Biology subjects

Machado, M. R.

Publications and source records attributed to Machado, M. R..

5 recordsLinked to original sources

bioRxiv2026

TNF-α-Driven NOX5 Activation Promotes Oxidative Stress and Umbilical Artery Dysfunction in Preeclampsia

BackgroundPreeclampsia (PE) is a hypertensive disorder of pregnancy characterized by systemic inflammation, oxidative stress, and endothelial dysfunction. Although maternal vascular dysfunction is well established in PE, the mechanisms underlying fetal vascular injury remain poorly understood. We investigated whether inflammatory signaling activates NADPH oxidase 5 (NOX5) and contributes to oxidative stress and dysfunction in human umbilical arteries from pregnancies complicated by PE. MethodsUmbilical arteries and serum samples were obtained from normotensive pregnant women (NP) and women with PE. Vascular reactivity, nitric oxide (NO) bioavailability, reactive oxygen species (ROS) generation, cytokine levels, and NOX isoform expression were evaluated in human umbilical arteries and EA.hy926 endothelial cells. Pharmacological inhibition of NOX5, TNF- neutralization, Ca{superscript 2} channel blockade, and siRNA-mediated NOX5 silencing were used to investigate mechanisms. ResultsPE umbilical arteries exhibited increased vasoconstrictor responses, oxidative stress, and NOX5 expression, accompanied by impairment of NO bioavailability. NOX5 inhibition reversed vascular hyperreactivity in PE vessels. Exposure of normotensive umbilical arteries to PE serum reproduced the PE vascular phenotype, characterized by enhanced ROS generation, reduced NO levels, and hypercontractility. In endothelial cells, PE serum induced TNF--dependent Ca{superscript 2} influx, oxidative stress, and reduced NO production. Both pharmacological and genetic inhibition of NOX5 prevented these alterations. ConclusionsPE promotes fetal vascular dysfunction through activation of a TNF-/Ca2+/NOX5 signaling pathway that amplifies oxidative stress and impairs NO bioavailability. These findings identify NOX5 as a previously unrecognized mediator of umbilical artery dysfunction in PE and suggest the TNF-/Ca2+/NOX5 axis as a potential therapeutic target in hypertensive pregnancies.

molecular biology↗

bioRxiv2021

Thiol-based mucolytics exhibit antiviral activity against SARS-CoV-2 through allosteric disulfide disruption in the spike glycoprotein

Small molecule therapeutics targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lagged far behind the development of vaccines in the fight to control the COVID-19 pandemic. Here, we show that thiol-based mucolytic agents, P2119 and P2165, potently inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity of repurposed mucolytic agents to the reduction of key disulfides, specifically, by disruption of the Cys379-Cys432 and Cys391-Cys525 pairs distal to the receptor binding motif (RBM) in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol warhead pointed directly towards Cys432. These collective findings establish the vulnerability of human coronaviruses to repurposed thiol-based mucolytics and lay the groundwork for developing these compounds as a potential treatment, preventative and/or adjuvant against infection.

microbiology↗

bioRxiv2020

SIRAH late harvest:coarse-grained models for protein glycosylation

Glycans constitute one of the most complex families of biological molecules. Despite their crucial role in a plethora of biological processes, they remain uncharacterized because of their high complexity. Their intrinsic flexibility, along with the vast variability associated with the many combination possibilities and relatively loose structural character, has hampered their experimental determination. Although theoretical methods have proven a valid alternative to the study of glycans, the large size associated with polysaccharides, proteoglycans, and glycolipids poses significant challenges to a fully atomistic description of biologically relevant glycoconjugates. On the other hand, the exquisite dependence on Hydrogen bonds to determine glycans' structure makes the development of simplified or coarse-grained (CG) representations extremely challenging. This is particularly the case when glycan representations are expected to be compatible with CG models of, for instance, proteins. We introduce a CG representation able to represent a wide variety of polysaccharides and most glycosylation motifs in proteins, which is fully compatible with the CG SIRAH force field. Examples of application to N-glycosylated proteins, including antibody recognition and Calcium-mediated glycan-protein interactions, highlight the versatility of the enlarged set of CG molecules provided by SIRAH.

biophysics↗

bioRxiv2019

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↗

bioRxiv2018

The SIRAH force field 2.0: Altius, Fortius, Citius

A new version of the coarse-grained (CG) SIRAH force field for proteins has been developed. Modifications to bonded and non-bonded interactions on the existing molecular topologies significantly ameliorate the structural description and flexibility of a non-redundant set of proteins. The SIRAH 2.0 force field has also been ported to the popular simulation package AMBER, which along with the former implementation in GROMACS expands significantly the potential range of users and performance of this CG force field on CPU/GPU codes.\n\nAs a non-trivial example of application, we undertook the structural and dynamical analysis of the most abundant and conserved calcium-binding protein, namely, Calmodulin (CaM). CaM is constituted by two calcium-binding motifs called EF-hands, which in presence of Calcium specifically recognize a cognate peptide by embracing it. CG simulations of CaM bound to four Calcium ions in the presence or absence of a binding peptide (holo and apo forms, respectively), resulted in good and stable ion coordination. The simulation of the holo form starting from an experimental structure sampled near-native conformations, retrieving quasi-atomistic precision. Removing the binding peptide enabled the EF-hands to perform large reciprocal movements, comparable to those observed in NMR structures. On the other hand, the isolated peptide starting from the helical conformation experienced spontaneous unfolding, in agreement with previous experimental data. However, repositioning the peptide in the neighborhood of one EF-hand not only prevented the peptide unfolding but also drove CaM to a fully bound conformation with both EF-hands embracing the cognate peptide, resembling the experimental holo structure.\n\nTherefore, SIRAH 2.0 showed the capacity to handle a number of structurally and dynamically challenging situations including metal ion coordination, unbiased conformational sampling, and specific protein-peptide recognition.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC=\"FIGDIR/small/436774_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@1d1ecc3org.highwire.dtl.DTLVardef@10f1a04org.highwire.dtl.DTLVardef@752a49org.highwire.dtl.DTLVardef@2b5746_HPS_FORMAT_FIGEXP M_FIG TOC. C_FIG

biophysics↗