Chemoproteomic identification of CO2-dependent lysine carboxylation in proteins

King, D.T.; Zhu, Sha; Hardie, Darryl B.; Serrano-Negrón, Jesús E; Madden, Zarina; Kolappan, Subramania; Vocadlo, David J.

doi:10.1038/s41589-022-01043-1

Cited by 19 publications

(18 citation statements)

References 57 publications

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“…It is important to note that in the crystal structure of mNG at pH 8, the K143 residue can be carboxylated up to 70 %, but there is no evidence that this modification exists in solution to such an extent [36] . Moreover, given the transient, reversible nature of lysine carboxylation, this modification likely does not contribute to our in vitro measurements [45, 46] . As such, non‐carboxylated K143 was used for all simulations.…”

Section: Resultsmentioning

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

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: Resultsmentioning

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

Angew Chem Int Ed

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“…To this end, TB medium without supplement of NaCl was used for recombinant gene expression and 50 mM Na 2 HPO 3 -NaH 2 PO 3 pH 7.5 was used as the buffer throughout protein purification and activity studies in this study. Studies of the state of carbamylation on lysine have always been challenging, given its labile nature 39 . To confirm that biphasic kinetics is not caused by chloride-dependent decarbamylation, we synthesized N -acetylated lysine (AcK, Fig.…”

Section: Resultsmentioning

confidence: 99%

Discovery and molecular basis of chloride as an allosteric activator and catalytic inhibitor for Class-D β-lactamases

Zhou

Bell

Catalán

et al. 2022

Preprint

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Oxacillinase (OXA)-48-like carbapenemases are epidemic class D β -lactamases in Enterobacterales, resulting in high mortality. Though the chemical mechanism has been clearly established, for decades, the link between the biphasic kinetic behaviour of these enzymes, which significantly impacts antibiotic efficacy, and the state of carbamylated lysine has been elusive. Here, substituting N-carbamylated lysine73 with a chemically-stable N-acetyl lysine allows us to prove the origin of catalytic inhibition is not decarbamylation and enables us to capture an unprecedented inactive acyl-intermediate wedged in place by a chloride ion against the conserved residue arginine250. We here identify chloride as a "Janus effector" acting by allosteric activation of the burst phase and inhibition of the steady-state for a series of β-lactam substrates in kinetic assays. Chloride ions are necessarily present in both laboratory and clinical OXA activity assays and their inseparable role is now identified. Our finding suggests a new direction for the discovery of next-generation antibiotics specific for β-lactamases of Class D.

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“…One possible mechanism by which molecular CO 2 might trigger alterations in gene expression is by carbamylation of regulatory proteins. Carbamylation by reaction of CO 2 with the amino group of lysine residues represents a recently described post-translational modification that can alter protein function 41,42 . Whether Zfhx3 or upstream components of a putative CO 2 signaling pathway undergo differential carbamylation at normal vs elevated levels of PCO 2 is another direction for future investigation.…”

Section: Discussionmentioning

confidence: 99%

MyeloidZfhx3Deficiency Protects Against Hypercapnia-induced Suppression of Host Defense Against Influenza A Virus

Casalino‐Matsuda

Chen

González-González

et al. 2023

Preprint

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SummaryHypercapnia, elevation of the partial pressure of CO2in blood and tissues, is a risk factor for mortality in patients with severe acute and chronic lung diseases. We previously showed that hypercapnia inhibits multiple macrophage and neutrophil antimicrobial functions, and that elevated CO2increases the mortality of bacterial and viral pneumonia in mice. Here, we show that normoxic hypercapnia downregulates innate immune and antiviral gene programs in alveolar macrophages (AMØs). We also show that zinc finger homeobox 3 (Zfhx3), mammalian ortholog of zfh2, which mediates hypercapnic immune suppression inDrosophila, is expressed in mouse and human MØs. Deletion ofZfhx3in the myeloid lineage blocked the suppressive effect of hypercapnia on immune gene expression in AMØs and decreased viral replication, inflammatory lung injury and mortality in hypercapnic mice infected with influenza A virus. Our results establish Zfhx3 as the first known mammalian mediator of CO2effects on immune gene expression and lay the basis for future studies to identify therapeutic targets to interrupt hypercapnic immunosuppression in patients with advanced lung diseases.Graphical abstract

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Chemoproteomic identification of CO2-dependent lysine carboxylation in proteins

Cited by 19 publications

References 57 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**

Discovery and molecular basis of chloride as an allosteric activator and catalytic inhibitor for Class-D β-lactamases

MyeloidZfhx3Deficiency Protects Against Hypercapnia-induced Suppression of Host Defense Against Influenza A Virus

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