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Enzymes are inherently dynamic entities, with their functions intricately governed by the interplay between conformational dynamics - ranging from local residue fluctuations to global motions - and biochemical activity. Deciphering how such dynamics coordinate higher-order cooperativity across multiple timescales to drive catalysis remains a fundamental challenge. This mini-review highlights the role of large-scale, collective motions involving domain-level displacements and hinge-based rearrangements, which not only facilitate substrate recognition, transformation, and release, but also emerge from and propagate through multidirectional allosteric interactions. Such dynamic mechanochemical coupling reflects evolutionary memory and provides a blueprint for enzyme design innovations.
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http://dx.doi.org/10.1016/j.sbi.2025.103131 | DOI Listing |
J Agric Food Chem
September 2025
Department of Applied Chemistry, College of Science, China Agriculture University, Beijing 100091, China.
l-glufosinate has garnered increasing attention as an ideal herbicide for weed control in agriculture. However, the underlying racemization process of l-glufosinate in the aqueous phase remains unclear. In this work, we elucidated the racemization mechanisms through heating reactions and theoretical calculations.
View Article and Find Full Text PDFJ Phys Chem B
September 2025
School of Science, RMIT University, Melbourne 3000, Australia.
Pentameric ligand-gated ion channels control synaptic neurotransmission via an allosteric mechanism, whereby agonist binding induces global protein conformational changes that open an ion-conducting pore. For the proton-activated bacterial () ligand-gated ion channel (GLIC), high-resolution structures are available in multiple conformational states. We used a library of atomistic molecular dynamics (MD) simulations to study conformational changes and to perform dynamic network analysis to elucidate the communication pathways underlying the gating process.
View Article and Find Full Text PDFArch Microbiol
September 2025
Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, India.
Salmonella enterica serovar Typhi, the etiological agent of Typhoid fever, remains a critical public health concern associated with high morbidity in many developing countries. The widespread emergence of multidrug-resistant (MDR) Salmonella Typhi strains against the fluoroquinolone group of antibiotics, particularly ciprofloxacin, poses a significant global therapeutic challenge with underlying resistance due to mutations in quinolone-resistance determining region (QRDR) of gyrA gene, encoding DNA gyrase subunit A (GyrA). In pursuit of alternative therapeutic candidates, the present study was designed to evaluate ciprofloxacin analogues against prevalent GyrA mutations (S83F, D87G, and D87N) to overcome fluoroquinolone resistance through machine learning (ML)-based approach.
View Article and Find Full Text PDFInorg Chem
September 2025
The Key Laboratory of the Materials for Energy Conversion and Storage of Shanxi Province, Institute of Molecular Science, Shanxi University, 92 Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China.
For over half a century, clusters exhibiting unconventional bonding have captivated researchers due to their unique electronic characteristics. While most elements in the periodic table demonstrate this remarkable structural feature, sulfur has been notably absent from known global minima with a planar pentacoordinate center. Herein, we report the first binary dianion cluster, SMg, featuring a planar pentacoordinate sulfur (ppS) atom.
View Article and Find Full Text PDFChaos
September 2025
School of Mathematical Sciences, Capital Normal University, Beijing 100048, China.
In this paper, we propose a general latent HIV infection model with general incidence and three distributed delays. We start with the analysis of the proposed model by establishing the positivity and boundedness of solutions and calculating basic reproduction number R0. Then, we show that the infection-free equilibrium is globally asymptotically stable when R0<1 (is globally attractive when R0=1), while the disease is uniformly persistent when R0>1.
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