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Streamlining Protein Fractional Synthesis Rates Using SP3 Beads and Stable Isotope Mass Spectrometry: A Case Study on the Plant Ribosome.
Bio Protoc
May 2024
Applied Metabolome Analysis, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
Ribosomes are an archetypal ribonucleoprotein assembly. Due to ribosomal evolution and function, r-proteins share specific physicochemical similarities, making the riboproteome particularly suited for tailored proteome profiling methods. Moreover, the structural proteome of ribonucleoprotein assemblies reflects context-dependent functional features.
View Article and Find Full Text PDFIntegrating Internal Fragments in the Interpretation of Top-Down Sequencing Data of Larger Oligonucleotides.
J Am Soc Mass Spectrom
October 2023
University of Connecticut, Storrs, Connecticut 06269, United States.
In the context of direct top-down analysis or concerted bottom-up characterization of nucleic acid samples, the waning yield of terminal fragments as a function of precursor ion size poses a significant challenge to the gas-phase sequencing of progressively larger oligonucleotides. In this report, we examined the behavior of oligoribonucleotide samples ranging from 20 to 364 nt upon collision-induced dissociation (CID). The experimental data showed a progressive shift from terminal to internal fragments as a function of size.
View Article and Find Full Text PDFAb Initio Studies of Hydrated Electron/Cation Contact Pairs: Hydrated Electrons Simulated with Density Functional Theory Are Too Kosmotropic.
J Phys Chem Lett
January 2023
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, United States.
We have performed the first DFT-based ab initio MD simulations of a hydrated electron () in the presence of Na, a system chosen because ion-pairing behavior in water depends sensitively on the local hydration structure. Experiments show that 's interact weakly with Na; the 's spectrum blue shifts by only a few tens of meV upon ion pairing without changing shape. We find that the spectrum of the DFT-simulated red shifts and changes shape upon interaction with Na, in contrast with experiment.
View Article and Find Full Text PDFCorrection to Chaotropic Perturbation of Noncovalent Interactions of the Hemagglutinin Tag Monoclonal Antibody Fragment Enables Superresolution Molecular Census.
ACS Nano
December 2022
Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States.
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