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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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Allosteric Regulation01:08

Allosteric Regulation

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Allosteric regulation of enzymes occurs when the binding of an effector molecule to a site that is different from the active site causes a change in the enzymatic activity. This alternate site is called an allosteric site, and an enzyme can contain more than one of these sites. Allosteric regulation can either be positive or negative, resulting in an increase or decrease in enzyme activity. Most enzymes that display allosteric regulation are metabolic enzymes involved in the degradation or...
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Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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...
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Related Experiment Video

Updated: Dec 14, 2025

Quantitative Analysis of Mitochondria-Associated Endoplasmic Reticulum Membrane (MAM) Stabilization in a Neural Model of Alzheimer's Disease (AD)
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Ensemble Allosteric Model for the Modified Wobble Hypothesis.

Aditya K Sarkar1, Joanna Sarzynska2, Ansuman Lahiri1

  • 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India.

The Journal of Physical Chemistry Letters
|July 24, 2020
PubMed
Summary
This summary is machine-generated.

The modified wobble hypothesis is supported by 2-thiouridine (s2U) in tRNAs. Molecular dynamics simulations show s2U shifts RNA structure from disordered to ordered, impacting codon recognition.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • The "modified wobble" hypothesis suggests tRNA modifications at the wobble position regulate codon recognition.
  • 2-thiouridine (s2U) is a key modification at the tRNA wobble position.

Purpose of the Study:

  • To investigate the structural impact of 2-thiouridine (s2U) modification on tRNA.
  • To elucidate the mechanism by which s2U influences RNA conformational dynamics and codon binding.

Main Methods:

  • Extensive molecular dynamics (MD) simulations were performed.
  • Custom χIDRP force field parameters were utilized for accurate simulation of the modified RNA.

Main Results:

  • The s2U modification induced a significant shift in the conformational ensemble of the RNA pentamer from a disordered to an ordered state.
  • Van der Waals interactions involving the sulfur atom of s2U were identified as the primary driver of this disorder-to-order transition.
  • The presence of s2U led to slower transitions between conformational clusters, indicating altered dynamics.

Conclusions:

  • The findings support the "modified wobble" hypothesis by demonstrating how s2U alters RNA structure and dynamics.
  • Ensemble allostery, driven by conformational redistribution and altered dynamics, is proposed as a key mechanism for wobble modification function in tRNAs.