# Determination of Nucleotide–Nucleotide and Nucleotide–Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations

## TL;DR

This paper uses detailed simulations to study how RNA and proteins interact at the molecular level, providing insights for modeling biomolecular condensates.

## Contribution

The study provides a detailed quantitative analysis of nucleotide–amino acid interactions using all-atom simulations and PMF calculations.

## Key findings

- Lys, Arg, Asp, Glu, Gln, Ser, and Asn amino acids consistently interact with RNA nucleotides through hydrogen bonding and cation−π interactions.
- Phosphate–Arg contacts and π–π stacking with aromatic residues are key for RNA–protein condensate cohesion.
- Salt concentration reduces electrostatic self-repulsion in phosphate–phosphate interactions.

## Abstract

Biomolecular condensates emerge from multivalent interactions
between
proteins and nucleic acids and are frequently modeled by using coarse-grained
molecular dynamics simulations. The parametrization of these models
critically depends on atomistic data describing the underlying molecular
interactions. In this work, we employ all-atom molecular dynamics
simulations and potential-of-mean-force (PMF) calculations to investigate
the landscape of interactions between RNA nucleotides and protein
amino acids. We begin by characterizing nucleotide–nucleotide
binding modes through canonical base-pairing analysis, observing notable
agreement in the predictions from both the AMBER03ws and CHARMM36
force fields. Further rationalization of different nucleotide–nucleotide
interaction modes involves the calculation of PMFs for ribose–ribose,
phosphate–phosphate, and RNA tertiary interactions such as
G-quadruplex formation. We also examine the effect of salt concentration
on these interactions, finding a reduction in electrostatic self-repulsion
for phosphate–phosphate binding upon increasing the ionic strength.
Expanding our analysis to amino acids, we first benchmark the performance
of both AMBER03ws and a99SB-disp force fields for describing pairwise
amino acid interactions, and then, we evaluate different nucleotide–amino
acid binding profiles. Our findings reveal a subset of amino acidsLys
and Arg (positively charged), Asp and Glu (negatively charged), and
Gln, Ser, and Asn (polar residues)that consistently engage
with the nitrogenous bases of different nucleotides. Such binding
is primarily mediated by hydrogen bonding and, in some cases, cation−π
interactions. Furthermore, we identify strong π–π
stacking interactions with aromatic residues and phosphate–Arg
contacts as key contributors to condensate cohesion in RNA–protein
condensates. Our comprehensive analysis provides a detailed library
of nucleotide–amino acid interactions, offering quantitative
insights to inform coarse-grained model parametrization and deepening
our understanding of condensate self-assembly, nucleic acid recognition,
and phase-separation regulation at the submolecular scale.