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Related Concept Videos

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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Cooperative Allosteric Transitions

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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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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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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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Mutations01:35

Mutations

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Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
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AlloSigMA: allosteric signaling and mutation analysis server.

Enrico Guarnera1, Zhen Wah Tan1, Zejun Zheng1

  • 1Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138671, Singapore.

Bioinformatics (Oxford, England)
|November 7, 2017
PubMed
Summary
This summary is machine-generated.

The AlloSigMA server offers a novel computational tool for analyzing protein allostery. It quantifies the energetic impact of mutations and ligand binding, aiding protein engineering and drug design.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Allostery is a fundamental mechanism for protein function regulation through exosites.
  • Existing resources lack efficient methods for assessing allosteric communication causality and energetics.

Purpose of the Study:

  • To introduce the AlloSigMA server for estimating allosteric effects.
  • To provide a framework for analyzing ligand binding and mutation impacts on protein allostery.

Main Methods:

  • Utilizes structure-based statistical mechanical models of allosteric signaling.
  • Provides an interactive computational framework for free energy estimation.

Main Results:

  • Enables estimation of allosteric free energy changes from ligand binding and mutations.
  • Facilitates detection and exploration of latent regulatory exosites and mutation effects.

Conclusions:

  • AlloSigMA aids protein engineering and allosteric drug design by quantifying allosteric effects.
  • The server offers a unique approach to understanding protein allosteric communication.