Amino Acids

, Volume 44, Issue 5, pp 1307–1316

S-linked protein homocysteinylation: identifying targets based on structural, physicochemical and protein–protein interactions of homocysteinylated proteins

  • Yumnam Silla
  • Elayanambi Sundaramoorthy
  • Puneet Talwar
  • Shantanu Sengupta
Original Article

Abstract

An elevated level of homocysteine, a thiol-containing amino acid is associated with a wide spectrum of disease conditions. A majority (>80 %) of the circulating homocysteine exist in protein-bound form. Homocysteine can bind to free cysteine residues in the protein or could cleave accessible cysteine disulfide bonds via thiol disulfide exchange reaction. Binding of homocysteine to proteins could potentially alter the structure and/or function of the protein. To date only 21 proteins have been experimentally shown to bind homocysteine. In this study we attempted to identify other proteins that could potentially bind to homocysteine based on the criteria that such proteins will have significant 3D structural homology with the proteins that have been experimentally validated and have solvent accessible cysteine residues either with high dihedral strain energy (for cysteine–cysteine disulfide bonds) or low pKa (for free cysteine residues). This analysis led us to the identification of 78 such proteins of which 68 proteins had 154 solvent accessible disulfide cysteine pairs with high dihedral strain energy and 10 proteins had free cysteine residues with low pKa that could potentially bind to homocysteine. Further, protein–protein interaction network was built to identify the interacting partners of these putative homocysteine binding proteins. We found that the 21 experimentally validated proteins had 174 interacting partners while the 78 proteins identified in our analysis had 445 first interacting partners. These proteins are mainly involved in biological activities such as complement and coagulation pathway, focal adhesion, ECM-receptor, ErbB signalling and cancer pathways, etc. paralleling the disease-specific attributes associated with hyperhomocysteinemia.

Keywords

Homocysteine Homologous structure Disulfide Dihedral strain energy pKa Protein–protein interaction 

Abbreviations

Hcy

Homocysteine

DSE

Dihedral strain energy

DSSP

Dictionary of secondary structure prediction

PPI

Protein–protein interaction

DAVID

Database for annotation, visualization and integrated discovery

GO

Gene ontology

CC

Cellular compartment

BP

Biological process

MF

Molecular function

Supplementary material

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Supplementary material 1 (PDF 864 kb)
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Supplementary material 2 (PDF 301 kb)
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Supplementary material 3 (PDF 227 kb)
726_2013_1465_MOESM4_ESM.pdf (8 kb)
Supplementary material 4 (PDF 8 kb)
726_2013_1465_MOESM5_ESM.pdf (85 kb)
Supplementary material 5 (PDF 85 kb)

References

  1. Ahamed J, Versteeg HH, Kerver M, Chen VM, Mueller BM et al (2006) Disulfide isomerization switches tissue factor from coagulation to cell signaling. Proc Natl Acad Sci USA 103:13932–13937PubMedCrossRefGoogle Scholar
  2. Anandakrishnan R, Aguilar B, Onufriev AV (2012) H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res 40:W537–W541PubMedCrossRefGoogle Scholar
  3. Andersson A, Lindgren A, Hultberg B (1995) Effect of thiol oxidation and thiol export from erythrocytes on determination of redox status of homocysteine and other thiols in plasma from healthy subjects and patients with cerebral infarction. Clin Chem 41:361–366PubMedGoogle Scholar
  4. Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24:282–284PubMedCrossRefGoogle Scholar
  5. Barsky A, Gardy JL, Hancock RE, Munzner T (2007) Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 23:1040–1042PubMedCrossRefGoogle Scholar
  6. Chuang CC, Chen CY, Yang JM, Lyu PC, Hwang JK (2003) Relationship between protein structures and disulfide-bonding patterns. Proteins 53:1–5PubMedCrossRefGoogle Scholar
  7. da Huang W, Sherman BT, Lempicki RA (2009a) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57CrossRefGoogle Scholar
  8. da Huang W, Sherman BT, Lempicki RA (2009b) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37:1–13CrossRefGoogle Scholar
  9. de Vries JI, Dekker GA, Huijgens PC, Jakobs C, Blomberg BM et al (1997) Hyperhomocysteinaemia and protein S deficiency in complicated pregnancies. Br J Obstet Gynaecol 104:1248–1254PubMedCrossRefGoogle Scholar
  10. Eikelboom JW, Lonn E, Genest J Jr, Hankey G, Yusuf S (1999) Homocyst(e)ine and cardiovascular disease: a critical review of the epidemiologic evidence. Ann Intern Med 131:363–375PubMedGoogle Scholar
  11. Gelly JC, Joseph AP, Srinivasan N, de Brevern AG (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res 39:W18–W23PubMedCrossRefGoogle Scholar
  12. Gilbert HF (1995) Thiol/disulfide exchange equilibria and disulfide bond stability. Methods Enzymol 251:8–28PubMedCrossRefGoogle Scholar
  13. Hernandez-Toro J, Prieto C, De las Rivas J (2007) APID2NET: unified interactome graphic analyzer. Bioinformatics 23:2495–2497PubMedCrossRefGoogle Scholar
  14. Jacobsen DW, Catanescu O, Dibello PM, Barbato JC (2005) Molecular targeting by homocysteine: a mechanism for vascular pathogenesis. Clin Chem Lab Med 43:1076–1083PubMedCrossRefGoogle Scholar
  15. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2537–2577CrossRefGoogle Scholar
  16. Kirke PN, Mills JL, Scott JM (1997) Homocysteine metabolism in pregnancies complicated by neural tube defects. Nutrition 13:994–995PubMedCrossRefGoogle Scholar
  17. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372:774–797PubMedCrossRefGoogle Scholar
  18. Majors AK, Sengupta S, Willard B, Kinter MT, Pyeritz RE et al (2002) Homocysteine binds to human plasma fibronectin and inhibits its interaction with fibrin. Arterioscler Thromb Vasc Biol 22:1354–1359PubMedCrossRefGoogle Scholar
  19. Mansoor MA, Svardal AM, Ueland PM (1992) Determination of the in vivo redox status of cysteine, cysteinylglycine, homocysteine, and glutathione in human plasma. Anal Biochem 200:218–229PubMedCrossRefGoogle Scholar
  20. Meigs JB, Jacques PF, Selhub J, Singer DE, Nathan DM et al (2001) Fasting plasma homocysteine levels in the insulin resistance syndrome: the Framingham offspring study. Diabetes Care 24:1403–1410PubMedCrossRefGoogle Scholar
  21. Minagawa H, Watanabe A, Akatsu H, Adachi K, Ohtsuka C et al (2010) Homocysteine, another risk factor for Alzheimer disease, impairs apolipoprotein E3 function. J Biol Chem 285:38382–38388PubMedCrossRefGoogle Scholar
  22. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536–540PubMedGoogle Scholar
  23. Perry IJ, Refsum H, Morris RW, Ebrahim SB, Ueland PM et al (1995) Prospective study of serum total homocysteine concentration and risk of stroke in middle-aged British men. Lancet 346:1395–1398PubMedCrossRefGoogle Scholar
  24. Regland B, Johansson BV, Grenfeldt B, Hjelmgren LT, Medhus M (1995) Homocysteinemia is a common feature of schizophrenia. J Neural Transm Gen Sect 100:165–169PubMedCrossRefGoogle Scholar
  25. Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G (1998) Homology modeling, model and software evaluation: three related resources. Bioinformatics 14:523–528PubMedCrossRefGoogle Scholar
  26. Schmidt B, Ho L, Hogg PJ (2006) Allosteric disulfide bonds. Biochemistry 45:7429–7433PubMedCrossRefGoogle Scholar
  27. Sengupta S, Wehbe C, Majors AK, Ketterer ME, DiBello PM et al (2001a) Relative roles of albumin and ceruloplasmin in the formation of homocystine, homocysteine-cysteine-mixed disulfide, and cystine in circulation. J Biol Chem 276:46896–46904PubMedCrossRefGoogle Scholar
  28. Sengupta S, Chen H, Togawa T, DiBello PM, Majors AK et al (2001b) Albumin thiolate anion is an intermediate in the formation of albumin-S-S-homocysteine. J Biol Chem 276:30111–30117PubMedCrossRefGoogle Scholar
  29. Seshadri S, Beiser A, Selhub J, Jacques PF, Rosenberg IH et al (2002) Plasma homocysteine as a risk factor for dementia and Alzheimer’s disease. N Engl J Med 346:476–483PubMedCrossRefGoogle Scholar
  30. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT et al (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504PubMedCrossRefGoogle Scholar
  31. Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH (2011) Improved treatment of ligands and coupling effects in empirical calculation and rationalization of pKa values. J Chem Theory Comput 7(7):2284–2295CrossRefGoogle Scholar
  32. Sundaramoorthy E, Maiti S, Brahmachari SK, Sengupta S (2008) Predicting protein homocysteinylation targets based on dihedral strain energy and pKa of cysteines. Proteins 71:1475–1543PubMedCrossRefGoogle Scholar
  33. Tang YS, Khan RA, Zhang Y, Xiao S, Wang M et al (2011) Incrimination of heterogeneous nuclear ribonucleoprotein E1 (hnRNP-E1) as a candidate sensor of physiological folate deficiency. J Biol Chem 286:39100–39115PubMedCrossRefGoogle Scholar
  34. Thangudu RR, Manoharan M, Srinivasan N, Cadet F, Sowdhamini R, Offmann B (2008) Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. BMC Struct Biol 8:55PubMedCrossRefGoogle Scholar
  35. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta SJ, Weiner P (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106:765–784CrossRefGoogle Scholar
  36. Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC et al (2006) The universal protein resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187–D191PubMedCrossRefGoogle Scholar
  37. Zemla A (2003) LGA:a method for finding 3D similarities in protein structures. Nucleic Acids Res 31:3370–3374PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Yumnam Silla
    • 1
  • Elayanambi Sundaramoorthy
    • 1
    • 2
  • Puneet Talwar
    • 1
  • Shantanu Sengupta
    • 1
  1. 1.CSIR-Institute of Genomics and Integrative BiologyDelhiIndia
  2. 2.Department of Oncology, Medical Research Council, Cancer Cell Unit Hutchison/MRC Research CentreUniversity of CambridgeCambridgeUK

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