Aromatic-aromatic interactions in proteins: Beyond the dimer

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 structu...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Biekofsky, Rodolfo Roberto, Estrin, Dario Ariel, Martí, Marcelo Adrián, Turjanski, Adrián Gustavo
Publicado:	2011
Materias:	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 Computer Simulation Dimerization Hydrocarbons, Aromatic Models, Chemical Models, Molecular Proteins
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499596_v51_n7_p1623_Lanzarotti http://hdl.handle.net/20.500.12110/paper_15499596_v51_n7_p1623_Lanzarotti
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_15499596_v51_n7_p1623_Lanzarotti
record_format	dspace
spelling	paper:paper_15499596_v51_n7_p1623_Lanzarotti2023-06-08T16:21:22Z Aromatic-aromatic interactions in proteins: Beyond the dimer Biekofsky, Rodolfo Roberto Estrin, Dario Ariel Martí, Marcelo Adrián Turjanski, Adrián Gustavo 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 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. Fil:Biekofsky, R.R. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Estrin, D.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marti, M.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Turjanski, A.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499596_v51_n7_p1623_Lanzarotti http://hdl.handle.net/20.500.12110/paper_15499596_v51_n7_p1623_Lanzarotti
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 Biekofsky, Rodolfo Roberto Estrin, Dario Ariel Martí, Marcelo Adrián Turjanski, Adrián Gustavo Aromatic-aromatic interactions in proteins: Beyond the dimer
topic_facet	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
description	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.
author	Biekofsky, Rodolfo Roberto Estrin, Dario Ariel Martí, Marcelo Adrián Turjanski, Adrián Gustavo
author_facet	Biekofsky, Rodolfo Roberto Estrin, Dario Ariel Martí, Marcelo Adrián Turjanski, Adrián Gustavo
author_sort	Biekofsky, Rodolfo Roberto
title	Aromatic-aromatic interactions in proteins: Beyond the dimer
title_short	Aromatic-aromatic interactions in proteins: Beyond the dimer
title_full	Aromatic-aromatic interactions in proteins: Beyond the dimer
title_fullStr	Aromatic-aromatic interactions in proteins: Beyond the dimer
title_full_unstemmed	Aromatic-aromatic interactions in proteins: Beyond the dimer
title_sort	aromatic-aromatic interactions in proteins: beyond the dimer
publishDate	2011
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15499596_v51_n7_p1623_Lanzarotti http://hdl.handle.net/20.500.12110/paper_15499596_v51_n7_p1623_Lanzarotti
work_keys_str_mv	AT biekofskyrodolforoberto aromaticaromaticinteractionsinproteinsbeyondthedimer AT estrindarioariel aromaticaromaticinteractionsinproteinsbeyondthedimer AT martimarceloadrian aromaticaromaticinteractionsinproteinsbeyondthedimer AT turjanskiadriangustavo aromaticaromaticinteractionsinproteinsbeyondthedimer
_version_	1768542195304890368

Aromatic-aromatic interactions in proteins: Beyond the dimer

Ejemplares similares