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Evaluation of synaptotagmin-1 action models by all-atom molecular dynamics simulations.
FEBS Open Bio
January 2025
Institute of Neurophysiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany.
Neurotransmitter release is triggered in microseconds by the two C domains of the Ca sensor synaptotagmin-1 and by SNARE complexes, which form four-helix bundles that bridge the vesicle and plasma membranes. The synaptotagmin-1 CB domain binds to the SNARE complex via a 'primary interface', but the mechanism that couples Ca-sensing to membrane fusion is unknown. Widespread models postulate that the synaptotagmin-1 Ca-binding loops accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers or helping bridge the membranes, but these models do not seem compatible with SNARE binding through the primary interface, which orients the Ca-binding loops away from the fusion site.
View Article and Find Full Text PDFMachine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.
J Chem Theory Comput
January 2025
Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States.
Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by the time-consuming process of generating the necessary training, validation, and test data for MLP models through QM/MM simulations. Furthermore, the entire process needs to be repeated for each specific enzyme system and reaction.
View Article and Find Full Text PDFMultiChem: predicting chemical properties using multi-view graph attention network.
BioData Min
January 2025
Department of Computer Science, Hanyang University, Seoul, Republic of Korea.
Background: Understanding the molecular properties of chemical compounds is essential for identifying potential candidates or ensuring safety in drug discovery. However, exploring the vast chemical space is time-consuming and costly, necessitating the development of time-efficient and cost-effective computational methods. Recent advances in deep learning approaches have offered deeper insights into molecular structures.
View Article and Find Full Text PDFClinical significance and pro-oncogenic function of DBF4 in clear cell renal cell carcinoma.
BMC Urol
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Institute of Clinical Medicine, The Second affiliated Hospital of Hainan Medical University, 368th Yehai Avenue, Haikou, Hainan, 570311, China.
Background: Clear cell renal cell carcinoma (ccRCC) is the most common malignant urological tumor, and regrettably, and is insensitive to chemotherapy and radiotherapy, resulting in poor patient outcomes. DBF4 plays a critical role in DNA replication and participates in various biological functions, making it an attractive target for cancer treatment. However, its significance in ccRCC has not yet been explored.
View Article and Find Full Text PDFAsthma-associated prostate enlargement and bladder smooth muscle hypercontractility: unveiling a potential link to LUTS.
BMC Urol
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Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510230, China.
Background: In male patients, benign prostate hyperplasia (BPH) and overactive bladder (OAB) secondary to BPH are the primary causes of Lower Urinary Tract Symptoms (LUTS). Recent clinical studies have reported an increased risk of LUTS, particularly severe LUTS conditions, in male asthmatic patients. However, the potential link and mechanism remain unclear.
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