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Filename: controllers/Detail.php
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File: /var/www/html/application/controllers/Detail.php
Line: 249
Function: _error_handler
File: /var/www/html/index.php
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Filename: controllers/Detail.php
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The utilization of tunnels and water transport within enzymes is crucial for their catalytic function as water molecules can stabilize bound substrates and help with unbinding processes of products and inhibitors. Since the choice of water models for molecular dynamics simulations was shown to determine the accuracy of various calculated properties of the bulk solvent and solvated proteins, we have investigated if and to what extent water transport through the enzyme tunnels depends on the selection of the water model. Here, we focused on simulating enzymes with various well-defined tunnel geometries. In a systematic investigation using haloalkane dehalogenase as a model system, we focused on the well-established TIP3P, OPC, and TIP4P-Ew water models to explore their impact on the use of tunnels for water molecule transport. The TIP3P water model showed significantly faster migration, resulting in the transport of approximately 2.5 times more water molecules compared to that of the OPC and 1.7 times greater than that of the TIP4P-Ew. Finally, the transport was 1.4-fold more pronounced in TIP4P-Ew than in OPC. The increase in migration of TIP3P water molecules was mainly due to faster transit times through dehalogenase tunnels. We observed similar behavior in two different enzymes with buried active sites and different tunnel network topologies, i.e., alditol oxidase and cytochrome P450, indicating that our findings are likely not restricted to a particular enzyme family. Overall, this study showcases the critical importance of water models in comprehending the use of enzyme tunnels for small molecule transport. Given the significant role of water availability in various stages of the catalytic cycle and the solvation of substrates, products, and drugs, choosing an appropriate water model may be crucial for accurate simulations of complex enzymatic reactions, rational enzyme design, and predicting drug residence times.
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http://dx.doi.org/10.1021/acs.jcim.4c01177 | DOI Listing |
AbstractClimate change will affect both the mean and the variability in environmental conditions and may have major negative impacts on population densities in the future. For annual plants that already live in an extreme environment like the Sonoran Desert, keeping a fraction of their seeds dormant underground (for possibly years at a time) is critical to survive. Here, we consider how this form of bet hedging (i.
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December 2024
Department of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Jiangxi Hospital, National Reginal Center for Neurological Disease, Honggutan District, No.266 Fenghe North Avenue, Nanchang, 330038, Jiangxi, China.
Acute injury and secondary injury caused by traumatic brain injury (TBI) seriously threaten the health of patients. The purpose of this study was to investigate the role of β-Asarone in TBI-induced neuroinflammation and injury. In this work, the effects of β-Asarone on nerve injury and neuronal apoptosis were investigated in mice with TBI by controlled cortical impingement.
View Article and Find Full Text PDFEnviron Geochem Health
December 2024
State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Beijing Normal University, Beijing, 100875, China.
Around 2.6 billion people are at risk of tooth carries and fluorosis worldwide. Quetta is the worst affected district in Balochistan plateau.
View Article and Find Full Text PDFCurr Microbiol
December 2024
School of Bio Science and Technology, VIT University, Vellore, Tamil Nadu, 632014, India.
Pseudomonas aeruginosa is a prevalent nosocomial pathogen and a significant reservoir of antimicrobial resistance genes in residential and built environments. It is also widespread in various indoor and outdoor settings, including sewage, surface waters, soil, recreational waters (both treated and untreated), and industrial effluents. Surveillance efforts for P.
View Article and Find Full Text PDFEnviron Sci Technol
December 2024
School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
The extensive use and longevity of nylon plastics pose substantial challenges for plastic management, recycling, and pollution control. Depolymerization and monomer recycling are potential solutions for valorizing waste plastics, but they often rely on complex and costly catalysts. Additionally, various additives in nylon plastics can negatively impact the catalyst efficiency.
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