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Lanzarotti, E.; Biekofsky, R.R.; Estrin, D.A.; Marti, M.A.; Turjanski, A.G. "Aromatic-aromatic interactions in proteins: Beyond the dimer" (2011) Journal of Chemical Information and Modeling. 51(7):1623-1633
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Abstract:

Aromatic residues are key widespread elements of protein structures and have been shown to be important for structure stability, folding, protein-protein recognition, and ligand binding. The interactions of pairs of aromatic residues (aromatic dimers) have been extensively studied in protein structures. Isolated aromatic molecules tend to form higher order clusters, like trimers, tetramers, and pentamers, that adopt particular well-defined structures. Taking this into account, we have surveyed protein structures deposited in the Protein Data Bank in order to find clusters of aromatic residues in proteins larger than dimers and characterized them. Our results show that larger clusters are found in one of every two unique proteins crystallized so far, that the clusters are built adopting the same trimer motifs found for benzene clusters in vacuum, and that they are clearly nonlocal brining primary structure distant sites together. We extensively analyze the trimers and tetramers conformations and found two main cluster types: a symmetric cluster and an extended ladder. Finally, using calmodulin as a test case, we show aromatic clsuters possible role in folding and protein-protein interactions. All together, our study highlights the relevance of aromatic clusters beyond the dimer in protein function, stability, and ligand recognition. © 2011 American Chemical Society.

Registro:

Documento: Artículo
Título:Aromatic-aromatic interactions in proteins: Beyond the dimer
Autor:Lanzarotti, E.; Biekofsky, R.R.; Estrin, D.A.; Marti, M.A.; Turjanski, A.G.
Filiación:Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, C1428EHA, Argentina
Departamento de Quimica Inorganica, Analitica y Quimica Fisica/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Buenos Aires, C1428EHA, Argentina
Palabras clave:Aromatic clusters; Aromatic molecules; Aromatic residues; Aromatic-aromatic interactions; Higher order; In-vacuum; Ligand binding; Ligand recognition; Nonlocal; Pentamers; Primary structures; Protein data bank; Protein functions; Protein structures; Protein-protein interactions; Protein-protein recognition; Structure stability; Test case; Tetramers; Well-defined structures; Aromatic compounds; Aromatization; Benzene; Dimers; Ligands; Calmodulin; aromatic hydrocarbon; calmodulin; protein; article; chemical model; chemical structure; chemistry; computer simulation; dimerization; Calmodulin; Computer Simulation; Dimerization; Hydrocarbons, Aromatic; Models, Chemical; Models, Molecular; Proteins
Año:2011
Volumen:51
Número:7
Página de inicio:1623
Página de fin:1633
DOI: http://dx.doi.org/10.1021/ci200062e
Título revista:Journal of Chemical Information and Modeling
Título revista abreviado:J. Chem. Inf. Model.
ISSN:15499596
CAS:protein, 67254-75-5; Calmodulin; Hydrocarbons, Aromatic; Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499596_v51_n7_p1623_Lanzarotti

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Citas:

---------- APA ----------
Lanzarotti, E., Biekofsky, R.R., Estrin, D.A., Marti, M.A. & Turjanski, A.G. (2011) . Aromatic-aromatic interactions in proteins: Beyond the dimer. Journal of Chemical Information and Modeling, 51(7), 1623-1633.
http://dx.doi.org/10.1021/ci200062e
---------- CHICAGO ----------
Lanzarotti, E., Biekofsky, R.R., Estrin, D.A., Marti, M.A., Turjanski, A.G. "Aromatic-aromatic interactions in proteins: Beyond the dimer" . Journal of Chemical Information and Modeling 51, no. 7 (2011) : 1623-1633.
http://dx.doi.org/10.1021/ci200062e
---------- MLA ----------
Lanzarotti, E., Biekofsky, R.R., Estrin, D.A., Marti, M.A., Turjanski, A.G. "Aromatic-aromatic interactions in proteins: Beyond the dimer" . Journal of Chemical Information and Modeling, vol. 51, no. 7, 2011, pp. 1623-1633.
http://dx.doi.org/10.1021/ci200062e
---------- VANCOUVER ----------
Lanzarotti, E., Biekofsky, R.R., Estrin, D.A., Marti, M.A., Turjanski, A.G. Aromatic-aromatic interactions in proteins: Beyond the dimer. J. Chem. Inf. Model. 2011;51(7):1623-1633.
http://dx.doi.org/10.1021/ci200062e