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Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2013; 18(3); 383-390; doi: 10.1007/s00775-013-0982-8

Interaction of dimeric horse cytochrome c with cyanide ion.

Abstract: We have previously shown that methionine-heme iron coordination is perturbed in domain-swapped dimeric horse cytochrome c. To gain insight into the effect of methionine dissociation in dimeric cytochrome c, we investigated its interaction with cyanide ion. We found that the Soret and Q bands of oxidized dimeric cytochrome c at 406.5 and 529 nm redshift to 413 and 536 nm, respectively, on addition of 1 mM cyanide ion. The binding constant of dimeric cytochrome c and cyanide ion was obtained as 2.5 × 10(4) M(-1). The Fe-CN and C-N stretching (ν (Fe-CN) and ν (CN)) resonance Raman bands of CN(-)-bound dimeric cytochrome c were observed at 443 and 2,126 cm(-1), respectively. The ν (Fe-CN) frequency of dimeric cytochrome c was relatively low compared with that of other CN(-)-bound heme proteins, and a relatively strong coupling between the Fe-C-N bending and porphyrin vibrations was observed in the 350-450-cm(-1) region. The low ν (Fe-CN) frequency suggests weaker binding of the cyanide ion to dimeric cytochrome c compared with other heme proteins possessing a distal heme cavity. Although the secondary structure of dimeric cytochrome c did not change on addition of cyanide ion according to circular dichroism measurements, the dimer dissociation rate at 45 °C increased from (8.9 ± 0.7) × 10(-6) to (3.8 ± 0.2) × 10(-5) s(-1), with a decrease of about 2 °C in its dissociation temperature obtained with differential scanning calorimetry. The results show that diatomic ligands may bind to the heme iron of dimeric cytochrome c and affect its stability.
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Publication Date: 2013-02-15 PubMed ID: 23412550DOI: 10.1007/s00775-013-0982-8Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research investigates the effects of cyanide ion interaction with a specific protein called dimeric horse cytochrome c which is known to have disturbed methionine-heme iron coordination. The study finds out that cyanide ion binding has an impact on the protein’s stability.

Research Overview

The study revolves around the interaction of a cyanide ion with dimeric horse cytochrome c. This particular protein has been previously known to present issues with methionine-heme iron coordination in its dimeric form.

Findings on Interaction

  • In the presence of 1mM cyanide ion, certain properties of the dimeric cytochrome c change: the Soret and Q bands of the oxidized form go through a ‘redshift’, moving from 406.5 and 529 nm to 413 and 536 nm respectively.
  • The cyanide ion binds to the dimeric cytochrome c with a binding constant of 2.5 × 10(4) M(-1).

Raman Resonance Bands Observations

  • The resonance Raman bands for Fe-CN and C-N stretching (denoted as ν (Fe-CN) and ν (CN)) in the CN-bound dimeric cytochrome c were seen to be at 443 and 2,126 cm(-1), respectively.
  • The Fe-CN frequency of the protein was found to be lower compared to other CN(-)-bound heme proteins. This indicates that the cyanide ion’s binding to dimeric cytochrome c is weaker compared to other heme proteins that have a distal heme cavity.
  • Coupling was observed between the bending of the Fe-C-N and vibrations of the porphyrin in the 350-450-cm(-1) region.

Stability of Cytochrome C in Cyandie Ion Presence

  • Circular dichroism measurements indicated that the secondary structure of dimeric cytochrome c did not change upon the addition of the cyanide ion. However, it was noted that the dimer dissociation rate increased significantly at 45°C.
  • Furthermore, using differential scanning calorimetry, it was seen that the dissociation temperature of the dimer decreased by about 2°C.
  • These findings suggest that the binding of diatomic ligands such as the cyanide ion to the heme iron of dimeric cytochrome c alters its stability.

Cite This Article

APA
Nugraheni AD, Nagao S, Yanagisawa S, Ogura T, Hirota S. (2013). Interaction of dimeric horse cytochrome c with cyanide ion. J Biol Inorg Chem, 18(3), 383-390. https://doi.org/10.1007/s00775-013-0982-8

Publication

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry
ISSN: 1432-1327
NlmUniqueID: 9616326
Country: Germany
Language: English
Volume: 18
Issue: 3
Pages: 383-390

Researcher Affiliations

Nugraheni, Ari Dwi
  • Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
Nagao, Satoshi
    Yanagisawa, Sachiko
      Ogura, Takashi
        Hirota, Shun

          MeSH Terms

          • Animals
          • Cyanides / metabolism
          • Cytochromes c / chemistry
          • Cytochromes c / metabolism
          • Horses / metabolism
          • Iron / metabolism
          • Methionine / chemistry
          • Methionine / metabolism
          • Models, Molecular
          • Protein Binding
          • Protein Multimerization
          • Protein Stability
          • Protein Structure, Secondary
          • Temperature

          References

          This article includes 50 references
          1. Pollock WB, Rosell FI, Twitchett MB, Dumont ME, Mauk AG. Bacterial expression of a mitochondrial cytochrome c. Trimethylation of lys72 in yeast iso-1-cytochrome c and the alkaline conformational transition.. Biochemistry 1998 Apr 28;37(17):6124-31.
            pubmed: 9558351doi: 10.1021/bi972188dgoogle scholar: lookup
          2. Weichsel A, Andersen JF, Champagne DE, Walker FA, Montfort WR. Crystal structures of a nitric oxide transport protein from a blood-sucking insect.. Nat Struct Biol 1998 Apr;5(4):304-9.
            pubmed: 9546222doi: 10.1038/nsb0498-304google scholar: lookup
          3. MARGOLIASH E, FROHWIRT N, WIENER E. A study of the cytochrome c haemochromogen.. Biochem J 1959 Mar;71(3):559-70.
            pubmed: 13638265doi: 10.1042/bj0710559google scholar: lookup
          4. Yeh SR, Takahashi S, Fan B, Rousseau DL. Ligand exchange during cytochrome c folding.. Nat Struct Biol 1997 Jan;4(1):51-6.
            pubmed: 8989324doi: 10.1038/nsb0197-51google scholar: lookup
          5. Hirota S, Ueda M, Hayashi Y, Nagao S, Kamikubo H, Kataoka M. Maintenance of the secondary structure of horse cytochrome c during the conversion process of monomers to oligomers by addition of ethanol.. J Biochem 2012 Dec;152(6):521-9.
            pubmed: 22923742doi: 10.1093/jb/mvs098google scholar: lookup
          6. Ying T, Zhong F, Xie J, Feng Y, Wang ZH, Huang ZX, Tan X. Evolutionary alkaline transition in human cytochrome c.. J Bioenerg Biomembr 2009 Jun;41(3):251-7.
            pubmed: 19593652doi: 10.1007/s10863-009-9223-9google scholar: lookup
          7. Bolognesi M, Rosano C, Losso R, Borassi A, Rizzi M, Wittenberg JB, Boffi A, Ascenzi P. Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.. Biophys J 1999 Aug;77(2):1093-9.
            pubmed: 10423453doi: 10.1016/S0006-3495(99)76959-6google scholar: lookup
          8. Filosa A, Ismail AA, English AM. FTIR-monitored thermal titration reveals different mechanisms for the alkaline isomerization of tuna compared to horse and bovine cytochromes c.. J Biol Inorg Chem 1999 Dec;4(6):717-26.
            pubmed: 10631603doi: 10.1007/pl00010652google scholar: lookup
          9. Bennett MJ, Choe S, Eisenberg D. Domain swapping: entangling alliances between proteins.. Proc Natl Acad Sci U S A 1994 Apr 12;91(8):3127-31.
            pubmed: 8159715doi: 10.1073/pnas.91.8.3127google scholar: lookup
          10. Bushnell GW, Louie GV, Brayer GD. High-resolution three-dimensional structure of horse heart cytochrome c.. J Mol Biol 1990 Jul 20;214(2):585-95.
            pubmed: 2166170doi: 10.1016/0022-2836(90)90200-6google scholar: lookup
          11. Ying T, Wang ZH, Lin YW, Xie J, Tan X, Huang ZX. Tyrosine-67 in cytochrome c is a possible apoptotic trigger controlled by hydrogen bonds via a conformational transition.. Chem Commun (Camb) 2009 Aug 14;(30):4512-4.
            pubmed: 19617967doi: 10.1039/b904347kgoogle scholar: lookup
          12. Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S. Domain swapping of the heme and N-terminal α-helix in Hydrogenobacter thermophilus cytochrome c(552) dimer.. Biochemistry 2012 Oct 30;51(43):8608-16.
            pubmed: 23035813doi: 10.1021/bi3011303google scholar: lookup
          13. Yao Y, Qian C, Ye K, Wang J, Bai Z, Tang W. Solution structure of cyanoferricytochrome c: ligand-controlled conformational flexibility and electronic structure of the heme moiety.. J Biol Inorg Chem 2002 Apr;7(4-5):539-47.
            pubmed: 11941512doi: 10.1007/s00775-001-0334-ygoogle scholar: lookup
          14. Sitter AJ, Reczek CM, Terner J. Observation of the FeIV=O stretching vibration of ferryl myoglobin by resonance Raman spectroscopy.. Biochim Biophys Acta 1985 Apr 29;828(3):229-35.
            pubmed: 3986209doi: 10.1016/0167-4838(85)90301-2google scholar: lookup
          15. Maes EM, Walker FA, Montfort WR, Czernuszewicz RS. Resonance Raman spectroscopic study of nitrophorin 1, a nitric oxide-binding heme protein from Rhodnius prolixus, and its nitrosyl and cyano adducts.. J Am Chem Soc 2001 Nov 28;123(47):11664-72.
            pubmed: 11716723doi: 10.1021/ja0031927google scholar: lookup
          16. Kagan VE, Tyurin VA, Jiang J, Tyurina YY, Ritov VB, Amoscato AA, Osipov AN, Belikova NA, Kapralov AA, Kini V, Vlasova II, Zhao Q, Zou M, Di P, Svistunenko DA, Kurnikov IV, Borisenko GG. Cytochrome c acts as a cardiolipin oxygenase required for release of proapoptotic factors.. Nat Chem Biol 2005 Sep;1(4):223-32.
            pubmed: 16408039doi: 10.1038/nchembio727google scholar: lookup
          17. Yu NT, Benko B, Kerr EA, Gersonde K. Iron-carbon bond lengths in carbonmonoxy and cyanomet complexes of the monomeric hemoglobin III from Chironomus thummi thummi: a critical comparison between resonance Raman and x-ray diffraction studies.. Proc Natl Acad Sci U S A 1984 Aug;81(16):5106-10.
            pubmed: 6591180doi: 10.1073/pnas.81.16.5106google scholar: lookup
          18. HORECKER BL, KORNBERG A. The cytochrome c-cyanide complex.. J Biol Chem 1946 Sep;165(1):11-20.
            pubmed: 21001180
          19. Hirota S, Hattori Y, Nagao S, Taketa M, Komori H, Kamikubo H, Wang Z, Takahashi I, Negi S, Sugiura Y, Kataoka M, Higuchi Y. Cytochrome c polymerization by successive domain swapping at the C-terminal helix.. Proc Natl Acad Sci U S A 2010 Jul 20;107(29):12854-9.
            pubmed: 20615990doi: 10.1073/pnas.1001839107google scholar: lookup
          20. Hirota S, Hayamizu K, Okuno T, Kishi M, Iwasaki H, Kondo T, Hibino T, Takabe T, Kohzuma T, Yamauchi O. Spectroscopic and electrochemical studies on structural change of plastocyanin and its tyrosine 83 mutants induced by interaction with lysine peptides.. Biochemistry 2000 May 30;39(21):6357-64.
            pubmed: 10828949doi: 10.1021/bi9929812google scholar: lookup
          21. Wang Z, Matsuo T, Nagao S, Hirota S. Peroxidase activity enhancement of horse cytochrome c by dimerization.. Org Biomol Chem 2011 Jul 7;9(13):4766-9.
            pubmed: 21625690doi: 10.1039/c1ob05552fgoogle scholar: lookup
          22. Banci L, Bertini I, Bren KL, Gray HB, Sompornpisut P, Turano P. 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.. Biochemistry 1995 Sep 12;34(36):11385-98.
            pubmed: 7547866doi: 10.1021/bi00036a011google scholar: lookup
          23. Yoshikawa S, O'Keeffe DH, Caughey WS. Investigations of cyanide as an infrared probe of hemeprotein ligand binding sites.. J Biol Chem 1985 Mar 25;260(6):3518-28.
            pubmed: 3972836
          24. Schejter A, Plotkin B. The binding characteristics of the cytochrome c iron.. Biochem J 1988 Oct 1;255(1):353-6.
            pubmed: 2848510
          25. Varhac R, Antalík M. Correlation of acid-induced conformational transition of ferricytochrome c with cyanide binding kinetics.. J Biol Inorg Chem 2008 Jun;13(5):713-21.
            pubmed: 18317818doi: 10.1007/s00775-008-0357-8google scholar: lookup
          26. Kitagawa T, Kyogoku Y, Iizuka T, Saito MI. Nature of the iron-ligand bond in ferrous low spin hemoproteins studied by resonance Raman scattering.. J Am Chem Soc 1976 Aug 18;98(17):5169-73.
            pubmed: 182732doi: 10.1021/ja00433a019google scholar: lookup
          27. Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap.. Protein Sci 2002 Jun;11(6):1285-99.
            pubmed: 12021428doi: 10.1110/ps.0201402google scholar: lookup
          28. Spiro TG, Burke JM. Protein control of porphyrin conformation. Comparison of resonance Raman spectra of heme proteins with mesoporphyrin IX analogues.. J Am Chem Soc 1976 Sep 1;98(18):5482-9.
            pubmed: 182734doi: 10.1021/ja00434a013google scholar: lookup
          29. Sutin N, Yandell JK. Mechanisms of the reactions of cytochrome c. Rate and equilibrium constants for ligand binding to horse heart ferricytochrome c.. J Biol Chem 1972 Nov 10;247(21):6932-6.
            pubmed: 4343163
          30. HORECKER BL, STANNARD JN. The cytochrome c-azide complex.. J Biol Chem 1948 Feb;172(2):589-97.
            pubmed: 18901178
          31. TSOU CL. Exogenous and endogenous cytochrome c.. Biochem J 1952 Feb;50(4):493-9.
            pubmed: 14925123doi: 10.1042/bj0500493google scholar: lookup
          32. Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly.. Protein Sci 1995 Dec;4(12):2455-68.
            pubmed: 8580836doi: 10.1002/pro.5560041202google scholar: lookup
          33. Rousseau F, Schymkowitz JW, Itzhaki LS. The unfolding story of three-dimensional domain swapping.. Structure 2003 Mar;11(3):243-51.
            pubmed: 12623012doi: 10.1016/s0969-2126(03)00029-7google scholar: lookup
          34. Varhac R, Tomásková N, Fabián M, Sedlák E. Kinetics of cyanide binding as a probe of local stability/flexibility of cytochrome c.. Biophys Chem 2009 Sep;144(1-2):21-6.
            pubmed: 19545938doi: 10.1016/j.bpc.2009.06.001google scholar: lookup
          35. Dickerson RE, Takano T, Eisenberg D, Kallai OB, Samson L, Cooper A, Margoliash E. Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 A resolution.. J Biol Chem 1971 Mar 10;246(5):1511-35.
            pubmed: 5545094
          36. Yeh SR, Rousseau DL. Ligand exchange during unfolding of cytochrome c.. J Biol Chem 1999 Jun 18;274(25):17853-9.
            pubmed: 10364230doi: 10.1074/jbc.274.25.17853google scholar: lookup
          37. Newcomer ME. Protein folding and three-dimensional domain swapping: a strained relationship?. Curr Opin Struct Biol 2002 Feb;12(1):48-53.
            pubmed: 11839489doi: 10.1016/s0959-440x(02)00288-9google scholar: lookup
          38. Pesce A, Couture M, Dewilde S, Guertin M, Yamauchi K, Ascenzi P, Moens L, Bolognesi M. A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.. EMBO J 2000 Jun 1;19(11):2424-34.
            pubmed: 10835341doi: 10.1093/emboj/19.11.2424google scholar: lookup
          39. Takahashi S, Yeh SR, Das TK, Chan CK, Gottfried DS, Rousseau DL. Folding of cytochrome c initiated by submillisecond mixing.. Nat Struct Biol 1997 Jan;4(1):44-50.
            pubmed: 8989323doi: 10.1038/nsb0197-44google scholar: lookup
          40. Henry ER, Rousseau DL, Hopfield JJ, Noble RW, Simon SR. Spectroscopic studies of protein-heme interactions accompanying the allosteric transition in methemoglobins.. Biochemistry 1985 Oct 8;24(21):5907-18.
            pubmed: 4084499doi: 10.1021/bi00342a033google scholar: lookup
          41. Reddy KS, Yonetani T, Tsuneshige A, Chance B, Kushkuley B, Stavrov SS, Vanderkooi JM. Infrared spectroscopy of the cyanide complex of iron (II) myoglobin and comparison with complexes of microperoxidase and hemoglobin.. Biochemistry 1996 Apr 30;35(17):5562-70.
            pubmed: 8611547doi: 10.1021/bi952596mgoogle scholar: lookup
          42. George P, Glauser SC, Schejter A. The reactivity of ferricytochrome c with ionic ligands.. J Biol Chem 1967 Apr 25;242(8):1690-5.
            pubmed: 6024762
          43. BUTT WD, KEILIN D. Absorption spectra and some other properties of cytochrome c and of its compounds with ligands.. Proc R Soc Lond B Biol Sci 1962 Nov 20;156:429-58.
            pubmed: 14040866doi: 10.1098/rspb.1962.0049google scholar: lookup
          44. Liu Y, Gotte G, Libonati M, Eisenberg D. Structures of the two 3D domain-swapped RNase A trimers.. Protein Sci 2002 Feb;11(2):371-80.
            pubmed: 11790847doi: 10.1110/ps.36602google scholar: lookup
          45. Belikova NA, Vladimirov YA, Osipov AN, Kapralov AA, Tyurin VA, Potapovich MV, Basova LV, Peterson J, Kurnikov IV, Kagan VE. Peroxidase activity and structural transitions of cytochrome c bound to cardiolipin-containing membranes.. Biochemistry 2006 Apr 18;45(15):4998-5009.
            pubmed: 16605268doi: 10.1021/bi0525573google scholar: lookup
          46. Rousseau F, Schymkowitz JW, Wilkinson HR, Itzhaki LS. Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues.. Proc Natl Acad Sci U S A 2001 May 8;98(10):5596-601.
            pubmed: 11344301doi: 10.1073/pnas.101542098google scholar: lookup
          47. Bennett MJ, Sawaya MR, Eisenberg D. Deposition diseases and 3D domain swapping.. Structure 2006 May;14(5):811-24.
            pubmed: 16698543doi: 10.1016/j.str.2006.03.011google scholar: lookup
          48. Chen YW, Stott K, Perutz MF. Crystal structure of a dimeric chymotrypsin inhibitor 2 mutant containing an inserted glutamine repeat.. Proc Natl Acad Sci U S A 1999 Feb 16;96(4):1257-61.
            pubmed: 9990011doi: 10.1073/pnas.96.4.1257google scholar: lookup
          49. Barrientos LG, Louis JM, Botos I, Mori T, Han Z, O'Keefe BR, Boyd MR, Wlodawer A, Gronenborn AM. The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures.. Structure 2002 May;10(5):673-86.
            pubmed: 12015150doi: 10.1016/s0969-2126(02)00758-xgoogle scholar: lookup
          50. Schymkowitz JW, Rousseau F, Wilkinson HR, Friedler A, Itzhaki LS. Observation of signal transduction in three-dimensional domain swapping.. Nat Struct Biol 2001 Oct;8(10):888-92.
            pubmed: 11573096doi: 10.1038/nsb1001-888google scholar: lookup

          Citations

          This article has been cited 4 times.
          1. Zhang M, Tai H, Yanagisawa S, Yamanaka M, Ogura T, Hirota S. Resonance Raman Studies on Heme Ligand Stretching Modes in Methionine80-Depleted Cytochrome c: Fe-His, Fe-O(2), and O-O Stretching Modes. J Phys Chem B 2023 Mar 23;127(11):2441-2449.
            doi: 10.1021/acs.jpcb.3c00514pubmed: 36919258google scholar: lookup
          2. Hirota S, Yamashiro N, Wang Z, Nagao S. Effect of methionine80 heme coordination on domain swapping of cytochrome c. J Biol Inorg Chem 2017 Jul;22(5):705-712.
            doi: 10.1007/s00775-017-1446-3pubmed: 28246923google scholar: lookup
          3. Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S. Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins. PLoS One 2015;10(4):e0123653.
            doi: 10.1371/journal.pone.0123653pubmed: 25853415google scholar: lookup
          4. Yamanaka M, Nagao S, Komori H, Higuchi Y, Hirota S. Change in structure and ligand binding properties of hyperstable cytochrome c555 from Aquifex aeolicus by domain swapping. Protein Sci 2015 Mar;24(3):366-75.
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