Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D

Nair, Aparna G; Perumalla, D. Sravanakumar; Anjukandi, Padmesh

doi:10.1039/d1cp05819c

Cited by 4 publications

(4 citation statements)

References 82 publications

(120 reference statements)

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“…A trend similar to Tyr 42 ‐Asp 68 interaction is observed between Tyr 40 and Asp 68 (red and green in Figure 2A and Figure S6), indicating strong hydrogen bond interaction. Unlike the case of oxidized nDsbD, [33] the formation of Tyr 40 O − is feasible in nDsbD Red . Hence there exist chances of generating two internal nucleophiles (Tyr 42 O − and Tyr 40 O − ) in the neighbourhood of the nDsbD Red active site.…”

Section: Resultsmentioning

confidence: 96%

“…A trend similar to Tyr 42 -Asp 68 interaction is observed between Tyr 40 and Asp 68 (red and green in Figure 2A and Figure S6), indicating strong hydrogen bond interaction. Unlike the case of oxidized nDsbD, [33] In pTyr42, for the QM/MM MD MTD simulations, the CVs were defined as the difference in coordination number between proton donor and acceptor atoms such that CV1 and CV2 account for the formation of Tyr 42 O À (2) and Cys 103 S À (3), respectively (Figure S7 and S8). From the CV evolution plot (Figure S9), the generation of both Tyr 42 O À (only CV1 � 0.5) and Cys 103 S À (both CV � 0.5) were characterized.…”

Section: Resultsmentioning

confidence: 99%

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Disulfide Isomerization in nDsbD‐DsbC Complex – Exploring an Internal Nucleophile Mediated Reaction Pathway

2022

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The disulfide bond redox chemistry of proteins is believed to be mostly governed by the proton motive force. The nucleophilic and α-elimination mechanisms are also found to supplement the formation and scission of the SÀ S bonds. On these grounds, the possibility for an internal nucleophile assisted disulfide bond formation in the nDsbD-DsbC complex was proposed way back. Using QM/MM MD metadynamics simulations, we explore the feasibility of the proposed mechanism. Our simulations highlight the formation of the internal nucleophile Tyr 42 O À and Tyr 40 O À which further generates Cys 103 S À necessary for the disulfide bond formation in nDsbD. Our results illustrate how the isomerase DsbC is functionally activated by nDsbD in gramnegative bacteria. Also, we foresee that the results will be important for modelling anti-bacterial compounds based on nDsbD.

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Section: Resultsmentioning

confidence: 96%

Section: Resultsmentioning

confidence: 99%

Disulfide Isomerization in nDsbD‐DsbC Complex – Exploring an Internal Nucleophile Mediated Reaction Pathway

2022

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“…The bonds can be reversibly reduced and re‐oxidized and has evolved into a cell signalling component. Disulfide bond stability often plays an important role in the biological system because disulfide formation is a reversible process [21] . The ability to form and break a particular disulfide bond depends on the type of the oxidant or reductant under appropriate biological conditions [22] .…”

Section: Introductionmentioning

confidence: 99%

“…Disulfide bond stability often plays an important role in the biological system because disulfide formation is a reversible process. [21] The ability to form and break a particular disulfide bond depends on the type of the oxidant or reductant under appropriate biological conditions. [22] As a result, the research on disulfide isomerization is particularly interesting for the pharmaceuticals and agrochemicals industry.…”

Section: Introductionmentioning

confidence: 99%

Boat‐, Cuboid‐, and Dumbbell‐Shaped Hierarchical Morphology of Cerium (IV) Hydroxidophosphate Materials for Oxidative Coupling Reaction

Sarkar

Patra

2022

ChemNanoMat

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A simple hydrothermal approach was used to obtain boat‐, cuboid‐, and dumbbell‐shaped hierarchical morphology of cerium (IV) hydroxidophosphate materials. The period of the reactions, pH, and types of bases play crucial roles in tuning the morphology of the material. PXRD, FE‐SEM, HR‐TEM, FT‐IR, XPS, EDX, and EPR spectroscopies were used to analyze the materials. FE‐SEM and HR‐TEM analysis show that the materials have hierarchical morphology. According to XPS and EPR analysis, the materials comprise a redox‐active Ce3+/Ce4+ couple. The thiol to disulfide oxidative coupling reaction is synergistically boosted by the hierarchical morphology and redox‐active Ce3+/Ce4+ couple. The catalyst has excellent catalytic activity both in aqueous as well as protic organic solvents. However, the catalyst exhibited no reactivity in common organic solvents such as CH3CN, DCM, and THF. The catalytic reaction was thoroughly investigated in the presence of various solvents, catalyst amounts, oxidising agents, and substrates. In the presence of H2O2, the yield is 99%, whereas in the presence of air, it is 79%. We found high yields for several aromatic thiols but aliphatic thiols exhibited relatively poor yields under identical conditions.

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Association between microplastics and the functionalities of human gut microbiome

Gao,

Chen,

et al. 2025

Ecotoxicology and Environmental Safety

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Towards solvent regulated self-activation of N-terminal disulfide bond oxidoreductase-D

Abstract: N-Terminal Disulfide Bond Oxidoreductase-D (nDsbD), an essential redox enzyme in Gram-negative bacteria, consists of a single disulfide bond (Cys 103 −Cys 109 ) in its active site. The enzymatic functions...

Cited by 4 publications

References 82 publications

Disulfide Isomerization in nDsbD‐DsbC Complex – Exploring an Internal Nucleophile Mediated Reaction Pathway

Disulfide Isomerization in nDsbD‐DsbC Complex – Exploring an Internal Nucleophile Mediated Reaction Pathway

Boat‐, Cuboid‐, and Dumbbell‐Shaped Hierarchical Morphology of Cerium (IV) Hydroxidophosphate Materials for Oxidative Coupling Reaction

Association between microplastics and the functionalities of human gut microbiome

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