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.
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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.
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1,480 citations
TL;DR: This paper applied continuum solvent models to investigate the relative stability of A-and B-form helices for three DNA sequences, d(CCAACGTTGG), d(ACCCGCGGGT), and d(CGCGAATTCGCG)2, a phosphoramidate-mod...
Abstract: We apply continuum solvent models to investigate the relative stability of A- and B-form helices for three DNA sequences, d(CCAACGTTGG)2, d(ACCCGCGGGT)2, and d(CGCGAATTCGCG)2, a phosphoramidate-mod...
1,407 citations
University of California, San Francisco1, University of Liège2, University of Oklahoma3, Columbia University4, Teikyo University5, Medical Research Council6, Scripps Research Institute7, University of Texas MD Anderson Cancer Center8, Harvard University9, Centre national de la recherche scientifique10, French Institute of Health and Medical Research11, Wayne State University12, University of Toronto13, Michigan State University14
1,098 citations
TL;DR: The Molecular Mechanics Poisson–Boltzmann Surface Area approach is an efficient method for the calculation of free energies of diverse molecular systems and has great potential that allows comparative free energy analyses for various molecular systems at low computational cost.
Abstract: Detailed knowledge of how molecules recognize interaction partners and of the conformational preferences of biomacromolecules is pivotal for understanding biochemical processes. Such knowledge also provides the foundation for the design of novel molecules, as undertaken in pharmaceutical research. Computer-based free energy calculations enable a detailed investigation of the energetic factors that are responsible for molecular stability or binding affinity. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) approach is an efficient method for the calculation of free energies of diverse molecular systems. Here we describe the concepts of this approach and outline the practical proceeding. Furthermore we give an overview of the wide spectrum of problems that have been addressed with this method and of successful analyses carried out, thereby focussing on ambitious and recent studies. Limits of the approach in terms of accuracy and applicability are discussed. Despite these limitations MM-PBSA is a method with great potential that allows comparative free energy analyses for various molecular systems at low computational cost.
744 citations
TL;DR: A brief introduction to the galectins as a protein family with some comments on nomenclature is given.
Abstract: Good evidence suggest roles of galectins in cancer, immunity and inflammation, and development, but a unifying picture of their biological function is lacking. Instead galectins appear to have a particularly diverse, bewildering but intriguing array of activities both inside and outside cells—“clear truths and mysteries are inextricably twined”. Fortunately this has not discouraged but rather enthused a large number of good galectin researchers, some of which have contributed to this special issue of Glycoconjugate Journal to provide a personal, critical status of the field. Here we will give a brief introduction to the galectins as a protein family with some comments on nomenclature. Published in 2004.
653 citations
"Investigation on the binding specif..." refers background in this paper
...In addition to N23L, ACG also recognizes extensively various b-galactosides, including lactose, N-Acetyl-lactosamines [Galb(1–3)GlcNAc and Galb(1–4)GlcNAc], Galb(1–3)GalNAc, and NeuAca2-3Galb(1–3)Glc.([6,8,10]) The binding specificity of lectins towards specific glycans can be enhanced by substitutions of either one or multiple amino acid residues inside the binding pocket of lectins....
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