Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH

Mattioli, Edoardo Jun; Rossi, Jacopo; Meloni, Maria Laura; Mia, Marcello De; Marchand, Christophe; Tagliani, Andrea; Fanti, Silvia; Falini, Giuseppe; Trost, Paolo Bernardo; Lemaire, Stéphane D.; Fermani, Simona; Calvaresi, Matteo; Zaffagnini, Mirko

doi:10.1016/j.redox.2022.102387

Cited by 7 publications

(6 citation statements)

References 69 publications

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“…At least one of the protein's Cys residues went from oxidized to reduced status in the majority of the proteins. The cysteine thiols are subjected to redox‐dependent PTMs as intermediate oxidation states (Mattioli et al, 2022 ). Glutathione and disulfide on cysteines at catalysis sites are shown to be the end‐product of the oxidation (Zaffagnini et al, 2019 ), and the structures of these oxidation states have been shown to significantly alter the GAP2 structures and even form insoluble aggregates.…”

Section: Discussionmentioning

confidence: 99%

“…We chose SNO as a model to explore the intermediate oxidation cysteines on GAP2. While SNO is transient and labile, it provides clues to the incremental structural changes (Mattioli et al, 2022 ) in the midst of the oxidation process. The investigation of bulky glutathione or disulfide bonds will be addressed in future work because they both induce significant conformational changes in GAP2, and a simple FEP tool may not be efficient.…”

Section: Discussionmentioning

confidence: 99%

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PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on protein structures and their impacts on dynamics and functions

Mejia‐Rodriguez,

Kim,

Sadler

et al. 2023

Protein Science

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Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi, integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on protein structures and their impacts on dynamics and functions

Mejia‐Rodriguez,

Kim,

Sadler

et al. 2023

Protein Science

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“…Sequence alignment of Arabidopsis ADHs. The alignment was performed as described in (Mattioli et al, 2022) The selection of residues found in the catalytic cavity of both ADH1 and GSNOR was based on their presence in the active site for more than 50% of the available structures (at least 3 for ADH1 and 5 for GSNOR). These residues are highlighted in bold and underlined.…”

Section: Figure S1mentioning

confidence: 99%

“…Depending on reactivity and microenvironment, Cys residues can undergo a wide range of redox post‐translational modifications (PTMs) that are able to modulate protein function or alter structural conformations (Mattioli et al., 2022; Trost et al., 2017; Zaffagnini, De Mia, et al., 2016; Zaffagnini, Fermani, et al., 2019). This property makes Cys residues exceptionally important for redox homeostasis in plant cells and cysteines are considered the primary sensor of reactive oxygen and nitrogen species (ROS and RNS, respectively).…”

Section: Introductionmentioning

confidence: 99%

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Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity

Meloni,

Rossi,

Fanti

et al. 2024

The Plant Journal

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SUMMARYAlcohol dehydrogenases (ADHs) are a group of zinc‐binding enzymes belonging to the medium‐length dehydrogenase/reductase (MDR) protein superfamily. In plants, these enzymes fulfill important functions involving the reduction of toxic aldehydes to the corresponding alcohols (as well as catalyzing the reverse reaction, i.e., alcohol oxidation; ADH1) and the reduction of nitrosoglutathione (GSNO; ADH2/GSNOR). We investigated and compared the structural and biochemical properties of ADH1 and GSNOR from Arabidopsis thaliana. We expressed and purified ADH1 and GSNOR and determined two new structures, NADH‐ADH1 and apo‐GSNOR, thus completing the structural landscape of Arabidopsis ADHs in both apo‐ and holo‐forms. A structural comparison of these Arabidopsis ADHs revealed a high sequence conservation (59% identity) and a similar fold. In contrast, a striking dissimilarity was observed in the catalytic cavity supporting substrate specificity and accommodation. Consistently, ADH1 and GSNOR showed strict specificity for their substrates (ethanol and GSNO, respectively), although both enzymes had the ability to oxidize long‐chain alcohols, with ADH1 performing better than GSNOR. Both enzymes contain a high number of cysteines (12 and 15 out of 379 residues for ADH1 and GSNOR, respectively) and showed a significant and similar responsivity to thiol‐oxidizing agents, indicating that redox modifications may constitute a mechanism for controlling enzyme activity under both optimal growth and stress conditions.

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Reactive Nitrogen Species in Plant Metabolism

et al. 2023

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Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH

Cited by 7 publications

References 69 publications

PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on protein structures and their impacts on dynamics and functions

PTM‐Psi: A python package to facilitate the computational investigation of post‐translational modification on protein structures and their impacts on dynamics and functions

Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity

Reactive Nitrogen Species in Plant Metabolism

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