title: Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations.
abstract: Characterization of the folding transition-state ensemble and the denatured-state ensemble is an important step toward a full elucidation of protein folding mechanisms. We report herein an investigation of the free-energy landscape of FSD-1 protein by a total of four sets of folding and unfolding molecular dynamics simulations with explicit solvent. The transition-state ensemble was initially identified from unfolding simulations at 500 K and was verified by simulations at 300 K starting from the ensemble structures. The denatured-state ensemble and the early-stage folding were studied by a combination of unfolding simulations at 500 K and folding simulations at 300 K starting from the extended conformation. A common feature of the transition-state ensemble was the substantial formation of the native secondary structures, including both the alpha-helix and beta-sheet, with partial exposure of the hydrophobic core in the solvent. Both the native and non-native secondary structures were observed in the denatured-state ensemble and early-stage folding, consistent with the smooth experimental melting curve. Interestingly, the contact orders of the transition-state ensemble structures were similar to that of the native structure and were notably lower than those of the compact structures found in early-stage folding, implying that chain and topological entropy might play significant roles in protein folding. Implications for FSD-1 folding mechanisms and the rate-limiting step are discussed. Analyses further revealed interesting non-native interactions in the denatured-state ensemble and early-stage folding and the possibility that destabilization of these interactions could help to enhance the stability and folding rate of the protein.
authors.affiliation: UC Davis Genome Center and Department of Applied Science, University of California, Davis, California 95616, USA.
authors.forename: Hongxing
authors.initials: H
authors.lastname: Lei
authors.forename: Shubhra Ghosh
authors.initials: SG
authors.lastname: Dastidar
authors.forename: Yong
authors.initials: Y
authors.lastname: Duan
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry*; D008958:Models, Molecular; D044367:Phase Transition; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D004268:DNA-Binding Proteins; C108466:FSD-1 protein, synthetic; D014157:Transcription Factors