Skip to main content
SpringerLink
Log in

Protein-Protein Interaction and Macromolecular Visualization

  • Chapter
Bioinformatics: A Concept-Based Introduction

  • 2908 Accesses

Abstract

Large-scale prediction and understanding of protein-protein interaction is important to elucidate biological function. Protein interactions play a key role in signaling pathways, transportation, and other structural/functional roles in a cell. Several experimental and theoretical methods have been developed to predict a protein’s interacting partners. Protein-protein docking is also gaining importance. A brief introduction to visualization tools for proteins is provided here.

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 39.99
Price excludes VAT (USA)
  • Available as 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
Hardcover Book
USD 54.99
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Archakov, A. I., Govorun, V. M., Dubanov, A. V., Ivanov, Y. D., Veselovsky, A. V., Lewi, P., and Janssen, P. (2003). Protein-protein interactions as a target for drugs in proteomics, ProteinSci1 3, 190–202.

    Google Scholar 

  • Bader, G. D., Betel, D., and Hogue, C. W. (2003). BIND: the Biomolecular Interaction Network Database, Nucleic Acids Res 31, 248–50.

    Article  PubMed  CAS  Google Scholar 

  • Bahadur, R. P., Chakrabarti, P., Rodier, F., and Janin, J. (2003). Dissecting subunit interfaces in homodimeric proteins, Proteins 53, 708–19.

    Article  PubMed  CAS  Google Scholar 

  • Bogan, A. A., and Thorn, K. S. (1998). Anatomy of hot spots in protein interfaces, J Mol Biol 280, 1–9.

    Article  PubMed  CAS  Google Scholar 

  • Brinda, K. V., Kannan, N., and Vishveshwara, S. (2002). Analysis of homodimeric protein interfaces by graph-spectral methods, Protein Eng 75, 265–77.

    Article  Google Scholar 

  • Caffrey, D. R, Somaroo, S., Hughes, J. D., Mintseris, I, and Huang, E. S. (2004). Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Sci 13, 190–202.

    Article  PubMed  CAS  Google Scholar 

  • Chakrabarti, P., and Janin, J. (2002). Dissecting protein-protein recognition sites, Proteins >47, 334–43.

    Article  PubMed  CAS  Google Scholar 

  • Chambers, J., Ames, R. S., Bergsma, D., Muir, A., Fitzgerald, L. R., Hervieu, G., Dytko, G. M., Foley, J. J., Martin, J., Liu, W. S., et al. (1999). Melanin-concentrating hormone is the cognate ligand for the orphan G-protein-coupled receptor SLC-1, Nature 400, 261–5.

    Article  PubMed  CAS  Google Scholar 

  • Chothia, C, and Janin, J. (1975). Principles of protein-protein recognition, Nature 256, 705–8.

    Article  PubMed  CAS  Google Scholar 

  • Dandekar, T., Snel, B., Huynen, M., and Bork, P. (1998). Conservation of gene order: a fingerprint of proteins that physically interact, Trends Biochem Sci 23, 324–8.

    Article  PubMed  CAS  Google Scholar 

  • Dasgupta, S., Iyer, G. H., Bryant, S. H., Lawrence, C. E., and Bell, J. A. (1997). Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers, Proteins 28, 494—514.

    Article  PubMed  CAS  Google Scholar 

  • Davies, D. R, and Cohen, G. H. (1996). Interactions of protein antigens with antibodies, Proc Natl Acad Sci U S A 93, 7–12.

    Article  PubMed  CAS  Google Scholar 

  • de Vos, A. M., Ultsch, M., and Kossiakoff, A. A. (1992). Human growth hormone and extracellular domain of its receptor: crystal structure of the complex, Science 255, 306–12.

    Article  PubMed  Google Scholar 

  • Dill, K. A. (1990). Dominant forces in protein folding, Biochemistry 29, 7133–55.

    Article  PubMed  CAS  Google Scholar 

  • Eisenberg, D., Marcotte, E. M., Xenarios, I., and Yeates, T. O. (2000). Protein function in the post-genomic era, Nature 405, 823–6.

    Article  PubMed  CAS  Google Scholar 

  • Enright, A. J., Iliopoulos, I., Kyrpides, N. C, and Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events, Nature 402, 86–90.

    Article  PubMed  CAS  Google Scholar 

  • Fryxell, K. J. (1996). The coevolution of gene family trees, Trends Genet 12, 364–9.

    Article  PubMed  CAS  Google Scholar 

  • Gavin, A. C, Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., et al. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature 415, 141–7.

    Article  PubMed  CAS  Google Scholar 

  • Glaser, F., Steinberg, D. M., Vakser, I. A., and Ben-Tal, N. (2001). Residue frequencies and pairing preferences at protein-protein interfaces, Proteins 43, 89–102.

    Article  PubMed  CAS  Google Scholar 

  • Goh, C. S., Bogan, A. A., Joachimiak, M., Walther, D., and Cohen, F. E. (2000). Co-evolution of proteins with their interaction partners, J Mol Biol 299, 283–93.

    Article  PubMed  CAS  Google Scholar 

  • Guinto, E. R., and Di Cera, E. (1996). Large heat capacity change in a protein-monovalent cation interaction, Biochemistry 35, 8800–4.

    Article  PubMed  CAS  Google Scholar 

  • Halperin, I., Wolfson, H., and Nussinov, R. (2004). Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking, Structure 12, 1027–38.

    Article  PubMed  CAS  Google Scholar 

  • Harpaz, Y., Gerstein, M., and Chothia, C. (1994). Volume changes on protein folding, Structure 2, 641–9.

    Article  PubMed  CAS  Google Scholar 

  • Hirakawa, H., Muta, S., and Kuhara, S. (1999). The hydrophobic cores of proteins predicted by wavelet analysis, Bioinformatics 75, 141–8.

    Article  Google Scholar 

  • Hsu, S. Y., Nakabayashi, K., Nishi, S., Kumagai, J., Kudo, M., Sherwood, O. D., and Hsueh, A. J. (2002). Activation of orphan receptors by the hormone relaxin, Science 295, 671–4.

    Article  PubMed  CAS  Google Scholar 

  • Hughes, A. L., and Yeager, M. (1999). Coevolution of the mammalian chemokines and their receptors, Immunogenetics 49, 115–24.

    Article  PubMed  CAS  Google Scholar 

  • Hurley, J. H., Thorsness, P. E., Ramalingam, V., Helmers, N. H., Koshland, D. E., Jr., and Stroud, R. M. (1989). Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase, Proc Natl Acad Sci U S A 86, 8635–9.

    Article  PubMed  CAS  Google Scholar 

  • Huynen, M., Snel, B., Lathe, W., 3rd, and Bork, P. (2000). Predicting protein function by genomic context: quantitative evaluation and qualitative inferences, Genome Res 10, 1204-10

    Article  PubMed  CAS  Google Scholar 

  • Ippolito, J. A., Alexander, R. S., and Christianson, D. W. (1990). Hydrogen bond stereochemistry in protein structure and function, J Mol Biol 215, 457–71.

    Article  PubMed  CAS  Google Scholar 

  • Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome, Proc Natl Acad Sci U S A 98, 4569–74.

    Article  PubMed  CAS  Google Scholar 

  • Janin, J., and Chothia, C. (1990). The structure of protein-protein recognition sites, J Biol Chem 265, 16027–30.

    PubMed  CAS  Google Scholar 

  • Janin, J., Miller, S., and Chothia, C. (1988). Surface, subunit interfaces and interior of oligomeric proteins, J Mol Biol 204, 155–64.

    Article  PubMed  CAS  Google Scholar 

  • Jones, S., Marin, A., and Thornton, J. M. (2000). Protein domain interfaces: characterization and comparison with oligomeric protein interfaces, Protein Eng 13, 77—82.

    Article  PubMed  CAS  Google Scholar 

  • Jones, S., and Thornton, J. M. (1995). Protein-protein interactions: a review of protein dimer structures, Prog Biophys Mol Biol 63, 31–65.

    Article  PubMed  CAS  Google Scholar 

  • Jones, S., and Thornton, J. M. (1996). Principles of protein-protein interactions, Proc Natl Acad Sci U S A 93, 13–20.

    Article  PubMed  CAS  Google Scholar 

  • Jones, S., and Thornton, J. M. (1997). Prediction of protein-protein interaction sites using inter faces, J Mol Biol 234, 946–50.

    Google Scholar 

  • Keskin, O., Ma, B., and Nussinov, R. (2005). Hot regions in protein-protein interactions: the organization and contribution of structurally conserved hot spot residues, J Mol Biol 345, 1281–94.

    Article  PubMed  CAS  Google Scholar 

  • Koretke, K. K., Lupas, A. N., Warren, P. V., Rosenberg, M., and Brown, J. R. (2000). Evolution of two-component signal transduction, Mol Biol Evol 17, 1956–70.

    PubMed  CAS  Google Scholar 

  • Korn, A. P., and Burnett, R. M. (1991). Distribution and complementarity of hydropathy in multisubunit proteins, Proteins 9, 37–55.

    Article  PubMed  CAS  Google Scholar 

  • Larsen, T. A., Olson, A. J., and Goodsell, D. S. (1998). Morphology of protein-protein interfaces, Structure 6, 421–7.

    Article  PubMed  CAS  Google Scholar 

  • Lawrence, M. C, and Colman, P. M. (1993). Shape complementarity at protein/protein interfaces, J Mol Biol 234, 946–50.

    Article  PubMed  CAS  Google Scholar 

  • Lichtarge, O., Bourne, H. R., and Cohen, F. E. (1996). An evolutionary trace method defines binding surfaces common to protein families, J Mol Biol 257, 342—58.

    Article  PubMed  CAS  Google Scholar 

  • Lijnzaad, P., and Argos, P. (1997). Hydrophobic patches on protein subunit interfaces: characteristics and prediction, Proteins 28, 333–43.

    Article  PubMed  CAS  Google Scholar 

  • Lockless, S. W., and Ranganathan, R. (1999). Evolutionarily conserved pathways of energetic connectivity in protein families, Science 286, 295–9.

    Article  PubMed  CAS  Google Scholar 

  • Lo Conte, L., Chothia, C, and Janin, J. (1999). The atomic structure of protein-protein recognition sites, J Mol Biol 285, 2177–98.

    Google Scholar 

  • Ma, B., Elkayam, T., Wolfson, H., and Nussinov, R. (2003). Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces, Proc Natl Acad Sci U S A 100, 5772–7.

    Article  PubMed  CAS  Google Scholar 

  • Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences, Science 285, 751–3.

    Article  PubMed  CAS  Google Scholar 

  • Mellor, J. C, Yanai, I., Clodfelter, K. H., Mintseris, J., and DeLisi, C. (2002). Predictome: a database of putative functional links between proteins, Nucleic Acids Res 30, 306–9.

    Article  PubMed  CAS  Google Scholar 

  • Meyer, M., Wilson, P., and Schomburg, D. (1996). Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking, J Mol Biol 264, 199–210.

    Article  PubMed  CAS  Google Scholar 

  • Miller, S., Lesk, A. M., Janin, J., and Chothia, C. (1987). The accessible surface area and stability of oligomeric proteins, Nature 328, 834–6.

    Article  PubMed  CAS  Google Scholar 

  • Musafia, B., Buchner, V., and Arad, D. (1995). Complex salt bridges in proteins: statistical analysis of structure and function, J Mol Biol 254, 761–70.

    Article  PubMed  CAS  Google Scholar 

  • Neuvirth, H., Raz, R., and Schreiber, G. (2004). ProMate: a structure based prediction program to identify the location of protein-protein binding sites, J Mol Biol 338, 181–99.

    Article  PubMed  CAS  Google Scholar 

  • Nicholls, A., Sharp, K. A., and Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons, Proteins 11, 281–96.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Novotny, J., and Sharp, K. (1992). Electrostatic fields in antibodies and antibody/antigen complexes, Prog Biophys Mol Biol 58, 203–24.

    Article  PubMed  CAS  Google Scholar 

  • Overbeek, R., Fonstein, M., D’Souza, M., Pusch, G. D., and Maltsev, N. (1999). The use of gene clusters to infer functional coupling, Proc Natl Acad Sci U S A 96, 2896–901.

    Article  PubMed  CAS  Google Scholar 

  • Pazos, F., and Valencia, A. (2001). Similarity of phylogenetic trees as indicator of protein-protein interaction, Protein Eng 14, 609–14.

    Article  PubMed  CAS  Google Scholar 

  • Pazos, F., and Valencia, A. (2002). In silico two-hybrid system for the selection of physically interacting protein pairs, Proteins 47, 219–27.

    Article  PubMed  CAS  Google Scholar 

  • Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc Natl Acad Sci U S A 96, 4285–8.

    Article  PubMed  CAS  Google Scholar 

  • Pruitt, K. D., and Maglott, D. R. (2001). RefSeq and LocusLink: NCBI gene-centered resources, Nucleic Acids Res 29, 137–40.

    Article  PubMed  CAS  Google Scholar 

  • Rajamani, D., Thiel, S., Vajda, S., and Camacho, C. J. (2004). Anchor residues in protein-protein interactions, Proc Natl Acad Sci U S A101, 11287–92.

    Article  PubMed  CAS  Google Scholar 

  • Roberts, V. A., Freeman, H. C, Olson, A. I, Tainer, J. A., and Getzoff, E. D. (1991). Electrostatic orientation of the electron-transfer complex between plastocyanin and cytochrome c, JBiol Chem 266, 13431–41.

    CAS  Google Scholar 

  • Russell, R. B., Alber, F., Aloy, P., Davis, F. P., Korkin, D., Pichaud, M., Topf, M., and Sali, A. (2004). A structural perspective on protein-protein interactions, Curr Opin Struct Biol 74, 313–24.

    Article  CAS  Google Scholar 

  • Rzhetsky, A., Iossifov, I., Koike, T., Krauthammer, M., Kra, P., Morris, M., Yu, H., Duboue, P. A., Weng, W., Wilbur, W. J., et al. (2004). GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data, J Biomed Inform 37, 43–53.

    Article  PubMed  CAS  Google Scholar 

  • Saito, Y., Nothacker, H. P., Wang, Z., Lin, S. H., Leslie, F., and Civelli, O. (1999). Molecular characterization of the melanin-concentrating-hormone receptor, Nature 400, 265–9.

    Article  PubMed  CAS  Google Scholar 

  • Sprinzak, E., and Margalit, H. (2001). Correlated sequence-signatures as markers of protein-protein interaction, J Mol Biol 311, 681–92.

    Article  PubMed  CAS  Google Scholar 

  • Stanfield, R. L., Takimoto-Kamimura, M., Rini, J. M., Profy, A. T., and Wilson, I. A. (1993). Major antigen-induced domain rearrangements in an antibody, Structure 1, 83–93.

    Article  PubMed  CAS  Google Scholar 

  • Stickle, D. F., Presta, L. G., Dill, K. A., and Rose, G. D. (1992). Hydrogen bonding in globular proteins, J Mol Biol 226, 1143–59.

    Article  PubMed  CAS  Google Scholar 

  • Stites, W. E. (1997). Proteinminus signProtein Interactions: Interface Structure, Binding Thermodynamics, and Mutational Analysis, Chem Rev 97, 1233–1250.

    Article  PubMed  CAS  Google Scholar 

  • Tong, A. H., Evangelista, M., Parsons, A. B., Xu, H., Bader, G. D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C. W., Bussey, H., et al. (2001). Systematic genetic analysis with ordered arrays of yeast deletion mutants, Science 294, 2364–8.

    Article  PubMed  CAS  Google Scholar 

  • Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, I, Berriz, G. F., Brost, R. L., Chang, M., et al. (2004). Global mapping of the yeast genetic interaction network, Science 303, 808–13.

    Article  PubMed  CAS  Google Scholar 

  • Tsai, C. J., Lin, S. L., Wolfson, H. J., and Nussinov, R. (1997). Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect, Protein Sci 6, 53–64.

    Article  PubMed  CAS  Google Scholar 

  • Tsai, C. J., and Nussinov, R. (1997). Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association, Protein Sci 6, 1426–37.

    Article  PubMed  CAS  Google Scholar 

  • Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae, Nature 403, 623–7.

    Article  PubMed  CAS  Google Scholar 

  • Valdar, W. S., and Thornton, J. M. (2001). Conservation helps to identify biologically relevant crystal contacts, J Mol Biol 313, 399–416.

    Article  PubMed  CAS  Google Scholar 

  • Wells, J. A. (1996). Binding in the growth hormone receptor complex, Proc Natl Acad Sci U S A 93, 1–6.

    Article  PubMed  CAS  Google Scholar 

  • Wilson, I. A., and Stanfield, R. L. (1994). Antibody-antigen interactions: new structures and new conformational changes, Curr Opin Struct Biol 4, 857–67.

    Article  PubMed  CAS  Google Scholar 

  • Xu, D., Tsai, C. J., and Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces, Protein Eng 10, 999–1012.

    Article  PubMed  CAS  Google Scholar 

  • Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M., and Cesareni, G. (2002). MINT: a Molecular INTeraction database, FEBS Lett 513, 135–40.

    Article  PubMed  CAS  Google Scholar 

  • Zhou, H. X., and Shan, Y. (2001). Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins 44, 336–43.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. University of Texas at Austin, USA

    Arun Ramani

  2. Roskamp Institute, 2040 Whitfield Avenue, Sarasota, Florida 34243, USA

    Venkatarajan S. Mathura

  3. Nanyang Technological University, Singapore

    Cui Zhanhua

  4. Biomedical Informatics, Pondicherry, India

    Pandjassarame Kangueane

Authors
  1. Arun Ramani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Venkatarajan S. Mathura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Cui Zhanhua
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Pandjassarame Kangueane
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Roskamp Institute, 2040 Whitfield Avenue, Sarasota, FL 34243

    Venkatarajan S. Mathura

  2. Biomed-Informatics, 17A Main Road, Irulan Chandai Annex, Pondicherry 607 402, India

    Pandjassarame Kangueane

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Ramani, A., Mathura, V.S., Zhanhua, C., Kangueane, P. (2009). Protein-Protein Interaction and Macromolecular Visualization. In: Mathura, V.S., Kangueane, P. (eds) Bioinformatics: A Concept-Based Introduction. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-84870-9_7

Download citation

Publish with us

Policies and ethics

Search

Navigation