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Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.
Antioxid Redox Signal. 2016 Mar 20; 24(9):502-17.AR

Abstract

AIMS

Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively).

RESULTS

Although AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA.

INNOVATION

Based on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation.

CONCLUSIONS

QM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 Å distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments.

Authors+Show Affiliations

1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26650776

Citation

Zaffagnini, Mirko, et al. "Tuning Cysteine Reactivity and Sulfenic Acid Stability By Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis Thaliana." Antioxidants & Redox Signaling, vol. 24, no. 9, 2016, pp. 502-17.
Zaffagnini M, Fermani S, Calvaresi M, et al. Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana. Antioxid Redox Signal. 2016;24(9):502-17.
Zaffagnini, M., Fermani, S., Calvaresi, M., Orrù, R., Iommarini, L., Sparla, F., Falini, G., Bottoni, A., & Trost, P. (2016). Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana. Antioxidants & Redox Signaling, 24(9), 502-17. https://doi.org/10.1089/ars.2015.6417
Zaffagnini M, et al. Tuning Cysteine Reactivity and Sulfenic Acid Stability By Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis Thaliana. Antioxid Redox Signal. 2016 Mar 20;24(9):502-17. PubMed PMID: 26650776.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana. AU - Zaffagnini,Mirko, AU - Fermani,Simona, AU - Calvaresi,Matteo, AU - Orrù,Roberto, AU - Iommarini,Luisa, AU - Sparla,Francesca, AU - Falini,Giuseppe, AU - Bottoni,Andrea, AU - Trost,Paolo, Y1 - 2016/02/01/ PY - 2015/12/10/entrez PY - 2015/12/10/pubmed PY - 2016/12/15/medline SP - 502 EP - 17 JF - Antioxidants & redox signaling JO - Antioxid. Redox Signal. VL - 24 IS - 9 N2 - AIMS: Cysteines and H2O2 are fundamental players in redox signaling. Cysteine thiol deprotonation favors the reaction with H2O2 that generates sulfenic acids with dual electrophilic/nucleophilic nature. The protein microenvironment surrounding the target cysteine is believed to control whether sulfenic acid can be reversibly regulated by disulfide formation or irreversibly oxidized to sulfinates/sulfonates. In this study, we present experimental oxidation kinetics and a quantum mechanical/molecular mechanical (QM/MM) investigation to elucidate the reaction of H2O2 with glycolytic and photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Arabidopsis thaliana (cytoplasmic AtGAPC1 and chloroplastic AtGAPA, respectively). RESULTS: Although AtGAPC1 and AtGAPA have almost identical 3D structure and similar acidity of their catalytic Cys149, AtGAPC1 is more sensitive to H2O2 and prone to irreversible oxidation than AtGAPA. As a result, sulfenic acid is more stable in AtGAPA. INNOVATION: Based on crystallographic structures of AtGAPC1 and AtGAPA, the reaction potential energy surface for Cys149 oxidation by H2O2 was calculated by QM. In both enzymes, sulfenic acid formation was characterized by a lower energy barrier than sulfinate formation, and sulfonate formation was prevented by very high energy barriers. Activation energies for both oxidation steps were lower in AtGAPC1 than AtGAPA, supporting the higher propensity of AtGAPC1 toward irreversible oxidation. CONCLUSIONS: QM/MM calculations coupled to fingerprinting analyses revealed that two Arg of AtGAPA (substituted by Gly and Val in AtGAPC1), located at 8-15 Å distance from Cys149, are the major factors responsible for sulfenic acid stability, underpinning the importance of long-distance polar interactions in tuning sulfenic acid stability in native protein microenvironments. SN - 1557-7716 UR - https://www.unboundmedicine.com/medline/citation/26650776/Tuning_Cysteine_Reactivity_and_Sulfenic_Acid_Stability_by_Protein_Microenvironment_in_Glyceraldehyde_3_Phosphate_Dehydrogenases_of_Arabidopsis_thaliana_ L2 - https://www.liebertpub.com/doi/full/10.1089/ars.2015.6417?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -