Inward-facing glycine residues create sharp turns in β-barrel membrane proteins.

Bacterial Outer Membrane Proteins / chemistry Escherichia coli Proteins / chemistry Glycine / chemistry Molecular Dynamics Simulation Protein Conformation, beta-Strand Protein Domains
Electrophysiology OmpX Outer membrane proteins (OMPs) Protein evolution β-Barrel shape

Journal

Biochimica et biophysica acta. Biomembranes
ISSN: 1879-2642
Titre abrégé: Biochim Biophys Acta Biomembr
Pays: Netherlands
ID NLM: 101731713

Informations de publication

Date de publication:
01 10 2021
Historique:
received: 16 01 2021
revised: 15 04 2021
accepted: 17 05 2021
pubmed: 8 6 2021
medline: 24 11 2021
entrez: 7 6 2021
Statut: ppublish

Résumé

The transmembrane region of outer-membrane proteins (OMPs) of Gram-negative bacteria are almost exclusively β-barrels composed of between 8 and 26 β-strands. To explore the relationship between β-barrel size and shape, we modeled and simulated engineered variants of the Escherichia coli protein OmpX with 8, 10, 12, 14, and 16 β-strands. We found that while smaller barrels maintained a roughly circular shape, the 16-stranded variant developed a flattened cross section. This flat cross section impeded its ability to conduct ions, in agreement with previous experimental observations. Flattening was determined to arise from the presence of inward-facing glycines at sharp turns in the β-barrel. An analysis of all simulations revealed that glycines, on average, make significantly smaller angles with residues on neighboring strands than all other amino acids, including alanine, and create sharp turns in β-barrel cross sections. This observation was generalized to 119 unique structurally resolved OMPs. We also found that the fraction of glycines in β-barrels decreases as the strand number increases, suggesting an evolutionary role for the addition or removal of glycine in OMP sequences.

Identifiants

DOI: 10.1016/j.bbamem.2021.183662 PMID: 34097860 PMC: PMC8380186
pubmed: 34097860
pii: S0005-2736(21)00112-7
doi: 10.1016/j.bbamem.2021.183662
pmc: PMC8380186
mid: NIHMS1718017
pii:
doi:

Substances chimiques

Bacterial Outer Membrane Proteins 0
Escherichia coli Proteins 0
Glycine TE7660XO1C

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

183662

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM123169
Pays : United States

Informations de copyright

Copyright © 2021 Elsevier B.V. All rights reserved.

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Auteurs

Zijian Zhang (Z)

School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America.

David Ryoo (D)

Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, United States of America.

Curtis Balusek (C)

School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America.

Atanu Acharya (A)

School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America.

Marcella Orwick Rydmark (MO)

Department of Biosciences, University of Oslo, Oslo, Norway.

Dirk Linke (D)

Department of Biosciences, University of Oslo, Oslo, Norway.

James C Gumbart (JC)

School of Physics, Georgia Institute of Technology, Atlanta, GA 30313, United States of America. Electronic address: gumbart@physics.gatech.edu.

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Classifications MeSH

Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines membranaires › Protéines de la membrane externe bactérienne › Inward-facing glycine residues create sharp...
Recherchemedicale.com › Acides aminés, peptides et protéines › Protéines › Protéines bactériennes › Protéines Escherichia coli › Inward-facing glycine residues create sharp...
Recherchemedicale.com › Acides aminés, peptides et protéines › Acides aminés › Glycine › Inward-facing glycine residues create sharp...
Recherchemedicale.com › Sciences de l'information › Méthodologies informatiques › Simulation numérique › Simulation de dynamique moléculaire › Inward-facing glycine residues create sharp...
Recherchemedicale.com › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structure secondaire des protéines › Structure en brin bêta › Inward-facing glycine residues create sharp...
Recherchemedicale.com › Phénomènes chimiques › Phénomènes biochimiques › Conformation moléculaire › Conformation des protéines › Structure tertiaire des protéines › Domaines protéiques › Inward-facing glycine residues create sharp...