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Unbiased picture of the ligand docking process for the hevein protein-oligosaccharide complex.
Sci Rep
January 2025
Department of Applied Chemistry, Faculty of Engineering, University of Miyazaki, 1-1 Nishi, Gakuen-Kibanadai, Miyazaki, 889-2192, Japan.
The ligand-docking behavior of hevein, the major latex protein from the rubber tree Hevea brasiliensis (Euphorbiaceae), has been investigated by the unguided molecular dynamics (MD) simulation method. An oligosaccharide molecule, initially placed in an arbitrary position, was allowed to move around hevein for a prolonged simulation time, on the order of microseconds, with the expectation of spontaneous ligand docking of the oligosaccharide molecule to the binding site of hevein. In the binary solution system consisting of a hevein molecule and a chito-trisaccharide (GlcNAc) molecule, three out of the six separate simulation runs successfully reproduced the complex structure of the observed binding from.
View Article and Find Full Text PDFLectin-carbohydrate analysis by molecular dynamics: Parkia lectins case study.
An Acad Bras Cienc
December 2024
Universidade Federal do Ceará, Departamento de Bioquímica e Biologia Molecular, Laboratório de Moléculas Biologicamente Ativas, Rua José Aurelio Camara, s/n, 60440-970 Fortaleza, CE, Brazil.
Understanding lectin-carbohydrate interactions at the structural and molecular levels is crucial to the field of lectins, as the diverse roles and biological activities exhibited by these proteins are fundamentally linked to their specific binding to target glycoconjugates. This study aimed to apply molecular dynamics to analyze the structure and binding properties of Parkia lectins. 3D structures of Parkia platycephala and P.
View Article and Find Full Text PDFUnveiling the structural and functional perspectives of a bifunctional α-l-arabinofuranosidase/endo-β-1,4-xylanase (BoGH43_35) from Bacteroides ovatus.
Arch Biochem Biophys
February 2025
Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India. Electronic address:
Article Synopsis
- - Arabinoxylan, a complex sugar, can be broken down by enzymes like α-l-arabinofuranosidase and xylanase; a new bifunctional enzyme (BoGH43_35) from Bacteroides ovatus has been studied for its ability to degrade these sugars.
- - The enzyme's structure features a stable 5-bladed β-propeller fold and carbohydrate-binding modules, with molecular dynamics confirming its compactness and stability during simulations.
- - Binding affinity analysis showed BoGH43_35 has the strongest interaction with arabinose and maintains stability in its complex forms, along with measurements suggesting good solubility and low aggregation in solution.
Sugar mimics and their probable binding sites: design and synthesis of thiazole linked coumarin-piperazine hybrids as galectin-1 inhibitors.
RSC Adv
November 2024
Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500037 India
Sugar mimics are valuable tools in medicinal chemistry, offering the potential to overcome the limitations of carbohydrate inhibitors, such as poor pharmacokinetics and non-selectivity. In our continued efforts to develop heterocyclic galectin-1 inhibitors, we report the synthesis and characterization of thiazole-linked coumarin piperazine hybrids (10a-10i) as Gal-1 inhibitors. The compounds were characterized using H NMR, C NMR and HRMS.
View Article and Find Full Text PDFImpact of mutations in carbohydrate binding sites of tandem-repeat type galectin from Takifugu obscurus on its antimicrobial activity.
Fish Shellfish Immunol
December 2024
Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization, College of Oceanography, Hohai University, Nanjing, 210024, China. Electronic address:
Galectins belong to a family of galactoside-binding proteins and exhibit diverse biological functions. In the present research, a tandem-repeat type galectin (named ToGalectin) was identified from obscure puffer Takifugu obscurus. The 296 amino acids ToGalectin contained two carbohydrate recognition domains (CRDs), one of which possessed two conserved carbohydrate binding motifs.
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