Skip to main content
SpringerLink
Log in

Protease-Antiprotease Interactions: An Overview of the Process from an “In Silico” Perspective

  • Chapter
  • First Online:
Proteases in Physiology and Pathology

  • 1056 Accesses

Abstract

Most if not all of the cellular processes involve protein-protein interactions (PPIs). The detailed information of the amino acid residues involved in PPIs may, therefore, be used in many important aspects like drug development, elucidation of molecular pathways, generation of protein mimetic, understanding of disease mechanisms, and development of docking methodologies to build structural models of protein complexes. Among the different physiological PPIs, protease-antiprotease interactions play a significant role. An imbalance between proteases and antiproteases is involved in many pathogenic reactions. This special class of PPI, therefore, needs a thorough scrutiny. There are different PPIs determining experimental tools. However, these tools are time-consuming and expensive. In response to these difficulties, a number of bioinformatic software tool have been developed. The algorithms are meant for prediction of three-dimensional structures of proteins as well as protein complexes. The structure prediction methods involve homology modeling, threading, and ab initio modeling. These methods have nearly 75%–80% overall accuracies. The other method is molecular docking which is meant to generate the three-dimensional conformations of protein complexes. The docking methods can broadly be classified as rigid body docking and flexible docking. In this chapter, the different aspects of experimental and computational modeling and docking strategies will be discussed. The basic terminologies will be revisited. This chapter is aimed at providing a firsthand knowledge on protein interaction methods using protease-antiprotease interactions as an example.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Lesk AM (2010) Introduction to protein science: artchitechture, function, and Genetics, 2nd Edition, Pg. no.: 17–38. Oxford University Press, New York

    Google Scholar 

  2. Branden C, Tooze A., (1998) Introduction to protein structure, 2nd edn. Garland Publishing Inc., New York, pp 373–392

    Google Scholar 

  3. Kessel A, Ben-Tal N (2010) Introduction to proteins: structure, function, and motion, 1st edn. Chapman & Hall CRC, Florida, pp 36–65

    Google Scholar 

  4. Whiteford D (2005) Proteins: structure and function, 1st edn. Wiley, Chichester, pp 189–244

    Google Scholar 

  5. Kurian J, Conforti B, Wemmer D (2012) The molecules of life: physical and chemical principles, 1st edn. Garland Science, New York, pp 530–787

    Google Scholar 

  6. Nelson DL, Cox MM (2012) Principles of biochemistry, 5th edn. W.H. Freemann & Company, New York, pp 157–237

    Google Scholar 

  7. Walsh G (2002) Proteins: biotechnology and biochemistry, 1st edn. Wiley, Chichester, pp 251–278

    Google Scholar 

  8. Creighton TE (1992) Proteins: structures and molecular properties, 2nd edn. W.H. Freemann & Company, New York

    Google Scholar 

  9. Park JS, Cochran JR (2009) Protein engineering and design, 1st edn. CRC Press, Florida, 131–150

    Google Scholar 

  10. Tropp BE (2011) Molecular biology: genes to proteins, 4th edn. Jones & Bartlett Learning, UK, pp 27–75

    Google Scholar 

  11. Greene CM, McEvanely NG (2009) Proteases and antiproteases in chronic neutrophilic lung disease – relevance to drug discovery. Br J Pharmacol 158:1048–1058

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Meyer M, Jaspers I (2015) Respiratory protease/antiprotease balance determines susceptibility to viral infection and can be modified by nutritional antioxidants. Am J Physiol Lung Cell Mol Physiol 308:L1189–L2010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hutchison DC (1987) The rôle of proteases and antiproteases in bronchial secretions. Eur J Respir Dis Suppl 153:78–85

    CAS  PubMed  Google Scholar 

  14. Testa V, Capasso G, Maffulli N et al (1994) Proteases and antiproteases in cartilage homeostasis. A brief review Clin Orthop Relat Res (308):79-84

    Google Scholar 

  15. Twigg MS, Brockbank S, Lowry P et al (2015) The role of serine proteases and Antiproteases in the cystic fibrosis lung. Mediat Inflamm 293053

    Google Scholar 

  16. Sandholm L (1986) Proteases and their inhibitors in chronic inflammatory periodontal disease. J Clin Periodontol 13:19–26

    Article  CAS  PubMed  Google Scholar 

  17. Hubbard RC, Crystal RG (1986) Antiproteases and antioxidants: strategies for the pharmacologic prevention of lung destruction. Respiration 50(Suppl 1):56–73

    CAS  PubMed  Google Scholar 

  18. Bourin M, Gautron J, Berges M et al (2012) Transcriptomic profiling of proteases and antiproteases in the liver of sexually mature hens in relation to vitellogenesis. BMC Genomics 13:457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kuhn, C 3rd (1986) The biochemical pathogenesis of chronic obstructive pulmonary diseases: protease-antiprotease imbalance in emphysema and diseases of the airways. J Thorac Imaging 1:1–6

    Google Scholar 

  20. Erickson S (1978) Proteases and protease inhibitors in chronic obstructive lung disease. Acta Med Scand 203:449–455

    Article  Google Scholar 

  21. Golemis E (2002) Protein-protein interactions: a molecular cloning manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor/New York, pp 1–50

    Google Scholar 

  22. Kerppola, T.K., (2008) Bimolecular fluorescence complementation: visualization of Molecular Interactions in Living Cells. Methods in Cell Biol 9:789–798

    Google Scholar 

  23. Bollag DM, Rozycki MD, Edelstein SJ (1996) Protein methods, 2nd edn. Wiley Publishers, New York, pp 1–83

    Google Scholar 

  24. Ausubel FM (1987) Current protocols in molecular biology. Wiley, New York/Boston, pp 15.1.1–15.1.14

    Google Scholar 

  25. Piehler J (2005) New methodologies for measuring protein interactions in vivo and in vitro. Current opinions in. Struct Biol 15:4–14

    CAS  Google Scholar 

  26. Puig O, Caspari F, Riquat G et al (2001) The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24:218–229

    Article  CAS  PubMed  Google Scholar 

  27. Rao VS, Srinivas K, Sujini GN et al (2014) Protein-protein interaction detection: methods and analysis. 147648

    Google Scholar 

  28. Braun, P. & Gingras., A.C. (2012) History of protein-protein interactions: from egg-white to complex networks. Proteomics 12: 1478–1498

    Google Scholar 

  29. Phizicky EM, Fields S (1995) Protein-protein interactions: methods for detection and analysis. Microbiol Rev 59:94–123

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Rigaut G, Shevchenko A, Rutz B et al (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol 17:1030–1032

    Article  CAS  PubMed  Google Scholar 

  31. Shoemaker BA, Panchenko AR (2007) Deciphering protein-protein interactions.Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3:e43

    Article  PubMed  PubMed Central  Google Scholar 

  32. Theofilatos K, Dimitrakopoulos C, Tsakalidis A et al (2011) Computational approaches for the prediction of protein-protein interactions-a survey. Curr Bioinforma 6:398–414

    Article  CAS  Google Scholar 

  33. Tuncbag N, Kar G, Keskin O et al (2009) A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform 10:217–232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Xiaoli L., Wu M, Chee-Kewong K et al (2010) Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics;11.

    Google Scholar 

  35. Skrabanek L, Saini HK, Bader GD et al (2008) Computational prediction of protein-protein interactions. Mol Biotechnol 38:1–17

    Article  CAS  PubMed  Google Scholar 

  36. Bader G et al (2003) BIND the biomolecular interaction network database. Nucleic Acids Res 31:248–250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Chatr-aryamontri A et al (2007) MINT the molecular INTeraction database. Nucleic Acids Res 35(Database):D572–D574

    Article  CAS  PubMed  Google Scholar 

  38. Peri S et al (2004) Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 32(Database issue):D497–D501

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Hermjakob L et al (2004) IntAct an open source molecular interaction database. Nucleic Acids Res 32:D452–D455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Breitkreutz BJ et al (2008) The BioGRID interaction database: 2008 update. Nucleic Acids Res 36(Database issue):D637–D640

    CAS  PubMed  Google Scholar 

  41. Puente XS, López-Otín C (2004) A genomic analysis of rat proteases and protease inhibitors. Genome Res 14:609–622

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Sims GK, Wander MM (2002) Proteolytic activity under nitrogen or sulfur limitation. Appl Soil Ecol 568:1–5

    Google Scholar 

  43. van der Hoorn RA (2008) Plant proteases: from phenotypes to molecular mechanisms. Annu Rev Plant Biol 59:191–223

    Article  PubMed  Google Scholar 

  44. Woessner, edited by Barrett AJ, Rawlings ND, Fred J (2004) Handbook of proteolytic enzymes, 3rd edn . London: Academic, Elsevier, pp 1–16

    Google Scholar 

  45. Oda K (2012) New families of carboxyl peptidases: serine-carboxyl peptidases and glutamic peptidases. J Biochem 151:13–25

    Article  CAS  PubMed  Google Scholar 

  46. Ofran Y, Rost B (2003a) Analysing six types of protein-protein interfaces. J Mol Biol 325:377–387

    Article  CAS  PubMed  Google Scholar 

  47. Bahadur RP, Chakrabarti P, Rodier F, Janin J (2004) A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 336:943–955

    Article  CAS  PubMed  Google Scholar 

  48. Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280:1–9

    Google Scholar 

  49. Keskin O, Ma B, Nussinov R (2005) Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol 345:1281–1294

    Article  CAS  PubMed  Google Scholar 

  50. Ofran Y, Rost B (2003b) Predicted protein-protein interaction sites from local sequence information. FEBS Lett 544:236–239

    Article  CAS  PubMed  Google Scholar 

  51. Sheinerman FB, Norel R, Honig B (2000) Electrostatic aspects of protein – protein interactions. Curr Opin Struct Biol:153–159

    Google Scholar 

  52. Schreiber G. (2002) Kinetic studies of protein – protein interactions.Curr. Opin. Struc. Bio.:41–7

    Google Scholar 

  53. Shenoy SR, Jayaram B (2010) Proteins: sequence to structure and function - Current status. Curr Protein Pept Sci 11:498–514

    Article  CAS  PubMed  Google Scholar 

  54. Nooren IM, Thornton JM (2003) Structural characterization and functional significance of transient protein-protein interactions. J Mol Biol 325:991–1018

    Article  CAS  PubMed  Google Scholar 

  55. Nooren IM (2003) New EMBO member’s review : diversity of protein-protein interactions. EMBO J 22:3486–3492

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Faisal M, Oliver JL, Kaattari SL (1999) Potential role of protease-anti-protease interactions in Perkinsus Marinus infection in Crassostrea sp. Bull Eur Ass Fish Pathol 19:269–276

    Google Scholar 

  57. Bradford JR, Needham CJ, Bulpitt AJ, Westhead DR (2006) Insights into protein-protein interfaces using a Bayesian network prediction method. J Mol Biol 362:365–386

    Article  CAS  PubMed  Google Scholar 

  58. Choong YS, Tye GJ, Lim TS (2013) Minireview: applied structural bioinformatics in proteomics. Protein J 32:505–511

    Article  CAS  PubMed  Google Scholar 

  59. Gallet X, Charloteaux B, Thomas a BR (2000) A fast method to predict protein interaction sites from sequences. J Mol Biol 302:917–926

    Article  CAS  PubMed  Google Scholar 

  60. Li JJ, Huang DS, Wang B, Chen P (2006) Identifying protein-protein interfacial residues in heterocomplexes using residue conservation scores. Int J Biol Macromol 38:241–247

    Article  CAS  PubMed  Google Scholar 

  61. Murakami Y, Mizuguchi K (2014) Homology-based prediction of interactions between proteins using averaged one-dependence estimators. BMC Bioinformatics 15:213

    Article  PubMed  PubMed Central  Google Scholar 

  62. Neuvirth H, Raz R, Schreiber G (2004) ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 338:181–199

    Article  CAS  PubMed  Google Scholar 

  63. Wang B, Chen P, Huang DS, Li JJ, Lok TM, Lyu MR (2006) Predicting protein interaction sites from residue spatial sequence profile and evolution rate. FEBS Lett 580:380–384

    Article  CAS  PubMed  Google Scholar 

  64. Lua RC, Marciano DC, Katsonis P, Adikesavan AK, Wilkins AD, Lichtarge O (2014) Prediction and redesign of protein–protein interactions. Prog Biophys Mol Biol 116:194–202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Lage K (2014) Protein-protein interactions and genetic diseases: the interactome. Biochim Biophys Acta Mol Basis Dis Elsevier BV 1842:1971–1980

    Article  CAS  Google Scholar 

  66. Cukuroglu E, Engin HB, Gursoy A, Keskin O (2014) Hot spots in protein-protein interfaces: towards drug discovery. Prog. Biophys Mol Biol Elsevier Ltd 1–9

    Google Scholar 

  67. Kobzar OL, Trush VV, Tanchuk VY, Zhilenkov AV, Troshin PA, Vovk AL (2014) Fullerene derivatives as a new class of inhibitors of protein tyrosine phosphatases. Bioorg Med Chem Lett Elsevier Ltd 24:3175–3179

    Article  CAS  Google Scholar 

  68. Kushwaha SK, Shakya M (2010) Protein interaction network analysis-approach for potential drug target identification in mycobacterium tuberculosis. J Theor Biol [internet]. Elsevier 262:284–294

    CAS  Google Scholar 

  69. You Z-H, Lei Y-K, Zhu L, Xia J, Wang B (2013) Prediction of protein-protein interactions from amino acid sequences with ensemble extreme learning machines and principal component analysis. BMC Bioinformatics. BioMed Central ltd 14. Suppl 8

    Google Scholar 

  70. Zahiri J, Yaghoubi O, Mohammad-Noori M, Ebrahimpour R, Masoudi-Nejad A (2013) PPIevo: protein-protein interaction prediction from PSSM based evolutionary information. Genomics Elsevier Inc 102:237–242

    CAS  Google Scholar 

  71. Pawson T, Nash P (2000) Protein-protein interactions define specificity in signal transduction. Genes Dev 14:1027–1047

    CAS  PubMed  Google Scholar 

Download references

Acknowledgment

The author would like to acknowledge the help rendered by the DBT-sponsored Bioinformatics Infrastructural Facility of the University of Kalyani. The author would also like to thank the Department of Biotechnology (DBT, India) for the financial support (SAN No. 102/IFD/SAN/1824/2015-2016). The author is grateful to the Virologie et Immunologie Moléculaires, INRA. UR892, Domaine de Vilvert 78352 Jouy-en-Josas, France, for the infrastructural support. The infrastructural help from the Department of Biochemistry and Biophysics, University of Kalyani, is duly acknowledged.

Author information

Authors and Affiliations

  1. Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, 741235, West Bengal, India

    Angshuman Bagchi

Authors
  1. Angshuman Bagchi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Angshuman Bagchi .

Editor information

Editors and Affiliations

  1. Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India

    Sajal Chakraborti

  2. St. Boniface Hospital Research Centre, University of Manitoba, Faculty of Health Sciences, College of Medicine, Institute of Cardiovascular Sciences, Manitoba, Winnipeg, Canada

    Naranjan S. Dhalla

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Nature Singapore Pte Ltd.

About this chapter

Cite this chapter

Bagchi, A. (2017). Protease-Antiprotease Interactions: An Overview of the Process from an “In Silico” Perspective. In: Chakraborti, S., Dhalla, N. (eds) Proteases in Physiology and Pathology. Springer, Singapore. https://doi.org/10.1007/978-981-10-2513-6_22

Download citation

Publish with us

Policies and ethics

Search

Navigation