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Related Concept Videos

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...
Cooperative Allosteric Transitions01:58

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 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...
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,...
SN2 Reaction: Transition State02:26

SN2 Reaction: Transition State

An SN2 reaction of an alkyl halide is a single-step process in which bond formation between the nucleophile and the substrate and bond breaking between the substrate and the halide occurs simultaneously through a transition state without forming an intermediate.
When the nucleophile approaches the electrophilic carbon with its lone pairs, the halide acts as a leaving group and moves away with the electron-pair bonded to the carbon. Dotted partial bonds represent the bonds being formed or broken...
Predicting Products: SN1 vs. SN202:27

Predicting Products: SN1 vs. SN2

Nucleophilic substitution reactions of alkyl halides can proceed via an SN1 or an SN2 mechanism. While in SN2 reactions, the nucleophile attacks the substrate simultaneously as the leaving group departs, in SN1 reactions, the substrate first dissociates to give the carbocation intermediate. Various factors such as the structure of the substrate, the strength of the nucleophile, and the nature of the solvent promote one mechanism over the other.
With increased substitution on the alkyl halide,...

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Related Experiment Video

Updated: Jun 14, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Size matters: side chain length affects SH2 substrate binding.

Christian F W Becker1

  • 1Center of Integrated Protein Science Munich and Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching b. München, Germany. christian.becker@ch.tum.de

Chemistry & Biology
|March 27, 2010
PubMed
Summary
This summary is machine-generated.

Researchers explored how lysine analogs affect Src Homology 2 (SH2) domain function. The study found that amino acid side chain length is crucial for recognizing phosphotyrosine peptides and influences binding specificity.

Related Experiment Videos

Last Updated: Jun 14, 2026

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability
09:49

Sedimentation Equilibrium of a Small Oligomer-forming Membrane Protein: Effect of Histidine Protonation on Pentameric Stability

Published on: April 2, 2015

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Protein Engineering

Background:

  • The Src Homology 2 (SH2) domain is a critical protein module involved in signal transduction by binding to phosphotyrosine residues.
  • Understanding the specificity of SH2 domain-peptide interactions is essential for deciphering cellular signaling pathways.

Discussion:

  • Virdee et al. (2010) investigated the role of lysine analogs in modifying SH2 domain variants.
  • This research focused on the impact of amino acid side chain length on the recognition of phosphotyrosine-containing substrate peptides.

Key Insights:

  • The study demonstrates a length-dependent contribution of a single amino acid side chain in SH2 domain binding.
  • Altering side chain length can lead to significant changes in the specificity of SH2 domain-peptide recognition.

Outlook:

  • Further exploration of amino acid side chain modifications could lead to novel tools for modulating protein-protein interactions.
  • These findings have implications for designing peptides with tailored binding specificities for therapeutic or diagnostic applications.