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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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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 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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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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Spatiotemporal Control of Protein Activity through Optogenetic Allosteric Regulation
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Exploring the Allosteric Territory of Protein Function.

Wei-Ven Tee1,2, Zhen Wah Tan1, Keene Lee1

  • 1Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, 138671, Singapore.

The Journal of Physical Chemistry. B
|April 12, 2021
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Summary
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This study demonstrates that allosteric mechanisms are universal across diverse proteins, including viral and metabolic enzymes. A computational framework is presented for controlling protein function and designing allosteric drugs.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Structural Biology
  • Computational Biology

Background:

  • Allostery is a fundamental mechanism regulating protein function.
  • Understanding allosteric regulation is crucial for drug discovery and understanding disease mechanisms.

Purpose of the Study:

  • To demonstrate the generic nature of allosteric mechanisms across various protein types.
  • To present a computational framework for analyzing and controlling protein allostery.
  • To explore the potential for designing allosteric effectors and drug candidates.

Main Methods:

  • Structure-based statistical mechanical model of allostery (SBSMMA).
  • Analysis of allosteric signaling in specific proteins: viroporin 3a, SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), isocitrate dehydrogenase 1 (IDH1), and fumarate hydratase (FH).
  • Prediction of allosteric sites and exploration of mutation effects.

Main Results:

  • Demonstrated the pervasive and generic nature of allosteric mechanisms.
  • Successfully analyzed allosteric signaling and predicted allosteric sites.
  • Explored the impact of mutations on protein allostery.
  • Showcased the framework's utility in inducing and tuning allosteric responses.

Conclusions:

  • Allosteric mechanisms are broadly applicable across diverse protein families.
  • The proposed computational framework enables comprehensive allosteric control and aids in designing allosteric drugs.
  • Further research into allosteric mechanisms is vital for biomedical applications, including cancer and viral diseases.