Sequence and stability of the goat cytochrome c.


Abstract

We have determined the sequence of mitochondrial cytochrome c (cyt-c) from the goat heart, and it was found to have a unique amino acid sequence among all amino acid sequences of cyt-c reported till date. Its sequence alignment with the bovine cytochrome c (b-cyt-c) led us to conclude that the goat cytochrome c (g-cyt-c) differs in amino acid sequence from b-cyt-c at only one position, i.e., Pro44(bovine) --> Ala44(goat). It has been observed that guanidinium chloride (GdmCl) induces a two-state transition between the native (N) and denatured (D) states of g-cyt-c. This conclusion is reached from the coincidence of GdmCl-induced transition curves monitored by measurements of absorbance at 405, 530 and 695 nm and circular dichroism (CD) at 222, 416 and 405 nm. Analysis of denaturation curves for the Gibbs energy of stabilization suggests that the stability of g-cyt-c is, within experimental errors, identical to that of b-cyt-c. We have also measured the effect of temperature on the equilibrium, N state <--> D state of g-cyt-c in the presence of different GdmCl concentrations. These measurements gave values of transition temperature (T(m)), changes in enthalpy (DeltaH(m)) and heat capacity (DeltaC(p)) of g-cyt-c in the absence of GdmCl, which are compared with those of b-cyt-c. We have used crystal structure coordinates of b-cyt-c to predict the structure and stability of g-cyt-c, which are compared with those of the bovine protein. Study holds ProTherm entries: 25565, 25566, 25567, 25568, 25569, 25570, 25571, 25572, 25573, 25574, 25575, 25576, 25577, 25578, 25579, 25580, 25581, 25582, 25583, 25584, 25585, 25586, 25587, 25588 Extra Details: monited by [theta]222 Folding and stability; Molecular modeling; Goat cytochrome c; Bovine cytochrome c; Circular dichroism

Submission Details

ID: fNkhmM4o

Submitter: Connie Wang

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

Version: 1

Publication Details
Rahaman H;Khan KA;Hassan I;Wahid M;Singh SB;Singh TP;Moosavi-Movahedi AA;Ahmad F,Biophys. Chem. (2008) Sequence and stability of the goat cytochrome c. PMID:18814948
Additional Information

Study Summary

Number of data points 54
Proteins Mitochondrial cytochrome c
Unique complexes 1
Assays/Quantities/Protocols Experimental Assay: dG_H2O units:kcal/mol ; Experimental Assay: dCp ; Experimental Assay: Tm details:Additives ; Experimental Assay: dHvH details:Additives ; Experimental Assay: Tm details:Additives GdnHCl 2.3 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.3 M ; Experimental Assay: Tm details:Additives GdnHCl 2.2 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.2 M ; Experimental Assay: Tm details:Additives GdnHCl 2.0 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.0 M ; Experimental Assay: Tm details:Additives GdnHCl 1.5 M ; Experimental Assay: dHvH details:Additives GdnHCl 1.5 M ; Experimental Assay: Tm details:Additives GdnHCl 1.0 M ; Experimental Assay: dHvH details:Additives GdnHCl 1.0 M ; Experimental Assay: Tm details:Additives GdnHCl 0.8 M ; Experimental Assay: dHvH details:Additives GdnHCl 0.8 M ; Experimental Assay: Tm details:Additives GdnHCl 0.6 M ; Experimental Assay: dHvH details:Additives GdnHCl 0.6 M ; Experimental Assay: Tm details:Additives GdnHCl 2.5 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.5 M ; Experimental Assay: Tm details:Additives GdnHCl 2.3 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.3 M ; Experimental Assay: Tm details:Additives GdnHCl 2.2 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.2 M ; Experimental Assay: Tm details:Additives GdnHCl 2.0 M ; Experimental Assay: dHvH details:Additives GdnHCl 2.0 M ; Experimental Assay: Tm details:Additives GdnHCl 1.5 M ; Experimental Assay: dHvH details:Additives GdnHCl 1.5 M ; Experimental Assay: Tm details:Additives GdnHCl 1.0 M ; Experimental Assay: dHvH details:Additives GdnHCl 1.0 M ; Experimental Assay: Tm details:Additives GdnHCl 0.8 M ; Experimental Assay: dHvH details:Additives GdnHCl 0.8 M ; Experimental Assay: Tm details:Additives GdnHCl 0.6 M ; Experimental Assay: dHvH details:Additives GdnHCl 0.6 M ; Experimental Assay: Cm ; Experimental Assay: m ; Experimental Assay: dG_H2O units:kJ/mol ; Experimental Assay: Cm ; Experimental Assay: m ; Experimental Assay: dG_H2O units:kJ/mol
Libraries Mutations for sequence GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAAGFSYTDANKNKGITWGEETLMEYLENPKKYIPGTKMIFAGIKKKGEREDLIAYLKKATNE

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
1LC2 2003-06-03 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR 30 Structures
1LC1 2003-06-03 Solution Structure Of Reduced Horse Heart Cytochrome c in 30% Acetonitrile Solution, NMR Minimized Average Structure
2N3B 2015-10-28 Structure of oxidized horse heart cytochrome c encapsulated in reverse micelles
1FI7 2000-08-23 Solution structure of the imidazole complex of cytochrome C
5ZKV 2019-05-22 Solution structure of molten globule state of L94G mutant of horse cytochrome-c
1GIW 1998-12-09 SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE
1I5T 2001-03-21 SOLUTION STRUCTURE OF CYANOFERRICYTOCHROME C
1FI9 2000-08-23 SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C
2FRC 1997-07-29 CYTOCHROME C (REDUCED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE
1AKK 1997-09-17 SOLUTION STRUCTURE OF OXIDIZED HORSE HEART CYTOCHROME C, NMR, MINIMIZED AVERAGE STRUCTURE
2GIW 1998-12-09 SOLUTION STRUCTURE OF REDUCED HORSE HEART CYTOCHROME C, NMR, 40 STRUCTURES
1OCD 1997-06-16 CYTOCHROME C (OXIDIZED) FROM EQUUS CABALLUS, NMR, MINIMIZED AVERAGE STRUCTURE
1M60 2002-08-07 Solution Structure of Zinc-substituted cytochrome c
5C0Z 2016-09-21 1.12 The structure of oxidized rat cytochrome c at 1.13 angstroms resolution
5DF5 2016-09-14 1.3 The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.
5C9M 2016-09-21 1.36 The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
2B4Z 2005-10-11 1.5 Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.
6FF5 2018-03-21 1.74 X-ray structure of bovine heart cytochrome c at high ionic strength
3O1Y 2012-01-25 1.75 Electron transfer complexes: Experimental mapping of the redox-dependent cytochrome c electrostatic surface
3WUI 2014-07-16 1.8 Dimeric horse cytochrome c formed by refolding from molten globule state
3WC8 2013-12-11 1.8 Dimeric horse cytochrome c obtained by refolding with desalting method
1WEJ 1998-12-09 1.8 IGG1 FAB FRAGMENT (OF E8 ANTIBODY) COMPLEXED WITH HORSE CYTOCHROME C AT 1.8 A RESOLUTION
1HRC 1994-11-01 1.9 HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF HORSE HEART CYTOCHROME C
3O20 2012-01-25 1.9 Electron transfer complexes:experimental mapping of the Redox-dependent Cytochrome C electrostatic surface
2YBB 2011-10-19 19.0 Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
5IY5 2017-01-11 2.0 Electron transfer complex of cytochrome c and cytochrome c oxidase at 2.0 angstrom resolution
1CRC 1996-03-08 2.08 CYTOCHROME C AT LOW IONIC STRENGTH
3NBT 2010-07-14 2.1 Crystal structure of trimeric cytochrome c from horse heart
4NFG 2014-09-24 2.11 K13R mutant of horse cytochrome c and yeast cytochrome c peroxidase complex
4RSZ 2015-01-14 2.19 The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c
3NBS 2010-07-14 2.2 Crystal structure of dimeric cytochrome c from horse heart
1KTD 2002-05-01 2.4 CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON CYTOCHROME C PEPTIDE
1U75 2004-09-28 2.55 Electron Transfer Complex between Horse Heart Cytochrome c and Zinc-Porphyrin Substituted Cytochrome c Peroxidase
2PCB 1993-07-15 2.8 CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C
3JBT 2015-11-18 3.8 Atomic structure of the Apaf-1 apoptosome
5JUY 2016-10-19 4.1 Active human apoptosome with procaspase-9
5WVE 2017-02-08 4.4 Apaf-1-Caspase-9 holoenzyme
3J2T 2013-04-10 9.5 An improved model of the human apoptosome

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
90.2 Mitochondrial cytochrome c P21665 CYC_VARVA
91.3 Mitochondrial cytochrome c P00022 CYC_CHESE
90.4 Mitochondrial cytochrome c P00019 CYC_STRCA
90.4 Mitochondrial cytochrome c P00024 CYC_LITCT
90.4 Mitochondrial cytochrome c Q52V08 CYC_MACSY
90.4 Mitochondrial cytochrome c P00002 CYC_MACMU
90.4 Mitochondrial cytochrome c P00018 CYC_DRONO
93.2 Mitochondrial cytochrome c P81280 CYC_ALLMI
90.4 Mitochondrial cytochrome c P00017 CYC_APTPA
91.3 Mitochondrial cytochrome c P67882 CYC_MELGA
91.3 Mitochondrial cytochrome c P67881 CYC_CHICK
94.1 Mitochondrial cytochrome c P00020 CYC_ANAPL
93.1 Mitochondrial cytochrome c P00021 CYC_COLLI
94.2 Mitochondrial cytochrome c P00013 CYC_MINSC
93.3 Mitochondrial cytochrome c P00014 CYC_MACGI
95.2 Mitochondrial cytochrome c P00012 CYC_MIRLE
92.3 Mitochondrial cytochrome c Q52V10 CYC_SAISC
94.2 Mitochondrial cytochrome c B4USV4 CYC_OTOGA
96.2 Mitochondrial cytochrome c P00004 CYC_HORSE
96.2 Mitochondrial cytochrome c P00011 CYC_CANLF
97.1 Mitochondrial cytochrome c P68096 CYC_EQUBU
97.1 Mitochondrial cytochrome c P68097 CYC_EQUAS
96.2 Mitochondrial cytochrome c P00008 CYC_RABIT
96.2 Mitochondrial cytochrome c P00007 CYC_HIPAM
97.1 Mitochondrial cytochrome c Q52V09 CYC_CEPBA
98.1 Mitochondrial cytochrome c P68098 CYC_LAMGU
98.1 Mitochondrial cytochrome c P68100 CYC_ESCRO
98.1 Mitochondrial cytochrome c P68099 CYC_CAMDR
98.1 Mitochondrial cytochrome c P62898 CYC_RAT
98.1 Mitochondrial cytochrome c P62897 CYC_MOUSE
99.0 Mitochondrial cytochrome c P62896 CYC_SHEEP
99.0 Mitochondrial cytochrome c P62895 CYC_PIG
99.0 Mitochondrial cytochrome c P62894 CYC_BOVIN