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Artículo

Detecting repetitions and periodicities in proteins by tiling the structural space

Parra, Rodrigo GonzaloIcon ; Espada, RocíoIcon ; Sánchez Miguel, Ignacio EnriqueIcon ; Sippl, Manfred J.; Ferreiro, DiegoIcon
Fecha de publicación: 06/2013
Editorial: American Chemical Society
Revista: Journal of Physical Chemistry B
ISSN: 1520-6106
Idioma: Inglés
Tipo de recurso: Artículo publicado
Clasificación temática:
Biofísica

Resumen

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.
Palabras clave: Repeat Protein , Protein Folding , Tiling
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info:eu-repo/semantics/openAccess Excepto donde se diga explícitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
Identificadores
URI: http://hdl.handle.net/11336/20829
DOI: http://dx.doi.org/10.1021/jp402105j
URL: http://pubs.acs.org/doi/abs/10.1021/jp402105j
Colecciones
Articulos(IQUIBICEN)
Articulos de INSTITUTO DE QUIMICA BIOLOGICA DE LA FACULTAD DE CS. EXACTAS Y NATURALES
Citación
Parra, Rodrigo Gonzalo; Espada, Rocío; Sánchez Miguel, Ignacio Enrique; Sippl, Manfred J.; Ferreiro, Diego; Detecting repetitions and periodicities in proteins by tiling the structural space; American Chemical Society; Journal of Physical Chemistry B; 117; 42; 6-2013; 12887-12897
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