Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular Dynamics

TL;DR

This study evaluates a nucleobase-driven backmapping method using steered Molecular Dynamics to convert coarse-grained RNA models into all-atom structures, highlighting its effectiveness and limitations in recovering native geometries.

Contribution

It introduces an analysis of how a nucleobase-focused backmapping procedure impacts interaction networks and backbone conformations in nucleic acids.

Findings

Target structures' geometry can be reliably recovered.

Limitations exist in regions with unpaired bases like bulges.

Folding pathways depend on ERMSD parameters and metrics used.

Abstract

Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential degrees of freedom and interactions for the description of a number of structures. With the aim to provide an all-atom representation in an explicit solvent to the predictions of our SPlit and conQueR (SPQR) coarse-grained model of RNA, we recently introduced a backmapping procedure which enforces the predicted structure into an atomistic one by means of steered Molecular Dynamics. These simulations minimize the ERMSD, a particular metric which deals exclusively with the relative arrangement of nucleobases, between the atomistic representation and the target structure. In this paper, we explore the effects of this approach on the resulting interaction networks and backbone conformations by applying it on a set of fragments using as a target their native structure. We find that the geometry of the target structures can be reliably recovered, with limitations in the regions with unpaired bases such as bulges. In addition, we observe that the folding pathway can also change depending on the parameters used in the definition of the ERMSD and the use of other metrics such as the RMSD.