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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding and Linkage00:49

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 the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Allosteric Proteins-ATCase01:19

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 pathway,...

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry
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AutoMap: a tool for analyzing protein-ligand recognition using multiple ligand binding modes.

Mark Agostino1, Ricardo L Mancera, Paul A Ramsland

  • 1Western Australian Biomedical Research Institute, Curtin Health Innovation Research Institute, School of Biomedical Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia. mark.agostino@curtin.edu.au

Journal of Molecular Graphics & Modelling
|February 5, 2013
PubMed
Summary

AutoMap enhances drug design by predicting protein residues crucial for ligand binding. This automated tool considers multiple binding modes, improving accuracy in identifying key interaction sites for various protein-ligand systems.

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Area of Science:

  • Computational chemistry and structural biology
  • Drug discovery and development

Background:

  • Predicting protein residues involved in ligand recognition is vital for structure-based drug design.
  • Current methods often overlook the importance of multiple ligand binding modes.

Purpose of the Study:

  • To present AutoMap, a partially automated implementation of the site mapping technique.
  • To evaluate AutoMap's ability to predict key ligand binding residues by considering multiple binding modes.

Main Methods:

  • AutoMap utilizes molecular docking outputs to generate protein binding site maps.
  • It analyzes hydrogen bonding and van der Waals interactions for each ligand pose.
  • An automated procedure optimizes cutoff selection for residue identification.

Main Results:

  • AutoMap successfully maps interactions to protein surfaces, identifying key residues.
  • Automated cutoff optimization rapidly identified appropriate parameters for tested systems.
  • AutoMap with optimized cutoffs demonstrated improved predictions compared to other methods in immunological test cases.

Conclusions:

  • The automated site mapping technique, AutoMap, offers a robust approach for predicting protein-ligand interaction sites.
  • Its ability to consider multiple binding modes and automated optimization enhances its utility in drug design.
  • AutoMap provides an opportunity for rapid deployment in diverse protein-ligand system investigations.