Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.
Many experimental and theoretical studies have suggested a significant role for nonnative interactions in protein folding pathways, but the energetic contributions of these interactions are not well understood. We have addressed the energetics and the position specificity of nonnative hydrophobic interactions by developing a continuum coarse-grained chain model with a native-centric potential augmented by sequence-dependent hydrophobic interactions. By modeling the effect of different hydrophobicity values at various positions in the Fyn SH3 domain, we predicted energetically significant nonnative interactions that led to acceleration or deceleration of the folding rate depending on whether they were more populated in the transition state or unfolded state. These nonnative contacts were centered on position 53 in the Fyn SH3 domain, which lies in an exposed position in a 3(10)-helix. The energetic importance of the predicted nonnative interactions was confirmed experimentally by folding kinetics studies combined with double mutant thermodynamic cycles. By attaining agreement of theoretical and experimental investigations, this study provides a compelling demonstration that specific nonnative interactions can significantly influence folding energetics. Moreover, we show that a coarse-grained model with a simple consideration of hydrophobicity is sufficient for the accurate prediction of kinetically important nonnative interactions.
Zarrine-Afsar
Arash
A
Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
Wallin
Stefan
S
Neculai
A Mirela
AM
Neudecker
Philipp
P
Howell
P Lynne
PL
Davidson
Alan R
AR
Chan
Hue Sun
HS
D019943:Amino Acid Substitution; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017510:Protein Folding; D051076:Proto-Oncogene Proteins c-fyn / Q000737:chemistry / Q000235:genetics; D013816:Thermodynamics; D018909:src Homology Domains
D051076:Proto-Oncogene Proteins c-fyn