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Related Concept Videos

Allosteric Regulation01:08

Allosteric Regulation

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...
Allosteric Regulation01:08

Allosteric Regulation

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Cooperative Allosteric Transitions01:58

Cooperative Allosteric Transitions

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...
Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

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 pathway,...

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Updated: Jun 19, 2026

Characterizing Modulators of Protease-Activated Receptors with a Calcium Mobilization Assay Using a Plate Reader
07:13

Characterizing Modulators of Protease-Activated Receptors with a Calcium Mobilization Assay Using a Plate Reader

Published on: May 24, 2024

Thrombin allosteric modulation revisited: a molecular dynamics study.

Hermes Luís Neubauer de Amorim1, Paulo Augusto Netz, Jorge Almeida Guimarães

  • 1Laboratório de Bioinformática Estrutural (LaBiE), Universidade Luterana do Brasil (ULBRA), Sala 122, Prédio 01, Av. Farroupilha 1001, Canoas, RS, Brazil. hamorim@cbiot.ufrgs.br

Journal of Molecular Modeling
|October 10, 2009
PubMed
Summary
This summary is machine-generated.

Thrombin

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Last Updated: Jun 19, 2026

Characterizing Modulators of Protease-Activated Receptors with a Calcium Mobilization Assay Using a Plate Reader
07:13

Characterizing Modulators of Protease-Activated Receptors with a Calcium Mobilization Assay Using a Plate Reader

Published on: May 24, 2024

Tracking Fibrinolysis of Chandler Loop-Formed Whole Blood Clots Under Shear Flow in An In-Vitro Thrombolysis Model
06:16

Tracking Fibrinolysis of Chandler Loop-Formed Whole Blood Clots Under Shear Flow in An In-Vitro Thrombolysis Model

Published on: April 19, 2024

Area of Science:

  • Biochemistry and Molecular Biology
  • Protein Dynamics and Regulation

Background:

  • Thrombin exhibits regulatory properties through distinct functional conformations.
  • Two equilibrium states, fast (procoagulant) and slow (anticoagulant), characterize thrombin.
  • Mechanisms of thrombin regulation by effectors remain incompletely understood.

Purpose of the Study:

  • To investigate dynamic events from sodium ion (Na+) and ligand interactions with thrombin.
  • To elucidate conformational changes at the active site and anion binding exosite 1 (ABE1).

Main Methods:

  • Molecular dynamics (MD) simulations of thrombin in various bound states.
  • Analysis of conformational changes induced by sodium ion displacement.

Main Results:

  • Sodium ion release promotes a closed thrombin conformation, resembling the slow form.
  • Key conformational changes include loop distortions, side-chain rotations, and loop projections.
  • Observed changes correlate with known structural properties of fast and slow thrombin forms.

Conclusions:

  • Evidence supports communication between diverse functional domains of thrombin.
  • MD simulations provide detailed structural insights complementing existing knowledge.
  • Findings advance the understanding of thrombin's structure-function relationship.