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Elucidating the therapeutic potential of indazole derivative bindarit against K-ras receptor: An analysis using molecular dynamics exploration.
Biochem Biophys Rep
March 2025
School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
Ras gene is frequently mutated in cancer. Among different subtypes of Ras gene, K-Ras mutation occurs in nearly 30 % of human cancers. K-Ras mutation, specifically K-Ras (G12D) mutation is prevalent in cancers like lung, colon and pancreatic cancer.
View Article and Find Full Text PDFStructure Characterization of a Disordered Peptide Using In-Droplet Hydrogen/Deuterium Exchange Mass Spectrometry and Molecular Dynamics.
ACS Phys Chem Au
January 2025
Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States.
In-droplet hydrogen/deuterium exchange (HDX)-mass spectrometry (MS) experiments have been conducted for peptides of highly varied conformational type. A new model is presented that combines the use of protection factors (PF) from molecular dynamics (MD) simulations with intrinsic HDX rates ( ) to obtain a structure-to-reactivity calibration curve. Using the model, the relationship of peptide structural flexibility and HDX reactivity for different peptides is elucidated.
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 PDFEvolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits.
PeerJ
January 2025
Department of Biological Science, University of Ulsan, Ulsan, Republic of South Korea.
The genus , a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus , with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea.
View Article and Find Full Text PDFNegative linear compressibility and structural stability of the energetic material -hexanitrostilbene under pressure.
Phys Chem Chem Phys
January 2025
School of Materials and Energy, University of Electronic Science and Technology of China, Chengdu 611731, Sichuan, China.
The structural stability of the energetic material 2,2',4,4',6,6'-hexanitrostilbene (-HNS) under high pressure is critical for optimizing its detonation performance and low sensitivity. However, its structural response to external pressure has not been sufficiently investigated. In this study, high-pressure single-crystal X-ray diffraction data of -HNS demonstrate that the sample exhibits pronounced anisotropic strain, demonstrating an unusual negative linear compressibility (NLC) along the axis, with a coefficient of -4.
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