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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...
The Two-State Receptor Model01:29

The Two-State Receptor Model

The two-state receptor model explains a drug's interaction with receptors, such as G protein-coupled receptors and ligand-gated ion channels, to induce or inhibit a biological response. When no natural ligands are present, a receptor exists in an equilibrium of inactive (Ri) and active (Ra) conformations. The inactive form does not produce a response, while the active form generates a basal effect known as constitutive activity.
The binding affinity of a drug determines its interaction with one...
G Protein-coupled Receptors01:15

G Protein-coupled Receptors

G Protein-Coupled Receptors or GPCRs are membrane-bound receptors that transiently associate with heterotrimeric G proteins and induce an appropriate response to sensory stimuli such as light, odors, hormones, cytokines, or neurotransmitters.
GPCRs are also called heptahelical, 7TM, or serpentine receptors, and consist of seven (H1-H7) transmembrane alpha-helices that span the bilayer to form a cylindrical core. The transmembrane helices are connected by three extracellular loops and three...
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...
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Predicting Toll-like receptor structures and characterizing ligand binding.

Joshua N Leonard1, Jessica K Bell, David M Segal

  • 1Experimental Immunology Branch, NCI, NIH, Bethesda, MD 20892-1360, USA.

Methods in Molecular Biology (Clifton, N.J.)
|April 21, 2009
PubMed
Summary
This summary is machine-generated.

This study presents novel methods for identifying non-consensus leucine-rich repeats (LRRs) in Toll-like receptors (TLRs). Understanding these unique TLR structures is crucial for developing new immunotherapies and antiviral drugs.

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07:48

Tracking Drug-induced Changes in Receptor Post-internalization Trafficking by Colocalizational Analysis

Published on: July 3, 2015

Area of Science:

  • Immunology
  • Structural Biology
  • Bioinformatics

Background:

  • Toll-like receptors (TLRs) possess ligand-binding domains with tandem leucine-rich repeat (LRR) motifs.
  • TLRs exhibit non-consensus LRR sequences, complicating identification by standard computational methods.

Purpose of the Study:

  • To develop and validate methods for identifying non-consensus LRRs in TLRs.
  • To investigate the structural impact of non-consensus LRRs on TLR3.
  • To establish protocols for producing TLR3 extracellular domain (ECD) protein for structural and binding studies.

Main Methods:

  • Development of computational approaches for non-consensus LRR identification.
  • Comparative analysis of hypothetical TLR3 models versus crystallographic data.
  • Establishment of methods for producing milligram quantities of recombinant TLR3-ECD.
  • Characterization of TLR3-ECD interaction with its ligand, double-stranded RNA (dsRNA).

Main Results:

  • Novel methods successfully identified non-consensus LRRs.
  • Hypothetical TLR models based on homology inaccurately predicted TLR3 structure.
  • Differences highlight the influence of non-consensus LRRs on TLR3 conformation.
  • Protocols for producing sufficient TLR3-ECD for structural and binding assays were established.

Conclusions:

  • Non-consensus LRRs significantly impact TLR structure, necessitating specialized identification methods.
  • Accurate TLR structural modeling requires accounting for these unique LRR variations.
  • The study provides a foundation for further research into TLR structure-function relationships and ligand interactions.