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
1KTD 2002-01-15T00:00:00+0000 2.4 CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO PIGEON CYTOCHROME C PEPTIDE
2B4Z 2005-09-27T00:00:00+0000 1.5 Crystal structure of cytochrome C from bovine heart at 1.5 A resolution.
2YBB 2011-03-02T00:00:00+0000 19.0 Fitted model for bovine mitochondrial supercomplex I1III2IV1 by single particle cryo-EM (EMD-1876)
3J2T 2012-12-23T00:00:00+0000 9.5 An improved model of the human apoptosome
5C0Z 2015-06-12T00:00:00+0000 1.12 The structure of oxidized rat cytochrome c at 1.13 angstroms resolution
5C9M 2015-06-28T00:00:00+0000 1.36 The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution.
5DF5 2015-08-26T00:00:00+0000 1.3 The structure of oxidized rat cytochrome c (T28E) at 1.30 angstroms resolution.
5JUY 2016-05-10T00:00:00+0000 4.1 Active human apoptosome with procaspase-9
6FF5 2018-01-03T00:00:00+0000 1.74 X-ray structure of bovine heart cytochrome c at high ionic strength
6N1O 2018-11-09T00:00:00+0000 1.55 Oxidized rat cytochrome c mutant (S47E)

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