To study the structure-biological effect correlation in the series of nucleoside analogues containing deazapurines, a number of 2-R-benzimidazole 1-beta-D-ribofuranosides (R = H, CF3, SCF3, CH2SCF3, CH2Ph, CH2CN) have been prepared by the modified silyl method. On the basis of CD and PMR data it was shown that the compounds exist in solution mainly as syn-conformers. Calculation of the furanose ring pseudorotation parameters in terms of N-S model indicates the predominance of S-population. In contrast to acyclonucleosides, the ribofuranosides obtained are nonactive against entheroviruses and more cytotoxic.
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Proc Natl Acad Sci U S A
January 2025
Max Perutz Labs, Vienna Biocenter Campus, Vienna 1030, Austria.
RNA G-quadruplexes (rG4s), the four-stranded structures formed by guanine-rich RNA sequences, are recognized by regions in RNA-binding proteins (RBPs) that are enriched in arginine-glycine repeats (RGG motifs). Importantly, arginine and glycine are encoded by guanine-rich codons, suggesting that some RGG motifs may both be encoded by and interact with rG4s in autogenous messenger RNAs (mRNAs). By analyzing transcriptome-wide rG4 datasets, we show that hundreds of RGG motifs in humans are at least partly encoded by rG4s, with an increased incidence for longer RGG motifs (~10 or more residues).
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637.
Many proteins form paralogous multimers-molecular complexes in which evolutionarily related proteins are arranged into specific quaternary structures. Little is known about the mechanisms by which they acquired their stoichiometry (the number of total subunits in the complex) and heterospecificity (the preference of subunits for their paralogs rather than other copies of the same protein). Here, we use ancestral protein reconstruction and biochemical experiments to study historical increases in stoichiometry and specificity during the evolution of vertebrate hemoglobin (Hb), an αβ heterotetramer that evolved from a homodimeric ancestor after a gene duplication.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
The glucose-6-phosphatase (G6Pase) is an integral membrane protein that catalyzes the hydrolysis of glucose-6-phosphate (G6P) in the endoplasmic reticulum lumen and plays a vital role in glucose homeostasis. Dysregulation or genetic mutations of G6Pase are associated with diabetes and glycogen storage disease 1a (GSD-1a). Studies have characterized the biophysical and biochemical properties of G6Pase; however, the structure and substrate recognition mechanism of G6Pase remain unclear.
View Article and Find Full Text PDFMol Biol Rep
January 2025
Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, Russia, 119071.
Background: TRIM28 plays a crucial role in maintaining genomic stability and establishing imprinting, facilitated by the diversity of KRAB zinc finger proteins. The SUMOylation of TRIM28 is essential for its function and is enhanced in the presence of the KRAB domain. Previously, we demonstrated that Kaiso, another factor capable of interacting with TRIM28, can promote its SUMOylation.
View Article and Find Full Text PDFBMC Bioinformatics
January 2025
Bioinformatics Research Group (BioRG), Knight Foundation School of Computing and Information Sciences, Florida International University, 11200 SW 8th 10 St, Miami, 33199, USA.
Background: While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurate and efficient scoring functions to differentiate between native and non-native binding complexes, the accuracy of current docking tools cannot be guaranteed. Although many innovative scoring functions have been proposed, a good scoring function for docking remains elusive.
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