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Related Concept Videos

Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...
Riboswitches01:56

Riboswitches

Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
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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.
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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...
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Cooperative Allosteric Transitions

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Using Modified Synthetic Oligonucleotides to Assay Nucleic Acid-Metabolizing Enzymes
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Published on: July 5, 2024

Mapping L1 ligase ribozyme conformational switch.

George M Giambaşu1, Tai-Sung Lee, William G Scott

  • 1BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.

Journal of Molecular Biology
|July 10, 2012
PubMed
Summary
This summary is machine-generated.

The L1 ligase (L1L) molecular switch uses a three-state process to transition between active and inactive states. This research clarifies the RNA catalyst

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Astrobiology

Background:

  • The L1 ligase (L1L) is a synthetic allosteric ribozyme.
  • L1L catalyzes a 5'-to-3' phosphodiester bond, a reaction crucial for prebiotic RNA self-replication.
  • The RNA world hypothesis posits RNA's central role in early life.

Purpose of the Study:

  • To understand the solution dynamics of L1L's active and inactive conformations.
  • To elucidate the mechanism of interconversion between L1L states.
  • To investigate the role of RNA catalysts in prebiotic chemistry.

Main Methods:

  • Explicit solvent molecular simulation.
  • Enhanced sampling method utilizing network theory concepts.
  • Conformational space network analysis.

Main Results:

  • The L1L switching mechanism follows a three-state, two-step process.
  • Step 1: Reorientation of stem C via a large-amplitude swing.
  • Step 2: Allosteric activation of the catalytic site through stem C contacts.
  • Distinct network topographical patterns characterize each step of the transition.

Conclusions:

  • L1L's switching mechanism provides a model for RNA-based catalysis.
  • The study reveals distinct pathways for stem C reorientation and catalytic site activation.
  • Findings support the feasibility of RNA self-replication in prebiotic scenarios.