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Article ; Online: Trapping and retaining intermediates in glycosyltransferases.

Guerin, Marcelo E

2023 Volume 299, Issue 8, Page(s) 105006

Abstract: Glycosyltransferases (GTs) attach sugar molecules to a broad range of acceptors, generating a remarkable amount of structural diversity in biological systems. GTs are classified as either "retaining" or "inverting" enzymes. Most retaining GTs typically ... ...

Abstract	Glycosyltransferases (GTs) attach sugar molecules to a broad range of acceptors, generating a remarkable amount of structural diversity in biological systems. GTs are classified as either "retaining" or "inverting" enzymes. Most retaining GTs typically use an S
MeSH term(s)	Glycosyltransferases/chemistry
Chemical Substances	Glycosyltransferases (EC 2.4.-)
Language	English
Publishing date	2023-07-01
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105006
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Article ; Online: Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.

Cifuente, Javier O / Colleoni, Christophe / Kalscheuer, Rainer / Guerin, Marcelo E

Chemical reviews

2024 Volume 124, Issue 8, Page(s) 4863–4934

Abstract: Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of ... ...

Abstract	Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
MeSH term(s)	Glucans/metabolism ; Glucans/chemistry ; Bacteria/enzymology ; Bacteria/metabolism ; Evolution, Molecular
Chemical Substances	Glucans
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.3c00811
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Article ; Online: Modulating antibody effector functions by Fc glycoengineering

García-Alija, Mikel / van Moer, Berre / Sastre, Diego E. / Azzam, Tala / Du, Jonathan J. / Trastoy, Beatriz / Callewaert, Nico / Sundberg, Eric J. / Guerin, Marcelo E.

Biotechnology Advances. 2023 Oct., v. 67 p.108201-

2023

Abstract: Antibody based drugs, including IgG monoclonal antibodies, are an expanding class of therapeutics widely employed to treat cancer, autoimmune and infectious diseases. IgG antibodies have a conserved N-glycosylation site at Asn297 that bears complex type ... ...

Abstract	Antibody based drugs, including IgG monoclonal antibodies, are an expanding class of therapeutics widely employed to treat cancer, autoimmune and infectious diseases. IgG antibodies have a conserved N-glycosylation site at Asn297 that bears complex type N-glycans which, along with other less conserved N- and O-glycosylation sites, fine-tune effector functions, complement activation, and half-life of antibodies. Fucosylation, galactosylation, sialylation, bisection and mannosylation all generate glycoforms that interact in a specific manner with different cellular antibody receptors and are linked to a distinct functional profile. Antibodies, including those employed in clinical settings, are generated with a mixture of glycoforms attached to them, which has an impact on their efficacy, stability and effector functions. It is therefore of great interest to produce antibodies containing only tailored glycoforms with specific effects associated with them. To this end, several antibody engineering strategies have been developed, including the usage of engineered mammalian cell lines, in vitro and in vivo glycoengineering.
Keywords	antibodies ; biotechnology ; complement ; half life ; mammals ; mannosylation ; therapeutics ; Antibody ; IgG ; Glycoengineering ; N-glycosylation ; Endoglycosidase ; Glycosynthase
Language	English
Dates of publication	2023-10
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	47165-3
ISSN	0734-9750
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2023.108201
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Article ; Online: Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis.

Guerin, Marcelo E / Stirnemann, Guillaume / Giganti, David

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 45, Page(s) 11525–11530

Abstract: An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino ... ...

Abstract	An immense repertoire of protein chemical modifications catalyzed by enzymes is available as proteomics data. Quantifying the impact of the conformational dynamics of the modified peptide remains challenging to understand the decisive kinetics and amino acid sequence specificity of these enzymatic reactions in vivo, because the target peptide must be disordered to accommodate the specific enzyme-binding site. Here, we were able to control the conformation of a single-molecule peptide chain by applying mechanical force to activate and monitor its specific cleavage by a model protease. We found that the conformational entropy impacts the reaction in two distinct ways. First, the flexibility and accessibility of the substrate peptide greatly increase upon mechanical unfolding. Second, the conformational sampling of the disordered peptide drives the specific recognition, revealing force-dependent reaction kinetics. These results support a mechanism of peptide recognition based on conformational selection from an ensemble that we were able to quantify with a torsional free-energy model. Our approach can be used to predict how entropy affects site-specific modifications of proteins and prompts conformational and mechanical selectivity.
MeSH term(s)	Biocatalysis ; Biomechanical Phenomena ; Connectin/chemistry ; Connectin/genetics ; Connectin/metabolism ; Endopeptidases/chemistry ; Endopeptidases/genetics ; Endopeptidases/metabolism ; Entropy ; Gene Expression ; Kinetics ; Models, Molecular ; Peptides/chemistry ; Peptides/genetics ; Peptides/metabolism ; Polyproteins/chemistry ; Polyproteins/genetics ; Polyproteins/metabolism ; Protein Conformation ; Protein Engineering ; Protein Unfolding ; Proteolysis ; Substrate Specificity
Chemical Substances	Connectin ; Peptides ; Polyproteins ; TTN protein, human ; Endopeptidases (EC 3.4.-) ; TEV protease (EC 3.4.-)
Language	English
Publishing date	2018-10-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1803872115
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Article ; Online: Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases.

Trastoy, Beatriz / Du, Jonathan J / García-Alija, Mikel / Li, Chao / Klontz, Erik H / Wang, Lai-Xi / Sundberg, Eric J / Guerin, Marcelo E

Current opinion in structural biology

2022 Volume 72, Page(s) 248–259

Abstract: Immunoglobulin G (IgG) monoclonal antibodies are a prominent and expanding class of therapeutics used for the treatment of diverse human disorders. The chemical composition of the N-glycan on the fragment crystallizable (Fc) region determines the ... ...

Abstract	Immunoglobulin G (IgG) monoclonal antibodies are a prominent and expanding class of therapeutics used for the treatment of diverse human disorders. The chemical composition of the N-glycan on the fragment crystallizable (Fc) region determines the effector functions through interaction with the Fc gamma receptors and complement proteins. The chemoenzymatic synthesis using endo-β-N-acetylglucosaminidases (ENGases) emerged as a strategy to obtain antibodies with customized glycoforms that modulate their therapeutic activity. We discuss the molecular mechanism by which ENGases recognize different N-glycans and protein substrates, especially those that are specific for IgG antibodies, in order to rationalize the glycoengineering of immunotherapeutic antibodies, which increase the impact on the treatment of myriad diseases.
MeSH term(s)	Antibodies, Monoclonal/chemistry ; Glycoside Hydrolases/metabolism ; Glycosylation ; Humans ; Immunoglobulin Fc Fragments/chemistry ; Immunoglobulin Fc Fragments/metabolism ; Immunoglobulin G/chemistry ; Immunoglobulin G/metabolism ; Polysaccharides/metabolism
Chemical Substances	Antibodies, Monoclonal ; Immunoglobulin Fc Fragments ; Immunoglobulin G ; Polysaccharides ; Glycoside Hydrolases (EC 3.2.1.-)
Language	English
Publishing date	2022-01-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2021.11.016
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Article ; Online: Quick-soaking of crystals reveals unprecedented insights into the catalytic mechanism of glycosyltransferases.

Albesa-Jové, David / Cifuente, Javier O / Trastoy, Beatriz / Guerin, Marcelo E

Methods in enzymology

2019 Volume 621, Page(s) 261–279

Abstract: Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from nucleotide-sugar or lipid-phospho-sugar donors to a wide range of acceptor substrates, generating a remarkable amount of structural diversity in biological systems. Glycosyl transfer ...

Abstract	Glycosyltransferases (GTs) catalyze the transfer of a sugar moiety from nucleotide-sugar or lipid-phospho-sugar donors to a wide range of acceptor substrates, generating a remarkable amount of structural diversity in biological systems. Glycosyl transfer reactions can proceed with either inversion or retention of the anomeric configuration with respect to the sugar donor substrate. In this chapter, we discuss the application of a quick soaking method of substrates and products into protein crystals to visualize native ternary complexes of retaining glycosyltransferases. The crystal structures provide different snapshots of the catalytic cycle, including the Michaelis complex. During this sequence of events, we visualize how the enzyme guides the substrates into the reaction center where the glycosyl transfer reaction takes place, and unveil the mechanism of product release, involving multiple conformational changes not only in the substrates and products but also in the enzyme. The methodology described here provides unprecedented insights into the catalytic mechanism of glycosyltransferases at the molecular level, and can be applied to the study a myriad of enzymatic mediated reactions.
MeSH term(s)	Animals ; Catalytic Domain ; Crystallization/methods ; Crystallography, X-Ray/methods ; Glycosyltransferases/chemistry ; Glycosyltransferases/metabolism ; Humans ; Models, Molecular ; Protein Conformation ; Substrate Specificity
Chemical Substances	Glycosyltransferases (EC 2.4.-)
Language	English
Publishing date	2019-03-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/bs.mie.2019.02.034
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Article ; Online: Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila.

Trastoy, Beatriz / Naegeli, Andreas / Anso, Itxaso / Sjögren, Jonathan / Guerin, Marcelo E

Nature communications

2020 Volume 11, Issue 1, Page(s) 4844

Abstract: Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune ... ...

Abstract	Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.
MeSH term(s)	Akkermansia ; Animals ; Binding Sites ; Crystallography, X-Ray ; Gastrointestinal Microbiome/physiology ; Glycopeptides/chemistry ; Humans ; Mammals ; Molecular Docking Simulation ; Mucin-1/metabolism ; Mucins/metabolism ; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase/chemistry ; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase/metabolism ; Polysaccharides/chemistry ; Protein Conformation ; Sequence Alignment ; Verrucomicrobia/enzymology ; Verrucomicrobia/metabolism
Chemical Substances	Glycopeptides ; Mucin-1 ; Mucins ; Polysaccharides ; Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase (EC 3.5.1.52)
Language	English
Publishing date	2020-09-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-18696-y
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Article ; Online: CryoEM analysis of the essential native UDP-glucose pyrophosphorylase from

Han, Xu / D'Angelo, Cecilia / Otamendi, Ainara / Cifuente, Javier O / de Astigarraga, Elisa / Ochoa-Lizarralde, Borja / Grininger, Martin / Routier, Francoise H / Guerin, Marcelo E / Fuehring, Jana / Etxebeste, Oier / Connell, Sean R

mBio

2023 Volume 14, Issue 4, Page(s) e0041423

Abstract: Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the ... ...

Abstract	Invasive aspergillosis is one of the most serious clinical invasive fungal infections, resulting in a high case fatality rate among immunocompromised patients. The disease is caused by saprophytic molds in the genus
Language	English
Publishing date	2023-07-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.00414-23
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Article ; Online: Mass Spectrometry-Based Methods to Determine the Substrate Specificities and Kinetics of N-Linked Glycan Hydrolysis by Endo-β-N-Acetylglucosaminidases.

Du, Jonathan J / Sastre, Diego / Trastoy, Beatriz / Roberts, Blaine / Deredge, Daniel / Klontz, Erik H / Flowers, Maria W / Sultana, Nazneen / Guerin, Marcelo E / Sundberg, Eric J

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2674, Page(s) 147–167

Abstract: Glycosylation is a common posttranslational modification of proteins and refers to the covalent addition of glycans, chains of polysaccharides, onto proteins producing glycoproteins. The glycans influence the structure, function, and stability of ... ...

Abstract	Glycosylation is a common posttranslational modification of proteins and refers to the covalent addition of glycans, chains of polysaccharides, onto proteins producing glycoproteins. The glycans influence the structure, function, and stability of proteins. They also play an integral role in the immune system, and aberrantly glycosylated proteins have wide ranging effects, including leading to diseases such as autoimmune conditions and cancer. Carbohydrate-active enzymes (CAZymes) are produced in bacteria, fungi, and humans and are enzymes which modify glycans via the addition or subtraction of individual or multiple saccharides from glycans. One of the hurdles in studying these enzymes is determining the types of substrates each enzyme is specific for and the kinetics of enzymatic activity. In this chapter, we discuss methods which are currently used to study the substrate specificity and kinetics of CAZymes and introduce a novel mass spectrometry-based technique which enables the specificity and kinetics of CAZymes to be determined accurately and efficiently.
MeSH term(s)	Humans ; Substrate Specificity ; Acetylglucosaminidase/metabolism ; Hydrolysis ; Kinetics ; Mass Spectrometry/methods ; Polysaccharides/chemistry
Chemical Substances	Acetylglucosaminidase (EC 3.2.1.52) ; Polysaccharides
Language	English
Publishing date	2023-05-30
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-3243-7_10
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Article ; Online: Modulating antibody effector functions by Fc glycoengineering.

García-Alija, Mikel / van Moer, Berre / Sastre, Diego E / Azzam, Tala / Du, Jonathan J / Trastoy, Beatriz / Callewaert, Nico / Sundberg, Eric J / Guerin, Marcelo E

Biotechnology advances

2023 Volume 67, Page(s) 108201

Abstract	Antibody based drugs, including IgG monoclonal antibodies, are an expanding class of therapeutics widely employed to treat cancer, autoimmune and infectious diseases. IgG antibodies have a conserved N-glycosylation site at Asn297 that bears complex type N-glycans which, along with other less conserved N- and O-glycosylation sites, fine-tune effector functions, complement activation, and half-life of antibodies. Fucosylation, galactosylation, sialylation, bisection and mannosylation all generate glycoforms that interact in a specific manner with different cellular antibody receptors and are linked to a distinct functional profile. Antibodies, including those employed in clinical settings, are generated with a mixture of glycoforms attached to them, which has an impact on their efficacy, stability and effector functions. It is therefore of great interest to produce antibodies containing only tailored glycoforms with specific effects associated with them. To this end, several antibody engineering strategies have been developed, including the usage of engineered mammalian cell lines, in vitro and in vivo glycoengineering.
MeSH term(s)	Animals ; Antibodies, Monoclonal/metabolism ; Immunoglobulin G/metabolism ; Glycosylation ; Polysaccharides ; Cell Line ; Mammals
Chemical Substances	Antibodies, Monoclonal ; Immunoglobulin G ; Polysaccharides
Language	English
Publishing date	2023-06-17
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	47165-3
ISSN	1873-1899 ; 0734-9750
ISSN (online)	1873-1899
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2023.108201
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