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Allosteric Proteins-ATCase

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...

Cooperative Allosteric Transitions

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...

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

Allosteric Regulation

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...

Protein Folding

Protein Folding

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

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Related Experiment Video

Updated: Aug 16, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Machine learning and protein allostery.

Sian Xiao¹, Gennady M Verkhivker², Peng Tao¹

¹Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75205, USA.

Trends in Biochemical Sciences

|December 23, 2022

Summary

This summary is machine-generated.

Machine learning is revolutionizing the study of allosteric proteins, crucial for cell signaling. These methods aid in understanding protein dynamics, predicting effects, and engineering proteins, including drug design for SARS-CoV-2.

Keywords:

allostery drug discovery machine learning mechanism prediction protein design

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Area of Science:

Biochemistry and computational biology

Background:

Allosterically regulated proteins are vital for signal transduction and cellular functions.
Machine learning (ML) methods are increasingly used to study protein dynamics and allosteric mechanisms.

Purpose of the Study:

To review recent advancements in applying ML to protein allostery.
To highlight ML's role in predicting allosteric effects and engineering allosteric proteins.
To discuss ML applications in SARS-CoV-2 drug design targeting allosteric mechanisms.

Main Methods:

Survey of recent literature on ML applications in protein allostery.
Analysis of ML strategies for characterizing allosteric mechanisms.
Review of ML in predicting allosteric effects and related properties.

Main Results:

ML facilitates theoretical and experimental studies of protein dynamics and allosteric mechanisms.
ML aids in predicting allosteric effects and allostery-related physicochemical properties.
ML is applied in allosteric protein engineering and drug design, notably for SARS-CoV-2.

Conclusions:

ML methods are essential for advancing the understanding of protein allosteric mechanisms.
Continued development of ML will bridge experimental and theoretical data-intensive technologies.
ML plays a critical role in drug discovery and protein engineering related to allostery.