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Related Concept Videos

Preparation and Reactions of Sulfides02:26

Preparation and Reactions of Sulfides

5.1K
Sulfides are the sulfur analog of ethers, just as thiols are the sulfur analog of alcohol. Like ethers, sulfides also consist of two hydrocarbon groups bonded to the central sulfur atom. Depending upon the type of groups present, sulfides can be symmetrical or asymmetrical. Symmetrical sulfides can be prepared via an SN2 reaction between 2 equivalents of an alkyl halide and one equivalent of sodium sulfide.
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SN2 Reaction: Stereochemistry02:23

SN2 Reaction: Stereochemistry

9.8K
In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
If the substrate is an achiral molecule at the α-carbon, the inversion of configuration is not...
9.8K
SN2 Reaction: Transition State02:26

SN2 Reaction: Transition State

10.1K
An SN2 reaction of an alkyl halide is a single-step process in which bond formation between the nucleophile and the substrate and bond breaking between the substrate and the halide occurs simultaneously through a transition state without forming an intermediate.
When the nucleophile approaches the electrophilic carbon with its lone pairs, the halide acts as a leaving group and moves away with the electron-pair bonded to the carbon. Dotted partial bonds represent the bonds being formed or broken...
10.1K
Preparation and Reactions of Thiols02:33

Preparation and Reactions of Thiols

6.6K
Thiols are prepared using the hydrosulfide anion as a nucleophile in a nucleophilic substitution reaction with alkyl halides. For instance, bromobutane reacts with sodium hydrosulfide to give butanethiol.
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SN2 Reaction: Mechanism02:27

SN2 Reaction: Mechanism

14.7K
The kinetic studies of SN2 reactions suggest an essential feature of its mechanism: it is a single-step process without intermediates. Here, both the nucleophile and the substrate participate in the rate-determining step.
The presence of the more electronegative halogen in the substrate creates a polarized carbon-halide bond. The halide pulls the electron cloud generating an electrophilic center at the carbon atom. Thus, the carbon atom carries a partial positive charge while the halide has a...
14.7K
Diels–Alder Reaction Forming Bridged Bicyclic Products: Stereochemistry01:29

Diels–Alder Reaction Forming Bridged Bicyclic Products: Stereochemistry

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Diels–Alder reactions between cyclic dienes locked in an s-cis configuration and dienophiles yield bridged bicyclic products.
4.7K

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Combining Non-reducing SDS-PAGE Analysis and Chemical Crosslinking to Detect Multimeric Complexes Stabilized by Disulfide Linkages in Mammalian Cells in Culture
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Combining Non-reducing SDS-PAGE Analysis and Chemical Crosslinking to Detect Multimeric Complexes Stabilized by Disulfide Linkages in Mammalian Cells in Culture

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Disulfide Isomerization in nDsbD-DsbC Complex - Exploring an Internal Nucleophile Mediated Reaction Pathway.

Aparna G Nair1, D Sravanakumar Perumalla1,2, Padmesh Anjukandi1

  • 1Department of Chemistry, Indian Institute of Technology, 678557, Palakkad, Kerala, India.

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
|July 20, 2022
PubMed
Summary

This study reveals how the nDsbD protein activates the DsbC isomerase in bacteria. It identifies specific tyrosine residues acting as internal nucleophiles to facilitate disulfide bond formation, crucial for bacterial function.

Keywords:
Ab initio molecular dynamicsdisulfide isomerizationmetadynamicsnucleophilesproton transfer

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Computational Chemistry

Background:

  • Protein disulfide bond formation is vital for cellular function.
  • Existing models suggest proton motive force and nucleophilic mechanisms govern S-S bond dynamics.
  • The role of internal nucleophiles in the nDsbD-DsbC complex was previously proposed.

Purpose of the Study:

  • To investigate the feasibility of internal nucleophile-assisted disulfide bond formation in the nDsbD-DsbC complex.
  • To elucidate the mechanism of DsbC activation by nDsbD in gram-negative bacteria.

Main Methods:

  • Utilized Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) metadynamics simulations.
  • Analyzed the dynamics of the nDsbD-DsbC complex to identify key reactive species.

Main Results:

  • Simulations confirmed the formation of internal nucleophiles Tyr42 O⁻ and Tyr40 O⁻.
  • These nucleophiles were shown to generate Cys103 S⁻, essential for disulfide bond formation in nDsbD.
  • Demonstrated the functional activation mechanism of DsbC isomerase by nDsbD.

Conclusions:

  • The study provides mechanistic insights into disulfide bond formation mediated by internal nucleophiles in the nDsbD-DsbC system.
  • Findings clarify how nDsbD activates DsbC in gram-negative bacteria.
  • Results offer a basis for developing novel antibacterial compounds targeting nDsbD.