title: Protein unfolding from free-energy calculations: integration of the Gaussian network model with bond binding energies.
abstract: Motivated by single molecule experiments, we study thermal unfolding pathways of four proteins, chymotrypsin inhibitor, barnase, ubiquitin, and adenylate kinase, using bond network models that combine bond energies and elasticity. The protein elasticity is described by the Gaussian network model (GNM), to which we add prescribed bond binding energies that are assigned to all (nonbackbone) connecting bonds in the GNM of native state and assumed identical for simplicity. Using exact calculation of the Helmholtz free energy for this model, we consider bond rupture single events. The bond designated for rupture is chosen by minimizing the free-energy difference for the process, over all (nonbackbone) bonds in the network. Plotting the free-energy profile along this pathway at different temperatures, we observe a few major partial unfolding, metastable or stable, states, that are separated by free-energy barriers and change role as the temperature is raised. In particular, for adenylate kinase we find three major partial unfolding states, which is consistent with single molecule FRET experiments [Pirchi et al., Nat. Commun. 2, 493 (2011)] for which hidden Markov analysis reveals between three and five such states. Such states can play a major role in enzymatic activity.
authors.affiliation: The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.
authors.forename: Amit
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.|The Ilse Katz Institute for Meso and Nanoscale Science and Technology, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel.
authors.forename: Rony
authors.initials: R
authors.lastname: Granek
mesh_terms: D000263:Adenylate Kinase / Q000737:chemistry; D001426:Bacterial Proteins; D002918:Chymotrypsin / Q000037:antagonists & inhibitors; D003198:Computer Simulation; D004548:Elasticity; D008958:Models, Molecular; D058767:Protein Unfolding; D012260:Ribonucleases / Q000737:chemistry; D013696:Temperature; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D025801:Ubiquitin; D000263:Adenylate Kinase; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D002918:Chymotrypsin