Toward an accurate determination of free energy landscapes in solution states of proteins

The dynamics of proteins plays a central role in their activity, including enzymatic catalysis and allosteric communication. Many advances have been made in recent years in the characterization of the equilibrium fluctuations of proteins through experimental and computational methods. We present evidence that the use of molecular dynamics simulations with ensemble-averaged structural restraints derived from nuclear magnetic resonance spectroscopy enables the determination of ensembles of structures representing the equilibrium populations of conformations explored during the thermal fluctuations of proteins. We obtained these results by using residual dipolar couplings to characterize the dynamics of ubiquitin and to derive its free-energy landscape under native conditions. © 2009 American Chemical Society.