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Parra, R.G.; Espada, R.; Sánchez, I.E.; Sippl, M.J.; Ferreiro, D.U. "Detecting repetitions and periodicities in proteins by tiling the structural space" (2013) Journal of Physical Chemistry B. 117(42):12887-12897
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Abstract:

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric, we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association toward higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information, we can identify structural units that can be encoded by a variety of distinct amino acid sequences. © 2013 American Chemical Society.

Registro:

Documento: Artículo
Título:Detecting repetitions and periodicities in proteins by tiling the structural space
Autor:Parra, R.G.; Espada, R.; Sánchez, I.E.; Sippl, M.J.; Ferreiro, D.U.
Filiación:Protein Physiology Lab, Departamento de Química Biológica, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
Department of Molecular Biology, Center of Applied Molecular Engineering, University of Salzburg, Salzburg, Austria
Palabras clave:Amino acid sequence; Analytical tool; Energy landscape; Folded structures; Protein architectures; Protein molecules; Structural repeats; Structural unit; Amino acids; Molecules; Tools; Proteins; protein; article; chemical structure; chemistry; metabolism; protein folding; protein motif; protein tertiary structure; thermodynamics; Amino Acid Motifs; Models, Molecular; Protein Folding; Protein Structure, Tertiary; Proteins; Thermodynamics
Año:2013
Volumen:117
Número:42
Página de inicio:12887
Página de fin:12897
DOI: http://dx.doi.org/10.1021/jp402105j
Título revista:Journal of Physical Chemistry B
Título revista abreviado:J Phys Chem B
ISSN:15206106
CODEN:JPCBF
CAS:protein, 67254-75-5
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n42_p12887_Parra

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Citas:

---------- APA ----------
Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J. & Ferreiro, D.U. (2013) . Detecting repetitions and periodicities in proteins by tiling the structural space. Journal of Physical Chemistry B, 117(42), 12887-12897.
http://dx.doi.org/10.1021/jp402105j
---------- CHICAGO ----------
Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J., Ferreiro, D.U. "Detecting repetitions and periodicities in proteins by tiling the structural space" . Journal of Physical Chemistry B 117, no. 42 (2013) : 12887-12897.
http://dx.doi.org/10.1021/jp402105j
---------- MLA ----------
Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J., Ferreiro, D.U. "Detecting repetitions and periodicities in proteins by tiling the structural space" . Journal of Physical Chemistry B, vol. 117, no. 42, 2013, pp. 12887-12897.
http://dx.doi.org/10.1021/jp402105j
---------- VANCOUVER ----------
Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J., Ferreiro, D.U. Detecting repetitions and periodicities in proteins by tiling the structural space. J Phys Chem B. 2013;117(42):12887-12897.
http://dx.doi.org/10.1021/jp402105j