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RNApedia: A Database of Protein-RNA Interactions

RNApedia collects data from the Protein Data Bank (PDB) and organizes structures into interaction pairs composed of a protein chain and an RNA chain. For each complex, RNApedia provides detailed information:

RNA Information

• RNA Type: Classification of RNA based on RNAcentral. Example: "misc_RNA" – for RNAs that do not fit other classifications.
• Base Composition (A|C|G|U): Number of each nitrogenous base in the RNA sequence.
• GC Content (%): Percentage of Guanine (G) and Cytosine (C), influencing stability.

RNA Secondary Structure

• Dot-Bracket Notation: Representation of secondary structure using symbols:
  • "(" and ")" indicate paired bases.
  • "." represents unpaired bases.
• Free Energy (kcal/mol): Stability measure calculated by RNAfold (negative values indicate more stability).

Protein Properties

• Molecular Weight (Da): Based on amino acid composition.
• Aromaticity: Fraction of aromatic amino acids (phenylalanine, tyrosine, tryptophan).
• Instability Index: In vitro stability measure (values >40 suggest instability).
• Isoelectric Point (pI): pH at which the protein has no net charge.

Binding Affinity Data

• ProNAB ID: Identification of the complex in ProNAB database.
• Kd - ProNAB (nM): Dissociation constant measuring molecule affinity (lower values = stronger interactions).
• ΔG - ProNAB (kcal/mol): Gibbs free energy of interaction (negative values indicate spontaneous binding).
• Kd - PDBbind v.2020: Dissociation constant from PDBbind 2020 database.

Accessible Surface Area (ASA) Calculations

• All-atoms ASA Protein/RNA/Complex: Measures exposure of molecules to solvent.
• ΔASA All-atoms: Difference between total ASA before and after complex formation.
• BSA All-atoms: Buried surface area, related to interaction stability.
• Non-polar ASA: Evaluates hydrophobic interaction contributions.
• Polar ASA: Measures potential for hydrogen bonding and electrostatic interactions.

Secondary Structure Mapping

RNApedia provides a detailed representation of RNA secondary structure, identifying internal loops, hairpins, and multi-loops. The format follows:

[TYPE] (Start_Position, End_Position) [Paired_Bases] ; (Start_Position, End_Position) [Paired_Bases]: [Energy]

Example:

Interior loop (1,117) GC; (2,116) CG: -340 kcal/mol

What is RpID?

RpID is the RNApedia entry ID. Each complex has an unique identification code composed of eight characteres (1ABC-X-X, i.e., PDB_ID-RNA_CHAIN-PROTEIN_CHAIN).

How to cite:

BASTOS, Luana Luiza et al. A strategy for refining the calculation of contacts in protein-RNA complexes. In: Simpósio Brasileiro de Bioinformática (BSB). SBC, 2024. p. 241-246.