Glycomics@ExPASy: Bridging the Gap

Mariethoz, Julien; Alocci, Davide; Gastaldello, Alessandra; Horlacher, Oliver; Gasteiger, Elisabeth; Rojas-Macias, Miguel A.; Karlsson, Niclas G.; Packer, Nicolle H.; Lisacek, Frédérique

doi:10.1074/mcp.ra118.000799

Cited by 64 publications

(44 citation statements)

References 58 publications

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“…These complexities are very difficult to resolve, requiring high levels of expertise and multi-layered orthogonal approaches [7][8][9][10]. Within this framework, the contribution of glycoinformatics tools and databases represents an essential resource to advance glycomics [11][12][13][14][15], while molecular simulations fit in very well as complementary and orthogonal techniques to support and advance structural glycobiology research. Indeed, current high performance computing (HPC) technology allows us to study realistic model systems [16,17] and to reach experimental timescales [18], so that computing can now contribute as one of the leading research methods in structural glycobiology.…”

Section: Introductionmentioning

confidence: 99%

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

Fogarty

Harbison

Dugdale

et al. 2020

Beilstein J. Org. Chem.

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The N-glycosylation is one of the most abundant and diverse post-translational modifications of proteins, implicated in protein folding and structural stability, and mediating interactions with receptors and with the environment. All N-glycans share a common core from which linear or branched arms stem from, with functionalization specific to different species and to the cells’ health and disease state. This diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans’ 3D architecture and dynamics, which remain for the large part unresolved and undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans’ 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We also compare these structural motifs and combine them with mammalian N-glycan motifs to devise strategies for the control of the N-glycan 3D structure through sequence. Our results suggest that the N-glycans’ architecture can be described in terms of the local spatial environment of groups of monosaccharides. We define these “glycoblocks” as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans’ 3D architecture can potentially lead to an easier prediction of sequence-to-structure relationships in complex carbohydrates, with important implications in glycoengineering design.

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Section: Introductionmentioning

confidence: 99%

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

Fogarty

Harbison

Dugdale

et al. 2020

Beilstein J. Org. Chem.

View full text Add to dashboard Cite

show abstract

“…These complexities are very difficult to resolve, requiring high levels of expertise and multi-layered orthogonal approaches [8][9][10]7]. Within this framework, the contribution of glycoinformatics tools and databases represents an essential resource to advance glycomics [11][12][13][14][15], while molecular simulations fit in very well as complementary and orthogonal techniques to support and advance structural glycobiology research. Indeed, current high performance computing (HPC) technology allows us to study realistic model systems [16,17] and to reach experimental timescales [18], so that computing can now contribute as one of the leading research methods in structural glycobiology.…”

Section: Introductionmentioning

confidence: 99%

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

Fogarty

Harbison

Dugdale

et al. 2020

Preprint

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N-glycosylation is one of the most abundant and diverse post-translational modifications of proteins, implicated in protein folding and structural stability, and mediating interactions with receptors and with the environment. All N-glycans share a common core from which linear or branched arms stem from, with functionalization specific to different species and to the cells' health and disease state. This diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans 3D architecture and dynamics, which remains for the large part unresolved and undetected because of intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We also compare these structural motifs and combine them with mammalian Nglycans motifs to devise strategies for the control of the N-glycan 3D structure through sequence. Our results suggest that the N-glycans architecture can be described in terms of the local spatial environment of groups of monosaccharides. We define these "glycoblocks" as self-contained 3D units, uniquely identified by the nature of the residues they comprise, their linkages and structural/dynamic features. This alternative description of glycans 3D architecture can potentially lead to an easier prediction of sequence-to-structure relationships in complex carbohydrates, with important implications in glycoengineering design.

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“…Manuscript to be reviewed (http://smart.embl-heidelberg.de/) (Letunic & Bork 2018) according to AtGELPs. The basic information for SaGELPs were predicted using ExPASy (https://web.expasy.org/protparam/) (Mariethoz et al 2018), including molecular weights, amino acid numbers and isoelectric point values.…”

Section: Identification Of Sagelps In S Alfredii Hancementioning

confidence: 99%

Peer Review #2 of "Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress (v0.1)"

2019

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The herb Sedum alfredii (S. alfredii) Hance is a hyper-accumulator of heavy metals [cadmium (Cd), zinc (Zn) and lead (Pb)]; therefore, it could be a candidate plant for efficient phytoremediation. The GDSL esterase/lipase protein (GELP) family plays important roles in plant defense and growth. Although the GELP family members in a variety of plants have been cloned and analyzed, there are limited studies on the family's responses to heavy metal-stress conditions. Methods: Multiple sequence alignments and phylogenetic analyses were performed according to the criteria described. A WGCNA was used to construct co-expression regulatory networks. The roots of S. alfredii seedlings were treated with 100 µM CdCl 2 for qRT-PCR to analyze expression levels in different tissues. SaGLIP8 was transformed into the Cd sensitive mutant strain yeast Δycf1 to investigate its role in resistance and accumulation to Cd. Results: We analyzed GELP family members from genomic data of S. alfredii. A phylogenetic tree divided the 80 identified family members into three clades. The promoters of the 80 genes contained certain elements related to abiotic stress, such as TC-rich repeats (defense and stress responsiveness), heat shock elements (heat stress) and MYB-binding sites (drought-inducibility). In addition, 66 members had tissue-specific expression patterns and significant responses to Cd stress. In total, 13 hub genes were obtained, based on an existing S. alfredii transcriptome database, that control 459 edge genes, which were classified into five classes of functions in a co-expression subnetwork: cell wall and defense function, lipid and esterase, stress and tolerance, transport and transcription factor activity. Among the hub genes, Sa13F.102 (SaGLIP8), with a high expression level in all tissues, could increase Cd tolerance and accumulation in yeast when overexressed. Conclusion: Based on genomic data of S. alfredii, we conducted phylogenetic analyses, as well as conserved domain, motif and expression profiling of the GELP family under Cd-stress conditions. SaGLIP8 could increase Cd tolerance and accumulation in yeast. These results indicated the roles of GELPs in plant responses to heavy metal exposure and provides a theoretical basis for further studies of the SaGELP family's functions.

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Glycomics@ExPASy: Bridging the Gap

Cited by 64 publications

References 58 publications

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

Peer Review #2 of "Identification and expression analysis of the GDSL esterase/lipase family genes, and the characterization of SaGLIP8 in Sedum alfredii Hance under cadmium stress (v0.1)"

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