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

Dhar, Rik; Feehan, Ryan; Slusky, Joanna S.G.

doi:10.1021/acs.jpcb.1c00878

Cited by 15 publications

(19 citation statements)

References 43 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In the initial design, all residues were polar in the interior and nonpolar in the exterior of the barrel, resulting in a binary pattern similar to β-sheets but opposite to the water-soluble barrel designs. The rationale aligned well with a recent analysis on native proteins suggesting that membrane barrels are taller, fatter and inside-out soluble barrels . However, experimental success was not achieved until additional destabilization with β-hairpins on the trans side and reduced β-sheets propensity were incorporated to slow down undesired nucleation and allowed proper folding of the structure.…”

Section: Novel Structures Assembly and Interaction Designsmentioning

confidence: 99%

Protein Design: From the Aspect of Water Solubility and Stability

et al. 2022

View full text Add to dashboard Cite

Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.

show abstract

Section: Novel Structures Assembly and Interaction Designsmentioning

confidence: 99%

Protein Design: From the Aspect of Water Solubility and Stability

et al. 2022

View full text Add to dashboard Cite

show abstract

“…The folding of soluble β-barrels, which are the “inside-out” version of membrane β-barrels (since the inward regions of the former exhibit similar hydrophobicity with the outward regions of the latter, and vice versa [ 28 ]), may not require special folding machinery, and may occur in an ATP-independent manner, as in the case of GFP-like proteins. Moreover, co-translational folding of GFP occurs more efficiently than after its chemical denaturation, which can be partially explained by the proposition that gradual polypeptide synthesis occurring in ribosomes facilitates the acquisition of more favorable conformations for correct folding [ 132 ].…”

Section: Folding Of β-Barrel Proteins and Their Aggregationmentioning

confidence: 99%

“…Similarly to amyloids, β-barrels represent a highly specific type of β-strand-enriched fold [ 17 , 24 , 25 , 26 ], which is widespread in nature and is presented by both membrane and cytoplasmic proteins [ 27 ]. Comparably to amyloidogenic proteins, β-barrel proteins are rich in hydrophobic residues [ 28 ]. β-barrels are composed of β-strands connected by loops.…”

Section: Introductionmentioning

confidence: 99%

β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis

Sulatskaya

Kosolapova

Bobylev

et al. 2021

IJMS

View full text Add to dashboard Cite

Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another—followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis (“on-pathway state”), or can be formed as a result of an alternative assembly of partially unfolded monomers (“off-pathway state”). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only “the tip of the iceberg”. Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.

show abstract

“…TolC forms a large rigid conduit in the outer membrane and periplasm ( Figure 3A ) with a water-filled lumen. The hydrophilic nature of the channel ( Dhar et al, 2021 ) coupled with the inflexibility of the outer-membrane-embedded barrel largely precludes the formation of any hydrophobic interfaces that are typically the basis of protein-protein interfaces involving helical peptides ( Eisenberg et al, 1982 ). Yet, we did observe specific polar contacts between colicin E1’s TolC box and the TolC barrel.…”

Section: Resultsmentioning

confidence: 99%

Colicin E1 opens its hinge to plug TolC

Budiardjo

Stevens

Calkins

et al. 2022

eLife

Self Cite

View full text Add to dashboard Cite

The double membrane architecture of Gram-negative bacteria forms a barrier that is impermeable to most extracellular threats. Bacteriocin proteins evolved to exploit the accessible, surface-exposed proteins embedded in the outer membrane to deliver cytotoxic cargo. Colicin E1 is a bacteriocin produced by, and lethal to, Escherichia coli that hijacks the outer membrane proteins TolC and BtuB to enter the cell. Here we capture the colicin E1 translocation domain inside its membrane receptor, TolC, by high-resolution cryoEM to obtain the first reported structure of a bacteriocin bound to TolC. Colicin E1 binds stably to TolC as an open hinge through the TolC pore-an architectural rearrangement from colicin E1's unbound conformation. This binding is stable in live E. coli cells as indicated by single-molecule fluorescence microscopy. Finally, colicin E1 fragments binding to TolC plug the channel, inhibiting its native efflux function as an antibiotic efflux pump and heightening susceptibility to three antibiotic classes. In addition to demonstrating that these protein fragments are useful starting points for developing novel antibiotic potentiators, this method could be expanded to other colicins to inhibit other outer membrane protein functions.

show abstract

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

Cited by 15 publications

References 43 publications

Protein Design: From the Aspect of Water Solubility and Stability

Protein Design: From the Aspect of Water Solubility and Stability

β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis

Colicin E1 opens its hinge to plug TolC

Contact Info

Product

Resources

About