DMSO might impact ligand binding, capsid stability, and RNA interaction in viral preparations

• Published in: Scientific reports 2024-12, Vol.14 (1), p.30408-9
• Main Authors: Wald, Jiri, Goessweiner-Mohr, Nikolaus, Real-Hohn, Antonio, Blaas, Dieter, Marlovits, Thomas C.
• Format: Article
• Language: English
• Subjects: 631/326/596/2148; 631/535/1258/1259; Antiviral Agents - chemistry; Antiviral Agents - pharmacology; Binding Sites; Capsid - chemistry; Capsid - drug effects; Capsid - metabolism; Capsid Proteins - chemistry; Capsid Proteins - metabolism; Cryoelectron Microscopy; Dimethyl sulfoxide; Dimethyl Sulfoxide - chemistry; Dimethyl Sulfoxide - pharmacology; DMSO; Electron microscopes; Electron microscopy; Fatty acids; Genomes; Heterogeneity; HRV; Humanities and Social Sciences; Humans; Hydrophobicity; Infections; Ligands; Microscopy; multidisciplinary; Pocket factor; Protein Binding; Protein structure; Proteins; Rhinovirus; Rhinovirus - drug effects; Ribonucleic acid; RNA; RNA, Viral - chemistry; RNA, Viral - metabolism; Science; Science (multidisciplinary); Solvents
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-81789-x

Dimethyl sulfoxide (DMSO) is a widely used solvent in drug research. However, recent studies indicate that even at low concentration DMSO might cause structural changes of proteins and RNA. The pyrazolopyrimidine antiviral OBR-5-340 dissolved in DMSO inhibits rhinovirus-B5 infection yet is inactive against RV-A89. This is consistent with our structural observation that OBR-5-340 is only visible at the pocket factor site in rhinovirus-B5 and not in RV-A89, where the hydrophobic pocket is collapsed. Here, we analyze the impact of DMSO in RV-A89 by high-resolution cryo-electron microscopy. Our 1.76 Å cryo-EM reconstruction of RV-A89 in plain buffer, without DMSO, reveals that the pocket-factor binding site is occupied by myristate and that the previously observed local heterogeneity at protein–RNA interfaces is absent. These findings suggest that DMSO elutes the pocket factor, leading to a collapse of the hydrophobic pocket of RV-A89. Consequently, the conformational heterogeneity observed at the RNA-protein interface in the presence of DMSO likely results from increased capsid flexibility due to the absence of the pocket factor and DMSO-induced affinity modifications. This local asymmetry may promote a directional release of the RNA genome during infection.