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DMSO might impact ligand binding, capsid stability, and RNA interaction in viral preparations.
Sci Rep
December 2024
Institute of Microbial and Molecular Sciences, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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.
View Article and Find Full Text PDFStructural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.
PLoS Comput Biol
December 2024
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
Protein-RNA interactions play a critical role in many cellular processes and pathologies. However, experimental determination of protein-RNA structures is still challenging, therefore computational tools are needed for the prediction of protein-RNA interfaces. Although evolutionary pressures can be exploited for structural prediction of protein-protein interfaces, and recent deep learning methods using protein multiple sequence alignments have radically improved the performance of protein-protein interface structural prediction, protein-RNA structural prediction is lagging behind, due to the scarcity of structural data and the flexibility involved in these complexes.
View Article and Find Full Text PDFSynchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.
Protein Sci
December 2024
Department of Physics, Sapienza University, Rome, Italy.
Investigating the binding between proteins and aptamers, such as peptides or RNA molecules, is of crucial importance both for understanding the molecular mechanisms that regulate cellular activities and for therapeutic applications in several pathologies. Here, a new computational procedure, employing mainly docking, clustering analysis, and molecular dynamics simulations, was designed to estimate the binding affinities between a protein and some RNA aptamers, through the investigation of the dynamical behavior of the predicted molecular complex. Using the state-of-the-art software catRAPID, we computationally designed a set of RNA aptamers interacting with the TAR DNA-binding protein 43 (TDP-43), a protein associated with several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS).
View Article and Find Full Text PDFReconstructing the sequence specificities of RNA-binding proteins across eukaryotes.
bioRxiv
October 2024
Department of Molecular Genetics, University of Toronto, Toronto, ON Canada.
RNA-binding proteins (RBPs) are key regulators of gene expression. Here, we introduce EuPRI (Eukaryotic Protein-RNA Interactions) - a freely available resource of RNA motifs for 34,736 RBPs from 690 eukaryotes. EuPRI includes binding data for 504 RBPs, including newly collected RNAcompete data for 174 RBPs, along with thousands of reconstructed motifs.
View Article and Find Full Text PDFInvestigation of RNA-binding protein NOVA1 in silico: Comparison of the modern human V197 with the archaic I197 variant present in Neanderthals.
Comput Biol Med
December 2024
Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; yΘμ Study Group, ProspED Polytechnic, Carlton, VIC, 3053, Australia; Baker Department of Cardiometabolic Health, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia. Electronic address:
Article Synopsis
- Researchers have identified specific genetic differences between archaic and modern human genomes, notably a switch in the NOVA1 gene linked to RNA regulation in neurons, changing an amino acid from isoleucine to valine.
- Using advanced modeling techniques, they compared the structures and binding interactions of the archaic and modern NOVA1 variants, finding similar binding free energies for protein-RNA complexes.
- The study suggests that although structural changes are modest, more research is needed to understand how mutations in NOVA1 affect alternative splicing and contribute to diseases, especially considering the roles of multiple mutations.
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