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Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Diels–Alder vs Retro-Diels–Alder Reaction: Thermodynamic Factors01:31

Diels–Alder vs Retro-Diels–Alder Reaction: Thermodynamic Factors

The Diels–Alder reaction is thermally reversible, meaning that the reaction reverts to the starting diene and dienophile under suitable temperatures. The forward reaction gives a cyclohexene derivative and is favored at low to medium temperatures. The reverse process, also called retro-Diels–Alder reaction, is a ring-opening process favored at high temperatures.
Diels–Alder Reaction Forming Cyclic Products: Stereochemistry01:28

Diels–Alder Reaction Forming Cyclic Products: Stereochemistry

The Diels–Alder reaction is one of the robust methods for synthesizing unsaturated six-membered rings. The reaction involves a concerted cyclic movement of six π electrons: four π electrons from the diene and two π electrons from the dienophile.
Diels–Alder Reaction: Characteristics of Dienes01:29

Diels–Alder Reaction: Characteristics of Dienes

The Diels–Alder reaction brings together a diene and a dienophile to form a six-membered ring. Both components have unique characteristics that influence the rate of the reaction.
Characteristics of the diene
Conformation
The simplest example of a diene is 1,3-butadiene, an acyclic conjugated π system. At room temperature, the molecule exists as a mixture of s-cis and s-trans conformers by virtue of rotation around the carbon–carbon single bond. Although the s-trans isomer is more stable, the...
Diels–Alder Reaction: Characteristics of Dienophiles01:24

Diels–Alder Reaction: Characteristics of Dienophiles

In a Diels–Alder reaction, the diene is usually an electron-rich system and acts as a nucleophile, whereas the dienophile is electron-deficient and functions as an electrophile. Much like the diene, the nature of the dienophile significantly impacts the outcome of the reaction.
Characteristics of Dienophiles
Generally, the best dienophiles are alkenes containing electron-withdrawing substituents such as carbonyl, nitrile, and nitro groups. The feasibility of a Diels–Alder reaction depends on...

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The Importance of Correct Protein Concentration for Kinetics and Affinity Determination in Structure-function Analysis
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Diels-Alder ribozyme catalysis: a computational approach.

Xiaohua Zhang1, Thomas C Bruice

  • 1Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA.

Journal of the American Chemical Society
|January 25, 2007
PubMed
Summary

This study computationally compares the Diels-Alderase ribozyme and water reactions. The ribozyme active site binds reactants in optimal positions and angles, enhancing catalysis compared to water.

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Area of Science:

  • Biochemistry
  • Computational Chemistry
  • Enzymology

Background:

  • The Diels-Alder reaction is a crucial carbon-carbon bond-forming reaction.
  • Ribozymes, RNA enzymes, can catalyze various chemical transformations, including Diels-Alder reactions.
  • Understanding enzyme active site mechanisms is key to designing efficient catalysts.

Purpose of the Study:

  • To computationally compare the Diels-Alder reaction mechanism catalyzed by a Diels-Alderase ribozyme with the uncatalyzed reaction in water.
  • To elucidate the role of the ribozyme active site structure and dynamics in catalysis.
  • To investigate the origins of rate enhancement by the Diels-Alderase ribozyme.

Main Methods:

  • Computational modeling using SCCDFTB/MM (Self-Consistent Charge Density Functional Tight Binding/Molecular Mechanics).
  • Umbrella sampling technique to calculate free energy barriers.
  • Analysis of reaction coordinates, transition states, and atomic charges.

Main Results:

  • The ribozyme active site holds reactants in favorable conformations, with a specific tilted approach angle for anthracene.
  • The active site stabilizes the product more than the transition state.
  • Calculated free energy barriers for the ribozyme-catalyzed reaction closely match experimental values.
  • Active site dynamics were found to contribute minimally to catalysis.

Conclusions:

  • The Diels-Alderase ribozyme enhances reaction rates by pre-organizing reactants in the active site.
  • The active site's specific geometry and reactant positioning are critical for catalytic proficiency.
  • Computational methods accurately reproduce experimental observations for ribozyme-catalyzed Diels-Alder reactions.