Biology subjects

Demyanenko, Y.

Publications and source records attributed to Demyanenko, Y..

8 recordsLinked to original sources

bioRxiv2025

High-throughput discovery of a dearomative cycloaddition enables dual photochemical-photophysical perturbative probing of protein function

Proteins exist in multiple conformations or states, often associated with different functional capacities. The ability to selectively identify and study these states is crucial for understanding the dynamic nature of proteins and their roles in cellular processes, yet can be currently limited by the artefacts of existing molecular labels and the lack of strategies to exploit them in diverse ways. Whilst i) methods for the photochemical perturbation of proteins and ii) photophysical protein probes and sensors are both known powerful tools, simultaneous methods for site- and context-specific photochemical modification of a protein side chain with concomitant modulation of photophysical properties would allow interrogation of protein function via diverse modes (potentially reporting simultaneously on structure and dynamics of ground- and reactive-state properties). Due to their mechanistic complexity, rational approaches for the design of suitable photochemical strategies can be difficult and non-intuitive. Here, we describe a high-throughput experimentation (HTE) strategy designed to allow the photochemical modification of a genetically-encoded, minimally disruptive ( zero-size), photophysically-active - yet typically unreactive and biologically-inert - unnatural amino acid (uAA) residue in proteins. The discovery of a novel dearomative, formal [4+3] photocycloaddition of imidazopyrimidine reagents which proceeds via photochemically generated C* intermediates with polyaromatic substrates enabled chemoselective application to the normally unreactive Trp-mimetic residue, 2-naphthylalanine (Npa). Npas site-selective installation allows dual photochemical and photophysical dearomative perturbation benignly and efficiently in proteins. Replacement of Trp in the archetypal apoptotic biosensor protein Annexin A5 (AnxV) enabled dual photochemical-photophysical determination of switched, conformationally-determined reactive states induced by Ca2+-binding, without any apparent functional perturbation of its in vitro or cellular recognition of phospholipids, indicating an ordered annexin mechanism. This ready and benign unification of photochemistry and photophysics suggests a general approach for using high-throughput light-mediated experimentation in artefact-free chemical biology to capture different functional states of proteins and to interrogate those states using combined photochemical-photophysical methods. HighlightsO_LIDevelopment of a general, high-throughput experimentation (HTE) approach enabled identification of an unprecedented photochemical reaction with potential for editing amino acid side chains within proteins. C_LIO_LIGenetic incorporation of 2-naphthylalanine, a minimally-disruptive ( zero-size) Trp mimic, enabled photochemical side chain editing with concomitant modulation of its distinctive photophysical properties in proteins. C_LIO_LIA naphthalene-tagged variant of the apoptotic biomarker protein AnxV enabled dual photochemical-photophysical exploration of its dynamic conformational states induced by Ca2+-binding whilst fully maintaining its functional capacity for in vitro or cellular recognition of phospholipids. C_LI

biochemistry↗

bioRxiv2025

Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3

In attempting to observe the behaviour of a protein of interest in vivo, akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or its host, leaving one uncertain as to whether natural behaviour remains unperturbed. The study of chromatin has mostly been restricted to defining its function in the nucleus, where histone proteins fulfil vital roles in packaging genomic DNA and regulating transcription. However, chromatin components can be released into the extracellular space, either intentionally via cellular secretion or during disease-induced cell death. These extracellular chromatin components, depending on the context, can consist of: free histones, free DNA, intact nucleosomes (histone octamers wrapped by DNA), or heterogeneous, higher order structures such as neutrophil extracellular traps (NETs). They have been associated with diverse pathologies such as inflammation, cancer, and sepsis, and distinct toxic effects. However, there is a widely acknowledged lack of methods that distinguish between them and between their unique functions. Here, we now address protein observer effects to explore the fate and function of extracellular free histones by utilizing FIRESCAPE ([18F]-Fluorine Isotopic Radiolabeling Enabling Scanning of Clearance After Proteolytic Events), a novel radiolabeling concept that leverages the unique, high-sensitivity properties of the radioisotope fluorine-18, 18F, and residue-specific protein editing chemistry. By installing close and then true 18F-containing protein sidechain mimics site-specifically, FIRESCAPE enables the hierarchical in vivo scanning of the half-lives, proteolytic susceptibility and clearance of single residues in a protein of interest, and at microdoses far below toxic levels (low nanomole). These radioequivalent proteins bearing near-zero-size, zero-background labels now precisely reveal the strikingly distinct distribution, half-lives, damage-inducing abilities and accumulation of free extracellular histones in cellulo and in vivo compared to intact nucleosomes. Free extracellular histone H3 is rapidly cleared from circulation, mediated first by proteolysis of the histone tail. By contrast, direct injection of free histones vs nucleosomes into tissue that is unprotected by such proteolysis (brain), provokes a starkly different response; free histones exhibited limited diffusion and swiftly promoted damage both in cell culture and in vivo, whilst intact nucleosomes were essentially passive and benign. Remarkably, synthetic extracellular histone H3 was observed to enter cells and integrate into chromatin, indistinguishable from native H3 in both localization and post-translational modification (PTM) accumulation, yet paired with cellular and tissue damage. The exploratory studies described here now provide much needed clarity to the distinct fates and effects of extracellular histones vs nucleosomes, in particular the strongly damaging effects of free histones, their rapid uptake into cells, and an associated histone-specific proteolysis pathway via the removal of the histone tail.

biochemistry↗

bioRxiv2025

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage

We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this ability to generate large datasets through multienzyme deep proteomics experiments for characterisation of these activation techniques. As a further step, motivated by the complexity generated by these dissociation techniques, we developed a single Prosit deep learning model for fragment ion intensity prediction covering all of these techniques. The generated model has been made publicly available and has been utilised in FragPipe within its MSBooster module. Rescoring allowed both data-dependent acquisition (DDA) and data-independent acquisition (DIA) to achieve on average more than 10% increase in protein identifications across all dissociation techniques and enzymatic digestions. We demonstrate that these alternative fragmentation approaches can now be used within standard data analysis pipelines and can produce data competitive to CID in terms of eficiency, but in the cases of EID and UVPD with far richer and more comprehensive spectra.

systems biology↗

bioRxiv2025

RNA binding regulation is a new dimension in the type I IFN response

The type I interferon (IFN-I) response shapes the intracellular environment to supress virus infection. Historically, this remodelling has been linked to the transcriptional induction of interferon stimulated genes (ISGs). However, IFN-I-driven post-translational regulation of proteins already present in the cell remains relatively unexplored. Here, we profiled the activity of cellular RNA-binding proteins (RBPs), which are key players in antiviral immunity. Using RNA interactome capture (RIC), we identified hundreds of RBPs whose association with RNA is regulated by IFN-I (IR-RBPs). Among these IR-RBPs are both known antiviral proteins and novel candidates identified in this study through a knockdown screen. By modifying RIC to study IR-RBPs phosphorylation states, we identified several putative instances of IFN-I-driven phospho-regulation of RNA binding. We experimentally confirmed this phospho-driven regulation for MATR3. Altogether, our results reveal a new dimension of the cells antiviral programme, in which the cellular RNA-bound proteome is remodelled by IFN-I.

biochemistry↗

bioRxiv2025

Are Solid Particles Ready for Prime-Time Proteomics?

We evaluate the performance of nonporous C-18 stationary phases in high-speed proteomics workflows. We employed two commercially available sub-2 {micro}m nonporous particle (NPP) materials, ODS-IIIE (1.5 {micro}m) and SOLAD (1.0 {micro}m), to fabricate analytical columns using 150 {micro}m internal diameter (i.d.) fused silica capillaries to ensure compatibility with nano-UHPLC and nano-HPLC pressure regimes. Using long NPP columns (15 - 25 cm) connected to a conventional nano-UHPLC, we found that both materials supported efficient peptide separations within the flow rate and pressure ranges typical of nano-UHPLC systems. Shorter columns, used with the 10- and 16-minute Whisper Zoom 120 and Zoom 80 methods on the Evosep One HPLC, demonstrated competitive separation performance compared to columns packed with fully porous (FPP) and superficially porous particles (SPP), achieving full-width at half maximum (FWHM) values below 2 seconds (Zoom 120) and 3 seconds (Zoom 80). DIA LC-MS/MS analysis of the same digest demonstrated that NPP columns provided comparable or superior performance relative to FPP and SPP materials. These findings establish NPP-based columns as a viable and competitive alternative to FPP and SPP materials, particularly suited for high-throughput and high-sensitivity proteomics applications.

systems biology↗

bioRxiv2024

Uukuniemi virus infection causes a pervasive remodelling of the RNA-binding proteome in tick cell cultures

Cellular RNA-binding proteins (RBPs) are pivotal for the viral lifecycle, mediating key host-virus interactions that promote or repress virus infection. While these interactions have been largely studied in the vertebrate host, no comprehensive analyses of protein-RNA interactions occurring in cells of arbovirus vectors, in particular ticks, have been performed to date. Here we systematically identified the responses of the RNA-binding proteome (RBPome) to infection with a prototype bunyavirus (Uukuniemi virus; UUKV) in tick cells and discovered changes in RNA-binding activity for 283 proteins. In an orthogonal approach, we analysed the composition of the viral ribonucleoprotein by immunoprecipitation of UUKV nucleocapsid protein (N) in infected cells. We found many tick RBPs that are regulated by UUKV infection and associate with viral nucleocapsid protein complexes. We confirmed experimentally that these RBPs impact UUKV infection. This includes the tick homolog of topoisomerase 3B (TOP3B), a protein able to manipulate the topology of RNA, which showed an effect on viral particle production. Our data thus reveals the first protein-RNA interaction map for infected tick cells. Research highlightsO_LIUUKV RNAs interact with nearly three hundred tick cell RBPs. C_LIO_LIDemonstrated an enrichment of N protein interactors within the upregulated RIC data suggesting a direct involvement in viral RNA metabolism and translation. C_LIO_LIDeveloped a robust methodology to silence gene expression in tick cell cultures. C_LIO_LIThe TOP3B complex facilitates efficient packaging of UUKV virions. C_LI

microbiology↗

bioRxiv2024

Removal of NHS-labelling by-products in Proteomic Samples

N-Hydroxysuccinimide (NHS) ester chemistry is used extensively across proteomics sample preparation. One of its increasingly prevalent applications is in isobaric reagent-based quantitation such as the iTRAQ (isobaric tags for relative and absolute quantitation) and TMT (tandem mass tag) approaches. In these methods, labelling on the primary amines of lysine residues and N-termini of tryptic peptides via amide formation (N-derivatives) from corresponding NHS ester reagents is the intended reactive outcome. However, the role of NHS esters as activated carboxyls can also drive the formation of serine-, tyrosine-, and threonine-derived esters (O-derivatives). These O-derivative peptides are typically classed as over-labelled and are disregarded for quantification, leading to loss of information and hence potential sensitivity. Their presence also unnecessarily increases sample complexity, which reduces the overall identification rates. One common approach for removing these unwanted labelling events has involved a quench with hydroxylamine. We show here that this approach is not fully efficient and can still leave substantial levels of unwanted over-labelled peptides. Through systematic screening of nucleophilic aminolysis reagents and reaction conditions, we have now developed a robust method to efficiently remove over-labelled peptides. The new method reduces the proportion of over-labelled peptides in the sample to less than 1% without affecting the labelling rate or introducing other modifications, leading to superior identification rates and quantitation precision.

systems biology↗

bioRxiv2024

Cheap, Robust and Versatile Two-Dimensional Chromatography system for Proteomics of Nanogram Scale Samples

In this work we describe a low loss fractionation system comprised of a reconfigured Evosep One LC system for the first dimension and a repurposed 3D-printer as a fraction collector. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP-RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 70% signal recovery at the peptide level and, more importantly, we observed over 30% increase on protein level intensity which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed more than 8,000 proteins to be identified from 50 ng of material. The utility of the 2D system was further investigated for phosphoproteomics (>21,000 phosphosites from 50 g starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP-RP system is highly versatile and powerful tool for many proteomics workflows.

systems biology↗