Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity

Schmitt, Christine; Bafna, Jayesh Arun; Schmid, Benedikt; Klingl, Stefan; Baier, Stephan; Hemmis, Birgit; Wagner, Richard; Winterhalter, Mathias; Voll, Lars M.

doi:10.1016/j.bbamem.2019.07.009

Cited by 7 publications

(8 citation statements)

References 60 publications

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“…For instance, the electrostatic potential in the pore of OmpG is higher than that of OmpC and OmpF, and the channel conductivity of OmpG is lower than that of OmpC and OmpF. 39,43 There are six glutamic acid residues (E15, E17, E31, E52, E152, and E174) with a negative charge and seven arginine residues (R68, R92, R111, R150, R194, R211, and R235) with a positive charge on the inner surface of the OmpG WT pore. 43 The OmpG − 4β(Δ1−80) pore on the inner surface consists of two glutamic acid residues (E152 and E174) and six arginine residues (R92, R111, R150, R194, R211, and R235), while the OmpG − 4β(Δ42−123) pore at the inner surface consists of five glutamic acid residues (E15, E17, E31, R152, and E174) and four arginine residues (R150, R194, R211, and R235) (Table S3).…”

Section: ■ Discussionmentioning

confidence: 99%

“…39,43 There are six glutamic acid residues (E15, E17, E31, E52, E152, and E174) with a negative charge and seven arginine residues (R68, R92, R111, R150, R194, R211, and R235) with a positive charge on the inner surface of the OmpG WT pore. 43 The OmpG − 4β(Δ1−80) pore on the inner surface consists of two glutamic acid residues (E152 and E174) and six arginine residues (R92, R111, R150, R194, R211, and R235), while the OmpG − 4β(Δ42−123) pore at the inner surface consists of five glutamic acid residues (E15, E17, E31, R152, and E174) and four arginine residues (R150, R194, R211, and R235) (Table S3). Therefore, the ion permeability of OmpG − 4β(Δ1−80) was higher than that of OmpG WT because the electrostatic potential of the inner surface in the OmpG − 4β(Δ1−80) pore is higher than that in the OmpG WT pore.…”

Section: ■ Discussionmentioning

confidence: 99%

“…On comparing the ion permeability and pore size of OmpG, OmpC, and OmpF, although the pore sizes of OmpC and OmpF were smaller than those of OmpG, the ion permeabilities of OmpC and OmpF were higher than those of OmpG. , Ion permeability does not depend on the pore size but on the inner surface structure of the pore because the electrostatic potential at the inner surface pore constriction plays an important role in determining channel conductivity. For instance, the electrostatic potential in the pore of OmpG is higher than that of OmpC and OmpF, and the channel conductivity of OmpG is lower than that of OmpC and OmpF. , There are six glutamic acid residues (E15, E17, E31, E52, E152, and E174) with a negative charge and seven arginine residues (R68, R92, R111, R150, R194, R211, and R235) with a positive charge on the inner surface of the OmpG WT pore . The OmpG – 4β(Δ1–80) pore on the inner surface consists of two glutamic acid residues (E152 and E174) and six arginine residues (R92, R111, R150, R194, R211, and R235), while the OmpG – 4β(Δ42–123) pore at the inner surface consists of five glutamic acid residues (E15, E17, E31, R152, and E174) and four arginine residues (R150, R194, R211, and R235) (Table S3).…”

Section: Discussionmentioning

confidence: 99%

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Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA

Tosaka

Kamiya

2022

ACS Appl. Nano Mater.

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The detection of single molecules such as singlestranded DNA (ssDNA) and other small molecules through biological nanopores is a powerful approach for analyzing DNA sequences and DNA shapes, as well as for disease diagnostics. The fixed diameter of biological nanopores restricts the size of biomolecules translocated through them. Although some nanopores such as ClyA, FraC, Phi29p, and γ-hemolysin have been shown to translocate double-stranded DNA (dsDNA), identifying the difference between dsDNA and three-way junction DNA is difficult using these native biological nanopores. OmpG, a major outer membrane protein, forms a nanosized pore with 14 β-strands.Here, we create a modified OmpG that expands and truncates βhairpins, allowing the generation of small or large nanopores compared to that of wild-type (WT) OmpG nanopores. To determine the pore diameters of modified OmpGs, the change in the current amplitude of the various modified OmpGs was measured in the presence or absence of poly(ethylene glycol) at different molecular weights. Finally, we demonstrated the detection of various structures of DNA (branched DNA) depending on the nanopore size using OmpG WT or mutated OmpG nanopores. Insights into the changes in pore diameters will be crucial to form precise pore diameters for the detection of various types of single biomolecules and for sequencing DNA, peptides, and proteins.

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Section: ■ Discussionmentioning

confidence: 99%

Section: ■ Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA

Tosaka

Kamiya

2022

ACS Appl. Nano Mater.

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“…The same effect was also observed for the strong polar interaction of two glutamine residues (see Figure S5) but not for the weak polar interaction of a serine pair (see Figure S6), indicating that interaction-specific differences in the induced effects of aIL incubation exist. Surprisingly, we also observed solvent-specific stabilization effects of aIL for like-charged residue pairs of Glu – , Arg + , or His + , which are common structural motifs in proteins despite their intuitively repelling natures ,− (Figures S7–S10 and Text S3 in the Supporting Information). For instance, the linear Glu – –Glu – interaction (Figure S7) was stabilized by ∼0.8 kcal mol –1 in high concentrations of aIL compared to water, resulting in a novel stable interaction minima of 0 kcal mol –1 at 4.4 Å.…”

Section: Resultsmentioning

confidence: 81%

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions

Harrar

Gohlke

2022

J. Chem. Inf. Model.

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The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein’s stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein’s stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein–residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol–1, depending on the residue pair, residue–residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion–residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.

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“…Unlike the strategy of strengthen anti-acid components, which focuses on finding unknown but effectively tolerant proteins, and expanding their effects by overexpression after being successfully identified, protein evolutionary engineering is based on known functional proteins, usually with the help of evolutionary rules to mutate amino acids to achieve functional enhancement. For example, OmpG is a diffusion pore protein of E.coli outer membrane β-barrels (OMBBs); Schmitt et al investigated the effect of charge distribution in the luminal ring of OmpG on substrate specificity, improved the transport function to double ponds of OmpG by amino acid substitution strategy, and identified the pH dependence of this sugar transport function on electrostatic interactions with charged residues to some extent (Dhar and Slusky 2021;Schmitt et al 2019).…”

Section: Protein Evolutionmentioning

confidence: 99%

The challenges and prospects of Escherichia coli as an organic acid production host under acid stress

Yang

Zhang

Zhu

et al. 2021

Appl Microbiol Biotechnol

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Objective Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production. Importance However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment. Elaboration This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application. Implication At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value. Key points • E. coli is a potential host for high value-added organic acids production.• Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules.• Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.

show abstract

Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity

Cited by 7 publications

References 60 publications

Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA

Modified Outer Membrane Protein-G Nanopores with Expanded and Truncated β-Hairpins for Recognition of Double-Stranded DNA

Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions

The challenges and prospects of Escherichia coli as an organic acid production host under acid stress

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