title: The folding mechanism of barstar: evidence for multiple pathways and multiple intermediates.
abstract: The mechanism of folding of the small protein barstar in the pre-transition zone at pH 7, 25 degrees C has been characterized using rapid-mixing techniques. Earlier studies had established the validity of the three-state US <--> UF <--> N mechanism for folding and unfolding in the presence of guanidine hydrochloride (GdnHCl) at concentrations greater than 2.0 M, where US and UF are the slow-refolding and fast-refolding unfolded forms, respectively, and N is the fully folded form. It is now shown that early intermediates, IS1 and IS2 as well as a late native-like intermediate, IN, are present on the folding pathways of US, and an early intermediate IF1 on the folding pathway of UF, when barstar is refolded in concentrations of GdnHCl below 2.0 M. The rates of formation and disappearance of IN, and the rates of formation of N at three different concentrations of GdnHCl in the pre-transition zone have been measured. The data indicate that in 1.5 M GdnHCl, IN is not fully populated on the US-->IS1-->IN-->N pathway because the rate of its formation is so slow that the US <--> UF <--> N pathway can effectively compete with that pathway. In 1.0 M GdnHCl, the US-->IS1-->IN transition is so fast that IN is fully populated. In 0.6 M GdnHCl, IN appears not to be fully populated because an alternative folding pathway, US-->IS2-->N, becomes available for the folding of US, in addition to the US-->IS1-->IN-->N pathway. Measurement of the binding of the hydrophobic dye 1-anilino-8-naphthalenesulphonate (ANS) during folding indicates that ANS binds to two distinct intermediates, IM1 and IM2, that form within 2 ms on the US-->IM1-->IS1-->IN-->N and US-->IM2-->IS2-->N pathways. There is no evidence for the accumulation of intermediates that can bind ANS on the folding pathway of UF.
authors.affiliation: National Centre for Biological Sciences, TIFR Centre, Indian Institute of Science Campus Bangalore.
authors.forename: M C
authors.initials: MC
authors.lastname: Shastry
authors.forename: J B
authors.initials: JB
authors.lastname: Udgaonkar
mesh_terms: D000817:Anilino Naphthalenesulfonates / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D005456:Fluorescent Dyes / Q000378:metabolism; D019791:Guanidine; D006146:Guanidines / Q000494:pharmacology; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry / Q000187:drug effects / Q000378:metabolism; D012260:Ribonucleases / Q000037:antagonists & inhibitors*; D013050:Spectrometry, Fluorescence
chemical_list: D000817:Anilino Naphthalenesulfonates; D001426:Bacterial Proteins; D005456:Fluorescent Dyes; D006146:Guanidines; D011994:Recombinant Proteins; C057438:barstar protein, Bacillus amyloliquefaciens; C027132:1-anilino-8-naphthalenesulfonate; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease; D019791:Guanidine