Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1021/acschembio.6b00798 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Proteins drive biochemical transformations by transitioning through distinct conformational states. Understanding these states is essential for modulating protein function. Although X-ray crystallography has enabled revolutionary advances in protein structure prediction by machine learning, this connection was made at the level of atomic models, not the underlying data.
View Article and Find Full Text PDFModeling of the Carbohydrate Oxacarbenium Ionic Intermediates of Glycosylation Reactions with Explicit Account for Protective Group Effects.
ACS Omega
January 2025
Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia.
O-Protected oxacarbenium ions are key intermediates of glycosylation reactions. The knowledge of their conformational preferences is crucial for choosing the correct blocking group pattern to achieve the required stereochemical outcome. This article describes a computational study of several glucosyl oxacarbenium cations.
View Article and Find Full Text PDFHigh-resolution analysis of human centromeric chromatin.
Life Sci Alliance
April 2025
National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, USA
Centromeres are marked by the centromere-specific histone H3 variant CENP-A/CENH3. Throughout the cell cycle, the constitutive centromere-associated network is bound to CENP-A chromatin, but how this protein network modifies CENP-A nucleosome conformations in vivo is unknown. Here, we purify endogenous centromeric chromatin associated with the CENP-C complex across the cell cycle and analyze the structures by single-molecule imaging and biochemical assays.
View Article and Find Full Text PDFNuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.
Nat Commun
January 2025
Department of Biological Sciences, Purdue University, West Lafayette, 47907, Indiana, USA.
RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures.
View Article and Find Full Text PDFSingle-molecule assay reveals the impact of composition, RNA duplex, and inhibitors on the binding dynamics of SARS-CoV-2 polymerase complex.
bioRxiv
January 2025
Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
The genome replication of SARS-CoV-2, the causative agent of COVID-19, involves a multi-subunit replication complex consisting of non-structural proteins (nsps) 12, 7 and 8. While the structure of this complex is known, the dynamic behavior of the subunits interacting with RNA is missing. Here we report a single-molecule protein-induced fluorescence enhancement (SM-PIFE) assay to monitor binding dynamics between the reconstituted or co-expressed replication complex and RNA.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!