Biology subjects

Orellana, L.

Publications and source records attributed to Orellana, L..

7 recordsLinked to original sources

bioRxiv2026

Leveraging elastic networks in a coarse-grained brownian simulation framework for protein conformational dynamics

Protein dynamics is fundamental to understand mechanisms. Although atomistic Molecular Dynamics (MD) remains the gold standard for predicting protein motions, its computational cost limits applications at large scales. Here, we present a coarse-grained (CG) simulation framework that combines Elastic Network Models (ENMs) with implicit-solvent Brownian Dynamics (BD) to efficiently generate protein conformational ensembles from native states. Benchmarking the method on more than 8,500 proteins against large datasets of atomistic MD trajectories and multi-state ensembles from Nucleic Magnetic Resonance (NMR), we show that short ENM-BD simulations can reproduce the residue fluctuation profiles and the dominant protein motions with remarkable accuracy. Correlations of residue fluctuations often exceeded 80%, with many proteins showing agreements above 90%, while Principal Component Analysis (PCA) revealed strong correspondences between the essential motions in the ENM-BD simulations and those observed in MD and NMR ensembles. Following CG-to-all-atom reconstruction and short energy minimization, the ENM-BD conformers also achieve high stereochemical quality, which enables their usage in downstream atomistic applications. Finally, we show that the stochastic dynamics emerging from BD trajectories closely aligns with the normal modes encoded in the underlying elastic network, highlighting that most of the intrinsic dynamics of proteins is already embedded in their native 3D topology.

biophysics↗

bioRxiv2026

Mutation-induced reshaping of protein conformational dynamics revealed by a coarse-grained modeling framework

Disease-related missense mutations reshape protein conformational energy landscapes, thereby altering biological function. However, mechanistically linking sequence variation to changes in conformational dynamics remains challenging for both experimental and computational approaches. Here, we introduce an internal-coordinate-based, essential-dynamics-refined elastic network model (ICed-ENM) that improves the physical fidelity of normal modes while capturing subtle mutation-induced side-chain effects and preserving computational efficiency. By constraining bond-length and bond-angle fluctuations and refining mode subspaces against experimentally observed collective motions, ICed-ENM provides a stable, structure-encoded description of intrinsic protein dynamics. Building on this framework, we developed a systematic mutation-scanning analysis that quantifies mutation impact as changes in vibrational entropy, providing a dynamic measure of mutation-induced redistribution within conformational energy landscapes. Validation against all-atom molecular dynamics simulations demonstrates that residues predicted as mutation hot spots induce substantial reshaping of free-energy landscapes, consistent with altered intrinsic conformational dynamics. Extending this analysis across a curated protein structure dataset reveals global patterns of mutation sensitivity across diverse structural and physicochemical contexts. Notably, these trends align with large-scale public mutation datasets, suggesting that our framework captures features relevant to pathogenic variation. Together, ICed-ENM and the associated mutation-scanning pipeline provide a scalable and mechanistically interpretable strategy to identify mutation-sensitive regions and substitutions, offering deeper insight into how sequence variation reshapes functional conformational landscapes.

biophysics↗

bioRxiv2026

A structure-aware framework for genomic variant interpretation in genetic skeletal disorders

BackgroundGenetic skeletal disorders (GSDs) comprise a heterogeneous group of rare, predominantly monogenic conditions that are increasingly diagnosed through high-throughput sequencing. While gene discovery has progressed rapidly, interpretation of pathogenic and uncertain variants remains a major bottleneck, in part because their functional consequences are determined at the protein structure level. However, a systematic assessment of structural knowledge across GSD-associated genes is currently lacking. Here, we present a comprehensive protein structure-centric analysis of 674 protein-coding genes implicated in GSDs. MethodsWe integrated experimental structures, AlphaFold2 (AF2) models, multimeric states, protein-protein interactions, and ClinVar variant annotations. ResultsWe quantify experimental structural availability and sequence coverage, revealing that 37% of GSD proteins lack any experimental structure and that, among proteins with structures, sequence coverage is often incomplete. We show that AF2 models provide high-confidence structural information for a substantial subset of proteins lacking experimental data, but that model reliability strongly correlates with existing structural coverage. Analysis of multimeric assemblies and co-occurring partners demonstrates that many GSD proteins function as obligate multimers, highlighting the importance of interface-level interpretation of variants. Finally, mapping clinically annotated missense variants onto representative protein structures illustrates how structural context can inform the interpretation of pathogenic and uncertain variants, particularly at interaction interfaces. ConclusionsTogether, this work provides a structure-aware reference framework for GSD genes, highlighting systematic gaps in current protein knowledge and demonstrating how integration of structural data can guide genomic variant interpretation. Our observations support a broader principle of structural equivalence, whereby distinct variants converge on shared structural perturbations that explain clustering patterns and enable mechanistic interpretation of nearby variants of uncertain significance.

genomics↗

bioRxiv2026

An essential dynamics-based elastic network model to unravel the conformational dynamics of DNA, RNA, and protein-nucleic acid complexes

The flexibility of DNA and RNA is known to play a central role in numerous biological processes, including chromatin organization and gene regulation. While a wide range of computational approaches have been developed to investigate the conformational dynamics and flexibility of proteins, analogous methods for nucleic acids remain comparatively underexplored. Elastic Network Models (ENMs) - coarse-grained mechanical representations in which macromolecules are modeled as networks of nodes connected by elastic springs - have been successfully applied to proteins, often allowing to capture experimentally observed conformational changes through a small number of harmonic normal modes. Building on a previously validated three-bead ENM for RNA, here we introduce edENM, an essential dynamics-refined ENM for DNA, RNA, and protein-nucleic acid complexes, parametrized using a diverse set of Molecular Dynamics simulations. The vibrational modes of the new edENM show good agreement with NMR data and experimental ensembles, while avoiding the unrealistic and localized deformability of previous ENM parametrizations. Additionally, we integrated this new edENM into eBDIMS, a Brownian Dynamics-based framework that enables the simulation of large-scale and anharmonic conformational transitions in protein assemblies. In this way, we are now able to explore functional motions in large protein-nucleic acid complexes such as chromatin subunits and ribosomes.

biophysics↗

bioRxiv2025

Structural basis for ATP regulation of human 5-lipoxygenase

5-Lipoxygenase catalyzes the committed step in the biosynthesis of the powerful proinflammatory leukotrienes and pro-resolving anti-inflammatory lipoxins. Here we present a 3.3 [A] cryo-EM structure of wild type 5-lipoxygenase in complex with ATP, one of its most important allosteric regulators. The nucleotide is located in a positively charged pocket of the catalytic domain and held in place by a complex network of amino acid side chains and backbone carbonyl and amino groups. Mutagenetic analysis suggests that ATP binding and action is primarily mediated via Lys320, assisted by Gln657. Further atomistic simulations demonstrate that ATP binding induces movements of the PLAT domain coupled to conformational rearrangements at the active center. These findings provide important structural and regulatory insights to a key enzyme in leukotriene biosynthesis, thus aiding in design of new antiphlogistic drugs.

biochemistry↗

bioRxiv2021

Structure and lipid-mediated remodelling mechanism of the Na+/H+ exchanger NHA2

Na+/H+ exchangers catalyse an ion-exchange activity that is carried out in most, if not all cells. SLC9B2, also known as NHA2, correlates with the long-sought after sodium/lithium (Na+/Li+) exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite its functional importance, structural information and the molecular basis of its ion-exchange mechanism have been lacking. Here, we report the cryo EM structures of bison NHA2 in detergent and in nanodiscs at 3.0 and 3.5 [A] resolution, respectively. NHA2 shares closest structural similarity to the bacterial electrogenic Na+/H+ antiporter NapA, rather than other mammalian SLC9A members. Nevertheless, SSM-based electrophysiology results with NHA2 show the catalysis of electroneutral rather than electrogenic ion exchange, and the ion-binding site is quite distinctive, with a tryptophan-arginine- glutamate triad separated from the well-established ion-binding aspartates. These triad residues fine-tune ion binding specificity, as demonstrated by a salt-bridge swap mutant that converts NHA2 into a Li+-specific transporter. Strikingly, an additional N-terminal helix in NHA2 establishes a unique homodimer with a large [~] 25 [A] intracellular gap between protomers. In the presence of phosphatidylinositol lipids, the N-terminal helix rearranges and closes this gap. We confirm that dimerization of NHA2 is required for activity in vivo, and propose that the N- terminal helix has evolved as a lipid-mediated remodelling switch for regulation of transport activity.

biophysics↗

bioRxiv2021

Transcriptomic and rRNA:rDNA signatures of environmental vs. enteric Enterococcus faecalis isolates under oligotrophic freshwater conditions

The use of enterococci as a fecal indicator bacterial group for public health risk assessment has been brought into question by recent studies showing that "naturalized" populations of E. faecalis exist in the extraenteric environment in a viable but not culturable (VBNC) state. The extent to which these naturalized or VBNC E. faecalis can confound water quality monitoring is unclear. To determine if strains isolated from different habitats display different survival strategies and responses, we compared the decay patterns of three E. faecalis isolates from the natural environment (environmental strains) against three human gut isolates (enteric strains) in laboratory mesocosms that simulate an oligotrophic, aerobic freshwater environment. Our results showed similar overall decay rates between enteric and environmental isolates based on viable plate and qPCR counts. However, the enteric isolates exhibited a spike in rRNA:rDNA ratios between days 1 and 3 of the mesocosm incubations that was not observed in environmental isolates, which could indicate a different stress response. Nevertheless, there was no strong evidence of differential expression of genes thought to be related to habitat adaptation in the accompanying mesocosm metatranscriptomes when compared between environmental and enteric isolates. Overall, our results provide novel information on how rRNA levels may vary over different metabolic states (i.e., alive vs. VBNC) for this important indicator bacteria. We also observed some evidence for habitat adaptation in E. faecalis; however, this adaptation may not be substantial or consistent enough for integration in water quality monitoring. IMPORTANCEEnterococci are commonly used worldwide to monitor environmental fecal contamination and public health risk for waterborne diseases. However, some species within this group can enter an inactive, viable but not culturable (VBNC) state that make it difficult to accurately quantify during routine monitoring. Furthermore, lower-risk, environmental enterococci strains may also confound water quality estimates. We developed an rRNA:rDNA viability assay for E. faecalis (a predominant species within this fecal group) and tested it against both enteric and environmental isolates in freshwater mesocosms to assess whether this approach can serve as a more sensitive water quality monitoring tool. We were unable to reliably distinguish the different isolate types using this assay under the conditions tested here; thus, environmental strains should continue to be counted during routine water monitoring. However, this assay could be useful for distinguishing more recent (i.e., higher risk) fecal pollution because rRNA levels significantly decreased after one week in all isolates.

microbiology↗