Biophysical and<i>in silico</i>characterization of NrtA: a protein-based host for aqueous nitrate and nitrite recognition

Ji, Ke; Baek, Kiheon; Peng, Weicheng; Alberto, Kevin; Torabifard, Hedieh; Nielsen, Steven O.; Dodani, Sheel C.

doi:10.1039/d1cc05879g

Cited by 5 publications

(5 citation statements)

References 49 publications

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Section: In Silico Characterizationmentioning

confidence: 99%

“…[19][20][21] To decode these supramolecular principles, we are actively investigating, engineering, and applying protein-based hosts for anions. [22][23][24][25][26][27][28] Along these lines, we have a growing program focused on anion sensors derived from the green fluorescent protein (GFP) family.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, protein engineering can be used to rapidly diversify the encoding sequence space and enrich for hosts with desired properties (e.g., selectivity, affinity) [19–21] . To decode these supramolecular principles, we are actively investigating, engineering, and applying protein‐based hosts for anions [22–28] . Along these lines, we have a growing program focused on anion sensors derived from the green fluorescent protein (GFP) family.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Ong

Pathiranage

et al. 2023

Angew Chem Int Ed

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Detection of anions in complex aqueous media is a fundamental challenge with practical utility that can be addressed by supramolecular chemistry. Biomolecular hosts such as proteins can be used and adapted as an alternative to synthetic hosts. Here, we report how the mutagenesis of the β-bulge residues (D137 and W138) in mNeonGreen, a bright, monomeric fluorescent protein, unlocks and tunes the anion preference at physiological pH for sulfate, resulting in the turn-off sensor SulfOFF-1. This unprecedented sensing arises from an enhancement in the kinetics of binding, largely driven by position 138. In line with these data, molecular dynamics (MD) simulations capture how the coordinated entry and gating of sulfate into the β-barrel is eliminated upon mutagenesis to facilitate binding and fluorescence quenching.

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Section: In Silico Characterizationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Ong

Pathiranage

et al. 2023

Angew Chem Int Ed

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“…Data was collected in triplicate from two protein preparations and is reported as the average with standard error of the mean. All experiments were carried out at room temperature (23)(24)(25) side of the β-barrel between them) (Figure 3). Of these, R140 is notably both near the β-bulge residues that are exposed to the bulk solvent and close to a nearby R195 residue located within the barrel, creating an outer and inner region of high positive charge.…”

Section: In Silico Characterizationmentioning

confidence: 99%

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Ong

Pathiranage

et al. 2023

Angewandte Chemie

Self Cite

View full text Add to dashboard Cite

Detection of anions in complex aqueous media is a fundamental challenge with practical utility that can be addressed by supramolecular chemistry. Biomolecular hosts such as proteins can be used and adapted as an alternative to synthetic hosts. Here, we report how the mutagenesis of the β‐bulge residues (D137 and W138) in mNeonGreen, a bright, monomeric fluorescent protein, unlocks and tunes the anion preference at physiological pH for sulfate, resulting in the turn‐off sensor SulfOFF‐1. This unprecedented sensing arises from an enhancement in the kinetics of binding, largely driven by position 138. In line with these data, molecular dynamics (MD) simulations capture how the coordinated entry and gating of sulfate into the β‐barrel is eliminated upon mutagenesis to facilitate binding and fluorescence quenching.

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“…23,41–44 These efforts are part of our larger program aimed at decoding the sequence level determinants of biological anion recognition. 45–47…”

Section: Introductionmentioning

confidence: 99%

Discovery of a monomeric green fluorescent protein sensor for chloride by structure-guided bioinformatics

et al. 2022

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Biophysical andin silicocharacterization of NrtA: a protein-based host for aqueous nitrate and nitrite recognition

Abstract: Nitrate and nitrite are key components of the global nitrogen cycle. As such, Nature has evolved proteins as biological supramolecular hosts for the recognition, translocation, and transformation of both nitrate...

Cited by 5 publications

References 49 publications

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Rational Design of the β‐Bulge Gate in a Green Fluorescent Protein Accelerates the Kinetics of Sulfate Sensing**

Discovery of a monomeric green fluorescent protein sensor for chloride by structure-guided bioinformatics

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