Biology subjects

Zeida, A.

Publications and source records attributed to Zeida, A..

4 recordsLinked to original sources

bioRxiv2026

Evolution of allostery without shape shifting: Internal dynamics drives functional diversification of a transcriptional repressor superfamily

Allostery enables proteins to couple environmental signals to functional outputs, yet how allosteric mechanisms diversify during evolution remains poorly understood. Here, we address this question in the ubiquitous and functionally diverse arsenic repressor (ArsR) superfamily by integrating information-theoretic bioinformatics, structural characterization of DNA recognition and NMR measurements of fast internal dynamics. We identify conserved residues that define the structural scaffold of ArsR proteins and subfamily-specific positions that encode inducer and DNA specificity. In the persulfide sensor SqrR, the crystal structure of the DNA-bound complex reveals how operator specificity is encoded by a limited set of residues, consistent with sequence-derived predictions functionally validated by in vitro transcription assays across divergent ArsR regulators. We further show that allosteric inhibition of DNA binding in SqrR occurs without large-scale conformational rearrangements and is instead associated with changes in internal dynamics, as previously observed for the zinc sensor CzrA. Together, these results support a model in which conformational entropy preserves allosteric connectivity while relaxing sequence constraints, thereby enabling functional diversification within a protein superfamily.

biochemistry↗

bioRxiv2025

Unraveling the Dual Immunomodulatory and Immunogenic Roles of the Central Conserved Cysteine-Rich Region in Respiratory Syncytial Virus G Protein

Respiratory syncytial virus (RSV) causes severe respiratory disease in infants and high-risk adults, in part by subverting host immunity. The RSV G glycoproteins central conserved cysteine-rich domain (CCD) contains a CX3C motif implicated in immune modulation, but the relationship between CCD redox state, structure and function is unresolved. We recombinantly expressed a CCD peptide (Gpep, residues 149-196) and combined structural and biophysical characterizations with cellular immunology and human serology to define how redox-dependent conformations govern immunogenicity and immunomodulation. Reduced Gpep is compact and rapidly folds via a dominant intermediate into an oxidized, extended monomer; at higher concentrations intermolecular disulfide isomerization produces covalent oligomers. Functionally, monomeric Gpep potently suppresses innate and adaptive activation inhibiting LPS- or UV-inactivated RSV-induced maturation of mouse bone marrow-derived dendritic cells, reducing antigen-specific CD4+ T cell proliferation and IFN-{gamma} production, and attenuating multiple human neutrophil responses (chemotaxis, CD11b upregulation, ROS, MPO release and NET formation), without cytotoxicity. Oligomerized Gpep lacks these suppressive activities. To link molecular mechanism and human exposure, analysis of sera from an ambulatory pediatric cohort (0-72 months) showed a progressive transient increase in the anti-F/anti-G IgG ratio with repeated early RSV exposures, maturating into a functional 2 to 3 ratio. This serologic shift is consistent with previously reported enrichment of F-directed neutralizing immunity. We propose a redox-dependent immune-evasion model in which soluble, monomeric G mediates transient immunosuppression that is removed by disulfide-driven oligomerization, which may occur in membrane-bound G. This may impact therapeutic strategies that commonly favor F-focused responses. ImportanceRespiratory syncytial virus (RSV) remains a leading cause of severe respiratory disease in young children and high-risk adults. This study identifies a chemical switch in a small conserved region of the RSV attachment protein that changes its shape and immune activity: when the region is present as a soluble, single chain, it transiently suppresses key innate and adaptive immune cells, but this activity is lost upon disulfide-mediated oligomerization. We also show that repetitive RSV exposures in early life bias the antibody response, initially boosting antibody responses toward the Fusion protein, rather than this conserved central region. Together, these results may uncover a mechanism by which RSV shapes the host immune response explaining the features of antibody development in children. Understanding this redox-dependent balance between immune evasion and antigenicity will inform safer vaccine and antibody strategies against RSV.

immunology↗

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↗

bioRxiv2019

Exploring the Conformational Transition Between the Fully Folded and Locally Unfolded Substates of the Escherichia coli Thiol Peroxidase

Thiol peroxidase from Escherichia coli (EcTPx) is a peroxiredoxin that catalyzes the reduction of different hydroperoxides. During the catalytic cycle of EcTPx, the peroxidatic cysteine (CP) is oxidized to a sulfenic acid by peroxide, then the resolving cysteine (CR) condenses with the sulfenic acid of CP to form a disulfide bond, which is finally reduced by thioredoxin. Purified EcTPx as dithiol and disulfide behaves as a monomer in close to physiological conditions. Although secondary structure rearrangements are present when comparing different redox states of the enzyme, no significant differences in unfolding free energies are observed under reducing and oxidizing conditions. A conformational change denominated fully folded (FF) to locally unfolded (LU) transition, involving a partial unfolding of H2 and H3 helices, must occur to enable the formation of the disulfide bond since the catalytic cysteines are 12 [A] apart in the FF conformation of EcTPx. To explore this crucial process, the mechanism of the FF[->]LU and the LU[->]FF transitions were studied using long time scale conventional molecular dynamic simulations and an enhanced conformational sampling technique for different oxidation and protonation states of CP and/or CR. Our results suggest that the FF[->]LU transition has a higher associated energy barrier than the refolding LU[->]FF process in agreement with the relatively slow experimental turnover number of EcTPx. Furthermore, in silico designed single-point mutants of the H3 enhanced locally unfolding events, suggesting that the native FF interactions in the active site are not evolutionary optimized to fully speed-up the conformational transition of wild-type EcTPx.

biophysics↗