title: Folding mechanism of a multiple independently-folding domain protein: double B domain of protein A.
abstract: The antibody binding properties of staphylococcal protein A (SpA) can be attributed to the presence of five highly homologous domains (E, D, A, B, and C). Although the folding of the B domain of protein A (BdpA) is well-characterized, the folding behavior of this domain in the context of full-length SpA in the cell remains unexplored. The sequence of the B domain is 89 and 91% identical to those of domains A and C, respectively. We have fused B domain sequences (BBdpA) as a close approximation of the A-B or B-C portion of SpA. Circular dichroism and fluorescence-detected denaturation curves of BBdpA are experimentally indistinguishable from those of BdpA. The rate constants for folding and unfolding from NMR line shape analysis for the single- and double-domain proteins are the same within experimental uncertainties (+/-20%). These results support the designation of SpA as a multiple independently-folding domain (MIFD) protein. We develop a mathematical model that describes the folding thermodynamics and kinetics of MIFD proteins. The model depicts MIFD protein folding and unfolding as a parallel network and explicitly calculates the flux through all parallel pathways. These fluxes are combined to give a complete description of the global thermodynamics and kinetics of the folding and unfolding of MIFD proteins. The global rates for complete folding and unfolding of a MIFD protein and those of the individual domains depend on the stability of the protein. We show that the global unfolding rate of a MIFD protein may be many orders of magnitude slower than that of the constituent domains.
authors.affiliation: Department of Chemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.
authors.forename: Pooja
authors.initials: P
authors.lastname: Arora
authors.forename: Gordon G
authors.initials: GG
authors.lastname: Hammes
authors.forename: Terrence G
authors.initials: TG
authors.lastname: Oas
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013050:Spectrometry, Fluorescence; D013205:Staphylococcal Protein A / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D013205:Staphylococcal Protein A