The role of sequence and structure in protein folding kinetics; the diffusion-collision model applied to proteins L and G.
The diffusion-collision model (DCM) is applied to the folding kinetics of protein L and protein G. In the DCM, the two proteins are treated as consisting of two beta-hairpins and one alpha-helix, so that they are isomorphous with the three-helix bundle DCM model. In the absence of sequence dependent factors, both proteins would fold in the same way in the DCM, with the coalescence of the N-terminal hairpin and the helix slightly favored over the C-terminal hairpin and the helix because the former are closer together than the latter. However, sequence dependent factors make the N-terminal hairpin of protein L and the C-terminal hairpin of protein G more stable in the ensemble of unfolded conformations. This difference in the stabilities gives rise to the difference in the calculated folding behavior, in agreement with experiment.
Structural Bioinformatics Group, Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London SW7 2AY, United Kingdom.
Suhail A
SA
Islam
Martin
M
Karplus
David L
DL
Weaver
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D004058:Diffusion; D007700:Kinetics; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D001426:Bacterial Proteins; C055047:Ig L-binding protein, Peptostreptococcus; C034284:IgG Fc-binding protein, Streptococcus