A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from https://link.springer.com/article/10.1007/s10439-010-0048-9 below:

Analysis of Hot Region Organization in Hub Proteins

References

  1. Ahmad, S., O. Keskin, A. Sarai, and R. Nussinov. Protein–DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins. Nucleic Acids Res. 36(18):5922–5932, 2008.

    Article  PubMed  CAS  Google Scholar 

  2. Bloom, J. D., and C. Adami. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein–protein interactions data sets. BMC Evol. Biol. 3:21, 2003.

    Article  PubMed  Google Scholar 

  3. Clackson, T., and J. A. Wells. A hot spot of binding energy in a hormone–receptor interface. Science 267(5196):383–386, 1995.

    Article  PubMed  CAS  Google Scholar 

  4. Ekman, D., S. Light, A. K. Bjorklund, and A. Elofsson. What properties characterize the hub proteins of the protein–protein interaction network of Saccharomyces cerevisiae? Genome Biol. 7(6):R45, 2006.

    Article  PubMed  CAS  Google Scholar 

  5. Fraser, H. B., D. P. Wall, and A. E. Hirsh. A simple dependence between protein evolution rate and the number of protein–protein interactions. BMC Evol. Biol. 3:11, 2003.

    Article  PubMed  Google Scholar 

  6. Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M. A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868):141–147, 2002.

    Article  PubMed  CAS  Google Scholar 

  7. Gsponer, J., and M. M. Babu. The rules of disorder or why disorder rules. Prog. Biophys. Mol. Biol. 99(2–3):94–103, 2009.

    Article  PubMed  CAS  Google Scholar 

  8. Gunasekaran, K., C. J. Tsai, and R. Nussinov. Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J. Mol. Biol. 341(5):1327–1341, 2004.

    Article  PubMed  CAS  Google Scholar 

  9. Han, J. D., N. Bertin, T. Hao, D. S. Goldberg, G. F. Berriz, L. V. Zhang, D. Dupuy, A. J. Walhout, M. E. Cusick, F. P. Roth, and M. Vidal. Evidence for dynamically organized modularity in the yeast protein–protein interaction network. Nature 430(6995):88–93, 2004.

    Article  PubMed  CAS  Google Scholar 

  10. Higurashi, M., T. Ishida, and K. Kinoshita. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci. 17(1):72–78, 2008.

    Article  PubMed  CAS  Google Scholar 

  11. Ito, T., T. Chiba, R. Ozawa, M. Yoshida, M. Hattori, and Y. Sakaki. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA 98(8):4569–4574, 2001.

    Article  PubMed  CAS  Google Scholar 

  12. Jordan, I. K., Y. I. Wolf, and E. V. Koonin. No simple dependence between protein evolution rate and the number of protein–protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3:1, 2003.

    Article  PubMed  Google Scholar 

  13. Kar, G., A. Gursoy, and O. Keskin. Human cancer protein–protein interaction network: a structural perspective. PLoS Comput. Biol. 5(12):e1000601, 2009.

    Article  PubMed  CAS  Google Scholar 

  14. Keskin, O., B. Ma, and R. Nussinov. Hot regions in protein–protein interactions: the organization and contribution of structurally conserved hot spot residues. J. Mol. Biol. 345(5):1281–1294, 2005.

    Article  PubMed  CAS  Google Scholar 

  15. Keskin, O., C. J. Tsai, H. Wolfson, and R. Nussinov. A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications. Protein Sci. 13(4):1043–1055, 2004.

    Article  PubMed  CAS  Google Scholar 

  16. Kim, P. M., L. J. Lu, Y. Xia, and M. B. Gerstein. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314(5807):1938–1941, 2006.

    Article  PubMed  CAS  Google Scholar 

  17. Kim, P. M., A. Sboner, Y. Xia, and M. Gerstein. The role of disorder in interaction networks: a structural analysis. Mol. Syst. Biol. 4:179, 2008.

    Article  PubMed  Google Scholar 

  18. Kleanthous, C. Protein–Protein Recognition, Frontiers in Molecular Biology. Oxford: Oxford University Press, 2000.

  19. Lo Conte, L., C. Chothia, and J. Janin. The atomic structure of protein–protein recognition sites. J. Mol. Biol. 285(5):2177–2198, 1999.

    Article  PubMed  CAS  Google Scholar 

  20. Ma, B., T. Elkayam, H. Wolfson, and R. Nussinov. Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA 100(10):5772–5777, 2003.

    Article  PubMed  CAS  Google Scholar 

  21. Meszaros, B., P. Tompa, I. Simon, and Z. Dosztanyi. Molecular principles of the interactions of disordered proteins. J. Mol. Biol. 372(2):549–561, 2007.

    Article  PubMed  CAS  Google Scholar 

  22. Noble, W. S. What is a support vector machine? Nat. Biotechnol. 24(12):1565–1567, 2006.

    Article  PubMed  CAS  Google Scholar 

  23. Patil, A., and H. Nakamura. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Lett. 580(8):2041–2045, 2006.

    Article  PubMed  CAS  Google Scholar 

  24. Reichmann, D., O. Rahat, S. Albeck, R. Meged, O. Dym, and G. Schreiber. The modular architecture of protein–protein binding interfaces. Proc. Natl Acad. Sci. USA 102(1):57–62, 2005.

    Article  PubMed  CAS  Google Scholar 

  25. Tsai, C. J., S. L. Lin, H. J. Wolfson, and R. Nussinov. A Dataset of Protein–Protein Interfaces Generated with a Sequence-Order-Independent Comparison Technique. J. Mol. Biol. 260(4):604–620, 1996.

    Article  PubMed  CAS  Google Scholar 

  26. Tsai, C. J., B. Ma, and R. Nussinov. Protein–Protein Interaction Networks: How Can a Hub Protein Bind So Many Different Partners? Trends Biochem. Sci. 34(12):594–600, 2009.

    Article  PubMed  CAS  Google Scholar 

  27. Tuncbag, N., A. Gursoy, E. Guney, R. Nussinov, and O. Keskin. Architectures and functional coverage of protein–protein interfaces. J. Mol. Biol. 381(3):785–802, 2008.

    Article  PubMed  CAS  Google Scholar 

  28. Tuncbag, N., A. Gursoy, and O. Keskin. Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. Bioinformatics 25(12):1513–1520, 2009.

    Article  PubMed  CAS  Google Scholar 

  29. Uetz, P., L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. M. Rothberg. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae. Nature 403(6770):623–627, 2000.

    Article  PubMed  CAS  Google Scholar 

  30. Wuchty, S. Evolution and topology in the yeast protein interaction network. Genome Res. 14(7):1310–1314, 2004.

    Article  PubMed  CAS  Google Scholar 

  31. Yu, H., P. Braun, M. A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, T. Hirozane-Kishikawa, F. Gebreab, N. Li, N. Simonis, T. Hao, J. F. Rual, A. Dricot, A. Vazquez, R. R. Murray, C. Simon, L. Tardivo, S. Tam, N. Svrzikapa, C. Fan, A. S. de Smet, A. Motyl, M. E. Hudson, J. Park, X. Xin, M. E. Cusick, T. Moore, C. Boone, M. Snyder, F. P. Roth, A. L. Barabasi, J. Tavernier, D. E. Hill, and M. Vidal. High-quality binary protein interaction map of the yeast interactome network. Science 322(5898):104–110, 2008.

    Article  PubMed  CAS  Google Scholar 

Download references

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4