ProtNAff: protein-bound Nucleic Acid filters and fragment libraries

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.