Outer membrane protein evolution

Dhar, Rik; Slusky, Joanna S.G.

doi:10.1016/j.sbi.2021.01.002

Cited by 14 publications

(6 citation statements)

References 56 publications

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“…No additional OM proteins have been identified for ColB toxicity, which may explain why, unlike most other colicins, ColB is composed of only two functional domains: an N-terminal domain that serves as both a receptor-binding domain and a translocation domain (ColB-RT) and a pore-forming, C-terminal cytotoxic domain ( 17 ). The ColB receptor FepA is a 22-stranded β-barrel TonB-dependent transporter (TBDT) with an N-terminal plug domain blocking its lumen ( 18 – 20 ).…”

Section: Introductionmentioning

confidence: 99%

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Cohen-Khait

Harmalkar

Pham

et al. 2021

mBio

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Section: Introductionmentioning

confidence: 99%

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Cohen-Khait

Harmalkar

Pham

et al. 2021

mBio

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“…Although almost all outer membrane proteins are β-barrels, the barrels are somewhat structurally heterogeneous. There are multiple classes among these barrels including some classes of barrels that convergently evolved the barrel structure. − …”

Section: Introductionmentioning

confidence: 99%

Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels

2021

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Up-and-down β-barrel topology exists in both the membrane and soluble environment. By comparing features of these structurally similar proteins, we can determine what features are particular to the environment rather than the fold. Here we compare structures of membrane β-barrels to soluble β-barrels and evaluate their relative size, shape, amino acid composition, hydrophobicity, and periodicity. We find that membrane β-barrels are generally larger than soluble β-barrels, with more strands per barrel and more amino acids per strand, making them wider and taller. We also find that membrane β-barrels are inside-out soluble β-barrels. The inward region of membrane β-barrels has similar hydrophobicity to the outward region of soluble β-barrels, and the outward region of membrane β-barrels has similar hydrophobicity to the inward region of the soluble β-barrels. Moreover, even though both types of β-barrel have been assumed to have strands with amino acids that alternate in direction and hydrophobicity, we find that the membrane β-barrels have more regular alternation than soluble β-barrels. These features give insight into how membrane barrels maintain their fold and function in the membrane.

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“…This warranted the use of only high conserved sequences which would allow the development of a broad-spectrum vaccine [65]. In the subcellular localization analysis, outer membrane, extracellular membrane, and periplasmic membrane proteins were considered as vaccine targets [83]. Surface localized proteins are more potent for generating an immune response compared to other localized proteins.…”

Section: Discussionmentioning

confidence: 99%

Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii

Ullah

Ahmad

Ismail

et al. 2021

IJERPH

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Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.

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Outer membrane protein evolution

Cited by 14 publications

References 56 publications

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Colicin-Mediated Transport of DNA through the Iron Transporter FepA

Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels

Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii

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