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The structural dynamics underlying molecular mechanisms of light-sensitive proteins can be studied by a variety of experimental and computational biophysical techniques. Here we review recent progress in combining time-resolved crystallography at X-ray free electron lasers and quantum chemical calculations to study structural changes in photoenzymes, photosynthetic proteins, photoreceptors, and photoswitchable fluorescent proteins following photoexcitation.
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http://dx.doi.org/10.1016/j.sbi.2022.102496 | DOI Listing |
J Phys Chem Lett
September 2025
Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, Oregon 97331, United States.
Carbon dots (CDs) represent a new class of nontoxic and sustainable nanomaterials with increasing applications. Among them, bright and large Stokes-shift CDs are highly desirable for display and imaging, yet the emission mechanisms remain unclear. We obtained structural signatures for the recently engineered green and red CDs by ground-state femtosecond stimulated Raman spectroscopy (FSRS), then synthesized orange CDs with similar size but much higher nitrogen dopants than red CDs.
View Article and Find Full Text PDFMol Divers
September 2025
Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al Kharj, Saudi Arabia.
Cyclin-dependent kinase 20 (CDK20), also known as cell cycle-related kinase (CCRK), plays a pivotal role in hepatocellular carcinoma (HCC) progression by regulating β-catenin signaling and promoting uncontrolled proliferation. Despite its emerging significance, selective small-molecule inhibitors of CDK20 remain unexplored. In this study, a known CDK20 inhibitor, ISM042-2-048, was employed as a reference to retrieve structurally similar compounds from the PubChem database using an 85% similarity threshold.
View Article and Find Full Text PDFJ Phys Chem Lett
September 2025
Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87106, United States.
Defects significantly influence charge transport in CHNHPbI (MAPbI) perovskite solar cells, particularly at interfaces. Using quantum dynamics simulation, we reveal a distinct interstitial iodine (I) defect behavior at different positions in the TiO/MAPbI system. In the perovskite bulk-like region, I exhibits high mobility and dissociates detrimental iodine trimers, facilitating small-to-large polaron transition and promoting shallow trap formation.
View Article and Find Full Text PDFSmall
September 2025
State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
Modifying cells to achieve desired functions has attracted extensive attention in bioengineering and bio-manufacturing. Approaches based on cell-surface engineering have the potential to endow cells with multiple functions and also create a protective shell around them. However, such shells are generally irreversible and lack functionality, leading to various drawbacks associated with irreversible dynamics.
View Article and Find Full Text PDFJ Chem Theory Comput
September 2025
Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077, Hong Kong China.
Coarse-grained (CG) lipid models enable efficient simulations of large-scale membrane events. However, achieving both speed and atomic-level accuracy remains challenging. Graph neural networks (GNNs) trained on all-atom (AA) simulations can serve as CG force fields, which have demonstrated success in CG simulations of proteins.
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