Methods for estimating milk production of dairy cows with full cow-calf contact.

The creatine transporter (CRT/SLC6A8) plays a key role in cellular energy homeostasis, yet the molecular mechanism underlying creatine transport remains poorly understood. Here, we reconstruct the complete transport cycle of human CRT using a hybrid simulation strategy that combines constant-force steered molecular dynamics (cf-sMD) with targeted molecular dynamics (tMD). This approach captures continuous progression through the outward-open, outward-occluded, inward-occluded, and inward-open states and reveals a water-assisted, sequential intracellular release of Na2, creatine, and Na1. Hydration analysis shows that progressive water penetration into the binding pocket weakens protein-substrate and protein-ion interactions and destabilizes the bound state before release. Residue-level contact analysis identifies residues that interact with creatine along the transport pathway, while dynamic network analysis reveals a TM1-TM6 communication backbone that mediates long-range coupling during transport. Together, these results provide a molecular framework for creatine transport and establish an approach for investigating transport mechanisms across the broader solute carrier family.

Lignocellulosic biomass can be converted into biofuels and other valuable bioproducts, but it must first undergo physicochemical and enzymatic degradation. Among the various enzymes involved in lignocellulose degradation, thermophilic glycoside hydrolase family 5 (GH5) cellulases have gained significant attention given their ability to sustain enzymatic activity at temperatures exceeding 60 °C. These high temperatures not only accelerate enzymatic reactions, improving reaction rates and process efficiency, but also enhance substrate solubility and reduce the risk of microbial contamination, making them highly valuable for the paper, food, feed, pharmaceutical, and biofuel industries. In this work, we identified five GH5 cellulases with predicted thermophilic properties from termite gut metagenomes and evaluated their structural features using machine-learning classification, comparative structural modeling, interatomic contact analysis, and temperature-dependent flexibility simulations. The candidates, spanning GH5 subfamilies 2, 25, 37, 39, and 40, displayed high structural confidence (pLDDT > 90) and aliphatic indices comparable to those of thermophilic references. Analysis of amino acid composition analysis revealed enrichment in aromatic and charged residues. Hydrophobic contact densities were consistently higher than in mesophilic controls and aligned with thermophilic benchmarks. Temperature-dependent flexibility simulations showed restrained RMSF profiles, more closely resembling the thermophilic reference enzyme than to the mesophilic control. These findings are consistent with a thermophilic profile, pending experimental confirmation, and provide useful insights for the selection and engineering of GH5 cellulases for high-temperature biotechnological applications.

Contact analysis and rotation angle of reverse-drive ball screws

Computer-aided drug discovery increasingly depends on virtual-screening workflows that remain reliable under severe class imbalance, chemical redundancy and early-recognition constraints. In this study, we developed a leakage-aware prioritization workflow for two cancer-relevant targets, pyruvate kinase M2 (PKM2) and mitogen-activated protein kinase 1 (MAPK1/ERK2), using the LIT-PCBA benchmark. The workflow combines canonical-SMILES curation, duplicate and label-conflict auditing, scaffold-aware validation, a non-learning nearest-active Tanimoto baseline, imbalance-aware machine-learning models, repeated-seed robustness analysis, isotonic probability calibration, ensemble-disagreement estimation, absorption, distribution, metabolism, excretion and toxicity (ADMET)-aware triage, molecular docking, and residue-level contact analysis. Benchmark enrichment is interpreted alongside calibration, ADMET filtering, docking and residue-contact evidence, rather than as a standalone discovery claim. PKM2 emerged as the clearer machine-learning case, with scaffold-aware tree models improving early recognition beyond the nearest-active similarity baseline and yielding top-ranked candidates supported by calibrated activity scores, ADMET profiles, docking scores, and residue-contact fingerprints. MAPK1 provided a biologically relevant contrast target, where ligand-neighborhood similarity remained competitive and downstream structural triage became more decisive than ligand-based ranking alone. These results support a conservative drug-discovery workflow in which leakage-aware benchmarking, calibration, uncertainty, and molecular-level triage remain visible throughout candidate prioritization.

Metallocarboxypeptidases (MCPs) are critical zinc-containing exopeptidases and promising therapeutic targets for conditions ranging from thromboembolic disorders to cancer. Despite their importance, the dynamic determinants governing subfamily-specific peptide recognition remain incompletely understood. In this study, we performed 200 ns molecular dynamics simulations on five distinct A/B MCP-peptide complexes and integrated contact analysis and per-residue energy decomposition (MM/PBSA) to systematically map their interaction profiles. We identified a core set of Grade A and B conserved hotspots-specifically Arg71, Arg127, Glu163, Thr164, and Tyr248-that mediate persistent interactions across the subfamilies. Based on their energetic and geometric profiles, we categorized these residues into three functional classes. Class I (functional hotspots): Such as Arg71 and Arg127, which act as near-permanent "anchoring hubs" with contact occupancies exceeding 90% and dominant negative binding free energies. Class II (topological hotspots): Such as Glu163, which maintains the structural integrity of the active site cleft. Class III (auxiliary energetic contributors): Which provide additional stabilization through transient or non-polar contacts. Furthermore, we identified complex-specific residues, such as Glu270 in hCPB1, that serve as selectivity filters. Collectively, this study highlights the key enzyme residues that mediate persistent interactions at the interface and provides molecular insights that may guide the rational design of novel metallocarboxypeptidase inhibitors.

Protein-carbohydrate interactions play a key role in numerous biological processes, including immune response, and glycan-based ligands that can target specific protein receptors on a cell surface represent promising candidates for therapeutics applications. For example, in retinoblastoma, the DC-SIGN mannose receptor is overexpressed on the surface of pathogenic cells and represents an interesting target for mannose-based ligands. At the same time, these ligands should not bind to the MRC1 receptor, which is expressed by adjacent, healthy, retinal pigment epithelial cells and presents a carbohydrate recognition domain (CRD) similar to the one of DC-SIGN. Therefore, the challenge remains to obtain a detailed picture of the recognition process between carbohydrates and proteins, in order to design effective and selective therapeutic compounds. In this work we used classical, all-atom molecular dynamics (MD) simulations to investigate the interaction between several mannose based ligands and the CRDs from DC-SIGN and MRC1. The analysis of the protein-carbohydrate contacts from the resulting trajectories highlights the variability of the mannose binding modes on both CRDs, and shows how the increased affinity of mannose for the MRC1 CRD can be related to a specific mannose binding state that is not accessible in the DC-SIGN CRD.

Dipeptidyl peptidase 4 (DPP4/CD26) is a clinically relevant serine protease involved in metabolic, immunological and viral processes. Although several crystal structures of DPP4–ligand complexes have been reported, the dynamic features that distinguish substrates from inhibitors remain less understood. In this study, 250 ns all-atom molecular dynamics simulations were performed for four structurally distinct ligand-bound states, a synthetic construct, a Neuropeptide Y (NPY) fragment, Diprotin A and an HIV-1 TAT peptide, to examine how ligand identity affects the conformational behavior of DPP4. All complexes maintained the global α/β-hydrolase and β-propeller architecture, with secondary-structure content remaining stable throughout the simulations. Ligand-dependent differences were mainly observed in the flexible loop regions near the catalytic cavity. The inhibitory ligands (Diprotin A and TAT) promoted reduced mobility and lower backbone RMSD values (1.5–2.0 Å), whereas the substrate and the synthetic construct allowed greater local flexibility (2.0–2.5 Å). Contact analyses showed a conserved anchoring network involving Glu205, Glu206 and Tyr662 across all systems, along with ligand-specific peripheral interactions, including Trp659, Tyr752 and Phe357, that influence the binding modes. These observations reveal a relationship among structure–dynamics–function, in which DPP4 maintains a stable interaction and modulates loop movements, including peripheral contacts, to differentiate substrates from inhibitors. The dynamic behavior of the enzyme offers mechanistic insights that allow for specific ligand recognition, which could support the design and development of new DPP4 modulators.

An efficient 3D finite element implementation for frictionless elliptical contact analysis in layered rough surfaces

ATP synthase (ATPase) is a crucial molecular motor in Mycobacterium tuberculosis (Mtb), essential for energy production and oxygen-dependent pathogenesis. The enzyme consists of two distinct rotors: a membrane-embedded Fₒunit and a cytosolic catalytic F1 unit, along with a stator, a central stalk, and a heterodimeric peripheral stalk (PS). As the F0 region hosts critical drug-binding pockets, it has gained significant interest. This study focuses on local structural dynamics at the leading site in the presence of bedaquiline (BDQ). All-atom molecular dynamics simulations were performed using GROMACS in a heterogeneous bilayer composed of phosphoinositol, phosphoethanolamine, phosphoglycerol, and cardiolipin (PI: PE: PG: CL) in a 32:42:4:50 ratio. The results revealed key interactions of BDQ with cL59, cF65, cE61, cA62, cI55, cI66, cG58, aI215, and aF219 at the a/c interface, consistent with energetically favored binding conformation. Quantitative lipid contact analysis revealed higher CL interactions with BDQ at leading site together with interfacial water molecules, whereas protein-lipid contacts based on only lipid headgroup (P-atoms) analysis remained independent of lipid abundance in the system. RMSD and RMSF revealed BDQ-induced fluctuations in the outer helix of subunit-c, while subunit-a remained comparatively more stable during the simulation. Distance analysis further indicated that the ligand remains confined within the binding region despite local flexibility. We further identified putative non-collinear proton channels, which showed no significant global perturbation upon BDQ binding. Residues aG195, aN105, aD220, aN190, aQ227, cE61 (inlet side), cE61 (outlet side), aE176, aE175, aA178, aK179, aS182, aY238, aQ110, aF192, aL122 form the two half channels in Mtb. The pooled water-count analysis for channels showed similar hydration levels in all simulated systems. We hypothesize that selective targeting of the leading pocket by newer drugs, in the presence of CL lipids, can modulate the proton inlet channel. The heterogeneous bilayer supports the structural and functional integrity of the membrane and ATPase complex. A CL-enriched membrane environment may provide a useful framework for investigating membrane-associated effects of BDQ and its analogs. Chain-wise analysis showed synchronous movement of the PS subunits and twisting of the δ-binding region, which may be perturbed in the presence of the F1 unit. The dynamics also revealed subunit-bδ involvement with the subunit-a at the leading pocket, a less studied PS and stator function. Identifying residue-specific interactions between PS could help to reveal its mechanical function. Together, these results provide complementary dynamic insights into BDQ at the leading pocket in a physiologically mimicked membrane environment and potentially support its relevance as a target site for the development of anti-TB compounds targeting ATPase.

Face-gear drive with novel tooth flanks: High-precision CNC skiving simulation and tooth contact analysis

ABSTRACTAs deformation is increasingly probed at nanometer scales, atomic‐level surface features become decisive in triggering crystal plasticity. Direct experimental elucidation of such effects has long been hindered by limited control over surface atomic arrangements. This challenge is particularly pronounced for GaN, a promising wide‐bandgap semiconductor that is hard to process, making ideal planarization nontrivial. Here, step–terrace GaN surfaces with monoatomic topography approaching the theoretical limit were realized using catalyst‐referred etching (CARE). On these surfaces, nanoindentation pop‐ins occurred in all 100 indents at the ideal strength (16.15 GPa) with a record‐low stress scatter of only 2.3%. As‐received surfaces, conventionally regarded as flat but lacking step–terrace ordering, exhibited pop‐ins at similar stress levels yet larger scatter, indicating that even atomic‐scale surface irregularities can perturb plasticity initiation. Mechanically buffed surfaces produced only 28/100 pop‐ins, evidencing a marked loss of reproducibility. Pop‐ins occurred at much lower stresses and with smaller bursts, consistent with heterogeneous dislocation nucleation and reduced elastic energy release. Equivalent‐radius contact analysis elucidated how local curvature affects stress estimation, decoupling topographic effects from incipient plasticity. These results shift nanoindentation evaluation standards from roughness metrics to atomic step–terrace structure and provide a reliable framework for analyzing incipient plasticity in crystals.

This study provides a preliminary investigation into the underlying factors of the M/V New Life contact incident with a pier of the 1915 Çanakkale Bridge on June 11, 2025. The novelty of this research lies in presenting the first academic analysis of a bridge-pier contact in the Çanakkale Strait prior to the release of the official accident report. Utilizing the fishbone (Ishikawa) method supported by a two-stage Delphi process with nine maritime experts, the study categorizes contributing factors into technical, human, organizational, and environmental domains. The reliability of the expert evaluations was validated using Kendall’s W coefficient of concordance, which yielded a value of 0.829, indicating a strong statistical consensus among the participants. Findings suggest that the incident resulted from a combination of multifaceted factors—primarily navigating without a pilot, probable crew fatigue, and non-compliance with COLREG (International Regulations for Preventing Collisions at Sea) rules. The study offers critical safety insights and policy recommendations for managing narrowed traffic separation schemes in international straits.

Understanding crystallizationmodifier mechanisms remains a centralchallenge in crystal engineering, particularly for growth promoterswhose modes of action are far less understood than inhibitors. Here,we investigate riboflavin (RF) as a crystallization promoter for ammoniumurate (NH4HU) using combined microfluidic experiments andmolecular dynamics simulations to elucidate its underlying mechanism.We discovered that RF reorganizes neighboring urate ions into growth-compatiblecoplanar conformations, contrasting with their naturally preferredgrowth-incompatible stacked arrangements. This identifies a solution-phasepreassembly mechanism for enhancing crystal growth, distinct fromclassical monomer addition or traditional surface-based pathways.We found that the modifier’s ability to reorganize surroundingurate correlates with its aromatic ring size, explaining why the largeRF framework exhibits unique promotion effects among known modifiers.Guided by detailed contact analysis between RF and urate ions, werationally designed RF derivatives with enhanced promotion capabilitiesand experimentally validated their predicted performance, with thenatural metabolite lumichrome showing a 40% growth enhancement comparedto the 20% enhancement observed for RF. Our findings establish solution-phasepreorganization as a viable mechanism for crystallization control.

The central channel of the nuclear pore complex (NPC) exhibits polydispersity in the FG-nucleoporin (FG-Nup) sequence length, with longer FG-Nups on the periphery and shorter FG-Nups in the interior of the pore. A minimal, coarse-grained model and Langevin dynamics simulations were used to investigate the functional role of FG-Nup polydispersity in NPC transport. The NPC was modelled as a cylindrical pore lined with a random copolymer brush composed of hydrophobic and hydrophilic segments, mimicking FG-Nups. Two model NPCs were considered to simulate the translocation of a karyopherin-bound spherical cargo (12 nm spherical tracers): a homogeneous NPC (h-NPC) with uniform FG-Nup lengths and an inhomogeneous NPC (ih-NPC) featuring shorter FG-Nups in the middle and longer FG-Nups at the periphery. The ih-NPC demonstrated enhanced selectivity and significantly higher passage probabilities for karyopherin-bound tracers, with an increase of up to 90% compared to the h-NPC. Analysis of binding contacts between tracers and FG-Nup hydrophobic segments revealed that tracer translocation was facilitated by a handover process between successive FG-Nups along the NPC length. This enhanced selectivity of the ih-NPC was attributed to an increase in binding contacts of the tracer with the shorter FG-Nups in its middle region. These findings provide a biophysical basis for the evolutionary significance of FG-Nup polydispersity in selective NPC transport.

Cyclotides are exceptionally stable plant peptides whose biological activity is widely attributed to interactions with lipid membranes, yet the molecular mechanisms underlying these interactions remain incompletely resolved. Here, we employ microsecond-scale (1 μs) all-atom molecular dynamics simulations to investigate the membrane association of the cyclotide kalata B1 with phospholipid bilayers of distinct headgroup composition, including POPC, POPE, and POPG. This extended timescale enables full bilayer equilibration and allows observation of slower peptide-induced membrane responses that are not accessible in shorter simulations. Across all systems, kalata B1 rapidly adsorbs to the membrane surface and remains predominantly surface-associated throughout the simulations, while the cyclic cystine knot motif remains structurally intact, confirming the exceptional robustness of the cyclotide fold during membrane engagement. Lipid-dependent differences arise primarily from variations in peptide orientation, conformational flexibility, and interfacial dynamics rather than deep bilayer insertion or pore formation. Zwitterionic POPC membranes favor compact, upright peptide configurations, whereas POPE and POPG bilayers promote enhanced lateral spreading and dynamic reorganization driven by hydrogen bonding and electrostatic interactions, respectively. Leaflet-resolved analyses of lipid contacts, membrane thickness, and area per lipid reveal localized, asymmetric perturbations confined to the peptide-exposed leaflet, with no evidence of sustained bilayer thinning or global destabilization. Together, these results support an interfacial, headgroup-dependent mechanism of cyclotide membrane activity and reconcile previous experimental observations. This work provides molecular-level insight into lipid selectivity and early-stage cyclotide-membrane interactions that may inform future design of cyclotide-based bioactive agents.

A method for quantitative assessment of occlusal contacts recorded by a digital occlusal analysis system.

There is a higher risk of subsidence following transforaminal lumbar interbody fusion (TLIF) relative to other approaches. Decreased subsidence risk is associated with anterior cage placement, speculated to be because of increased apophyseal ring contact. However, this hypothesis is largely based on in vitro evidence and, to date, has not been investigated in a clinical cohort. Pre-operative and post-operative computed tomography (CT) images from 42 TLIF patients were used to segment the endplate and cages. The apophyseal ring boundary was manually landmarked for each endplate. The pre-operative endplates were rigidly registered with the post-operative cage position, and an iterative closest point approach was used to calculate the contact area between the cage, apophyseal ring, and endplate. Subsidence was categorised based on severity (No Subsidence: <2mm; Moderate Subsidence: 2-4mm; Severe Subsidence: ≥4mm) from post-operative CT. Apophyseal ring contact was significantly lower in both Moderate and Severe Subsidence, relative to No Subsidence (Moderate: -19.6±7.0%; Severe: -21.5±6.5%; P<0.05), and negatively correlated with subsidence depth (P<0.05). Injury risk analysis demonstrated that a 50% subsidence risk was associated with 45.7% (38.4-53.6%) apophyseal ring contact. Suprajacent endplate apophyseal ring contact, but not subjacent, was significantly predictive of subsidence at the respective endplate (P<0.05). The risk of subsidence in TLIF patients can be mitigated by ensuring that at least half of the interbody cage surface area is in contact with the peripheral endplate rim, particularly at the endplate superior to the cage.

Mapping the conformational variability in mutants of the amyloid precursor protein intracellular domain.

The proline-rich domain (PRD) of the tumor suppressor p53 plays a central role in modulating conformational dynamics and molecular interactions, yet its intrinsic structural behavior remains incompletely understood. Here, we combine extensive all-atom molecular dynamics simulations with biophysical validation to characterize the conformational ensemble of the p53 PRD. The domain behaves as an intrinsically disordered region, sampling a highly heterogeneous ensemble with average end-to-end distance and radius of gyration of 52.5 Å and 21.8 Å, respectively. Despite this disorder, transient local structure is prominent: unordered conformations dominate, followed by substantial polyproline II (PPII) content, with β-bends and turns linking conserved PXXP motifs. Circular dichroism and small-angle X-ray scattering experiments corroborate the largely disordered yet partially structured nature of the PRD. Ramachandran and contact analyses reveal that consecutive prolines, particularly Pro71-Pro72, impose steric constraints that stabilize locally extended conformations and restrict backbone collapse. To approximate the PRD within full-length p53, additional simulations were performed with restrained terminal distances, yielding reduced conformational variability and improved agreement with small-angle X-ray scattering data while preserving secondary-structure propensities. PPII helices emerge as particularly robust features, acting as stiff spacers linking the transactivation domain to downstream regions. Finally, simulations of clinically relevant variants reveal mutation-specific local perturbations: P72R disrupts consecutive proline rigidity and increases flexibility, whereas P82L abolishes a PXXP motif and its associated PPII helix. These results identify proline-mediated rigidity and transient PPII structure as key determinants of the dynamic conformational landscape of the p53 PRD.