Abstract
In this chapter we address two aspects – the static physical interactions which allow the information transfer for the function to be performed; and the dynamic, i.e. how the information is transmitted between the binding sites in the single protein molecule and in the network. We describe the single protein molecules and their complexes; and the analogy between protein folding and protein binding. Eventually, to fully understand the interactome and how it performs the essential cellular functions, we have to put all together - and hierarchically progress through the system.
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References
Argos, P. (1988) An investigation of protein subunit and domain interfaces. Protein Eng 2, 101–113.
Arkin, M. R., Randal, M., DeLano, W. L., Hyde, J., Luong, T. N., Oslob, J. D., Raphael, D. R., Taylor, L., Wang, J., McDowell, R. S., Wells, J. A., and Braisted, A. C. (2003) Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A 100, 1603–1608.
Batada, N. N., Hurst, L. D., and Tyers, M. (2006) Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2, e88.
Cheng, Y. S., Yin, F. H., Foundling, S., Blomstrom, D., and Kettner, C. A. (1990) Stability and activity of human immunodeficiency virus protease: comparison of the natural dimer with a homologous, single-chain tethered dimer. Proc Natl Acad Sci U S A 87, 9660–9664.
Daily, M. D., and Gray, J. J. (2007) Local motions in a benchmark of allosteric proteins. Proteins 67, 385-399.
Ekman, D., Light, S., Bjorklund, A. K., and Elofsson, A. (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol 7, R45.
Fetler, L., Kantrowitz, E. R., and Vachette, P. (2007) Direct observation in solution of a preexisting structural equilibrium for a mutant of the allosteric aspartate transcarbamoylase. Proc Natl Acad Sci U S A 104, 495–500.
Finkelstein, A. V., Badretdinov, A., and Gutin, A. M. (1995) Why do protein architectures have Boltzmann-like statistics? Proteins 23, 142–150.
Grigoriev, A. (2003) On the number of protein-protein interactions in the yeast proteome. Nucleic Acids Res 31, 4157–4161.
Gunasekaran, K., Ma, B., and Nussinov, R. (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57, 433–443.
Han, J. D., Bertin, N., Hao, T., Goldberg, D. S., Berriz, G. F., Zhang, L. V., Dupuy, D., Walhout, A. J., Cusick, M. E., Roth, F. P., and Vidal, M. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430, 88–93.
Hawkins, R. J., and McLeish, T. C. (2004) Coarse-grained model of entropic allostery. Phys Rev Lett 93, 098104.
Homans, S. W. (2005) Probing the binding entropy of ligand-protein interactions by NMR. Chembiochem 6, 1585–1591.
Janin, J., and Chothia, C. (1990) The structure of protein-protein recognition sites. J Biol Chem 265, 16027-16030.
Janin, J., Miller, S., and Chothia, C. (1988) Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 204, 155–164.
Jones, S., and Thornton, J. M. (1996) Principles of protein-protein interactions. Proc Natl Acad Sci U S A 93, 13–20.
Keskin, O., Tsai, C. J., Wolfson, H., and Nussinov, R. (2004) A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci 13, 1043–1055.
Kippen, A. D., Sancho, J., and Fersht, A. R. (1994) Folding of barnase in parts. Biochemistry 33, 3778–3786.
Kumar, S., Ma, B., Tsai, C. J., Wolfson, H., and Nussinov, R. (1999) Folding funnels and conformational transitions via hinge-bending motions. Cell Biochem Biophys 31, 141–164.
Liang, H., Sandberg, W. S., and Terwilliger, T. C. (1993) Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding. Proc Natl Acad Sci U S A 90, 7010–7014.
Lindsley, J. E., and Rutter, J. (2006) Whence cometh the allosterome? Proc Natl Acad Sci U S A 103, 10533–10535.
Ma, B., Kumar, S., Tsai, C. J., and Nussinov, R. (1999) Folding funnels and binding mechanisms. Protein Eng 12, 713–720.
Mintseris, J., and Weng, Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A 102, 10930–10935.
Moult, J., and Melamud, E. (2000) From fold to function. Curr Opin Struct Biol 10, 384–389.
Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247, 536–540.
Nagano, N., Orengo, C. A., and Thornton, J. M. (2002) One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 321, 741–765.
Nooren, I. M., and Thornton, J. M. (2003) Diversity of protein-protein interactions. Embo J 22, 3486–3492.
Orengo, C. A., Todd, A. E., and Thornton, J. M. (1999) From protein structure to function. Curr Opin Struct Biol 9, 374–382.
Popovych, N., Sun, S., Ebright, R. H., and Kalodimos, C. G. (2006) Dynamically driven protein allostery. Nat Struct Mol Biol 13, 831–838.
Swain, J. F., and Gierasch, L. M. (2006) The changing landscape of protein allostery. Curr Opin Struct Biol 16, 102–108.
Thornton, J. M., Todd, A. E., Milburn, D., Borkakoti, N., and Orengo, C. A. (2000) From structure to function: approaches and limitations. Nat Struct Biol 7 Suppl, 991–994.
Todd, A. E., Orengo, C. A., and Thornton, J. M. (2002) Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10, 1435–1451.
Tsai, C. J., Kumar, S., Ma, B., and Nussinov, R. (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8, 1181–1190.
Tsai, C. J., Ma, B., and Nussinov, R. (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci U S A 96, 9970–9972.
Valente, A. X., and Cusick, M. E. (2006) Yeast Protein Interactome topology provides framework for coordinated-functionality. Nucleic Acids Res 34, 2812–2819.
Wand, A. J. (2001) Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat Struct Biol 8, 926–931.
Wilson, C. J., Zhan, H., Swint-Kruse, L., and Matthews, K. S. (2007) The lactose repressor system: paradigms for regulation, allosteric behavior and protein folding. Cell Mol Life Sci 64, 3–16.
Wu, L. C., Grandori, R., and Carey, J. (1994) Autonomous subdomains in protein folding. Protein Sci 3, 369–371.
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Keskin, O., Gursoy, A., Nussinov, R. (2008). Principles of Protein Recognition and Properties of Protein-protein Interfaces. In: Panchenko, A., Przytycka, T. (eds) Protein-protein Interactions and Networks. Computational Biology, vol 9. Springer, London. https://doi.org/10.1007/978-1-84800-125-1_3
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DOI: https://doi.org/10.1007/978-1-84800-125-1_3
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