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 UniProtKB Entries

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