Research

SoutheRNA group participating in the RNA puzzles Round V (Horacio V. Guzman consortium formation, lead: Fabrizio Pucci ULB)

Here, several groups worked collectively for the advancement of #RNA 3D strct. prediction ➡️ Challenges have been identified like avoidance(after detailed analysis) of entanglements🪢, + more #multiscalingRNA #compchemmore...

M. Domingo, Horacio V. Guzman, M. Kanduč, and J. Faraudo

These are results of the first visting Ph.D. student we received in my group, Marc Domingo (from ICMAB's CSIC)!

Here we compute the electrostatic interaction between WT, Delta and Omicron Spike proteins with charged surfaces using a new method (based on Debye–Hückel theory) that provides efficiently general results as a function of the surface charge density σ. We found that the interaction of the WT and Delta variant spikes with charged surfaces is dominated by repulsive image forces proportional to σ2 originating at the protein/water interface...

A. Bosch, Horacio V. Guzman*, R. Perez*  

Here, we investigate the role of the receptor-binding domain (RBD) of the spike protein mutations on the adsorption of SARS-CoV-2 to hydrophobic and hydrophilic surfaces employing molecular simulations. To contextualize our findings, we contrast the interactions on inanimate surfaces with those on native biological interfaces, specifically the angiotensin-converting enzyme 2. Notably, we identify a 2-fold increase in structural deformations for the protein’s receptor binding motif (RBM) onto inanimate surfaces, indicative of enhanced shock-absorbing mechanisms. Furthermore...

W. Menacho, K. Catalan, Tomas P. Corrales, Horacio V. Guzman*,  

We combined Atomic Force-Microscopy (AFM) experiments, analytical theory, and simulations are combined to determine the elastic properties of the nanofibers as a function of relative humidity. The effect of morphological changes from the adsorbed water-layer, and an ensemble of inter-chain interaction strength and morphological changes at peak-forces are explored. For PVA nanofibers, considerable differences are found, which are strongly dependent on the molecular signatures of hydration-adsorption at a polymer-chain level. Here, the semi-empirical model plays a key role in properly interpreting experiments by evaluating only a few observables...

C.D. Cooper, I. Addison-Smith, Horacio V. Guzman*,  

Electrostatic interactions are crucial for the assembly, disassembly, and stability of proteinaceous viral capsids. Moreover, at the molecular scale, elucidating the organization and structure of the capsid proteins in response to an approaching nanoprobe is a major challenge in biomacromolecular research. Here, the team led by Dr. Guzman reports on a generalized electrostatic model, based on the Poisson-Boltzmann equation that quantifies the subnanometric electrostatic interactions between an AFM tip and a proteinaceous capsid from molecular snapshots...

Guo, et al., Horacio V. Guzman & T. Tsuboi,  Single-chain models illustrate the 3D RNA folding shape during translation

The three-dimensional conformation of RNA is important in the function and fate of the molecule. The common conformation of mRNA is formed based on the closed-loop structure and internal base pairings with the activity of the ribosome movements. However, recent reports suggest that the closed-loop structure might not be formed in many mRNAs. This implies that mRNA can be considered as a single polymer in the cell...

S. Poblete, A. Bozic, M. Kanduc, R. Podgornik, Horacio V. Guzman*,  RNA secondary structure regulates fragments’ adsorption onto flat substrates

RNA molecules present different adsorption mechanisms based on the secondary structure underneath its 3D conformations. In this context a generalizable multiscale model of RNA and substrates, allow us to explore different interaction regimes for RNA adsorption, which contribute in unveiling further mechanisms of self-association of certain RNA fragments.

S. Poblete, Horacio V. Guzman*, Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models

Could 3D structure of RNA genome be reconstructed avoiding topological defects, like knots? Here we present a first algorithm to reconstruct the whole genome of a virus in and outside the capsid based on experimental secondary structures. Happy RNA assembling!

M. Martinez, C. D. Cooper, A. Poma, Horacio V. Guzman*, Free energies of the disassembly of viral

capsids from a multiscale molecular simulation approach, Journal of Chem. Inf. and Modeling (2020)

R.A. Moreira, M. Chwastyk, J.L. Baker, Horacio V. Guzman, A. Poma, Quantitative determination of mechanical stability in the novel coronavirus spike protein, Nanoscale (2020)

Horacio V. Guzman*, N. Tretyakov, H. Kobayashi, A. Fogarty, K. Kreis, J. Krajniak, C. Junghans, K. Kremer, T. Stuehn, Advanced methods for multiscale molecular simulation, Comp. Phys. Comm. (2019)

A. B. Poma, Horacio V. Guzman, M. S. Li, P. E. Theodorakis, Mechanical and thermodynamic properties of biological fibrils from molecular-scale simulation, Beilstein J. Nanotechnol. (2019)

Horacio V. Guzman*, C. Junghans, K. Kremer, T. Stuehn, Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes, Phys. Rev. E (2017)

Horacio V. Guzman*, Scaling law to determine peak forces in tapping mode AFM experiments on finite elastic soft matter systems, Beilstein J. Nanotechnol. (2017)

Horacio V. Guzman*, P.D. Garcia, R. Garcia, Dynamic force microscopy simulator (dForce): A tool for planning and understanding tapping and bimodal AFM experiments, Beilstein J. Nanotechnol. (2015)

Horacio V. Guzman*, A.P. Perrino, R. Garcia, Peak forces in high-resolution imaging of soft matter in liquid, ACS nano (2013)