scholarly journals Phylogenetic and specificity studies of two-domain GNA-related lectins: generation of multispecificity through domain duplication and divergent evolution

2007 ◽  
Vol 404 (1) ◽  
pp. 51-61 ◽  
Author(s):  
Els J. M. Van Damme ◽  
Sachiko Nakamura-Tsuruta ◽  
David F. Smith ◽  
Maté Ongenaert ◽  
Harry C. Winter ◽  
...  
Keyword(s):  
Binding Sites ◽  
Sequence Divergence ◽  
Structural Data ◽  
Divergent Evolution ◽  
Carbohydrate Binding ◽  
Dual Specificity ◽  
Domain Duplication ◽  
Galanthus Nivalis ◽  
High Mannose ◽  
Microarray Analyses

A re-investigation of the occurrence and taxonomic distribution of proteins built up of protomers consisting of two tandem arrayed domains equivalent to the GNA [Galanthus nivalis (snowdrop) agglutinin] revealed that these are widespread among monotyledonous plants. Phylogenetic analysis of the available sequences indicated that these proteins do not represent a monophylogenetic group but most probably result from multiple independent domain duplication/in tandem insertion events. To corroborate the relationship between inter-domain sequence divergence and the widening of specificity range, a detailed comparative analysis was made of the sequences and specificity of a set of two-domain GNA-related lectins. Glycan microarray analyses, frontal affinity chromatography and surface plasmon resonance measurements demonstrated that the two-domain GNA-related lectins acquired a marked diversity in carbohydrate-binding specificity that strikingly contrasts the canonical exclusive specificity of their single domain counterparts towards mannose. Moreover, it appears that most two-domain GNA-related lectins interact with both high mannose and complex N-glycans and that this dual specificity relies on the simultaneous presence of at least two different independently acting binding sites. The combined phylogenetic, specificity and structural data strongly suggest that plants used domain duplication followed by divergent evolution as a mechanism to generate multispecific lectins from a single mannose-binding domain. Taking into account that the shift in specificity of some binding sites from high mannose to complex type N-glycans implies that the two-domain GNA-related lectins are primarily directed against typical animal glycans, it is tempting to speculate that plants developed two-domain GNA-related lectins for defence purposes.

scholarly journals Removal of two high-mannose N-linked glycans on gp120 renders human immunodeficiency virus 1 largely resistant to the carbohydrate-binding agent griffithsin

2011 ◽  
Vol 92 (10) ◽  
pp. 2367-2373 ◽  
Author(s):  
Xin Huang ◽  
Wei Jin ◽  
George E. Griffin ◽  
Robin J. Shattock ◽  
Qinxue Hu
Keyword(s):  
Human Immunodeficiency Virus ◽  
Neutralizing Antibodies ◽  
Site Directed Mutagenesis ◽  
Carbohydrate Binding ◽  
Immunodeficiency Virus ◽  
Galanthus Nivalis ◽  
High Mannose ◽  
Topical Microbicides ◽  
Marked Resistance ◽  
Hiv 1

High-mannose N-linked glycans recognized by carbohydrate-binding agents (CBAs) are potential targets for topical microbicides. To better understand the mechanisms by which CBAs inhibit human immunodeficiency virus (HIV)-1 infection at the molecular level, we systematically analysed the contribution of site-specific glycans to the anti-HIV activity of CBAs by site-directed mutagenesis. Our results demonstrate that a single deglycosylation at N295 or N448 in a range of primary and T-cell-line-adapted HIV-1 isolates resulted in marked resistance to griffithsin (GRFT) but maintained the sensitivity to cyanovirin (CV-N), Galanthus nivalis agglutinin (GNA) and a range of neutralizing antibodies. Unlike CV-N and GNA, the interaction between GRFT and gp120 appeared to be dependent on the specific trimeric ‘sugar tower’ including N295 and N448. This was further strengthened by the results of GRFT–Env binding experiments. Our study identifies GRFT-specific gp120 glycans and may provide information for the design of novel CBA antiviral strategies.

scholarly journals The barley lectin, horcolin, binds high-mannose glycans in a multivalent fashion, enabling high-affinity, specific inhibition of cellular HIV infection

2020 ◽  
Vol 295 (34) ◽  
pp. 12111-12129
Author(s):  
Nisha Grandhi Jayaprakash ◽  
Amrita Singh ◽  
Rahul Vivek ◽  
Shivender Yadav ◽  
Sanmoy Pathak ◽  
...  
Keyword(s):  
Hiv Infection ◽  
Binding Sites ◽  
Neutralizing Antibodies ◽  
Titration Calorimetry ◽  
Carbohydrate Binding ◽  
High Affinity ◽  
Mannose Binding ◽  
Surface Envelope ◽  
High Mannose ◽  
Anti Hiv

N-Linked glycans are critical to the infection cycle of HIV, and most neutralizing antibodies target the high-mannose glycans found on the surface envelope glycoprotein-120 (gp120). Carbohydrate-binding proteins, particularly mannose-binding lectins, have also been shown to bind these glycans. Despite their therapeutic potency, their ability to cause lymphocyte proliferation limits their application. In this study, we report one such lectin named horcolin (Hordeum vulgare lectin), seen to lack mitogenicity owing to the divergence in the residues at its carbohydrate-binding sites, which makes it a promising candidate for exploration as an anti-HIV agent. Extensive isothermal titration calorimetry experiments reveal that the lectin was sensitive to the length and branching of mannooligosaccharides and thereby the total valency. Modeling and simulation studies demonstrate two distinct modes of binding, a monovalent binding to shorter saccharides and a bivalent mode for higher glycans, involving simultaneous interactions of multiple glycan arms with the primary carbohydrate-binding sites. This multivalent mode of binding was further strengthened by interactions of core mannosyl residues with a secondary conserved site on the protein, leading to an exponential increase in affinity. Finally, we confirmed the interaction of horcolin with recombinant gp120 and gp140 with high affinity and inhibition of HIV infection at nanomolar concentrations without mitogenicity.

scholarly journals New Hepatitis B Virus of Cranes That Has an Unexpected Broad Host Range

2003 ◽  
Vol 77 (3) ◽  
pp. 1964-1976 ◽  
Author(s):  
Alexej Prassolov ◽  
Heinz Hohenberg ◽  
Tatyana Kalinina ◽  
Carola Schneider ◽  
Lucyna Cova ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Host Range ◽  
Sequence Divergence ◽  
Divergent Evolution ◽  
Broad Host Range ◽  
Virus Propagation ◽  
Direct Dna Sequencing ◽  
Duck Hepatitis ◽  
B Virus

ABSTRACT All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation.

scholarly journals Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions

2016 ◽  
Vol 15 ◽  
pp. CIN.S39968
Author(s):  
Ji-Hyun Lim ◽  
Natasha S. Latysheva ◽  
Richard D. Iggo ◽  
Daniel Barker
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
P53 Protein ◽  
Species Conservation ◽  
Structural Data ◽  
Functional Differentiation ◽  
Dna Binding Domain ◽  
Response Elements ◽  
Cycle Arrest ◽  
Important Regulator

p53 is an important regulator of cell cycle arrest, senescence, apoptosis and metabolism, and is frequently mutated in tumors. It functions as a tetramer, where each component dimer binds to a decameric DNA region known as a response element. We identify p53 binding site subtypes and examine the functional and evolutionary properties of these subtypes. We start with over 1700 known binding sites and, with no prior labeling, identify two sets of response elements by unsupervised clustering. When combined, they give rise to three types of p53 binding sites. We find that probabilistic and alignment-based assessments of cross-species conservation show no strong evidence of differential conservation between types of binding sites. In contrast, functional analysis of the genes most proximal to the binding sites provides strong bioinformatic evidence of functional differentiation between the three types of binding sites. Our results are consistent with recent structural data identifying two conformations of the L1 loop in the DNA binding domain, suggesting that they reflect biologically meaningful groups imposed by the p53 protein structure.

scholarly journals Man-Specific, GalNAc/T/Tn-Specific and Neu5Ac-Specific Seaweed Lectins as Glycan Probes for the SARS-CoV-2 (COVID-19) Coronavirus

Marine Drugs ◽  
2020 ◽  
Vol 18 (11) ◽  
pp. 543
Author(s):  
Annick Barre ◽  
Els J.M. Van Damme ◽  
Mathias Simplicien ◽  
Hervé Benoist ◽  
Pierre Rougé
Keyword(s):  
Influenza Virus ◽  
Antiviral Agents ◽  
Host Cells ◽  
Carbohydrate Binding ◽  
Complex Type ◽  
Enveloped Viruses ◽  
High Mannose ◽  
Hiv 1 ◽  
Biomedical Interest

Seaweed lectins, especially high-mannose-specific lectins from red algae, have been identified as potential antiviral agents that are capable of blocking the replication of various enveloped viruses like influenza virus, herpes virus, and HIV-1 in vitro. Their antiviral activity depends on the recognition of glycoprotein receptors on the surface of sensitive host cells—in particular, hemagglutinin for influenza virus or gp120 for HIV-1, which in turn triggers fusion events, allowing the entry of the viral genome into the cells and its subsequent replication. The diversity of glycans present on the S-glycoproteins forming the spikes covering the SARS-CoV-2 envelope, essentially complex type N-glycans and high-mannose type N-glycans, suggests that high-mannose-specific seaweed lectins are particularly well adapted as glycan probes for coronaviruses. This review presents a detailed study of the carbohydrate-binding specificity of high-mannose-specific seaweed lectins, demonstrating their potential to be used as specific glycan probes for coronaviruses, as well as the biomedical interest for both the detection and immobilization of SARS-CoV-2 to avoid shedding of the virus into the environment. The use of these seaweed lectins as replication blockers for SARS-CoV-2 is also discussed.

scholarly journals StackCBPred: A stacking based prediction of protein-carbohydrate binding sites from sequence

2019 ◽  
Vol 486 ◽  
pp. 107857 ◽  
Author(s):  
Suraj Gattani ◽  
Avdesh Mishra ◽  
Md Tamjidul Hoque
Keyword(s):  
Binding Sites ◽  
Carbohydrate Binding

scholarly journals Developmentally regulated enzymes and cyclic AMP-binding sites in Dictyostelium discoideum cells blocked during development by α-chymotrypsin

1982 ◽  
Vol 206 (2) ◽  
pp. 185-193
Author(s):  
J A Schmidt ◽  
J L Stirling
Keyword(s):  
Cyclic Amp ◽  
Dictyostelium Discoideum ◽  
Binding Sites ◽  
Glycogen Phosphorylase ◽  
Specific Activity ◽  
Tyrosine Aminotransferase ◽  
Carbohydrate Binding ◽  
Threonine Deaminase ◽  
Developmentally Regulated ◽  
Beta Glucosidase

When cells of the slime mould Dictyostelium discoideum are allowed to starve in the presence of alpha-chymotrypsin, they are blocked in development at the stage where tight aggregates form tips. Analysis of developmentally regulated enzymes has shown that alpha-mannosidase, beta-N-acetylglucosaminidase, threonine deaminase, tyrosine aminotransferase, beta-glucosidase and the carbohydrate-binding protein discoidin are unaffected, but enzymes that show an increase in specific activity during post-aggregative development, namely glycogen phosphorylase, UDP-glucose pyrophosphorylase, UDP-galactose 4-epimerase, UDP-galactose polysaccharide transferase and alkaline phosphatase, did not show the characteristic increase when development was blocked by alpha-chymotrypsin. Recovery of cells from the effects of alpha-chymotrypsin was accompanied by the formation of fruiting bodies and a concomitant increase in the specific activity of UDP-glucose pyrophosphorylase. Uptake or efflux of 45Ca2+ was not altered in the presence of alpha-chymotrypsin. Cells allowed to develop in alpha-chymotrypsin, or treated with the enzyme for 15 min, had a markedly reduced ability to bind cyclic AMP with low affinity; high-affinity binding was unaffected. Pronase had a similar effect on cyclic AMP binding, but trypsin, which does not alter developmental processes, has no effect on cyclic AMP binding to D. discoideum cells.

Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii

2020 ◽  
Vol 76 (5) ◽  
pp. 447-457
Author(s):  
Ping Huang ◽  
Shiwang Wu ◽  
Shaoqing Yang ◽  
Qiaojuan Yan ◽  
Zhengqiang Jiang
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Structural Basis ◽  
Carbohydrate Binding ◽  
Type I ◽  
Debranching Enzyme ◽  
Crystal Forms ◽  
Aromatic Residues ◽  
Starch Debranching Enzyme ◽  
Paenibacillus Barengoltzii

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

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