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Studying DNA Looping by Single-Molecule FRET
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Conformational elasticity can facilitate TALE-DNA recognition.

Hongxing Lei1, Jiya Sun2, Enoch P Baldwin3

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; UC Davis Genome Center and Department of Biomedical Engineering, One Shields Avenue, Davis, California, USA.

Advances in Protein Chemistry and Structural Biology
|March 18, 2014
PubMed
Summary

Transcription activator-like effector (TALE) proteins exhibit high elasticity, allowing conformational changes between unbound and DNA-bound states with minimal energy cost. Computational analysis reveals TALE repeat-variable di-residues (RVDs) effectively discriminate cognate DNA bases, ensuring binding specificity.

Keywords:
BoundElasticitySpecificityTALEUnbound

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Area of Science:

  • Genetics and Genomics
  • Molecular Biology
  • Biophysics

Background:

  • Transcription activator-like effector (TALE) proteins are crucial for genome engineering.
  • TALE proteins undergo conformational changes between open (unbound) and compact (DNA-bound) states.
  • The mechanisms governing TALE conformational transitions and DNA base discrimination by repeat-variable di-residues (RVDs) remain incompletely understood.

Purpose of the Study:

  • To computationally investigate the energetics and dynamics of TALE-DNA interactions.
  • To elucidate the conformational flexibility of TALE proteins.
  • To understand the molecular basis of RVD-mediated DNA base specificity.

Main Methods:

  • Molecular dynamics simulations of DNA-free TALE structures.
  • Free energy calculations using Poisson-Boltzmann surface area (PBSA) for various RVD-base combinations.
  • Analysis of TALE conformational sampling and binding affinities.

Main Results:

  • TALE proteins display significant elasticity, readily transitioning between apo and DNA-bound conformations with a low free energy barrier.
  • Molecular dynamics simulations revealed a wide range of sampled conformations for DNA-free TALE structures.
  • PBSA calculations demonstrated that native RVD-base pairings exhibit lower binding free energies than mismatched pairings for most RVDs.

Conclusions:

  • TALE protein conformational flexibility facilitates efficient DNA binding without substantial energetic penalties.
  • The inherent elasticity of TALE structures contributes to their adaptability in genome engineering applications.
  • Computational methods provide valuable insights into the dynamics and specificity of TALE-DNA recognition.