Glycan-Binding Proteins
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Targeted Metabolic Labeling of Yeast N-Glycans with Unnatural Sugars
Targeted metabolic labeling of yeast N-glycans with unnatural sugars Mark A. Breidenbacha, Jennifer E. G. Gallagherb, David S. Kingc, Brian P. Smarta, Peng Wua,2, and Carolyn R. Bertozzia,b,c,d,1 aDepartments of Chemistry; bMolecular and Cell Biology; and cHoward Hughes Medical Institute, University of California, Berkeley, CA 94720; and dThe Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Edited by David A. Tirrell, California Institute of Technology, Pasadena, CA, and approved December 23, 2009 (received for review September 30, 2009) Metabolic labeling of glycans with synthetic sugar analogs has and mass spectrometric analyses of proteins displaying the nonna- emerged as an attractive means for introducing nonnatural chemi- tural chemical functionality (5, 6). cal functionality into glycoproteins. However, the complexities of While existing glycan labeling methodology is suitable for stud- glycan biosynthesis prevent the installation of nonnatural moieties ies that require only stochastic insertion of analogs at low levels, at defined, predictable locations within glycoproteins at high levels the technique is inadequate for applications in which specific of incorporation. Here, we demonstrate that the conserved monosaccharides must be reliably targeted for metabolic replace- N-acetyglucosamine (GlcNAc) residues within chitobiose cores of ment. For example, high-efficiency and predictable installation of N-glycans in the model organism Saccharomyces cerevisiae can sugar analogs could dramatically facilitate biophysical studies of be specifically targeted for metabolic replacement by unnatural glycoprotein structure and function via site-specific introduction sugars. We introduced an exogenous GlcNAc salvage pathway into of fluorophores and heavy atoms. Unfortunately, site-specific me- yeast, allowing cells to metabolize GlcNAc provided as a supple- tabolic labeling of glycans is hindered by multiple factors. -
High Affinity Biomolecular Interactions That Can Mediate Binding of Pathogenic Bacteria to Host Cells
Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells Christopher J. Daya,1, Elizabeth N. Tranb, Evgeny A. Semchenkoa, Greg Trama, Lauren E. Hartley-Tassella, Preston S. K. Nga, Rebecca M. Kinga, Rachel Ulanovskya, Sarah McAtamneya, Michael A. Apicellac, Joe Tiralongoa, Renato Moronab,2, Victoria Korolika,2, and Michael P. Jenningsa,1,2 aInstitute for Glycomics, Griffith University Gold Coast Campus, Gold Coast, QLD 4222, Australia; bSchool of Biological Sciences, Department of Molecular and Cellular Biology, University of Adelaide, Adelaide, SA 5005, Australia; and cDepartment of Microbiology, University of Iowa, Iowa City, IA 52242 Edited by Rino Rappuoli, GSK Vaccines, Siena, Italy, and approved November 10, 2015 (received for review November 3, 2014) Cells from all domains of life express glycan structures attached to Interestingly, there are specific reports of several bacteria lipids and proteins on their surface, called glycoconjugates. Cell-to- expressing truncated surface polysaccharides and oligosaccharides cell contact mediated by glycan:glycan interactions have been that are significantly less adherent than wild-type equivalents considered to be low-affinity interactions that precede high- (10, 11), or that their adherence can be blocked by extracted affinity protein–glycan or protein–protein interactions. In several LOS/LPS (10), indicating a role for bacterial surface glycans in pathogenic bacteria, truncation of surface glycans, lipooligosac- adherence to host cells. This decreased adherence of rough strains charide (LOS), or lipopolysaccharide (LPS) have been reported to or blocking of adherence using the free lipooligosaccharide (LOS)/ significantly reduce bacterial adherence to host cells. Here, we lipopolysaccharide (LPS) in both cell-based and animal infection show that the saccharide component of LOS/LPS have direct, models has been noted in a range of Gram-negative bacteria in- high-affinity interactions with host glycans. -
Metabolomics Analysis of Skeletal Muscles from FKRP-Deficient Mice
www.nature.com/scientificreports OPEN Metabolomics Analysis of Skeletal Muscles from FKRP-Defcient Mice Indicates Improvement After Gene Received: 21 March 2019 Accepted: 28 June 2019 Replacement Therapy Published: xx xx xxxx Charles Harvey Vannoy 1, Victoria Leroy1, Katarzyna Broniowska2 & Qi Long Lu1 Muscular dystrophy-dystroglycanopathies comprise a heterogeneous and complex group of disorders caused by loss-of-function mutations in a multitude of genes that disrupt the glycobiology of α-dystroglycan, thereby afecting its ability to function as a receptor for extracellular matrix proteins. Of the various genes involved, FKRP codes for a protein that plays a critical role in the maturation of a novel glycan found only on α-dystroglycan. Yet despite knowing the genetic cause of FKRP-related dystroglycanopathies, the molecular pathogenesis of disease and metabolic response to therapeutic intervention has not been fully elucidated. To address these challenges, we utilized mass spectrometry- based metabolomics to generate comprehensive metabolite profles of skeletal muscle across diseased, treated, and normal states. Notably, FKRP-defcient mice elicit diverse metabolic abnormalities in biomarkers of extracellular matrix remodeling and/or aging, pentoses/pentitols, glycolytic intermediates, and lipid metabolism. More importantly, the restoration of FKRP protein activity following AAV-mediated gene therapy induced a substantial correction of these metabolic impairments. While interconnections of the afected molecular mechanisms remain unclear, -
A Systematic Review on the Implications of O-Linked Glycan Branching and Truncating Enzymes on Cancer Progression and Metastasis
cells Review A Systematic Review on the Implications of O-linked Glycan Branching and Truncating Enzymes on Cancer Progression and Metastasis 1, 1, 1 1,2,3, Rohitesh Gupta y, Frank Leon y, Sanchita Rauth , Surinder K. Batra * and Moorthy P. Ponnusamy 1,2,* 1 Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68105, USA; [email protected] (R.G.); [email protected] (F.L.); [email protected] (S.R.) 2 Fred and Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 681980-5900, USA 3 Department of Pathology and Microbiology, UNMC, Omaha, NE 68198-5900, USA * Correspondence: [email protected] (S.K.B.); [email protected] (M.P.P.); Tel.: +402-559-5455 (S.K.B.); +402-559-1170 (M.P.P.); Fax: +402-559-6650 (S.K.B. & M.P.P.) Equal contribution. y Received: 21 January 2020; Accepted: 12 February 2020; Published: 14 February 2020 Abstract: Glycosylation is the most commonly occurring post-translational modifications, and is believed to modify over 50% of all proteins. The process of glycan modification is directed by different glycosyltransferases, depending on the cell in which it is expressed. These small carbohydrate molecules consist of multiple glycan families that facilitate cell–cell interactions, protein interactions, and downstream signaling. An alteration of several types of O-glycan core structures have been implicated in multiple cancers, largely due to differential glycosyltransferase expression or activity. Consequently, aberrant O-linked glycosylation has been extensively demonstrated to affect biological function and protein integrity that directly result in cancer growth and progression of several diseases. -
Agency Response Letter GRAS Notice No. GRN 000675
. Janet Oesterling Novozymes North America, Inc. 77 Perry Chapel Church Road Franklinton, NC 27525 Re: GRAS Notice No. GRN 000675 Dear Ms. Oesterling: The Food and Drug Administration (FDA, we) completed our evaluation of GRN 000675. We received the notice, dated October 10, 2016, that you submitted in accordance with the agency’s proposed regulation, proposed 21 CFR 170.36 (62 FR 18938; April 17, 1997; Substances Generally Recognized as Safe (GRAS); the GRAS proposal) on July 17, 2016, and filed it on October 14, 2016. We received amendments containing clarifying information on February, 22, 2017 and March 09, 2017. FDA published the GRAS final rule on August 17, 2016 (81 FR 54960), with an effective date of October 17, 2016. As GRN 000675 was pending on the effective date of the GRAS final rule, we requested some additional information consistent with the format and requirements of the final rule. We received an amendment responding to this request on October 24, 2016. The subject of the notice is xylanase enzyme preparation produced by Trichoderma reesei carrying a xylanase gene from Talaromyces leycettanus (xylanase enzyme preparation). The notice informs us of the view of Novozymes North America, Inc. (Novozymes) that xylanase enzyme preparation is GRAS, through scientific procedures, for use as an enzyme at levels up to 48.33 mg Total Organic Solids (TOS) per kg raw material in brewing, cereal beverage processing, baking, and processing of cereal grains such as corn, wheat, barley, and oats. Commercial enzyme preparations that are used in food processing typically contain an enzyme component that catalyzes the chemical reaction as well as substances used as stabilizers, preservatives, or diluents. -
Novel Xylan Degrading Enzymes from Polysaccharide Utilizing Loci of Prevotella Copri DSM18205
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Novel xylan degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205 Javier A. Linares-Pastén1*, Johan Sebastian Hero2, José Horacio Pisa2, Cristina Teixeira1, Margareta Nyman3, Patrick Adlercreutz1, M. Alejandra Martinez2,4, Eva Nordberg Karlsson1** 1Biotechnology, Dept of Chemistry, Lund University, P.O.Box 124, 221 00 Lund, Sweden. 2Planta Piloto de Procesos Industriales Microbiológicos PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, San Miguel de Tucumán, Argentina. 3 Dept Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden. 4Facultad de Ciencias Exactas y Tecnología, UNT. Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina. Corresponding authors: *e-mail: [email protected] ** e-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Prevotella copri DSM18205 is a bacterium, classified under Bacteroidetes that can be found in the human gastrointestinal tract (GIT). The role of P. copri in the GIT is unclear, and elevated numbers of the microbe have been reported both in dietary fiber- induced improvement in glucose metabolism but also in conjunction with certain inflammatory conditions. -
Exogenous Enzymes As Zootechnical Additives in Animal Feed: a Review
catalysts Review Exogenous Enzymes as Zootechnical Additives in Animal Feed: A Review Brianda Susana Velázquez-De Lucio 1, Edna María Hernández-Domínguez 1, Matilde Villa-García 1, Gerardo Díaz-Godínez 2, Virginia Mandujano-Gonzalez 3, Bethsua Mendoza-Mendoza 4 and Jorge Álvarez-Cervantes 1,* 1 Cuerpo Académico Manejo de Sistemas Agrobiotecnológicos Sustentables, Posgrado Biotecnología, Universidad Politécnica de Pachuca, Zempoala 43830, Hidalgo, Mexico; [email protected] (B.S.V.-D.L.); [email protected] (E.M.H.-D.); [email protected] (M.V.-G.) 2 Centro de Investigación en Ciencias Biológicas, Laboratorio de Biotecnología, Universidad Autónoma de Tlaxcala, Tlaxcala 90000, Tlaxcala, Mexico; [email protected] 3 Ingeniería en Biotecnología, Laboratorio Biotecnología, Universidad Tecnológica de Corregidora, Santiago de Querétaro 76900, Querétaro, Mexico; [email protected] 4 Instituto Tecnológico Superior del Oriente del Estado de Hidalgo, Apan 43900, Hidalgo, Mexico; [email protected] * Correspondence: [email protected]; Tel.: +52-771-5477510 Abstract: Enzymes are widely used in the food industry. Their use as a supplement to the raw Citation: Velázquez-De Lucio, B.S.; material for animal feed is a current research topic. Although there are several studies on the Hernández-Domínguez, E.M.; application of enzyme additives in the animal feed industry, it is necessary to search for new Villa-García, M.; Díaz-Godínez, G.; enzymes, as well as to utilize bioinformatics tools for the design of specific enzymes that work in Mandujano-Gonzalez, V.; certain environmental conditions and substrates. This will allow the improvement of the productive Mendoza-Mendoza, B.; Álvarez-Cervantes, J. -
Biomolecule Purification, Characterization, and Analyses Biomolecule Purification, Characterization, and Analyses Characterization, Purification, Biomolecule
Biomolecule Purification, Characterization, and Analyses Biomolecule Purification, Characterization, Analyses and “Quality is always about having a consistent product.” ~ Aoife Hayes, Technical Service Manager, Wexford, Ireland 239 Benchmarking, Method Development, and Troubleshooting: MassPREP Contents Peptide Standard .......................................................273 Phosphorylated Peptide Standards and Sample Preparation Kits..........................273 Innovative HPLC, UHPLC, Delta-Pak HPLC and UHPLC and UPLC Chemistry Consumables Columns ..............................................................................274 for Bioseparations ....................................................241 RapiGest SF Surfactant for Protein Digestions .....................................................275 Amino Acids ................................................................242 AccQ•Tag Ultra Derivatization Protein Separations ...............................................276 Reaction ..............................................................................242 ACQUITY UPLC SEC System Solution ..276 AccQ•Tag Amino Acid Analysis Turn Key Solution .......................................................243 Waters Insulin HMWP HPLC and UHPLC Columns .............................................278 Glycans and Glycoproteins ..............................247 XBridge Protein BEH SEC, 125Å, HILIC for Released 200Å, and 450Å Columns and N-Glycan Analysis .....................................................248 Protein Standard Test -
Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application
biomolecules Review Microbial Beta Glucosidase Enzymes: Recent Advances in Biomass Conversation for Biofuels Application 1, , 2 3 1 4, Neha Srivastava * y, Rishabh Rathour , Sonam Jha , Karan Pandey , Manish Srivastava y, Vijay Kumar Thakur 5,* , Rakesh Singh Sengar 6, Vijai K. Gupta 7,* , Pranab Behari Mazumder 8, Ahamad Faiz Khan 2 and Pradeep Kumar Mishra 1,* 1 Department of Chemical Engineering and Technology, IIT (BHU), Varanasi 221005, India; [email protected] 2 Department of Bioengineering, Integral University, Lucknow 226026, India; [email protected] (R.R.); [email protected] (A.F.K.) 3 Department of Botany, Banaras Hindu University, Varanasi 221005, India; [email protected] 4 Department of Physics and Astrophysics, University of Delhi, Delhi 110007, India; [email protected] 5 Enhanced Composites and Structures Center, School of Aerospace, Transport and Manufacturing, Cranfield University, Bedfordshire MK43 0AL, UK 6 Department of Agriculture Biotechnology, College of Agriculture, Sardar Vallabhbhai Patel, University of Agriculture and Technology, Meerut 250110, U.P., India; [email protected] 7 Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia 8 Department of Biotechnology, Assam University, Silchar 788011, India; [email protected] * Correspondence: [email protected] (N.S.); vijay.Kumar@cranfield.ac.uk (V.K.T.); [email protected] (V.K.G.); [email protected] (P.K.M.); Tel.: +372-567-11014 (V.K.G.); Fax: +372-620-4401 (V.K.G.) These authors have equal contribution. y Received: 29 March 2019; Accepted: 28 May 2019; Published: 6 June 2019 Abstract: The biomass to biofuels production process is green, sustainable, and an advanced technique to resolve the current environmental issues generated from fossil fuels. -
Mapping the Transglycosylation Relevant Sites of Cold-Adapted -D
International Journal of Molecular Sciences Article Mapping the Transglycosylation Relevant Sites of Cold-Adapted β-d-Galactosidase from Arthrobacter sp. 32cB Maria Rutkiewicz 1,2,* , Marta Wanarska 3 and Anna Bujacz 1 1 Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924 Lodz, Poland; [email protected] 2 Macromolecular Structure and Interaction, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany 3 Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland; [email protected] * Correspondence: [email protected] Received: 30 June 2020; Accepted: 24 July 2020; Published: 28 July 2020 Abstract: β-Galactosidase from Arthrobacter sp. 32cB (ArthβDG) is a cold-adapted enzyme able to catalyze hydrolysis of β-d-galactosides and transglycosylation reaction, where galactosyl moiety is being transferred onto an acceptor larger than a water molecule. Mutants of ArthβDG: D207A and E517Q were designed to determine the significance of specific residues and to enable formation of complexes with lactulose and sucrose and to shed light onto the structural basis of the transglycosylation reaction. The catalytic assays proved loss of function mutation E517 into glutamine and a significant drop of activity for mutation of D207 into alanine. Solving crystal structures of two new mutants, and new complex structures of previously presented mutant E441Q enables description of introduced changes within active site of enzyme and determining the importance of mutated residues for active site size and character. -
Synthesis of Three Advanced Biofuels from Ionic Liquid-Pretreated Switchgrass Using Engineered Escherichia Coli
Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli Gregory Bokinskya,b, Pamela P. Peralta-Yahyaa,b, Anthe Georgea,c, Bradley M. Holmesa,c, Eric J. Steena,d, Jeffrey Dietricha,d, Taek Soon Leea,e, Danielle Tullman-Erceka,f, Christopher A. Voigtg, Blake A. Simmonsa,c, and Jay D. Keaslinga,b,d,e,f,1 aJoint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, CA 94608; bQB3 Institute, University of California, San Francisco, CA 94158; cSandia National Laboratories, P.O. Box 969, Livermore, CA 94551; dDepartment of Bioengineering, and ePhysical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; fDepartment of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720; and gDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 Edited by Alexis T. Bell, University of California, Berkeley, CA, and approved November 2, 2011 (received for review May 2, 2011) One approach to reducing the costs of advanced biofuel production Unfortunately, several challenges must be overcome before from cellulosic biomass is to engineer a single microorganism to lignocellulose can be considered an economically competitive both digest plant biomass and produce hydrocarbons that have feedstock for biofuel production. One of the more significant chal- the properties of petrochemical fuels. Such an organism would lenges is the need for large quantities of glycoside hydrolase (GH) require pathways for hydrocarbon -
Enzyme Applications in Pulp and Paper Industry
Enzyme Applications in Pulp and Paper: An Introduction to Applications Dr. Richard Venditti Associate Professor - Director of Graduate Programs Department of Wood and Paper Science Biltmore Hall Room 1204 Raleigh NC 27695-8005 Tel. (919) 515-6185 Fax. (919) 515-6302 Email: [email protected] Slides courtesy of Phil Hoekstra. Endo-Beta 1,4 Xylanase Enzymes • Are proteins that catalyze chemical reactions • Biological cells need enzymes to perform needed functions • The starting molecules that enzymes process are called substrates and these are converted to products Endo-Beta 1,4 Xylanase Cellulase enzyme which acts on cellulose substrate to make product of glucose. Endo-Beta 1,4 Xylanase Enzymes • Are extremely selective for specific substrates • Activity affected by inhibitors, pH, temperature, concentration of substrate • Commercial enzyme products are typically mixtures of different enzymes, the enzymes often complement the activity of one another Endo-Beta 1,4 Xylanase Types of Enzymes in Pulp and Paper and Respective Substrates • Amylase --- starch • Cellulase --- cellulose fibers • Protease --- proteins • Hemicellulases(Xylanase) ---hemicellulose • Lipase --- glycerol backbone, pitch • Esterase --- esters, stickies • Pectinase --- pectins Endo-Beta 1,4 Xylanase Enzyme Applications in Pulp and Paper • Treat starches for paper applications • Enhanced bleaching • Treatment for pitch • Enhanced deinking • Treatment for stickies in paper recycling • Removal of fines • Reduce refining energy • Cleans white water systems • Improve