Biology subjects

Dramicanin, M.

Publications and source records attributed to Dramicanin, M..

4 recordsLinked to original sources

bioRxiv2026

Structural basis for inefficient G protein coupling by Frizzled receptors

Frizzleds (FZDs) are class F G protein-coupled receptors (GPCRs) that primarily signal through Dishevelled (DVL) to initiate Wnt signalling, with evidence for context-specific coupling to heterotrimeric G proteins. Every FZD-G protein structure to date has been determined without an agonist, implying that agonist binding is not required for stable complex formation in vitro and directly contradicting the difficulty of demonstrating G protein coupling in cells. All these structures contain unassigned density between the receptor and the heterotrimeric G protein. From structures generated by single-particle cryo-electron microscopy (cryo-EM) of FZD7-Gs and FZD5-Gq, we identify this density as the detergent lauryl maltose neopentyl glycol (LMNG), which bridges the receptor and G protein to stabilise a weak, shallow interface. Absence of LMNG - in biochemical preparations and molecular dynamics simulations - destabilises the complex, showing that constitutive FZD-G protein engagement is intrinsically weak. The weak G protein coupling is governed by a conserved intracellular interface that when mutated differentially influences DVL and G protein signalling. Our findings show that LMNG has masked the instability of purified FZD-G protein complexes and provide the structural basis of FZDs as inherently weak G protein activators that are predisposed to DVL signalling.

biochemistry↗

bioRxiv2026

Active Learning Enables Efficient Directed Evolution of a Far-Red Fluorescent Protein with Minimal Experimental Data

Fluorescent proteins are fundamental tools for cellular imaging. Most fluorescent proteins in routine use, including GFP, are derived from the jellyfish Aequorea victoria and emit blue-green light, which is strongly absorbed and scattered by tissue, limiting imaging depth. Far-red and near-infrared fluorescent proteins, engineered from bacteriophytochromes, address this limitation because far-red light penetrates tissue considerably further. However, these proteins are typically much dimmer than their A. victoria -derived counterparts. Improving brightness by conventional directed evolution requires screening large random mutant libraries, a process that is slow, labor-intensive, and often impractical outside specialized laboratories. We utilized an active-learning-guided directed evolution workflow that identified improved variants from substantially less data than conventional screening. Each round coupled automated, miniaturized cell-free protein expression directly from a DNA template without cloning or cell culture, with a machine-learning model retrained on cumulative sequence-function data to nominate the most informative variants for the next round. Applied to miRFP670nano3, this workflow screened 120 variants across successive rounds and identified twelve with improved brightness, the best four-fold brighter in bacterial systems. However, these gains did not translate when the variants were evaluated in mammalian cells, indicating that performance can be strongly dependent on cellular context. Retrospective simulation across benchmark datasets from ProteinGym showed that performing more experimental batches with fewer samples per batch consistently accelerated convergence to high-fitness sequences. Incorporating protein-language-model derived zero-shot fitness priors also accelerated convergence, but only in proportion to how well each prior score correlated with the true fitness landscape. Together, these findings established generalizable design rules, favoring smaller acquisition batches and confidence-weighted priors, for engineering proteins from minimal experimental data. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=55 SRC="FIGDIR/small/744534v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@14cd238org.highwire.dtl.DTLVardef@7d8334org.highwire.dtl.DTLVardef@30e9f2org.highwire.dtl.DTLVardef@14f3a0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Inhibiting heme-piracy by pathogenic Escherichia coli using de novo-designed proteins

Iron is an essential nutrient for most bacteria and is often growth-limiting during infection, due to the host sequestering free iron as part of the innate immune response. To obtain the iron required for growth, many bacterial pathogens encode transporters capable of extracting the iron-containing cofactor heme directly from host proteins. Pathogenic E. coli and Shigella spp. produce the outer membrane transporter ChuA, which binds host hemoglobin and extracts its heme cofactor, before importing heme into the cell. Heme extraction by ChuA is a dynamic process, with the transporter capable of rapidly extracting heme from hemoglobin in the absence of an external energy source, without forming a stable ChuA-hemoglobin complex. In this work, we utilise a combination of structural modelling, Cryo-EM, X-ray crystallography, mutagenesis, and phenotypic analysis to understand the mechanistic detail of this process. Based on this understanding we utilise artificial intelligence-based protein design to create binders capable of inhibiting E. coli growth by blocking hemoglobin binding to ChuA. By screening a limited number of these designs, we identify several binders that inhibit E. coli growth at low nanomolar concentrations, without experimental optimisation. We determine the structure of a subset of these binders, alone and in complex with ChuA, demonstrating that they closely match the computational design. This work demonstrates the utility of de novo-designed proteins for inhibiting bacterial nutrient uptake and uses a workflow that could be applied to integral membrane proteins in other organisms.

biochemistry↗

bioRxiv2020

Structural basis of substrate recognition and catalysis by fucosyltransferase 8

Fucosylation of the inner-most N-acetyl-glucosamine (GlcNAc) of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can have a dramatic impact on the activity and half-life of glycoproteins. These effects are relevant to understanding the invasiveness of some cancers, the development of monoclonal antibody therapeutics, and to a congenital disorder of glycosylation. The acceptor substrate preferences of FUT8 are well characterised and provide a framework for understanding N-glycan maturation in the Golgi, however the structural basis for these substrate preferences and the mechanism through which catalysis is achieved remains unknown. Here, we describe several structures of mouse and human FUT8 in the apo state and in complex with guanosine diphosphate (GDP), a mimic of the donor substrate, and a glycopeptide acceptor substrate. These structures provide insights into: a unique conformational change associated with donor substrate binding; common strategies employed by fucosyltransferases to coordinate GDP; features that define acceptor substrate preferences; and a likely mechanism for enzyme catalysis. Together with molecular dynamics simulations, the structures also reveal how FUT8 dimerisation plays an important role in defining the acceptor substrate binding site. Collectively, this information significantly builds on our understanding of the core-fucosylation process.

biochemistry↗