Biology subjects

Pickersgill, R. W.

Publications and source records attributed to Pickersgill, R. W..

5 recordsLinked to original sources

bioRxiv2026

Assembly and activation of the AAA+ motor of the multi-subunit cobaltochelatase

Cobalamin is a complex yet essential cobalt-containing cofactor synthesized exclusively by prokaryotes and archaea. Aerobic cobalamin biosynthesis requires the CobNST multi-subunit class I cobaltochelatase for cobalt incorporation. Cobalt chelation is dependent on the energy transfer from the CobST AAA+/VWA motor unit to the substrate-binding catalytic unit (CobN). However, the mechanism for assembly and function of CobNST cobaltochelatase remains poorly understood. Here, we used cryo-EM to solve the structures of the AAA+ motor CobS, in the absence and presence of ATP and its VWA-partner protein CobT. Our data reveal that the AAA+ CobS assembles into various conformations, including hexameric planar rings and different spiral left-handed assemblies: hexamers, double rings and filaments. In the absence of nucleotide, the CobT N-terminal domain interacts with CobS left-handed oligomers, remaining in a half-assembled, nonfunctional motor unit. In the CobST complex, ATP induces conformational rearrangement of CobS from left-handed helical oligomers to a right-handed closed hexamer. The simultaneous repositioning of the CobT VWA domain to the AAA+ central pore shifts the motor unit to a functional state, ready-to-drive CobN-catalyzed chelation reaction. These findings define the mechanism for assembly and activation of the class I cobaltochelatase CobST motor.

biochemistry↗

bioRxiv2026

Learning fragment-based segmentation of binding sites from molecular dynamics: a proof-of-concept on cardiac myosin.

The geometric and chemical features of protein binding sites tend to change as a consequence of conformational dynamics. In the ligand-unbound (apo) state, a binding site might be only transiently organised in a way that can accommodate a given ligand, with the relevant regions of the protein coming together in a suitable arrangement only in a subset of conformations. Ligand binding itself can also induce further changes in the binding site. Because most ligands can be decomposed into smaller fragments, we hypothesised that mapping onto the binding site surface the propensity of binding specific fragments could be used to monitor changes in the overall ability of the site to bind a ligand. This task can be formulated as semantic segmentation, which can now be performed successfully using deep learning methods. Here we introduce the Fragment-Based protein Ensemble semantic Segmentation Tool for Myosin (FragBEST-Myo), a deep learning method based on a 3D U-Net architecture, trained to partition the omecamtiv mecarbil (OM) binding site of cardiac myosin into fragment-specific regions using only local shape and physico-chemical features. The model was trained on labelled Molecular Dynamics (MD) trajectories of OM-bound myosin in both post-rigor (PR) and pre-power-stroke (PPS) states, achieving an accuracy of ~95% and a mean Intersection over Union (mIoU) > 0.75 on unseen trajectories from both states. When applied to apo trajectories, FragBEST-Myo-derived descriptors produced rankings consistent with similarity to holo conformations. Moreover, selecting apo frames based on FragBEST-Myo ranking increased the chance of recovering holo-like OM docking poses relative to randomly chosen control frames, supporting its use as a screening tool for ensemble docking. Beyond frame selection, fragment maps provide a compact representation to assess docking poses and to guide fragment-based design. Our proof-of-concept provides a basis for developing future general models applicable to a broader range of proteins and ligands, with the fragment-based formulation offering a natural route to generalisation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/703009v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1551255org.highwire.dtl.DTLVardef@26bf73org.highwire.dtl.DTLVardef@1e3181forg.highwire.dtl.DTLVardef@44baf7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2022

Enzyme encapsulation peptides bind to the groove between tessellating subunits of the bacterial microcompartment shell

Bacterial microcompartments are prokaryotic organelles consisting of encapsulated enzymes within a thin protein shell. They are involved in metabolic processing including propanediol, choline, glycerol and ethanolamine utilization, and carbon fixation. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the binding-site has not been revealed. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating tiles of major shell proteins. In silico docking studies provide a compelling model of peptide binding to this hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell proteins faces the lumen of the microcompartment. Binding between shell protein tiles explains why the encapsulation peptide binding site has been elusive, how encapsulation-peptide bearing enzymes can promote shell assembly, and how the presence of cargo affects the size and shape of the bacterial microcompartment.

biochemistry↗

bioRxiv2021

Scaffolding protein GspB/OutB facilitates assembly of the Dickeya dadantii type 2 secretion system by anchoring the outer membrane secretin pore to the inner membrane and to the peptidoglycan cell wall.

The phytopathogenic proteobacterium Dickeya dadantii secretes an array of plant cell wall degrading enzymes and other virulence factors via the type 2 secretion system (T2SS). T2SSs are widespread among important plant, animal and human bacterial pathogens. This multi-protein complex spans the double membrane cell envelope and secretes fully folded proteins through a large outer membrane pore formed by 15 subunits of the secretin GspD. Secretins are also found in the type 3 secretion system and the type 4 pili. Usually, specialized lipoproteins termed as pilotins assist the targeting and assembly of secretins into the outer membrane. Here, we show that in Dickeya, the pilotin acts in concert with the scaffolding protein GspB. Deletion of gspB profoundly impacts secretin assembly, pectinase secretion, and virulence. Structural studies reveal that GspB possesses a conserved periplasmic Homology Region domain that interacts directly with the N-terminal secretin domain. Site-specific photo cross-linking unravels molecular details of the GspB-GspD complex in vivo. We show that GspB facilitates outer membrane targeting and assembly of the secretin pores and anchors them to the inner membrane while the C-terminal extension of GspB scaffolds the secretin channel in the peptidoglycan cell wall. Phylogenetic analysis shows that in other bacteria, GspB homologs vary in length and domain composition and act in concert with either a cognate ATPase GspA or a pilotin GspS. ImportanceGram-negative bacteria have two cell membranes sandwiching a peptidoglycan net that form together a robust protective cell envelope. To translocate effector proteins across this multilayer envelope, bacteria have evolved several specialized secretion systems. In the type 2 secretion system and some other bacterial machineries, secretins form large multimeric pores that allow transport of effector proteins or filaments across the outer membrane. The secretins are essential for nutrient acquisition and pathogenicity and constitute a target for development of new antibacterials. Targeting of secretin subunits into the outer membrane is often facilitated by a special class of lipoproteins called pilotins. Here, we show that in Dickeya and some other bacteria, the scaffolding protein GspB acts in concert with pilotin, facilitating the assembly of the secretin pore and its anchoring to both the inner membrane and the bacterial cell wall. GspB homologs of varied domain composition are present in many other T2SSs.

microbiology↗

bioRxiv2018

Structure analysis of human Prion protein involved in Sporadic Fatal Insomnia

Prion disorders are the root cause of Transmissible Spongiform Encephalopathies (TSE), a group of lethal diseases portrayed by progressive neurodegeneration and spongiosis. In recent years, researchers have come to understand that it is not the endogenous presence of Prions itself that causes neurodegeneration, but the amount of prion proteins that accumulates in the nervous tissue, leading them to exert neurotoxicity. More specifically, the cause of these disorders is mapped to several mutations that can bring the prion protein structure to a disordered permanent misfolded state. Our research is focused on Sporadic Fatal Insomnia (sFI), a rare TSE characterized by severe and chronic insomnia, leading to a life expectancy estimation of about two and a half years, from the onset of the first symptoms. The goal of this work was to analyze through computational studies the structure of the native human Prion Protein (PrPnat) and compare it with the toxic form (FI-Prion) which causes disease. Our findings show that the structure of the human mutant FI-Prion, responsible for Sporadic Fatal Insomnia is more flexible than the native human form PrPnat. Specific regions of the mutant seem to fluctuate more freely than the corresponding loops in the native form. We also identified amino acids Tyr128 and Met129 to be the key residues playing a major role in the manifestation of the disease. Therefore, weve learnt that the FI-Prion is more flexible than PrPnat. In addition, we also confirmed that sporadic fatal insomnia is undoubtedly an infectious disease.

bioinformatics↗