DOCSLIB.ORG

The Structure and Function of the Starch Utilization System in Bacteroides Thetaiotaomicron

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Structure and Function of the Starch Utilization System in Bacteroides Thetaiotaomicron The Structure and Function of the Starch Utilization System in Bacteroides thetaiotaomicron by Elizabeth Ann Cameron A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Microbiology and Immunology) in the University of Michigan 2014 Doctoral Committee: Assistant Professor Eric C. Martens, Chair Assistant Professor Nicole M. Koropatkin Associate Professor Maria B. Sandkvist Associate Professor Mark A. Saper Professor Michele S. Swanson Acknowledgements I would first like to thank my thesis mentor Dr. Eric Martens for all of his support and guidance over the past five years. Thank you for pushing me to test my hypotheses from every angle and always listening to and valuing my ideas. You have always been my biggest advocate, which has given me the confidence to become a more independent scientist. I have been very lucky to have another fantastic mentor in Dr. Nicole Koropatkin. Nicole you have consistently challenged me to think about things in new and different ways and have taught me to always consider the bigger picture. I also thank you for your constant support in lab and in life. I would like to thank my committee members: Dr. Michele Swanson, Dr. Maria Sandkvist and Dr. Mark Saper. Thank you for your feedback and guidance. I would like to thank Michele Swanson in particular for her advice and support during my search for a post- doctoral position. I would like to thank all current and past members of the Martens and Koropatkin labs for your helpful advice and input over the years. I would particularly like to thank Nick Pudlo for helping me in countless ways and making the lab a fun place to work. I am grateful to the entire University of Michigan Microbiology and Immunology Department for the opportunity to complete my doctoral work at such a fantastic training institution. I would like to thank all of the faculty and staff for useful discussions and advice throughout my dissertation work. ii The work described here would not have been possible without funding from the University of Michigan Genetics Training Program, the Rackham Predoctoral Fellowship and the NIH. Finally, I would like to thank my family and friends for their love and support. In particular I am grateful to my husband, Jamie Cameron for his constant encouragement, patience and love. iii Table of Contents Acknowledgements ....................................................................................................................... ii List of Figures ............................................................................................................................... vi List of Tables .............................................................................................................................. viii Abstract ......................................................................................................................................... ix Chapter I: Introduction The human gut microbiota ...................................................................................................1 Bacterial glycan utilization shapes the gut microbiota ........................................................2 Glycan diversity in the human gut .......................................................................................9 Starch is an important dietary glycan .................................................................................12 The Bacteroides thetaiotaomicron Starch Utilization System ...........................................15 Expansion of Sus-like systems...........................................................................................19 Summary and chapter outline ............................................................................................21 Notes ..................................................................................................................................23 References ..........................................................................................................................23 Chapter II: Multi-domain carbohydrate binding proteins involved in Bacteroides thetaiotaomicron starch metabolism Abstract ..............................................................................................................................33 Introduction ........................................................................................................................34 Results and Discussion ......................................................................................................37 Prospectus ..........................................................................................................................59 Materials and methods .......................................................................................................63 Notes ..................................................................................................................................68 References ..........................................................................................................................69 Chapter III: Multi-functional nutrient binding proteins adapt human symbiotic bacteria for glycan competition in the gut Abstract ..............................................................................................................................73 Introduction ........................................................................................................................73 Results ................................................................................................................................77 Discussion ........................................................................................................................108 Materials and methods .....................................................................................................111 Notes ................................................................................................................................117 References ........................................................................................................................118 iv Chapter IV: Discussion Chapter Summary ............................................................................................................121 Similarities between the Bt Sus and other Sus-like systems ............................................125 Bacteroides glycan catabolism is involved in intestinal disease ......................................131 Future research .................................................................................................................136 Final conclusions .............................................................................................................139 References ........................................................................................................................140 Appendix I: Super-resolution imaging captures carbohydrate utilization dynamics in human gut symbionts Abstract ............................................................................................................................144 Introduction ......................................................................................................................145 Results ..............................................................................................................................148 Discussion ........................................................................................................................172 Materials and Methods .....................................................................................................175 Notes ................................................................................................................................180 References ........................................................................................................................180 v List of Figures Figure 1.1 Sources and chemical variation of glycans in the gut ..............................................................10 1.2 Starch is a structurally diverse carbohydrate ...........................................................................13 1.3 A model of the Bacteroides thetaiotaomicron Starch Utilization System ...............................16 2.1 SusE and SusF are exposed on the surface of Bt .....................................................................38 2.2 Ribbon diagram of SusE and SusF structures ..........................................................................42 2.3 Overlay of the N-terminal domains of SusF and SusE (predicted) .........................................45 2.4 Close-up view of the three starch-binding sites in SusF ..........................................................47 2.5 Close-up view of the starch-binding sites in SusE ...................................................................50 2.6 Protein binding to insoluble cornstarch ...................................................................................56 2.7 Model of Sus outer-membrane protein interactions with starch ..............................................61 3.1 Model of the Bt Starch utilization system (Sus) incorporating findings in this study .............76 3.2 SusC, D and G mutant growth curves on maltoOS .................................................................79 3.3 The SusD* protein is unable to bind starch, stable on the Bt surface, and leads to a phenotype distinct from wild-type
Load more

Recommended publications
  • Immunological Approaches to Biomass Characterization and Utilization
    REVIEW published: 28 October 2015 doi: 10.3389/fbioe.2015.00173 Immunological approaches to biomass characterization and utilization Sivakumar Pattathil1,2* , Utku Avci1,2 , Tiantian Zhang1 , Claudia L. Cardenas1† and Michael G. Hahn1,2 1 Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, 2 Oak Ridge National Laboratory, BioEnergy Science Center (BESC), Oak Ridge, TN, USA Plant biomass is the major renewable feedstock resource for sustainable generation of alternative transportation fuels to replace fossil carbon-derived fuels. Lignocellulosic cell walls are the principal component of plant biomass. Hence, a detailed understanding of plant cell wall structure and biosynthesis is an important aspect of bioenergy research. Cell walls are dynamic in their composition and structure, varying considerably among Edited by: Jason Lupoi, different organs, cells, and developmental stages of plants. Hence, tools are needed that University of Queensland, USA are highly efficient and broadly applicable at various levels of plant biomass-based bioen- Reviewed by: ergy research. The use of plant cell wall glycan-directed probes has seen increasing use Xu Fang, Shandong University, China over the past decade as an excellent approach for the detailed characterization of cell Arumugam Muthu, walls. Large collections of such probes directed against most major cell wall glycans are Council of Scientific and Industrial currently available worldwide. The largest and most diverse set of such probes consists Research, India of cell wall glycan-directed monoclonal antibodies (McAbs). These McAbs can be used *Correspondence: Sivakumar Pattathil as immunological probes to comprehensively monitor the overall presence, extractability, [email protected] and distribution patterns among cell types of most major cell wall glycan epitopes using †Present address: two mutually complementary immunological approaches, glycome profiling (an in vitro Claudia L.
    [Show full text]
  • Designing Tools for Studying the Dynamic Glycome John F
    Marshall University Marshall Digital Scholar Chemistry Faculty Research Chemistry Winter 12-2012 Designing Tools for Studying the Dynamic Glycome John F. Rakus Marshall University, [email protected] Follow this and additional works at: http://mds.marshall.edu/chemistry_faculty Part of the Organic Chemistry Commons Recommended Citation Rakus, J. F. (2012, December). Designing tools for studying the dynamic glycome. Invited Lecture at Sonoma State University, Rohnert Park, CA. This Presentation is brought to you for free and open access by the Chemistry at Marshall Digital Scholar. It has been accepted for inclusion in Chemistry Faculty Research by an authorized administrator of Marshall Digital Scholar. For more information, please contact [email protected]. NYU Cover Cells are primarily compose of three types of biomolecules Protein (50% dry weight) HeLa cell Nucleic acid (25% dry weight) Carbohydrate (10% dry weight) Carbohydrates are pervasive and involved in many cellular interactions Holgersson et al, Immuno Cell Biol, 2005 Laughlin et al, Science, 2008 Nucleic acids and proteins are synthesized with a defined template and dedicated polymerases Macromolecule: Nucleic acid Macromolecule: polypeptide Polymerase: DNA Pol or RNA Pol Polymerase: Ribosome Template: DNA strand Template: mRNA strand Glycan biosynthesis lacks a dedicated polymerase and genetic template Formation of Glc3Man9GlcNAc2-DolPP, an intermediate in the N-linked glycosylation pathway, requires 12 separate enzymes Essentially, each linkage in an oligosaccharide is
    [Show full text]
  • Combinatorial Glycomic Analyses to Direct Cazyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides
    microorganisms Article Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides Kristin E. Low 1 , Xiaohui Xing 1,2, Paul E. Moote 1,3, G. Douglas Inglis 1,3,4 , Sivasankari Venketachalam 5,6, Michael G. Hahn 5,6,7 , Marissa L. King 1, Catherine Y. Tétard-Jones 8, Darryl R. Jones 1, William G. T. Willats 8, Bogdan A. Slominski 9 and D. Wade Abbott 1,2,4,* 1 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; [email protected] (K.E.L.); [email protected] (X.X.); [email protected] (P.E.M.); [email protected] (G.D.I.); [email protected] (M.L.K.); [email protected] (D.R.J.) 2 Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada 3 Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada 4 Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada 5 Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; [email protected] (S.V.); [email protected] (M.G.H.) 6 Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA 7 Department of Plant Biology, University of Georgia, Athens, GA 30602, USA 8 School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK; [email protected] (C.Y.T.-J.); [email protected] (W.G.T.W.) 9 Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; [email protected] * Correspondence: [email protected] Received: 30 September 2020; Accepted: 20 November 2020; Published: 29 November 2020 Abstract: Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and lignin.
    [Show full text]
  • The N-Glycome Regulates the Endothelial-To-Hematopoietic Transition
    bioRxiv preprint doi: https://doi.org/10.1101/602912; this version posted August 6, 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. Title: The N-Glycome regulates the endothelial-to-hematopoietic transition Authors: Dionna M. Kasper1, 2, 4, Jared Hintzen1, 2, 4, Yinyu Wu1, 2, 4, Joey J. Ghersi1, 2, 4, Hanna K. Mandl1, 5 2, 4, Kevin E. Salinas1, 2, 4, William Armero1, 2, 4, Zhiheng He1, 2, 4, Ying Sheng7, Yixuan Xie7, Daniel W. Heindel5, Eon Joo Park3, 4, William C. Sessa3, 4, Lara K. Mahal5,6, Carlito Lebrilla7, Karen K. Hirschi1, 2, 4, 8*, Stefania Nicoli1,2,3,4* Affiliations: 10 1Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA 2Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA 15 3 Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA 4Vascular Biology & Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520, USA 20 5Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, NY 10003, USA 6Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada 25 7Department of Chemistry, University of California, Davis, CA 95616 8Developmental Genomics Center, Cell Biology Department, University of Virginia School of Medicine, Charlottesville, VA 22908 30 * Correspondence to: [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/602912; this version posted August 6, 2020.
    [Show full text]
  • Handbook of Polysaccharides
    Handbook of Polysaccharides Toolbox for Polymeric sugars Polysaccharide Review I 2 Global Reach witzerland - taad lovakia - Bratislava Synthetic laboratories Synthetic laboratories Large-scale manufacture Large-scale manufacture Distribution hub Distribution hub apan - Tokyo Sales office United Kingdom - Compton India - Chennai Synthetic laboratories Sales office United tates - an iego Distribution hub Distribution hub China - Beijing, inan, uzhou outh Korea - eoul Synthetic laboratories Sales office Large-scale manufacture Distribution hub Table of contents Section Page Section Page 1.0 Introduction 1 6.2 Examples of Secondary & Tertiary Polysaccharide Structures 26 About Biosynth Carbosynth 2 6.2.1 Cellulose 26 Product Portfolio 3 6.2.2 Carrageenan 27 Introduction 4 6.2.3 Alginate 27 2.0 Classification 5 6.2.4 Xanthan Gum 28 3.0 Properties and Applications 7 6.2.5 Pectin 28 4.0 Polysaccharide Isolation and Purification 11 6.2.6 Konjac Glucomannan 28 4.1 Isolation Techniques 12 7.0 Binary & Ternary Interactions Between Polysaccharides 29 4.2 Purification Techniques 12 7.1 Binary Interactions 30 5.0 Polysaccharide Structure Determination 13 7.2 Ternary Interactions 30 5.1 Covalent Primary Structure 13 8.0 Polysaccharide Review 31 5.1.1 Basic Structural Components 13 Introduction 32 5.1.2 Monomeric Structural Units and Substituents 13 8.1 Polysaccharides from Higher Plants 32 5.2 Linkage Positions, Branching & Anomeric Configuration 15 8.1.1 Energy Storage Polysaccharides 32 5.2.1 Methylation Analysis 16 8.1.2 Structural Polysaccharides 33 5.2.2
    [Show full text]
  • Three-Dimensional Structures of Carbohydrates and Where to Find Them
    International Journal of Molecular Sciences Review Three-Dimensional Structures of Carbohydrates and Where to Find Them Sofya I. Scherbinina 1,2,* and Philip V. Toukach 1,* 1 N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia 2 Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia * Correspondence: [email protected] (S.I.S.); [email protected] (P.V.T.) Received: 26 September 2020; Accepted: 16 October 2020; Published: 18 October 2020 Abstract: Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed. Keywords: carbohydrate; spatial structure; model build; database; web-tool; glycoinformatics; structure validation; PDB glycans; structure visualization; molecular modeling 1. Introduction Knowledge of carbohydrate spatial (3D) structure is crucial for investigation of glycoconjugate biological activity [1,2], vaccine development [3,4], estimation of ligand-receptor interaction energy [5–7] studies of conformational mobility of macromolecules [8], drug design [9], studies of cell wall construction aspects [10], glycosylation processes [11], and many other aspects of carbohydrate chemistry and biology. Therefore, providing information support for carbohydrate 3D structure is vital for the development of modern glycomics and glycoproteomics.
    [Show full text]
  • A Site-Specific Map of the Human Plasma Glycome and Its Age And
    www.nature.com/scientificreports OPEN A site‑specifc map of the human plasma glycome and its age and gender‑associated alterations Alexander A. Merleev1, Dayoung Park2,3, Yixuan Xie3, Muchena J. Kailemia3, Gege Xu3, L. Renee Ruhaak3,4, Kyoungmi Kim5, Qiuting Hong3, Qiongyu Li3, Forum Patel1, Yu‑Jui Yvonne Wan6, Alina I. Marusina1, Iannis E. Adamopoulos7,8, Nelvish N. Lal1, Anupum Mitra5, Stephanie T. Le1, Michiko Shimoda1, Guillaume Luxardi1, Carlito B. Lebrilla3,9,10* & Emanual Maverakis1* Alterations in the human glycome have been associated with cancer and autoimmunity. Thus, constructing a site‑specifc map of the human glycome for biomarker research and discovery has been a highly sought‑after objective. However, due to analytical barriers, comprehensive site‑specifc glycoprofling is difcult to perform. To develop a platform to detect easily quantifable, site‑specifc, disease‑associated glycan alterations for clinical applications, we have adapted the multiple reaction monitoring mass spectrometry method for use in glycan biomarker research. The adaptations allow for highly precise site‑specifc glycan monitoring with minimum sample prep. Using this technique, we successfully mapped out the relative abundances of the most common 159 glycopeptides in the plasma of 97 healthy volunteers. This plasma glycome map revealed 796 signifcant (FDR < 0.05) site‑ specifc inter‑protein and intra‑protein glycan associations, of which the vast majority were previously unknown. Since age and gender are relevant covariants in biomarker research, these variables were also characterized. 13 glycopeptides were found to be associated with gender and 41 to be associated with age. Using just fve age‑associated glycopeptides, a highly accurate age prediction model was constructed and validated (r2 = 0.62 ± 0.12).
    [Show full text]
  • Quantitative Secretome and Glycome of Primary Human Adipocytes During
    Lim et al. Clinical Proteomics 2014, 11:20 http://www.clinicalproteomicsjournal.com/content/11/1/20 CLINICAL PROTEOMICS RESEARCH Open Access Quantitative secretome and glycome of primary human adipocytes during insulin resistance Jae-Min Lim1,2,5, Edith E Wollaston-Hayden1,3, Chin Fen Teo1,3, Dorothy Hausman4 and Lance Wells1,2,3* Abstract Adipose tissue is both an energy storage depot and an endocrine organ. The impaired regulation of the secreted proteins of adipose tissue, known as adipocytokines, observed during obesity contributes to the onset of whole-body insulin resistance and the pathobiology of type 2 diabetes mellitus (T2DM). In addition, the global elevation of the intracellular glycosylation of proteins by O-linked β-N-acetylglucosamine (O-GlcNAc) via either genetic or pharmacological methods is sufficient to induce insulin resistance in both cultured cells and animal models. The elevation of global O-GlcNAc levels is associated with the altered expression of many adipocytokines. We have previously characterized the rodent adipocyte secretome during insulin sensitive and insulin resistant conditions. Here, we characterize and quantify the secretome and glycome of primary human adipocytes during insulin responsive and insulin resistant conditions generated by the classical method of hyperglycemia and hyperinsulinemia or by the pharmacological manipulation of O-GlcNAc levels. Using a proteomic approach, we identify 190 secreted proteins and report a total of 20 up-regulated and 6 down-regulated proteins that are detected in both insulin resistant conditions. Moreover, we apply glycomic techniques to examine (1) the sites of N-glycosylation on secreted proteins, (2) the structures of complex N- and O-glycans, and (3) therelativeabundanceofcomplexN-andO-glycans structures in insulin responsive and insulin resistant conditions.
    [Show full text]
  • Immunoglobulin G Glycome Composition in Transition from Pre-Menopause to Menopause
    medRxiv preprint doi: https://doi.org/10.1101/2021.04.10.21255252; this version posted April 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . 1 Immunoglobulin G glycome composition in transition from pre-menopause to menopause 2 3 Domagoj Kifer1, Helena Deriš2, Ana Cindrić2, Tea Petrović2, Ana Cvetko1, Irena Trbojević- 4 Akmačić2, Louise Newson3, Tim Spector4, Cristina Menni4, and Gordan Lauc1,2 5 6 7 1Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb 10000, Croatia 8 2Genos Glycoscience Research Laboratory, Zagreb 10000, Croatia 9 3Newson Health Menopause & Wellbeing Centre, Church Street Stratford-Upon-Avon 10 CV37 6HB, UK 11 4Department of Twin Research and Genetic Epidemiology, King’s College London, 12 Westminster Bridge Road, SE17EH London, UK 13 14 15 NOTE: This preprint reports new research that has not been certified1 by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2021.04.10.21255252; this version posted April 17, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license . 16 Abstract 17 Background 18 Glycosylation of immunoglobulin G (IgG) is an important regulator of the immune system 19 and its changes are believed to be a significant contributor to inflammaging.
    [Show full text]
  • UDP-Glucose Pyrophosphorylase 2, a Regulator of Glycogen Synthesis and Glycosylation, Is Critical for Pancreatic Cancer Growth
    UDP-glucose pyrophosphorylase 2, a regulator of glycogen synthesis and glycosylation, is critical for pancreatic cancer growth Andrew L. Wolfea, Qingwen Zhoub, Eneda Toskac, Jacqueline Galeasa, Angel A. Kua,d, Richard P. Kochee, Sourav Bandyopadhyaya,d, Maurizio Scaltritic,f, Carlito B. Lebrillab,g,h, Frank McCormicka,i,1,2, and Sung Eun Kima,1,2,3,4 aHelen Diller Comprehensive Cancer Center, University of California, San Francisco, CA 94158; bDepartment of Chemistry, University of California, Davis, CA 95616; cHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065; dBioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158; eCenter for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065; fDepartment of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065; gDepartment of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616; hFoods for Health Institute, University of California, Davis, CA 95616; and iNational Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701 Contributed by Frank McCormick, June 28, 2021 (sent for review February 26, 2021; reviewed by Adrian L. Harris and Alec Kimmelman) UDP-glucose pyrophosphorylase 2 (UGP2), the enzyme that synthe- We further characterize two regulatory functions of UGP2 in sizes uridine diphosphate (UDP)-glucose, rests at the convergence of PDAC cells: first, that
    [Show full text]
  • CONSIDERATION of GLYCOSIDIC TORSION ANGLE PREFERENCES and CH/Π INTERACTIONS in PROTEIN-CARBOHYDRATE DOCKING by Anita Karen Nive
    CONSIDERATION OF GLYCOSIDIC TORSION ANGLE PREFERENCES AND CH/π INTERACTIONS IN PROTEIN-CARBOHYDRATE DOCKING by Anita Karen Nivedha (Under the direction of Robert J. Woods) ABSTRACT Carbohydrates play a pivotal role in various life processes including energy metabolism, storage, immune recognition, transportation, signaling and biosynthesis. In these roles, they often interact with other integral components of the living system such as proteins and lipids. An understanding of how these molecules interact can further our knowledge of crucial biological processes, and begins with the knowledge of the three-dimensional structures of these complexes. However, owing to challenges involved in crystallizing oligosaccharide structures, theoretical modeling methods such as molecular docking are often used to predict how oligosaccharides interact with protein receptors. But, docking programs have generalized scoring functions which often produce unnatural oligosaccharide conformations during docking. In this thesis, we present two approaches to improve protein-carbohydrate docking by accounting for specific intra- and intermolecular interaction energies relating to carbohydrates, which are not currently dealt with by existing docking methodologies. In the first approach, we developed a set of Carbohydrate Intrinsic (CHI) energy functions in order to account for intramolecular energies of carbohydrate ligands primarily determined by the conformations of glycosidic torsion angles connecting individual saccharides. This work resulted in the development of Vina-Carb (incorporation of the CHI energy functions within the scoring function of AutoDock Vina), which significantly improved the conformations of oligosaccharide binding mode predictions. In the second approach, we developed a scoring function by fitting a mathematical model to data from literature describing the energy contributed by CH/π interactions.
    [Show full text]
  • Determination of Glycoside Hydrolase Specificities During Hydrolysis of Plant Cell Walls Using Glycome Profiling
    Lawrence Berkeley National Laboratory Recent Work Title Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. Permalink https://escholarship.org/uc/item/0z0563wg Journal Biotechnology for biofuels, 10(1) ISSN 1754-6834 Authors Walker, Johnnie A Pattathil, Sivakumar Bergeman, Lai F et al. Publication Date 2017 DOI 10.1186/s13068-017-0703-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Walker et al. Biotechnol Biofuels (2017) 10:31 DOI 10.1186/s13068-017-0703-6 Biotechnology for Biofuels RESEARCH Open Access Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling Johnnie A. Walker1,2†, Sivakumar Pattathil3,4†, Lai F. Bergeman1,2, Emily T. Beebe1,2, Kai Deng5,6, Maryam Mirzai3,4, Trent R. Northen5,7, Michael G. Hahn3,4 and Brian G. Fox1,2* Abstract Background: Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine solu- ble sugar products of their reactions. Results: Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant bio- mass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses.
    [Show full text]