A native tertiary interaction stabilizes the A state of cytochrome c.


Abstract

Certain kinetic intermediates in protein folding are similar to the molten globule, or A state, an equilibrium state of many proteins that is populated under high salt and low pH conditions. Many A states are nearly as compact as native proteins and have native-like secondary structure, but the extent to which nonlocal interactions stabilize the A state is unclear. In this study, thermal denaturation, monitored by circular dichroism, was used to determine the free energy of denaturation of the A state (delta GA<-->D) for Saccharomyces cerevisiae iso-1-ferricytochrome c. Specifically, we examined the wild-type protein, seven variants with amino acid substitutions at the interface between the N- and C-terminal helices, and two variants with mutations at a position close to, but not involved in, the interface. A plot of delta GA<-->D versus delta GN<-->D (the free energy of denaturation of the native state) has a slope near unity, showing that the evolutionarily conserved helix-helix interaction stabilizes the A state to the same degree that it stabilizes the native state. Study holds ProTherm entries: 5296, 5297, 5298, 5299, 5300, 5301, 5302, 5303, 5304 Extra Details: tertiary interaction; molten globule; secondary structure;,nonlocal interactions; helix-helix interaction

Submission Details

ID: NYT23GqK3

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:29 p.m.

Version: 1

Publication Details
Marmorino JL;Pielak GJ,Biochemistry (1995) A native tertiary interaction stabilizes the A state of cytochrome c. PMID:7880808
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
1FHB 1995-09-15 THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE CYANIDE ADDUCT OF A MET80ALA VARIANT OF SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C. IDENTIFICATION OF LIGAND-RESIDUE INTERACTIONS IN THE DISTAL HEME CAVITY
2JQR 2008-04-22 Solution model of crosslinked complex of cytochrome c and adrenodoxin
2MHM 2014-10-29 Solution structure of cytochrome c Y67H
2N18 2015-05-13 Dominant form of the low-affinity complex of yeast cytochrome c and cytochrome c peroxidase
1LMS 2003-03-18 Structural model for an alkaline form of ferricytochrome c
2LIT 2011-12-07 NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in reduced states
2GB8 2006-11-21 Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase
2ORL 2007-04-24 Solution structure of the cytochrome c- para-aminophenol adduct
2JTI 2008-07-22 Solution structure of the yeast iso-1-cytochrome c (T12A) : yeast cytochrome c peroxidase complex
1YFC 1997-03-12 Solution nmr structure of a yeast iso-1-ferrocytochrome C
2LIR 2011-12-07 NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in oxidized states
2HV4 2006-09-26 NMR solution structure refinement of yeast iso-1-ferrocytochrome c
1NMI 2003-02-04 Solution structure of the imidazole complex of iso-1 cytochrome c
1YIC 1997-07-23 THE OXIDIZED SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C, NMR, 20 STRUCTURES
4N0K 2014-09-10 1.05 Atomic resolution crystal structure of a cytochrome c-calixarene complex
6GD6 2018-08-29 1.2 Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with ammonium sulfate
1YCC 1991-07-15 1.23 HIGH-RESOLUTION REFINEMENT OF YEAST ISO-1-CYTOCHROME C AND COMPARISONS WITH OTHER EUKARYOTIC CYTOCHROMES C
5LFT 2017-07-12 1.25 Crystal structure of cytochrome c - Bromo-trisulfonatocalix[4]arene complexes
4YE1 2015-05-13 1.39 A cytochrome c plus calixarene structure - alternative ligand binding mode
3TYI 2012-05-02 1.4 Crystal Structure of Cytochrome c - p-Sulfonatocalix[4]arene Complexes
4MU8 2014-06-04 1.45 Crystal structure of an oxidized form of yeast iso-1-cytochrome c at pH 8.8
5NCV 2018-03-14 1.5 Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene
6GD7 2018-08-29 1.55 Cytochrome c in complex with Sulfonato-calix[8]arene, H3 form with PEG
5T8W 2017-11-01 1.6 Cytochrome c - calixarene free
5KPF 2017-07-12 1.7 Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex
2BCN 2006-02-28 1.7 Solvent isotope effects on interfacial protein electron transfer between cytochrome c and cytochrome c peroxidase
5KKE 2017-03-22 1.7 Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with CYMAL5
1CIH 1995-01-26 1.8 STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
1CIE 1995-01-26 1.8 STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
1CIG 1995-01-26 1.8 STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
5LYC 2017-05-10 1.8 Cytochrome c in complex with phosphonato-calix[6]arene
1CSU 1995-01-26 1.81 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
4Q5P 2015-04-22 1.87 Lysine-Ligated Yeast Iso-1 Cytochrome C
1S6V 2004-04-27 1.88 Structure of a cytochrome c peroxidase-cytochrome c site specific cross-link
1CSV 1995-01-26 1.9 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
1CRH 1994-01-31 1.9 THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C
1IRV 1997-01-11 1.9 CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR
2YCC 1992-07-15 1.9 OXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C
1CTZ 1993-07-15 1.9 MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT
1RAQ 1993-10-31 1.9 THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REPLACEMENTS IN CYTOCHROME C
1CSW 1995-01-26 1.9 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
1CIF 1995-01-26 1.9 STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
1CHJ 1994-12-20 1.9 STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C
3CX5 2008-05-13 1.9 Structure of complex III with bound cytochrome c in reduced state and definition of a minimal core interface for electron transfer.
1CSX 1995-01-26 1.9 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
1CHH 1994-12-20 1.97 STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C
5KLU 2017-03-22 1.99 Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside
5T7H 2017-03-22 2.0 Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6
1IRW 1997-01-11 2.0 CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY ALA AND CYS 102 REPLACED BY THR
1CHI 1994-12-20 2.0 STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C
1CRG 1994-01-31 2.0 THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C
1CRI 1994-01-31 2.0 THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C
5CIF 2016-08-03 2.01 Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c
4P4Q 2015-03-25 2.01 Complex of yeast cytochrome c peroxidase (W191F) with iso-1 cytochrome c
1CRJ 1994-01-31 2.05 THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN CYTOCHROME C
5CIG 2016-08-03 2.06 Complex of yeast cytochrome c peroxidase (W191G) with iso-1 cytochrome c
5CIC 2016-08-03 2.1 Complex of yeast cytochrome c peroxidase (W191G) bound to 3-aminobenzotrifluoride with iso-1 cytochrome c
4QAO 2015-08-05 2.1 Lysine-ligated cytochrome c with F82H
6EGZ 2018-10-10 2.17 Crystal structure of cytochrome c in complex with di-PEGylated sulfonatocalix[4]arene
1CTY 1993-07-15 2.2 MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT
1RAP 1993-10-31 2.25 THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REPLACEMENTS IN CYTOCHROME C
2B11 2005-10-25 2.3 Crystal structure of the protein-protein complex between F82W cytochrome c and cytochrome c peroxidase
2PCC 1993-07-15 2.3 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C
1U74 2004-09-28 2.4 Electron Transfer Complex between cytochrome C and cytochrome C peroxidase
6GD8 2018-08-29 2.5 Cytochrome c in complex with Sulfonato-calix[8]arene, P31 form
5CIH 2016-08-03 2.6 Complex of yeast cytochrome c peroxidase (W191Y) with iso-1 cytochrome c
5CIE 2016-08-03 2.6 Complex of yeast cytochrome c peroxidase (W191G) bound to aniline with iso-1 cytochrome c
6RGI 2019-07-10 2.64 Partially unfolded cytochrome c in complex with sulfonatocalix[6]arene
6GD9 2018-08-29 2.65 Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form
2B0Z 2005-10-25 2.7 Crystal structure of the protein-protein complex between F82I cytochrome c and cytochrome c peroxidase
6EGY 2018-10-10 2.7 Crystal structure of cytochrome c in complex with mono-PEGylated sulfonatocalix[4]arene
5CID 2016-08-03 2.76 Complex of yeast cytochrome c peroxidase (W191G) bound to o-toluidine with iso-1 cytochrome c
6GDA 2019-05-01 2.8 Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine
2B10 2005-10-25 2.8 Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase
1KYO 2002-03-06 2.97 YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C
5CIB 2016-08-03 3.01 Complex of yeast cytochrome c peroxidase (W191G) bound to 2,4-dimethylaniline with iso-1 cytochrome c
2B12 2005-10-25 3.02 Crystal structure of the protein-protein complex between F82Y cytochrome c and cytochrome c peroxidase

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.0 Cytochrome c iso-1 P25400 CYC_CANGA
100.0 Cytochrome c iso-1 P00044 CYC1_YEAST