title: Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.
abstract: OBJECTIVE
  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.
  
  
  METHODS
  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.affiliation: 1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.
authors.forename: Mirko
authors.initials: M
authors.lastname: Zaffagnini
authors.affiliation: 2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .
authors.forename: Simona
authors.initials: S
authors.lastname: Fermani
authors.affiliation: 2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .
authors.forename: Matteo
authors.initials: M
authors.lastname: Calvaresi
authors.affiliation: 1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Orrù
authors.affiliation: 1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.
authors.forename: Luisa
authors.initials: L
authors.lastname: Iommarini
authors.affiliation: 1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Sparla
authors.affiliation: 2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Falini
authors.affiliation: 2 Department of Chemistry "G. Ciamician," University of Bologna , Bologna, Italy .
authors.forename: Andrea
authors.initials: A
authors.lastname: Bottoni
authors.affiliation: 1 Department of Pharmacy and Biotechnology, University of Bologna , Bologna, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Trost
mesh_terms: D017360:Arabidopsis / Q000378:metabolism*; D001665:Binding Sites; D020134:Catalytic Domain; D002736:Chloroplasts / Q000378:metabolism; D003545:Cysteine / Q000378:metabolism*; D003593:Cytoplasm / Q000378:metabolism; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases / Q000737:chemistry / Q000378:metabolism*; D006861:Hydrogen Peroxide / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation; D013434:Sulfenic Acids / Q000378:metabolism*
chemical_list: D013434:Sulfenic Acids; D006861:Hydrogen Peroxide; D005987:Glyceraldehyde-3-Phosphate Dehydrogenases; D003545:Cysteine