IR-spectroscopic characterization of an elongated OmpG mutant

Korkmaz, Filiz; Pee, Katharina van; Yıldız, Özkan

doi:10.1016/j.abb.2015.04.010

Cited by 10 publications

(5 citation statements)

References 18 publications

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“…The prominence of the penultimate strands in OMBB folding may explain unsuccessful attempts at design as well. For instance, the unsuccessful attempt to increase the number of strands in OmpG by duplicating the final hairpin pushed the penultimate hairpin out of the penultimate position(Korkmaz et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Franklin

Nepomnyachyi

Feehan

et al. 2018

eLife

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Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria. These proteins have diverse functions but a single topology: the β-barrel. Sequence analysis has suggested that this common fold is a β-hairpin repeat protein, and that amplification of the β-hairpin has resulted in 8–26-stranded barrels. Using an integrated approach that combines sequence and structural analyses, we find events in which non-amplification diversification also increases barrel strand number. Our network-based analysis reveals strand-number-based evolutionary pathways, including one that progresses from a primordial 8-stranded barrel to 16-strands and further, to 18-strands. Among these pathways are mechanisms of strand number accretion without domain duplication, like a loop-to-hairpin transition. These mechanisms illustrate perpetuation of repeat protein topology without genetic duplication, likely induced by the hydrophobic membrane. Finally, we find that the evolutionary trace is particularly prominent in the C-terminal half of OMPs, implicating this region in the nucleation of OMP folding.

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Section: Discussionmentioning

confidence: 99%

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Franklin

Nepomnyachyi

Feehan

et al. 2018

eLife

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“…Although an attempt to widen the barrel of OmpG using two strands at its C-terminus was not successful [30], duplication of two strands at the N-terminus of FhuA successfully increased both its pore size and diffusion kinetics[31]. Conversely, removing one and two strands from the middle of the VDAC1 barrel resulted in a smaller barrel [32].…”

Section: Outer Membrane Protein Designmentioning

confidence: 99%

Outer membrane protein design

Slusky

2017

Current Opinion in Structural Biology

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Membrane proteins are the gateway to the cell. These proteins are also a control center of the cell as information from the outside is passed through membrane protein signaling networks to the cellular machinery. The design of membrane proteins seeks to harness the power of these gateways and signaling networks. This review will focus on the design of the membrane proteins that are in the outer membrane, a membrane which only exists for gram negative bacteria, mitochondria and chloroplasts. Unlike other membrane proteins, outer membrane proteins are uniquely shaped as β-barrels. Herein, I describe most known examples of outer-membrane, β-barrel design to date, focusing particularly on categorizing designs as 1) structural deconstruction, 2) structural changes, 3) chemical function design, and 4) the creation of new folds.

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“…Duplication studies of OmpX also successfully folded, as long as the strands of the middle hairpin (strands 4 and 5) were included (Arnold, et al 2007). This may explain unsuccessful attempts as well; to create a 16-stranded barrel by adding to the C-terminus, the last hairpin was duplicated in the 14-stranded OmpG but IR studies revealed that this additional hairpin never formed as part of the barrel (Korkmaz, et al 2015).…”

Section: Discussionmentioning

confidence: 99%

Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane

Franklin

Nepomnyaciy

Feehan

et al. 2018

Preprint

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Outer membrane beta barrels (OMBBs) are the proteins on the surface of Gram negative bacteria. These proteins have diverse functions but only a single topology, the beta barrel. It has been suggested that this common fold is a repeat protein with the repeating unit of a beta hairpin. By grouping structurally solved OMBBs by sequence, a detailed evolutionary story unfolds. A strand-number based pathway manifests with progression from a primordial 8-stranded barrel to 16-stranded and then to 18-stranded barrels. The transitions from 16- to 18-stranded barrels show mechanisms of strand number variation without domain duplication, such as a loop to hairpin transition. This indicates that repeat protein topology can be perpetuated without genetic duplication likely because the topology is being enforced by the membrane environment. Moreover, we find the evolutionary trace is particularly prominent in the C-terminal half of OMBBs which may be relevant to understanding OMBB folding pathways.

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IR-spectroscopic characterization of an elongated OmpG mutant

Cited by 10 publications

References 18 publications

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

Outer membrane protein design

Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane

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