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Identifying Sequence Effects on Chain Dimensions of Disordered Proteins by Integrating Experiments and Simulations.
JACS Au
December 2024
Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
It has become increasingly evident that the conformational distributions of intrinsically disordered proteins or regions are strongly dependent on their amino acid compositions and sequence. To facilitate a systematic investigation of these sequence-ensemble relationships, we selected a set of 16 naturally occurring intrinsically disordered regions of identical length but with large differences in amino acid composition, hydrophobicity, and charge patterning. We probed their conformational ensembles with single-molecule Förster resonance energy transfer (FRET), complemented by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy as well as small-angle X-ray scattering (SAXS).
View Article and Find Full Text PDFMachine-Learning-Aided Engineering Hemoglobin as Carbene Transferase for Catalyzing Enantioselective Olefin Cyclopropanation.
JACS Au
December 2024
Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130023, P. R. China.
In this study, we developed a machine-learning-aided protein design strategy for engineering hemoglobin (VHb) as carbene transferase. A Natural Language Processing (NLP) model was used for the first time to construct an algorithm (EESP, enzyme enantioselectivity score predictor) and predict the enantioselectivity of VHb. We identified critical amino acid residue sites by molecular docking and established a simplified mutation library by site-saturated mutagenesis.
View Article and Find Full Text PDFDiscovery of New Synthetic Routes of Amino Acids in Prebiotic Chemistry.
JACS Au
December 2024
Faculty of Synthetic Biology, Shenzhen University of Advanced Technology, Shenzhen 518055, China.
The origin of life on Earth remains one of the most perplexing challenges in biochemistry. While numerous bottom-up experiments under prebiotic conditions have provided valuable insights into the spontaneous chemical genesis of life, there remains a significant gap in the theoretical understanding of the complex reaction processes involved. In this study, we propose a novel approach using a roto-translationally invariant potential (RTIP) formulated with pristine Cartesian coordinates to facilitate the simulation of chemical reactions.
View Article and Find Full Text PDFCholinesterase Inhibitory Activity of Paeoniflorin: Molecular Dynamics Simulation, and In Vitro Mechanistic Investigation.
Biochem Res Int
December 2024
Kentucky College of Osteopathic Medicine, University of Pikeville, Pikeville 41501, Kentucky, USA.
Alzheimer's disease (AD), a neurological disorder, is one of the major reasons for memory loss in the world. AD is characterized by a sequela of cognitive and functional decline caused by brain cell degeneration. Paeoniflorin is a monoterpenoid glycoside found in plants of the Paeoniaceae family, which are known for their medicinal properties including dementia.
View Article and Find Full Text PDFRapid and Large-Scale Synthesis of Chiral and Fluorescent Sulfur Quantum Dots for Intracellular Temperature Monitoring.
Chem Biomed Imaging
December 2024
College of Chemistry and Materials Science, Jinan University, Guangzhou, Guangdong 510632, China.
The large-scale preparation of fluorescent nanomaterials with laboratory-relevant chemical and optical properties will greatly forward their consumer market applications; however, it still remains challenging. In this work, a universal strategy was developed for the rapid and large-scale synthesis of fluorescent sulfur quantum dots that recently has drawn great attention because of their unique optical characteristics. From the fact that empty 3d orbitals of sulfide species are able to bind with lone-pair π electrons of the heteroatomic groups, many amino-group containing compounds, such as amino acid and polyethylenimine molecules, were exploited to synthesize sulfur quantum dots.
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