Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation.
Solid-state NMR can provide atomic-resolution information about protein motions occurring on a vast range of time scales under similar conditions to those of X-ray diffraction studies and therefore offers a highly complementary approach to characterizing the dynamic fluctuations occurring in the crystal. We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales. We discover that the potential complexity of relaxation-active motion can lead to significant under- or overestimation of dynamic amplitudes if different components are not taken into consideration.
†Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France.
Luca
L
Mollica
‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
Maria
M
Baias
§Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom.
Józef R
JR
Lewandowski
⊥Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States.
Benjamin J
BJ
Wylie
#Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States.
Lindsay J
LJ
Sperling
∥Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States.
Chad M
CM
Rienstra
‡CNRS/ENS-Lyon/UCB-Lyon 1, Centre de RMN à Très Hauts Champs, Université de Lyon, 5 rue de la Doua, 69100 Villeurbanne, France.
Lyndon
L
Emsley
†Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, Grenoble 38027, France.
Martin
M
Blackledge
NMR; conformational dynamics; crystalline protein; molecular dynamics; protein dynamics