Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein

• Published in: Journal of molecular biology 2005-10, Vol.353 (1), p.196-210
• Main Authors: Ravindranathan, Krishna Pratap, Gallicchio, Emilio, Levy, Ronald M.
• Format: Article
• Language: English
• Subjects: Allosteric Regulation; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - metabolism; Crystallography, X-Ray; free energy profiles; Hydrogen Bonding; ligand-induced conformational change; Models, Molecular; protein allostery; Protein Conformation; Ribose - chemistry; Ribose - metabolism; ribose-binding protein; Thermodynamics; umbrella sampling molecular dynamics
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.08.009

The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation upon binding to ribose. The crystal structures of RBP in open and closed conformations have been solved. It has been hypothesized that the open and closed conformations exist in a dynamic equilibrium in solution, and that sugar binding shifts the population from open conformations to closed conformations. Here, we study by computer simulations the thermodynamic changes that accompany this conformational change, and model the structural changes that accompany the allosteric transition, using umbrella sampling molecular dynamics and the weighted histogram analysis method. The open state is comprised of a diverse ensemble of conformations; the open ribose-free X-ray crystal conformations being representative of this ensemble. The unligated open form of RBP is stabilized by conformational entropy. The simulations predict detectable populations of closed ribose-free conformations in solution. Additional interdomain hydrogen bonds stabilize this state. The predicted shift in equilibrium from the open to the closed state on binding to ribose is in agreement with experiments. This is driven by the energetic stabilization of the closed conformation due to ribose–protein interactions. We also observe a significant population of a hitherto unobserved ribose-bound partially open state. We believe that this state is the one that has been suggested to play a role in the transfer of ribose to the membrane-bound permease complex.