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.
Islam
Suhail A
SA
Structural Bioinformatics Group, Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London SW7 2AY, United Kingdom.
Karplus
Martin
M
Weaver
David L
DL
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