Hostname: page-component-f554764f5-246sw Total loading time: 0 Render date: 2025-04-10T00:55:42.502Z Has data issue: false hasContentIssue false
  • English
  • Français

Protein–protein interaction and quaternary structure

Published online by Cambridge University Press:  24 September 2008

Joël Janin ,
Ranjit P. Bahadur  and
Pinak Chakrabarti
Joël Janin*
Affiliation:
Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Université Paris-Sud, Orsay, France
Ranjit P. Bahadur
Affiliation:
School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
Pinak Chakrabarti
Affiliation:
Department of Biochemistry, Bose Institute, Calcutta, India
*
*Author for correspondence: J. Janin, Yeast Structural Genomics, IBBMC UMR 8619 Université Paris-Sud, 91405 Orsay, France. Tel.: +33 1 69 15 79 66; Fax: +33 1 69 85 37 15; Email: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Protein–protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein–protein complexes, oligomeric proteins, viral capsids and protein–nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 41 , Issue 2 , May 2008 , pp. 133 - 180
Copyright
Copyright © 2008 Cambridge University Press

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Article purchase

Temporarily unavailable

References

Alber, F., Dokudovskaya, S., Veenhoff, L. M., Zhang, W., Kipper, J., Devos, D., Suprapto, A., Karni-Schmidt, O., Williams, R., Chait, B. T., Sali, A. & Rout, M. P. (2007). The molecular architecture of the nuclear pore complex. Nature 450, 695–701.CrossRefGoogle ScholarPubMed
Alberts, B. (1998). The cell as a collection of protein machines: preparing the next generation of molecular biologists. Cell 92, 291–294.CrossRefGoogle ScholarPubMed
Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A. C., Bork, P., Superti-Furga, G., Serrano, L. & Russell, R. B. (2004). Structure-based assembly of protein complexes in yeast. Science 303, 2026–2029.CrossRefGoogle ScholarPubMed
Aloy, P., Ceulemans, H., Stark, A. & Russell, R. B. (2003). The relationship between sequence and interaction divergence in proteins. Journal of Molecular Biology 332, 989–998.CrossRefGoogle ScholarPubMed
Aloy, P., Pichaud, M. & Russell, R. B. (2005). Protein complexes: structure prediction challenges for the 21st century. Current Opinion in Structural Biology 15, 15–22.CrossRefGoogle ScholarPubMed
Aloy, P. & Russell, R. B. (2003). InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 19, 161–162.CrossRefGoogle ScholarPubMed
Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A. et al. (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Research 29, 37–40.CrossRefGoogle ScholarPubMed
Argos, P. (1988). An investigation of protein subunit and domain interfaces. Protein Engineering 2, 101–113.CrossRefGoogle ScholarPubMed
Armon, A., Graur, D. & Ben-Tal, N. (2001). ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface-mapping of phylogenetic Information. Journal of Molecular Biology 307, 447–463.CrossRefGoogle ScholarPubMed
Aurenhammer, F. (1987). Power diagrams: properties, algorithms and applications. SIAM Journal on Computing 16, 78–96.CrossRefGoogle Scholar
Bahadur, R. P., Chakrabarti, P., Rodier, F. & Janin, J. (2003). Dissecting subunit interfaces in homodimeric proteins. Proteins 53, 708–719.CrossRefGoogle ScholarPubMed
Bahadur, R. P., Chakrabarti, P., Rodier, F. & Janin, J. (2004). A dissection of specific and non-specific protein–protein interfaces. Journal of Molecular Biology 336, 943–955.CrossRefGoogle ScholarPubMed
Bahadur, R. P. & Janin, J. (2008). Residue conservation in viral capsid assembly. Proteins 71, 407–414.CrossRefGoogle ScholarPubMed
Bahadur, R. P., Rodier, F. & Janin, J. (2007). A dissection of the protein–protein interfaces in icosahedral virus capsids. Journal of Molecular Biology 367, 574–590.CrossRefGoogle ScholarPubMed
Bahadur, R. P., Zacharias, M. & Janin, J. (2008). Dissecting protein–RNA sites. Nucleic Acids Research 26, 2705–2716.CrossRefGoogle Scholar
Baldwin, J. & Chothia, C. (1979). Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism. Journal of Molecular Biology 129, 175–220.CrossRefGoogle ScholarPubMed
Ban, Y. E. A., Edelsbrunner, H. & Rudolph, J. (2004). Interface surfaces for protein–protein complexes. In Proceedings of the Eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), pp. 205–212. San Diego, CA.CrossRefGoogle Scholar
Benesch, J. L. & Robinson, C. V. (2006). Mass spectrometry of macromolecular assemblies: preservation and dissociation. Current Opinion in Structural Biology 16, 245–251.CrossRefGoogle ScholarPubMed
Berchanski, A., Segal, D. & Eisenstein, M. (2005). Modeling oligomers with C n or D n symmetry: application to CAPRI target 10. Proteins 60, 202–206.CrossRefGoogle ScholarPubMed
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research 28, 235–242.CrossRefGoogle ScholarPubMed
Bernauer, J., Bahadur, R. P., Rodier, F., Janin, J. & Poupon, A. (2008). DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions. Bioinformatics 24, 652–658.CrossRefGoogle ScholarPubMed
Bhat, T. N., Bentley, G. A., Boulot, G., Greene, M. I., Tello, D., Dall'Acqua, W., Souchon, H., Schwarz, F. P., Mariuzza, R. A. & Poljak, R. J. (1994). Bound water molecules and conformational stabilization help mediate an antigen–antibody association. Proceedings of the National Academy of Sciences USA 91, 1089–1093.CrossRefGoogle ScholarPubMed
Birtalan, S., Zhang, Y., Fellouse, F. A., Shao, L., Schaefer, G. & Sidhu, S. S. (2008). The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. Journal of Molecular Biology 377, 1518–1528.CrossRefGoogle Scholar
Block, P., Paern, J., Hüllermeier, E., Sanschagrin, P., Sotriffer, C. A. & Klebe, G. (2006). Physicochemical descriptors to discriminate protein–protein interactions in permanent and transient complexes selected by means of machine learning algorithms. Proteins 65, 607–622.CrossRefGoogle ScholarPubMed
Bode, W., Wei, A. Z., Huber, R., Meyer, E., Travis, J. & Neumann, S. (1986). X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor. EMBO Journal 5, 2453–2458.CrossRefGoogle ScholarPubMed
Bogan, A. A. & Thorn, K. S. (1998). Anatomy of hot spots in protein interfaces. Journal of Molecular Biology 280, 1–9.CrossRefGoogle ScholarPubMed
Braden, B. C. & Poljak, R. J. (2000). Structure and energetics of anti-lysozome antibodies. In Protein–protein recognition (ed. Kleanthous, C.), pp. 126–161. Oxford University Press.CrossRefGoogle Scholar
Bradley, P., Misura, K. M. & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868–1871.CrossRefGoogle ScholarPubMed
Bressanelli, S., Stiasny, K., Allison, S. L., Stura, E. A., Duquerroy, S., Lescar, J., Heinz, F. X. & Rey, F. A. (2004). Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO Journal 23, 728–738.CrossRefGoogle ScholarPubMed
Caffrey, D., Somaroo, S., Hughes, J., Mintseris, J. & Huang, E. (2004). Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science 13, 190–202.CrossRefGoogle Scholar
Carugo, O. & Argos, P. (1997). Protein–protein crystal-packing contacts. Protein Science 6, 2261–2263.CrossRefGoogle ScholarPubMed
Carugo, O. & Pongor, S. (2001). A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Science 10, 1470–1473.CrossRefGoogle ScholarPubMed
Caspar, D. L. (1980). Movement and self-control in protein assemblies. Quasi-equivalence revisited. Biophysical Journal 10, 103–135.CrossRefGoogle Scholar
Caspar, D. L. & Klug, A. (1962). Physical principles in the construction of regular viruses. Cold Spring Harbor Symposia on Quantitative Biology 27, 1–24.CrossRefGoogle ScholarPubMed
Cazals, F., Proust, F., Bahadur, R. P. & Janin, J. (2006). Revisiting the Voronoi description of protein–protein interfaces. Protein Science 15, 2082–2092.CrossRefGoogle ScholarPubMed
Chakrabarti, P. & Janin, J. (2002). Dissecting protein–protein recognition sites. Proteins 47, 334–343.CrossRefGoogle ScholarPubMed
Chakravarty, S. & Varadarajan, R. (1999). Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7, 723–732.CrossRefGoogle ScholarPubMed
Chaudhury, S., Sircar, A., Sivasubramanian, A., Berrondo, M. & Gray, J. J. (2007). Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12. Proteins 69, 793–800.CrossRefGoogle ScholarPubMed
Chen, H. & Skolnick, J. (2008). M-TASSER: an algorithm for protein quaternary structure prediction. Biophysical Journal 94, 918–928.CrossRefGoogle ScholarPubMed
Chothia, C. (1974). Hydrophobic bonding and accessible surface area in proteins. Nature 248, 338–339.CrossRefGoogle ScholarPubMed
Chothia, C. & Janin, J. (1975). Principles of protein–protein recognition. Nature 256, 705–708.CrossRefGoogle ScholarPubMed
Clackson, T. & Wells, J. A. (1995). A hot spot of binding energy in a hormone–receptor interface. Science 267, 383–386.CrossRefGoogle Scholar
Comeau, S. R., Gatchell, D. W., Vajda, S. & Camacho, C. J. (2004). ClusPro: a fully automated algorithm for protein–protein docking. Nucleic Acids Research 32, W96–W99.CrossRefGoogle ScholarPubMed
Connolly, M. L. (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709–713.CrossRefGoogle ScholarPubMed
Copley, R. R., Ponting, C. P., Schultz, J. & Bork, P. (2002). Sequence analysis of multidomain proteins: past perspectives and future directions. Advances in Protein Chemistry 61, 75–98.CrossRefGoogle ScholarPubMed
Crick, F. H. & Watson, J. D. (1956). Structure of small viruses. Nature 177, 473–475.CrossRefGoogle ScholarPubMed
Crosio, M. P., Janin, J. & Jullien, M. (1992). Crystal packing in six crystal forms of pancreatic ribonuclease. Journal of Molecular Biology 228, 243–251.CrossRefGoogle ScholarPubMed
Crowley, P. B. & Carrondo, M. A. (2004). The architecture of the binding site in redox protein complexes: implications for the fast dissociation. Proteins 55, 603–612.CrossRefGoogle ScholarPubMed
Darnall, D. W. & Klotz, I. M. (1975). Subunit constitution of proteins: a table. Archives of Biochemistry and Biophysics 166, 651–682.CrossRefGoogle ScholarPubMed
Das, R., Qian, B., Raman, S., Vernon, R., Thompson, J., Bradley, P., Khare, S., Tyka, M. D., Bhat, D., Chivian, D., Kim, D. E., Sheffler, W. H., Malmström, L., Wollacott, A. M., Wang, C., Andre, I. & Baker, D. (2007). Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 69, 118–128.CrossRefGoogle ScholarPubMed
Dasgupta, S., Iyer, G. H., Bryant, S. H., Lawrence, C. E. & Bell, J. A. (1997). Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers. Proteins 28, 494–514.3.0.CO;2-A>CrossRefGoogle ScholarPubMed
de Vries, S. J., van Dijk, A. D., Krzeminski, M., van Dijk, M., Thureau, A., Hsu, V., Wassenaar, T. & Bonvin, A. M. (2007). HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. Proteins 69, 726–733.CrossRefGoogle ScholarPubMed
DeLano, W. L. (2002). Unraveling hot spots in binding interfaces: progress and challenges. Current Opinion in Structural Biology 12, 14–20.CrossRefGoogle ScholarPubMed
Dokland, T. (2000). Freedom and restraint: themes in virus assembly. Structure 8, R157–R162.CrossRefGoogle Scholar
Dokland, T., Bernal, R. A., Burch, A., Pletnev, S., Fane, B. A. & Rossmann, M. G. (1999). The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174. Journal of Molecular Biology 288, 595–608.CrossRefGoogle ScholarPubMed
Dominguez, C., Boelens, R. & Bonvin, A. M. (2003). HADDOCK: a protein–protein docking approach based on biochemical or biophysical information. Journal of the American Chemical Society 125, 1731–1737.CrossRefGoogle ScholarPubMed
Dupuis, F., Sadoc, J., Jullien, R., Angelov, B. & Mornon, J. P. (2005). Voro3D: 3D Voronoi tesselation applied to protein structures. Bioinformatics 21, 1715–1716.CrossRefGoogle ScholarPubMed
Dutta, S. & Berman, H. M. (2005). Large macromolecular complexes in the Protein Data Bank: a status report. Structure 13, 381–388.CrossRefGoogle Scholar
Edelsbrunner, H. & Mucke, E. P. (1994). Three-dimensional alpha-shapes. ACM Transactions on Graphics 13, 43–72.CrossRefGoogle Scholar
Eisenberg, D., Marcotte, E. M., Xenarios, I. & Yeates, T. O. (2000). Protein function in the post-genomic era. Nature 405, 823–826.CrossRefGoogle ScholarPubMed
Elcock, A. & McCammon, J. (2001). Identification of protein oligomerization states by analysis of interface conservation. Proceedings of the National Academy of Sciences USA 98, 2990–2994.CrossRefGoogle ScholarPubMed
Ellis, J. J., Broom, M. & Jones, S. (2007). Protein–RNA interactions: structural analysis and functional classes. Proteins 66, 903–911.CrossRefGoogle ScholarPubMed
Ellis, J. J. & Jones, S. (2008). Evaluating conformational changes in protein structures binding RNA. Proteins 70, 1518–1526.CrossRefGoogle ScholarPubMed
Finn, R. D., Marshall, M. & Bateman, A. (2005). iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions. Bioinformatics 21, 410–412.CrossRefGoogle ScholarPubMed
Fu, H.(Ed.) (2004). Protein–Protein Interactions: Methods in Molecular Biology, vol. 261, 532 pp. Totowa NJ: Humana Press.CrossRefGoogle Scholar
Gabb, H. A., Jackson, R. M. & Sternberg, M. J. (1997). Modelling protein docking using shape complementarity, electrostatics and biochemical information. Journal of Molecular Biology 272, 106–120.CrossRefGoogle ScholarPubMed
Gao, Y., Douguet, D., Tovchigrechko, A. & Vakser, I. A. (2007). DOCKGROUND system of databases for protein recognition studies: unbound structures for docking. Proteins 69, 845–851.CrossRefGoogle ScholarPubMed
Gavin, A. C., Aloy, P., Grandi, P., Krause, R. et al. (2006). Proteome survey reveals modularity of the yeast cell machinery. Nature 440, 631–636.CrossRefGoogle ScholarPubMed
Gellatly, B. J. & Finney, J. L. (1982). Calculation of protein volumes: an alternative to the Voronoi procedure. Journal of Molecular Biology 161, 305–322.CrossRefGoogle Scholar
Gerstein, M. & Chothia, C. (1996). Packing at the protein–water interface. Proceedings of the National Academy of Sciences USA 93, 10167–10172.CrossRefGoogle ScholarPubMed
Gerstein, M., Tsai, J. & Levitt, M. (1995). The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. Journal of Molecular Biology 249, 955–966.CrossRefGoogle ScholarPubMed
Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B. et al. (2003). A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736.CrossRefGoogle ScholarPubMed
Glaser, F., Steinberg, D. M., Vakser, I. A. & Ben-Tal, N. (2001). Residue frequencies and pairing preferences at protein–protein interfaces. Proteins 43, 89–102.3.0.CO;2-H>CrossRefGoogle ScholarPubMed
Goodsell, D. S. & Olson, A. J. (2000). Structural symmetry and protein function. Annual Review of Biophysics and Biomolecular Structure 29, 105–153.CrossRefGoogle ScholarPubMed
Gray, J. (2006). High-resolution protein–protein docking. Current Opinion in Structural Biology 16, 150–169.CrossRefGoogle ScholarPubMed
Gray, J. J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C. A. & Baker, D. (2003). Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology 331, 281–299.CrossRefGoogle ScholarPubMed
Grimes, J. M., Burroughs, J. N., Gouet, P., Diprose, J. M., Malby, R., Ziéntara, S., Mertens, P. P. & Stuart, D. I. (1998). The atomic structure of the bluetongue virus core. Nature 395, 470–478.CrossRefGoogle ScholarPubMed
Grimm, V., Zhang, Y. & Skolnick, J. (2006). Benchmarking of dimeric threading and structure refinement. Proteins 63, 457–465.CrossRefGoogle ScholarPubMed
Grünberg, R., Nilges, M. & Leckner, J. (2006). Flexibility and conformational entropy in protein–protein binding. Structure 14, 683–693.CrossRefGoogle ScholarPubMed
Guharoy, M. & Chakrabarti, P. (2005). Conservation and relative importance of residues across protein–protein interfaces. Proceedings of the National Academy of Sciences USA 102, 15447–15452.CrossRefGoogle ScholarPubMed
Guharoy, M. & Chakrabarti, P. (2007). Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein–protein interactions. Bioinformatics 15, 1909–1918.CrossRefGoogle Scholar
Hadfield, A. T., Lee, W., Zhao, R., Oliveira, M. A., Minor, I., Rueckert, R. R. & Rossmann, M. G. (1997). The refined structure of human rhinovirus 16 at 2.15 Å resolution: implications for the viral life cycle. Structure 5, 427–441.CrossRefGoogle ScholarPubMed
Halperin, I., Ma, B., Wolfson, H. & Nussinov, R. (2002). Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47, 409–443.CrossRefGoogle Scholar
Halperin, I., Wolfson, H. & Nussinov, R. (2004). Protein–protein interactions: coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure 12, 1027–1038.CrossRefGoogle ScholarPubMed
Halperin, I., Wolfson, H. & Nussinov, R. (2006). Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin–Dockerin families. Proteins 63, 832–845.CrossRefGoogle Scholar
Harpaz, Y., Gerstein, M. & Chothia, C. (1994). Volume changes on protein folding. Structure 2, 641–649.CrossRefGoogle ScholarPubMed
Harrison, S. C., Olson, A. J., Schutt, C. E., Winkler, F. K. & Bricogne, G. (1978). Tomato bushy stunt virus at 2·9 Å resolution. Nature 276, 368–373.CrossRefGoogle ScholarPubMed
Headd, J. J., Ban, Y. E., Brown, P., Edelsbrunner, H., Vaidya, M. & Rudolph, J. (2007). Protein–protein interfaces: properties, preferences, and projections. Journal of Proteome Research 6, 2576–2586.CrossRefGoogle ScholarPubMed
Henrick, K. & Thornton, J. M. (1998). PQS: a protein quaternary structure file server. Trends in Biochemical Sciences 23, 358–361.CrossRefGoogle ScholarPubMed
Hubbard, S. J. & Argos, P. (1994). Cavities and packing at protein interfaces. Protein Science 3, 2194–2206.CrossRefGoogle ScholarPubMed
Hwang, H., Pierce, B., Mintseris, J., Janin, J. & Weng, Z. (2008). Protein–protein docking benchmark version 3.0. Proteins [Epub ahead of print] May 19.CrossRefGoogle ScholarPubMed
Inbar, Y., Benyamini, H., Nussinov, R. & Wolfson, H. J. (2005). Prediction of multimolecular assemblies by multiple docking. Journal of Molecular Biology 349, 435–447.CrossRefGoogle ScholarPubMed
Janin, J. (1997). Specific versus non-specific contacts in protein crystals. Nature Structural & Molecular Biology 4, 973–974.CrossRefGoogle ScholarPubMed
Janin, J. (1999). Wet and dry interfaces: the role of solvent in protein–protein and protein–DNA recognition. Structure Fold Design 7, R277–R279.CrossRefGoogle ScholarPubMed
Janin, J. (2005). Assessing predictions of protein–protein interaction: the CAPRI experiment. Protein Science 14, 278–283.CrossRefGoogle ScholarPubMed
Janin, J. (2007). Structural genomics: winning the second half of the game. Structure 15, 1347–1349.CrossRefGoogle ScholarPubMed
Janin, J. & Chothia, C. (1976). Stability and specificity of protein–protein interactions: the case of the trypsin–trypsin inhibitor complexes. Journal of Molecular Biology 100, 197–211.CrossRefGoogle ScholarPubMed
Janin, J. & Chothia, C. (1990). The structure of protein–protein recognition sites. Journal of Biological Chemistry 265, 16027–16030.CrossRefGoogle ScholarPubMed
Janin, J., Henrick, K., Moult, J., Eyck, L. T., Sternberg, M. J., Vajda, S., Vakser, I. & Wodak, S. J. (2003). CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 52, 2–9.CrossRefGoogle Scholar
Janin, J., Miller, S. & Chothia, C. (1988). Surface, subunit interfaces and interior of oligomeric proteins. Journal of Molecular Biology 204, 155–164.CrossRefGoogle ScholarPubMed
Janin, J. & Rodier, F. (1995). Protein–protein interaction at crystal contacts. Proteins 23, 580–587.CrossRefGoogle ScholarPubMed
Janin, J., Rodier, F., Chakrabarti, P. & Bahadur, R. P. (2007). Macromolecular recognition in the Protein Data Bank. Acta Crystallographica. Section D, Biological Crystallography 63, 1–8.CrossRefGoogle ScholarPubMed
Janin, J. & Wodak, S. J.(Eds.) (2003). Protein Modules and Protein–Protein Interaction: Advances in Protein Chemistry, vol. 61, 333 pp. San Diego, LondonAcademic Press.Google Scholar
Janin, J. & Wodak, S. (2007). The third CAPRI assessment meeting. Structure 15, 755–759.CrossRefGoogle ScholarPubMed
Johnson, J. E. & Speir, J. A. (1997). Quasi-equivalent viruses: a paradigm for protein assemblies. Journal of Molecular Biology 269, 665–675.CrossRefGoogle ScholarPubMed
Jones, S., Daley, D., Luscombe, N., Berman, H. M. & Thornton, J. M. (2001). Protein–RNA interactions: a structural analysis. Nucleic Acids Research 29, 943–954.CrossRefGoogle ScholarPubMed
Jones, S. & Thornton, J. M. (1995). Protein–protein interactions: a review of protein dimer structures. Progress in Biophysics and Molecular Biology 63, 31–65.CrossRefGoogle ScholarPubMed
Jones, S. & Thornton, J. M. (1996). Principles of protein–protein interactions. Proceedings of the National Academy of Sciences USA 93, 13–20.CrossRefGoogle ScholarPubMed
Jones, S. & Thornton, J. M. (1997). Analysis of protein–protein interaction sites using surface patches. Journal of Molecular Biology 272, 121–132.CrossRefGoogle ScholarPubMed
Jones, S. & Thornton, J. M. (2000). Analysis and classification of protein–protein interactions from a structural perspective. In Protein–Protein Recognition, Frontiers in Molecular Biology, vol. 31 (ed. Kleanthous, C.), pp. 33–59. New York: Oxford University Press.CrossRefGoogle Scholar
Jones, S., van Heyningen, P., Berman, H. M. & Thornton, J. M. (1999). Protein–DNA interactions: a structural analysis. Journal of Molecular Biology 287, 877–896.CrossRefGoogle ScholarPubMed
Juan, D., Pazos, F. & Valencia, A. (2008). Co-evolution and co-adaptation in protein networks. FEBS Letters 582, 1225–1230.CrossRefGoogle ScholarPubMed
Kelly, C. A., Nishiyama, M., Ohnishi, Y., Beppu, T. & Birktoft, J. J. (1993). Determinants of protein thermostability observed in the 1.9-Å crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. Biochemistry 32, 3913–3922.CrossRefGoogle ScholarPubMed
Keskin, O., Bahar, I., Badretdinov, A. Y., Ptitsyn, O. B. & Jernigan, R. L. (1998). Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Science 7, 2578–2586.CrossRefGoogle ScholarPubMed
Keskin, O., Ma, B. & Nussinov, R. (2005). Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues. Journal of Molecular Biology 345, 1281–1294.CrossRefGoogle ScholarPubMed
Kleanthous, C.ed. (2000). Protein–Protein Recognition: Frontiers in Molecular Biology, 314 pp., New York: Oxford University Press.CrossRefGoogle Scholar
Krissinel, E. & Henrick, K. (2007). Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology 372, 774–797.CrossRefGoogle ScholarPubMed
Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A. P., Punna, T., Peregrín-Alvarez, J. M., Shales, M., Zhang, X., Davey, M., Robinson, M. D., Paccanaro, A., Bray, J. E., Sheung, A., Beattie, B., Richards, D. P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M. M., Vlasblom, J., Wu, S., Orsi, C., Collins, S. R., Chandran, S., Haw, R., Rilstone, J. J., Gandi, K., Thompson, N. J., Musso, G., St Onge, P., Ghanny, S., Lam, M. H., Butland, G., Altaf-Ul, A. M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J. S., Ingles, C. J., Hughes, T. R., Parkinson, J., Gerstein, M., Wodak, S. J., Emili, A. and Greenblatt, J. F. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637–643.CrossRefGoogle ScholarPubMed
Krol, M., Chaleil, R. A., Tournier, A. L. & Bates, P. A. (2007). Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 69, 750–757.CrossRefGoogle ScholarPubMed
Lambright, D. G., Sondek, J., Bohm, A., Skiba, N. P., Hamm, H. E. & Sigler, P. B. (1996). The 2·0 Å crystal structure of a heterotrimeric G protein. Nature 379, 311–319.CrossRefGoogle ScholarPubMed
Larsen, T. A., Olson, A. J. & Goodsell, D. S. (1998). Morphology of protein–protein interfaces. Structure 6, 421–427.CrossRefGoogle ScholarPubMed
Laskowski, R. A. (1995). SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Journal of Molecular Graphics 13, 323–330.CrossRefGoogle ScholarPubMed
Lawrence, M. C. & Colman, P. M. (1993). Shape complementarity at protein/protein interfaces. Journal of Molecular Biology 234, 946–950.CrossRefGoogle ScholarPubMed
Lee, B. K. & Richards, F. M. (1971). The interpretation of protein structures: estimation of static accessibility. Journal of Molecular Biology 55, 379–400.CrossRefGoogle ScholarPubMed
Leiman, P. G., Kanamaru, S., Mesyanzhinov, V. V., Arisaka, F. & Rossmann, M. G. (2003). Structure and morphogenesis of bacteriophage T4. Cellular and Molecular Life Sciences 60, 2356–2370.CrossRefGoogle ScholarPubMed
Lensink, M. F., Méndez, R. & Wodak, S. J. (2007). Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 69, 704–718.CrossRefGoogle ScholarPubMed
Lévy, E. D. (2007). PiQSi: protein quaternary structure investigation. Structure 15, 1364–1367.CrossRefGoogle ScholarPubMed
Lévy, E. D., Erba, E. B., Robinson, C. V. & Teichmann, S. A. (2008). Assembly reflects evolution of protein complexes. Nature 453, 1262–1265.CrossRefGoogle ScholarPubMed
Lévy, E. D., Pereira-Leal, J. B., Chothia, C. & Teichmann, S. A. (2006). 3D complex: a structural classification of protein complexes. PLoS Computational Biology 2, e155.CrossRefGoogle ScholarPubMed
Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P. O., Han, J. D., Chesneau, A., Hao, T., Goldberg, D. S., Li, N., Martinez, M., Rual, J. F., Lamesch, P., Xu, L., Tewari, M., Wong, S. L., Zhang, L. V., Berriz, G. F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H. W., Elewa, A., Baumgartner, B., Rose, D. J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S. E., Saxton, W. M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K. C., Harper, J. W., Cusick, M. E., Roth, F. P., Hill, D. E. & Vidal, M. (2004). A map of the interactome network of the metazoan C. elegans. Science 303, 540–543.CrossRefGoogle ScholarPubMed
Li, Y., Huang, Y., Swaminathan, C. P., Smith-Gill, S. J. & Mariuzza, R. A. (2005). Magnitude of the hydrophobic effect at central versus peripheral sites in protein–protein interfaces. Structure 13, 297–307.CrossRefGoogle ScholarPubMed
Lichtarge, O., Bourne, H. & Cohen, F. (1996). An evolutionary trace method defines binding surfaces common to protein families. Journal of Molecular Biology, 257, 342–358.CrossRefGoogle ScholarPubMed
Lichtarge, O. & Sowa, M. (2002). Evolutionary predictions of binding surfaces and interactions. Current Opinion in Structural Biology 12, 21–27.CrossRefGoogle ScholarPubMed
Liljas, L. (1999). Virus assembly. Current Opinion in Structural Biology 9, 129–134.CrossRefGoogle ScholarPubMed
Liljas, L., Unge, T., Jones, T. A., Fridborg, K., Lövgren, S., Skoglund, U. & Strandberg, B. (1982). Structure of satellite tobacco necrosis virus at 3.0 Å resolution. Journal of Molecular Biology 159, 93–108.CrossRefGoogle ScholarPubMed
Linderström-Lang, K. U. & Schellman, J. A. (1959). Protein structure and enzyme activity. In The Enzymes, vol. 1, 2nd edn (eds. Boyer, D., Lardy, H & Myrback, K.), pp. 443–510. New York: Academic Press.Google Scholar
Lo Conte, L., Chothia, C. & Janin, J. (1999). The atomic structure of protein–protein recognition sites. Journal of Molecular Biology 285, 2177–2198.CrossRefGoogle ScholarPubMed
Ma, B., Elkayam, T., Wolfson, H. & Nussinov, R. (2003). Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proceedings of the National Academy of Sciences USA 100, 5772–5777.CrossRefGoogle ScholarPubMed
Marshall, G. R. & Vakser, I. A. (2005). Protein–protein docking methods. In Proteomics and Protein–Protein Interaction: Biology, Chemistry, Bioinformatics, and Drug Design (ed.Waksman, G.), pp. 115–146. New York: Springer.CrossRefGoogle Scholar
May, A. & Zacharias, M. (2007). Protein–protein docking in CAPRI using ATTRACT to account for global and local flexibility. Proteins 69, 774–780.CrossRefGoogle ScholarPubMed
McDonald, I. K. & Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology 238, 777–793.CrossRefGoogle ScholarPubMed
Méndez, R., Leplae, R., De Maria, L. & Wodak, S. J. (2003). Assessment of blind predictions of protein–protein interactions: current status of docking methods. Proteins 52, 51–67.CrossRefGoogle ScholarPubMed
Méndez, R., Leplae, R., Lensink, M. F. & Wodak, S. J. (2005). Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures. Proteins 60, 150–169.CrossRefGoogle ScholarPubMed
Mihalek, I., Res, I. & Lichtarge, O. (2006). Evolutionary trace report_maker: a new type of service for comparative analysis of proteins. Bioinformatics 22, 1656–1657.CrossRefGoogle Scholar
Mihalek, I., Res, I. & Lichtarge, O. (2007). On itinerant water molecules and detectability of protein–protein interfaces through comparative analysis of homologues. Journal of Molecular Biology 369, 584–595.CrossRefGoogle ScholarPubMed
Miller, S., Janin, J., Lesk, A. M. & Chothia, C. (1987). Interior and surface of monomeric proteins. Journal of Molecular Biology 196, 641–656.CrossRefGoogle ScholarPubMed
Mintseris, J., Pierce, B., Wiehe, K., Anderson, R., Chen, R. & Weng, Z. (2007). Integrating statistical pair potentials into protein complex prediction. Proteins 69, 511–520.CrossRefGoogle ScholarPubMed
Mintseris, J. & Weng, Z. (2005). Structure, function and evolution of transient and obligate protein–protein interactions. Proceedings of the National Academy of Sciences USA 102, 10930–10935.CrossRefGoogle ScholarPubMed
Monod, J., Changeux, J. P. & Jacob, F. (1963). Allosteric proteins and cellular control systems. Journal of Molecular Biology 6, 306–329.CrossRefGoogle ScholarPubMed
Monod, J., Wyman, J. & Changeux, J. P. (1965). On the nature of allosteric transitions: a plausible model. Journal of Molecular Biology 12, 88–118.CrossRefGoogle ScholarPubMed
Moont, G., Gabb, H. A. & Sternberg, M. J. E. (1999). Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 35, 364–373.3.0.CO;2-4>CrossRefGoogle ScholarPubMed
Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. Journal of Molecular Biology 247, 536–540.CrossRefGoogle ScholarPubMed
Nadassy, K., Tomas-Oliveira, I., Alberts, I., Janin, J. & Wodak, S. J. (2001). Standard atomic volumes in double-stranded DNA and packing of protein–DNA interfaces. Nucleic Acids Research 29, 3362–3376.CrossRefGoogle ScholarPubMed
Nadassy, K., Wodak, S. & Janin, J. (1999). Structural features of protein–nucleic acid recognition sites. Biochemistry 38, 1999–2017.CrossRefGoogle ScholarPubMed
Nicholls, A., Sharp, K. A. & Honig, B. (1991). Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296.CrossRefGoogle ScholarPubMed
Noreen, I. M. & Thornton, J. M. (2003a). Diversity of protein–protein interactions. EMBO Journal 22, 3486–3492.CrossRefGoogle Scholar
Noreen, I. M. & Thornton, J. M. (2003b). Structural characterisation and functional significance of transient protein–protein interactions. Journal of Molecular Biology 325, 991–1018.CrossRefGoogle Scholar
Ofran, Y. & Rost, B. (2003). Analysing six types of protein–protein interfaces. Journal of Molecular Biology 325, 377–387.CrossRefGoogle ScholarPubMed
Ofran, Y. & Rost, B. (2007). ISIS: interaction sites identified from sequence. Bioinformatics 23, e13–e16.CrossRefGoogle ScholarPubMed
Pal, A., Chakrabarti, P., Bahadur, R., Rodier, F. & Janin, J. (2007). Peptide segments in protein–protein interfaces. Journal of Biosciences 32, 101–111. Erratum in Journal of Biosciences 2007 32, 805.CrossRefGoogle ScholarPubMed
Pauling, L. & Corey, R. B. (1951). Configuration of polypeptide chains. Nature 168, 550–551.CrossRefGoogle ScholarPubMed
Pazos, F. & Valencia, A. (2002). In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 47, 219–227.CrossRefGoogle ScholarPubMed
Perutz, M. F. (1960). Structure of hemoglobin. Brookhaven Symposia in Biology 13, 165–183.Google ScholarPubMed
Perutz, M. F. (1970). Stereochemistry of cooperative effects in haemoglobin. Nature 228, 726–739.CrossRefGoogle ScholarPubMed
Peschard, P., Kozlov, G., Lin, T., Mirza, I. A., Berghuis, A. M., Lipkowitz, S., Park, M. & Gehring, K. (2007). Structural basis for ubiquitin-mediated dimerization and activation of the ubiquitin protein ligase Cbl-b. Molecular Cell 27, 474–485.CrossRefGoogle ScholarPubMed
Pierce, B., Tong, W. & Weng, Z. (2005). M-ZDOCK: a grid-based approach for C n symmetric multimer docking. Bioinformatics 21, 1472–1478.CrossRefGoogle ScholarPubMed
Ponstingl, H., Henrick, K. & Thornton, J. M. (2000). Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 41, 47–57.3.0.CO;2-8>CrossRefGoogle ScholarPubMed
Ponstingl, H., Kabir, T., Gorse, D. & Thornton, J. M. (2005). Morphological aspects of oligomeric protein structures. Progress in Biophysics and Molecular Biology 89, 9–35.CrossRefGoogle ScholarPubMed
Ponstingl, H., Kabir, T. & Thornton, J. M. (2003). Automatic inference of protein quaternary structure from crystals. Journal of Applied Crystallography 36, 1116–1122.CrossRefGoogle Scholar
Pontius, J., Richelle, J. & Wodak, S. J. (1996). Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology 264, 121–136.CrossRefGoogle ScholarPubMed
Poole, A. M. & Ranganathan, R. (2006). Knowledge-based potentials in protein design. Current Opinion in Structural Biology 16, 508–513.CrossRefGoogle ScholarPubMed
Poupon, A. (2004). Voronoi and Voronoi-related tessellations in studies of protein structure and interaction. Current Opinion in Structural Biology 14, 233–241.CrossRefGoogle ScholarPubMed
Poupon, A. & Janin, J. (in press). Analysis and prediction of protein quaternary structure. In Biological Data Mining, Methods in Molecular Biology (ed. Carugo, O.), (In press). Totowa, NJ: Humana Press.Google Scholar
Prevelige, P. E. Jr., Thomas, D. & King, J. (1993). Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells. Biophysical Journal 64, 824–835.CrossRefGoogle ScholarPubMed
Reddy, V. S., Giesing, H. A., Morton, R. T., Kumar, A., Post, C. B., Brooks, C. L. 3rd & Johnson, J. E. (1998). Energetics of quasiequivalence: computational analysis of protein–protein interactions in icosahedral viruses. Biophysical Journal 74, 546–558.CrossRefGoogle ScholarPubMed
Reichmann, D., Rahat, O., Albeck, S., Meged, R., Dym, O. & Schreiber, G. (2005). The modular architecture of protein–protein binding interfaces. Proceedings of the National Academy of Sciences USA 102, 57–62.CrossRefGoogle ScholarPubMed
Reichmann, D., Rahat, O., Cohen, M., Neuvirth, H. & Schreiber, G. (2007). The molecular architecture of protein–protein binding sites. Current Opinion in Structural Biology 17, 67–76.CrossRefGoogle ScholarPubMed
Res, I. & Lichtarge, O. (2005). Character and evolution of protein–protein interfaces. Physical Biology 2, S36–S43.CrossRefGoogle ScholarPubMed
Richards, F. M. (1974). The interpretation of protein structures: total volume, group volume distributions and packing density. Journal of Molecular Biology 82, 1–14.CrossRefGoogle ScholarPubMed
Robinson, C. V., Sali, A. & Baumeister, W. (2007). The molecular sociology of the cell. Nature 450, 973–982.CrossRefGoogle ScholarPubMed
Rodier, F., Bahadur, R. P., Chakrabarti, P. & Janin, J. (2005). Hydration of protein–protein interfaces. Proteins 60, 36–45.CrossRefGoogle ScholarPubMed
Rossmann, M. G., Arnold, E., Erickson, J. W., Frankenberger, E. A., Griffith, J. P., Hecht, H. J., Johnson, J. E., Kamer, G., Luo, M., Mosser, A. G., Rueckert, R. R., Sherry, B. & Vriend, G. (1985). Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317, 145–153.CrossRefGoogle ScholarPubMed
Rossmann, M. G. & Johnson, J. E. (1989). Icosahedral RNA virus structure. Annual Review of Biochemistry 58, 533–573.CrossRefGoogle ScholarPubMed
Russell, R. B., Alber, F., Aloy, P., Davis, F. P., Korkin, D., Pichaud, M., Topf, M. & Sali, A. (2004). A structural perspective on protein–protein interactions. Current Opinion in Structural Biology 14, 313–324.CrossRefGoogle ScholarPubMed
Saha, R. P., Bahadur, R. P. & Chakrabarti, P. (2005). Interresidue contacts in proteins and protein–protein interfaces and their use in characterizing the homodimeric interface. Journal of Proteome Research 4, 1600–1609.CrossRefGoogle ScholarPubMed
Saha, R. P., Bahadur, R. P., Pal, A., Mandal, S. & Chakrabarti, P. (2006). ProFace: a server for the analysis of the physicochemical features of protein–protein interfaces. BMC Structural Biology 6, 11.CrossRefGoogle ScholarPubMed
Sali, A. (1998). 100 000 protein structures for the biologist. Nature Structural Biology 5, 1029–1032.CrossRefGoogle Scholar
Sander, C. & Schneider, R. (1993). The HSSP data base of protein structure–sequence alignments. Nucleic Acids Research 21, 3105–3109.CrossRefGoogle ScholarPubMed
Sanger, F. & Thompson, E. O. (1953). The amino-acid sequence in the glycyl chain of insulin. I. The identification of lower peptides from partial hydrolysates. Biochemical Journal 53, 353–366.CrossRefGoogle ScholarPubMed
Sarai, A. & Kono, H. (2005). Protein–DNA recognition patterns and predictions. Annual Review of Biophysics and Biomolecular Structure 34, 379–398.CrossRefGoogle ScholarPubMed
Scheffzek, K., Ahmadian, M. R., Kabsch, W., Wiesmüller, L., Lautwein, A., Schmitz, F. & Wittinghofer, A. (1997). The Ras–RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants. Science 277, 333–338.CrossRefGoogle ScholarPubMed
Schnackenberg, J., Than, M. E., Mann, K., Wiegand, G., Huber, R. & Reuter, W. (1999). Amino acid sequence, crystallization and structure determination of reduced and oxidized cytochrome c6 from the green alga Scenedesmus obliquus. Journal of Molecular Biology 290, 1019–1030.CrossRefGoogle ScholarPubMed
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. & Wolfson, H. J. (2005a). Geometry-based flexible and symmetric protein docking. Proteins 60, 224–231.CrossRefGoogle ScholarPubMed
Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. & Wolfson, H. J. (2005b). PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Research 33, W363–W367.CrossRefGoogle ScholarPubMed
Schreiber, G. & Fersht, A. R. (1993). Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering. Biochemistry 32, 5145–5150.CrossRefGoogle ScholarPubMed
Schreiber, G., Shaul, Y. & Gottschalk, K. E. (2006). Electrostatic design of protein–protein association rates. Methods in Molecular Biology 340, 235–249.Google ScholarPubMed
Schueler-Furman, O., Wang, C., Bradley, P., Misura, K. & Baker, D. (2005). Progress in modeling of protein structures and interactions. Science 310, 638–642.CrossRefGoogle ScholarPubMed
Sheinerman, F. B., Norel, R. & Honig, B. (2000). Electrostatic aspects of protein–protein interactions. Current Opinion in Structural Biology 10, 153–159.CrossRefGoogle ScholarPubMed
Shepherd, C. M., Borelli, I. A., Lander, G., Natarajan, P., Siddavanahalli, V., Bajaj, C., Johnson, J. E., Brooks, C. L. 3rd & Reddy, V. S. (2006). VIPERdb: a relational database for structural virology. Nucleic Acids Research 34, D386–D389.CrossRefGoogle ScholarPubMed
Smith, G. R. & Sternberg, M. J. (2002). Prediction of protein–protein interactions by docking methods. Current Opinion in Structural Biology 12, 28–35.CrossRefGoogle ScholarPubMed
Soyer, A., Chomilier, J., Mornon, J. P., Jullien, R. & Sadoc, J. (2000). Voronoi tesselation reveals the condensed matter character of folded proteins. Physical Review Letters 85, 3532–3535.CrossRefGoogle ScholarPubMed
Stein, A., Russell, R. B. & Aloy, P. (2005). 3did: interacting protein domains of known three-dimensional structure. Nucleic Acids Research 33, D413–D417.CrossRefGoogle ScholarPubMed
Steven, A. C., Heymann, J. B., Cheng, N., Trus, B. L. & Conway, J. F. (2005). Virus maturation: dynamics and mechanism of a stabilizing structural transition that leads to infectivity. Current Opinion in Structural Biology 15, 227–236.CrossRefGoogle ScholarPubMed
Steven, A. C., Trus, B. L., Booy, F. P., Cheng, N., Zlotnick, A., Caston, J. R. & Conway, J. F. (1997). The making and breaking of symmetry in virus capsid assembly: glimpses of capsid biology from cryoelectron microscopy. FASEB Journal 11, 733–742.CrossRefGoogle ScholarPubMed
Stock, D., Gibbons, C., Arechaga, I., Leslie, A. G. & Walker, J. E. (2000). The rotary mechanism of ATP synthase. Current Opinion in Structural Biology 10, 672–679.CrossRefGoogle ScholarPubMed
Stock, D., Leslie, A. G. & Walker, J. E. (1999). Molecular architecture of the rotary motor in ATP synthase. Science 286, 1700–1705.CrossRefGoogle ScholarPubMed
Stockley, P. G., Rolfsson, O., Thompson, G. S., Basnak, G., Francese, S., Stonehouse, N. J., Homans, S. W. & Ashcroft, A. E. (2007). A simple, RNA-mediated allosteric switch controls the pathway to formation of a T=3 viral capsid. Journal of Molecular Biology 369, 541–552.CrossRefGoogle ScholarPubMed
Sundberg, E. J. & Mariuzza, R. A. (2002). Molecular recognition in antibody–antigen complexes. Advances in Protein Chemistry 61, 119–160.CrossRefGoogle ScholarPubMed
Sundberg, E. J., Urrutia, M., Braden, B. C., Isern, J., Tsuchiya, D., Fields, B. A., Malchiodi, E. L., Tormo, J., Schwarz, F. P. & Mariuzza, R. A. (2000). Estimation of the hydrophobic effect in an antigen–antibody protein–protein interface. Biochemistry 39, 15375–15387.CrossRefGoogle Scholar
Svedberg, T. (1927). The ultracentrifuge. Nobel Lectures, Chemistry 1922–1941, Elsevier Publishing Company, Amsterdam, 1966.Google Scholar
Thorn, K. S. & Bogan, A. A. (2001). ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions. Bioinformatics 17, 284–285.CrossRefGoogle ScholarPubMed
Thornton, J. M., Edwards, M. S., Taylor, W. R. & Barlow, D. J. (1986). Location of ‘continuous’ antigenic determinants in the protruding regions of proteins. EMBO Journal 5, 409–413.CrossRefGoogle ScholarPubMed
Tovchigrechko, A. & Vakser, I. A. (2006). GRAMM-X public web server for protein–protein docking. Nucleic Acids Research 34, W310–W314.CrossRefGoogle ScholarPubMed
Tovchigrechko, A., Wells, C. A. & Vakser, I. A. (2002). Docking of protein models. Protein Science 11, 1888–1896.CrossRefGoogle ScholarPubMed
Treger, M. & Westhof, E. (2001). Statistical analysis of atomic contacts at RNA–protein interfaces. Journal of Molecular Recognition 14, 199–214.CrossRefGoogle Scholar
Tsai, C. J., Lin, S. L., Wolfson, H. J. & Nussinov, R. (1997). Studies of protein–protein interfaces: a statistical analysis of the hydrophobic effect. Protein Science 6, 53–64.CrossRefGoogle Scholar
Tsai, J. & Gerstein, M. (2002). Calculation of protein volumes: sensitivity analysis and parameter database. Bioinformatics 18, 985–995.CrossRefGoogle ScholarPubMed
Tsai, J., Taylor, R., Chothia, C. & Gerstein, M. (1999). The packing density in proteins: standard radii and volumes. Journal of Molecular Biology 290, 253–266.CrossRefGoogle ScholarPubMed
Vajda, S., Weng, Z. & DeLisi, C. (1995). Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Engineering 11, 1081–1092.CrossRefGoogle Scholar
Valdar, W. S. & Thornton, J. M. (2001). Protein–protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42, 108–124.3.0.CO;2-O>CrossRefGoogle ScholarPubMed
Valencia, A. & Pazos, F. (2002). Computational methods for the prediction of protein interactions. Current Opinion in Structural Biology 12, 368–373.CrossRefGoogle ScholarPubMed
van Dijk, A. D., de Vries, S. J., Dominguez, C., Chen, H., Zhou, H. X. & Bonvin, A. M. (2005). Data-driven docking: HADDOCK's adventures in CAPRI. Proteins 60, 232–238.CrossRefGoogle Scholar
Wang, C., Schueler-Furman, O., Andre, I., London, N., Fleishman, S. J., Bradley, P., Qian, B. & Baker, D. (2007). RosettaDock in CAPRI rounds 6–12. Proteins 69, 758–763.CrossRefGoogle ScholarPubMed
Wells, J. A. & McClendon, C. L. (2007). Reaching for high-hanging fruit in drug discovery at protein–protein interfaces. Nature 450, 1001–1009.CrossRefGoogle ScholarPubMed
Wiehe, K., Peterson, M. W., Pierce, B., Mintseris, J. & Weng, Z. (2007). Protein–protein docking: overview and performance analysis. Methods in Molecular Biology 413, 283–314.Google Scholar
Xie, Z. & Hendrix, R. W. (1995). Assembly in vitro of bacteriophage HK97 proheads. Journal of Molecular Biology 253, 74–85.CrossRefGoogle ScholarPubMed
Xu, Q., Canutescu, A., Obradovic, Z. & Dunbrack, R. L. Jr. (2006). ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics 22, 2876–2882.CrossRefGoogle ScholarPubMed
Zhang, Y., Arakaki, A. K. & Skolnick, J. (2005). TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61, 91–98.CrossRefGoogle ScholarPubMed
Zhang, Y. & Skolnick, J. (2004). Automated structure prediction of weakly homologous proteins on a genomic scale. Proceedings of the National Academy of Sciences USA 101, 7594–7599.CrossRefGoogle ScholarPubMed
Zhu, H., Domingues, F. S., Sommer, I. & Lengauer, T. (2006). NOXclass: prediction of protein–protein interaction types. BMC Bioinformatics 7, 27.CrossRefGoogle ScholarPubMed
Zlotnick, A. (2005). Theoretical aspects of virus capsid assembly. Journal of Molecular Recognition 18, 479–490.CrossRefGoogle ScholarPubMed