Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure

Area of Science:

• Molecular Biology
• Computational Biology
• Biophysics

Background:

• Single-stranded nucleic acid binding proteins (e.g., HIV nucleocapsid protein, bacterial RecA) are crucial in biological processes.
• These proteins significantly influence nucleic acid secondary structure.
• Accurate modeling of these interactions is vital for understanding biological mechanisms.

Purpose of the Study:

• To develop and implement a computational model for predicting nucleic acid secondary structure in the presence of single-stranded binding proteins.
• To extend the existing Vienna RNA Package with protein-binding capabilities.

Main Methods:

• The model extends the Vienna RNA Package, incorporating protein footprint and sequence-dependent binding affinity as adjustable parameters.
• Utilizes previously determined parameters for nucleic acid secondary structure prediction without proteins.

Main Results:

• Predicts the probability of protein binding along the nucleic acid sequence.
• Determines the protein's impact on nucleic acid base pairing.
• Calculates end-to-end distance distributions and Förster Resonance Energy Transfer (FRET) distributions.

Conclusions:

• The developed model provides a powerful tool for studying nucleic acid-protein interactions.
• Enables accurate prediction of structural changes induced by binding proteins.
• Facilitates a deeper understanding of biological processes involving these interactions.