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Deciphering allosteric mechanisms in KRAS activation: insights from GTP-induced conformational dynamics and interaction network reorganization.
RSC Adv
January 2025
College of Agriculture and Biological Science, Dali University Dali 671000 China
The conformational dynamics and activation mechanisms of KRAS proteins are of great importance for targeted cancer therapy. However, the detailed molecular mechanics of KRAS activation induced by GTP binding remains unclear. In this study, we systematically investigated how GTP/GDP exchange affects the thermodynamic and kinetic properties of KRAS and explored the activation mechanism using molecular dynamics (MD) simulations, Markov state models (MSMs), and neural relational inference (NRI) models.
View Article and Find Full Text PDFFTIR microscopic study on biomolecular alterations in placental tissues of intrahepatic cholestasis of pregnancy.
Anal Methods
January 2025
Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai 200092, China.
Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder that typically leads to severe pregnancy outcomes. Although genetic, endocrine, and environmental factors are involved in the etiology of ICP, the role of metabolic disorders remains unclear. Here we report an examination of the biomolecular alterations in placental tissues of women with ICP and healthy pregnant women at a molecular level.
View Article and Find Full Text PDFReaction and interaction dynamics of azobenzene-tethered DNA with T7 RNA polymerase.
Phys Chem Chem Phys
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Reaction and interaction dynamics of azobenzene-tethered DNA (photoresponsive DNA) with T7 RNA polymerase (T7RNAP) were studied after photoisomerization of azobenzene from the - to -forms using the transient grating (TG) and time-resolved fluorescence polarization techniques. Two types of photoresponsive DNA were examined: AzoPBD, tethered at the protein binding site, and AzoTATA, tethered at the unwinding site. A diffusion change was observed after photoexcitation of -AzoPBD within 1 ms, and this change is explained in terms of a structural change from a bent to an extended conformation upon the -to- photoisomerization.
View Article and Find Full Text PDFdescribes the ability of biological macromolecules to transmit signals spatially through the molecule from an site – a site that is distinct from binding sites of primary, endogenous ligands – to the functional or active site. This review starts with a historical overview and a description of the classical example of allostery – hemoglobin – and other well-known examples (aspartate transcarbamoylase, Lac repressor, kinases, G-protein-coupled receptors, adenosine triphosphate synthase, and chaperonin). We then discuss fringe examples of allostery, including intrinsically disordered proteins and inter-enzyme allostery, and the influence of dynamics, entropy, and conformational ensembles and landscapes on allosteric mechanisms, to capture the essence of the field.
View Article and Find Full Text PDFPharmacological and structural insights into nanvuranlat, a selective LAT1 (SLC7A5) inhibitor, and its N-acetyl metabolite with implications for cancer therapy.
Sci Rep
January 2025
Department of Bio-System Pharmacology, Graduate School of Medicine, Osaka University, 2-2, Yamadaoka, Suita, Osaka, 565-0871, Japan.
L-type amino acid transporter 1 (LAT1, SLC7A5), overexpressed in various cancers, mediates the uptake of essential amino acids crucial for tumor growth. It has emerged as a promising target for cancer therapy. Nanvuranlat (JPH203/KYT-0353), a LAT1 inhibitor, has shown antitumor activity in preclinical studies and efficacy in biliary tract cancer during clinical trials.
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