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Related Concept Videos

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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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Related Experiment Video

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Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

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Published on: April 26, 2013

Structural modeling of TAL effector-DNA interactions.

Philip Bradley1

  • 1Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, M1-B514, Seattle, Washington 98109, USA. pbradley@fhcrc.org

Protein Science : a Publication of the Protein Society
|February 16, 2012
PubMed
Summary
This summary is machine-generated.

Transcriptional activator-like (TAL) effectors bind DNA with high specificity. Our models reveal TAL proteins form a superhelical structure that wraps around B-form DNA, with specific repeat residues dictating DNA base recognition.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Transcriptional activator-like (TAL) effectors are DNA-binding proteins.
  • TAL effectors exhibit a unique 1:1 mapping between repeat residues and DNA bases for target recognition.
  • The structural basis for this specific TAL-DNA interaction remains largely unknown.

Purpose of the Study:

  • To elucidate the structural mechanism underlying TAL effector DNA binding.
  • To investigate how the 1:1 repeat-base recognition is accommodated by DNA structure.
  • To provide insights into the overall structure of TAL proteins in complex with DNA.

Main Methods:

  • Development of a structure prediction protocol specifically for the TAL-DNA system.
  • Computational simulations to model TAL-DNA interactions.
  • Analysis of repeat-base associations and overall TAL protein structure.

Main Results:

  • TAL repeat domains form a superhelical structure that encircles B-form DNA.
  • This structure runs parallel to the DNA major groove.
  • Specific contacts between repeat position 13 and the DNA sense strand determine recognition specificity.

Conclusions:

  • The proposed model explains the observed TAL-DNA repeat-base associations.
  • TAL-DNA recognition is achieved through a superhelical wrap around undistorted B-form DNA.
  • Position 13 of the TAL repeat is crucial for sequence-specific DNA binding.