Biology subjects

Barcenas, O.

Publications and source records attributed to Barcenas, O..

3 recordsLinked to original sources

bioRxiv2026

Shedding light on Gaussia Luciferase conformational space using multi-conformation enhanced sampling simulation

Gaussia luciferase (GLuc) has broad biotechnological applications owing to its bioluminescence, yet its catalytic mechanism remains poorly understood and rational engineering efforts are hindered by the absence of a structural model. This gap stems from GLuc's highly dynamic nature, which allows it to populate a wide range of conformations rather than adopt a single, well-defined fold. Aiming to bridge this gap, in this work we employ structure predictors and conformational sampling techniques to prod GLuc's structure. Our results indicate that structure predictors such as AlphaFold, as well as ensemble predictors such as BioEmu, fail to adequately sample this conformational space, and even extended molecular dynamics simulations do not yield converged conformational ensembles. However, enhanced sampling via PT-WTE provides a more satisfactory description of GLu's conformational landscape, allowing us to cluster distinct conformational basins, identify loosely defined substrate-binding pockets, and characterize the conformational changes induced by substrate binding. These insights advance our understanding of GLuc's catalytic mechanism and inform future efforts to engineer improved variants.

biophysics↗

bioRxiv2026

Full-Length Molecular Models of Brain-Derived α-Synuclein Fibrils Reveal a Fuzzy-Coat-Mediated Mechanism for Selective Peptide Binding

Parkinsons disease (PD) is characterized by the aggregation of -synuclein (aSyn) into amyloid fibrils that seed further aggregation and contribute to pathological spreading. Peptides that bind aggregated aSyn are promising therapeutic leads, but their validation is slow, difficult to standardize, and often relies on structural models limited to the ordered cross-{beta} core. Here, we built models of brain-derived full-length aSyn fibrils by extending the Lewy-fold cryo-EM structure with disordered N- and C-terminal segments and sampling the resulting ensembles with the CALVADOS coarse-grained force field. The resulting fibrils display a dynamic fuzzy coat in which the termini, especially the acidic C-terminal tails, form recurrent transient contacts with the core, including the aggregation-prone {beta}5 and {beta}9 motifs. We then used these full-length fibrils in a standardized in silico assay for peptide binding. Simulations of the validated peptide binders PSM3 and LL-37 reproduced their relative binding behavior and converged on a common mechanism in which electrostatic capture by the anionic fuzzy coat precedes stabilization on recurrent P2 and P3 hotspots within the structured core. Control simulations with monomeric aSyn or core-only fibrils showed that persistent association is lost in the absence of the full-length architecture, providing a mechanism for selectivity toward aggregated species. Finally, screening 123 peptides from aSynPEP-DB using a relative contact-based binding score yielded a ranked set of candidate binders and identified net positive charge as the dominant determinant of sustained association, with hydrophobicity acting as a secondary modulator. Together, these results establish full-length, brain-derived fibril ensembles as a practical framework for understanding ligand recognition at pathological amyloid surfaces and for prioritizing therapeutic peptide binders targeting aggregated aSyn. SignificanceParkinsons disease is driven by the assembly of -synuclein into amyloid fibrils, yet most structural models of these aggregates omit the disordered termini that form the fibrillar "fuzzy coat" in vivo. Here we use coarse-grained simulations to reconstruct full-length, brain-derived -synuclein fibrils and show that this fuzzy coat transiently contacts the Lewy-fold core, reshaping access to cross-{beta} surface motifs. Using these ensembles in a computational assay, we recapitulate the relative binding behavior of validated peptide inhibitors and reveal a two-step mechanism in which cationic and amphipathic peptides are first captured by the anionic fuzzy coat and then engage recurrent core hotspots. This framework explains selective recognition of aggregated -synuclein and provides a practical route to prioritize therapeutic peptide binders.

bioinformatics↗

bioRxiv2025

Liquid-liquid phase separation (LLPS) as a sensing and adaptation mechanism: An evidence-based hypothesis on AP2 transcription factors in the malaria parasite

BackgroundProtein liquid-liquid phase separation (LLPS) can be driven by prion-like domains (PrLDs) inside intrinsically disordered regions (IDRs). The causing agent of the deadliest form of human malaria, Plasmodium falciparum, has abundant prion-like proteins whose aggregation is presumed to have a functional role. Multiple members of the largest family of transcription factors in P. falciparum, AP2 (PfAP2), responsible for adapting the parasite gene response in different scenarios, were found in aggregation-prone protein screenings. ResultsWe show that the PfAP2s members carry the physicochemical determinants to perform LLPS forming biomolecular condensates in vivo. The long IDRs of PfAP2s could sense changes in the cellular microenvironment, and their PrLDs could drive conformational rearrangements. PfAP2s do not function as centralizing hubs for protein-protein interaction networks, but display significant preferred interactions among themselves, establishing a large, connected subnetwork. Predictions suggest that all PfAP2s have regions to localize into LLPS-condensates, while larger PfAP2s could initiate condensation. We show that four PfAP2 members co-localize in live P. falciparum, bearing the potential to be engaged in LLPS-condensates. ConclusionWe present bioinformatics analyses and experimental data obtained in live parasites suggesting that PfAP2s are able to direct LLPS in P. falciparum. We propose a model in which sensing by the parasite of cellular stresses like host transfer, temperature changes and energy depletion, and the corresponding gene responses are driven by LLPS where the PfAP2 family plays a fundamental role. Finally, we postulate targeting PfAP2 as a new therapeutic antimalarial strategy to curb the emergence of drug-resistant parasites.

bioinformatics↗