Perspectives in glycomics and lectin engineering.

This chapter would like to provide a short survey of the most promising concepts applied recently in analysis of glycoproteins based on lectins. The first part describes the most exciting analytical approaches used in the field of glycoprofiling based on integration of nanoparticles, nanowires, nanotubes, or nanochannels or using novel transducing platforms allowing to detect very low levels of glycoproteins in a label-free mode of operation. The second part describes application of recombinant lectins containing several tags applied for oriented and ordered immobilization of lectins. Besides already established concepts of glycoprofiling several novel aspects, which we think will be taken into account for future, more robust glycan analysis, are described including modified lectins, peptide lectin aptamers, and DNA aptamers with lectin-like specificity introduced by modified nucleotides. The last part of the chapter describes a novel concept of a glycocodon, which can lead to a better understanding of glycan-lectin interaction and for design of novel lectins with unknown specificities and/or better affinities toward glycan target or for rational design of peptide lectin aptamers or DNA aptamers.

[1]  W. Alley,et al.  Analytical glycobiology at high sensitivity: current approaches and directions , 2013, Glycoconjugate Journal.

[2]  Lakshmi Krishnamoorthy,et al.  Glycomic analysis: an array of technologies. , 2009, ACS chemical biology.

[3]  S. Ståhl,et al.  Affinity proteins and their generation , 2013 .

[4]  D. Jarvis,et al.  Letter to the Glyco-Forum: Effective glycoanalysis with Maackia amurensis lectins requires a clear understanding of their binding specificities , 2011 .

[5]  Massimo Di Giulio,et al.  An extension of the coevolution theory of the origin of the genetic code. , 2008 .

[6]  J. Švitel,et al.  Glycan and lectin microarrays for glycomics and medicinal applications , 2010, Medicinal research reviews.

[7]  Andrew G. Watts,et al.  Mechanism-Based Covalent Neuraminidase Inhibitors with Broad-Spectrum Influenza Antiviral Activity , 2013, Science.

[8]  Lupei Du,et al.  Selecting aptamers for a glycoprotein through the incorporation of the boronic acid moiety. , 2008, Journal of the American Chemical Society.

[9]  Jason J. Davis,et al.  Peptide aptamers in label-free protein detection: 2. Chemical optimization and detection of distinct protein isoforms. , 2009, Analytical chemistry.

[10]  S. Laurenson,et al.  Design and validation of a neutral protein scaffold for the presentation of peptide aptamers. , 2005, Journal of molecular biology.

[11]  Mubarak Ali,et al.  Carbohydrate-Mediated Biomolecular Recognition and Gating of Synthetic Ion Channels , 2013 .

[12]  Roger Brent,et al.  Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2 , 1996, Nature.

[13]  Anne Imberty,et al.  Electronic detection of lectins using carbohydrate-functionalized nanostructures: graphene versus carbon nanotubes. , 2012, ACS nano.

[14]  Chen-zhong Li,et al.  Detection and discrimination of alpha-fetoprotein with a label-free electrochemical impedance spectroscopy biosensor array based on lectin functionalized carbon nanotubes. , 2013, Talanta.

[15]  Peter H Seeberger,et al.  Optimization of localized surface plasmon resonance transducers for studying carbohydrate-protein interactions. , 2012, Analytical chemistry.

[16]  Jan Tkac,et al.  Peptide aptamers in label-free protein detection: 1. Characterization of the immobilized scaffold. , 2007, Analytical chemistry.

[17]  A. Libchaber,et al.  Emergence of a Code in the Polymerization of Amino Acids along RNA Templates , 2009, PloS one.

[18]  Richard D. Cummings,et al.  The repertoire of glycan determinants in the human glycome. , 2009, Molecular bioSystems.

[19]  Xiliang Luo,et al.  Electrical Biosensors and the Label Free Detection of Protein Disease Biomarkers , 2013 .

[20]  Hiroaki Tateno,et al.  Lectin microarrays: concept, principle and applications. , 2013, Chemical Society reviews.

[21]  Carla Oliveira,et al.  Recombinant lectins: an array of tailor-made glycan-interaction biosynthetic tools , 2013, Critical reviews in biotechnology.

[22]  G. Sánchez-Pomales,et al.  Recent Advances in Electrochemical Glycobiosensing , 2011 .

[23]  David F. Smith,et al.  Application of Microarrays for Deciphering the Structure and Function of the Human Glycome* , 2013, Molecular & Cellular Proteomics.

[24]  Fu-Hsiang Ko,et al.  Real-time and label-free detection of the prostate-specific antigen in human serum by a polycrystalline silicon nanowire field-effect transistor biosensor. , 2013, Analytical chemistry.

[25]  Jozef Nahalka Glycocodon theory--the first table of glycocodons. , 2012, Journal of theoretical biology.

[26]  J. Tkáč,et al.  Comparison of three distinct ELLA protocols for determination of apparent affinity constants between Con A and glycoproteins. , 2012, Colloids and surfaces. B, Biointerfaces.

[27]  David F. Smith,et al.  Shotgun Glycomics: A Microarray Strategy for Functional Glycomics , 2010, Nature Methods.

[28]  Lai-Xi Wang,et al.  A combined method for producing homogeneous glycoproteins with eukaryotic N-glycosylation , 2010, Nature chemical biology.

[29]  D. Burton,et al.  Highly Antigenically Diverse Viruses Broadly Neutralizing Antibodies Present New Prospects to Counter , 2012 .

[30]  J. Švitel,et al.  Lectinomics II. A highway to biomedical/clinical diagnostics. , 2009, Biotechnology advances.

[31]  Kenji Ikehara,et al.  A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis , 2002, Journal of Molecular Evolution.

[32]  Milan Mikula,et al.  Ultrasensitive impedimetric lectin based biosensor for glycoproteins containing sialic acid , 2012, Microchimica Acta.

[33]  Dan Schneider,et al.  Expanding the chemistry of DNA for in vitro selection. , 2010, Journal of the American Chemical Society.

[34]  Anil Wipat,et al.  Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant. , 2011, Protein engineering, design & selection : PEDS.

[35]  W. Yi,et al.  Overexpression and topology of bacterial oligosaccharyltransferase PglB. , 2010, Biochemical and biophysical research communications.

[36]  Ardemis A. Boghossian,et al.  Transduction of glycan-lectin binding using near-infrared fluorescent single-walled carbon nanotubes for glycan profiling. , 2011, Journal of the American Chemical Society.

[37]  Minyong Li,et al.  Carbohydrate recognition by boronolectins, small molecules, and lectins , 2009, Medicinal research reviews.

[38]  Michel H M Eppink,et al.  Alternative affinity tools: more attractive than antibodies? , 2011, The Biochemical journal.

[39]  S. Yokoyama,et al.  Generation of high-affinity DNA aptamers using an expanded genetic alphabet , 2013, Nature Biotechnology.

[40]  M. DeLisa,et al.  Expanding the glycoengineering toolbox: the rise of bacterial N-linked protein glycosylation. , 2013, Trends in biotechnology.

[41]  Chi-Huey Wong,et al.  Enzymes in the synthesis of glycoconjugates. , 2011, Chemical reviews.

[42]  J Christopher Love,et al.  Emergent properties of nanosensor arrays: applications for monitoring IgG affinity distributions, weakly affined hypermannosylation, and colony selection for biomanufacturing. , 2013, ACS nano.

[43]  H. Gabius,et al.  The Third Dimension of Reading the Sugar Code by Lectins: Design of Glycoclusters with Cyclic Scaffolds as Tools with the Aim to Define Correlations between Spatial Presentation and Activity , 2013, Molecules.

[44]  K. Khoo,et al.  BAD-lectins: boronic acid-decorated lectins with enhanced binding affinity for the selective enrichment of glycoproteins. , 2013, Analytical chemistry.

[45]  Jason J. Davis Engineering the bioelectronic interface : applications to analyte biosensing and protein detection , 2009 .

[46]  Jesús Jiménez-Barbero,et al.  From lectin structure to functional glycomics: principles of the sugar code. , 2011, Trends in biochemical sciences.

[47]  Carolyn R. Bertozzi,et al.  Essentials of Glycobiology , 1999 .

[48]  M. Strano,et al.  Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. , 2012, Chemical Society reviews.

[49]  Carolyn R. Bertozzi,et al.  Chemical Glycobiology , 2001, Science.

[50]  Guo-Jun Zhang,et al.  Label-free detection of carbohydrate-protein interactions using nanoscale field-effect transistor biosensors. , 2013, Analytical chemistry.

[51]  Juewen Liu,et al.  Functional nucleic acid sensors. , 2009, Chemical reviews.

[52]  L. Mahal,et al.  Fabrication of an oriented lectin microarray. , 2010, Chembiochem : a European journal of chemical biology.

[53]  Michaela Gebauer,et al.  Engineered protein scaffolds as next-generation antibody therapeutics. , 2009, Current opinion in chemical biology.

[54]  K. Nagashima,et al.  HIV-1 and microvesicles from T-cells share a common glycome, arguing for a common origin , 2009, Nature chemical biology.

[55]  I. Lazar,et al.  Glycoproteomics on the rise: Established methods, advanced techniques, sophisticated biological applications , 2013, Electrophoresis.

[56]  S. Tope,et al.  Aptamers as therapeutics , 2013 .

[57]  J. Kamerling,et al.  The Chemistry and Biology of Trypanosomal trans-Sialidases: Virulence Factors in Chagas Disease and Sleeping Sickness , 2011 .

[58]  R. Knight,et al.  RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code , 2009, Journal of Molecular Evolution.

[59]  Xiangqun Zeng,et al.  Carbohydrate–protein interactions and their biosensing applications , 2012, Analytical and Bioanalytical Chemistry.

[60]  Thomas Alava,et al.  Control of the graphene-protein interface is required to preserve adsorbed protein function. , 2013, Analytical chemistry.

[61]  Anne Imberty,et al.  Binding sugars: from natural lectins to synthetic receptors and engineered neolectins. , 2013, Chemical Society reviews.

[62]  B. Bany,et al.  Tumor necrosis factor receptor subfamily 9 (Tnfrsf9) gene is expressed in distinct cell populations in mouse uterus and conceptus during implantation period of pregnancy , 2011, Cell and Tissue Research.

[63]  Yan Liu,et al.  A Potent and Broad Neutralizing Antibody Recognizes and Penetrates the HIV Glycan Shield , 2011, Science.

[64]  L. Joshi,et al.  Glycobiomimics and glycobiosensors. , 2010, Biochemical Society transactions.

[65]  G. Mayer,et al.  Dressed for success – applying chemistry to modulate aptamer functionality , 2013 .

[66]  P. Parren,et al.  Anti-galactose-α-1,3-galactose IgE from allergic patients does not bind α-galactosylated glycans on intact therapeutic antibody Fc domains , 2011, Nature Biotechnology.

[67]  J. Furukawa,et al.  Recent Advances in Cellular Glycomic Analyses , 2013, Biomolecules.

[68]  Michael S Strano,et al.  Carbon nanotubes as optical biomedical sensors. , 2013, Advanced drug delivery reviews.

[69]  W. Hancock,et al.  Modulation of glycan detection on specific glycoproteins by lectin multimerization. , 2013, Analytical chemistry.

[70]  M. Aebi,et al.  Substrate specificity of bacterial oligosaccharyltransferase suggests a common transfer mechanism for the bacterial and eukaryotic systems. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[71]  N. Sharon,et al.  Lectins: Carbohydrate-Specific Proteins That Mediate Cellular Recognition. , 1998, Chemical reviews.

[72]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[73]  N. Sharon,et al.  Recombinant plant lectins and their mutants. , 2003, Methods in enzymology.

[74]  Lokesh Joshi,et al.  Glyco-biosensors: recent advances and applications for the detection of free and bound carbohydrates. , 2010, The Analyst.

[75]  Sergei Svarovsky,et al.  Label-free impedimetric detection of glycan-lectin interactions. , 2007, Analytical chemistry.

[76]  M. Eigen,et al.  The Hypercycle , 2004, Naturwissenschaften.

[77]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[78]  Lara K Mahal,et al.  New technologies for glycomic analysis: toward a systematic understanding of the glycome. , 2011, Annual review of analytical chemistry.

[79]  Andrei Yakovlev Mathematical Biology in Biology Direct , 2008, Biology Direct.

[80]  P. Conroy,et al.  Aberrant PSA glycosylation—a sweet predictor of prostate cancer , 2013, Nature Reviews Urology.

[81]  Ku-Lung Hsu,et al.  A simple strategy for the creation of a recombinant lectin microarray. , 2008, Molecular bioSystems.

[82]  Jan Tkac,et al.  Ultrasensitive impedimetric lectin biosensors with efficient antifouling properties applied in glycoprofiling of human serum samples. , 2013, Analytical chemistry.

[83]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[84]  J. Tkáč,et al.  Electrochemical lectin based biosensors as a label-free tool in glycomics , 2012, Microchimica Acta.

[85]  Radoslav Goldman,et al.  Glycoprotein Disease Markers and Single Protein-omics* , 2013, Molecular & Cellular Proteomics.

[86]  Milos V. Novotny,et al.  High-sensitivity analytical approaches for the structural characterization of glycoproteins. , 2013, Chemical reviews.

[87]  K. Ikehara Possible steps to the emergence of life: the [GADV]-protein world hypothesis. , 2005, Chemical record.

[88]  M. Ferens-Sieczkowska,et al.  Seminal plasma glycoproteins in male infertility and prostate diseases: is there a chance for glyco-biomarkers? , 2013, Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals.

[89]  Peter H Seeberger,et al.  Cantilever array sensors detect specific carbohydrate-protein interactions with picomolar sensitivity. , 2011, ACS nano.

[90]  Joachim O Rädler,et al.  Discrimination of Escherichia coli strains using glycan cantilever array sensors. , 2012, Nano letters.

[91]  Milan Mikula,et al.  Label-free detection of glycoproteins by the lectin biosensor down to attomolar level using gold nanoparticles. , 2013, Talanta.

[92]  Ron Diskin,et al.  HIV therapy by a combination of broadly neutralizing antibodies in humanized mice , 2012, Nature.

[93]  Shan X. Wang,et al.  Emerging protein array technologies for proteomics , 2013, Expert review of proteomics.

[94]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[95]  Ilaria Palchetti,et al.  Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. , 2012, Angewandte Chemie.

[96]  Peter Wiktor,et al.  NanoMonitor: a miniature electronic biosensor for glycan biomarker detection. , 2010, Nanomedicine.

[97]  Jozef Nahalka Quantification of Peptide Bond Types in Human Proteome Indicates How DNA Codons were Assembled at Prebiotic Conditions , 2011 .

[98]  Anne Imberty,et al.  Nanoelectronic detection of lectin-carbohydrate interactions using carbon nanotubes. , 2011, Nano letters.

[99]  P. Gemeiner,et al.  Lectinomics I. Relevance of exogenous plant lectins in biomedical diagnostics , 2009, Biologia.

[100]  Raz Jelinek,et al.  Carbohydrate biosensors. , 2004, Chemical reviews.

[101]  Chi‐Huey Wong,et al.  Fabrication of an oriented Fc-fused lectin microarray through boronate formation. , 2008, Angewandte Chemie.

[102]  F. Pontén,et al.  Correlations between RNA and protein expression profiles in 23 human cell lines , 2009, BMC Genomics.

[103]  Lianghai Hu,et al.  Aptamer in bioanalytical applications. , 2011, Analytical chemistry.

[104]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[105]  J. Reichert,et al.  A triumph for glyco-engineering , 2012 .

[106]  J. Paulson,et al.  Glycomics: an integrated systems approach to structure-function relationships of glycans , 2005, Nature Methods.

[107]  Maria D. L. Oliveira,et al.  Electrochemical evaluation of lectin-sugar interaction on gold electrode modified with colloidal gold and polyvinyl butyral. , 2008, Colloids and surfaces. B, Biointerfaces.

[108]  L. Mahal,et al.  Orientation of GST-tagged lectins via in situ surface modification to create an expanded lectin microarray for glycomic analysis. , 2011, Molecular bioSystems.

[109]  Shohei Koide,et al.  High-affinity single-domain binding proteins with a binary-code interface , 2007, Proceedings of the National Academy of Sciences.

[110]  R. Ley,et al.  The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine , 2011, Science.