title: Structural comparison of the two alternative transition states for folding of TI I27.
abstract: TI I27, a beta-sandwich domain from the human muscle protein titin, has been shown to fold via two alternative pathways, which correspond to a change in the folding mechanism. Under physiological conditions, TI I27 folds by a classical nucleation-condensation mechanism (diffuse transition state), whereas at extreme conditions of temperature and denaturant it switches to having a polarized transition state. We have used experimental Phi-values as restraints in ensemble-averaged molecular dynamics simulations to determine the ensembles of structures representing the two transition states. The comparison of these ensembles indicates that when native interactions are substantially weakened, a protein may still be able to fold if it can access an alternative transition state characterized by a much larger entropic contribution. Analysis of the probability distribution of Phi-values derived from ensemble averaged simulations, enables us to identify residues that form contacts in some members of the ensemble but not in others illustrating that many interactions present in transition states are not strictly required for the successful completion of the folding process.
authors.affiliation: Department of Chemistry, Medical Research Council Centre for Protein Engineering, University of Cambridge, Cambridge CB2 1EW, United Kingdom.
authors.forename: Christian D
authors.initials: CD
authors.lastname: Geierhaas
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
authors.forename: Emanuele
authors.initials: E
authors.lastname: Paci
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
authors.forename: Jane
authors.initials: J
authors.lastname: Clarke
mesh_terms: D003198:Computer Simulation; D064211:Connectin; D019277:Entropy; D008956:Models, Chemical; D008958:Models, Molecular; D009124:Muscle Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D044367:Phase Transition; D011487:Protein Conformation; D017510:Protein Folding; D011494:Protein Kinases / Q000737:chemistry* / Q000648:ultrastructure*; D013329:Structure-Activity Relationship
chemical_list: D064211:Connectin; D009124:Muscle Proteins; C577285:TTN protein, human; D011494:Protein Kinases