Skip to main content
SpringerLink
Log in
Book cover

Fractal Symmetry of Protein Exterior pp 17–31Cite as

Characterization of Protein–Protein Interfaces, Considering Surface-Roughness and Local Shape

  • Chapter
  • First Online:

  • 563 Accesses

Part of the book series: SpringerBriefs in Biochemistry and Molecular Biology ((BRIEFSBIOCHEM))

Abstract

This chapter attempts to provide an account of works that have attempted to characterize protein–protein interaction interfaces, with fractal dimension. However, such characterization of interfaces is not solely dependent upon interface roughness. Without involving the biophysical factors, we will concentrate only on geometric characterization of these interfaces. To be specific, we will attempt to talk about a possible algorithm to quantify the changes in two parameters describing any protein–protein interaction interface; namely, the curvature of shape of protein–protein interaction interface and the surface roughness of it. One can connect these two parameters through a novel methodology, ‘extended unit iterated shuffle transformation’. Results show that although the interface patch for enzyme-inhibitor interaction is flatter and smoother than the non-interfacial surface patches, absolute magnitudes of shape curvatures and surface roughness of bound interfaces are greater than what they were in unbound states of concerned entities. Trends observed on antigen–antibody interfaces are found to be somewhat contradictory to the trends observed in case of enzyme-inhibitor interfaces. Antigen–antibody interfaces, like the enzyme-inhibitor interfaces, are found to be flatter and smoother than the non-interfacial surface patches. However, unlike the enzyme-inhibitor interfaces, absolute magnitudes of shape curvatures and surface roughness of bound antigen–antibody interfaces are observed to be less than what they were in unbound states of concerned entities. Algorithm proposed in the present work could quantify the effects due to changes in two extremely important interfacial parameters, through a unified scheme.

This is a preview of subscription content, 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   39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Learn about institutional subscriptions

References

  • Aqvist J, Tapia O (1987) Surface fractality as a guide for studying protein–protein interactions. J Mol Graph 5:30–34

    Article  Google Scholar 

  • Argos P (1988) An investigation of protein subunit and domain interfaces. Protein Eng 2:101–113

    Article  PubMed  CAS  Google Scholar 

  • Arkin M, Randal M, DeLano W, Hyde J, Luong T, Oslob J, Raphael D, Taylor L, Wang J, McDowell R, Wells J, Braisted A (2003) Binding of small molecules to an adaptive protein–protein interface. Proc Natl Acad Sci USA 100:1603–1608

    Article  PubMed  CAS  Google Scholar 

  • Bartlett GJ, Porter CT, Borkakoti N, Thornton JM (2002) Analysis of catalytic residues in enzyme active sites. J Mol Biol 324:105–121

    Article  PubMed  CAS  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H (2000) Shindyalov i.n., bourne p.e., the protein data bank. Nucleic Acids Res 28(1):235–242

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Bowman RL (1995) Fractal metamorphosis: a brief student tutorial. Comput Graph 19(1):157–164

    Article  Google Scholar 

  • Bradford JR, Westhead DR (2005) Improved prediction of protein–protein binding sites using a support vector machines approach. Bioinformatics 21(8):1487–1494

    Article  PubMed  CAS  Google Scholar 

  • Chen R, Weng Z (2003) A novel shape complementarity scoring function for protein–protein docking, PROTEINS: structure. Funct Genet 51:397–408

    Article  CAS  Google Scholar 

  • Chothia C, Janin J (1975) Principles of protein–protein recognition. Nature 256:705–708

    Article  PubMed  CAS  Google Scholar 

  • Connolly ML (1986) Measurement of protein surface shape by solid angles. J Mol Graph 4:3–6

    Article  CAS  Google Scholar 

  • DeLano WL, Ultsch MH, de Vos AM, Wells JA (2000) Convergent solution to binding at a protein–protein interface. Science 287:1279–1283

    Article  PubMed  CAS  Google Scholar 

  • DeLano WL (2002) Unraveling hot spots in binding interfaces: progress and challenges. Curr Opin Struct Biol 12:14–20

    Article  PubMed  CAS  Google Scholar 

  • Dewey TG (1994) Fractal analysis of proton exchange kinetics in lysozyme. Proc Natl Acad Sci USA 91:12101–12104

    Article  PubMed  CAS  Google Scholar 

  • Fujimoto T, Chiba N (2004) Fractal deformation using displacement vectors and their increasing rates based on extended unit iterated shuffle transformation, “Thinking in patterns: fractals and related phenomena in nature”. World Scientific, Ed. Miroslav M Novak, pp 57–68

    Book  Google Scholar 

  • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003) Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 331:281–299

    Article  PubMed  CAS  Google Scholar 

  • Holliday GL, Almonacid DE, Bartlett GJ, O’Boyle NM, Torrance JW, Murray-Rust P, Mitchell JBO, Thornton JM (2007) MACiE (mechanism, annotation and classification in enzymes): novel tools for searching catalytic mechanisms. Nucleic Acids Res 35:D515–D520

    Article  PubMed  CAS  Google Scholar 

  • Hutchinson JE (1981) Fractals and self similarity. Indiana Univ Math J 30:713–747

    Article  Google Scholar 

  • Islam SA, Weaver DL (1991) Variation of folded polypeptide surface area with probe size. Proteins Struct Funct Genet 10(4):300–314

    Article  PubMed  CAS  Google Scholar 

  • Janin J (1995) Principles of protein–protein recognition from structure to thermodynamics. Biochimie 77:497–505

    Article  PubMed  CAS  Google Scholar 

  • Janin J (1997) Specific versus non-specific contacts in protein crystals. Nat Struct Biol 4:973–974

    Article  PubMed  CAS  Google Scholar 

  • Jefferson E, Walsh T, Barton G (2006) Biological units and their effect upon the properties and prediction of protein–protein interactions. J Mol Biol 364:1118–1129

    Article  PubMed  CAS  Google Scholar 

  • Joachimiak LA, Kortemme T, Stoddard BL, Baker D (2006) Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein–protein interface. J Mol Biol 361:195–208

    Article  PubMed  CAS  Google Scholar 

  • Jones S, Thornton JM (1996) Principles of protein–protein interactions. Proc Natl Acad Sci USA 93:13–20

    Article  PubMed  CAS  Google Scholar 

  • Jones S, Thornton JM (1997) Analysis of protein–protein interaction sites using surface patches. J Mol Biol 272:121–132

    Article  PubMed  CAS  Google Scholar 

  • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 89:2195–2199

    Article  PubMed  CAS  Google Scholar 

  • Keskin O, Mab B, Nussinov R (2005) Hot Regions in Protein–Protein Interactions: The Organization and Contribution of Structurally Conserved Hot Spot Residues. J Mol Biol 345(5):1281–1294

    Article  PubMed  CAS  Google Scholar 

  • Kuhlmann UC, Pommer AJ, Moore GR, James R, Kleanthous C (2000) Specificity in protein–protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes. J Mol Biol 301:1163–1178

    Article  PubMed  CAS  Google Scholar 

  • Lawrence MC, Colman PM (1993) Shape complementarity at protein–protein interfaces. J Mol Biol 234:946–950

    Article  PubMed  CAS  Google Scholar 

  • Lewis M, Rees DC (1985) Fractal surfaces of proteins. Science 230:1163–1165

    Article  PubMed  CAS  Google Scholar 

  • Li X, Keskin O, Ma B, Nussinov R, Liang J (2004) Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol 344:781–795

    Article  PubMed  CAS  Google Scholar 

  • Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations, Protein Sci 11:184–197

    Google Scholar 

  • Nagle JK (1990) atomic polarizability and electronegativity. J Am Chem Soc 112(12):4741–4747

    Article  CAS  Google Scholar 

  • Nooren IMA, Thornton JM (2003) Structural characterisation and functional significance of transient protein–protein interactions. J Mol Biol 325:991–1018

    Article  PubMed  CAS  Google Scholar 

  • Noorizadeh S, Parhizgara M (2005) The atomic and group compressibility. J Mol Str Theochem 725(1–3):23–26

    Article  CAS  Google Scholar 

  • Novotný J, Handschumacher M, Haber E, Bruccoleri RE, Carlson WB, Fanning DW, Smith JA, Rose GD (1986) Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains). Proc Natl Acad Sci USA 83(2):226–230

    Article  PubMed  Google Scholar 

  • Pfeifer P, Welz U, Wippermann H (1985) Fractal surface dimension of proteins: lysozyme. Chem Phys Lett 113:535–540

    Article  CAS  Google Scholar 

  • Rajamani D, Thiel S, Vajda S, Camacho CJ (2004) Anchor residues in protein–protein interactions. Proc Natl Acad Sci USA 101:11287–11292

    Article  PubMed  CAS  Google Scholar 

  • Sederberg TW, Parry SR (1986) Free-form deformation of solid geometric models. ACM Comput Graph 20(4):151–160

    Article  Google Scholar 

  • Smith GR, Sternberg MJE, Bates PA (2005) The relationship between the flexibility of proteins and their conformational states on forming protein–protein complexes with an application to protein–protein docking. J Mol Biol 347:1077–1101

    Article  PubMed  CAS  Google Scholar 

  • Todd A, Orengo C, Thornton J (2002) Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10:1435–1451

    Article  PubMed  CAS  Google Scholar 

  • Yogurtcu ON, Erdemli SB, Nussinov R, Turkay M, Keskin O (2008) Restricted mobility of conserved residues in protein–protein interfaces in molecular simulations. Biophys J 94:3475–3485

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Bioinformatics Centre, University of Pune, Pune, 411007, India

    Anirban Banerji

Authors
  1. Anirban Banerji
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anirban Banerji .

Rights and permissions

Reprints and permissions

Copyright information

© 2013 The Author(s)

About this chapter

Cite this chapter

Banerji, A. (2013). Characterization of Protein–Protein Interfaces, Considering Surface-Roughness and Local Shape. In: Fractal Symmetry of Protein Exterior. SpringerBriefs in Biochemistry and Molecular Biology. Springer, Basel. https://doi.org/10.1007/978-3-0348-0654-1_2

Download citation

Publish with us

Policies and ethics

Search

Navigation