Biology subjects

Olivos-Ramirez, G. E.

Publications and source records attributed to Olivos-Ramirez, G. E..

4 recordsLinked to original sources

bioRxiv2026

Structural modelling and biophysical analyses reveal a dimeric coiled-coil architecture in the FAZ10 central region of Trypanosoma brucei

Trypanosoma brucei relies on the flagellum attachment zone (FAZ) to coordinate flagellum positioning, cell morphology, and cytokinesis. The giant FAZ10 protein, which contains both repetitive and structured regions, is essential for correct cleavage-furrow placement, yet its molecular organization remains unresolved due to its exceptional size. In this study, we define the architecture of the FAZ10 central region through structural modelling and biophysical validation. AlphaFold2 and molecular dynamics simulations defined a parallel coiled-coil dimer flanked by symmetric globular domains, with canonical hydrophobic core packing, complementary interhelical contacts, and local heptad discontinuities, including a stammer-stutter pair that modulates the superhelical geometry. Biophysical analyses show that this region forms a stable dimer in solution, mediated by the coiled-coil domain and consistent with a predominantly -helical structure. Together, these findings identify the FAZ10 central region as a semi-flexible dimeric scaffold that provides a structural framework for understanding FAZ supramolecular organization and the integration of large cytoskeletal assemblies in trypanosomatids.

biophysics↗

bioRxiv2026

Exploring Conformational Transitions of RNA Dimers via Machine Learning Potentials

RNA is a flexible biopolymer that adopts diverse conformations while forming structural motifs essential for its function. Classical RNA force fields often show limited transferability and inefficient sampling of transitions between stable states, particularly in moderately large RNA. To address these limitations, quantum-informed machine learning (ML) potentials have recently emerged as a promising alternative, offering improved accuracy and transferability relative to classical force fields. Here, we assess ML potentials for exploring RNA conformations using the adenine-adenine dinucleoside monophosphate (ApA) dimer, a fundamental RNA building block. We generated an extensive quantum-mechanical (QM) dataset for ApA conformations obtained from temperature replica exchange molecular dynamics (TREMD) simulations. Despite its small size, the ApA dimer exhibits six conformations in which quantum effects and solvent-mediated interactions play crucial roles. Using this dataset, we parameterized ML potentials based on the equivariant MACE architecture and informed by both ab-initio and semi-empirical data. The resulting potentials reproduce key conformational features of the ApA system, including base stacking, sugar puckering, and backbone flexibility, and provide broader coverage of structural transitions than the general-purpose SO3LR and MACE-OFF24 models. These findings highlight the importance of quantum-accurate RNA force fields towards the structural and energetic characterization of RNA complexes.

biophysics↗

bioRxiv2025

A Comparative Nanomechanical Study of Antibody and Nanobody Binding to SARS-CoV-2 Variants

The receptor-binding domain of the SARS-CoV-2 spike protein is the principal target of neutralizing antibodies (Abs) and nanobodies (Nbs). Although their thermodynamic binding properties have been extensively characterized, their stability under mechanical force remains less understood. Here, we perform a comparative nanomechanical analysis of three Abs (PDI-231, S2X259, and R1-32) and three Nbs (R14, C1, and n3113.1) bound to the RBD from the WT strain and the Omicron BA.4 and JN.1 variants. Using coarse-grained steered molecular dynamics within the G[o]Martini 3 framework, we identified distinct force-response behaviors shaped by epitope topology, binding architecture, and variant-specific mutations. Ab/RBD dissociation was characterized by asymmetric rupture events, variant-dependent unfolding of RBD segments, and occasional deformation of antibody constant domains. Analysis of single-chain systems revealed that the heavy chain acts as the main load-bearing element, while the light chain sustains a consistent but weaker mechanical response. For the two-chain Ab system, the cooperative action of both chains enhances stability, enabling complexes to withstand rupture forces in the range of 500 pN. By contrast, Nb/RBD complexes dissociated primarily through rigid-body mechanisms, transmitting force more directly to the RBD interface with minimal structural disruption. Together, these results demonstrate that mechanical resilience emerges from immune complex topology and inter-chain cooperation, providing complementary insights beyond affinity into the design of therapeutics resilient to viral evolution.

biophysics↗

bioRxiv2024

Occurrence of the Humboldt Penguin (Spheniscus humboldti, Meyen, 1834) in El Ferrol Bay, Chimbote, Peru, and strategies for its conservation

The Humboldt penguin is an emblematic species of the Humboldt ecosystem of Peru and Chile, declared as vulnerable in The IUCN Red List of Threatened Species in 2020. By 2023, its population was estimated around 9,900 pairs, which means a decrease of 93% of its population in 70 years. In response to a warning of its occurrence on the Guaneras Islands located in El Ferrol Bay (Chimbote, Peru), the objective of this study was to verify its presence in situ. Between October and November 2024, four expeditions were carried out on the leeward side of the Islote Pena Blanca (White Rock Islet), Isla Blanca (White Island), Isla Ferrol del Norte (Northern Ferrol Island), Isla Ferrol del Centro (Central Ferrol Island), and Isla Ferrol del Sur (Southern Ferrol Island). The presence of 149 individuals, 5 of them juveniles, and one chick accompanied by its parent, was verified on Northern Ferrol Island, Central Ferrol Island, and Southern Ferrol Island. It is estimated that the presence of these organisms is explained by the improvement of oceanographic conditions in this bay. Considering the high vulnerability of the species, the local community must articulate efforts to guarantee the establishment of its population in this particular habitat.

ecology↗