Serge Perez

French National Centre for Scientific Research - Grenoble University Alpes · Centre de Recherches sur les Macromolécules Végétales (CERMAV) CNRS

Hyaluronan (HA) is a naturally occurring non-sulfated glycosaminoglycan (GAG) localized to the cell surface and the tissue extracellular matrix (ECM). It is composed of disaccharides containing glucuronic acid and N-acetylglucosamine, is synthesized by the HA synthase (HAS) enzymes and is degraded by hyaluronidase (HYAL) or reactive oxygen and nitr...

Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conform...

The present report assesses the capability of a soluble glycosyltransferase to modify glycolipids organized in two synthetic membrane systems that are attractive models to mimic cell membranes: giant unilamellar vesicles (GUVs) and supported lipid bilayers (SLBs). The objective was to synthesize the Gb3 antigen (Galα1,4Galβ1,4Glcβ-Cer), a cancer bi...

Nonulosonic acids or non-2-ulosonic acids (NulOs) are an ancient family of 2-ketoaldonic acids (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in a 3-deoxy form (referred to as “sialic acids”) or in a 3,9-dideoxy “sialic-acid-like” form. The former sialic acids are most common in the deuterostome lineag...

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequence...

Emerging SARS-CoV-2 variants raise concerns about our ability to withstand the Covid-19 pandemic, and therefore, understanding mechanistic differences of those variants is crucial. In this study, we investigate disparities between the SARS-CoV-2 wild type and five variants that emerged in late 2020, focusing on the structure and dynamics of the spi...

Glycosaminoglycans are complex polysaccharides exhibiting a large structural and conformational diversity. These key biological players organize the extracellular matrix, contribute to cell–matrix interactions, and regulate cell signaling. Natural and synthetic libraries of glycosaminoglycans have been spotted on microarrays to find glycosaminoglyc...

With the increasing need for hydrogels with tunable properties for specific biomedical applications, a complete understanding of the structure-function relationship of polymers used for hydrogel development remains crucial for their optimal use. In the present study, by combining experimental and theoretical approaches, the structure-function relat...

During processing of plant-based foods, cell wall polysaccharides and polyphenols, such as procyanidins, interact extensively, thereby affecting their physicochemical properties along with their potential health effects. Although hemicelluloses are second only to pectins in affinity for procyanidins in cell walls, a detailed study of their interact...

Pdf version of an e-chapter available at glycopedia.eu

Glycosaminoglycans (GAGs) are linear, anionic polysaccharides that consist of repeating disaccharides of hexosamine and hexuronic acid [...]

This book is written in the context of the bioeconomy, which is the renewable segment of the circular economy. It is dedicated to a variety of audiences. Chitin is the second most abundant natural polymer in the world after cellulose. It is a linear polysaccharide composed of β-1,4-linked 2-acetamido-2-deoxy-D-glucopyranose, which plays the role of...

The exopolysaccharide Infernan, from the bacterial strain GY785, has a complex repeating unit of nine monosaccharides established on a double-layer of sidechains. A cluster of uronic and sulfated monosaccharides confers to Infernan functional and biological activities. We characterized the 3-dimensional structures and dynamics along Molecular Dynam...

Glycosaminoglycans (GAGs) are complex linear polysaccharides. GAG-DB is a curated database that classifies the three-dimensional features of the six mammalian GAGs (chondroitin sulfate, dermatan sulfate, heparin, heparan sulfate, hyaluronan, and keratan sulfate) and their oligosaccharides complexed with proteins. The entries are structures of GAG a...

The starch granule is Nature’s way to store energy in green plants over long periods. Irrespective of their origins, starches display distinct structural features that are the fingerprints of levels of organization over six orders of magnitude. We hypothesized that Nature retains hierarchical material structures at all levels and that some general...

Lectins are non-covalent glycan-binding proteins mediating cellular interactions but their annotation in newly sequenced organisms is lacking. The limited size of functional domains and the low level of sequence similarity challenge usual bioinformatics tools. The identification of lectin domains in proteomes requires the manual curation of sequen...

The ubiquitous occurrences of glycans (from oligo to polysaccharides) as cell components to significant constituents of the terrestrial biomass provide the glycans with a panel of biological functions and physicochemical properties. The progress made in algorithms and computational power allows for the simulation of glycans in their natural environ...

Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard rep...

Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visu-alisation and modelling of glycans. The article also provides details on the standard re...

Chloroplast membranes have a high content of the uncharged galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). These galactolipids are essential for the biogenesis of plastids and functioning of the photosynthetic machinery. A monotopic glycosyltransferase, monogalactosyldiacylglycerol synthase synthesizes the b...

Preface of a book

The search for new biomolecules requires a clear understanding of biosynthesis and degradation pathways. This view applies to most metabolites as well as other molecule types such as glycans whose repertoire is still poorly characterized. Lectins are proteins that recognize specifically and interact noncovalently with glycans. This particular class...

Glycoscience is an interdisciplinary field, which leads to different industrial applications derived from physicochemical and/or biological properties of carbohydrates. The aim of this paper is to understand the different innovation potentials based on glycoscience research. We consider three main value-chains related to the two main properties of...

Mono- and digalactosyldiacylglycerol are essential galactolipids for the biogenesis of plastids and functioning of the photosynthetic machinery. In Arabidopsis, the first step of galactolipid synthesis is catalyzed by monogalactosyldiacylglycerol synthase 1 (MGD1), a monotopic protein located in the inner envelope membrane of chloroplasts, which tr...

Lectins with a β-propeller fold bind glycans on the cell surface through multivalent binding sites and appropriate directionality. These proteins are formed by repeats of short domains, raising questions about evolutionary duplication. However, these repeats are difficult to detect in translated genomes and seldom correctly annotated in sequence da...

Derrière l'acception commune « le sucre », se cachent en réalité des molécules complexes autrement appelées « glycanes ». Ces glycanes de toutes formes, de toutes tailles règnent sur le vivant. Objets d'étude des glycosciences, ils protègent et soignent notre corps, diagnostiquent la maladie, constituent la biomasse végétale terrestre et inspirent...

Glycoscience is a rapidly developing and emerging scientific discipline. Like many other scientific disciplines, glycoscience is adapting to the exciting rise of accessible scientific data, which now impacts research and modifies its practice. The accumulation of information along with the development of enabling technologies has laid the foundatio...

Mammalian glycosaminoglycans are linear complex polysaccharides comprising heparan sulfate, heparin, dermatan sulfate, chondroitin sulfate, keratan sulfate and hyaluronic acid. They bind to numerous proteins and these interactions mediate their biological activities. GAG–protein interaction data reported in the literature are curated mostly in Matr...

This article covers nomenclature, sources, biosynthesis, preparation, uses, microcrystalline cellulose, structural chemistry, reactions, solvents, and liquid crystals. Cellulose for commercial purposes comes mostly from wood and cotton, whereas cellulose for research comes from bacteria, algae, and ramie (also a textile fiber). Preparation includes...

This article offers a general background for scientists embarking in the field of glycoscience to grasp an essential component i.e. the alphabet of the building blocks that constitute the many naturally occurring glycans and complex carbohydrates. There is a need to conform to the recommendations of nomenclatures of carbohydrates whilst the constra...

Les glycanes (glucides complexes) jouent un rôle important dans de nombreux processus importants sur le plan biomédical, tels que la réponse inflammatoire, l'activité hormonale, la malignité, les infections virales et bactériennes et la différenciation cellulaire. Cet article de synthèse présente l'apport de la glycobiotechnologie au domaine de la...

MatrixDB (http://matrixdb.univ-lyon1.fr/) is an interaction database focused on biomolecular interactions established by extracellular matrix (ECM) proteins and glycosaminoglycans (GAGs). It is an active member of the International Molecular Exchange (IMEx) consortium (https://www.imexconsortium.org/). It has adopted the HUPO Proteomics Standards I...

The EPS Database (EPS-DB) is a web-based, platform-independent database of bacterial exopolysaccharides (EPSs) providing access to detailed structural, taxonomic, growth conditions, functional properties, genetic, and bibliographic information for EPSs. It is freely available on the Internet as a website at http://www.epsdatabase.com. Several struc...

Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on liga...

Mammalian glycosaminoglycans are linear complex polysaccharides comprising heparan sulfate, heparin, dermatan sulfate, chondroitin sulfate, keratan sulfate and hyaluronic acid. They bind to numerous proteins and these interactions mediate their biological activities. GAG-protein interaction data reported in the literature are curated mostly in Matr...

Bacterial adhesion to human epithelia via lectins constitutes a therapeutic opportunity to prevent infection. Specifically, BambL (the lectin from Burkholderia ambifaria) is implicated in cystic fibrosis, where lectin-mediated bacterial adhesion to fucosylated lung epithelia is suspected to play an important role. We have employed structure-based v...

Glyco3D is a portal for structural glycobiology of several interlinked databases that is covering the three-dimensional features of monosaccharides, disaccharides, oligosaccharides, polysaccharides, glycosyltransferases, lectins, monoclonal antibodies, and glycosaminoglycan-binding proteins. Collection of annotated NMR data of bioactive oligosaccha...

This chapter offers a general background for researchers embarking in glycoscience to grasp the evolution and present status of the nomenclature(s) and representation(s) of glycans and complex carbohydrates. The availability of high-performance computing and the application of data mining are opening new paths to discovery. The field of structural...

Synchrotron radiation is the most versatile way to explore biological materials in different states: monocrystalline, polycrystalline, solution, colloids and multiscale architectures. Steady improvements in instrumentation have made synchrotrons the most flexible intense X-ray source. The wide range of applications of synchrotron radiation is comme...

Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respirat...

Within the family of plant cell wall polysaccharides rhamnogalacturonans I are the most diverse and structurally complex members. In the present study we characterize the 3-dimensional structures and dynamic features of the constituents of RG-I along MD trajectories. It is demonstrated that extended threefold helical structure of the rhamnogalactur...

Polysaccharides form the most abundant and diverse family of biopolymers. With several hundreds of known examples, they offer a great diversity of chemical structures ranging from simple linear homopolymers to branched heteropolymers, having repeating units that consist of up to octasaccharides. Polysaccharides may also be branched, which is a uniq...

Understanding the dynamics of protein-ligand interactions, which lie at the heart of host-pathogen recognition, represents a crucial step to clarify the molecular determinants implicated in binding events, as well as to optimize the design of new molecules with therapeutic aims. Over the last decade, advances in complementary biophysical and spectr...

Histo-blood group epitopes are fucosylated branched oligosaccharides with well-defined conformations in solution that are recog-nized by receptors, such as lectins from pathogens. We report here the results of a series of experimental and computational en-deavours revealing the unusual distortion of histo-blood group antigens by bacterial and funga...

Introduction aux biotechnologies en santé présente un panorama des différents types de biotechnologies devenues incontournables dans le domaine de la santé, qu’elles soient actuellement sur le marché ou en cours de développement .Après un rappel historique des évolutions et des découvertes scientifiques et un point sur l’apport prépondérant de l’in...

The present study reports a comprehensive NMR characterization and a systematic conformational sampling of the conformational preferences of 170 glycan moieties of glycosphingolipids as produced in large scale quantities by bacterial fermentation. These glycans span across a variety of families including the blood group antigens (A, B & O), core st...

The present work describes, in a detailed way, a family of databases covering the three-dimensional features of monosaccharides, disaccharides, oligosaccharides, polysaccharides, glycosyltransferases, lectins, monoclonal antibodies against carbohydrates, and glycosaminoglycan-binding proteins. These databases have been developed with non-proprietar...

The third variable region (V3 peptide) of the HIV-1 gp120 is a major immunogenic domain of HIV-1. Controlling the formation of the immunologically active conformation is a crucial step to the rational design of full synthetic candidate vaccines. Herein, we present the modulation and stabilisation of either the α-helix or β-strand conformation of th...

Because of their ubiquitous functions in deciphering the structural information encoded in glycoconjugates at the cell surface, lectins have been the focus of many structural investigations. The 3D-lectin database aims at classifying threedimensional structural features of lectins of all origins. Information about protein fold, oligomerization stat...

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of c...

A molecular visualization program tailored to deal with the range of 3D structures of complex carbohydrates and polysaccharides, either alone or in their interactions with other biomacromolecules, has been developed using advanced technologies elaborated by the video games industry. All the specific structural features displayed by the simplest to...

This paper describes an update of POLYS, the POLYSaccharide builder, for generating three-dimensional structures of polysaccharides and complex carbohydrates [1]. POLYS is written in portable ANSI C and is now released under an open source license. Using this software, complex branched carbohydrate structures and polysaccharides can be constructed...