Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins

The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic resid...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Mikhail Yu. Lobanov, Leonid B. Pereyaslavets, Ilya V. Likhachev, Bakhyt T. Matkarimov, Oxana V. Galzitskaya
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Aromatic residues Conformation Exhaustive enumeration Stacking Server Protein Data Bank Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/446e6f61aad0401e93e34ed10df033fd
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:446e6f61aad0401e93e34ed10df033fd
record_format	dspace
spelling	oai:doaj.org-article:446e6f61aad0401e93e34ed10df033fd2021-11-14T04:31:40ZIs there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins2001-037010.1016/j.csbj.2021.10.036https://doaj.org/article/446e6f61aad0401e93e34ed10df033fd2021-01-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S200103702100458Xhttps://doaj.org/toc/2001-0370The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/.Mikhail Yu. LobanovLeonid B. PereyaslavetsIlya V. LikhachevBakhyt T. MatkarimovOxana V. GalzitskayaElsevierarticleAromatic residuesConformationExhaustive enumerationStackingServerProtein Data BankBiotechnologyTP248.13-248.65ENComputational and Structural Biotechnology Journal, Vol 19, Iss , Pp 5960-5968 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Aromatic residues Conformation Exhaustive enumeration Stacking Server Protein Data Bank Biotechnology TP248.13-248.65
spellingShingle	Aromatic residues Conformation Exhaustive enumeration Stacking Server Protein Data Bank Biotechnology TP248.13-248.65 Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
description	The aim of this study was to evaluate the favorability of different conformations of aromatic residues in proteins by analysing the occurrence of particular conformations. The clustering of protein structures from the Protein Data Bank (PDB) was performed. Conformations of interacting aromatic residues were analyzed for 511 282 pairs in 35 493 protein structures sharing less than 50% identity. Pairs with a parallel arrangement of aromatic residues made up 6.2% of all possible ones, which was twice as much as expected. Pairs with a perpendicular arrangement of aromatic residues made up 25%. We demonstrate that the most favorable arrangement was at an angle of 60° between the interacting aromatic residues. Among all possible aromatic pairs, the His-His pair was twice as frequent as expected, and the His-Phe pair was less frequent than expected. A server (CARP – Contacts of Aromatic Residues in Proteins) has been created for calculating essential structural features of interacting aromatic residues in proteins: http://bioproteom.protres.ru/arom_q_prog/.
format	article
author	Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya
author_facet	Mikhail Yu. Lobanov Leonid B. Pereyaslavets Ilya V. Likhachev Bakhyt T. Matkarimov Oxana V. Galzitskaya
author_sort	Mikhail Yu. Lobanov
title	Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
title_short	Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
title_full	Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
title_fullStr	Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
title_full_unstemmed	Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins
title_sort	is there an advantageous arrangement of aromatic residues in proteins? statistical analysis of aromatic interactions in globular proteins
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/446e6f61aad0401e93e34ed10df033fd
work_keys_str_mv	AT mikhailyulobanov isthereanadvantageousarrangementofaromaticresiduesinproteinsstatisticalanalysisofaromaticinteractionsinglobularproteins AT leonidbpereyaslavets isthereanadvantageousarrangementofaromaticresiduesinproteinsstatisticalanalysisofaromaticinteractionsinglobularproteins AT ilyavlikhachev isthereanadvantageousarrangementofaromaticresiduesinproteinsstatisticalanalysisofaromaticinteractionsinglobularproteins AT bakhyttmatkarimov isthereanadvantageousarrangementofaromaticresiduesinproteinsstatisticalanalysisofaromaticinteractionsinglobularproteins AT oxanavgalzitskaya isthereanadvantageousarrangementofaromaticresiduesinproteinsstatisticalanalysisofaromaticinteractionsinglobularproteins
_version_	1718429952454426624

Is there an advantageous arrangement of aromatic residues in proteins? Statistical analysis of aromatic interactions in globular proteins

Ejemplares similares