Biology subjects

Orozco, M.

Publications and source records attributed to Orozco, M..

3 recordsLinked to original sources

bioRxiv2018

Side chain to main chain hydrogen bonds stabilize polyglutamine helices in transcription factors

Polyglutamine (polyQ) tracts are regions of low sequence complexity of variable length found in more than one hundred human proteins. These tracts are frequent in activation domains of transcription factors and their length often correlates with transcriptional activity. In addition, in nine proteins, tract elongation beyond specific thresholds causes polyQ disorders. To study the structural basis of the association between tract length, transcriptional activity and disease, here we addressed how the conformation of the polyQ tract of the androgen receptor (AR), a transcription factor associated with the polyQ disease spinobulbar muscular atrophy (SBMA), depends on its length. We found that the tract folds into a helical structure stabilized by unconventional hydrogen bonds between glutamine side chains and main chain carbonyl groups. These bonds are bifurcate with the conventional main chain to main chain hydrogen bonds stabilizing -helices. In addition, since tract elongation provides additional interactions, the helicity of the polyQ tract directly correlates with its length. These findings suggest a plausible rationale for the association between polyQ tract length and AR transcriptional activity and have implications for establishing the mechanistic basis of SBMA.

biophysics↗

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↗

bioRxiv2017

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

Native mass spectrometry coupled to ion mobility spectrometry is a promising tool for structural biology. Intact complexes can be transferred to the mass spectrometer and, if native conformations survive, collision cross sections give precious information on the structure of each species in solution. Based on several successful reports for proteins and their complexes, the conformation survival becomes more and more taken for granted. Here we report on the fate of nucleic acids conformation in the gas phase. Disturbingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions ([≥] 100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for short (12-bp) and long (36-bp) duplexes, and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semi-empirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb-driven expansion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.

biophysics↗