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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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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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Production of Disulfide-stabilized Transmembrane Peptide Complexes for Structural Studies
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One short cysteine-rich sequence pattern - two different disulfide-bonded structures - a molecular dynamics

Sonja A Dames1,2

  • 1Biomolecular NMR Spectroscopy, Department of Chemistry, Technische Universität München, 85747, Garching, Germany.

Journal of Peptide Science : an Official Publication of the European Peptide Society
|March 18, 2015
PubMed
Summary

Molecular dynamics simulations reveal that distinct structural preferences in cysteine-rich domains (CRDs) of Hydra proteins NW1 and Mcol1C dictate their unique disulfide bond patterns, crucial for understanding protein folding and therapeutics.

Keywords:
GROMOSNOWAcysteine-rich domaindisulfide bond patternhydraminicollagen-1molecular dynamics simulationsoxidative folding

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Dynamics

Background:

  • Nematocyst walls in Hydra are constructed from proteins featuring cysteine-rich domains (CRDs).
  • Two specific CRDs, NW1 and Mcol1C, possess six conserved cysteines but form different disulfide bond structures.
  • Understanding these structural differences is key to elucidating protein folding mechanisms.

Purpose of the Study:

  • To investigate the structural preferences of NW1 and Mcol1C in their non-disulfide bonded states.
  • To determine if these preferences explain the distinct disulfide bond connectivities observed in NW1 and Mcol1C.
  • To explore the folding mechanisms of these proteins using computational simulations.

Main Methods:

  • Molecular dynamics (MD) simulations were conducted at various temperatures (e.g., 283 K) for 100 ns.
  • Analysis of backbone dihedral angles (Φ/ψ) to assess turn propensities.
  • Comparison of simulation data with existing NMR residual dipolar coupling data.

Main Results:

  • NW1 adopted a compact fold stabilized by hydrogen bonds during MD simulations.
  • Mcol1C exhibited more structural fluctuations but remained largely compact.
  • Distinct turn propensities were identified for NW1 and Mcol1C, correlating with their amino acid sequences and side-chain influences.
  • NW1 folding may follow a precursor mechanism, while Mcol1C might employ a quasi-stochastic folding model with disulfide reshuffling.

Conclusions:

  • MD simulations effectively detect local structural preferences in dynamic protein states.
  • These preferences, encoded in the amino acid sequence, guide disulfide bond formation.
  • Findings advance the understanding of oxidative folding and the design of disulfide-stabilized therapeutics.