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Related Concept Videos

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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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...

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Published on: August 9, 2019

Inferring protein-DNA interaction parameters from SELEX experiments.

Marko Djordjevic1

  • 1Faculty of Biology, Department of Chemistry and Physics, University of Belgrade, Arkansas State University, Studentski trg 16, 11000 Belgrade, Serbia. dmarko@bio.bg.ac.rs

Methods in Molecular Biology (Clifton, N.J.)
|September 10, 2010
PubMed
Summary
This summary is machine-generated.

Systematic Evolution of Ligands by EXponential enrichment (SELEX) can now accurately determine protein-DNA interactions. This method aids in predicting transcription factor binding sites without prior specificity data.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics and Computational Biology

Background:

  • Systematic Evolution of Ligands by EXponential enrichment (SELEX) isolates high-affinity oligonucleotides for molecular targets.
  • SELEX has significant applications in research, diagnostics, and therapeutics.
  • Recent SELEX modifications enable precise inference of protein-DNA interaction parameters.

Purpose of the Study:

  • To detail the experimental and computational procedures for accurately determining protein-DNA interaction parameters using SELEX.
  • To highlight the capability of SELEX to predict transcription factor binding sites without prior specificity information.

Main Methods:

  • Utilizing modified SELEX protocols to generate high-affinity binding sequences.
  • Employing computational procedures for the analysis of SELEX data.
  • Integrating experimental and computational approaches for parameter inference.

Main Results:

  • Accurate determination of protein-DNA interaction parameters is achievable.
  • Precise prediction of transcription factor binding sites is possible, even without a priori information.
  • New SELEX modifications enhance the accuracy of interaction parameter inference.

Conclusions:

  • Modified SELEX combined with computational analysis offers unprecedented accuracy in determining protein-DNA interactions.
  • This approach facilitates the prediction of binding sites for various transcription factors.
  • The discussed methods provide a robust framework for advancing research in molecular recognition and gene regulation.