Mapping the Native Conformational Ensemble of Proteins from a Combination of Simulations and Experiments: New Insight into the src-SH3 Domain.
The biological function of a protein is strongly tied to the ensemble of three-dimensional conformations populated at physiological temperature, and dynamically transforming into each other. Experimental techniques such as nuclear magnetic resonance spectroscopy (NMR) provide a wealth of structural and dynamical information, which, in combination with an accurate atomic-level computational modeling, can disclose the details of protein behavior. We here propose a fast and efficient protocol employing molecular dynamics (MD) simulations and NMR chemical shifts, which allows one to reconstruct the detailed conformational ensemble of small globular proteins. In the case of the well-studied src-SH3 domain, we are able to obtain new important insight including the existence of a helical state in the RT loop and a pathway for single-file water diffusion in and out of the core.
†Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
Fabio
F
Pietrucci
‡Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, F-38027 Grenoble, France.
Luca
L
Mollica
‡Protein Dynamics and Flexibility, Institut de Biologie Structurale, CEA, CNRS, UJF-Grenoble 1, 41 Rue Jules Horowitz, F-38027 Grenoble, France.
Martin
M
Blackledge
NMR chemical shifts; SH3 domain; conformational ensemble; free energy landscape; molecular dynamics