Databases and Associated Tools for Glycomics and Glycoproteomics

Lisacek, Frédérique; Mariethoz, Julien; Alocci, Davide; Rudd, Pauline M.; Abrahams, Jodie L.; Campbell, Matthew P.; Packer, Nicolle H.; Ståhle, Jonas; Widmalm, Göran; Mullen, Elaine; Adamczyk, B; Rojas-Macias, Miguel A.; Jin, Chunsheng; Karlsson, Niclas G.

doi:10.1007/978-1-4939-6493-2_18

Cited by 46 publications

(31 citation statements)

References 58 publications

(2 reference statements)

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“…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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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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show abstract

“…In some cases, conformers can increase the number of drift peaks although the number of individual analytes remains the same, which complicates the analysis of the measured data [21]. The identification confidence can be increased by comparing obtained CCSs with reference values of comprehensive databases [22][23][24] or theoretical values.…”

Section: Top-down Fragment Analysismentioning

confidence: 99%

Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy

Manz

Pagel

2018

Current Opinion in Chemical Biology

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Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics.

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“…The database contains over 600 fluorescently labeled N‐ and O‐linked glycans including their structure and retention times calculated from published values . GlycoMod, GlycoWorkbench, and UniCarb‐DB are MS databases that aid in prediction of monosaccharide composition of N‐ and O‐linked glycans, annotation of MS data with corresponding glycan structure and provide comparisons of end user experimental data to data collected in the database …”

Section: Glycomicsmentioning

confidence: 99%

CHO‐Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction

Stolfa

Smonskey

Boniface

et al. 2017

Biotechnology Journal

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CHO cells are the most prevalent platform for modern bio-therapeutic production. Currently, there are several CHO cell lines used in bioproduction with distinct characteristics and unique genotypes and phenotypes. These differences limit advances in productivity and quality that can be achieved by the most common approaches to bioprocess optimization and cell line engineering. Incorporating omics-based approaches into current bioproduction processes will complement traditional methodologies to maximize gains from CHO engineering and bioprocess improvements. In order to highlight the utility of omics technologies in CHO bioproduction, the authors discuss current applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, lipidomics, fluxomics, glycomics, and multi-omics approaches and the potential they hold for the future of bioproduction. Multiple omics approaches are currently being used to improve CHO bioprocesses; however, the application of these technologies is still limited. As more CHO-omic datasets become available and integrated into systems models, the authors expect significant gains in product yield and quality. While individual omics technologies provide incremental improvements in bioproduction, the authors will likely see the most significant gains by applying multi-omics and systems biology approaches to individual CHO cell lines.

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Databases and Associated Tools for Glycomics and Glycoproteomics

Cited by 46 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

Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy

CHO‐Omics Review: The Impact of Current and Emerging Technologies on Chinese Hamster Ovary Based Bioproduction

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