VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes

Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macr...

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Autores principales:	Vitor Pimentel, Diego Mariano, Letícia Xavier Silva Cantão, Luana Luiza Bastos, Pedro Fischer, Leonardo Henrique Franca de Lima, Alexandre Victor Fassio, Raquel Cardoso de Melo-Minardi
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	protein interactions structural bioinformatics structural alignment contacts rational design of enzymes Computer applications to medicine. Medical informatics R858-859.7
Acceso en línea:	https://doaj.org/article/48e3df2b9e28426ba537a648ed17e6b3
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spelling	oai:doaj.org-article:48e3df2b9e28426ba537a648ed17e6b32021-11-08T06:40:29ZVTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes2673-764710.3389/fbinf.2021.730350https://doaj.org/article/48e3df2b9e28426ba537a648ed17e6b32021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fbinf.2021.730350/fullhttps://doaj.org/toc/2673-7647Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macromolecular structures such as proteins. Here we show VTR, a new method for the detection of analogous contacts in protein pairs. The VTR web tool performs structural alignment between proteins and detects interactions that occur in similar regions. To evaluate our tool, we proposed three case studies: we 1) compared vertebrate myoglobin and truncated invertebrate hemoglobin; 2) analyzed interactions between the spike protein RBD of SARS-CoV-2 and the cell receptor ACE2; and 3) compared a glucose-tolerant and a non-tolerant β-glucosidase enzyme used for biofuel production. The case studies demonstrate the potential of VTR for the understanding of functional similarities between distantly sequence-related proteins, as well as the exploration of important drug targets and rational design of enzymes for industrial applications. We envision VTR as a promising tool for understanding differences and similarities between homologous proteins with similar 3D structures but different sequences. VTR is available at http://bioinfo.dcc.ufmg.br/vtr.Vitor PimentelDiego MarianoLetícia Xavier Silva CantãoLuana Luiza BastosPedro FischerLeonardo Henrique Franca de LimaAlexandre Victor FassioRaquel Cardoso de Melo-MinardiFrontiers Media S.A.articleprotein interactionsstructural bioinformaticsstructural alignmentcontactsrational design of enzymesComputer applications to medicine. Medical informaticsR858-859.7ENFrontiers in Bioinformatics, Vol 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	protein interactions structural bioinformatics structural alignment contacts rational design of enzymes Computer applications to medicine. Medical informatics R858-859.7
spellingShingle	protein interactions structural bioinformatics structural alignment contacts rational design of enzymes Computer applications to medicine. Medical informatics R858-859.7 Vitor Pimentel Diego Mariano Letícia Xavier Silva Cantão Luana Luiza Bastos Pedro Fischer Leonardo Henrique Franca de Lima Alexandre Victor Fassio Raquel Cardoso de Melo-Minardi VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
description	Evolutionarily related proteins can present similar structures but very dissimilar sequences. Hence, understanding the role of the inter-residues contacts for the protein structure has been the target of many studies. Contacts comprise non-covalent interactions, which are essential to stabilize macromolecular structures such as proteins. Here we show VTR, a new method for the detection of analogous contacts in protein pairs. The VTR web tool performs structural alignment between proteins and detects interactions that occur in similar regions. To evaluate our tool, we proposed three case studies: we 1) compared vertebrate myoglobin and truncated invertebrate hemoglobin; 2) analyzed interactions between the spike protein RBD of SARS-CoV-2 and the cell receptor ACE2; and 3) compared a glucose-tolerant and a non-tolerant β-glucosidase enzyme used for biofuel production. The case studies demonstrate the potential of VTR for the understanding of functional similarities between distantly sequence-related proteins, as well as the exploration of important drug targets and rational design of enzymes for industrial applications. We envision VTR as a promising tool for understanding differences and similarities between homologous proteins with similar 3D structures but different sequences. VTR is available at http://bioinfo.dcc.ufmg.br/vtr.
format	article
author	Vitor Pimentel Diego Mariano Letícia Xavier Silva Cantão Luana Luiza Bastos Pedro Fischer Leonardo Henrique Franca de Lima Alexandre Victor Fassio Raquel Cardoso de Melo-Minardi
author_facet	Vitor Pimentel Diego Mariano Letícia Xavier Silva Cantão Luana Luiza Bastos Pedro Fischer Leonardo Henrique Franca de Lima Alexandre Victor Fassio Raquel Cardoso de Melo-Minardi
author_sort	Vitor Pimentel
title	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
title_short	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
title_full	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
title_fullStr	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
title_full_unstemmed	VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes
title_sort	vtr: a web tool for identifying analogous contacts on protein structures and their complexes
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/48e3df2b9e28426ba537a648ed17e6b3
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VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes

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