Detecting repetitions and periodicities in proteins by tiling the structural space

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 symmetri...

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Autores principales:	Parra, R.G., Espada, R., Sánchez, I.E., Sippl, M.J., Ferreiro, D.U.
Formato:	JOUR
Materias:	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 Thermodynamics
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_15206106_v117_n42_p12887_Parra
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	todo:paper_15206106_v117_n42_p12887_Parra
record_format	dspace
spelling	todo:paper_15206106_v117_n42_p12887_Parra2023-10-03T16:20:27Z Detecting repetitions and periodicities in proteins by tiling the structural space Parra, R.G. Espada, R. Sánchez, I.E. Sippl, M.J. Ferreiro, D.U. 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 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_15206106_v117_n42_p12887_Parra
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 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
topic_facet	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
description	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.
format	JOUR
author	Parra, R.G. Espada, R. Sánchez, I.E. Sippl, M.J. Ferreiro, D.U.
author_facet	Parra, R.G. Espada, R. Sánchez, I.E. Sippl, M.J. Ferreiro, D.U.
author_sort	Parra, R.G.
title	Detecting repetitions and periodicities in proteins by tiling the structural space
title_short	Detecting repetitions and periodicities in proteins by tiling the structural space
title_full	Detecting repetitions and periodicities in proteins by tiling the structural space
title_fullStr	Detecting repetitions and periodicities in proteins by tiling the structural space
title_full_unstemmed	Detecting repetitions and periodicities in proteins by tiling the structural space
title_sort	detecting repetitions and periodicities in proteins by tiling the structural space
url	http://hdl.handle.net/20.500.12110/paper_15206106_v117_n42_p12887_Parra
work_keys_str_mv	AT parrarg detectingrepetitionsandperiodicitiesinproteinsbytilingthestructuralspace AT espadar detectingrepetitionsandperiodicitiesinproteinsbytilingthestructuralspace AT sanchezie detectingrepetitionsandperiodicitiesinproteinsbytilingthestructuralspace AT sipplmj detectingrepetitionsandperiodicitiesinproteinsbytilingthestructuralspace AT ferreirodu detectingrepetitionsandperiodicitiesinproteinsbytilingthestructuralspace
_version_	1782028014146551808

Detecting repetitions and periodicities in proteins by tiling the structural space

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