title: Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.
abstract: The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.
authors.affiliation: Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Agnieszka G
authors.initials: AG
authors.lastname: Lipska
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Seidman
authors.affiliation: Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
authors.affiliation: Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Artur
authors.initials: A
authors.lastname: Giełdoń
authors.affiliation: Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.affiliation: Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry*; D057446:Hydrodynamics; D007700:Kinetics; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry*; D000072417:Protein Domains; D017510:Protein Folding; D013205:Staphylococcal Protein A / Q000737:chemistry*
chemical_list: D002352:Carrier Proteins; D010446:Peptide Fragments; D013205:Staphylococcal Protein A