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Bioinformatic analysis of the protein/DNA interface.

Bohdan Schneider1, Jirí Cerný, Daniel Svozil

  • 1Institute of Biotechnology AS CR, Videnska 1083, CZ-142 20 Prague, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology Prague, Technická 5, CZ-166 28 Prague, Czech Republic, INSERM, U665, DSIMB, F-75739 Paris, France, University of Paris Diderot, Sorbonne Paris Cité, UMR_S 665, F-75739 Paris, France, Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France and Laboratoire d'Excellence GR-Ex, F-75739 Paris, France.

Nucleic Acids Research
|December 17, 2013
PubMed
Summary

This study analyzed protein-DNA complex structures, revealing distinct interaction patterns based on protein type and DNA groove. Water molecules play a key role in these interactions, particularly in transcription factor complexes.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Molecular Interactions

Background:

  • Protein-DNA recognition is fundamental to cellular processes.
  • Understanding these interactions requires analyzing complex structural data.

Purpose of the Study:

  • To investigate the principles governing protein-DNA recognition.
  • To classify and analyze structural elements and their interactions within protein-DNA complexes.

Main Methods:

  • Analysis of over a thousand crystal structures of protein/DNA complexes.
  • Classification of protein conformations using structural alphabets (protein blocks).
  • Classification of DNA conformations using dinucleotide conformers.

Main Results:

  • Identified distinct interaction patterns for different protein types (transcription factors, nucleases).
  • Revealed differences in interaction patterns between DNA major and minor grooves.
  • Highlighted the significant role of water-mediated contacts, especially in minor groove interactions and transcription factor complexes.
  • Attributed A-DNA form induction to A-like and intermediate A/B conformers, which are rare in unbound DNA.

Conclusions:

  • Protein-DNA recognition involves specific structural element correlations and conformer preferences.
  • Water molecules are crucial mediators of protein-DNA interactions.
  • DNA conformation changes upon binding are more nuanced than previously thought.