Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions.

Communications Correlated motions can be accurately extracted from molecular dynamics (MD) simulations that are compatible with the measured NMR spectroscopic data (NOE and order parameters) for two different proteins (Cov: covariance matrix). B. de Groot and co-workers discuss the results of MD simulations on a fragment of protein G in their Communication on the following pages.

[1]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997 .

[2]  A. Palmer,et al.  Nmr probes of molecular dynamics: overview and comparison with other techniques. , 2001, Annual review of biophysics and biomolecular structure.

[3]  P. Agarwal,et al.  Network of coupled promoting motions in enzyme catalysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Bernard R. Brooks,et al.  Molecular Dynamics of Staphylococcal Nuclease: Comparison of Simulation with 15N and 13C NMR Relaxation Data , 1998 .

[5]  A. Joshua Wand,et al.  Dynamic activation of protein function: A view emerging from NMR spectroscopy , 2001, Nature Structural Biology.

[6]  S. Benkovic,et al.  A Perspective on Enzyme Catalysis , 2003, Science.

[7]  L. Regan,et al.  Covariation of backbone motion throughout a small protein domain , 2003, Nature Structural Biology.

[8]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[9]  David A Case,et al.  Molecular dynamics and NMR spin relaxation in proteins. , 2002, Accounts of chemical research.

[10]  L. Kay,et al.  Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. , 1989, Biochemistry.

[11]  G L Gilliland,et al.  Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. , 1994, Biochemistry.

[12]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[13]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[14]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[15]  Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. , 2001, Journal of the American Chemical Society.

[16]  G. Marius Clore,et al.  Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration , 1999 .

[17]  A. Gronenborn,et al.  A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. , 1993, Science.

[18]  G. Lipari.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules , 1982 .

[19]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[20]  García,et al.  Large-amplitude nonlinear motions in proteins. , 1992, Physical review letters.

[21]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[22]  Andrew L. Lee,et al.  Microscopic origins of entropy, heat capacity and the glass transition in proteins , 2001, Nature.

[23]  Rieko Ishima,et al.  Protein dynamics from NMR , 2000, Nature Structural Biology.

[24]  M. Philippopoulos,et al.  Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics , 1997, Proteins.

[25]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[26]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[27]  P. Wright,et al.  Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance carbon-13 heteronuclear NMR spectroscopy , 1991 .

[28]  Julie D. Forman-Kay,et al.  The 'dynamics' in the thermodynamics of binding , 1999, Nature Structural Biology.

[29]  K. Mayo,et al.  Motional Model Analyses of Protein and Peptide Dynamics Using 13C and 15N NMR Relaxation , 1997 .

[30]  A. Szabó,et al.  Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity , 1982 .