3CQT

N53I V55L MUTANT of FYN SH3 DOMAIN

Summary for 3CQT

• Entry DOI: 10.2210/pdb3cqt/pdb
• Descriptor: Proto-oncogene tyrosine-protein kinase Fyn (2 entities in total)
• Functional Keywords: beta barrel, atp-binding, developmental protein, kinase, lipoprotein, manganese, metal-binding, myristate, nucleotide-binding, palmitate, phosphoprotein, proto-oncogene, sh2 domain, sh3 domain, transferase, tyrosine-protein kinase
• Biological source: Gallus gallus (Chicken)
• Total number of polymer chains: 1
• Total formula weight: 9337.11

Authors

Neculai, A.M.,Zarrine-Afsar, A.,Howell, P.L.,Davidson, A.,Chan, H.S. (deposition date: 2008-04-03, release date: 2008-07-01, Last modification date: 2023-08-30)

Primary citation

Zarrine-Afsar, A.,Wallin, S.,Neculai, A.M.,Neudecker, P.,Howell, P.L.,Davidson, A.R.,Chan, H.S.
Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.
Proc.Natl.Acad.Sci.Usa, 105:9999-10004, 2008

PubMed Abstract: 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.

PubMed: 18626019
DOI: 10.1073/pnas.0801874105

Experimental method

X-RAY DIFFRACTION (1.6 Å)