BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins

Understanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accura...

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Autores principales:	Sankar Basu, Simon S. Assaf, Fabian Teheux, Marianne Rooman, Fabrizio Pucci
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	computational prediction membrane protein structure and stability folding free energy frustration statistical potentials Leucine Transporters Computer applications to medicine. Medical informatics R858-859.7
Acceso en línea:	https://doaj.org/article/cc33f4ed640446bd910d23e1e1275813
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spelling	oai:doaj.org-article:cc33f4ed640446bd910d23e1e12758132021-12-02T11:42:00ZBRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins2673-764710.3389/fbinf.2021.742843https://doaj.org/article/cc33f4ed640446bd910d23e1e12758132021-12-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fbinf.2021.742843/fullhttps://doaj.org/toc/2673-7647Understanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accurate method to evaluate the per-residue contributions to the overall stability of membrane proteins. It is based on an extended set of recently introduced statistical potentials derived from membrane protein structures, which better describe the stability properties of this class of proteins than standard potentials derived from globular proteins. We defined a per-residue membrane propensity index from combinations of these potentials, which can be used to identify residues which strongly contribute to the stability of the transmembrane region or which would, on the contrary, be more stable in extramembrane regions, or vice versa. Large-scale application to membrane and globular proteins sets and application to tests cases show excellent agreement with experimental data. BRANEart thus appears as a useful instrument to analyze in detail the overall stability properties of a target membrane protein, to position it relative to the lipid bilayer, and to rationally modify its biophysical characteristics and function. BRANEart can be freely accessed from http://babylone.3bio.ulb.ac.be/BRANEart.Sankar BasuSankar BasuSimon S. AssafFabian TeheuxMarianne RoomanMarianne RoomanFabrizio PucciFabrizio PucciFrontiers Media S.A.articlecomputational predictionmembrane protein structure and stabilityfolding free energyfrustrationstatistical potentialsLeucine TransportersComputer applications to medicine. Medical informaticsR858-859.7ENFrontiers in Bioinformatics, Vol 1 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	computational prediction membrane protein structure and stability folding free energy frustration statistical potentials Leucine Transporters Computer applications to medicine. Medical informatics R858-859.7
spellingShingle	computational prediction membrane protein structure and stability folding free energy frustration statistical potentials Leucine Transporters Computer applications to medicine. Medical informatics R858-859.7 Sankar Basu Sankar Basu Simon S. Assaf Fabian Teheux Marianne Rooman Marianne Rooman Fabrizio Pucci Fabrizio Pucci BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
description	Understanding the role of stability strengths and weaknesses in proteins is a key objective for rationalizing their dynamical and functional properties such as conformational changes, catalytic activity, and protein-protein and protein-ligand interactions. We present BRANEart, a new, fast and accurate method to evaluate the per-residue contributions to the overall stability of membrane proteins. It is based on an extended set of recently introduced statistical potentials derived from membrane protein structures, which better describe the stability properties of this class of proteins than standard potentials derived from globular proteins. We defined a per-residue membrane propensity index from combinations of these potentials, which can be used to identify residues which strongly contribute to the stability of the transmembrane region or which would, on the contrary, be more stable in extramembrane regions, or vice versa. Large-scale application to membrane and globular proteins sets and application to tests cases show excellent agreement with experimental data. BRANEart thus appears as a useful instrument to analyze in detail the overall stability properties of a target membrane protein, to position it relative to the lipid bilayer, and to rationally modify its biophysical characteristics and function. BRANEart can be freely accessed from http://babylone.3bio.ulb.ac.be/BRANEart.
format	article
author	Sankar Basu Sankar Basu Simon S. Assaf Fabian Teheux Marianne Rooman Marianne Rooman Fabrizio Pucci Fabrizio Pucci
author_facet	Sankar Basu Sankar Basu Simon S. Assaf Fabian Teheux Marianne Rooman Marianne Rooman Fabrizio Pucci Fabrizio Pucci
author_sort	Sankar Basu
title	BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
title_short	BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
title_full	BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
title_fullStr	BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
title_full_unstemmed	BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins
title_sort	braneart: identify stability strength and weakness regions in membrane proteins
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/cc33f4ed640446bd910d23e1e1275813
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BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins

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