Biology subjects

Dans, P. D.

Publications and source records attributed to Dans, P. D..

3 recordsLinked to original sources

bioRxiv2022

The Pseudo-Torsional Space of RNA

The characterization of the conformational landscape of the RNA backbone is rather complex due to the ability of RNA to assume a big variety of conformations. These backbone conformations can be depicted by pseudo-torsional angles linking RNA backbone atoms, from which Ramachandran-like plots can be built. We explored here different definitions of these pseudo-torsional angles, finding that the most accurate ones are the traditional {eta} (eta) and {theta} (theta) angles, which represent the relative position of RNA backbone atoms P and C4. We explore the distribution of {eta}-{theta} in known experimental structures, comparing the pseudo-torsional space generated with structures determined exclusively by one experimental technique. We found that the complete picture only appears when combining data from different sources. The maps provide a quite comprehensive representation of the RNA accessible space, which can be used in RNA-structural prediction. Finally, our results highlight that protein interactions leads to significant changes in the population of the {eta}-{theta} space, pointing towards the role of induced-fit mechanisms in protein-RNA recognition.

bioinformatics↗

bioRxiv2022

A fijivirus major viroplasm protein shows RNA-stimulated ATPase activity by adopting pentameric and hexameric assemblies of dimers

The fijivirus Mal de Rio Cuarto virus (MRCV) causes a devastating maize disease. Its non-structural protein P9-1, which shows ATPase and RNA binding activities, is the major component of the intracellular viroplasm where virus replication takes place. Here, we established that the 24 C-terminal residues (C-arm) of P9-1 are required for the formation of viroplasm-like structures (VLS) in vivo and for the protein multimerization in vitro. Employing an integrative structural approach, we found that the C-arm is dispensable for P9-1 dimer assembly, but essential for the formation of doughnut-shaped pentamers and hexamers of dimers (decamers and dodecamers). Both assemblies, larger than those reported for other reoviruses, contain disordered loops oriented towards the inner pore of the structures, where RNA binding sites and conditional proteasome-mediated degradation signals (PEST) were predicted. In vitro assays demonstrated that ssRNA binding is favored towards P9-1 (do)decamers over the dimeric {Delta}C-arm version. In addition, although both P9-1 and P9-1{Delta}C-arm catalyze the hydrolysis of ATP with similar activity values, an RNA-stimulated ATPase activity was only observed in the full-length protein, indicating a C-arm-mediated interaction between the ATP catalytic site and the allosteric RNA binding sites in the (do)decameric assemblies. Computational studies revealed a stronger preference of phosphate moieties to the decamer in the pore and the C-arm regions, suggesting that the allosteric communication between the ATP and RNA binding sites is favored with this protein arrangement. Overall, our work reveals the structural versatility of a major viroplasm protein providing unprecedented insights into fijivirus viroplasm assembly and function and establishes the structural basis for the development of antiviral strategies against the Mal de Rio Cuarto crop disease.

biochemistry↗

bioRxiv2018

The intimate knowledge of DNA crystals revealed by molecular dynamics simulations

X-ray crystallography has been traditionally considered as the primary tool for the determination of biomolecular structures and its derived models are taken as the gold standard in structural biology. However, contacts formed through the crystal lattice are known to affect the structures, especially in the case of small and flexible molecules, like DNA oligos, introducing drastic changes in the structure with respect to the solution phase. Furthermore, it is still unknown why molecules crystallize in certain symmetry groups and how the associated lattice impacts their structure. The role of crystallization additives and whether they are just innocuous and unspecific catalyzers of the crystallization process also remains unclear. On account of a massive computational effort and the use of the latest generation force field, we were able to describe with unprecedented level of detail the nature of intermolecular forces that participate in the stabilization of B-DNA crystals in various symmetry groups and in different solvent environments. We showed that the stability of the crystal lattice and the type of crystallization additives are tightly coupled, and certain symmetry groups are only stable in the presence of a specific crystallization additive (i.e., spermine). Additives and crystal contacts induce small but non-negligible changes in the physical properties of DNA.

biophysics↗