Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity

Rojas-Macias, Miguel A.; Lütteke, Thomas

doi:10.1007/978-1-4939-2343-4_16

Cited by 13 publications

(17 citation statements)

References 16 publications

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“…Sialic acid receptors of different origin have structural similarities in the architecture of their carbohydrate recognition domains (CRDs), pertaining, for instance, to the three‐dimensional (3D) arrangement of certain amino acid residues . In addition to arginine residues, aromatic amino acids, such as tryptophan and tyrosine are often involved in these interactions, leading to a stable complex formation.…”

Section: Resultsmentioning

confidence: 99%

“…Due to their important role in nervous system regeneration and neuro‐oncological processes, polySia receptors (e.g., lectins) are of the highest clinical importance . The involvement of polySia and sulfated oligosaccharides, such as the HNK‐1 epitope, in neurite outgrowth allows development of new therapeutic strategies with strong supportive impact on nervous system regeneration in mammals . NCAM, as well as other polySia‐carrying proteins, which are neuropilin‐2 and the synaptic cell adhesion molecule SynCAM1, interact with these receptors through a repeating unit, the disaccharide α2,8‐linked sialic acid building block.…”

Section: Introductionmentioning

confidence: 99%

“…[16][17][18][19] The involvement of polySia and sulfated oligosaccharides, such as the HNK-1 epitope, in neuriteo utgrowth allows development of new therapeutic strategies with strongs upportive impact on nervous system regeneration in mammals. [7,[20][21][22][23][24] NCAM, as well as other polySia-carryingp roteins, which are neuropilin-2 and the synaptic cella dhesion molecule SynCAM1, interactw ith these receptors througharepeatingu nit, the disaccharide a2,8-linked sialic acid building block. In our study,w ef ocused on the polySia receptors MARCKS, a-defensins HNP 1, 2, 3a nd HD5, and al ectin from the Chinese bird-hunting spider,S HL-1, to describe the molecular basis of polySia-protein interactions.…”

Section: Introductionmentioning

confidence: 99%

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Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides

et al. 2016

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Polysialic acid (polySia) and polySia glycomimetic molecules support nerve cell regeneration, differentiation, and neuronal plasticity. With a combination of biophysical and biochemical methods, as well as data mining and molecular modeling techniques, it is possible to correlate specific ligand-receptor interactions with biochemical processes and in vivo studies that focus on the potential therapeutic impact of polySia, polySia glycomimetics, and sulfated polysaccharides in neuronal diseases. With this strategy, the receptor interactions of polySia and polySia mimetics can be understood on a submolecular level. As the HNK-1 glycan also enhances neuronal functions, we tested whether similar sulfated oligo- and polysaccharides from seaweed could be suitable, in addition to polySia, for finding potential new routes into patient care focusing on an improved cure for various neuronal diseases. The knowledge obtained here on the structural interplay between polySia or sulfated polysaccharides and their receptors can be exploited to develop new drugs and application routes for the treatment of neurological diseases and dysfunctions.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides

et al. 2016

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“…This is why it is also important to understand how glycans will interact with the protein residues. GlyVicinity [26] is a tool that statistically analyzes the amino acids closest to a chosen type of carbohydrates.…”

Section: Glycosylation and Modellingmentioning

confidence: 99%

Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol

Besancon

Guillot

Blaise

et al. 2020

Methods

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A B S T R A C TN-glycosylation is a post-translational modification heavily impacting protein functions. Some alterations of glycosylation, such as sialic acid hydrolysis, are related to protein dysfunction. Because of their high flexibility and the many reactive groups of the glycan chains, studying glycans with in vitro methods is a challenging task. Molecular dynamics is a useful tool and probably the only one in biology able to overcome this problem and gives access to conformational information through exhaustive sampling. To better decipher the impact of Nglycans, the analysis and visualization of their influence over time on protein structure is a prerequisite. We developed the Umbrella Visualization, a graphical method that assigns the glycan intrinsic flexibility during a molecular dynamics trajectory. The density plot generated by this method brought relevant informations regarding glycans dynamics and flexibility, but needs further development in order to integrate an accurate description of the protein topology and its interactions. We propose here to transform this analysis method into a visualization mode in UnityMol. UnityMol is a molecular editor, viewer and prototyping platform, coded in C#. The new representation of glycan chains presented in this study takes into account both the main positions adopted by each antenna of a glycan and their statistical relevance. By displaying the collected data on the protein surface, one is then able to investigate the protein/glycan interactions. Thr and Asn-X-Ser, where X is any amino acid but not proline [10]. In

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“…Molecular modeling (Kar et al 2016;Zhang et al 2016) and data mining (Lütteke et al 2005;Rojas-Macias & Lütteke, 2015) tools are necessary for general discussions of the principles of carbohydrate-protein interactions. In order to gain insight into the binding mode for disaccharide 1, molecular Table S1) after the addition of disaccharide 1 onto the 3D structure of lysozyme; the atoms are indicated as green spheres.…”

Section: Molecular Modeling Of the Interaction Between Hl And Disacchmentioning

confidence: 99%

Lysozyme's lectin-like characteristics facilitates its immune defense function

Zhang

Eckert

et al. 2017

Quart. Rev. Biophys.

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Abstract. Interactions between human lysozyme (HL) and the lipopolysaccharide (LPS) of Klebsiella pneumoniae O1, a causative agent of lung infection, were identified by surface plasmon resonance. To characterize the molecular mechanism of this interaction, HL binding to synthetic disaccharides and tetrasaccharides representing one and two repeating units, respectively, of the O-chain of this LPS were studied. pH-dependent structural rearrangements of HL after interaction with the disaccharide were observed through nuclear magnetic resonance. The crystal structure of the HL-tetrasaccharide complex revealed carbohydrate chain packing into the A, B, C, and D binding sites of HL, which primarily occurred through residue-specific, direct or water-mediated hydrogen bonds and hydrophobic contacts. Overall, these results support a crucial role of the Glu35/Asp53/Trp63/Asp102 residues in HL binding to the tetrasaccharide. These observations suggest an unknown glycan-guided mechanism that underlies recognition of the bacterial cell wall by lysozyme and may complement the HL immune defense function.

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Statistical Analysis of Amino Acids in the Vicinity of Carbohydrate Residues Performed by GlyVicinity

Cited by 13 publications

References 16 publications

Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides

Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides

Umbrella Visualization: A method of analysis dedicated to glycan flexibility with UnityMol

Lysozyme's lectin-like characteristics facilitates its immune defense function

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