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Journal ArticleDOI

Investigation on the binding specificity of Agrocybe cylindracea galectin towards α(2,6)-linked sialyllactose by molecular modeling and molecular dynamics simulations

TL;DR: Analysis of the interaction patterns of the carbohydrate at the binding site of wild type and mutated lectins revealed that sialic acid contributed more to the binding when compared with other sugar units in the trisaccharide and enhanced the binding specificity of ACG towards α(2,6)-linked sialyllactose.
About: This article is published in Journal of Carbohydrate Chemistry.The article was published on 2019-07-09. It has received 1 citations till now. The article focuses on the topics: Galectin.
Citations
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Journal ArticleDOI
TL;DR: In this article , the structural flexibility of glycosidic linkage and intramolecular interactions between molecules was investigated for human breast milk oligosaccharide (HMOs), lacto-N-fucopentaose (LNFP) I and II, investigated through MD simulation for 250 ns, and its replicate.

1 citations

References
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Journal ArticleDOI
TL;DR: Ten mutants of human galectin-3 are produced, with changes in these adjacent sites that have altered carbohydrate-binding fine specificity but that retain the basic β-galactoside binding activity, and help to define the differences in fine specificity shown by Xenopus, mouse, and human galector-3 and, as such, the evidence for adaptive change during evolution.

97 citations


"Investigation on the binding specif..." refers methods in this paper

  • ...Carbohydrate binding specificity of ACG has been investigated by surface plasmon resonance and frontal affinity chromatography using ACG mutants.([11,14]) For example, Leguminous Bauhinia purpurea lectin was used to design artificial lectins with distinct and desired carbohydrate binding properties by random mutations at cDNA levels....

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Book ChapterDOI
Hakon Leffler1
TL;DR: The 20 or so galectins expected to be found in man, and their many possible functional effects promise a rich and fruitful research field in the future, but the field lacks the cohesion of knowing basic galectin function.
Abstract: The 20 or so galectins expected to be found in man, and their many possible functional effects promise a rich and fruitful research field in the future. At present, the biomedically most promising areas for use of galectins or their ligands are in inflammation, immunity, and cancer. Many good stories can be formulated, but the field lacks the cohesion of knowing basic galectin function. The only basic common denominators among galectins are beta-galactoside binding, and the unusual combination of intra- and extracellular expression with non-classical secretion in between. Maybe that is all there is, and nature has used these properties for multiple, otherwise unrelated functions. Then again, maybe there is some deeper common function that has so far been overlooked. If it exists, this probably lies somewhere in the detailed integration of galectin activity in the complexities of cell physiology.

84 citations

Journal ArticleDOI
TL;DR: The statistical analyses of interaction contacts of the antibiotic ampicillin with residues based on MD trajectories suggest that two Zn ions are essential for maintaining the binding of AMP with NDM-1 and double-Zn coordination exerts strong restriction on the motions of loop L10 relative to loops L3 and L4.
Abstract: The hydrolysis of a β-lactam core ring caused by new Delphi metallo-β-lactamase 1 (NDM-1) with the help of two zinc cofactors induces significant resistance toward β-lactam antibiotics. Molecular dynamics (MD) simulations and the umbrella sampling method are integrated to study the conformational change mechanism of NDM-1 mediated by zinc ion binding. The statistical analyses of interaction contacts of the antibiotic ampicillin (AMP) with residues based on MD trajectories suggest that two Zn ions are essential for maintaining the binding of AMP with NDM-1. Umbrella sampling simulations further reveal that double-Zn coordination exerts strong restriction on the motions of loop L10 relative to loops L3 and L4. Principal component (PC) analysis also demonstrates that zinc ion binding totally inhibits the motion extent of NDM-1 and changes internal motion modes in NDM-1. We expect that the current study can provide significant dynamical information involving conformational changes of NDM-1 for the development of efficient inhibitors to decrease drug resistance of NDM-1 toward antibiotics.

63 citations

Journal ArticleDOI
TL;DR: A lectin was isolated from fruiting bodies of Agrocybe cylindracea by two ion-exchange chromatographies and gel filtration on Toyopearl HW55F and strongly interacted with glycoconjugates containing NeuAcα2,3Galβ1,3GlcNAc-/GalNAc sequences.
Abstract: A lectin was isolated from fruiting bodies of Agrocybe cylindracea by two ion-exchange chromatographies and gel filtration on Toyopearl HW55F. The lectin was homogeneous on polyacrylamide gel electrophoresis and its molecular mass was determined to be 30 000 by gel filtration, and 15 000 by sodium dodecylsulfate polyacrylamide gel electrophoresis, signifying a dimeric protein.

56 citations


"Investigation on the binding specif..." refers background in this paper

  • ...The Neu5Ac unit of N26L had a substantial contribution to the binding of ACG2 by making 9 direct and 4 water-mediated hydrogen bonds (Table 2) as reported earlier in the literature.([5,10]) A representative plot indicating these direct and water-mediated hydrogen bonds is given in Figure 10....

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