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Pervushin, K.

Publications and source records attributed to Pervushin, K..

8 recordsLinked to original sources

Modulation of liposome membranes by the C-terminal domain of the coronavirus envelope protein

The coronavirus envelope (E) protein is a viroporin that plays a key role in viral assembly, release, budding and pathogenesis. E protein forms oligomeric ion channels that can activate immune responses. However, high-resolution structural data for its extramembrane domains is limited. The C-terminal domain of SARS-CoV has been shown previously to form amyloid fibers, and here we show that these fibers can modulate the shape of liposomes. The propensity to form fibrils, and their effect on liposomes, was examined for sequences belonging to the four clades of coronaviruses. Electron microscopy data shows that the C-terminal domain in E protein adopts a filamentous structure. These findings demonstrate the potential of these peptides to modulate membranes, providing a possible mechanism by which E protein interacts with membranes in the host cell.

biophysics↗

NMR as a Video-(game): Constructing Super-Resolution Cross-peak Trajectories in Protein Spectroscopy

High-resolution multidimensional NMR spectroscopy of proteins remains limited by long acquisition times, sensitivity constraints, and severe peak overlap, particularly for larger systems. Conventional 3D and higher-dimensional experiments trade experimental efficiency for resolution, while post-acquisition analysis often becomes the dominant bottleneck. Here, we present a new framework that redefines both how NMR experiments are constructed and how they are executed and analyzed, by treating an AI agent-controllable series of 2D spectra as a spatiotemporal dataset analogous to a video. Our approach is based on temperature-dependent series of reduced-dimensionality 2D HSQC and novel RDL-TROSY experiments, in which each 2D [1H,15N] cross-peak is controllably shifted and split in proportion to the 13C chemical shift of the J-coupled carbons. We propose treating a variable-temperature (VT) series as a pseudo-temporal video sequence in which each cross-peak traces a physically motivated trajectory through frequency space. The proportionality coefficient () of this reduced-dimensionality encoding is systematically and programmatically varied together with the temperature providing full control for constructing optimal cross-peak trajectories. As a result, individual resonances follow predictable, spectral acquisition time-controllable trajectories in the 2D spectral plane across the series, which can be executed by an autonomous AI agent directly interacting with the NMR GUI layer. Each spectrum represents a single "frame," while temperature and RD controls serves as the temporal dimension. We describe two complementary super-resolution strategies: a cross-peak model-independent approach based on the deep-learning video super-resolution that leverages temporal redundancy to sharpen per-frame peak shapes, and a model-based approach that derives the exact mathematical form of the peak trajectories and uses it to design acquisition schedules that render individual peak paths maximally distinct and amenable for algorithmic deconvolution. As a result, we obtained full backbone resonance assignment in the wide temperature range (279-315 K) with one degree Kelvin resolution in a test protein in an automatic manner in the time frame typically required for collection of a single 3D NMR dataset.

biophysics↗

Hierarchical structural organization in bioinspired peptide coacervate microdroplets

This study explores the dynamic and hierarchical structural organization of peptide coacervate microdroplets at the meso-to atomic-scale resolution using a combination of Transferred Nuclear Overhauser Effect Spectroscopy (TrNOESY), Small Angle Neutron Scattering (SANS), and confocal microscopy. Dynamic interactions driving the self-association of peptide clusters are revealed, highlighting the critical roles of interacting residues. These phase-separating model peptides form small oligomers at low pH, which aggregate into larger clusters at neutral pH. These clusters organize into a porous network within the droplets, facilitating size-selective cargo sequestration. The findings underscore the significance of the dynamic spatio-temporal properties of peptide-based coacervates, contributing to our understanding of phase separation at the atomic and molecular levels. Critically, this approach enables the investigation of coacervate structures in their native state, offering insights into the physical and dynamic interactions governing droplet formation and cargo encapsulation. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/602323v4_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15aadb2org.highwire.dtl.DTLVardef@41be55org.highwire.dtl.DTLVardef@36f0d8org.highwire.dtl.DTLVardef@fe1af8_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Complete sequences of the velvet worm slime proteins reveal that slime formation is enabled by disulfide bonds and intrinsically disordered regions

The slime of velvet worms (Onychophora) is a strong and fully biodegradable protein material, which upon ejection undergoes a fast liquid-to-solid transition to ensnare prey. However, the molecular mechanisms of slime self-assembly are still not well understood, notably because the primary structures of slime proteins are yet unknown. Combining transcriptomic and proteomic studies, we have obtained the complete primary sequences of slime proteins and identified key features for slime self-assembly. The high molecular weight slime proteins contain Cys residues at the N- and C-termini that mediate the formation of multi-protein complexes via disulfide bonding. Low complexity domains in the N-termini were also identified and their propensity for liquid-liquid phase separation established, which may play a central role for slime biofabrication. Using solid-state nuclear magnetic resonance, rigid and flexible domains of the slime proteins were mapped to specific peptide domains. The complete sequencing of major slime proteins is an important step towards sustainable fabrication of polymers inspired by the velvet worm slime.

bioengineering↗

Liquid-Liquid Phase Separation Protects Amyloidogenic and Aggregation-Prone Peptides in Heterologous Expression Systems

Studying pathogenic effects of amyloids requires homogeneous amyloidogenic peptide samples. Recombinant production of these peptides is challenging due to their susceptibility to aggregation and chemical modifications. Thus, chemical synthesis is primarily used to produce amyloidogenic peptides suitable for high resolution structural studies. Here, we exploited the shielded environment of protein condensates formed via liquid-liquid phase separation (LLPS) as a protective mechanism against premature aggregation. We designed a fusion protein tag undergoing LLPS in E. coli and linked it to highly amyloidogenic peptides, including A{beta} amyloid. We find that the fusion proteins form membraneless organelles during overexpression and remain soluble. We also developed a facile purification method of functional A{beta} peptides free of chromatography steps. The strategy exploiting LLPS can be applied to other amyloidogenic, hydrophobic, and repetitive peptides that are otherwise difficult to produce.

molecular biology↗

Conjugates of neuroprotective chaperone L-PGDS provide MRI contrast for detection of amyloid β-rich regions in live Alzheimer's Disease mouse model brain

Endogenous brain proteins can recognize the toxic oligomers of amyloid-{beta} (A{beta}) peptides implicated in Alzheimers disease (AD) and interact with them to prevent their aggregation. Lipocalin-type Prostaglandin D Synthase (L-PGDS) is a major A{beta}-chaperone protein in the human cerebrospinal fluid. Here we demonstrate that L-PGDS detects amyloids in diseased mouse brain. Conjugation of L-PGDS with magnetic nanoparticles enhanced the contrast for magnetic resonance imaging. We conjugated the L-PGDS protein with ferritin nanocages to detect amyloids in the AD mouse model brain. We show here that the conjugates administered through intraventricular injections co-localize with amyloids in the mouse brain. These conjugates can target the brain regions through non-invasive intranasal administration, as shown in healthy mice. These conjugates can inhibit the aggregation of amyloids in vitro and show potential neuroprotective function by breaking down the mature amyloid fibrils.

biochemistry↗

Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain

A population of >6 million people worldwide at high risk of Alzheimers disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of {beta}-amyloid-(A{beta})-precursor-protein gene. We report AD-like pathology in cerebral organoids grown in vitro from non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar A{beta} deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss. Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome-21-gene BACE2, but prevented by combined chemical {beta} and {gamma}-secretase inhibition. We found that T21-organoids secrete increased proportions of A{beta}-preventing (A{beta}1-19) and A{beta}-degradation products (A{beta}1-20 and A{beta}1-34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2-trisomy and cross-inhibited by clinically trialled BACE1-inhibitors. Combined, our data prove the physiological role of BACE2 as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in [~]30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.

neuroscience↗

Xenobiotic compounds modulate cytotoxicity of Aβ amyloids and interact with neuroprotective chaperone L-PGDS

A positive association of the exposure to different classes of xenobiotics such as commonly prescribed drugs and polycyclic aromatic hydrocarbons (PAH) typically those found in air pollution-related particulate matter with Alzheimers disease (AD) may point to direct physical interaction of those compounds with the amyloid formation and clearance processes. In this study, for the first time, we provide evidence of such interactions for three representative compounds from prescription drugs and air pollution, e.g. anticholinergic drugs Chlorpheniramine, a common antihistamine, and Trazodone, an antidepressant as well as 9,10-PQ, a common PAH anthraquinone abundantly present in diesel exhaust and associated with AD. We demonstrate that these three compounds bind to the lipophilic compound carrier and neuroprotective amyloid beta (A{beta}) chaperone lipocalin-type prostaglandin D synthase (L-PGDS) with high affinity attenuating its neuroprotective chaperone function with Chlorpheniramine exhibiting markedly stronger inhibitory effects. We also show that these compounds directly interact with A{beta}(1-40) increasing the fibrils yield with altered fibril morphology and increased the cytotoxicity of the resulting fibrils. We propose that exposure to some xenobiotics in the peripheral tissues such as gut and lungs might result in the accumulation of these compounds in the brain facilitated by the carrier function of L-PGDS. This might lead to attenuation of its neuroprotective function and direct modification of A{beta} amyloid morphology and cytotoxicity. This hypothesis might provide a mechanistic link between exposure to xenobiotic compounds and the increased risk of Alzheimers disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/920884v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@14a4d92org.highwire.dtl.DTLVardef@12aadeeorg.highwire.dtl.DTLVardef@100e5e1org.highwire.dtl.DTLVardef@1f44b9b_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗