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E1 Reaction: Kinetics and Mechanism02:46

E1 Reaction: Kinetics and Mechanism

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Here, in contrast to the E2 reaction mechanism, we delve into the aspects of the E1 reaction mechanism, which has two steps: rate-limiting loss of the leaving group and abstraction of the beta hydrogen by a weak base. Typically, the experimental proof for the E1 mechanism is via kinetic studies or isotope studies. While the former demonstrates the first-order kinetics—the dependence of the reaction solely on substrate concentration—the latter proves the abstraction of hydrogen only...
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E2 Reaction: Kinetics and Mechanism02:45

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SN2 substitutions and E2 eliminations of alkyl halides proceed via a concerted pathway. While the nucleophile attacks the alpha carbon in SN2 reactions, it functions as a strong base and abstracts a beta hydrogen in the E2 mechanism. The rate-limiting transition state in E2 elimination reactions is characterized by partially broken carbon–hydrogen and carbon–halogen bonds and a partially formed pi bond between the alpha and beta carbons. The beta hydrogen and halide are eliminated...
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Energy Diagrams, Transition States, and Intermediates02:13

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Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
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Biosynthesis of Nucleic Acids01:28

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Nucleic acid biosynthesis is a fundamental biochemical process that produces the purine and pyrimidine nucleotides essential for DNA and RNA synthesis. This pathway maintains a balanced nucleotide pool, preventing imbalances that could jeopardize genetic integrity and cellular function. Given the crucial role of nucleotides, their synthesis is tightly regulated to ensure proper cellular homeostasis.Purine BiosynthesisThe biosynthesis of purine nucleotides begins with ribose-5-phosphate, a...
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E1 Reaction: Stereochemistry and Regiochemistry02:43

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One of the critical aspects of the E1 reaction mechanism, as also observed in E2, is the regiochemistry, with multiple regioisomers obtained as products. In the example discussed, the presence of water as a weak base favors elimination over substitution to generate two alkenes. Given that alkenes’ stability increases with the number of alkyl groups across the double bond, typically, E1 reactions lead to the Zaitsev product, for this is more substituted and stable than the Hofmann product.
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E2 Reaction: Stereochemistry and Regiochemistry02:43

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Elimination reactions of alkyl halides can yield one or more alkenes depending on the specific regiochemical and stereochemical considerations. While the regiochemistry of the reaction governs the location of the double bond in the product, the stereochemical requirements often influence the geometry.
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Structures, Properties, and Dynamics of Intermediates in eEF2-Diphthamide Biosynthesis.

Jean-Marc Billod1, Patricia Saenz-Mendez2, Anders Blomberg

  • 1Department of Chemical and Physical Biology, Center for Biological Research, CIB-CSIC , 28040 Madrid, Spain.

Journal of Chemical Information and Modeling
|August 16, 2016
PubMed
Summary

Diphthamide (DTA), a unique modification in eukaryotic translation Elongation Factor 2 (eEF2), is targeted by diphtheria toxin (DT). This study reveals DTA’s specific hydrogen bond interaction with asparagine, explaining DT’s mechanism and suggesting mutations to reduce toxin susceptibility.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Eukaryotic translation Elongation Factor 2 (eEF2) is crucial for protein synthesis.
  • eEF2 features a unique histidine modification to diphthamide (DTA) via intermediate steps.
  • DTA is susceptible to NAD(+)-dependent ADP-ribosylase toxins like diphtheria toxin (DT).

Purpose of the Study:

  • To investigate the differential susceptibility of diphthamide (DTA) and its biosynthetic precursors to bacterial toxins.
  • To elucidate the structural basis for DTA’s vulnerability to diphtheria toxin (DT).

Main Methods:

  • In silico structural and dynamic motion analysis of His699 intermediates (HIS, ACP, DTI, DTA).
  • Computational investigation of the interaction between DTA and diphtheria toxin (DT).
  • In silico mutagenesis of the DTA-modified protein to disrupt key interactions.

Main Results:

  • Diphthamide (DTA) forms a critical hydrogen bond with an asparagine residue, potentially mediating diphtheria toxin (DT) ADP-ribosylation.
  • In silico mutations designed to disrupt this hydrogen bond reduced the susceptibility of the modified protein to DT.
  • The mutant structure exhibited reduced DT susceptibility, similar to the diphthine (DTI) intermediate.

Conclusions:

  • The specific hydrogen bond interaction between DTA and asparagine is a key factor in diphtheria toxin (DT) targeting.
  • Targeting this interaction through protein modification offers a potential strategy to confer resistance to DT.
  • Understanding these molecular interactions is vital for developing novel therapeutic or protective approaches against bacterial toxins.