Journal ArticleDOI
Investigation on the binding specificity of Agrocybe cylindracea galectin towards α(2,6)-linked sialyllactose by molecular modeling and molecular dynamics simulations
Ponnusamy Parasuraman,Jeyasigamani F. A. Selvin,M. Michael Gromiha,Kazuhiko Fukui,K. Veluraja +4 more
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TLDR
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.read more
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Structural and conformational dynamics of human milk oligosaccharides, lacto-N-fucopentaose I and II, through molecular dynamics simulation
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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Journal ArticleDOI
Structural Basis of a Fungal Galectin from Agrocybe cylindracea for Recognizing Sialoconjugate
TL;DR: The refined structure shows that ACG is a "proto"-type galectin composed of a beta-sandwich of two antiparallel sheets, each with six strands, in contrast to the five and six strands in animal galectins, which is among the "layer"-type.
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Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling.
TL;DR: The calculations of potential of mean force (PMF) based on umbrella sampling simulations indicate that the free energies of inhibitor-L1196M ALKs are lower than those of inhibitors-wild ALKS, which would help in the design of potent inhibitors alleviating the drug resistance of L1196m in ALK.
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Comparative molecular dynamics simulations of histone deacetylase-like protein: Binding modes and free energy analysis to hydroxamic acid inhibitors
TL;DR: The binding of HDLP to these four hydroxamic acid inhibitors is mainly driven by van der Waals/nonpolar interactions, which can be a guide for the optimization of HDAC inhibitors and future design of new therapeutic agents for the treatment of cancer.
Journal ArticleDOI
Conformational dynamics of sialyl Lewisx in aqueous solution and its interaction with selectinE. A study by molecular dynamics.
K. Veluraja,Claudio J. Margulis +1 more
TL;DR: It appears from this study that when the oligosaccharide is free in solution the NeuNAca(2–3)Gal segment favors glycosidic conformation in three different regions in the plane with propensity of populations in the ratio 1:8:1.
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Engineering of the glycan-binding specificity of Agrocybe cylindracea galectin towards α(2,3)-linked sialic acid by saturation mutagenesis.
TL;DR: It was found that E86D mutant (Glu86 substituted with Asp) substantially lost the binding ability to LacNAc and T-antigen, while it retained the high affinity for 3'-sialyl lactose, and frontal affinity chromatography analysis confirmed that the E85D mutant had a strong preference for α(2,3)-disialo biantennary N-linked glycan.