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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2013
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n42_p12887_Parra http://hdl.handle.net/20.500.12110/paper_15206106_v117_n42_p12887_Parra |
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paper:paper_15206106_v117_n42_p12887_Parra2023-06-08T16:19:08Z Detecting repetitions and periodicities in proteins by tiling the structural space 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n42_p12887_Parra 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 |
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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 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. |
| 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 |
| publishDate |
2013 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v117_n42_p12887_Parra http://hdl.handle.net/20.500.12110/paper_15206106_v117_n42_p12887_Parra |
| _version_ |
1768543199927730176 |