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1
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0029586380
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Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: Comparison to X-ray and NMR data
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Li A., Daggett V. Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to X-ray and NMR data. Protein Eng. 8:1995;1117-1128.
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(1995)
Protein Eng
, vol.8
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Li, A.1
Daggett, V.2
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2
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0032584783
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Reversible peptide folding in solution by molecular dynamics simulation
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The authors describe an interesting series of simulations of a small peptide in methanol simulated as a function of temperature. Equilibrium is obtained: conformational populations are found to be independent of the starting structure. Also noteworthy is the finding that the pathways of folding and unfolding are similar, and that the pathways are independent of temperature, which is good news for high-temperature denaturation simulations
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Daura X., Jaun B., Seebach D., van Gunsteren W.F., Mark A.E. Reversible peptide folding in solution by molecular dynamics simulation. J Mol Biol. 280:1998;925-932. The authors describe an interesting series of simulations of a small peptide in methanol simulated as a function of temperature. Equilibrium is obtained: conformational populations are found to be independent of the starting structure. Also noteworthy is the finding that the pathways of folding and unfolding are similar, and that the pathways are independent of temperature, which is good news for high-temperature denaturation simulations.
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(1998)
J Mol Biol
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, pp. 925-932
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Daura, X.1
Jaun, B.2
Seebach, D.3
Van Gunsteren, W.F.4
Mark, A.E.5
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3
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0033557181
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Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations
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Daura X., van Gunsteren W.F., Mark A.E. Folding-unfolding thermodynamics of a β-heptapeptide from equilibrium simulations. Proteins. 34:1999;269-280.
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Proteins
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, pp. 269-280
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Daura, X.1
Van Gunsteren, W.F.2
Mark, A.E.3
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4
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0032800402
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The effect of motional averaging on the calculation of NMR-derived structural properties
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Daura X., Antes I., van Gunsteren W.F., Thiel W., Mark A.E. The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins. 36:1999;542-555.
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(1999)
Proteins
, vol.36
, pp. 542-555
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Daura, X.1
Antes, I.2
Van Gunsteren, W.F.3
Thiel, W.4
Mark, A.E.5
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5
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0033578828
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Is protein unfolding the reverse of protein folding? A lattice simulation analysis
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Dinner A.R., Karplus M. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J Mol Biol. 292:1999;403-419.
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J Mol Biol
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Dinner, A.R.1
Karplus, M.2
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6
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0032867335
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Long-range electrostatic effects on peptide folding
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Åqvist J. Long-range electrostatic effects on peptide folding. FEBS Lett. 457:1999;414-418.
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(1999)
FEBS Lett
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, pp. 414-418
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Åqvist, J.1
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7
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0032561237
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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
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An impressive computational achievement is described
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Duan Y., Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:1998;740-744. An impressive computational achievement is described.
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Science
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, pp. 740-744
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Duan, Y.1
Kollman, P.A.2
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8
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0029633167
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Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
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Levitt M., Hirshberg M., Sharon R., Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp Phys Commun. 91:1995;215-231.
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Comp Phys Commun
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, pp. 215-231
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Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
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10
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0032790341
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Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study
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An interesting simulation of an amphipathic peptide at a hexane-water interface is presented. Simulations begin with the peptide in an extended conformation in the water, but the peptide quickly absorbs to the interface and adjusts itself to optimize interactions with both solvents
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Chipot C., Maigret B., Pohorille A. Early events in the folding of an amphipathic peptide: a multinanosecond molecular dynamics study. Proteins. 36:1999;383-399. An interesting simulation of an amphipathic peptide at a hexane-water interface is presented. Simulations begin with the peptide in an extended conformation in the water, but the peptide quickly absorbs to the interface and adjusts itself to optimize interactions with both solvents.
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(1999)
Proteins
, vol.36
, pp. 383-399
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Chipot, C.1
Maigret, B.2
Pohorille, A.3
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11
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0032567163
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Folding and translocation of the undecamer of poly L-leucine across the water-hexane interface. A multi-nanosecond molecular dynamics study
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Chipot C., Pohorille A. Folding and translocation of the undecamer of poly L-leucine across the water-hexane interface. A multi-nanosecond molecular dynamics study. J Am Chem Soc. 120:1998;11912-11924.
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J Am Chem Soc
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Chipot, C.1
Pohorille, A.2
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13
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0034602807
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Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
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Multiple unfolding simulations of the B- and E-domains of protein A illustrate how differences in the sequence can affect the structure and dynamics of both the native and denatured states. Overall properties, such as radius of gyration and tertiary contacts, are shown to provide a poor description of the unfolding reaction coordinate
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Alonso D.O.V., Daggett V. Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains. Proc Natl Acad Sci USA. 97:2000;133-138. Multiple unfolding simulations of the B- and E-domains of protein A illustrate how differences in the sequence can affect the structure and dynamics of both the native and denatured states. Overall properties, such as radius of gyration and tertiary contacts, are shown to provide a poor description of the unfolding reaction coordinate.
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(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 133-138
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Alonso, D.O.V.1
Daggett, V.2
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14
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0029151245
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First-principles calculation of the folding free energy of a three-helix bundle protein
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Boczko E.M., Brooks C.L. III First-principles calculation of the folding free energy of a three-helix bundle protein. Science. 269:1995;393-396.
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(1995)
Science
, vol.269
, pp. 393-396
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Boczko, E.M.1
Brooks C.L. III2
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15
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0030967896
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Exploring the folding free energy surface of a three-helix bundle protein
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Guo Z., Brooks C.L. III, Boczko E.M. Exploring the folding free energy surface of a three-helix bundle protein. Proc Natl Acad Sci USA. 94:1997;10161-10166.
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Proc Natl Acad Sci USA
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Guo, Z.1
Brooks C.L. III2
Boczko, E.M.3
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16
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0030755502
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Absence of a stable intermediate on the folding pathway of protein A
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Bai Y., Karimi A., Dyson J., Wright P.E. Absence of a stable intermediate on the folding pathway of protein A. Protein Sci. 6:1997;1449-1457.
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Protein Sci
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Bai, Y.1
Karimi, A.2
Dyson, J.3
Wright, P.E.4
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17
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0028608099
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The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy
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Bottomley S.P., Popplewell A.G., Seawen M., Wan T., Sutton B.J., Gore M.G. The stability and unfolding of an IgG binding protein based upon the B domain of protein A from Staphylococcus aureus probed by tryptophan substitution and fluorescence spectroscopy. Protein Eng. 7:1994;1463-1470.
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Protein Eng
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Bottomley, S.P.1
Popplewell, A.G.2
Seawen, M.3
Wan, T.4
Sutton, B.J.5
Gore, M.G.6
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18
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0032484148
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Non-native interactions in protein folding intermediates: Molecular dynamics simulations of hen lysozyme
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Kazmirski S.L., Daggett V. Non-native interactions in protein folding intermediates: molecular dynamics simulations of hen lysozyme. J Mol Biol. 284:1998;793-806.
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J Mol Biol
, vol.284
, pp. 793-806
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Kazmirski, S.L.1
Daggett, V.2
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19
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0026630480
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Simulation of the thermal denaturation of hen egg white lysozyme: Trapping the molten globule state
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Mark A.E., van Gunsteren W.F. Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state. Biochemistry. 31:1992;7745-7748.
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Biochemistry
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Mark, A.E.1
Van Gunsteren, W.F.2
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20
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0028926875
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Computational approaches to study protein unfolding: Hen egg white lysozyme as a case study
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Hunenberger P.H., Mark A.E., van Gunsteren W.F. Computational approaches to study protein unfolding: hen egg white lysozyme as a case study. Proteins. 21:1995;196-213.
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Proteins
, vol.21
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Hunenberger, P.H.1
Mark, A.E.2
Van Gunsteren, W.F.3
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22
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0033955055
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Protein dynamics in enzymatic catalysis: Exploration of dihydrofolate reductase
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The authors present interesting simulations addressing the effect of dynamics on different aspects of the dihydrofolate reductase catalyzed reaction. Many mutations known to affect catalysis reside in regions of the protein that display coupled correlated motion in the Michaelis complex
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Radkiewicz J.L., Brooks C.L. III Protein dynamics in enzymatic catalysis: exploration of dihydrofolate reductase. J Am Chem Soc. 122:2000;225-231. The authors present interesting simulations addressing the effect of dynamics on different aspects of the dihydrofolate reductase catalyzed reaction. Many mutations known to affect catalysis reside in regions of the protein that display coupled correlated motion in the Michaelis complex.
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(2000)
J Am Chem Soc
, vol.122
, pp. 225-231
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Radkiewicz, J.L.1
Brooks C.L. III2
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23
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0028912595
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A sampling problem in molecular dynamics simulations of macromolecules
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Clarage J.B., Romo T., Andrews B.K., Pettitt B.M., Phillips G.N. A sampling problem in molecular dynamics simulations of macromolecules. Proc Natl Acad Sci USA. 92:1995;3288-3292.
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Proc Natl Acad Sci USA
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Clarage, J.B.1
Romo, T.2
Andrews, B.K.3
Pettitt, B.M.4
Phillips, G.N.5
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24
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0343870703
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Protein dynamics: A theoretical perspective
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Kazmirski S.L., Daggett V. Protein dynamics: a theoretical perspective. Adv Mol Cell Biol. 22B:1997;339-390.
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(1997)
Adv Mol Cell Biol
, vol.22
, pp. 339-390
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Kazmirski, S.L.1
Daggett, V.2
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25
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0031472252
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Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
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Bond C.J., Wong K., Clarke J., Fersht A.R., Daggett V. Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proc Natl Acad Sci USA. 94:1997;13409-13413.
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Proc Natl Acad Sci USA
, vol.94
, pp. 13409-13413
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Bond, C.J.1
Wong, K.2
Clarke, J.3
Fersht, A.R.4
Daggett, V.5
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26
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0034628913
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Towards complete characterization of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
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Wong K., Clarke J., Bond C.J., Neira J.L., Freund S.M.V., Fersht A.R., Daggett V. Towards complete characterization of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J Mol Biol. 296:2000;1257-1258.
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J Mol Biol
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Wong, K.1
Clarke, J.2
Bond, C.J.3
Neira, J.L.4
Freund, S.M.V.5
Fersht, A.R.6
Daggett, V.7
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27
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0032571391
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The structural and dynamic properties of unfolded proteins: Simulations of the "molten coil" state of BPTI
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Kazmirski S., Daggett V. The structural and dynamic properties of unfolded proteins: simulations of the "molten coil" state of BPTI. J Mol Biol. 277:1998;487-506.
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J Mol Biol
, vol.277
, pp. 487-506
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Kazmirski, S.1
Daggett, V.2
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28
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0028965968
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Molecular dynamics simulations of protein unfolding and limited refolding: Characterization of partially unfolded states of ubiquitin in methanol and in pure water
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Alonso D.O.V., Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in methanol and in pure water. J Mol Biol. 247:1995;501-520.
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J Mol Biol
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Alonso, D.O.V.1
Daggett, V.2
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29
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0031965674
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Molecular dynamics simulations of hydrophobic collapse of ubiquitin
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Alonso D.O.V., Daggett V. Molecular dynamics simulations of hydrophobic collapse of ubiquitin. Protein Sci. 7:1998;860-874.
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(1998)
Protein Sci
, vol.7
, pp. 860-874
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Alonso, D.O.V.1
Daggett, V.2
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30
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0030057477
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Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues
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Khorasanizadeh S., Peters I.D., Roder H. Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat Struct Biol. 3:1996;193-205.
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Nat Struct Biol
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Khorasanizadeh, S.1
Peters, I.D.2
Roder, H.3
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31
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0029963345
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Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
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Li A., Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol. 257:1996;412-429.
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J Mol Biol
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Li, A.1
Daggett, V.2
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32
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0031465967
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"new view" of protein folding reconciled with the old through multiple unfolding simulations
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Lazaridis T., Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science. 278:1997;1928-1931.
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Science
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, pp. 1928-1931
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Lazaridis, T.1
Karplus, M.2
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33
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0031910020
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Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
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Caves L.S.D., Evanseck J.D., Karplus M. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci. 7:1998;649-666.
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Protein Sci
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Caves, L.S.D.1
Evanseck, J.D.2
Karplus, M.3
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34
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0345411345
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Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
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Tsai J., Levitt M., Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol. 291:1999;215-225.
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(1999)
J Mol Biol
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Tsai, J.1
Levitt, M.2
Baker, D.3
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35
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0033516512
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Analysis methods for comparison of molecular dynamics trajectories: Applications to protein unfolding pathways and denatured ensembles
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Kazmirski S., Li A., Daggett V. Analysis methods for comparison of molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles. J Mol Biol. 290:1999;283-304.
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J Mol Biol
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Kazmirski, S.1
Li, A.2
Daggett, V.3
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