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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Ligand Binding and Linkage00:49

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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...
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Ligand Binding Sites02:40

Ligand Binding Sites

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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...
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Conservation of Protein Domains Over Different Proteins02:26

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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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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...
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Peptide-based Identification of Functional Motifs and their Binding Partners
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Peptide-based Identification of Functional Motifs and their Binding Partners

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Using Linear Motif Database Resources to Identify SH2 Domain Binders.

Hugo Sámano-Sánchez1,2,3, Toby J Gibson1, Lucía B Chemes4,5,6

  • 1Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

Methods in Molecular Biology (Clifton, N.J.)
|September 5, 2023
PubMed
Summary
This summary is machine-generated.

Short linear motifs (SLiMs) binding SH2 domains are crucial for cell signaling and pathogen interactions. This study presents bioinformatics strategies to identify these motifs, aiding in understanding protein complex regulation.

Keywords:
Binding specificityCell signalingPathogen hijackPhosphotyrosineRegular expressionSH2 domainShort linear motif (SLiM)

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Cellular Signaling

Background:

  • SH2-binding phosphotyrosine motifs are critical for intracellular signaling and pathogen interactions.
  • Predicting SH2 domain-motif binding is complex due to cooperative binding effects.
  • Existing methods like peptide arrays do not fully capture binding specificities.

Purpose of the Study:

  • To provide bioinformatics strategies for identifying SH2-binding motifs in proteins.
  • To offer a table of motif patterns for motif hunting.
  • To aid researchers in predicting functional protein-protein interactions.

Main Methods:

  • Utilizing bioinformatics tools and resources for motif prediction.
  • Analyzing conserved phosphotyrosine residues in intrinsically disordered protein regions.
  • Leveraging tissue and cell type expression data to refine interactor lists.

Main Results:

  • A framework for predicting candidate SH2-binding motifs is established.
  • Four distinct bioinformatics strategies are presented for motif hunting.
  • The study highlights the importance of considering cooperative binding and expression data.

Conclusions:

  • Bioinformatics approaches can effectively identify potential SH2-binding motifs.
  • These strategies assist in understanding motif-mediated signaling and pathogen interactions.
  • Experimental validation is crucial for confirming functional SH2 domain-motif partnerships.