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A careful comparison between molecular dynamics simulations of DMSO-solvated linear and cyclic APB peptides, and femtosecond time-resolved spectroscopy attempted to validate the simulations. Absorbance spectra were compared for several 1 ns simulations in a spectral region that possessed no ground state absorption. The simulations were in good agreement with the experiments, which occurred on identical timescales, leading the authors to associate ballistic cis/trans isomerization motions with the observed spectral features.
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Sporlein S., Carstens H., Satzger H., Renner C., Behrendt R., Moroder L., Tavan P., Zinth W., Wachtveitl J. Ultrafast spectroscopy reveals subnanosecond peptide conformation dynamics and validates molecular dynamics simulation. Proc. Natl. Acad. Sci. U.S.A. 99:2002;7998-8002 A careful comparison between molecular dynamics simulations of DMSO-solvated linear and cyclic APB peptides, and femtosecond time-resolved spectroscopy attempted to validate the simulations. Absorbance spectra were compared for several 1 ns simulations in a spectral region that possessed no ground state absorption. The simulations were in good agreement with the experiments, which occurred on identical timescales, leading the authors to associate ballistic cis/trans isomerization motions with the observed spectral features.
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Absolute comparison of simulated and experimental protein-folding dynamics
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The authors carried out a detailed comparison of the measured and calculated folding rates for the mini-protein BBA5. The calculation consists of thousands of 10-50 ns (700 μs total simulation time) simulations using a GB/SA implicit solvent model. There is a very good agreement between measured and calculated folding rates. This study might represent the first example of a truly synergistic collaboration between theoretical and experimental work.
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Snow C.D., Nguyen N., Pande V.S., Gruebele M. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 42:2002;102-106 The authors carried out a detailed comparison of the measured and calculated folding rates for the mini-protein BBA5. The calculation consists of thousands of 10-50 ns (700 μs total simulation time) simulations using a GB/SA implicit solvent model. There is a very good agreement between measured and calculated folding rates. This study might represent the first example of a truly synergistic collaboration between theoretical and experimental work.
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Snow, C.D.1
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5] using an implicit solvent model. The forcefield is good enough to fold both β and α peptides. Folding and unfolding rates show the non-Arrhenius temperature dependence seen in simple lattice models. Folding is more cooperative for the β peptide than the α peptide, and is slower for the β peptide than the α peptide.
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5] using an implicit solvent model. The forcefield is good enough to fold both β and α peptides. Folding and unfolding rates show the non-Arrhenius temperature dependence seen in simple lattice models. Folding is more cooperative for the β peptide than the α peptide, and is slower for the β peptide than the α peptide.
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2 peptides using Amber and Charm forcefields. Whereas the potentials of mean force from the two potentials were markedly different, the end-to-end contact times were found to be quite similar. The authors found that the measured quenching rates were consistent with the simulations [40].
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2 peptides using Amber and Charm forcefields. Whereas the potentials of mean force from the two potentials were markedly different, the end-to-end contact times were found to be quite similar. The authors found that the measured quenching rates were consistent with the simulations [40].
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In this work, the folding of a peptide has been simulated for the longest time that has ever been reported for a peptide of this size. This simulation has allowed the authors to directly observe folding events that occur on the microsecond timescale.
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Zagrovic B., Sorin E.J., Pande V.S. β-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:2002;151-169 In this work, the folding of a peptide has been simulated for the longest time that has ever been reported for a peptide of this size. This simulation has allowed the authors to directly observe folding events that occur on the microsecond timescale.
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On the simulation of protein folding by short time scale molecular dynamics and distributed computing
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In this paper, Fersht criticizes the use of multiple short simulations to study folding kinetics. He argues that protein folding is not an elementary kinetic step, because it involves a series of early conformational steps that lead to lag phases at the beginning of the kinetics. The presence of these lag phases can bias short simulations toward selecting minor pathways that have fewer or faster lag steps, and so the major folding pathways could be missed.
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Fersht A.R. On the simulation of protein folding by short time scale molecular dynamics and distributed computing. Proc. Natl. Acad. Sci. U.S.A. 99:2002;14122-14125 In this paper, Fersht criticizes the use of multiple short simulations to study folding kinetics. He argues that protein folding is not an elementary kinetic step, because it involves a series of early conformational steps that lead to lag phases at the beginning of the kinetics. The presence of these lag phases can bias short simulations toward selecting minor pathways that have fewer or faster lag steps, and so the major folding pathways could be missed.
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An excellent illustration of the use of umbrella sampling to sample the free energy surface of a peptide, betanova. The free energy surfaces obtained with explicit and implicit solvent models are very similar.
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Bursulaya B.D., Brooks C.L. Comparative study of the folding free energy landscape of a three-stranded beta-sheet protein with explicit and implicit solvent models. J. Phys. Chem. B. 104:2000;12378-12383 An excellent illustration of the use of umbrella sampling to sample the free energy surface of a peptide, betanova. The free energy surfaces obtained with explicit and implicit solvent models are very similar.
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An REMD simulation of the GB1 peptide in explicit solvent shows that the peptide samples multiple free energy minima with different secondary structure.
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Garcia A.E., Sanbonmatsu K.Y. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins. 42:2001;345-354 An REMD simulation of the GB1 peptide in explicit solvent shows that the peptide samples multiple free energy minima with different secondary structure.
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Lapidus L.J., Steinbach P.J., Eaton W.A., Szabo A., Hofrichter J. Effects of chain stiffness on the dynamics of loop formation in polypeptides. Testing a 1-dimensional diffusion model of peptide dynamics. J. Phys. Chem. B. 106:2002;11628-11640.
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3 were analyzed using bounds on the mean contact times for a general Gaussian chain. Although correlation functions of the end-to-end vector were found to be non-Gaussian, the simulated diffusion-limited contact time agrees with the Gaussian bounds if the diffusion coefficient is reduced to match the simulated end-to-end distance relaxation.
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3 were analyzed using bounds on the mean contact times for a general Gaussian chain. Although correlation functions of the end-to-end vector were found to be non-Gaussian, the simulated diffusion-limited contact time agrees with the Gaussian bounds if the diffusion coefficient is reduced to match the simulated end-to-end distance relaxation.
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REMD simulations in explicit solvent examined the mechanism of the helix-coil transition and addressed the issues of adequate sampling and forcefield accuracy. It was found that Parm94 exaggerates helix formation, whereas Parm96, designed to address this deficiency, produces predominately β-hairpin conformations for the Ala-21 system. A simple modification of the Parm94 forcefield was shown to produce σ values with the correct order of magnitude (0.004) and reasonable values for the α-helix melting temperature.
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Garcia A.E., Sanbonmatsu K.Y. α-Helical stabilization by side chain shielding of backbone hydrogen bonds. Proc. Natl. Acad. Sci. U.S.A. 99:2002;2782-2787 REMD simulations in explicit solvent examined the mechanism of the helix-coil transition and addressed the issues of adequate sampling and forcefield accuracy. It was found that Parm94 exaggerates helix formation, whereas Parm96, designed to address this deficiency, produces predominately β-hairpin conformations for the Ala-21 system. A simple modification of the Parm94 forcefield was shown to produce σ values with the correct order of magnitude (0.004) and reasonable values for the α-helix melting temperature.
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Vila J.A., Ripoll D.R., Scheraga H.A. Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl. Acad. Sci. U.S.A. 97:2002;13075-13079.
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Assessing equilibrium and convergence in biomolecular simulations
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The authors attempt to establish criteria for assessing the quality of sampling achieved during a simulation. The intermolecular energy, rmsd, number of clusters as determined from a cluster analysis, number of intermolecular hydrogen bonds and number of torsion angle transitions were used as measures of equilibration. These quantities were compared for various molecular dynamics simulations of α helices and β hairpins at several different temperatures. This study revealed that different measures have different convergence times. Whereas the rmsd and intermolecular interaction energy stabilize quickly (∼3 ns), the number of hydrogen bonds and number of clusters require significantly more time to equilibrate (30-50 ns).
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Smith L.J., Daura X., van Gunsteren W.F. Assessing equilibrium and convergence in biomolecular simulations. Proteins. 48:2002;487-496 The authors attempt to establish criteria for assessing the quality of sampling achieved during a simulation. The intermolecular energy, rmsd, number of clusters as determined from a cluster analysis, number of intermolecular hydrogen bonds and number of torsion angle transitions were used as measures of equilibration. These quantities were compared for various molecular dynamics simulations of α helices and β hairpins at several different temperatures. This study revealed that different measures have different convergence times. Whereas the rmsd and intermolecular interaction energy stabilize quickly (∼3 ns), the number of hydrogen bonds and number of clusters require significantly more time to equilibrate (30-50 ns).
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Smith, L.J.1
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Peng Y., Hansmann U.H.E. Solvation model dependency of helix-coil transition in polyalanine. Biophys. J. 82:2002;3269-3276.
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Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta-beta-alpha-motif
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Jang S., Shin S., Pak Y. Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta-beta-alpha-motif. J. Am. Chem. Soc. 124:2002;4976-4979.
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Molecular dynamics simulations of a beta-hairpin fragment of protein G: Balance between side-chain and backbone forces
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Ma B., Nussinov R. Molecular dynamics simulations of a beta-hairpin fragment of protein G: balance between side-chain and backbone forces. J. Mol. Biol. 296:2000;1091-1104.
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The free energy landscape for beta hairpin folding in explicit water
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Zhou R.H., Berne B.J., Germain R. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. U.S.A. 98:2001;14931-14936.
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Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?
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REMD calculations of the free energy surface of the GB1 β hairpin in explicit and implicit (GB/SA) solvent models are in great disagreement. The authors argue that GB/SA and implicit solvent models need to improve on the energetics of ion pair formation.
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Zhou R.H., Berne B.J. Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc. Natl. Acad. Sci. U.S.A. 99:2002;12777-12782 REMD calculations of the free energy surface of the GB1 β hairpin in explicit and implicit (GB/SA) solvent models are in great disagreement. The authors argue that GB/SA and implicit solvent models need to improve on the energetics of ion pair formation.
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Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation
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Wu H.W., Wang S.M., Brooks B.R. Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation. J. Am. Chem. Soc. 124:2002;5282-5283.
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Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study
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Roccatano D., Colombo G., Fioroni M., Mark A.E. Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: a molecular dynamics study. Proc. Natl. Acad. Sci. U.S.A. 99:2002;12179-12184.
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Two-dimensional correlation analysis of peptide unfolding: Molecular dynamics simulations of beta hairpins
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Lee J., Shin S. Two-dimensional correlation analysis of peptide unfolding: molecular dynamics simulations of beta hairpins. J. Phys. Chem. B. 106:2002;8796-8802.
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Understanding protein folding with energy landscape theory: Part I: Basic concepts
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Plotkin S.S., Onuchic J.N. Understanding protein folding with energy landscape theory: part I: basic concepts. Q Rev. Biophys. 35:2002;111-167.
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Generalized Born models of macromolecular solvation effects
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Bashford D., Case D.A. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51:2000;129-152.
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Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models
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Shen M.Y., Freed K.F. Long time dynamics of met-enkephalin: comparison of explicit and implicit solvent models. Biophys. J. 82:2002;1791-1808.
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The beta-peptide hairpin in solution: Conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation
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A detailed conformational study on a β-hexapeptide in methanol at two different temperatures, 298K and 340K. Reversible folding to the hairpin conformation was observed at both temperatures. It was found that the ensemble of structures from the simulation at 340K reproduced the room temperature NMR-derived data, such as NOEs, better than those obtained from the simulation at 298K. It was suggested that the disagreement in the temperature could be a result of improper parameterization.
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Daura X., Gademann K., Schafer H., Jaun B., Seebach D., van Gunsteren W.F. The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation. J. Am. Chem. Soc. 123:2001;2393-2404 A detailed conformational study on a β-hexapeptide in methanol at two different temperatures, 298K and 340K. Reversible folding to the hairpin conformation was observed at both temperatures. It was found that the ensemble of structures from the simulation at 340K reproduced the room temperature NMR-derived data, such as NOEs, better than those obtained from the simulation at 298K. It was suggested that the disagreement in the temperature could be a result of improper parameterization.
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Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
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Peter C., Daura X., van Gunsteren W.F. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. J. Biomol. NMR. 20:2001;297-310.
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A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides
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6> for clustered conformations and, subsequently, spectral densities were obtained from a Lorentz function using these averages. In the third approach, the average distances are assumed to be proportional to intensities. It was found that, regardless of the methodology chosen, the correlations between experimental and theoretical intensities were identical.
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6> for clustered conformations and, subsequently, spectral densities were obtained from a Lorentz function using these averages. In the third approach, the average distances are assumed to be proportional to intensities. It was found that, regardless of the methodology chosen, the correlations between experimental and theoretical intensities were identical.
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