Biochemistry has a strong interest in ion channels, a diverse group of membrane proteins. This group has long remained difficult to study at the structural level, but much progress has been made in recent decades with improvements in biochemical methods and computational procedures. Voltage-gated ion channels undergo conformational changes upon functioning, and multiple models of activation mechanisms were proposed based on experimental data. This review focuses on the structural studies of the functioning of voltage-gated ion channels, which are accompanied by conformational changes in proteins, and the methodological advances that allow their observation. Particular attention is paid to the lipid modulation of ion channels, as well as to the use of various lipids and membrane mimetics to stabilize specific conformations of ion channels. Modern experimental methods that allow obtaining ion channel proteins in specific functional states are discussed, including cryoelectron microscopy and cryoelectron tomography. NMR (Nuclear Magnetic Resonance) spectroscopy approaches and molecular modeling studies of conformational dynamics of ion channels and their isolated domains are also discussed. Finally, new algorithms for studying the conformational mobility of proteins have been recently developed, which help to better understand the mechanisms of ion channel domain movements.

Nicotinic acetylcholine receptor of α7 type (α7-nAChR) is a ligand-gated ion channel composed of five identical α7 subunits. Secreted lymphocyte antigen-6 urokinase-type plasminogen activator receptor (Ly6/uPAR)-related protein-1 (SLURP-1) controls carcinoma progression by negative modulation of oncogenic α7-nAChR. In this study, we observed dramatic decrease of SLURP-1 plasma level in patients with metastatic melanoma. We suggested usage of recombinant analog of human SLURP-1 (rSLURP-1) to compensate this deficiency for metastatic melanoma treatment. rSLURP-1 did not affect viability of different patient-derived metastatic melanoma cells, but reduced migration of some of them. Metastatic melanoma cells of other lines were resistant to rSLURP-1. Antimigratory rSLURP-1 effect was mediated by α7-nAChR, whereas resistance to rSLURP-1 correlated with overexpression of human-specific CHRFAM7A gene, which encodes the α7 subunit with truncated N-terminal region (dupα7) able to form hybrid α7/dupα7-nAChR channels. Electrophysiological study in Xenopus laevis oocytes showed that rSLURP-1 inhibits α7/dupα7-nAChR weaker than α7-nAChR. In contrast, "Oncotag" peptide, which mimics the loop I of SLURP-1, inhibited α7/dupα7- and α7-nAChRs with similar efficiency. Oncotag suppressed metastatic melanoma cell migration independently on dupα7 expression. Computer modeling provided rationale for altered activities of rSLURP-1 and Oncotag on α7/dupα7-nAChR. The Cancer Genome Atlas Program (TCGA) database analysis revealed correlation between CHRNΑ7 and CHRFAM7A gene expression and worse survival prognosis for patients with metastatic melanoma. Thus, 1) low plasma SLURP-1 level may be a specific marker of metastatic melanoma development, 2) metastatic melanoma progression can be controlled by α7-nAChR inhibition, and 3) dupα7 overexpression is a new molecular mechanism of melanoma resistance to internal cholinergic control and new target for melanoma treatment.NEW & NOTEWORTHY Metastatic melanoma is aggressive skin tumor often resistant to standard therapies. High α7-nAChR expression negatively correlates with survival of patients with metastatic melanoma, who are characterized by SLURP-1 drop in the plasma. Targeting α7-nAChR with recombinant SLURP-1 could significantly suppress metastatic melanoma cell migration; however, overexpression of human-specific dupα7 subunit forming hybrid α7/dupα7-nAChRs causes melanoma resistance to SLURP-1. This resistance can be overcome by the SLURP-1 mimicking peptide Oncotag, which exhibits activity against hybrid α7/dupα7-nAChRs.

G-quadruplexes (G4s) are prevalent at promoters and superenhancers (SEs), exclude nucleosomes, and recruit transcription factors. This study sought to determine whether the nucleosome exclusion affects the recruitment of the SE marker BRD4, which typically binds to acetylated histones and facilitates SE-promoter contacts via the phase separation-dependent mechanism. Analyses of the available whole-genome data revealed that SEs with the highest G4 density were depleted of nucleosomes but not of BRD4. This led us to test the possibility of histone-independent BRD4 maintenance at G4-rich SEs. A typical SE G4 destabilized a nearby nucleosome in vitro and, unlike B-DNA, bound weakly to BRD4 bromodomains. Similar to an acetylated nucleosome, the G4 promoted phase separation in BRD4 solutions. This effect was not altered by the histone competitor JQ1. However, it was attenuated by two known G4 ligands, suggesting that they could disrupt SE-promoter communication in cells. Consistently, these ligands downregulated several genes regulated by G4-rich SE-contacting promoters more efficiently than they did SE-independent genes. Our findings underscore the significance of G4-rich SEs as transcriptional regulators and provide new insights into their organization.

Prostate stem cell antigen (PSCA) is a Ly6/uPAR protein that targets neuronal nicotinic acetylcholine receptors (nAChRs). It exists in membrane-tethered and soluble forms, with the latter upregulated in Alzheimer’s disease. We hypothesize that PSCA may be linked to a wider spectrum of neurological diseases and could induce neuroinflammation. Indeed, PSCA expression is significantly upregulated in the brain of patients with multiple sclerosis, Huntington’s disease, Down syndrome, bipolar disorder, and HIV-associated dementia. To investigate PSCA’s structure, pharmacology, and inflammatory function, we produced a correctly folded water-soluble recombinant analog (ws-PSCA). In primary hippocampal neurons and astrocytes, ws-PSCA differently regulates secretion of inflammatory factors and adhesion molecules and induces pro-inflammatory responses by increasing TNFβ secretion. Heteronuclear NMR and 15N relaxation measurements reveal a classical β-structural three-finger fold with conformationally disordered loops II and III. Positive charge clustering on the molecular surface suggests the functional importance of ionic interactions by these loops. Electrophysiological studies in Xenopus oocytes point on ws-PSCA inhibition of α3β2-, high-, and low-sensitive variants of α4β2- (IC50 ~50, 27, and 15 μM, respectively) but not α4β4-nAChRs, suggesting targeting of the β2 subunit. Ensemble docking and molecular dynamics simulations predict PSCA binding to high-sensitive α4β2-nAChR at α4/β2 and β2/β2 interfaces. Complexes are stabilized by ionic and hydrogen bonds between PSCA’s loops II and III and the primary and complementary receptor subunits, including glycosyl groups. This study gives new structural and functional insights into PSCA’s interaction with molecular targets and provides clues to understand its role in the brain function and mental disorders.

Recently, we found that Lystar5 protein from coelomic cells of A. rubens starfish interacts with nicotinic acetylcholine receptors (nAChRs) and integrin α8-like protein. We hypothesized that Lystar5 mediates detachment of coelomic cells from the matrix and their migration. Skin wound healing in humans is based on keratinocytes migration and is regulated by nAChRs and integrins. Here, we revealed that Lystar5 stimulates migration of human skin HaCaT keratinocytes and peripheral blood monocytes. Using ELISA, we found that Lystar5 binds to the membrane fraction of coelomic cells with its loops I and II, which form an active site of Lystar5 and resemble its pro-migratory activity. In keratinocytes and monocytes, Lystar5 and the peptides mimicking its loops I and II bound with α3, α4, and β2 nAChR and α5, αV, and β1 integrin subunits, which form molecular complexes. In keratinocytes, Lystar5 and its mimetics promoted short-term E/N cadherin switch and upregulated expression of α5 and αV integrins, EGFR, and ICAM-1. In keratinocytes and monocytes, Lystar5 and its mimetics upregulated E-selectin secretion. The ability of Lystar5 and its mimetics to stimulate skin keratinocyte migration and immune cell infiltration may be considered promising for the development of new wound-healing agents.

Inflammation is a physiological response of the immune system to infectious agents or tissue injury, which involves a cascade of vascular and cellular events and the activation of biochemical pathways depending on the type of harmful agent and the stimulus generated. The Kunitz peptide HCIQ2c1 of sea anemone Heteractis magnifica is a strong protease inhibitor and exhibits neuroprotective and analgesic activities. In this study, we investigated the anti-inflammatory potential of HCIQ2c1 in histamine- and lipopolysaccharide (LPS)-activated RAW 264.7 macrophages as well as in LPS-induced systemic inflammation and carrageenan-induced paw edema models in CD-1 mice. We found that 10 μM HCIQ2c1 dramatically decreases histamine-induced intracellular Ca2+ release and LPS-induced reactive oxygen species (ROS) production in RAW 264.7 macrophages. Moreover, HCIQ2c1 significantly inhibited the production of LPS-induced tumor necrosis factor α (TNF-α), inducible NO-synthase (iNOS), and 5-lipoxygenase (5-LO) but slightly influenced the IL-1β and cyclooxygenase-2 (COX-2) expression level in macrophages. Furthermore, intravenous administration by HCIQ2c1 at 0.1 mg/kg dose reduced LPS-induced TNF-α, IL-1β, COX-2, and iNOS gene expression in CD-1 mice. The subplantar administration of HCIQ2c1 at 0.1 mg/kg dose to mice significantly reduced carrageenan-induced paw edema by a factor of two, which is comparable to the effect of diclofenac at 1 mg/kg dose. Thus, peptide HCIQ2c1 has a strong anti-inflammatory potential by the attenuation of systemic and local inflammatory effects through the inhibition of intracellular Ca2+ release, the production of ROS and pro-inflammatory cytokines, and enzymes involved in arachidonic acid metabolism.

One of the approaches for treatment of COVID-19 is a use of neutralizing antibodies (nAbs). The study of the mechanisms by which nAbs recognize different strains of SARS-CoV-2 may facilitate the development of new drugs and vaccines against the coronavirus infection. In this work, we present the 3.1 & Aring; resolution cryo-electron microscopy structure of a full-length trimeric spike-protein (S-protein) of the SARS-CoV-2 Alpha (B.1.1.7) variant in complex with the Fab of the REGN10987 nAb. In the complex, two receptor-binding domains (RBDs) of the Sprotein were observed in the 'up' state, whereas third RBD was in the 'down' state. This distinguishes the obtained structure from the complex of Delta (B.1.617.2) S-protein with REGN10987-Fab, where only one RBD was in the 'up' state. Probably some of the substituted residues (K478T, A570D, and S982A) located at the interprotomer interfaces are responsible for the greater Alpha S-protein opening upon the REGN10987-Fab binding. The Fab identically binds to the RBD in the both 'up' and 'down' conformations. The RBD-Fab interaction interface was refined to a resolution of 3.6 & Aring;. The antibody binds to the receptor-binding motif (RBM), which prevents the S-protein from the binding to its receptor, angiotensin-converting enzyme 2 (ACE-2). Comparison with the structures of the Wuhan (wild type) and Delta RBD variants in complex with REGN10987-Fab revealed that the N501Y and T478K/L452R mutations presented in the RBM of the Alpha and Delta variants, respectively, do not affect the mode of the RBD-Fab interaction.

Background/Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant global health threat due to its increasing resistance to conventional antibiotics. Antimicrobial peptides (AMPs) derived from natural sources represent a promising alternative. Fragments of spider membrane-active toxins can serve as AMPs with anti-MRSA activity. Methods: To demonstrate this, amino acid sequences of approximately 2000 linear spider venom peptides were fragmented into 9–22-residue-long moieties (75,235 in total) and pre-trained neural networks were used to predict their anti-MRSA activity. As many as 15 peptides with high predicted activity were synthesized, and three AMPs with high anti-MRSA and low hemolytic activities were selected. One of these peptides was studied using high-resolution 1H-, 13C-, and 15N-NMR spectroscopy in an aqueous solution and lyso-palmitoylphosphatidylglycerol (LPPG) micelles. Wide-line 31P-NMR was applied to multilamellar phospholipid liposomes composed of phosphatidylcholine (PC) or phosphatidylglycerol (PG). Results: Low hemolytic activity is explained by non-specific interaction with PC whereas high antibacterial activity arises from specific interaction with PG accompanied with the formation of a tight complex between the N-terminal tripeptide fragment and PG headgroup. The structure of a such complex, stabilized by an ionic interaction between the N-terminal NH3+ group and the lipid phosphate, was determined based on peptide–LPPG NOEs. The most favorable ratio between anti-MRSA and hemolytic activities, i.e., selectivity of the peptides, is attained when the tripeptide consists exclusively of phenylalanine and tryptophan residues. Confocal microscopy confirmed that the most selective peptide deteriorates the plasma membrane of S. aureus. Conclusions: This approach may enable the production of highly selective AMPs against Stapylococci, including MRSA.

Wound healing is a complex process based on the regulation of proliferation and migration of epithelial cells. Chronic wounds are characterized by increased proliferation and lack of migration of epidermal cells. The secreted human protein SLURP-2 regulates the growth and differentiation of epithelial cells. It has previously been shown that the targets of SLURP-2 are various types of nicotinic acetylcholine receptors (nAChRs), as well as muscarinic acetylcholine receptors involved in the regulation of epithelial cell homeostasis. In this work, we found that the previously demonstrated acceleration of keratinocyte migration under the incubation with SLURP-2 is due to its interaction with α7 type nAChR. Using alanine scanning mutagenesis, we showed that the R20A mutation of the SLURP-2 molecule increases the inhibitory activity of SLURP-2 towards α7-nAChR and leads to an even greater stimulation of Het-1A keratinocyte migration, while, in contrast to SLURP-2, does not stimulate, but suppresses the proliferation of Het-1A cells. At the same time, other SLURP-2 mutations simultaneously lead to inhibition of α7-nAChR, proliferation and migration of keratinocytes. Thus, new information was obtained about the localization of regions of the SLURP-2 molecule, the replacement of which can lead to a targeted change in the biological activity of SLURP-2. Further research into the possibility of regulating the activity of SLURP-2 and the creation of targeted drugs based on it may be useful for the development of new drugs that stimulate wound healing.

Study of mechanisms by which antibodies recognize different viral strains is necessary for the development of new drugs and vaccines to treat COVID-19 and other infections. Here, we report 2.5 Å cryo-EM structure of the SARS-CoV-2 Delta trimeric S-protein in complex with Fab of the recombinant analog of REGN10987 neutralizing antibody. S-protein adopts "two RBD-down and one RBD-up" conformation. Fab interacts with RBDs in both conformations, blocking the recognition of angiotensin converting enzyme-2. Three-dimensional variability analysis reveals high mobility of the RBD/Fab regions. Interaction of REGN10987 with Wuhan, Delta, Omicron BA.1, and mutated variants of RBDs is analyzed by microscale thermophoresis, molecular dynamics simulations, and ΔG calculations with umbrella sampling and one-dimensional potential of mean force. Variability in molecular dynamics trajectories results in a large scatter of calculated ΔG values, but Boltzmann weighting provides an acceptable correlation with experiment. REGN10987 evasion of the Omicron variant is found to be due to the additive effect of the N440K and G446S mutations located at the RBD/Fab binding interface with a small effect of Q498R mutation. Our study explains the influence of known-to-date SARS-CoV-2 RBD mutations on REGN10987 recognition and highlights the importance of dynamics data beyond the static structure of the RBD/Fab complex.

Three-finger proteins (TFPs), or Ly6/uPAR proteins, are characterized by the beta-structural LU domain containing three protruding “fingers” and stabilized by four conserved disulfide bonds. TFPs were initially characterized as snake alpha-neurotoxins, but later many studies showed their regulatory roles in different organisms. Despite a known expression of TFPs in vertebrates, they are poorly studied in other taxa. The presence of TFPs in starfish was previously shown, but their targets and functional role still remain unknown. Here, we analyzed expression, target, and possible function of the Lystar5 protein from the Asterias rubens starfish using bioinformatics, qPCR, and immunoassay. First, the presence of Lystar5 homologues in all classes of echinoderms was demonstrated. qPCR revealed that mRNA of Lystar5 and LyAr2 are expressed mainly in coelomocytes and coelomic epithelium of Asterias, while mRNA of other TFPs, LyAr3, LyAr4, and LyAr5, were also found in a starfish body wall. Using anti-Lystar5 serum from mice immunized by a recombinant Lystar5, we confirmed that this protein is expressed on the surface of coelomocytes and coelomic epithelium cells. According to ELISA, a recombinant analogue of Lystar5 bound to the membrane fraction of coelomocytes and coelomic epithelium but not to the body wall or starfish arm tip. Analysis by LC-MALDI MS/MS suggested integrin α-8-like protein expressed in the coelomocytes and coelomic epithelium as a target of Lystar5. Thus, our insights propose the important role of TFPs in regulation of starfish physiology and show prospects for their further research.

Capitellacin is the β-hairpin membrane-active cationic antimicrobial peptide from the marine polychaeta Capitella teleta. Capitellacin exhibits antibacterial activity, including against drug-resistant strains. To gain insight into the mechanism of capitellacin action, we investigated the structure of the peptide in the membrane-mimicking environment of dodecylphosphocholine (DPC) micelles using high-resolution NMR spectroscopy. In DPC solution, two structural forms of capitellacin were observed: a monomeric β-hairpin was in equilibrium with a dimer formed by the antiparallel association of the N-terminal β-strands and stabilized by intermonomer hydrogen bonds and Van der Waals interactions. The thermodynamics of the enthalpy-driven dimerization process was studied by varying the temperature and molar ratios of the peptide to detergent. Cooling the peptide/detergent system promoted capitellacin dimerization. Paramagnetic relaxation enhancement induced by lipid-soluble 12-doxylstearate showed that monomeric and dimeric capitellacin interacted with the surface of the micelle and did not penetrate into the micelle interior, which is consistent with the “carpet” mode of membrane activity. An analysis of the known structures of β-hairpin AMP dimers showed that their dimerization in a membrane-like environment occurs through the association of polar or weakly hydrophobic surfaces. A comparative analysis of the physicochemical properties of β-hairpin AMPs revealed that dimer stability and hemolytic activity are positively correlated with surface hydrophobicity. An additional positive correlation was observed between hemolytic activity and AMP charge. The data obtained allowed for the provision of a more accurate description of the mechanism of the oligomerization of β-structural peptides in biological membranes.

TRPA1 is a homotetrameric non-selective calcium-permeable channel. It contributes to chemical and temperature sensitivity, acute pain sensation, and development of inflammation. HCIQ2c1 is a peptide from the sea anemone Heteractis magnifica that inhibits serine proteases. Here, we showed that HCIQ2c1 significantly reduces AITC- and capsaicin-induced pain and inflammation in mice. Electrophysiology recordings in Xenopus oocytes expressing rat TRPA1 channel revealed that HCIQ2c1 binds to open TRPA1 and prevents its transition to closed and inhibitor-insensitive ‘hyperactivated’ states. NMR study of the 15N-labeled recombinant HCIQ2c1 analog described a classical Kunitz-type structure and revealed two dynamic hot-spots (loops responsible for protease binding and regions near the N- and C-termini) that exhibit simultaneous mobility on two timescales (ps–ns and μs–ms). In modelled HCIQ2c1/TRPA1 complex, the peptide interacts simultaneously with one voltage-sensing-like domain and two pore domain fragments from different channel’s subunits, and with lipid molecules. The model explains stabilization of the channel in the open conformation and the restriction of ‘hyperactivation’, which are probably responsible for the observed analgetic activity. HCIQ2c1 is the third peptide ligand of TRPA1 from sea anemones and the first Kunitz-type ligand of this channel. HCIQ2c1 is a prototype of efficient analgesic and anti-inflammatory drugs.

We report the molecular mechanism of action of gausemycins and the isolation of new members of the family, gausemycins C (1c), D (1d), E (1e), and F (1f), the minor components of the mixture. To elucidate the mechanism of action of gausemycins, we investigated the antimicrobial activity of the most active compounds, gausemycins A and B, in the presence of Ca2+, other metal ions, and phosphate. Gausemycins require a significantly higher Ca2+ concentration for maximum activity than daptomycin but lower than that required for malacidine and cadasides. Species-specific antimicrobial activity was found upon testing against a wide panel of Gram-positive bacteria. Membranoactivity of gausemycins was demonstrated upon their interactions with model lipid bilayers and micelles. The pore-forming ability was found to be dramatically dependent on the Ca2+ concentration and the membrane lipid composition. An NMR study of gausemycin B in zwitterionic and anionic micelles suggested the putative structure of the gausemycin/membrane complex and revealed the binding of Ca2+ by the macrocyclic domain of the antibiotic.

The secreted human protein SLURP-2 is a regulator of epithelial homeostasis, which enhances the viability and migration of keratinocytes. The targets of SLURP-2 in keratinocytes are nicotinic and muscarinic acetylcholine receptors. This work is devoted to the search for the SLURP-2 functional regions responsible for enhancing keratinocyte viability and migration. We produced synthetic peptides corresponding to the SLURP-2 loop regions and studied their effect on the viability and migration of HaCaT skin keratinocytes using the WST-8 test and scratch-test, respectively. The highest activity was exhibited by a loop II-mimicking peptide that enhanced the viability of keratinocytes and stimulated their migration. The peptide activity was mediated by interactions with α7- and α3β2-nAChRs and suppression of the p38 MAPK intracellular signaling pathway. Thus, we obtained new data that explain the mechanisms underlying SLURP-2 regulatory activity and indicate the promise of further research into loop II-mimicking peptides as prototypes of wound healing drugs.

Animal venoms contain a huge variety of bioactive molecules—namely, toxins—with an almost combinatorial spectrum of biological activities [...]