arXiv subjects

Simón Poblete

Publications and source records attributed to Simón Poblete.

4 recordsLinked to original sources

arXiv2023

The GōMartini approach: Revisiting the concept of contact maps and the modelling of protein complexes

We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance-threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g. distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust GōMartini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō-like approach for the study of protein-sugar complexes, and also limitations of this approach are discussed. The GōMartini approach was first introduced by Poma et al. J. Chem. Theory Comput. 2017, 13(3), 1366-1374 in Martini 2 force field and recently, it has gained the status of gold-standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support to this approach in the context of the biophysical community.

cond-mat.soft↗

arXiv2017

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

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.

physics.bio-ph↗

arXiv2017

A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs

We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the ESCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-base model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the coarse-grained representation.

q-bio.BM↗

arXiv2011

Characterization of the Melting Transition in Two Dimensions at Vanishing External Pressure Using Molecular Dynamics Simulations

A molecular dynamics study of a two dimensional system of particles interacting through a Lennard-Jones pairwise potential is performed at fixed temperature and vanishing external pressure. As the temperature is increased, a solid-to-liquid transition occurs. When the melting temperature $T_c$ is approached from below, there is a proliferation of dislocation pairs and the elastic constant approaches the value predicted by the KTHNY theory. In addition, as $T_c$ is approached from above, the relaxation time increases, consistent with an approach to criticality. However, simulations fail to produce a stable hexatic phase using systems with up to 90,000 particles. A significant jump in enthalpy at $T_c$ is observed, consistent with either a first order or a continuous transition. The role of external pressure is discussed.

cond-mat.stat-mech↗