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Exploring transition states of protein conformational changes via out-of-distribution detection in the hyperspherical latent space.
Nat Commun
January 2025
Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA.
Identifying transitional states is crucial for understanding protein conformational changes that underlie numerous biological processes. Markov state models (MSMs), built from Molecular Dynamics (MD) simulations, capture these dynamics through transitions among metastable conformational states, and have demonstrated success in studying protein conformational changes. However, MSMs face challenges in identifying transition states, as they partition MD conformations into discrete metastable states (or free energy minima), lacking description of transition states located at the free energy barriers.
View Article and Find Full Text PDFCurcumenol regulates Histone H3K27me3 demethylases KDM6B affecting Succinic acid metabolism to alleviate cartilage degeneration in knee osteoarthritis.
Phytomedicine
October 2024
Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong, China; The Fifth Clinical College of Guangzhou University of Chinese Medicine, Guangzhou 510095, Guangdong, China; Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou 510095, Guangdong, China; Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, Guangdong, China. Electronic address:
Article Synopsis
- The study investigates the effects of Curcumenol, a compound from traditional Chinese medicine, on cartilage metabolism dysregulation in knee osteoarthritis (KOA), aiming to clarify its mechanisms of action through advanced techniques like transcriptomics and metabolomics.
- Using a mouse model of KOA, the researchers administered different doses of Curcumenol and employed various methods to assess its impact on cartilage health and cellular functions.
- Results showed that Curcumenol reduced cartilage damage, enhanced cartilage repair, and positively influenced extracellular matrix metabolism by regulating specific proteins associated with cartilage health.
Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems.
J Chem Theory Comput
August 2024
Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States.
This study introduces a novel method named multiple parameter replica exchange Gaussian accelerated molecular dynamics (MP-Rex-GaMD), building on the Gaussian accelerated molecular dynamics (GaMD) algorithm. GaMD enhances sampling and retrieves free energy information for biomolecular systems by adding a harmonic boost potential to smooth the potential energy surface without the need for predefined reaction coordinates. Our innovative approach advances the acceleration power and energetic reweighting accuracy of GaMD by incorporating a replica exchange algorithm that enables the exchange of multiple parameters, including the GaMD boost parameters of force constant and energy threshold, as well as temperature.
View Article and Find Full Text PDFAims: This study evaluates the antibacterial characteristics and mechanisms of combined tea polyphenols (TPs), Nisin, and ε-polylysine (PL) against Streptococcus canis, Streptococcus minor, Streptococcus mutans, and Actinomyces oris, common zoonotic pathogens in companion animals.
Methods And Results: Pathogenic strains were isolated from feline oral cavities and assessed using minimum inhibitory concentration (MIC) tests, inhibition zone assays, growth kinetics, and biofilm inhibition studies. Among single agents, PL exhibited the lowest MIC values against all four pathogens.
Targeted suppression of MEP pathway genes DXS, IspD and IspF to explore the mycobacterial metabolism and survival.
Int J Biol Macromol
June 2024
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India; Dr.Reddy's Institute of Life Science, Hyderabad 500046, India. Electronic address:
Due to the uniqueness and essentiality of MEP pathway for the synthesis of crucial metabolites- isoprenoids, hopanoids, menaquinone etc. in mycobacterium, enzymes of this pathway are considered promising anti-tubercular drug targets. In the present study we seek to understand the consequences of downregulation of three of the essential genes- DXS, IspD, and IspF of MEP pathway using CRISPRi approach combined with transcriptomics in Mycobacterium smegmatis.
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