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ProtNAff: protein-bound Nucleic Acid filters and fragment libraries.

Antoine Moniot1, Yann Guermeur1, Sjoerd Jacob de Vries2,3

  • 1LORIA (CNRS - INRIA - Université de Lorraine), Nancy 54000, France.

Bioinformatics (Oxford, England)
|July 1, 2022
PubMed
Summary

This study introduces protNAff, a novel pipeline for creating searchable databases of protein-bound nucleic acid (NA) fragments. It enables detailed analysis of NA structures and their interactions with proteins, addressing NA flexibility challenges.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Atomistic models of nucleic acid (NA) fragments are crucial for studying protein-NA interactions.
  • High NA flexibility, particularly in single-stranded regions, poses a significant modeling challenge.
  • Existing databases lack the capacity to handle diverse contextual variations in NA structures.

Purpose of the Study:

  • To present protNAff, a new pipeline for generating searchable databases of protein-bound NA structures and fragments.
  • To enable the selection of context-specific NA structures using flexible filtering.
  • To facilitate the creation of specialized NA fragment libraries for various modeling problems.

Main Methods:

  • Development of a modular pipeline (protNAff) for processing protein-bound NA data.
  • Implementation of filters for selecting NA structures based on 2D and 3D properties.
  • Creation of context-specific NA fragment libraries from filtered structures.
  • Application of the pipeline to analyze sequence-specificity, conformational diversity, protein binding effects, and hairpin loop propensity.

Main Results:

  • protNAff allows for the creation of searchable databases of protein-bound NA.
  • The pipeline successfully extracts context-specific NA fragments.
  • Demonstrated quantitative analysis of sequence-specificity, RNA conformational diversity, protein binding impacts, and hairpin loop properties.
  • The modularity of protNAff allows adaptation to diverse modeling needs.

Conclusions:

  • protNAff provides a versatile solution for analyzing protein-NA interactions through context-specific fragment libraries.
  • The pipeline enhances the study of NA flexibility and structural variations in biological contexts.
  • The developed tools and databases are publicly available, supporting further research in structural biology and bioinformatics.