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Cooperative Allosteric Transitions

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...

Cooperative Allosteric Transitions

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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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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Predicting Allosteric Changes from Conformational Ensembles.

Martin Zacharias¹

¹Physics Department T38, Technical University of Munich, James-Franck-Straße 1, 85748 Garching, Germany; Center for Integrated Protein Science, 81377 Munich, Germany.

Structure (London, England : 1993)

|March 9, 2017

Summary

This summary is machine-generated.

Researchers developed a computational method to predict protein flexibility and binding sites. This approach uses two experimental structures to generate protein conformational ensembles, aiding in drug discovery.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Structural biology
Computational biology
Biophysics

Background:

Understanding protein dynamics is crucial for drug discovery.
Existing methods for predicting protein conformational ensembles can be computationally intensive.

Purpose of the Study:

To present a novel computational approach for generating protein conformational ensembles.
To enable rapid prediction of global protein flexibility.
To identify potential allosteric effector binding sites on proteins.

Main Methods:

A new computational method was developed.
The approach utilizes two experimental input structures.
It generates conformational ensembles of proteins.

Main Results:

The method successfully generates conformational ensembles.
It demonstrates potential for rapid prediction of protein flexibility.
Putative binding sites for allosteric effectors were identified.

Conclusions:

The described computational method offers a promising tool for protein dynamics prediction.
This approach can accelerate the identification of allosteric binding sites, relevant for drug development.