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CC and CXC chemokines are distinct chemokine subfamilies. CC chemokines usually do not bind CXC‐chemokine receptors and vice versa. CCR5 and CXCR4 receptors are activated by CCL5 and CXCL12 chemokines, respectively, and are also used as HIV‐1 coreceptors. CCL5 contains one conserved binding site for a sulfated tyrosine residue, whereas CXCL12 is unique in having two additional sites for sulfated/nonsulfated tyrosine residues. In this study, N‐terminal (Nt) CXCR4 peptides were found to bind CCL5 with somewhat higher affinities in comparison to those of short Nt‐CCR5(8–20) peptides with the same number of sulfated tyrosine residues. Similarly, a long Nt‐CCR5(1–27)(sY3,sY10,sY14) peptide cross reacts with CXCL12 and with lower KD in comparison to its binding to CCL5. Intermolecular nuclear overhauser effect (NOE) measurements were used to decipher the mechanism of the chemokine/Nt‐receptor peptide binding. The Nt‐CXCR4 peptides interact with the conserved CCL5 tyrosine sulfate‐binding site by an allovalency mechanism like that observed for CCL5 binding of Nt‐CCR5 peptides. Nt‐CCR5 peptides bind CXCL12 in multiple modes analogous to their binding to HIV‐1 gp120 and interact with all three tyrosine/sulfated tyrosine‐binding pockets of CXCL12. We suggest that the chemokine‐receptors Nt‐segments bind promiscuously to cognate and non‐cognate chemokines and in a mechanism that is dependent on the number of binding pockets for tyrosine residues found on the chemokine. In conclusion, common features shared among the chemokine‐receptors' Nt‐segments such as multiple tyrosine residues that are potentially sulfated, and a large number of negatively charged residues are the reason of the cross binding observed in this study. [ABSTRACT FROM AUTHOR]

The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5′- and 3′-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5′-untranslated region (5′-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5′-UUUCGU-3′ hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy. [ABSTRACT FROM AUTHOR]

Residues 184 through 200 appear to be the binding site on the alpha-subunit of the nicotinic acetylcholine receptor for alpha-bungarotoxin. This neurotoxin from snake venom inhibits neuromuscular transmission.

The solution structure of the complex between [Alpha]-bungarotoxin ([Alpha]-BTX) and a 13-residue library-derived peptide (MRYYESSLKSYPD) has been solved using two-dimensional proton-NMR spectroscopy. The bound pep-tide adopts an almost-globular conformation resulting from three turns that surround a hydrophobic core formed by Tyr-11 of the peptide. The peptide fills an [Alpha]-BTX pocket made of residues located at fingers I and II, as well as at the C-terminal region. Of the peptide residues, the largest contact area is formed by Tyr-3 and Tyr-4. These findings are in accord with the previous data in which it had been shown that substitution of these aromatic residues by aliphatic amino acids leads to loss of binding of the modified peptide with [Alpha]-BTX. Glu-5 and Leu-8, which also remarkably contribute to the contact area with the toxin, are present in all the library-derived peptides that bind strongly to [Alpha]-BTX. The structure of the complex may explain the fact that the library-derived peptide binds [Alpha]-BTX with a 15-fold higher affinity than that shown by the acetylcholine receptor peptide ([Alpha]185-196). Although both peptides bind to similar sites on [Alpha]-BTX, the latter adopts an extended conformation when bound to the toxin [Basus, V., Song, G. & Hawrot, E. (1993) Biochemistry 32, 12290-12298], whereas the library peptide is nearly globular and occupies a larger surface area of [Alpha]-BTX binding site.

Nuclear Overhauser effect spectroscopy examined the intramolecular interactions in bound cholera toxin peptide (CTP3) in three antibody complexes. Two beta-turns were found in the bound peptide that were not expressed in the free peptide. The beta-turn formations gave CTP3 a compact structure and greater flexibility in its conformation than in other secondary structures. Results showed that Tyr 32L, Tyr 32H and Trp 50H aromatic residues functioned in nonspecific hydrophobic interactions with the antigen.

Several NMR studies are conducted to determine the structures of the different third variable region (V3) peptides of the HIV-1 envelope glycoprotein used for neutralizing antibodies. The cyclic V3 peptides are shown to exhibit a minimized conformational space, as compared to their linear counterparts.

Two-dimensional nuclear magnetic resonance (2D NMR) provides contemporary tools available for the elucidation of molecular structure, function, and dynamics. Hundreds of different 2D NMR pulse sequences are used in almost all areas of experimental science, ranging from solid-state chemistry and physics, through inorganic, and biochemistry, and onto various areas of in vivo experimentation and diagnosis.

Snake-venom [Alpha]-bungarotoxin is a member of the [Alpha]-neurotoxin family that binds with very high affinity to the nicotinic acetylcholine receptor (AChR) at the neuromuscular junction. The structure of the complex between [Alpha]-bungarotoxin and a 13-mer peptide (WRYYESSLEPYPD) that binds the toxin with high affinity, thus inhibiting its interactions with AChR with an [IC.sub.50] of 2 nM, has been solved by [sup.1]H-NMR spectroscopy. The bound peptide folds into a [Beta]-hairpin structure created by two antiparallel [Beta]-strands, which combine with the already existing triple-stranded [Beta]-sheet of the toxin to form a five-stranded intermolecular, antiparallel [Beta]-sheet. Peptide residues [Y3.sup.P], [E5.sup.P], and [L8.sup.P] have the highest intermolecular contact area, indicating their importance in the binding of [Alpha]-bungarotoxin; [W1.sup.P], [R2.sup.P], and [Y4.sup.P] also contribute significantly to the binding. A large number of characteristic hydrogen bonds and electrostatic and hydrophobic interactions are observed in the complex. The high-affinity peptide exhibits inhibitory potency that is better than any known peptide derived from AChR, and is equal to that of the whole [Alpha]-subunit of AChR. The high degree of sequence similarity between the peptide and various types of AChRs implies that the binding mode found within the complex might possibly mimic the receptor binding to the toxin. The design of the high-affinity peptide was based on our previous findings: (i) the detection of a lead peptide (MRYYESSLKSYPD) that binds [Alpha]-bungarotoxin, using a phage-display peptide library, (ii) the information about the three-dimensional structure of [Alpha]-bungarotoxin/lead-peptide complex, and (iii) the amino acid sequence analysis of different AChRs.