Journal Of Structural Biology[JOURNAL]
Sun
200 papers
MLAC: MicroED-assisted ligand structure analysis in complexes and its application to hERG-ligand complexes.
Tanaka K, Miyashita Y, Iwasaki K … +4 more , Saito T, Yamada Y, Murata T, Adachi N
J Struct Biol · 2026 Jul · PMID 42398788 · Publisher ↗
Accurate determination of ligand structures in protein-ligand complexes is essential for elucidating molecular recognition mechanisms and advancing structure-based drug discovery. Cryogenic electron microscopy (cryo-EM)...
Accurate determination of ligand structures in protein-ligand complexes is essential for elucidating molecular recognition mechanisms and advancing structure-based drug discovery. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful technique for determining macromolecular structures; however, reliable identification of small-molecule ligands from cryo-EM maps remains challenging, particularly in the absence of accurate initial ligand models. Here, we present MLAC (MicroED-assisted Ligand structure Analysis in Complexes), an integrative framework that combines microcrystal electron diffraction (MicroED) with cryo-EM single-particle analysis (SPA). In MLAC, high-resolution ligand structures determined by MicroED from submicrometer-sized crystals are used as initial models for fitting into cryo-EM maps of protein-ligand complexes. As a proof of concept, previously reported hERG-ligand complexes were reanalyzed. MicroED structures of representative hERG ligands-astemizole, pimozide, and E-4031-were determined at resolutions of 0.66-0.92 Å and then used for model fitting and refinement. Several quantitative metrics, including Q-score, atom inclusion, model-to-map correlation coefficients, clash analysis, and Mogul analysis, together with visual inspection, indicated that MicroED-derived ligand structures can facilitate ligand modeling for astemizole and, to a lesser extent, pimozide, whereas no clear advantage was observed for E-4031. Notably, MicroED frequently revealed structural polymorphs that provided alternative ligand conformations and helped resolve modeling ambiguities, including the chair-boat conformational variability of the piperidine ring and alternative ligand placements in the hERG-astemizole complex. Collectively, these findings support MLAC as a proof-of-concept framework that provides experimentally determined starting models to complement computational ligand-generation approaches.
Ultrastructural evidence of autophagy-related processes and mitochondrial remodeling in the myxozoan parasite Henneguya piaractus.
Capodifoglio KRH, Schneberger F, Maia AAM … +1 more , Ranzani de Paiva MJT
J Struct Biol · 2026 Jun · PMID 42302954 · Publisher ↗
Henneguya piaractus is a myxozoan parasite infecting the gills of Piaractus mesopotamicus, yet its cellular biology remains poorly understood. Here, we investigated mitochondrial organization and the occurrence of autoph...
Henneguya piaractus is a myxozoan parasite infecting the gills of Piaractus mesopotamicus, yet its cellular biology remains poorly understood. Here, we investigated mitochondrial organization and the occurrence of autophagy-related processes using an integrated approach combining confocal laser microscopy and transmission electron microscopy. SSU rDNA sequencing (1546 bp) confirmed species identity, showing 99.7% similarity to available H. piaractus sequences. Confocal microscopy revealed clear labeling of nuclei, polar capsules, and valves, whereas no signal indicative of mitochondrial activity was detected in mature myxospores. Ultrastructural analysis showed a plasmodium surrounded by a single membrane with numerous pinocytotic channels and mitochondria with well-developed cristae in the ectoplasmic region. Sporogenesis occurred asynchronously at the periphery, where sporoblasts and immature myxospores were observed. This region also exhibited double-membrane vesicles consistent with autophagosome-like structures, as well as phagophore-like membranes associated with damaged mitochondria. In addition, mitochondria-endoplasmic reticulum contact sites (MERCs) were identified. In contrast, centrally located mature myxospores contained mitochondria lacking cristae. Together, these findings indicate stage-dependent mitochondrial remodeling and suggest an autophagy-related process, possibly involving mitochondrial degradation. However, as these observations are based primarily on morphological evidence, the involvement of canonical autophagy pathways requires further molecular confirmation. This study provides novel insights into organelle dynamics in H. piaractus and contributes to a better understanding of cellular adaptations in myxozoan parasites.
Architecture and dynamics of a supramolecular oxygen transport system in human homogentisate 1,2-Dioxygenase.
Trezza A, Finetti R, Roncaglia B … +3 more , Giuliani F, Furlan F, Santucci A
J Struct Biol · 2026 Jun · PMID 42276179 · Publisher ↗
Alkaptonuria (AKU) is an ultra-rare inherited metabolic disorder caused by impaired activity of homogentisate 1,2-dioxygenase (HGD), a Fe(II)-dependent enzyme that catalyzes the oxidative cleavage of homogentisic acid in...
Alkaptonuria (AKU) is an ultra-rare inherited metabolic disorder caused by impaired activity of homogentisate 1,2-dioxygenase (HGD), a Fe(II)-dependent enzyme that catalyzes the oxidative cleavage of homogentisic acid in the tyrosine degradation pathway. Although high-resolution structures of human HGD have been solved, a fundamental mechanistic question has remained unresolved: how molecular oxygen reaches the deeply buried catalytic iron required for catalysis. Here, we identify a previously unreported AKU-associated HGD variant, c.925G>A (p.G309R), and use it as a mechanistic perturbation reference to dissect the structural determinants of oxygen access. By integrating replicated classical and steered molecular dynamics simulations with transient pocket detection, tunnel mapping, O spatial-occupancy analysis, residue-level tunnel composition, and PCA/tICA-based dynamic validation, we identify a structurally accessible and dynamically supported O-translocation architecture connecting the central pore of the hexameric enzyme to the non-heme Fe(II) active sites. This pathway is not intrinsic to a single subunit but emerges from a cooperative arrangement of residues contributed by three protomers, generating six symmetry-related O-access routes per hexamer. The G309R substitution perturbs the architecture and continuity of this tunnel system, providing a mechanistic explanation for enzyme dysfunction without evidence of active-site structural perturbation or global destabilization. Together, our findings support oxygen-tunnel integrity as a previously unrecognized mechanistic requirement for human HGD activity and introduce disruption of oxygen trafficking as an additional pathogenic mode in AKU, with implications for structure-guided variant interpretation and precision-medicine strategies.
Connecting pathways between mineralized fibrocartilage and bone at the Achilles tendon insertion.
Tits A, Blouin S, Rummler M … +5 more , Kaux JF, Drion P, Weinkamer R, Hartmann MA, Ruffoni D
J Struct Biol · 2026 Jun · PMID 42264160 · Publisher ↗
At entheses, tendons and bones are bridged by mineralized fibrocartilage, joined to tissues through dedicated interfaces. Tendons and bones are characterized by cells interconnected thanks to their underlying dense netwo...
At entheses, tendons and bones are bridged by mineralized fibrocartilage, joined to tissues through dedicated interfaces. Tendons and bones are characterized by cells interconnected thanks to their underlying dense networks. Nanotubes connect tenocytes in tendons, allowing cellular crosstalk and providing biomechanical stability. Osteocytes are involved in bone mechanoresponsiveness and mineralization: they are encased into cavities and their cellular processes run through channels, forming the osteocyte lacunocanalicular network. Here, we explore the structural connectivity between fibrocartilage and bone, exploiting rat enthesis as model system and focusing on two specific regions: the Achilles tendon insertion into calcaneus and the periosteal fibrocartilage, facilitating tendon sliding. Those regions are used to characterize the impact of loading environment on tissue connectivity. Central to our approach is rhodamine staining, employed to trace connections between tissues. This information is interpreted using data on tissue microstructure, organization and composition, acquired combining high-resolution imaging methods. At the enthesis, we observe potential connections between trabecular bone marrow and mineralized fibrocartilage through a subchondral channel network perforating the interface. Direct cellular connections between bone and fibrocartilage cells are rare: canaliculi mostly stop or switch direction at the cement line. Yet, we observed a high density of canaliculi around perforating channels, which reach fibrochondrocyte lacunae. Such connections seem practically absent at the periosteal region. Our findings are preliminary but suggest that inter-tissue connectivity is required to support the enthesis load-bearing function. To understand multi-tissue biochemical cellular crosstalk, the physical infrastructure enabling this communication is also a critical feature to investigate.
Structural and functional characterization of thermostable EstS1 esterase for BHET degradation.
Verma S, Aggarwal D, Ashar M … +6 more , Pandey AK, Sutradhar A, Pandey S, Sircar D, Singla J, Kumar P
J Struct Biol · 2026 Jun · PMID 42264159 · Publisher ↗
Enzymatic degradation of plastics has been extensively investigated, but its applications have remained limited due to the low stability and efficiency of enzymes in diverse environmental conditions. The present study el...
Enzymatic degradation of plastics has been extensively investigated, but its applications have remained limited due to the low stability and efficiency of enzymes in diverse environmental conditions. The present study elucidates the structural and functional characteristics of the thermostable EstS1 Esterase from Sulfobacillus acidophilus DSM10332 in the degradation of bis(2-hydroxyethyl) terephthalate (BHET), the primary intermediate of PET degradation. The co-crystal structure of wild-type EstS1 with BHET revealed binding of BHET and its degradation products, mono(2-hydroxyethyl) terephthalate (MHET), and ethylene glycol in the active site tunnel, with MHET interacting with the catalytic triad. The structure of the EstS1 Ser154Ala mutant with bound substrate showed two BHET molecules, of which one interacted with the mutated catalytic triad and the oxyanion hole, and the other was positioned in front of the first towards cavity 2. Further, structural analysis suggested that the hydrophobic nature of cavity 1, formed by the cap domain, plays a critical role in substrate binding, orientation, and catalysis. Kinetic analyses demonstrated that EstS1 degraded 75% of BHET within 1 h, producing MHET and terephthalate as end products. These findings indicate the remarkable ability of EstS1 to consecutively cleave two ester bonds. Molecular dynamics (MD) simulation revealed highly stable interactions between BHET and the active site of EstS1 throughout the 1 μs trajectory. Overall, this study provides structural insights into the EstS1-BHET interaction mechanism and demonstrates the potential of EstS1 esterase to directly convert BHET into terephthalate. These findings establish a strong foundation for future enzyme engineering efforts aimed at developing efficient PET plastic degradation technologies.
Following the white rabbit: multiscale 2D3D correlative imaging of bone structure.
Mahfouz C, Reiss T, Aimedieu P … +4 more , Vallet M, Smaniotto B, Vennat E, Le Cann S
J Struct Biol · 2026 Jun · PMID 42263961 · Publisher ↗
Bridging scales in bone research is challenging due to bone's heterogeneities and anisotropy at different scales. High-resolution imaging is often limited to volumes too small to reveal its complete hierarchical structur...
Bridging scales in bone research is challenging due to bone's heterogeneities and anisotropy at different scales. High-resolution imaging is often limited to volumes too small to reveal its complete hierarchical structure, a limitation that is further compounded by site-specific variability. Although bone multiscale structural organization has been extensively studied in humans, extrapolating these findings across species remains difficult. The study of bone pathologies or dynamic processes still relies on in vivo models, as these experiments cannot be performed on humans. In particular, rabbit bone represents a common model for bone studies but remains underexplored, especially at small scales. In this work, we investigate bone hierarchical structure and porosities in the rabbit across scales by combining 3D volumetric global (voxel size ∼ 15 μm) and local (voxel size ∼ 2 μm) micro-computed X-ray tomography with high-resolution 2D scanning electron microscopy (pixel size < 0.5 μm) and transmission electron microscopy (pixel size < 50 nm). 2D images were integrated into the spatial context of the 3D data through image registration, to highlight site-specific differences between endosteal, mid-cortex and periosteal regions. Osteocyte lacunae 2D morphology varied between primary osteons, secondary osteons and periosteal bone. These findings motivate further three-dimensional characterization of osteocyte lacunar morphology across osteon types and in larger cohorts, to clarify the role of osteocytes in bone remodeling. More broadly, our work highlights the potential of sequential multimodal workflows in giving a broader spatial context to sub-micron and nanoscale structural findings, reducing the "blindness" compromise that comes with high-resolution detail.
The mantis shrimp eye imaged in 3D using 4th generation synchrotron multiscale phase contrast tomography.
Faaborg AMM, Østergaard M, Langdal NK … +3 more , Kantor I, Christensen TEK, Birkedal H
J Struct Biol · 2026 Jun · PMID 42235654 · Publisher ↗
The stomatopod eye is a fascinating biological system capable of detecting both colour and polarization of light, making it a highly complex, mixed-tissue sample. In the investigation of complex biological systems, three...
The stomatopod eye is a fascinating biological system capable of detecting both colour and polarization of light, making it a highly complex, mixed-tissue sample. In the investigation of complex biological systems, three-dimensional methods spanning multiple length scales with the power to resolve soft tissues are required. In this study, propagation-based phase contrast X-ray computed tomography with stitching at a 4th generation synchrotron was used to image a full stomatopod eye with sub-micron voxel size to illustrate how this method accommodates these demands. The images are based on natural X-ray contrast and without any added labels or staining agents. Key features of the eye were identified and segmented. Utilizing these segmentations, photo filter volumes, chitin porosity volumes, and muscle fiber periodicities were measured, demonstrating the ability to perform quantitative as well as qualitative investigations. Neural compartments and associated cells were discernable, showing the power of 4th generation synchrotron phase contrast for the study of soft tissues. The illustrated properties along with its non-invasive nature proves phase contrast synchrotron X-ray computed tomography with stitching to be a powerful tool for the investigation of biological materials.
TAM receptor-ligand interfaces in zebrafish and mammals: A comparative structural and electrostatic analysis.
Torres Alegre EO
J Struct Biol · 2026 May · PMID 42217689 · Publisher ↗
Efficient resolution of neuroinflammation and debris clearance are key determinants of successful central nervous system (CNS) regeneration. Regenerative vertebrates such as Danio rerio often show faster immune resolutio...
Efficient resolution of neuroinflammation and debris clearance are key determinants of successful central nervous system (CNS) regeneration. Regenerative vertebrates such as Danio rerio often show faster immune resolution and debris clearance than mammals, yet the molecular determinants underlying these differences remain incompletely understood. TAM receptor tyrosine kinases (Tyro3, Axl, and Mertk) and their ligands Gas6 and Protein S are central regulators of phagocytosis and immune resolution in the nervous system, but whether intrinsic structural properties of these receptor-ligand complexes may modulate TAM signaling across species with distinct regenerative capacities has not been systematically explored. Here, I perform a comparative in silico analysis of TAM receptors and ligands from zebrafish, human, and mouse, integrating sequence evolution, high-confidence structural modeling, interface characterization, and electrostatic analysis. Despite substantial sequence divergence between mammals and zebrafish, ligand-binding domains retain strong structural conservation, supporting a conserved global mode of TAM-ligand engagement. At the interface level, zebrafish complexes exhibit enhanced electrostatic contributions and increased salt-bridge density, particularly in the Tyro3-Protein S interaction. Residue-resolved electrostatic analysis identifies clustered interface hotspots that are conserved in spatial organization and physicochemical function across species, despite evolutionary rewiring of individual contacts. Together, these findings suggest that TAM receptor-ligand interfaces are evolutionarily tuned through subtle electrostatic and geometric variation rather than large-scale structural changes. This conserved yet adaptable electrostatic framework supports the hypothesis that interface-level features may modulate TAM receptor-ligand engagement across vertebrates. However, these structural and electrostatic properties should be interpreted as potential modulatory contributions to TAM signaling rather than definitive determinants of regenerative capacity.
Crystallographic analysis of a putative FAD-dependent oxidoreductase identifies a potentially misfolded apo structure in a soluble monomeric state.
Xu J, Han L, Qi H … +4 more , Han Y, Chen B, Ju Y, Zhou H
J Struct Biol · 2026 May · PMID 42208745 · Publisher ↗
Misfolded proteins, if not refolded by molecular chaperones, are typically targeted for degradation by cellular quality control systems or tend to aggregate. In the present study, we report a rarely observed crystal stru...
Misfolded proteins, if not refolded by molecular chaperones, are typically targeted for degradation by cellular quality control systems or tend to aggregate. In the present study, we report a rarely observed crystal structure of a misfolded structure that exists as a stable monomer in solution. The CT375 protein from Chlamydia trachomatis, annotated as a putative d-amino acid dehydrogenase (DAADH), was confirmed to contain the flavin adenine dinucleotide (FAD) through ultraviolet-visible absorption spectroscopy and liquid chromatography-mass spectrometry analyses. However, high-resolution electron density maps excluded the presence of an FAD cofactor bound within the crystallized CT375. This abnormal apo conformation cannot be explained by the loss of FAD during crystallization, as the loop aberrantly occupying the active pocket cannot transition between its current conformation and the FAD-bound conformation observed in homologous oxidoreductases without passing through a two-stranded β-sheet. It is likely that the interactions between this misfolded loop, instead of FAD, and the active pocket residues contribute to stabilizing the overall fold of CT375 in this misfolded state, and that the misfolded protein, present within the heterogeneous CT375 sample, was fortuitously crystallized. The structure of misfolded CT375 underscores the critical role of the cofactor in correct protein folding and provides a valuable model for advancing the understanding of protein misfolding and its potential mechanisms underlying protein dysfunction.
Suppression of TLR4 dimerization by terahertz irradiation inhibits LPS-induced inflammation: A molecular dynamics study.
Shang S, Lin Y, Zhao X … +3 more , Li X, Wang H, Lu X
J Struct Biol · 2026 May · PMID 42203186 · Publisher ↗
Toll-like receptor 4 (TLR4) plays a pivotal role in the innate immune system by recognizing lipopolysaccharide (LPS) and triggering inflammatory signaling pathways. Previous studies have shown that 0.1 THz irradiation ca...
Toll-like receptor 4 (TLR4) plays a pivotal role in the innate immune system by recognizing lipopolysaccharide (LPS) and triggering inflammatory signaling pathways. Previous studies have shown that 0.1 THz irradiation can alleviate LPS-induced inflammation, but the specific mechanisms underlying this effect remain unclear. This study investigated the anti-inflammatory role of 0.1 THz irradiation by exploring its impact on TLR4 dimerization and LPS-induced inflammatory responses, using molecular dynamics simulations combined with in vitro validation. Results demonstrated that 0.1 THz irradiation significantly reduced the expression of TLR4 and its downstream signaling molecule MyD88 in LPS-stimulated HaCaT cells, inhibited the degradation of IκBα and phosphorylation of p65, and crucially suppressed LPS-induced TLR4 dimerization. This suppression of TLR4 dimerization further blocked the activation of the NF-κB inflammatory pathway. Molecular dynamics simulations revealed that 0.1 THz irradiation induced structural alterations of the (TLR4/MD-2/LPS)₂ complex, disrupted TLR4 dimerization, and altered the hydrogen bond distribution between proteins and surrounding water molecules. These structural changes likely interfere with the conformational prerequisites required for TLR4 dimerization and the subsequent activation of downstream signaling. Our findings clarify that 0.1 THz irradiation exerts anti-inflammatory effects by inhibiting TLR4 dimerization and downstream inflammatory signaling, which provides novel insights into the anti-inflammatory mechanisms of THz irradiation. This study also highlights the potential of terahertz technology as a promising strategy for the intervention and management of skin inflammatory.
Structural basis for TCR recognition of a Rac1 neoantigen arising from anchor residue mutation.
Zeng Y, Yang D, Zhao J … +5 more , Yuan P, Jin H, Liao W, Chen G, Wu D
J Struct Biol · 2026 May · PMID 42190883 · Publisher ↗
T cell receptor (TCR)-based immunotherapy can drive cancer regression by targeting neoantigens derived from mutations in self-proteins. Most neoantigens result from mutations in solvent-exposed residues creating neoepito...
T cell receptor (TCR)-based immunotherapy can drive cancer regression by targeting neoantigens derived from mutations in self-proteins. Most neoantigens result from mutations in solvent-exposed residues creating neoepitopes that allow highly specific TCR recognition. Here, we describe a melanoma neoantigen (Rac1) caused by a mutation at a primary anchor residue. Unlike typical cases, the immunogenicity of Rac1 stems from this anchor mutation, which permits MHC presentation of the mutant peptide but not the wild-type counterpart. We determined the structures of both the mutant Rac1-HLA-A2 complex and its complex with the tumor-specific TCR 5934. These structures show how the P29S mutation makes a Rac1 self- peptide visible to T cells. Notably, TCR 5934 primarily engages the C-terminal, non-mutated P8 threonine residue of Rac1 -far from the N-terminal mutated P2 serine. This contrasts with most neoantigen-specific TCRs, which typically focus on the mutated residue to distinguish mutant from wild-type peptides. Together, these findings provide a structural framework to guide the development of TCR-based cancer immunotherapies.
Crystal structure, thermostability and temperature-dependent enzymatic activity of an exo-β-d-glucosaminidase from Pyrococcus chitonophagus.
Biniek-Antosiak K, Baranowski D, Śliwiak J … +3 more , Milik M, Bejger M, Rypniewski W
J Struct Biol · 2026 May · PMID 42177926 · Publisher ↗
Pch-GlmA is a hyperthermophilic GH35 exo-β-d-glucosaminidase whose structure closely resembles its archaeal homologs, yet its functional behavior differs markedly. Calorimetric and fluorimetric temperature scans consiste...
Pch-GlmA is a hyperthermophilic GH35 exo-β-d-glucosaminidase whose structure closely resembles its archaeal homologs, yet its functional behavior differs markedly. Calorimetric and fluorimetric temperature scans consistently reveal a complex thermodynamic profile of the enzyme, characterized by distinct thermal transitions. The freshly purified protein appears to be monomeric and required thermal annealing to attain its biologically relevant dimeric state. Catalytic activity is observed only above 75 °C, where the enzyme specifically hydrolyses the glycosidic bond of GlcN-GlcNAc. These findings support a sequential role for Pch-GlmA alongside Pch-Dac in the processing of chitin-derived carbohydrates. Comparison with related GlmA proteins demonstrates that substantial structural similarity does not necessarily translate into equivalent enzymatic properties and that hyperthermophilic enzymes may operate within narrow temperature ranges. Overall, this work underscores the importance of experimental validation when interpreting or predicting the activity of enzymes derived from extremophiles.
Allosteric mechanisms of post-translational modification regulation in human cyclic GMP-AMP synthase catalytic activity from molecular dynamics simulations.
Gul M, Fakhar M, Li W
J Struct Biol · 2026 May · PMID 42177925 · Publisher ↗
Cyclic GMP-AMP synthase (cGAS) activation is regulated by post-translational modifications (PTMs), yet the structural basis by which these modifications tune DNA binding, nucleotide engagement, and dimer-dependent activa...
Cyclic GMP-AMP synthase (cGAS) activation is regulated by post-translational modifications (PTMs), yet the structural basis by which these modifications tune DNA binding, nucleotide engagement, and dimer-dependent activation remains unclear. Here, we investigated human cGAS catalytic-core complexes bound to dsDNA and ATP, comparing wild type with S305-phosphorylated and K384-, K394-, and K414-acetylated monomeric systems, followed by 2:2 cGAS-DNA dimeric assemblies focused on K394 acetylation. Monomeric simulations showed that PTMs regulate cGAS in a site-specific manner rather than through broad destabilization of the complex. S305 phosphorylation and K414 acetylation weakened ATP engagement by perturbing the catalytic-pocket environment, with K414 showing an allosteric effect through helix α7 rearrangement. K384 acetylation mainly altered the Zn-finger/DNA-contacting region, whereas K394 acetylation produced comparatively modest effects in the monomeric state. Because cGAS activity requires DNA-induced dimerization, we further analyzed WT_WT, WT_acK394, and acK394_acK394 dimers containing ATP, Mg, and Zn over 1000 ns. The WT_WT dimer maintained the most stable DNA association and ATP-pocket organization, whereas WT_acK394 showed intermediate perturbation and acK394_acK394 displayed the strongest reduction in DNA-protein contacts, hydrogen bonding, and ATP-pocket stability. Together, these results indicate that PTMs remodel cGAS through residue-specific effects on catalytic and DNA-binding hotspots, with K394 acetylation exerting a stronger destabilizing influence in the dimeric assembly than in the monomer. This monomer-to-dimer analysis provides mechanistic insight into how PTM-dependent structural remodeling may tune cGAS activation and innate immune signaling.
Rational design, antimicrobial mechanisms of non-perfectly amphipathic peptides with α-helical propensity.
Shi K, Su C, Hou J … +1 more , Jiang Z
J Struct Biol · 2026 May · PMID 42167663 · Publisher ↗
Antimicrobial peptides (AMPs) are natural substances, gaining attention for prevention of drug-resistant characteristics. To optimize the antibacterial efficacy and cellular selectivity of the AMPs, the antimicrobial pep...
Antimicrobial peptides (AMPs) are natural substances, gaining attention for prevention of drug-resistant characteristics. To optimize the antibacterial efficacy and cellular selectivity of the AMPs, the antimicrobial peptide with the sequence LKKISQYYQKFA was designated as L-0, extracted from sheep α-casein, which was used as a template to design five peptides through the mirror symmetry and amino acid substitution. Among these designed peptides, W-4, which featured an imperfect amphipathic α-helical structure, exhibited the strongest antimicrobial activity, comparable to cefixime. In addition, both the cellular selectivity and condition stability of W-4 were improved, compared with the template peptide. Molecular docking was further performed to show that W-4 preferentially targeted bacterial membrane mimics than L-0, thus exerting strong antimicrobial activity with minimal damage to eukaryotic membranes. W-4 exerted stronger bactericidal activity than the template peptide, due to its greater capacity to permeabilize and disrupt the cell membrane. Therefore, imperfect amphipathic peptides have strong antibacterial activities and are promising candidates for traditional antibiotics in food and pharmaceutical industries.
Machine learning for predicting young's modulus of soft tissues from atomic force microscopy data.
Abdoli M, Taheri M
J Struct Biol · 2026 Jun · PMID 42142679 · Publisher ↗
Atomic force microscopy (AFM) is an advanced tool applied to investigate the mechanical properties of a wide variety of material classes, including soft biological tissues. Force-indentation curves obtained through AFM c...
Atomic force microscopy (AFM) is an advanced tool applied to investigate the mechanical properties of a wide variety of material classes, including soft biological tissues. Force-indentation curves obtained through AFM can be analyzed using appropriate contact models to extract key material parameters, notably Young's modulus. The measurement of the Young's modulus of biological materials imposes significant constraints. However, a persistent challenge in the adoption of AFM lies in the complexity of data analysis, which is often time-intensive and requires highly specialized personnel with robust expertise in physics and mathematics. As a result, recent efforts have concentrated on alternative methodologies, particularly machine learning (ML) models, to enhance and facilitate this analysis process. This work introduces a customized regressor to predict Young's modulus from force-indentation (F-I) curves, specifically targeting values between 1 and 50 kPa. The model was exclusively trained on synthetic datasets generated based the Johnson-Kendall-Roberts (JKR) contact theory. An MLP regressor was employed for model training, alongside a Grid-Search library to optimize the hyperparameters. Model accuracy was validated through regressor testing against theoretical and laboratory force-indentation curves obtained from AFM nano-indentation studies. By delivering precise predictions with optimized computational efficiency, this regressor demonstrates the potential of deep learning approaches to support comprehensive evaluation of AFM nanoindentations, paving the way for further advancements in overcoming the current limitations associated with AFM.
Scientific Laudatio for Professor Andreas Engel.
Fotiadis D, Müller SA, Müller DJ
J Struct Biol · 2026 Jun · PMID 42103177 · Publisher ↗
With the passing of Andreas Engel on 1 April 2026, the structural biology and biophysics communities have lost one of their most visionary and influential scientists. Over a career spanning more than five decades, Andrea...
With the passing of Andreas Engel on 1 April 2026, the structural biology and biophysics communities have lost one of their most visionary and influential scientists. Over a career spanning more than five decades, Andreas fundamentally shaped how we visualize and understand biological macromolecules at the nanoscale. His pioneering contributions to scanning transmission electron microscopy (STEM), atomic force microscopy (AFM) and electron crystallography opened entirely new avenues for studying the architecture and function of membrane proteins and supramolecular protein complexes.
In situ loading and patterns of trabecular deformation in the intermediale of the vertebral centrum of a great hammerhead.
Parker JT, Comes JS, Passerotti MS … +4 more , Natanson LJ, Seto J, Parkinson DY, Stock SR
J Struct Biol · 2026 Jun · PMID 42081960 · Publisher ↗
The vertebral centra of sharks consist of cartilage, and many species' centra are mineralized. The main centrum structures, the corpus calcareum and intermedialia, consist of an interconnected network of thin, closely-sp...
The vertebral centra of sharks consist of cartilage, and many species' centra are mineralized. The main centrum structures, the corpus calcareum and intermedialia, consist of an interconnected network of thin, closely-spaced, mineralized trabeculae and of unmineralized volumes which are also interconnected. In vivo, the centra survive millions of cycles of large amplitude compressions, and we hypothesized that reversible trabecular deflections/rotations make this possible. The hypothesis was directly tested using in situ compression of three small blocks cut from a great hammerhead intermediale and synchrotron microComputed Tomography. The BoneJ plugin for ImageJ was used to quantify trabecular spacings and trabecular thicknesses at multiple subvolumes within each block. Changes in applied strain of 4% produced little change in trabecular thickness and appreciable changes in trabecular spacing, confirming the hypothesis that the large applied strain was accommodated by deflections/rotations of trabeculae.
Conformational changes on the third PDZ domain of PSD95 upon phosphorylation of Tyr397.
Salinas-Garcia MC, Murciano-Calles J, Andujar-Sánchez M … +3 more , Ortiz-Salmerón E, Martínez JC, Cámara-Artigas A
J Struct Biol · 2026 Jun · PMID 42067080 · Publisher ↗
PSD95, a member of the membrane-associated guanylate kinase family, plays a key role in synaptic transmission. In this multidomain protein, the third PDZ domain has a complex regulatory mechanism that modulates its bindi...
PSD95, a member of the membrane-associated guanylate kinase family, plays a key role in synaptic transmission. In this multidomain protein, the third PDZ domain has a complex regulatory mechanism that modulates its binding of carboxyl-terminal sequences. Phosphorylation of Tyr397, located in the additional α3 helix of this PDZ domain, has been shown to affect the domain's binding affinity. To explore the molecular basis of these changes in affinity, the crystal structure of the mutant Tyr397Glu, a point mutation intended to mimic phosphorylated tyrosine, has been determined. The crystal structure of this mutant reveals conformational changes induced by the introduction of a negative charge into the extra-domain α3 helix, suggesting communication between distant secondary-structure elements that may affect the binding affinity of this domain. Additionally, DSC folding studies show a noticeable decrease in the mutant's stability, indicating significant conformational changes. Altogether, the experimental results included in this work demonstrate that α3 is part of an electrostatic network that regulates stability and conformational changes at distant sites, including the β-hairpin at the binding site.
Structural implications of glycosylation on the voltage-gated sodium channel β3-subunit.
Beaudoin CA, Hayes J, Liu H … +8 more , Namadurai S, Deery MJ, August EA, Krasner S, Hamaia SW, Salvage SC, Huang CL, Jackson AP
J Struct Biol · 2026 Jun · PMID 42034256 · Publisher ↗
Voltage-gated sodium (Na) channel α-subunits are modulated by associated β-subunits affecting their localization, trafficking and gating behaviour. The β-subunits are members of the immunoglobulin (Ig) domain family of c...
Voltage-gated sodium (Na) channel α-subunits are modulated by associated β-subunits affecting their localization, trafficking and gating behaviour. The β-subunits are members of the immunoglobulin (Ig) domain family of cell-adhesion molecules and the interactions between their extracellular Ig-domains may modify channel clustering. The full-length β3-subunit can form cis trimers on the plasma membrane. The atomic resolution structure of a deglycosylated trimeric β3-subunit Ig-domain has been solved by X-ray crystallography. However, it is not clear whether this particular trimeric Ig-domain structure is plausible for cell-expressed, glycosylated β3-subunits. Here we use glycan profiling to confirm an extensive and heterogeneous pattern of β3-subunit glycosylation, with the majority of glycans being bi- and tri-antennary structures with one or two terminal sialic acids. Two tryptic peptides of the β3 Ig-domain are predicted to contain potential N-linked glycosylation sites. When the isolated, glycosylated full-length β3-subunit was trypsin-digested and analysed by LC-MS/MS, only one of these peptides - containing an N-linked glycosylation site at residue N95 and located close to the trimer interface - was identified in its unmodified form, suggesting that residue N95 is under-glycosylated. All-atom molecular dynamics simulations of the glycosylated, membrane-bound full-length β3 trimer confirmed that glycans can be accommodated with the Ig-domain trimer and indeed, may contribute to protein-membrane and inter-protomer interactions within the full-length, membrane-embedded trimer. Further biochemical studies are warranted to explore the interactions between oligomeric β-subunits with corresponding α-subunit sodium channels.
Molecular structure of the third immunoglobulin domain (Ig3) of human Muscle-Specific kinase (MuSK).
Canciani A, Palamini M, Forneris F
J Struct Biol · 2026 Jun · PMID 41956176 · Publisher ↗
The Muscle-Specific Kinase (MuSK) is a monotopic transmembrane receptor responsible for key signaling events during development and maintenance of neuromuscular junctions. The N-terminal extracellular portion of MuSK is...
The Muscle-Specific Kinase (MuSK) is a monotopic transmembrane receptor responsible for key signaling events during development and maintenance of neuromuscular junctions. The N-terminal extracellular portion of MuSK is characterized by multiple domains, extensively involved in molecular interactions with co-receptor LRP4 during MuSK activation. The molecular mechanisms underlying MuSK activation through self- and non-self- molecular interactions are still poorly understood. In this work, we have recombinantly produced and characterized the third Ig domain of human MuSK (hMuSK-Ig3) using X-ray crystallography. Long-wavelength experimental phasing serendipitously revealed several potassium ions bound to the ten copies of hMuSK-Ig3 found in the crystallographic asymmetric unit, arranged in a super-helical fashion with paired antiparallel inter-domain molecular contacts involving β-sheets from two neighboring molecules. Collectively, our data highlight unique structural features of this domain, including metal ion binding and surface contact hot-spots possibly suggestive of contact sites relevant for interactions with co-receptor LRP4 and/or other molecular partners involved in MuSK signaling.
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