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Dimeric interactions and complex formation using direct coevolutionary couplings (2015)

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  • USP affiliated authors: ANDRICOPULO, ADRIANO DEFINI - IFSC
  • USP Schools: IFSC
  • DOI: 10.1038/srep13652
  • Subjects: PROTEÍNAS; FÁRMACOS (DESENVOLVIMENTO); DOENÇAS DEGENERATIVAS
  • Language: Inglês
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    Informações sobre o DOI: 10.1038/srep13652 (Fonte: oaDOI API)
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    Título do periódico: Scientific Reports

    ISSN: 2045-2322

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    Informações sobre o Citescore
  • Título: Scientific Reports

    ISSN: 2045-2322

    Citescore - 2017: 4.36

    SJR - 2017: 1.533

    SNIP - 2017: 1.245


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    • ABNT

      SANTOS, Ricardo N.; MORCOS, Faruck; JANA, Biman; ANDRICOPULO, Adriano Defini; ONUCHIC, Jose Nelson. Dimeric interactions and complex formation using direct coevolutionary couplings. Scientific Reports, London, Nature, v. 5, p. 13652-1-13652-10, 2015. Disponível em: < http://dx.doi.org/10.1038/srep13652 > DOI: 10.1038/srep13652.
    • APA

      Santos, R. N., Morcos, F., Jana, B., Andricopulo, A. D., & Onuchic, J. N. (2015). Dimeric interactions and complex formation using direct coevolutionary couplings. Scientific Reports, 5, 13652-1-13652-10. doi:10.1038/srep13652
    • NLM

      Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN. Dimeric interactions and complex formation using direct coevolutionary couplings [Internet]. Scientific Reports. 2015 ; 5 13652-1-13652-10.Available from: http://dx.doi.org/10.1038/srep13652
    • Vancouver

      Santos RN, Morcos F, Jana B, Andricopulo AD, Onuchic JN. Dimeric interactions and complex formation using direct coevolutionary couplings [Internet]. Scientific Reports. 2015 ; 5 13652-1-13652-10.Available from: http://dx.doi.org/10.1038/srep13652

    Referências citadas na obra
    Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. Atomic model of the actin filament. Nature 347, 44–49 (1990).
    Reisler, E. Actin molecular structure and function. Curr Opin Cell Biol 5, 41–47 (1993).
    Dominguez, R. & Holmes, K. C. Actin structure and function. Annu. Rev. Biophys 40, 169–186 (2011).
    Caudron, N., Arnal, I., Buhler, E., Job, D. & Valiron, O. Microtubule nucleation from stable tubulin oligomers. J. Biol. Chem. 277, 50973–50979 (2002).
    Bermudes, D., Hinkle, G. & Margulis, L. Do prokaryotes contain microtubules? Microbiol. Rev. 58, 387–400 (1994).
    Bieniossek, C. et al. The molecular architecture of the metalloprotease FtsH. Proc. Natl. Acad. Sci. USA 103, 3066–3071 (2006).
    Langklotz, S., Baumann, U. & Narberhaus, F. Structure and function of the bacterial AAA protease FtsH. Bba-Mol. Cell. Res. 1823, 40–48 (2012).
    Lee, K. A. Dimeric transcription factor families: it takes two to tango but who decides on partners and the venue? J. Cell. Sci. 103 (Pt 1), 9–14 (1992).
    Klemm, J. D., Schreiber, S. L. & Crabtree, G. R. Dimerization as a regulatory mechanism in signal transduction. Annu. Rev. Immunol. 16, 569–592 (1998).
    Ali, M. H. & Imperiali, B. Protein oligomerization: How and why. Bioorgan. Med. Chem. 13, 5013–5020 (2005).
    Matthews, J. M. in Protein Dimerization and Oligomerization in Biology (ed. Matthews, J. M. ) Ch. 1, 1–18 (Springer: New York,, 2012).
    Ispolatov, I., Yuryev, A., Mazo, I. & Maslov, S. Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res. 33, 3629–3635 (2005).
    Morcos, F., Hwa, T., Onuchic, J. N. & Weigt, M. in Protein Structure Prediction, Methods in Molecular Biology 3rd ed Vol. 1137 (ed. Kihara, D. ) Ch. 5, 55–70 (Humana Press, 2014).
    Ekeberg, M., Lovkvist, C., Lan, Y. H., Weigt, M. & Aurell, E. Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models. Phys. Rev. E 87 (2013).
    Kamisetty, H., Ovchinnikov, S. & Baker, D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc. Natl. Acad. Sci. USA 110, 15674–15679 (2013).
    Lockless, S. W. & Ranganathan, R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295–299 (1999).
    Liu, Z., Chen, J. & Thirumalai, D. On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model. Proteins Struct. Func. Bioinf 77, 823–831 (2009).
    Dima, R. & Thirumalai, D. Determination of network of residues that regulate allostery in protein families using sequence analysis. Protein Sci. 15, 258–268 (2006).
    Sulkowska, J. I., Morcos, F., Weigt, M., Hwa, T. & Onuchic, J. N. Genomics-aided structure prediction. Proc. Natl. Acad. Sci. USA 109, 10340–10345 (2012).
    Marks, D. S. et al. Protein 3D structure computed from evolutionary sequence variation. PLoS ONE 6, e28766 (2011).
    Hopf, T. A. et al. Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149, 1607–1621 (2012).
    Morcos, F. et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc. Natl. Acad. Sci. USA 108, E1293–1301 (2011).
    Taylor, W. R., Jones, D. T. & Sadowski, M. I. Protein topology from predicted residue contacts. Protein Sci. 21, 299–305 (2012).
    Kloczkowski, A. et al. Distance matrix-based approach to protein structure prediction. J. Struct. Funct. Genomics 10, 67–81 (2009).
    Wu, D., Cui, F., Jernigan, R. & Wu, Z. PIDD: database for Protein Inter-atomic Distance Distributions. Nucleic Acids Res. 35, D202–207 (2007).
    Halabi, N., Rivoire, O., Leibler, S. & Ranganathan, R. Protein sectors: evolutionary units of three-dimensional structure. Cell 138, 774–786 (2009).
    Morcos, F., Jana, B., Hwa, T. & Onuchic, J. N. Coevolutionary signals across protein lineages help capture multiple protein conformations. Proc. Natl. Acad. Sci. USA 110, 20533–20538 (2013).
    Weigt, M., White, R. A., Szurmant, H., Hoch, J. A. & Hwa, T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc. Natl. Acad. Sci. USA 106, 67–72 (2009).
    Schug, A., Weigt, M., Onuchic, J. N., Hwa, T. & Szurmant, H. High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci USA 106, 22124–22129 (2009).
    Procaccini, A., Lunt, B., Szurmant, H., Hwa, T. & Weigt, M. Dissecting the specificity of protein-protein interaction in bacterial two-component signaling: orphans and crosstalks. PLoS one 6, e19729 (2011).
    Cheng, R. R., Morcos, F., Levine, H. & Onuchic, J. N. Toward rationally redesigning bacterial two-component signaling systems using coevolutionary information. Proc. Natl. Acad. Sci. USA 111, E563–571 (2014).
    Tamir, S. et al. Integrated strategy reveals the protein interface between cancer targets Bcl-2 and NAF-1. Proc. Natl. Acad. Sci. USA 111, 5177–5182 (2014).
    Jana, B., Morcos, F. & Onuchic, J. N. From structure to function: the convergence of structure based models and co-evolutionary information. Phys. Chem. Chem. Phys. 16, 6496–6507 (2014).
    Ovchinnikov, S., Kamisetty, H. & Baker, D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Elife 3, e02030 (2014).
    Pierce, B., Tong, W. & Weng, Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics 21, 1472–1478 (2005).
    de Vries, S. J., van Dijk, M. & Bonvin, A. M. The HADDOCK web server for data-driven biomolecular docking. Nat. Protoc 5, 883–897 (2010).
    Mukherjee, S. & Zhang, Y. Protein-protein complex structure predictions by multimeric threading and template recombination. Structure 19, 955–966 (2011).
    Kim, S. K. & Jacobson, K. A. Computational prediction of homodimerization of the A3 adenosine receptor. J. Mol. Graph. Model 25, 549–561 (2006).
    La, D., Kong, M., Hoffman, W., Choi, Y. I. & Kihara, D. Predicting permanent and transient protein-protein interfaces. Proteins 81, 805–818 (2013).
    Esquivel-Rodriguez, J., Filos-Gonzalez, V., Li, B. & Kihara, D. Pairwise and multimeric protein-protein docking using the LZerD program suite. Methods Mol. Biol. 1137, 209–234 (2014).
    Zheng, W., Schafer, N. P., Davtyan, A., Papoian, G. A. & Wolynes, P. G. Predictive energy landscapes for protein-protein association. Proc. Natl. Acad. Sci. USA 109, 19244–19249 (2012).
    Miyashita, N., Straub, J. E., Thirumalai, D. & Sugita, Y. Transmembrane structures of amyloid precursor protein dimer predicted by replica-exchange molecular dynamics simulations. J. Am. Chem. Soc. 131, 3438–3439 (2009).
    Sgourakis, N. G. & Garcia, A. E. The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J. Mol. Biol. 398, 161–173 (2010).
    Sgourakis, N. G., Patel, M. M., Garcia, A. E., Makhatadze, G. I. & McCallum, S. A. Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. J Mol Biol 396, 1128–1144 (2010).
    Lammert, H., Schug, A. & Onuchic, J. N. Robustness and generalization of structure-based models for protein folding and function. Proteins Struct. Func. Bioinf 77, 881–891 (2009).
    Morcos, F., Schafer, N. P., Cheng, R. R., Onuchic, J. N. & Wolynes, P. G. Coevolutionary information, protein folding landscapes and the thermodynamics of natural selection. Proc. Natl. Acad. Sci. USA 111, 12408–12413 (2014).
    Laub, M. T. & Goulian, M. Specificity in two-component signal transduction pathways. Annu Rev Genet 41, 121–145 (2007).
    Hoch, J. A. Two-component and phosphorelay signal-transduction. Curr. Opin. Microbiol. 3, 165–170 (2000).
    Fabret, C., Feher, V. A. & Hoch, J. A. Two-component signal transduction in Bacillus subtilis: how one organism sees its world. J. Bacteriol. 181, 1975–1983 (1999).
    Bachhawat, P., Swapna, G. V., Montelione, G. T. & Stock, A. M. Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states. Structure 13, 1353–1363 (2005).
    King-Scott, J. et al. The structure of a full-length response regulator from Mycobacterium tuberculosis in a stabilized three-dimensional domain-swapped, activated state. J. Biol. Chem. 282, 37717–37729 (2007).
    Sola, M., Gomis-Ruth, F. X., Serrano, L., Gonzalez, A. & Coll, M. Three-dimensional crystal structure of the transcription factor PhoB receiver domain. J. Mol. Biol. 285, 675–687 (1999).
    Baumkotter, F. et al. Amyloid precursor protein dimerization and synaptogenic function depend on copper binding to the growth factor-like domain. J. Neurosci. 34, 11159–11172 (2014).
    Baulac, S., LaVoie, M. J., Strahle, J., Schlossmacher, M. G. & Xia, W. Dimerization of Parkinson’s disease-causing DJ-1 and formation of high molecular weight complexes in human brain. Mol. Cell. Neurosci. 27, 236–246 (2004).
    Tompa, P., Tusnady, G. E., Friedrich, P. & Simon, I. The role of dimerization in prion replication. Biophys. J 82, 1711–1718 (2002).
    Zheng, W., Schafer, N. P. & Wolynes, P. G. Free energy landscapes for initiation and branching of protein aggregation. Proc. Natl. Acad. Sci. USA 110, 20515–20520 (2013).
    Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res. 38, D211–222 (2010).
    Finn, R. D., Clements, J. & Eddy, S. R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–37 (2011).
    Fraczkiewicz, R. & Braun, W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comput. Chem. 19, 319–333 (1998).
    Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000).
    Bordoli, L. & Schwede, T. Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal. Methods Mol. Biol. 857, 107–136 (2012).
    Noel, J. K., Whitford, P. C., Sanbonmatsu, K. Y. & Onuchic, J. N. SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res. 38, W657–661 (2010).
    Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).