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...

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Autores principales:	Lanzarotti, E., Biekofsky, R.R., Estrin, D.A., Marti, M.A., Turjanski, A.G.
Formato:	JOUR
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:	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	todo:paper_15499596_v51_n7_p1623_Lanzarotti
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spelling	todo:paper_15499596_v51_n7_p1623_Lanzarotti2023-10-03T16:23:14Z Aromatic-aromatic interactions in proteins: Beyond the dimer Lanzarotti, E. Biekofsky, R.R. Estrin, D.A. Marti, M.A. Turjanski, A.G. 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. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar 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 Lanzarotti, E. Biekofsky, R.R. Estrin, D.A. Marti, M.A. Turjanski, A.G. 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.
format	JOUR
author	Lanzarotti, E. Biekofsky, R.R. Estrin, D.A. Marti, M.A. Turjanski, A.G.
author_facet	Lanzarotti, E. Biekofsky, R.R. Estrin, D.A. Marti, M.A. Turjanski, A.G.
author_sort	Lanzarotti, E.
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
url	http://hdl.handle.net/20.500.12110/paper_15499596_v51_n7_p1623_Lanzarotti
work_keys_str_mv	AT lanzarottie aromaticaromaticinteractionsinproteinsbeyondthedimer AT biekofskyrr aromaticaromaticinteractionsinproteinsbeyondthedimer AT estrinda aromaticaromaticinteractionsinproteinsbeyondthedimer AT martima aromaticaromaticinteractionsinproteinsbeyondthedimer AT turjanskiag aromaticaromaticinteractionsinproteinsbeyondthedimer
_version_	1807320344205197312

Aromatic-aromatic interactions in proteins: Beyond the dimer

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