Dataset Information

Membrane thinning and lateral gating are consistent features of BamA across multiple species.

ABSTRACT: In Gram-negative bacteria, the folding and insertion of ?-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the ?-barrel assembly machinery (BAM) complex. Two leading models of this process have been put forth: the hybrid barrel model, which claims that a lateral gate in BamA's ?-barrel can serve as a template for incoming OMPs, and the passive model, which claims that a thinned membrane near the lateral gate of BamA accelerates spontaneous OMP insertion. To examine the key elements of these two models, we have carried out 45.5 ?s of equilibrium molecular dynamics simulations of BamA with and without POTRA domains from Escherichia coli, Salmonella enterica, Haemophilus ducreyi and Neisseria gonorrhoeae, together with BamA's homolog, TamA from E. coli, in their native, species-specific outer membranes. In these equilibrium simulations, we consistently observe membrane thinning near the lateral gate for all proteins. We also see occasional spontaneous lateral gate opening and sliding of the ?-strands at the gate interface for N. gonorrhoeae, indicating that the gate is dynamic. An additional 14 ?s of free-energy calculations shows that the energy necessary to open the lateral gate in BamA/TamA varies by species, but is always lower than the Omp85 homolog, FhaC. Our combined results suggest OMP insertion utilizes aspects of both the hybrid barrel and passive models.

SUBMITTER: Liu J

PROVIDER: S-EPMC7652284 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Membrane thinning and lateral gating are consistent features of BamA across multiple species.

Liu Jinchan J Gumbart James C JC

PLoS computational biology 20201028 10

In Gram-negative bacteria, the folding and insertion of β-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the β-barrel assembly machinery (BAM) complex. Two leading models of this process have been put forth: the hybrid barrel model, which claims that a lateral gate in BamA's β-barrel can serve as a template for incoming OMPs, and the passive model, which claims that a thinned membrane near the lateral gate of BamA accelerates spontaneous OMP insertion. To examine the ...[more]

PMID: 33112853

Similar Datasets

Project description:Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressive neurodegenerative disease that primarily affects motor neurons. Recently, three causative genes have been implicated in both ALS and glaucoma. However, it is still uncertain whether patients with ALS have neurodegeneration in their retinas. If so, retinal thickness measurements might be a useful biomarker for ALS progression. Previous work in this area has been inconclusive, as it has not taken into account the effect of ophthalmic diseases on retinal thinning.To determine whether there are differences in retinal neurons in ALS patients utilizing spectral-domain optical coherence tomography (SD-OCT). We tested the hypothesis that ALS patients exhibit retinal neurodegeneration that is not associated with ophthalmic diseases.Observational, comparative, cross-sectional study performed on patients recruited from the Duke University Medical Center ALS clinic. Patients underwent a comprehensive ophthalmologic examination to rule out ocular pathology. 21 patients met inclusion criteria. Two eyes with ocular pathology were excluded, leading to a total of 40 eyes of 21 patients included in the study. Retinal neurodegeneration was assessed by retinal nerve fiber layer (RNFL) thickness measurement using SD-OCT (Spectralis; Heidelberg Engineering).ALS disease severity, determined through the ALS Functional Rating Scale (ALSFRS-R); mean and six sector RNFL thickness values compared to age-adjusted values in the normative database provided by Heidelberg Engineering; RNFL thickness correlation with ALSFRS-R, ALSFRS-R progression rate, forced vital capacity (FVC), and visual acuity.ALSFRS-R mean score was 30+/-10. Mean RNFL thickness in ALS patients was 88.95 +/- 10.8 microns, significantly thinner than values in the normative database (95.81 +/- 0.8). These RNFL thickness values did not demonstrate correlation to ALSFRS-R score, ALSFRS-R progression rate, FVC, intraocular pressure, or visual acuity.Using SD-OCT, our study shows that ALS patients without ocular pathology exhibit thinned retinal layers. Future studies are warranted to clarify the clinical relationship between retinal thinning and motor neuron loss in ALS.

Dataset Information

Membrane thinning and lateral gating are consistent features of BamA across multiple species.

Publications

Membrane thinning and lateral gating are consistent features of BamA across multiple species.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets