Cytochrome c folds through a smooth funnel.


Abstract

A dominant feature of folding of cytochrome c is the presence of nonnative His-heme kinetic traps, which either pre-exist in the unfolded protein or are formed soon after initiation of folding. The kinetically trapped species can constitute the majority of folding species, and their breakdown limits the rate of folding to the native state. A temperature jump (T-jump) relaxation technique has been used to compare the unfolding/folding kinetics of yeast iso-2 cytochrome c and a genetically engineered double mutant that lacks His-heme kinetic traps, H33N,H39K iso-2. The results show that the thermodynamic properties of the transition states are very similar. A single relaxation time tau(obs) is observed for both proteins by absorbance changes at 287 nm, a measure of solvent exclusion from aromatic residues. At temperatures near Tm, the midpoint of the thermal unfolding transitions, tau(obs) is four to eight times faster for H33N,H39K iso-2 (tau(obs) approximately 4-10 ms) than for iso-2 (tau(obs) approximately 20-30 ms). T-jumps show that there are no kinetically unresolved (tau < 1-3 micros T-jump dead time) "burst" phases for either protein. Using a two-state model, the folding (k(f)) and unfolding (k(u)) rate constants and the thermodynamic activation parameters standard deltaGf, standard deltaGu, standard deltaHf, standard deltaHu, standard deltaSf, standard deltaSu are evaluated by fitting the data to a function describing the temperature dependence of the apparent rate constant k(obs) (= tau(obs)(-1)) = k(f) + k(u). The results show that there is a small activation enthalpy for folding, suggesting that the barrier to folding is largely entropic. In the "new view," a purely entropic kinetic barrier to folding is consistent with a smooth funnel folding landscape. Study holds ProTherm entries: 8053, 8054 Extra Details:

Submission Details

ID: o2yTTMR64

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:35 p.m.

Version: 1

Publication Details
Panda M;Benavides-Garcia MG;Pierce MM;Nall BT,Protein Sci. (2000) Cytochrome c folds through a smooth funnel. PMID:10752615
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
1YTC 1996-03-08 1.8 THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION RELATIONSHIPS IN UNFOLDED PROTEINS
1YEA 1993-10-31 1.9 STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN
1YEB 1993-10-31 1.95 STRUCTURE DETERMINATION AND ANALYSIS OF YEAST ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN
3CXH 2008-05-13 2.5 Structure of yeast complex III with isoform-2 cytochrome c bound and definition of a minimal core interface for electron transfer.

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Cytochrome c iso-2 P00045 CYC7_YEAST
100.0 Cytochrome c mitochondrial import factor CYC2 P38909 CYC2_YEAST