonding pattern of HEWL changes to maintain its compactness and thus the structural stability of the ester-linked lysozymes...
  47. ncbi request reprint Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding
    Haibo Yu
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, 8093 Zurich, Switzerland
    Proteins 54:116-27. 2004
    ..Together with the available experimental data, these simulation studies indicate that Hao-containing peptides may serve as inhibitors of beta-sheet interactions between proteins...
  48. doi request reprint Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation
    Clara D Christ
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    J Comput Chem 30:1664-79. 2009
    ..In this reference state not all barriers between all pairs of states are reduced. Instead a minimum spanning tree of states is calculated, which connects states that are "closest" in configuration space...
  49. ncbi request reprint Interpreting experimental data by using molecular simulation instead of model building
    Zrinka Gattin
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Chemistry 15:6389-98. 2009
    ....
  50. ncbi request reprint Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D
    Anna Pitschna E Kunz
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    J Phys Chem A 113:11570-9. 2009
    ....
  51. ncbi request reprint Using one-step perturbation to predict the effect of changing force-field parameters on the simulated folding equilibrium of a beta-peptide in solution
    Zhixiong Lin
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH 8093, Zurich, Switzerland
    J Comput Chem 31:2419-27. 2010
    ..The evaluated methodology constitutes an efficient tool in force-field development for molecular simulation by reducing the number of required separate simulations by orders of magnitude...
  52. doi request reprint What stabilizes the 3(14)-helix in beta3-peptides? A conformational analysis using molecular simulation
    Bettina Keller
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zurich, CH 8093 Zurich, Switzerland
    Proteins 78:1677-90. 2010
    ..The folded state of beta-peptides is stabilized by a different mechanism than that of alpha-peptides...
  53. ncbi request reprint Mechanism and thermodynamics of binding of the polypyrimidine tract binding protein to RNA
    Nathan Schmid
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    Biochemistry 46:6500-12. 2007
    ..Furthermore, the low-energy conformations of the complexes that were found provided additional information about the mechanism of binding...
  54. ncbi request reprint Free energy calculations using flexible-constrained, hard-constrained and non-constrained molecular dynamics simulations
    Markus Christen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    Chemphyschem 8:1557-64. 2007
    ..7 (4.3) kJ mol(-1) are observed. These values are smaller than the differences observed between the three different pairs of methanol/water models: up to 5 % in density and up to 8.5 kJ mol(-1) in (excess) free energy...
  55. pmc Explicit-solvent molecular dynamics simulations of the polysaccharide schizophyllan in water
    David B Kony
    Laboratory of Physical Chemistry, ETH Zurich, CH 8093 Zurich, Switzerland
    Biophys J 93:442-55. 2007
    ....
  56. ncbi request reprint Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein
    Dirk Bakowies
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
    Proteins 47:534-45. 2002
    ..Differences between the two forms of the protein are observed and discussed...
  57. ncbi request reprint Orientation and conformational preference of leucine-enkephalin at the surface of a hydrated dimyristoylphosphatidylcholine bilayer: NMR and MD simulation
    Indira Chandrasekhar
    Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
    J Am Chem Soc 128:159-70. 2006
    ..The conformational behavior of lenk at the DMPC surface is compared to that in the aqueous solution, both in the neutral and in the zwitterionic forms...
  58. ncbi request reprint Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA
    Jozica Dolenc
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH 8093 Zurich, Switzerland
    J Phys Chem B 114:11164-72. 2010
    ..Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively...
  59. ncbi request reprint Molecular dynamics simulations of a double unit cell in a protein crystal: volume relaxation at constant pressure and correlation of motions between the two unit cells
    Regula Walser
    Laboratory of Physical Chemistry, Eidgenossische Technische Hochschule Zurich, ETH Zentrum, Zurich, Switzerland
    Proteins 48:327-40. 2002
    ..The results of the double-unit-cell simulations are closely similar to the results of the single-unit-cell simulations, and little motional correlation is found between the two unit cells...
  60. ncbi request reprint Unfolded state of peptides
    Xavier Daura
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, CH 8093 Zurich
    Adv Protein Chem 62:341-60. 2002
  61. ncbi request reprint Multi-resolution simulation of biomolecular systems: a review of methodological issues
    Katharina Meier
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich ETH, 8093 Zurich, Switzerland
    Angew Chem Int Ed Engl 52:2820-34. 2013
    ....
  62. doi request reprint Structural effects of an atomic-level layer of water molecules around proteins solvated in supra-molecular coarse-grained water
    Sereina Riniker
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    J Phys Chem B 116:8873-9. 2012
    ..4 to 2.0 nm...
  63. ncbi request reprint Are NMR-derived model structures for beta-peptides representative for the ensemble of structures adopted in solution?
    Alice Glättli
    Laboratorium fur Physikalische Chemie, ETH, ETH Honggerberg, HCI, 8093 Zurich, Switzerland
    Angew Chem Int Ed Engl 43:6312-6. 2004
  64. ncbi request reprint Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models
    Haibo Yu
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, 8093 Zurich, Switzerland
    J Comput Chem 27:1494-504. 2006
    ..In particular, the experimental dielectric permittivity of 32 could be reproduced, which had been shown to be difficult when using nonpolarizable models...
  65. doi request reprint Comparing geometric and kinetic cluster algorithms for molecular simulation data
    Bettina Keller
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, CH 8093 Zurich, Switzerland
    J Chem Phys 132:074110. 2010
    ....
  66. pmc Catalytic mechanism of cyclophilin as observed in molecular dynamics simulations: pathway prediction and reconciliation of X-ray crystallographic and NMR solution data
    Daniel Trzesniak
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
    Protein Sci 15:2544-51. 2006
    ..These results illustrate the use of MD simulation at atomic resolution to model structural transitions and to interpret experimental data...
  67. ncbi request reprint A photoinducible beta-hairpin
    Andreas Aemissegger
    Laboratorium für Organische Chemie and Laboratorium für Physikalische Chemie, Swiss Federal Institute of Technology, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Am Chem Soc 127:2929-36. 2005
    ..These results suggest that suitably substituted azobenzenes can be used as photoinducible turn elements to investigate and control the folding and stability of beta-sheets...
  68. doi request reprint Definition and testing of the GROMOS force-field versions 54A7 and 54B7
    Nathan Schmid
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
    Eur Biophys J 40:843-56. 2011
    ..The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained...
  69. doi request reprint Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors
    Sereina Riniker
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zurich, Switzerland
    J Chem Phys 135:024105. 2011
    ..In addition, two different schemes to determine automatically the EDS reference state parameters and two different topology approaches are compared...
  70. doi request reprint Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide
    Zrinka Gattin
    Swiss Federal Institute of Technology, ETH, Zurich, Switzerland
    J Phys Chem B 113:8695-703. 2009
    ..Helv. Chim. Acta 2005, 88, 266-280) may lead to molecular structures that are not representative for the ensemble of molecular conformations...
  71. ncbi request reprint A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
    Indira Chandrasekhar
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Hoenggerberg, 8093, Zurich, Switzerland
    Eur Biophys J 32:67-77. 2003
    ..An optimal set of simulation parameters for which the GROMOS96 parameter set 45A3 yields a head group area, chain order parameters and a lateral diffusion coefficient in accordance with the experimental data is listed...
  72. ncbi request reprint Structure and dynamics of two beta-peptides in solution from molecular dynamics simulations validated against experiment
    Bojan Zagrovic
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
    Eur Biophys J 37:903-12. 2008
    ..The central members of all of the clusters populating more than 5% of all of the structures are shown, together with the most dominant hydrogen bonds and the corresponding percentages of cluster members containing them...
  73. ncbi request reprint Force field evaluation for biomolecular simulation: free enthalpies of solvation of polar and apolar compounds in various solvents
    Daan P Geerke
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Hönggerberg HCI, 8093 Zurich, Switzerland
    Chemphyschem 7:671-8. 2006
    ....
  74. ncbi request reprint Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalene-hopene cyclase
    Fabienne Schwab
    Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, Zurich, CH 8093, Switzerland
    Biochemistry 47:2945-51. 2008
    ..Detailed comparisons and potential reasons for this are given...
  75. doi request reprint Coarse-grained models for the solvents dimethyl sulfoxide, chloroform, and methanol
    Jane R Allison
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    J Chem Phys 136:054505. 2012
    ..The inclusion of polarizability greatly improves the reproduction of thermodynamic data measured experimentally and calculated from AL simulations for both the pure liquids and binary mixtures...
  76. doi request reprint Current computer modeling cannot explain why two highly similar sequences fold into different structures
    Jane R Allison
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    Biochemistry 50:10965-73. 2011
    ....
  77. ncbi request reprint Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
    Chris Oostenbrink
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
    Proteins 54:237-46. 2004
    ....
  78. doi request reprint A molecular dynamics study of the ASC and NALP1 pyrin domains at neutral and low pH
    Zrinka Gattin
    Laboratory for Physical Chemistry, ETH Zurich, Hoenggerberg, HCI G236, 8093 Zurich, Switzerland
    Chembiochem 9:923-33. 2008
    ..The results show that the particular protonation states of acidic side chains in the protein interior might be crucial to properly modeling these proteins at low pH...
  79. pmc A comparison of the different helices adopted by α- and β-peptides suggests different reasons for their stability
    Jane R Allison
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    Protein Sci 19:2186-95. 2010
    ..The observed energetic and entropic differences can be traced to differences in the polarity of the solvent-accessible surface area and, in particular, the solute dipole moments, suggesting different reasons for their stability...
  80. ncbi request reprint Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1
    Jozica Dolenc
    Laboratory of Physical Chemistry, ETH, Swiss Federal Institute of Technology, 8093, Zurich, Switzerland
    J Biomol NMR 47:221-35. 2010
    ..e. measured NMR data...
  81. ncbi request reprint Principles of carbopeptoid folding: a molecular dynamics simulation study
    Riccardo Baron
    Laboratorium fur Physikalische Chemie, ETH, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Pept Sci 11:74-84. 2005
    ..The simulations provide an atomic picture of molecular conformational variability that is consistent with the available experimental data...
  82. doi request reprint Cyclic beta-helical/beta-hairpin D,L-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics
    Katharina Meier
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich ETH, 8093 Zurich, Switzerland
    J Phys Chem A 114:1852-9. 2010
    ..Due to the high barriers to (un)folding, a folding/unfolding equilibrium could not be established...
  83. doi request reprint A refined, efficient mean solvation force model that includes the interior volume contribution
    Jane R Allison
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, Zürich, Switzerland
    J Phys Chem B 115:4547-57. 2011
    ....
  84. ncbi request reprint On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
    Markus Christen
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH, CH 8093 Zurich, Switzerland
    J Comput Chem 29:157-66. 2008
    ..The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest...
  85. ncbi request reprint On using oscillating time-dependent restraints in MD simulation
    Bettina Keller
    Laboratorium fur Physikalische Chemie, ETH Zurich, Zurich, CH 8093, Switzerland
    J Biomol NMR 37:1-14. 2007
    ..The introduction of a factor oscillating with time into the restraining penalty function alleviates this problem and enhances the restrained conformational sampling...
  86. ncbi request reprint A comparison of the potential energy parameters of aliphatic alkanes: molecular dynamics simulations of triacylglycerols in the alpha phase
    Indira Chandrasekhar
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Zentrum, 8092 Zurich, Switzerland
    Eur Biophys J 31:89-101. 2002
    ..The last parameter set tested, 45A3-45x12, also performs well when combined with either set of partial charges, although the system expands in the plane of the bilayer...
  87. doi request reprint A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation
    Adam Lange
    Physical Chemistry, ETH Zurich, Wolfgang Pauli Strasse 10, Zurich, Switzerland
    Chembiochem 10:1657-65. 2009
    ..Simulations at different temperatures indicated that the network is highly dynamic and that it contributes to the thermostability of the HET-s(218-289) amyloids...
  88. ncbi request reprint Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation
    Roland Bürgi
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, Zurich, Switzerland
    Proteins 47:469-80. 2002
    ..The method is tested on the acidic residues of the protein hen egg white lysozyme. It is shown that small structural changes may have a big effect on the pK(A) values of titratable residues...
  89. ncbi request reprint Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water
    Dirk Bakowies
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zurich, 8093, Switzerland
    J Mol Biol 315:713-36. 2002
    ..Solvent inside apo-FABP, for example, shows characteristics of a water droplet, while solvent in holo-FABP benefits from interactions with the ligand headgroup and slightly stronger interactions with protein residues...
  90. ncbi request reprint Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study
    Haibo Yu
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, 8093 Zurich, Switzerland
    Carbohydr Res 339:1697-709. 2004
    ..It was found that methylation at O-2 has the biggest effect, in agreement with experiment...
  91. ncbi request reprint Can one derive the conformational preference of a beta-peptide from its CD spectrum?
    Alice Glättli
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zurich, ETH Honggerberg, CH 8093 Zurich, Switzerland
    J Am Chem Soc 124:12972-8. 2002
    ..To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required...
  92. ncbi request reprint On the calculation of velocity-dependent properties in molecular dynamics simulations using the leapfrog integration algorithm
    Michel A Cuendet
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    J Chem Phys 127:184102. 2007
    ..We show the consequences when the system is coupled to a thermostat and a barostat...
  93. ncbi request reprint Investigation of stability and disulfide bond shuffling of lipid transfer proteins by molecular dynamics simulation
    Jane R Allison
    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland
    Biochemistry 49:6916-27. 2010
    ....
  94. pmc Unusual compactness of a polyproline type II structure
    Bojan Zagrovic
    Department of Chemistry, Laboratory of Physical Chemistry, Eidgenossische Technische Hochschule Zurich, Honggerberg, 8093 Zurich, Switzerland
    Proc Natl Acad Sci U S A 102:11698-703. 2005
    ....
  95. ncbi request reprint Assessing equilibration and convergence in biomolecular simulations
    Lorna J Smith
    Oxford Centre for Molecular Sciences, Central Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
    Proteins 48:487-96. 2002
    ..This is particularly the case if the analysis includes a comparison of multiple trajectories calculated for the same system from different starting structures...
  96. ncbi request reprint Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation
    Sofia Calero
    Department of Chemical Engineering, Faculty of Science, University of Amsterdam, NL 1018 WV Amsterdam
    Chem Biodivers 1:505-19. 2004
    ..The proposed polyproline-type-II helicity appears only locally, and the peptide displays substantial flexibility. It is found that the peptide residues Lys10 to Tyr12 could be responsible for most of the specificity of the interaction...
  97. ncbi request reprint Molecular dynamics simulations of Hydrogenobacter thermophilus cytochrome c552: comparisons of the wild-type protein, a b-type variant, and the apo state
    Lorna J Smith
    Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom
    Proteins 65:702-11. 2006
    ..In the absence of heme, in the apo state simulations, these residues form short but persistent regions of beta-sheet secondary structure. These could provide nucleation sites for the conversion to amyloid fibrils...
  98. ncbi request reprint A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides
    K Anton Feenstra
    BIOSON Research Institute and Laboratory of Biophysical Chemistry, University of Groningen, The Netherlands
    J Biomol NMR 23:181-94. 2002
    ....
  99. ncbi request reprint Computational study of ground-state chiral induction in small peptides: comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations
    Yu Zhou
    Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
    J Comput Chem 27:857-67. 2006
    ....
  100. ncbi request reprint Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations
    Ricard Boned
    Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
    Chemistry 14:5039-46. 2008
    ..The results illustrate the power of current molecular simulation force fields and techniques in establishing the link between thermodynamic quantities and conformational distributions...
  101. ncbi request reprint beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution
    Clara M Santiveri
    Instituto de Quimica Fisica Rocasolano, Consejo Superior de Investigaciones Cientificas, E 28006 Madrid, Spain
    J Pept Sci 10:546-65. 2004
    ..Nevertheless, the fine organization of the turn region appears to be a late event in the folding process...