Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding.


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. Study holds ProTherm entries: 24648, 24649, 24650, 24651, 24652, 24653, 24654, 24655, 24656, 24657, 24658, 24659, 24660, 24661, 24662, 24663, 24664, 24665, 24666, 24667, 24668, 24669, 24670, 24671, 24672, 24673, 24674, 24675 Extra Details: 0.2 mM EDTA was added in the experiment double mutant cycles; Fyn tyrosine kinase; Go models; HP model; Langevin dynamics

Submission Details

ID: stPVeEap3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:55 p.m.

Version: 1

Publication Details
Zarrine-Afsar A;Wallin S;Neculai AM;Neudecker P;Howell PL;Davidson AR;Chan HS,Proc. Natl. Acad. Sci. U.S.A. (2008) Theoretical and experimental demonstration of the importance of specific nonnative interactions in protein folding. PMID:18626019
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1NYG 1996-11-08 NMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINASE, FAMILY OF 20 STRUCTURES
1AOU 1998-01-14 NMR STRUCTURE OF THE FYN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROSYL PEPTIDE, 22 STRUCTURES
1ZBJ 2005-05-03 Inferential Structure Determination of the Fyn SH3 domain using NOESY data from a 15N,H2 enriched protein
1NYF 1996-11-08 NMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINASE, MINIMIZED AVERAGE (PROBMAP) STRUCTURE
1AZG 1998-02-25 NMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINASE KINASE COMPLEXED WITH THE SYNTHETIC PEPTIDE P2L CORRESPONDING TO RESIDUES 91-104 OF THE P85 SUBUNIT OF PI3-KINASE, MINIMIZED AVERAGE (PROBMAP) STRUCTURE
2LP5 2012-05-16 Native Structure of the Fyn SH3 A39V/N53P/V55L
2MRK 2015-07-15 Fyn SH2 domain in complex with the natural inhibitory phosphotyrosine peptide
2MRJ 2015-07-15 Structure of Fyn protein SH2 bound
2MQI 2015-07-29 human Fyn SH2 free state
1A0N 1998-02-25 NMR STUDY OF THE SH3 DOMAIN FROM FYN PROTO-ONCOGENE TYROSINE KINASE COMPLEXED WITH THE SYNTHETIC PEPTIDE P2L CORRESPONDING TO RESIDUES 91-104 OF THE P85 SUBUNIT OF PI3-KINASE, FAMILY OF 25 STRUCTURES
2L2P 2011-09-14 Folding Intermediate of the Fyn SH3 A39V/N53P/V55L from NMR Relaxation Dispersion Experiments
1AOT 1998-01-14 NMR STRUCTURE OF THE FYN SH2 DOMAIN COMPLEXED WITH A PHOSPHOTYROSYL PEPTIDE, MINIMIZED AVERAGE STRUCTURE
6IPY 2018-11-28 1.34 His-tagged Fyn SH3 domain R96I mutant
6EDF 2018-08-29 1.4 Fragment of a tyrosine-protein kinase
4U1P 2015-07-29 1.4 Human Fyn-SH2 domain in complex with a synthetic high-affinity phospho-peptide
3UA7 2012-07-25 1.5 Crystal Structure of the Human Fyn SH3 domain in complex with a peptide from the Hepatitis C virus NS5A-protein
6IPZ 2018-11-28 1.58 Fyn SH3 domain R96W mutant, crystallized with 18-crown-6
3CQT 2008-07-01 1.6 N53I V55L MUTANT of FYN SH3 DOMAIN
4EIK 2013-04-10 1.6 Crystal Structure of the Human Fyn SH3 domain in complex with the synthetic peptide VSL12
3H0H 2010-04-21 1.76 human Fyn SH3 domain R96I mutant, crystal form I
3UA6 2012-07-25 1.85 Crystal Structure of the Human Fyn SH3 domain
1SHF 1993-10-31 1.9 CRYSTAL STRUCTURE OF THE SH3 DOMAIN IN HUMAN FYN; COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF SH3 DOMAINS IN TYROSINE KINASES AND SPECTRIN
3UF4 2011-12-07 1.98 Crystal structure of a SH3 and SH2 domains of FYN protein (Proto-concogene Tyrosine-protein kinase Fyn) from Mus musculus at 1.98 A resolution
4U17 2015-07-29 1.99 Swapped dimer of the human Fyn-SH2 domain
4ZNX 2016-06-29 2.1 Crystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12
3H0I 2010-04-21 2.2 human Fyn SH3 domain R96I mutant, crystal form II
1FYN 1996-11-08 2.3 PHOSPHOTRANSFERASE
1EFN 1997-01-11 2.5 HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN
1M27 2003-05-06 2.5 Crystal structure of SAP/FynSH3/SLAM ternary complex
4D8D 2013-01-16 2.52 Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant
1G83 2001-05-30 2.6 CRYSTAL STRUCTURE OF FYN SH3-SH2
3H0F 2010-04-21 2.61 Crystal structure of the human Fyn SH3 R96W mutant
2DQ7 2006-07-04 2.8 Crystal Structure of Fyn kinase domain complexed with staurosporine
1AVZ 1998-03-25 3.0 V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.5 Tyrosine-protein kinase Fyn F1RDG9 FYNB_DANRE
93.2 Tyrosine-protein kinase Fyn Q6EWH2 FYNA_DANRE
96.8 Tyrosine-protein kinase Fyn P13406 FYN_XENLA
98.3 Tyrosine-protein kinase Fyn Q05876 FYN_CHICK
100.0 Tyrosine-protein kinase Fyn Q62844 FYN_RAT
100.0 Tyrosine-protein kinase Fyn A1Y2K1 FYN_PIG
100.0 Tyrosine-protein kinase Fyn P39688 FYN_MOUSE
100.0 Tyrosine-protein kinase Fyn P06241 FYN_HUMAN
100.0 Tyrosine-protein kinase Fyn A0JNB0 FYN_BOVIN
92.6 Tyrosine-protein kinase Fyn P27446 FYN_XIPHE