Compressing the free energy range of substructure stabilities in iso-1-cytochrome c.


Abstract

Evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-HCl. Mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. The limited proteolysis data yield a free energy of 3.8 +/- 0.4 kcal mol(-1) to unfold the least stable substructure compared with 5.05 +/- 0.30 kcal mol(-1) for global unfolding of iso-1-cytochrome c. Thus, substructure stabilities of iso-1-cytochrome c span only approximately 1.2 kcal mol(-1) compared with approximately 8 kcal mol(-1) for horse cytochrome c. Consistent with the less cooperative folding thus expected for the horse protein, the guanidine-HCl m-values are approximately 3 kcal mol(-1)M(-1) versus approximately 4.5 kcal mol(-1)M(-1) for horse versus yeast cytochrome c. The tight free energy spacing of the yeast cytochrome c substructures suggests that its folding has more branch points than for horse cytochrome c. Studies on a variant of iso-1-cytochrome c with an H26N mutation indicate that the least and most stable substructures unfold sequentially and the two least stable substructures unfold independently as for horse cytochrome c. Thus, important aspects of the substructure architecture of horse cytochrome c, albeit compressed energetically, are preserved evolutionally in yeast iso-1-cytochrome c. Study holds ProTherm entries: 24965, 24966 Extra Details: protein folding; limited proteolysis; protein substructures; evolutionary conservation; folding cooperativity; alkaline transition

Submission Details

ID: sA5aFZhr

Submitter: Connie Wang

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

Version: 1

Publication Details
Duncan MG;Williams MD;Bowler BE,Protein Sci. (2009) Compressing the free energy range of substructure stabilities in iso-1-cytochrome c. PMID:19472325
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
2JQR 2008-04-22 Solution model of crosslinked complex of cytochrome c and adrenodoxin
1YIC 1997-07-23 THE OXIDIZED SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C, NMR, 20 STRUCTURES
2HV4 2006-09-26 NMR solution structure refinement of yeast iso-1-ferrocytochrome c
2ORL 2007-04-24 Solution structure of the cytochrome c- para-aminophenol adduct
2MHM 2014-10-29 Solution structure of cytochrome c Y67H
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
2N18 2015-05-13 Dominant form of the low-affinity complex of yeast cytochrome c and cytochrome c peroxidase
2JTI 2008-07-22 Solution structure of the yeast iso-1-cytochrome c (T12A) : yeast cytochrome c peroxidase complex
1LMS 2003-03-18 Structural model for an alkaline form of ferricytochrome c
2GB8 2006-11-21 Solution structure of the complex between yeast iso-1-cytochrome c and yeast cytochrome c peroxidase
1NMI 2003-02-04 Solution structure of the imidazole complex of iso-1 cytochrome c
2LIT 2011-12-07 NMR Solution Structure of Yeast Iso-1-cytochrome c Mutant P71H in reduced states
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
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
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
5KPF 2017-07-12 1.7 Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex
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
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
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
1CHJ 1994-12-20 1.9 STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C
1CIF 1995-01-26 1.9 STRUCTURAL AND FUNCTIONAL EFFECTS OF MULTIPLE MUTATIONS AT DISTAL SITES IN CYTOCHROME C
1CSX 1995-01-26 1.9 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
1RAQ 1993-10-31 1.9 THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REPLACEMENTS IN CYTOCHROME C
1CTZ 1993-07-15 1.9 MUTATION OF TYROSINE-67 IN CYTOCHROME C SIGNIFICANTLY ALTERS THE LOCAL HEME ENVIRONMENT
1IRV 1997-01-11 1.9 CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ILE 75 REPLACED BY MET AND CYS 102 REPLACED BY THR
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.
2YCC 1992-07-15 1.9 OXIDATION STATE-DEPENDENT CONFORMATIONAL CHANGES IN CYTOCHROME C
1CSV 1995-01-26 1.9 REPLACEMENTS IN A CONSERVED LEUCINE CLUSTER IN THE HYDROPHOBIC HEME POCKET OF CYTOCHROME C
1CSW 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
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
1IRW 1997-01-11 2.0 CYTOCHROME C ISOZYME 1, REDUCED, MUTANT WITH ASN 52 REPLACED BY ALA AND CYS 102 REPLACED BY THR
1CRI 1994-01-31 2.0 THE ROLE OF A CONSERVED INTERNAL WATER MOLECULE AND ITS ASSOCIATED HYDROGEN BOND NETWORK IN 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
1CHI 1994-12-20 2.0 STRUCTURAL STUDIES OF THE ROLES OF RESIDUES 82 AND 85 AT THE INTERACTIVE FACE OF CYTOCHROME C
5T7H 2017-03-22 2.0 Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6
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
5CIE 2016-08-03 2.6 Complex of yeast cytochrome c peroxidase (W191G) bound to aniline with iso-1 cytochrome c
5CIH 2016-08-03 2.6 Complex of yeast cytochrome c peroxidase (W191Y) 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
2B10 2005-10-25 2.8 Crystal Structure of the Protein-Protein Complex between F82S cytochrome c and cytochrome c peroxidase
6GDA 2019-05-01 2.8 Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine
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