NMR structure of the channel-former zervamicin IIB in isotropic solvents

AbstractSpatial structure of the membrane channel-forming hexadecapeptide, zervamicin IIB, was studied by NMR spectroscopy in mixed solvents of different polarity ranging from CDCl3/CD3OH (9:1, v/v) to CD3OH/H2O (1:1, v/v). The results show that in all solvents used the peptide has a very similar structure that is a bent amphiphilic helix with a mean backbone root mean square deviation (rmsd) value of ca. 0.3 Å. Side chains of Trp1, Ile2, Gln3, Ile5 and Thr6 are mobile. The results are discussed in relation to the validity of the obtained structure to serve as a building block of zervamicin IIB ion channels

Long-range 1H-15N J couplings providing a method for direct studies of the structure and azide-tetrazole equilibrium in a series of azido-1,2,4-triazines and azidopyrimidines

The selectively 15N labeled azido-1,2,4-triazine 2*A and azidopyrimidine 4*A were synthesized by treating hydrazinoazines with 15N-labeled nitrous acid. The synthesized compounds were studied by 1H, 13C, and 15N NMR spectroscopy in DMSO, TFA, and DMSO/TFA solutions, where the azide-tetrazole equilibrium could lead to the formation of two tetrazoles (T, T′) and one azide (A) isomer for each compound. The incorporation of the 15N label led to the appearance of long-range 1H-15N coupling constants (JHN), which can be measured easily by using amplitude-modulated 1D 1H spin-echo experiments with selective inversion of the 15N nuclei. The observed JHN patterns enable the unambiguous determination of the mode of fusion between the azole and azine rings in the two groups of tetrazole isomers (2*T′, 4*T′ and 2*T, 4*T), even for minor isoforms with a low concentration in solution. However, the azide isomers (2*A and 4*A) are characterized by the absence of detectable J HN coupling. The analysis of the JHN couplings in 15N-labeled compounds provides a simple and efficient method for direct NMR studies of the azide-tetrazole equilibrium in solution. © 2013 American Chemical Society

Spin-spin coupling constants 13C-15N and 1H-15N in the investigation of azido-tetrazole tautomerism in a series of 2-azidopyrimidines

A new method was developed for the investigation of an azido-tetrazole equilibrium based on using a complex analysis of 13C-15N and 1H-15N spin-spin coupling constants. The use of this approach became possible due to the selective inclusion of 15N isotopes into the structures of 2-azidopyrimidines and their cyclic analogs tetrazolo[1,5-a]pyrimidines. © 2013 Springer Science+Business Media New York

Abstract OR-3: Integrative Structural Study of the Complex of Snake Toxin WTX with α7-type Nicotinic Acetylcholine Receptor

Background: Nicotinic acetylcholine receptors are ligand-gated ion channels present in the nervous system, epithelium, and the immune system. The α7-type nicotinic receptor (α7-nAChR) is a homopentameric membrane protein containing five ligand binding sites located at the interface between subunits in the extracellular domain of the receptor. α7-nAChR is considered a promising target for the treatment of cancer and cognitive dysfunction in Alzheimer's disease, schizophrenia, and depression. WTX is a non-conventional three-finger neurotoxin from the Naja kaouthia venom inhibiting α7-nAChR. WTX structure consists of three loops protruding from the “head” (core) stabilized by a system of disulfide bonds. Methods: The complex of the α7-nAChR extracellular domain with a recombinant analogue of WTX was studied by cryo-electron microscopy. The structure of the complex of full-length α7-nAChR with the toxin in the membrane environment was reconstructed by in silico molecular modeling. Interaction of WTX with the lipid membrane was confirmed by NMR-spectroscopy. Results: Analysis of electronic images confirmed the homopentameric organization of the extracellular domain with a diameter of ~ 9 nm and a height of ~ 7 nm. On the electron density map, additional regions corresponding to five WTX molecules located at the intersubunit interfaces of the domain were observed. Fitting the known spatial structures of the extracellular domain and the WTX toxin into the obtained electron density made it possible to reconstruct the structure of the complex (although with a low resolution of ~ 8 Ǻ due to the predominant orientation of particles in the ice) and to determine the topology of the toxin-receptor interaction. It was revealed that WTX interacts with the extracellular domain of α7-nAChR by the loop II, while the loop I and the toxin’s head seem to interact with the surface of the lipid membrane surrounding the receptor. Model of the complex of the full-length α7-nAChR receptor with WTX in the membrane environment corresponding to the neuronal membrane was constructed using computer simulation methods. Molecular dynamics for >1500 ns confirmed the stability of the complex. The predicted membrane-active site of the WTX molecule includes residues Lys13 and Arg18. The study of WTX and its mutants Lys13Ala and Arg18Ala by NMR-spectroscopy confirmed the importance of these residues for interaction with lipid membrane. Conclusion: Interaction mode of non-conventional neurotoxins with nAChR has been determined for the first time

Circular proteins from plants and fungi

Circular proteins, defined as head-to-tail cyclized polypeptides originating from ribosomal synthesis, represent a novel class of natural products attracting increasing interest. From a scientific point of view, these compounds raise questions of where and why they occur in nature and how they are formed. From a rational point of view, these proteins and their structural concept may be exploited for crop protection and novel pharmaceuticals. Here, we review the current knowledge of three protein families: cyclotides and circular sunflower trypsin inhibitors from the kingdom of plants and the Amanita toxins from fungi. A particular emphasis is placed on their biological origin, structure, and activity. In addition, the opportunity for discovery of novel circular proteins and recent insights into their mechanism of action are discussed

Identification and structural characterization of a novel cyclotide with activity against an insect pest of sugar cane

Cyclotides are a family of plant-derived cyclic peptides comprising six conserved cysteine residues connected by three intermolecular disulfide bonds that form a knotted structure known as a cyclic cystine knot (CCK). This structural motif is responsible for the pronounced stability of cyclotides against chemical, thermal, or proteolytic degradation and has sparked growing interest in this family of peptides. Here, we isolated and characterized a novel cyclotide from Palicourea rigida (Rubiaceae), which was named parigidin-br1. The sequence indicated that this peptide is a member of the bracelet subfamily of cyclotides. Parigidin-br1 showed potent insecticidal activity against neonate larvae of Lepidoptera (Diatraea saccharalis), causing 60% mortality at a concentration of 1 mu M but had no detectable antibacterial effects. A decrease in the in vitro viability of the insect cell line from Spodoptera frugiperda (SF-9) was observed in the presence of parigidin-br1, consistent with in vivo insecticidal activity. Transmission electron microscopy and fluorescence microscopy of SF-9 cells after incubation with parigidin-br1 or parigidin-br1-fluorescein isothiocyanate, respectively, revealed extensive cell lysis and swelling of cells, consistent with an insecticidal mechanism involving membrane disruption. This hypothesis was supported by in silico analyses, which suggested that parigidin-br1 is able to complex with cell lipids. Overall, the results suggest promise for the development of parigidin-br1 as a novel biopesticide

Betaine–N-Heterocyclic Carbene Interconversions of Quinazolin-4-One Imidazolium Mesomeric Betaines. Sulfur, Selenium, and Borane Adduct Formation

Reaction of N-alkylated imidazoles with 2-chloro-4-quinazolinone gave mesomeric betaines, 2-(1-alkyl-1H-imidazolium-3-yl)quinazolin-4-olates, for which three tautomeric forms of N-heterocyclic carbenes (NHCs) can be formulated, in addition to an anionic NHC after deprotonation. The NHC tautomers were trapped with sulfur, selenium, triethylborane, and triphenylborane as thiones, selenones and borane adducts, respectively. We obtained two isomers of the cyclic borane adducts, diazaboroloquinazolinones with [1,5-a] and [5,1-b]-type fusion between the quinazolinone and the diazaborole rings. They correspond to two different NHC tautomers and to the anionic NHC derived thereof. The third NHC tautomer was trapped as a non-cyclic adduct with tris(pentafluorophenyl)borane by coordination to the quinazoline oxygen atom. 2D 1H-15N HMBC experiments of 15N-labeled quinazolinone fragments, quantitative measurements of long-range 1H-15N coupling constants (JHN), and five X-ray single crystal analyses have been carried out for the structure elucidations and to gain insight into the NMR spectroscopic properties of these compounds. © 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.Russian Foundation for Basic Research, RFBR: 17-03-01029Deutscher Akademischer Austauschdienst, DAADMinistry of Education and Science of the Russian Federation, Minobrnauka: 4.6351.2017/8.9This work was supported by the Russian Ministry of Education and Science (State contract 4.6351.2017/8.9) and the Russian Foundation for Basic Research (grant 17-03-01029). Single crystal X-ray analysis of 23b was performed at the User Facilities Centers of IGIC RAS within the State Assignment on Fundamental Research to the Kurnakov Institute of General and Inorganic Chemistry. We thank the Deutscher Akademischer Austauschdienst DAAD for the financial support of the internship of S. D. at Clausthal University of Technology, Germany

Antiviral drug Triazavirin, selectively labeled with 2H, 13C, and 15N stable isotopes. Synthesis and properties

[Figure not available: see fulltext.] Isotope-labeled antiviral drug Triazavirin containing 2H, 13C, and 15N atoms in its structure has been synthesized. 13C2H3I and KS13CN served as donors of 13C isotopes. The use of 13С-MeI containing 2H atoms made it possible to additionally incorporate deuterium labels into the structure of the compound. The 15N atoms were incorporated using 15N-enriched sodium nitrite, aminoguanidine carbonate, and ethyl nitroacetate. The resulting 2H3,13C2,15N3-Triazavirin was characterized by NMR spectroscopy. © 2021, Springer Science+Business Media, LLC, part of Springer Nature.This work was supported by the Russian Foundation for Basic Research (grant 20-03-00842) and the Ministry of Science and Higher Education of the Russian Federation (project No. FEUZ-2020-0058 (N687.42B.223/20))

NMR Investigation of Structures of G-Protein Coupled Receptor Folding Intermediates

Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot et al., Biochemistry 29(1990), 4031) is postulated to proceed in 2 steps: Partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two and the first three transmembrane (TM) segments, as well as a construct comprising TM1-TM2 covalently linked to TM7 were examined. We observed that the isolated TM1 does not form a stable helix nor does it integrate well into the micelle. TM1 is significantly stabilized upon interaction with TM2, forming a helical hairpin reported previously (Neumoin et al., Biophys. J. 96(2009), 3187), and in this case the protein integrates into the hydrophobic interior of the micelle. TM123 displays a strong tendency to oligomerize, but hydrogen exchange data reveal that the center of TM3 is solvent exposed. In all GPCRs so-far structurally characterized TM7 forms many contacts with TM1 and TM2. In our study TM127 integrates well into the hydrophobic environment, but TM7 does not stably pack against the remaining helices. Topology mapping in microsomal membranes also indicates that TM1 does not integrate in a membrane-spanning fashion, but that TM12, TM123 and TM127 adopt predominantly native-like topologies. The data from our study would be consistent with the retention of individual helices of incompletely synthesized GPCRs in the vicinity of the translocon until the complete receptor is released into the membrane interior