Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy

Phineus R. L. Markwick; Guillaume Bouvignies; Martin Blackledge

doi:10.1021/ja0687668

journal article Mar 22, 2007

Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy

Phineus R. L. Markwick Guillaume Bouvignies Martin Blackledge

Journal of the American Chemical Society Vol. 129 No. 15 pp. 4724-4730 · American Chemical Society (ACS)

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References

61

[1]

The Energy Landscapes and Motions of Proteins

Hans Frauenfelder, Stephen G. Sligar, Peter G. Wolynes

Science 1991 10.1126/science.1749933

[2]

Benkovic S. J. Science (2003) 10.1126/science.1085515

[3]

Mittermaier A. Science (2006) 10.1126/science.1124964

[4]

Kay L. E. Biochemistry (1989)

[5]

Palmer A. G. Annu. Rev. Biophys. Biomol. Struct. (2001)

[6]

Bruschweiler R. Curr. Opin. Struct. Biol. (2003) 10.1016/s0959-440x(03)00036-8

[7]

Tousignant A. Chem. Biol. (2004) 10.1016/j.chembiol.2004.06.007

[8]

Rousseau F. Curr. Opin. Struct. Biol. (2005) 10.1016/j.sbi.2005.01.007

[9]

The role of dynamics in allosteric regulation

Dorothee Kern, Erik RP Zuiderweg

Current Opinion in Structural Biology 2003 10.1016/j.sbi.2003.10.008

[10]

Enzyme Dynamics During Catalysis

Elan Zohar Eisenmesser, Daryl A. Bosco, Mikael Akke et al.

Science 2002 10.1126/science.1066176

[11]

Frans A.A. Mulder, Anthony Mittermaier, Bin Hon et al.

Nature Structural Biology 2001 10.1038/nsb1101-932

[12]

Eisenmesser E. Z. Nature (2005) 10.1038/nature04105

[13]

Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR

Dmitry M. Korzhnev, Xavier Salvatella, Michele Vendruscolo et al.

Nature 2004 10.1038/nature02655

[14]

The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis

David D. Boehr, Dan McElheny, H. Jane Dyson et al.

Science 2006 10.1126/science.1130258

[15]

Direct Measurement of Distances and Angles in Biomolecules by NMR in a Dilute Liquid Crystalline Medium

Nico Tjandra, Ad Bax

Science 1997 10.1126/science.278.5340.1111

[16]

NMR evidence for slow collective motions in cyanometmyoglobin

J. R. Tolman, J. M. Flanagan, M. A. Kennedy et al.

Nature Structural Biology 1997 10.1038/nsb0497-292

[17]

Bax A. Protein Sci. (2003)

[18]

Prestegard J. H. Chem. Rev. (2004) 10.1021/cr030419i

[19]

Prestegard J. H. Rev. Biophys. (2000) 10.1017/s0033583500003656

[20]

Blackledge M. Prog. Nucl. Magn. Reson. Spectrosc. (2005) 10.1016/j.pnmrs.2004.11.002

[21]

Meiler J. J. Am. Chem. Soc. (2001) 10.1021/ja010002z

[22]

Peti W. J. Am. Chem. Soc. (2002) 10.1021/ja011883c

[23]

Briggman K. B. J. Am. Chem. Soc. (2003) 10.1021/ja035904+

[24]

Evaluation of Backbone Proton Positions and Dynamics in a Small Protein by Liquid Crystal NMR Spectroscopy

Tobias S. Ulmer, Benjamin E. Ramirez, Frank Delaglio et al.

Journal of the American Chemical Society 2003 10.1021/ja0350684

[25]

How Much Backbone Motion in Ubiquitin Is Required To Account for Dipolar Coupling Data Measured in Multiple Alignment Media as Assessed by Independent Cross-Validation?

G. Marius Clore, Charles D. Schwieters

Journal of the American Chemical Society 2004 10.1021/ja0386804

[26]

Bernado P. J. Am. Chem. Soc. (2004)

[27]

Bernado P. J. Am. Chem. Soc. (2004)

[28]

Bouvignies G. J. Magn. Reson. (2005) 10.1016/j.jmr.2005.01.001

[29]

Lienin S. F. J. Am. Chem. Soc. (1998) 10.1021/ja9810179

[30]

Bouvignies G. Proc. Natl. Acad. Sci. U.S.A. (2005) 10.1073/pnas.0505129102

[31]

Derrick J. P. J. Mol. Biol. (1994) 10.1006/jmbi.1994.1691

[32]

Molecular dynamics simulations of biomolecules

Martin Karplus, J. Andrew McCammon

Nature Structural Biology 2002 10.1038/nsb0902-646

[33]

Molecular dynamics and protein function

M. Karplus, John Kuriyan

Proceedings of the National Academy of Sciences 2005 10.1073/pnas.0408930102

[34]

Levy R. M. J. Am. Chem. Soc. (1981) 10.1021/ja00410a003

[35]

Bruschweiler R. J. Am. Chem. Soc. (1992)

[36]

Case D. A. Acc. Chem. Res. (2002)

[37]

Chandrasekhar I. J. Mol. Biol. (1992) 10.1016/0022-2836(92)90136-8

[38]

Schlitter J. J. Mol. Graph. (1994) 10.1016/0263-7855(94)80072-3

[39]

TRANSITIONPATHSAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark

Peter G. Bolhuis, David Chandler, Christoph Dellago et al.

Annual Review of Physical Chemistry 2002 10.1146/annurev.physchem.53.082301.113146

[40]

Amadei A. J. Proteins (1993)

[41]

Muller E. M. J. Chem. Phys. (2002)

[42]

Mitsutake A. J. Chem. Phys. (2003)

[43]

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling

G.M. Torrie, J.P. Valleau

Journal of Computational Physics 1977 10.1016/0021-9991(77)90121-8

[44]

Kleinjung J. FEBS Lett. (2000) 10.1016/s0014-5793(00)01295-3

[45]

Elber R. Curr. Opin. Struct. Biol. (2005) 10.1016/j.sbi.2005.02.004

[46]

Hamelberg D. J. Chem. Phys. (2004) 10.1063/1.1755656

[47]

Hamelberg D. J. Am. Chem. Soc. (2005)

[48]

Meier S. J. Am. Chem. Soc. (2003) 10.1021/ja028740q

[49]

Nederveen A. J. J. Chem. Theory Comp. (2005) 10.1021/ct0498829

[50]

Hall J. B. J. Biomol. NMR (2003)

Showing 50 of 61 references

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Details

Published: Mar 22, 2007
Vol/Issue: 129(15)
Pages: 4724-4730

Authors

P

Phineus R. L. Markwick

Contribution from the Institute de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR 5075, 41 rue Jules Horowitz, F-38027 Grenoble, Cedex, France.

G

Guillaume Bouvignies

Contribution from the Institute de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR 5075, 41 rue Jules Horowitz, F-38027 Grenoble, Cedex, France.

M

Martin Blackledge

Contribution from the Institute de Biologie Structurale Jean-Pierre Ebel, CNRS, CEA, UJF, UMR 5075, 41 rue Jules Horowitz, F-38027 Grenoble, Cedex, France.

Cite This Article

Phineus R. L. Markwick, Guillaume Bouvignies, Martin Blackledge (2007). Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy. Journal of the American Chemical Society, 129(15), 4724-4730. https://doi.org/10.1021/ja0687668

Exploring Multiple Timescale Motions in Protein GB3 Using Accelerated Molecular Dynamics and NMR Spectroscopy

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