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Related Concept Videos

Introduction to Mechanisms of Enzyme Catalysis01:13

Introduction to Mechanisms of Enzyme Catalysis

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For many years, scientists thought that enzyme-substrate binding took place in a simple "lock-and-key" fashion. This model stated that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view scientists call induced fit. The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes...
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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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Allosteric Proteins-ATCase01:19

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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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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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Induced-fit Model01:13

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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Ligand Binding and Linkage00:49

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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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Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences.

Heidi Klem1, Martin McCullagh2, Robert S Paton1

  • 1Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.

Topics in Catalysis
|October 28, 2022
PubMed
Summary
This summary is machine-generated.

Understanding enzyme dynamics and allostery is crucial for drug discovery and enzyme design. This study explores multistate models and structural clustering to bridge quantum mechanics and molecular dynamics for better computational enzyme modeling.

Keywords:
AllosteryBiocatalysisComputational chemistryConformational ensemblesMolecular DynamicsMolecular modelingReaction mechanisms

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Area of Science:

  • Biochemistry and enzymology
  • Computational chemistry
  • Structural biology

Background:

  • Enzymatic mechanisms are key for biologics discovery, biocatalysis, and enzyme design.
  • Quantum mechanical (QM) methods like Density Functional Theory (DFT) enable detailed study of enzymatic reactions.
  • Large-scale enzyme conformational changes in allosteric enzymes pose challenges for QM and molecular mechanics (MM) methods.

Purpose of the Study:

  • To provide an overview of multistate models for enzyme catalysis and allostery.
  • To discuss the challenges posed by large-scale conformational changes in allosteric enzymes for computational modeling.
  • To highlight structural clustering as a method to integrate molecular dynamics and QM cluster models.

Main Methods:

  • Review of multistate models for enzyme catalysis and allostery.
  • Discussion of QM, QM/MM, and MM potentials for enzyme simulations.
  • Application of structural clustering to bridge conformational sampling and quantum chemical models.
  • Case study using Imidazole Glycerol Phosphate Synthase (IGPS).

Main Results:

  • Multistate models are essential for understanding enzyme catalysis and allostery.
  • Bridging timescales and length scales of enzyme dynamics requires integrated computational approaches.
  • Structural clustering effectively connects MM-based conformational sampling with QM-based catalytic models.
  • Imidazole Glycerol Phosphate Synthase (IGPS) exemplifies the importance of multiple conformations.

Conclusions:

  • Accurate computational modeling of allosteric enzymes requires accounting for multiple conformations.
  • Structural clustering offers a promising strategy for quantitative modeling of enzyme allostery.
  • Further development in computational methods is needed to fully capture enzyme dynamics and allosteric regulation.