MD simulation of the interaction between sialoglycans and the second sialic acid binding site of influenza A virus N1 neuraminidase

The neuraminidases (NAs) of avian influenza viruses (IAVs) contain a second sialic acid-binding site (2SBS), historically known as the hemadsorption site, which is separated from the sialyl-hydrolase catalytic site and serves to facilitate NA catalytic activity towards multivalent sialyl-capped glycoconjugates. Transmission and adaptation of avian IAVs to humans decreases hemadsorption and catalytic activities of the NA. Here, we report the molecular recognition features of the NA 2SBS of two pandemic H1N1 IAVs, A/Brevig Mission /1/1918 (BM18) and A/California/04/2009 (CA09), differing by their 2SBS activity. Using explicit solvent MD simulation, molecular mechanics, and glycosidic conformation analysis we initially analyzed the interactions of BM18 2SBS with two sialyllacto-N-tetraose pentasaccharides, 3′SLN-LC and 6′SLN-LC, which are models for the glycan receptors of IAVs in birds and humans, respectively. These studies characterize the binding specificity of BM18 2SBS towards human-type and avian-type receptors and identifies the key amino acids that affects binding. We next compared the interactions of the 2SBSs of BM18 and CA09 with 6′SLN-LC, revealing the critical effect of amino acid 372 on binding. Our results expand the current knowledge of the molecular features of NA 2SBSs and its alteration during the adaptation of avian IAVs to humans.

Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming a Pseudo-loop

Bone remodeling is a fine-tuned process principally regulated by a cascade triggered by interaction of receptor activator of NF-κB (RANK) and RANK ligand (RANKL). Excessive activity of the RANKL gene leads to increased bone resorption and can influence the incidence of osteoporosis. Although much has been learned about the intracellular signals activated by RANKL/RANK complex, significantly less is known about the molecular mechanisms of regulation of RANKL expression. Here, we report on the structure of an unprecedented DNA G-quadruplex, well-known secondary structure-mediated gene expression regulator, formed by a G-rich sequence found in the regulatory region of a RANKL gene. Solution-state NMR structural study reveals the formation of a three-layered parallel-type G-quadruplex characterized by an unique features, including a G-A bulge. Although a guanine within a G-tract occupies syn glycosidic conformation, bulge-forming residues arrange in a pseudo-loop conformation to facilitate partial 5/6-ring stacking, typical of G-quadruplex structures with parallel G-tracts orientation. Such distinctive structural features protruding from the core of the structure can represent a novel platform for design of highly specific ligands with anti-osteoporotic function. Additionally, our study suggests that the expression of RANKL gene may be regulated by putative folding of its G-rich region into non-B-DNA structure(s).

Structure and conformation of 5-methoxymethyl-1-(2′-deoxy-β-D-lyxofuranosyl)uracil

The structure of the nucleoside 5-methoxymethyl-1-(2′-deoxy-β-D-lyxofuranosyl)uracil (MMdLU) was deduced by X-ray crystallographic analysis. MMdLU crystallized in space group P21 with a = 8.719(4), b = 13.188(3), c = 5.701(3) Å, β = 109.56(2)° and Z = 2; R = 0.040 for 1208 unique reflections with net I > 2σ(I). The furanose ring adopts the rare C(4′)—exo envelope conformation (4E). The glycosyl linkage is anti (χ = 243.5°) and the C(5′) side chain has the t conformation. The conformation was also determined in solution by nmr analysis. The sugar ring exists in the N-conformation (97 ± 5%), the populations of the three rotamers about the exocyclic C(4′)—C(5′) bond were estimated to be g+:t:g− = 23%:59%:18% and the glycosidic conformation is predominantly anti.