Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil.


Abstract

We measured whether solvent viscosity, and hence chain diffusion, plays a role in the rate-limiting step of the folding reactions of GCN4-p2', a simple alpha-helical coiled coil derived from the leucine zipper region of bZIP transcriptional activator GCN4. To deconvolute the dual effects of viscosogenic solvents on both viscosity, eta, and stability, earlier attempts assumed that the cosolvent and denaturant interact to the same degree in the transition state. Applying this analysis to GCN4-p2' yielded a nearly 1/eta dependence between folding rates and viscosity for both the dimeric and the cross-linked, monomeric versions of the coiled coil, but it revealed no such coherent relationship for cytochrome c. We also developed a method to determine the relative viscosity dependence of the dimeric and monomeric forms of the coiled coil independent of the assumption concerning the transition state's relative interaction with cosolvents and denaturants. Application of this method indicated that the effect of viscosity on both the folding and the unfolding rates was the same for the dimeric and monomeric versions, further supporting the view that the folding of the dimeric version is folding-limited rather than encounter-limited. The finding that GCN4-p2' folding appears to exhibit a 1/eta viscosity dependence implies that the rate-limiting step in folding is opposed predominantly by solvent-derived rather than internal frictional forces. These results are interpreted in relation to various models for protein folding. Study holds ProTherm entries: 16362, 16363, 16364, 16365, 16366, 16367, 16368, 16369, 16370, 16371, 16372, 16373, 16374, 16375, 16376 Extra Details: alpha-helical coiled coil from leucine zipper region, dimeric. equilibrium. GCN4-p2, cytochrome c, folding kinetics, transcriptional activator

Submission Details

ID: zBqP2Xsy3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:47 p.m.

Version: 1

Publication Details
Bhattacharyya RP;Sosnick TR,Biochemistry (1999) Viscosity dependence of the folding kinetics of a dimeric and monomeric coiled coil. PMID:10029555
Additional Information

Study Summary

Number of data points 30
Proteins Cytochrome c ; General control protein GCN4 ; General control protein GCN4 ; Cytochrome c
Unique complexes 2
Assays/Quantities/Protocols Experimental Assay: m buffers:Imidazole: 50 mM, pH:7.0, prot_conc:10-20 micro M, details:Additives Glycerol(25% (w/w)), ; Experimental Assay: dG_H2O buffers:Imidazole: 50 mM, pH:7.0, prot_conc:10-20 micro M, details:Additives Glycerol(25% (w/ ; Experimental Assay: m buffers:Imidazole: 50 mM, pH:7.0, prot_conc:10-20 micro M, details:Additives Glucose(21% (w/w)), ; Experimental Assay: dG_H2O buffers:Imidazole: 50 mM, pH:7.0, prot_conc:10-20 micro M, details:Additives Glucose(21% (w/w ; Experimental Assay: m buffers:Imidazole: 50 mM, details:Additives Ethylene glycol(27% (w/w)),, prot_conc:10-20 micro M, ; Experimental Assay: dG_H2O buffers:Imidazole: 50 mM, details:Additives Ethylene glycol(27% (w/w)),, prot_conc:10-20 micr ; Experimental Assay: m buffers:Imidazole: 50 mM, details:Additives , prot_conc:10-20 micro M, pH:7.0 ; Experimental Assay: dG_H2O buffers:Imidazole: 50 mM, details:Additives , prot_conc:10-20 micro M, pH:7.0 ; Experimental Assay: m prot_conc:34.1 micro M, buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives glycerol (9%), ; Experimental Assay: dG_H2O prot_conc:34.1 micro M, buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives glycerol (9% ; Experimental Assay: m buffers:Sodium acetate: 20 mM, pH:5.5, prot_conc:2-10 micro M, details:Additives glycerol (15.2%), ; Experimental Assay: dG_H2O buffers:Sodium acetate: 20 mM, pH:5.5, prot_conc:2-10 micro M, details:Additives glycerol (15 ; Experimental Assay: m prot_conc:34.1 micro M, buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives glycerol (15.2%), ; Experimental Assay: dG_H2O prot_conc:34.1 micro M, buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives glycerol (15 ; Experimental Assay: m buffers:Sodium acetate: 20 mM, pH:5.5, prot_conc:2-10 micro M, details:Additives glycerol (9%), ; Experimental Assay: dG_H2O buffers:Sodium acetate: 20 mM, pH:5.5, prot_conc:2-10 micro M, details:Additives glycerol (9% ; Experimental Assay: m buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives , prot_conc:2-10 micro M ; Experimental Assay: dG_H2O buffers:Sodium acetate: 20 mM, pH:5.5, details:Additives , prot_conc:2-10 micro M ; Experimental Assay: m prot_conc:34.1 micro M, details:Additives , buffers:Sodium acetate: 20 mM, pH:5.5 ; Experimental Assay: dG_H2O prot_conc:34.1 micro M, details:Additives , buffers:Sodium acetate: 20 mM, pH:5.5
Libraries Mutations for sequence RMKQLEDKVEELLSKNYHLENEVARLKKLVGER ; Mutations for sequence GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKKATNE

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
1KTD 2002-01-15T00:00:00+0000 2.4 CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON CYTOCHROME C PEPTIDE
2B4Z 2005-09-27T00:00:00+0000 1.5 Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.
2YBB 2011-03-02T00:00:00+0000 19.0 Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
3J2T 2012-12-23T00:00:00+0000 9.5 An improved model of the human apoptosome
5C0Z 2015-06-12T00:00:00+0000 1.12 The structure of oxidized rat cytochrome c at 1.13 angstroms resolution
5C9M 2015-06-28T00:00:00+0000 1.36 The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
5DF5 2015-08-26T00:00:00+0000 1.3 The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.
5JUY 2016-05-10T00:00:00+0000 4.1 Active human apoptosome with procaspase-9
6FF5 2018-01-03T00:00:00+0000 1.74 X-ray structure of bovine heart cytochrome c at high ionic strength
6N1O 2018-11-09T00:00:00+0000 1.55 Oxidized rat cytochrome c mutant (S47E)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.3 Cytochrome c P00021 CYC_COLLI
92.2 Cytochrome c P00020 CYC_ANAPL
92.3 Cytochrome c P81280 CYC_ALLMI
90.5 Cytochrome c Q52V10 CYC_SAISC
93.3 Cytochrome c P00012 CYC_MIRLE
93.3 Cytochrome c Q52V09 CYC_CEPBA
93.3 Cytochrome c P00013 CYC_MINSC
93.3 Cytochrome c P00014 CYC_MACGI
94.3 Cytochrome c P00011 CYC_CANLF
94.3 Cytochrome c P62898 CYC_RAT
94.3 Cytochrome c P00008 CYC_RABIT
94.3 Cytochrome c P62897 CYC_MOUSE
95.2 Cytochrome c P68098 CYC_LAMGU
95.2 Cytochrome c P68100 CYC_ESCRO
95.2 Cytochrome c P68099 CYC_CAMDR
94.3 Cytochrome c P00007 CYC_HIPAM
97.1 Cytochrome c P62896 CYC_SHEEP
97.1 Cytochrome c P62895 CYC_PIG
97.1 Cytochrome c P62894 CYC_BOVIN
99.0 Cytochrome c P68096 CYC_EQUBU
99.0 Cytochrome c P68097 CYC_EQUAS
100.0 Cytochrome c P00004 CYC_HORSE
100.0 General control protein GCN4 P03069 GCN4_YEAST
90.3 Cytochrome c B4USV4 CYC_OTOGA