Special Issue "Challenges in Glycan, Glycoprotein and Proteoglycan Research"
A special issue of Biomolecules (ISSN 2218-273X).
Deadline for manuscript submissions: closed (30 November 2012)
Prof. Dr. Hans Vliegenthart
Bijvoet Center, Division Bioorganic Chemistry, Utrecht University, Padualaan 8, NL 3584 CH Utrecht, The Netherlands
Phone: +3130 253 2168/2281
Interests: carbohydrates; glycoconjugates; unsaturated fatty acids; lipoxygenase and related enzymes
In the past decades Glycoscience has evolved tremendously. The progress that has been made in the analytical and synthetic aspects is spectacular. The introduction of high resolution NMR spectroscopy and Mass spectrometry has enabled the unravelling of the structure of glycans derived from glycoconjugates like glycoproteins, proteoglycans and glycolipids as well as of oligo- and polysaccharides. Improvements in the synthetic procedures, e.g., the development of solid state synthesis and of oligosaccharide synthesizers have rendered the synthesis of complex glycans possible in a reasonable period of time. Intriguing are the roles glycans can play at the molecular level in a large diversity of biological processes like normal and abnormal cell growth and development, recognition and interaction phenomena, adhesion of pathogens.
The biological features imply that the borders with (micro)biology, medicine, immunology, vaccines etc. have definitively been crossed. Many new challenges are waiting in the field.
To illustrate for the readers of “Biomolecules” the importance of Glycoscience as a multidisciplinary field of research, this special issue is intended to show the various aspects, possibilities, applications and challenges of glycans and related compounds.
We look forward to reading your contributions,
Prof. Dr. Hans Vliegenthart
Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.
Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed Open Access quarterly journal published by MDPI.
Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.
Biomolecules 2012, 2(3), 389-414; doi:10.3390/biom2030389
Received: 2 August 2012; in revised form: 6 September 2012 / Accepted: 18 September 2012 / Published: 24 September 2012| Download PDF Full-text (2103 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 415-434; doi:10.3390/biom2040415
Received: 23 August 2012; in revised form: 17 September 2012 / Accepted: 25 September 2012 / Published: 8 October 2012| Download PDF Full-text (642 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 435-466; doi:10.3390/biom2040435
Received: 29 August 2012; in revised form: 27 September 2012 / Accepted: 30 September 2012 / Published: 11 October 2012| Download PDF Full-text (853 KB) | Download XML Full-text
Biomolecules 2012, 2(4), 467-482; doi:10.3390/biom2040467
Received: 2 September 2012; in revised form: 27 September 2012 / Accepted: 29 September 2012 / Published: 12 October 2012| Download PDF Full-text (502 KB) | Download XML Full-text
Article: Hyaluronidases Have Strong Hydrolytic Activity toward Chondroitin 4-Sulfate Comparable to that for Hyaluronan
Biomolecules 2012, 2(4), 549-563; doi:10.3390/biom2040549
Received: 13 October 2012; in revised form: 22 October 2012 / Accepted: 8 November 2012 / Published: 12 November 2012| Download PDF Full-text (613 KB) | Download XML Full-text
Article: Comparative Ultrastructure and Carbohydrate Composition of Gastroliths from Astacidae, Cambaridae and Parastacidae Freshwater Crayfish (Crustacea, Decapoda)
Biomolecules 2013, 3(1), 18-38; doi:10.3390/biom3010018
Received: 25 October 2012; in revised form: 27 November 2012 / Accepted: 28 November 2012 / Published: 21 December 2012| Download PDF Full-text (1427 KB) | Download XML Full-text
Article: Binding of Sperm to the Zona Pellucida Mediated by Sperm Carbohydrate-Binding Proteins is not Species-Specific in Vitro between Pigs and Cattle
Biomolecules 2013, 3(1), 85-107; doi:10.3390/biom3010085
Received: 28 November 2012; in revised form: 7 January 2013 / Accepted: 16 January 2013 / Published: 25 January 2013| Download PDF Full-text (984 KB) | Download XML Full-text
Article: Application of Metabolic 13C Labeling in Conjunction with High-Field Nuclear Magnetic Resonance Spectroscopy for Comparative Conformational Analysis of High Mannose-Type Oligosaccharides
Biomolecules 2013, 3(1), 108-123; doi:10.3390/biom3010108
Received: 19 December 2012; in revised form: 10 January 2013 / Accepted: 15 January 2013 / Published: 25 January 2013| Download PDF Full-text (682 KB) | Download XML Full-text
Biomolecules 2013, 3(1), 198-225; doi:10.3390/biom3010198
Received: 2 December 2012; in revised form: 28 January 2013 / Accepted: 14 February 2013 / Published: 21 February 2013| Download PDF Full-text (691 KB) | Download XML Full-text
Biomolecules 2013, 3(2), 270-286; doi:10.3390/biom3020270
Received: 20 February 2013; in revised form: 14 March 2013 / Accepted: 15 March 2013 / Published: 26 March 2013| Download PDF Full-text (1972 KB) | Supplementary Files
The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.
Type of Paper: Article
Title: Comparative ultrastructure and carbohydrate composition of gastroliths from Astacidea, Parastacidea and Cambaridea freshwater crayfish (Crustacea, Decapoda)
Author: Gilles Luquet
Affiliation: UMR 5561 CNRS Biogéosciences, Université de Bourgogne, 6 Boulevard Gabriel, 21000 Dijon, France; E-Mail: email@example.com
Abstract: Crustaceans have to cyclically replace their rigid exoskeleton for growing. Most of the crustaceans harden this external cuticle by a calcification process. Some decapods (mainly land crabs, lobsters and crayfish) elaborate calcium storage structures as a reservoir of calcium ions in their stomach wall, as so-called gastroliths. For a better understanding of the cyclic elaboration of these calcium carbonate structures, we studied the ultrastructure of gastroliths from different freshwater crayfish species by using a combination of microscopic and physical techniques. Sugars being molecules putatively involved in the elaboration process of these biomineralizations, we also determined their carbohydrate composition. This study was performed in an evolutionary perspective comparing the results obtained from 5 different crayfish species belonging to 3 families of the Astacoidea superfamily (Decapoda, Malacostraca): Astacus astacus and Pacifastacus leniusculus (Astacidae family), Cherax quadricarinatus (Parastacidae family), Orconectes limosus and Procambarus clarkii (Cambaridae family). We observed that all the gastroliths present a similar dense network of protein-chitin fibers from macro- to nanoscale, concentrically and transversally distributed, forming pockets of different sizes within which CaCO3 is precipitated as amorphous calcium carbonate. Nevertheless, they are not completely similar at the molecular level, notably as regards their carbohydrate composition. Beside glucosamine, the basic carbohydrate component of chitin, representing from 65 to 72% of the matrix sugar content, we also observed the presence of other sugars, some of which could be linked to proteoglycan components.
Type of Paper: Article
Title: Nucleocytoplasmic plant lectins and their interaction with glycan structures
Authors: Elke Fouquaert and Els J.M. Van Damme *
Affiliation Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, 9000 Ghent, Belgium; E-Mail: ElsJM.vanDamme@Ugent.be (E.J.M.V.D.)
Abstract: Plant lectins are a heterogeneous group of proteins, classified together based on their ability to recognize and specifically bind carbohydrate ligands. For a long time plant lectins were regarded as abundant proteins that are located in the vacuolar/extracellular compartment of the plant cell. In recent years evidence has accumulated that plants also synthesize small amounts of well-defined carbohydrate-binding proteins upon exposure to stresses like drought, high salt, wounding, treatment with some plant hormones or pathogen attack. In contrast to the 'classical’ plant lectins, this new class of inducible lectins is located in the cytoplasm and the nucleus. Hitherto, six families of such nucleocytoplasmic lectins have been identified in plants. This review will focus on the carbohydrate-binding properties of some of these inducible lectins. Taking into account that any physiological role of plant lectins most likely relies on their specific carbohydrate-binding activity and specificity, the discovery of these stress-related lectins provides strong evidence for the importance of protein-carbohydrate-interactions in plant cells.
Type of Paper: Article
Title: Hyaluronidases Preferentially Act on Chondroitin 4-sulfate Rather than Hyaluronan
Author: Shuhei Yamada
Affiliation: Laboratory of Proteoglycan Signaling and Therapeutics, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan; E-Mail: firstname.lastname@example.org
Abstract: Chondroitin sulfate (CS) chains are involved in the regulation of various biological processes. The cellular degradation of CS occurs predominantly in lysosomes. Following the fragmentation of polysaccharides by an endo-type hydrolase, the oligosaccharide products are degraded sequentially from the nonreducing end by exo-type glycosidases and sulfatases to liberate monosaccharide moieties. Hyaluronan (HA)-degrading enzymes, hyaluronidases, are considered to be the enzymes acting at the initial stage of the degradation process, because HA is similar in structure to nonsulfated CS, chondroitin (Chn). Although human hyaluronidase-1 (HYAL1) and testicular hyaluronidase (PH-20) can degrade not only HA but also CS, it has been considered that they digest CS to a limited extent and therefore that their preferred substrate is HA rather than CS. However, the distinct preference of the substrate recognition by hyaluronidases had not been determined. In this study, the hydrolytic activity of HYAL1 and PH-20 toward various substrates was quantitatively analyzed. HYAL1 depolymerized CS-A and HA to a similar extent. PH-20 also exhibited the activity to degrade CS-A, Chn, and HA to similar extents. CS is widely distributed from very primitive organisms to humans, whereas HA has been reported to be present only in vertebrates except for a mollusk. Therefore, the genuine substrate of HYAL1 appears to be CS rather than HA.
Type of Paper: Review
Title: Glycobiology Aspects of the Cell Envelope of the Periodontal Pathogen Tannerella forsythia
Authors: Gerald Posch, Gerhard Sekot, Valentin Friedrich, Zoë Megson, Paul Messner and Christina Schäffer
Affiliation: Department of NanoBiotechnology, NanoGlycobiology unit, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria; E-Mails: email@example.com (C.S.); firstname.lastname@example.org (P.M.)
Abstract: Cell surface glycosylation is an important element in defining the life of the periodontal pathogen Tannerella forsythia. The glycosylated surface (S-) layer of this bacterium is formed by co-assembly of two glycoproteins into a square 2D lattice with a spacing of 10.1±0.7 nm. The S-layer would be anchored to the cell wall by a novel type of rough lipopolysaccharide. The S-layer glycan is a so far unique oligosaccharide with the structure 4-Me-β-ManpNAcCONH2-(1→3)-[Pse5Am7Gc-(2→4)-]-β-ManpNAcA-(1→4)-[4-Me-α-Galp-(1→2)-]-α-Fucp-(1→4)-[-α-Xylp-(1→3)-]-β-GlcpA-(1→3)-[-β-Digp-(1→2)-]-α-Galp that is O-glycosidically linked to distinct serine and threonine residues within the (D)(S/T)(A/I/L/M/T/V) motif. Also several other Tannerella proteins are modified with that oligosaccharide, most of which are found in the outer membrane. This pinpoints to the presence of a general O-glycosylation system in this bacterium. It obviously impacts the life style of T. forsythia since a defined mutant carrying truncated S-layer glycans favors biofilm formation. While the S-layer has also been shown to delay the bacterium's recognition by the innate immune system, the contribution of glycosylation to this phenomenon is currently being assessed. This review focuses on a general protein O-glycosylation system in T. forsythia that is essential for creating a rich glycoproteome and which has possible relevance for the virulence of this bacterium.
Title: Decorin Content and Near Infrared Spectroscopy Analysis of Dried Collagenous Biomaterial Samples
Authors: Mila L. Aldema-Ramos 1*, Joan Carles Castell 2, Zerlina Muir 1, José Ma Adzet 2, Rosa Sabé 2 and Suzanne Schreyer 3
Affiliations: 1 U.S.Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid LN, Wyndmoor, PA 19038 USA; E-Mail: email@example.com
2 Asociación de Investigación de la Industria de Curtidos y Anexas (AIICA). Pla de la Massa, s/n, Igualada, Spain; E-Mail: Info@aiica.com
3 Chemometrics Applications, Thermo Fisher Scientific, Tewksbury, MA 01876, USA
Abstract: The efficient removal of proteoglycans, such as decorin, from the hide when processing it traditionally to leather is generally acceptable and beneficial for leather quality, especially for softness and flexibility. A patented waterless or acetone dehydration method that can generate a product similar to leather called Dried Collagenous Biomaterial (coined as BCD) was developed but has no clue on decorin removal efficiency. The Alcian Blue colorimetric technique was used to assay the sulfated glycosaminoglycan (sGAG) portion of decorin. The corresponding residual decorin content was correlated to the mechanical properties of the BCD samples and was comparable to the control leather made traditionally. The waterless dehydration and instantaneous chrome tanning process is a good eco-friendly alternative in transforming hides to leather because no additional harmful effects were observed when monitored by a non-invasive near infrared (NIR) spectroscopy technique.
Keywords: proteoglycan; decorin; sulfated glycosaminoglycan (sGAG); alcian blue; near infrared, Principal component analysis (PCA); leather quality; waterless dehydration; BCD
Title: Overcoming Challenges and Opening New Opportunities in Glycoproteomics.
Authors: Ten-Yang Yen and Bruce A. Macher
Affiliations: Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132 USA; E-Mail: firstname.lastname@example.org (B.A.M.)
Abstract: Protein glycosylation is a common post-translational modification in mammalian cells, and is altered in cells undergoing normal differentiation and carcinogenic transformation. Glycoproteins often serve as biomarkers and therapeutic targets for diseases, including cancer. Thus, identification of glycoproteins (glycoproteomics) has been a prime area of interest in the proteomics field. Since glycoproteins are expressed at relatively low levels in cells enrichment methods have been developed to improve their detection. Among these approaches is the capture of glycoproteins via oxidation of their glycan chains and covalently binding via hydrazide modified resins. Peptides released from the bound glycoproteins, usually via the action of trypsin, and N-linked glycopeptides, usually released via the action of PNGase F, are identified by LC/ESI-MS/MS. The enzyme, PNGase F, catalyzes the removal of N-linked glycans from glycoproteins and converts the glycosite Asn to Asp with a molecular weight increase of 0.984 Da. For a low resolution MS this mass difference could result in the misidentification of the monoisotopic peak vs. the 13C isotope peak. Thus, there is a significant chance for false positive glycosite identifications. In this study, we demonstrate that compared to a low resolution LTQ ion trap MS, a high resolution Q Exactive MS delivers a higher confidence identification of glycopeptides and their N-linked glycosylation sites.
Last update: 18 October 2012