title: Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain.
abstract: The purpose of this work is to show how mutation, truncation, and change of temperature can influence the folding kinetics of a protein. This is accomplished by principal component analysis of molecular-dynamics-generated folding trajectories of the triple β-strand WW domain from formin binding protein 28 (FBP28) (Protein Data Bank ID: 1E0L) and its full-size, and singly- and doubly-truncated mutants at temperatures below and very close to the melting point. The reasons for biphasic folding kinetics [i.e., coexistence of slow (three-state) and fast (two-state) phases], including the involvement of a solvent-exposed hydrophobic cluster and another delocalized hydrophobic core in the folding kinetics, are discussed. New folding pathways are identified in free-energy landscapes determined in terms of principal components for full-size mutants. Three-state folding is found to be a main mechanism for folding the FBP28 WW domain and most of the full-size and truncated mutants. The results from the theoretical analysis are compared to those from experiment. Agreements and discrepancies between the theoretical and experimental results are discussed. Because of its importance in understanding protein kinetics and function, the diffusive mechanism by which the FBP28 WW domain and its full-size and truncated mutants explore their conformational space is examined in terms of the mean-square displacement and principal component analysis eigenvalue spectrum analyses. Subdiffusive behavior is observed for all studied systems.
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.
authors.forename: Gia G
authors.initials: GG
authors.lastname: Maisuradze
authors.forename: Rui
authors.initials: R
authors.lastname: Zhou
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.forename: Yi
authors.initials: Y
authors.lastname: Xiao
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D025341:Principal Component Analysis; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013696:Temperature; D013816:Thermodynamics
chemical_list: D002352:Carrier Proteins; C473939:formin binding protein 28, human