Biology subjects

Petridis, L.

Publications and source records attributed to Petridis, L..

6 recordsLinked to original sources

bioRxiv2026

Conformational Reorganization of a Processive Cellulase on Crystalline Cellulose

Enzymes that degrade insoluble polymers must couple catalytic chemistry to productive engagement with heterogeneous substrate interfaces, yet direct structural information on these interfacial states remains limited. We investigated the conformational organization of the processive cellulase Trichoderma reesei Cel7A both free in solution and bound to an insoluble cellulose substrate using small-angle neutron scattering (SANS). Use of biosynthetically deuterated bacterial cellulose allowed the scattering contribution of the cellulose-associated Cel7A holoenzyme to be selectively highlighted using SANS with contrast matching. SANS measurements performed under conditions supporting high or low catalytic activity revealed distinct differences between the free and cellulose-bound enzyme. Under poorly active conditions, the conformational distributions of free and bound Cel7A were similar. In contrast, catalytically favorable conditions produced an additional interdomain correlation in the bound enzyme, consistent with redistribution toward a substrate-selected conformational ensemble. Molecular dynamics simulations showed that free Cel7A samples can assume compact, intermediate, and extended conformations, but these solution-state ensembles did not reproduce the structural features of cellulose-bound Cel7A. These results identify productive cellulose engagement as a structurally distinct state of the Cel7A holoenzyme and support a dynamic model in which the linker and carbohydrate-binding module modulate interfacial positioning of the catalytic domain rather than functioning as a rigid mechanical unit during processive hydrolysis. More broadly, the findings suggest that heterogeneous biocatalysis depends not only on substrate binding and active-site chemistry, but also on interface-selected conformational states that determine whether binding becomes productive. The study further demonstrates how deuteration and neutron contrast variation can reveal functional macromolecular conformations directly within complex interfacial environments.

biochemistry↗

bioRxiv2026

Conformational Preference Classification of Integrin-Binding Ligands Using Free Energy Perturbation

Integrins are crucial cell adhesion receptors and attractive therapeutic targets, but developing safe small-molecule inhibitors has been challenging, at least in part due to inadvertent partial agonism caused by stabilization of the integrins open, high-affinity state. To address this challenge, we present a computational approach using Absolute Binding Free Energy Perturbation (AB-FEP) calculations to predict whether a ligand will stabilize the open or closed integrin states, leveraging the difference between the ligands binding free energy to the respective end states. Despite challenges posed by Ca and Mg ions, metal-coordinating residues in the binding pocket, and the subtlety of structural differences between states, AB-FEP achieved excellent classification performance on a set of known opening and closing ligands, significantly outperforming docking scores and MM-GBSA results. We also showed a good correlation between AB-FEP binding free energy differences and experimental values. Furthermore, AB-FEP provided insights into intermediate integrin states and analysis of simulation trajectories confirmed the formation of a water-mediated hydrogen bond network with an ion in the binding pocket to be characteristic for closing ligands. This work demonstrates AB-FEP as a robust method for classifying integrin ligands by the conformation they stabilize and for understanding their functional mechanisms, offering valuable guidance for designing safe and conformationally selective integrin therapeutics. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/721214v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@1a0b8eforg.highwire.dtl.DTLVardef@cd6b56org.highwire.dtl.DTLVardef@420cc0org.highwire.dtl.DTLVardef@533963_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

The interaction of relative age with maturation and body size in female handball talent selection based on only sport-specific criteria

Talent identification is often affected by the relative age effects (RAEs) and/or maturation. Previous research has suggested that talent selection should include sport-specific technical tasks instead of body size and/or physical test measurements, assuming that the technical tasks are less influenced by interindividual variability in maturation. Our purpose was to examine the prevalence of RAEs and how biological maturity, body size, and body composition in relation to relative age affect talent selection among female handball players. Handball-specific drills and in-game performance were the criteria of a single talent selection program. Birth distribution of U14 female (N = 3198) handball players were analyzed. Body size, body composition, and bone age were assessed on 264 selected and 266 not-selected players. Body composition was assessed with InBody 720, whereas biological age from bone age. Chi-square was used to examine quartile distributions, and logistic regression to determine the effects of the predictors on the selection. In terms of all registered players, there was no difference in birth distribution. RAEs appeared at the first selection level and were evident at all levels. Quartiles differed only between the first and the last quartiles in body size and muscle mass. Only bone age differed between consecutive quartile or semi-year groups. Body size, body composition, and maturity had a significant, but of moderate power, effect on the selection. Larger body height increased selection odds by about 12%, larger muscle mass by 12% to 25%, larger percent body fat decreased selection odds by 7%, while larger bone age by 3.5-4 times. RAEs affected talent selection when applying sport-specific drills as selection criteria. Relative age was connected to bone age, but not convincingly to body size and muscle mass. Bone age had the largest effect on the selection, but this was not associated with larger body size or muscle mass.

physiology↗

bioRxiv2020

Small molecule FGF23 inhibitors increase serum phosphate and improve skeletal abnormalities in Hyp mice

Fibroblast growth factor 23 (FGF23) is a bone-derived hormone that binds to binary FGFR/-Klotho receptor complexes in the kidney tubules to inhibit phosphate reabsorption and 1,25(OH)2D production. Excess FGF23 causes X-linked hypophosphatemia (XLH) and tumor induced osteomalacia (TIO). Recently, Burosumab, an FGF23 blocking antibody, was approved for treating these hypophosphatemic disorders. A small molecule inhibitor that specifically binds to FGF23 to prevent activation of FGFR/-Klotho complexes has potential advantages over a systemically administered FGF23 blocking antibody. We previously identified the small molecule ZINC13407541 (N-[[2-(2-phenylethenyl)cyclopenten-1-yl]methylidene]hydroxylamine) as a therapeutic lead FGF23 antagonist. Additional structure-activity studies developed a series of ZINC13407541 analogues with enhanced drug-like properties. In this study, we tested in a pre-clinical Hyp mouse homologue of XLH a direct connect analogue (8n) [(E)-2-(4-(tert-butyl)phenyl)cyclopent-1-ene-1-carbaldehyde oxime] that exhibited the greatest stability in microsomal assays, and 13a [(E)-2-((E)-4-methylstyryl)benzaldehyde oxime] that exhibited increased in vitro potency. We found that pharmacological inhibition of FGF23 with either of these compounds blocked FGF23 signaling and significantly increased serum phosphate and 1,25(OH)2D concentrations in Hyp mice. Long-term parenteral treatment with 8n or 13a also enhanced linear bone growth, increased mineralization of bone, and narrowed the growth plate in Hyp mice. The more potent 13a compound showed greater therapeutic efficacy in Hyp mice. Further optimization of these FGF23 inhibitors may lead to versatile drugs to treat FGF23-mediated disorders.

pharmacology and toxicology↗

bioRxiv2020

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy in the force fields and inadequate sampling. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD led to unbiased ensembles of unprecedented accuracy, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of variable sequence properties using two recently optimized force fields. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues).

biophysics↗

bioRxiv2020

Mesophilic enzyme function at high temperature: moleculardynamics of hyperthermophilic and mesophilicpyrophosphatases

The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermoccoccus thioreducens, whereas, the homolog protein from the hyperthermophilic organism (TtPPase) cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein:water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.

biophysics↗