title: The origins of asymmetry in the folding transition states of protein L and protein G.
abstract: Topology has been shown to be an important determinant of many features of protein folding; however, the delineation of sequence effects on folding remains obscure. Furthermore, differentiation between the two influences proves difficult due to their intimate relationship. To investigate the effect of sequence in the absence of significant topological differences, we examined the folding mechanisms of segment B1 peptostreptococcal protein L and segment B1 of streptococcal protein G. These proteins share the same highly symmetrical topology. Despite this symmetry, neither protein folds through a symmetrical transition state. We analyzed the origins of this difference using theoretical models. We found that the strength of the interactions present in the N-terminal hairpin of protein L causes this hairpin to form ahead of the C-terminal hairpin. The difference in chain entropy associated with the formation of the hairpins of protein G proves sufficient to beget initiation of folding at the shorter C-terminal hairpin. Our findings suggest that the mechanism of folding may be understood by examination of the free energy associated with the formation of partially folded microstates.
authors.affiliation: Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: John
authors.initials: J
authors.lastname: Karanicolas
authors.forename: Charles L
authors.initials: CL
authors.lastname: Brooks
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins; D019295:Computational Biology; D004268:DNA-Binding Proteins / Q000378:metabolism*; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000378:metabolism*; D017510:Protein Folding; D017434:Protein Structure, Tertiary / Q000502:physiology; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C029152:G-substrate; C116593:L-protein, Peptococcus magnus; D009419:Nerve Tissue Proteins