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Barrera, E. E.

Publications and source records attributed to Barrera, E. E..

4 recordsLinked to original sources

Ursolic Acid Inhibits Rotavirus Replication Through Modulation Of Lipid Droplet Homeostasis

Rotavirus (RV) replication occurs within viroplasms (VP), which are globular, membrane-less cytosolic inclusions primarily assembled by the viral NSP5 and NSP2 proteins. Among host factors, lipid droplets (LD) are strictly required for VP biogenesis. LD are ubiquitous organelles consisting of a neutral lipid core surrounded by a phospholipid monolayer and associated proteins. Ursolic acid (UA), a pentacyclic triterpenoid widely present in plants and fruits, displays multiple biological activities, including modulation of lipid metabolism, and exhibits antiviral activity against RV, as we have previously demonstrated. Here, we investigated the molecular mechanism underlying the antiviral effect of UA. Using biophysical approaches, we first examined the impact of UA on LD formation, finding that it impairs LD biogenesis, consistent with reduced LD budding from the endoplasmic reticulum. We then employed cell-based assays to assess LD turnover and observed that UA acts as a lipolytic stimulus, leading to a marked reduction in LD abundance. Notably, we found that autophagic pathways contribute to LD degradation in the presence of UA. Finally, molecular dynamics simulations proposed that UA, owing to its intrinsic lipid-partitioning capacity, inserts into the LD phospholipid monolayer, establishing interactions with interdigitated neutral lipids. Together, our results indicate that UA both hampers LD biogenesis and accelerates LD degradation, likely through its association with and destabilization of the LD membrane. This dual effect leads to LD depletion, thereby impairing VP formation and ultimately inhibiting RV replication. IMPORTANCEDiarrheal diseases caused by a wide range of pathogens, including bacteria and viruses, remain a major global public health concern, accounting for more than one million deaths annually. These diseases mainly affect children under five years of age, with RV being the primary cause of diarrheal mortality in this age group. The burden is particularly severe in low- and middle-income countries. To address RV-associated disease, coordinated public health interventions have been implemented worldwide, including improvements in water, sanitation, hygiene, the introduction of vaccines, and the widespread use of oral rehydration therapy. Although these measures have substantially reduced the global burden of diarrheal diseases, the lack of a specific antiviral treatment against RV highlights the need for continued research. The development of antiviral strategies could provide a valuable complementary approach to existing interventions and help further reduce morbidity and mortality in infected children.

microbiology↗

Dissecting the role of glutamine in seeding peptide aggregation.

Poly glutamine and glutamine-rich peptides play a central role in a plethora of pathological aggregation events. However, biophysical characterization of soluble oligomers --the most toxic species involved in these processes-- remains elusive due to their structural heterogeneity and dynamical nature. Here, we exploit the high spatio-temporal resolution of simulations as a computational microscope to characterize the aggregation propensity and morphology of a series of polyglutamine and glutamine-rich peptides. Comparative analysis of ab-initio aggregation pinpointed a double role for glutamines. In the first phase, glutamines mediate seeding by pairing monomeric peptides, which serve as primers for higher-order nucleation. According to the glutamine content, these low molecular-weight oligomers may then proceed to create larger aggregates. Once within the aggregates, buried glutamines continue to play a role in their maturation by optimizing solvent-protected hydrogen bonds networks. TOC / Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/381632v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@251f33org.highwire.dtl.DTLVardef@123506borg.highwire.dtl.DTLVardef@174d9cdorg.highwire.dtl.DTLVardef@875f00_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Evolutionary and Structural Constraints Influencing Apolipoprotein A-I Amyloid Behavior

Apolipoprotein A-I (apoA-I) has a key function in the reverse cholesterol transport mediated by the high density lipoprotein (HDL) particles. However, aggregation of apoA-I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural impacts introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA-I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation-prone regions (APRs) present in apoA-I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA-I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA-I. Structural properties of the full-length apoA-I model suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Following we set up to study the effect of natural mutations on protein conformation and stability. Compared to natural silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of apoA-I amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha-helix bundle with the concomitant exposure of APR1 to the solvent and the formation of beta-sheet segments at the C-terminus of apoA-I, giving a possible hint about the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA-I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region. This information contributes to our understanding of how apoA-I, with its high degree of structural flexibility, maintains a delicate equilibrium between its monomeric native structure and intrinsic tendency to form amyloid aggregates. In addition, our stability measurements could be used as a proxy to interpret the structural impact of new mutations.

bioinformatics↗

Fat SIRAH: Coarse-grained phospholipids to explore membrane-protein dynamics.

Tne capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here we introduce the parameterization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths, partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium -SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parameterization is implemented in the GROMACS and AMBER simulation packages facilitating its use to a wide portion of the Biocomputing community.

biophysics↗