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Short linear peptide motifs play important roles in cell signaling. They can act as modification sites for enzymes and as recognition sites for peptide binding domains. SH2 domains bind specifically to tyrosine-phosphorylated proteins, with the affinity of the interaction depending strongly on the flanking sequence.
View Article and Find Full Text PDFTyrosine phosphorylation is an important post-translational modification that regulates many biochemical signaling networks in multicellular organisms. To date, 46,000 tyrosines have been observed in human proteins, but relatively little is known about the function and regulation of most of these sites. A major challenge has been producing recombinant phospho-proteins in order to test the effects of phosphorylation.
View Article and Find Full Text PDFRHEB neddylation by the UBE2F-SAG axis enhances mTORC1 activity and aggravates liver tumorigenesis.
EMBO J
January 2025
Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, China.
Small GTPase RHEB is a well-known mTORC1 activator, whereas neddylation modifies cullins and non-cullin substrates to regulate their activity, subcellular localization and stability. Whether and how RHEB is subjected to neddylation modification remains unknown. Here, we report that RHEB is a substrate of NEDD8-conjugating E2 enzyme UBE2F.
View Article and Find Full Text PDFUnveiling the promise of peptide nucleic acids as functional linkers for an RNA imaging platform.
RSC Chem Biol
December 2024
Department of Biochemistry, University of Colorado Boulder CO 80309-0596 USA +1 303 492 5894 +1 303 735 2159 +1 303 492 1945.
Linkers in chemical biology provide more than just connectivity between molecules; their intrinsic properties can be harnessed to enhance the stability and functionality of chemical probes. In this study, we explored the incorporation of a peptide nucleic acid (PNA)-based linker into RNA-targeting probes to improve their affinity and specificity. By integrating a PNA linker into a small molecule probe of the Riboglow platform, we enabled dual binding events: cobalamin (Cbl)-RNA structure-based recognition and sequence-specific PNA-RNA interaction.
View Article and Find Full Text PDFStabilization of small organic molecules on VC and VCO MXenes: first-principles insights into the performance of van der Waals functionals and the effect of oxygen vacancies.
RSC Adv
January 2025
New Industry Creation Hatchery Center, Tohoku University Sendai 980-8579 Japan.
The adsorption of small organic molecules on pristine VC MXene and its derivatives is investigated by first-principles density functional theory calculations. By employing state-of-the-art van der Waals (vdW) density functionals, the binding affinity of studied molecules, , CH, CO, and HO on MXene adsorbents is well described by more recent vdW functionals, , SCAN-rvv10. Although both CH and CO are nonpolar molecules, on pristine and oxygen-vacancy surfaces, they show a different range of adsorption energies, in which CH is more inert and has weaker binding than CO.
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