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Turjanski, P.; Parra, R.G.; Espada, R.; Becher, V.; Ferreiro, D.U. "Protein Repeats from First Principles" (2016) Scientific Reports. 6
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Abstract:

Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.

Registro:

Documento: Artículo
Título:Protein Repeats from First Principles
Autor:Turjanski, P.; Parra, R.G.; Espada, R.; Becher, V.; Ferreiro, D.U.
Filiación:Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires-CONICET-IQUIBICEN, Buenos Aires, Argentina
Palabras clave:quantitative study; algorithm; biology; chemistry; Markov chain; protein database; protein domain; protein folding; protein motif; statistical model; amino acid; protein; Algorithms; Amino Acid Motifs; Amino Acids; Computational Biology; Databases, Protein; Markov Chains; Models, Statistical; Protein Domains; Protein Folding; Proteins
Año:2016
Volumen:6
DOI: http://dx.doi.org/10.1038/srep23959
Título revista:Scientific Reports
Título revista abreviado:Sci. Rep.
ISSN:20452322
CAS:amino acid, 65072-01-7; protein, 67254-75-5; Amino Acids; Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20452322_v6_n_p_Turjanski

Referencias:

  • Kajava, A.V., Tandem repeats in proteins: From sequence to structure (2012) J Struct Biol, 179, pp. 279-288
  • Espada, R., Repeat proteins challenge the concept of structural domains (2015) Biochem Soc Trans, 43, pp. 844-849
  • Parra, R., Espada, R., Sánchez, I., Sippl, M., Ferreiro, D., Detecting repetitions and periodicities in proteins by tiling the structural space (2013) J Phys Chem B, 117, pp. 12887-12897
  • Espada, R., Parra, R., Mora, T., Walczak, A., Ferreiro, D., Capturing coevolutionary signals inrepeat proteins (2015) BMC Bioinformatics, 16, p. 207
  • Luo, H., Nijveen, H., Understanding and identifying amino acid repeats (2014) Brief Bioinform, 15, pp. 582-591
  • Marsella, L., Sirocco, F., Trovato, A., Seno, F., Tosatto, S.C., Repetita: Detection and discrimination of the periodicity of protein solenoid repeats by discrete fourier transform (2009) Bioinformatics, 25, pp. i289-i295
  • Crochemore, M., Rytter, W., (2002) Jewels of Stringology, , World Scientific
  • Gusfield, D., (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, , Cambridge University Press
  • Becher, V., Deymonnaz, A., Heiber, P., Efficient computation of all perfect repeats in genomic sequences of up to half a gigabyte, with a case study on the human genome (2009) Bioinformatics, 25, pp. 1746-1753
  • Mosavi, L.K., Cammett, T.J., Desrosiers, D.C., Peng, Z., The ankyrin repeat as molecular architecture for protein recognition (2004) Protein Sci, 13, pp. 1435-1448
  • Mosavi, L.K., Minor, D.L., Peng, Z., Consensus-derived structural determinants of the ankyrin repeat motif (2002) Proc Natl Acad Sci U SA, 99, pp. 16029-16034
  • Binz, H., Stumpp, M.T., Forrer, P., Amstutz, P., Plückthun, A., Designing repeat proteins: Well-expressed, soluble and stable proteins from combinatorial libraries of consensus ankyrin repeat proteins (2003) J Mol Biol, 332, pp. 489-503
  • Di Domenico, T., Repeatsdb: A database of tandem repeat protein structures (2014) Nucleic Acids Res, 42, pp. D352-D357
  • Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T., Tramontano, A., Critical assessment of methods of protein structure prediction (casp)-round x (2014) Proteins, 82, pp. 1-6
  • Voth, D., Thanks for the repeat: Intracellular pathogens exploit a common eukaryotic domain (2011) Cell Logist, 1, pp. 128-132
  • Parra, R., Espada, R., Verstraete, N., Ferreiro, D., Structural and energetic characterization of the ankyrin repeat protein family (2015) PLoS Comput Biol, 11
  • Myers, J.K., Nick Pace, C., Martin Scholtz, J., Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding (1995) Protein Sci, 4, pp. 2138-2148
  • Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., Wu, C.H., Uniref: Comprehensive and non-redundant uniprot reference clusters (2007) Bioinformatics, 23, pp. 1282-1288
  • Fox, N., Brenner, S., Chandonia, J., Scope: Structural classification of proteins-extended, integrating SCOP and ASTRAL data and classification of new structures (2014) Nucleic Acids Res, 42, pp. D304-D309

Citas:

---------- APA ----------
Turjanski, P., Parra, R.G., Espada, R., Becher, V. & Ferreiro, D.U. (2016) . Protein Repeats from First Principles. Scientific Reports, 6.
http://dx.doi.org/10.1038/srep23959
---------- CHICAGO ----------
Turjanski, P., Parra, R.G., Espada, R., Becher, V., Ferreiro, D.U. "Protein Repeats from First Principles" . Scientific Reports 6 (2016).
http://dx.doi.org/10.1038/srep23959
---------- MLA ----------
Turjanski, P., Parra, R.G., Espada, R., Becher, V., Ferreiro, D.U. "Protein Repeats from First Principles" . Scientific Reports, vol. 6, 2016.
http://dx.doi.org/10.1038/srep23959
---------- VANCOUVER ----------
Turjanski, P., Parra, R.G., Espada, R., Becher, V., Ferreiro, D.U. Protein Repeats from First Principles. Sci. Rep. 2016;6.
http://dx.doi.org/10.1038/srep23959