Syllabus: BIOL 7290 Fall 2006
"Glycobiology" Biochemistry of Complex Carbohydrates
Instructor: Roger A. Laine, Professor of Biochemistry
(Depts. Of Biological Sciences, and Chemistry), and Adjunct Professor, Entomology)
Contacts: rogerlaine@gmail.com
cell phone 268-3052(easiest)
lab 578-4691
fax 578-4695
Office Hours: 1:30-2:30 T (otherwise by appointment): 512 Choppin Hall
Class time and Room: 2:40-5:30, Tureaud 117
Text: No Text required: Readings from current and classic literature.
Brief: A large number of novel differentiation markers, cell surface receptors, specific cell adhesion molecules are specified by complex carbohydrates. The outside surfaces of all prokaryotic and eukaryotic plasma membranes are covered with a carbohydrate-rich complex surface called the “Glycocalyx”. Members of compounds attached and peripheral to the membrane are glycolipids and glycoproteins. A number of these kinds of compounds are involved in cell adhesion, cell signaling, antigenic recognition, and other structure-specific biological recognition events. The ABO blood group system is an example. Gram negative prokaryotes have an additional lipopolysaccharide membrane which also contains a glycocalyx. All serological types are based on these structures. Aberrant forms of these compounds are associated with tumor differentiation, tumor antigens, for another example. A large number of drugs in development are sugar structures. The chemical diversity of this major class of biochemicals is much higher than possible in either proteins or nucleic acids, the latter of which is a polysaccharide linked by phosphate groups. No biochemists education is complete without an introduction to this major area of R&D.
Structure of the course and review:
Structure of the course: There will be 2 weeks of didactics and assigned papers to bring the class up to speed in structure, analytical techniques, and the nomenclature and stereochemistry of complex carbohydrates. During these first 2 weeks we will review common sugar structures and nomenclature of glucose, galactose, mannose, hexosamine, sialic acid, neuraminic acid, gluconic acid, glucuronic acid, and the terms aldose, ketose, anomeric configuration, acetal, ketal, hemiacetal, linkage position, glycoprotein, glycolipid, glycosaminoglycan, peptidoglycan,lipopolysaccharide and other verbiage and concepts common to the field, a part of the biochemical vocabulary to which you have already been introduced in prerequisite courses. We will consider the potential in these structures for biological information, including binding proteins.
STUDENT PRESENTATIONS:
Following the first 2 weeks, the class will comprise assigned student presentations using Powerpoint, Keynote or other presentation software. We will utilize current and classic literature representing important biomedical areas of “glycobiology”, topics of which are listed below. During these classes of 2.5 hours (50 minutes times 3 = 150 minutes, or 2 hours, 30 minutes), we will take 2 hours of class time for student presentations, and 30 minutes for discussions, elaborations of the topics, and questions.
For student presentations: use about 40-50 minutes for the talk, beginning with about 20 minutes of Historical review of the subject, chemical structures of relevant carbohydrates, biological activity, and for the last 20-30 minutes show data from one or more published paper(s) and results (with a critical assessment of experimental approach, results, data and conclusions of the authors) You can choose, with my consent, to describe the experiments in detail of one or more recent papers in the field or from a classic paper. Most days, 2 students will present, and we will allot time for discussion, and elaboration of the subject matter.
A review presentation on a lab computer (510 Choppin Hall) will be required 2 days before the class or earlier. This will be critiqued, corrected if necessary, there may be requested additions, and there may be another review required the day before the class presentation to allow adequate time to make a finished presentation .
A number of suggested topics are listed below for selected student presentations, although this is not meant to be comprehensive. You may trade topics, ask for special topics of particular interest, and suggest topics desired for presentations. The key will be the research approach to the subject, and especially, strategies and thinking related to experimentation to solve biochemical problems.
If more than one student signs up for a topic we will have a negotiation
for a decision on an assignment of parts of the topic.
The Instructor will help each student with sources for information and literature regarding each presentation. These will be provided as websites, links, literature, patents, etc., usually by email communication.
The Final Version of the Presentation will be emailed to me the night before the presentation, so I have it in the Morning.
The student will come to the class with his/her presentation burned on a CD, and will have emailed me the final version the day before the class. Upload to PAWS
Topics list: This list is for choices of topics by students for presentation, and obviously, not all of these topics will fit within a one semester course. It is also not all-inclusive. The list of possible topics can be incremented.
Carbohydrates and Cancer Therapy: Angiogenesis, tumor antigens, immunotherapy.
1. “Group B” streptococcal polysaccharide (GBS antiangiogenesis toxin)
a. Anti-angiogenesis and solid tumor cancer therapeutics,
b. Recovery of spinal cord injury, and prevention of scar formation.
c. Vaccine against solid tumor cancers by immunization with GB59
2. Melanoma and GM3 ganglioside therapy
3. T-cell antigens and failed human therapy after successful lower primate tests
Lectins: non-immune carbohydrate-specific binding proteins:
1. Selectins and antagonists and the inflammatory response (3 presentations)
a. L-selectin, P-selectin, E-selectin, specificity for cell types and ligands
b. Antibody against P-selectin soluble selectin approaches
c. structure-activity relationships, carbohydrate ligands and analogs.
2. Galectins, galactose binding lectins in differentiation, Cancer
3. Siglecs: Family of sialic acid binding lectins important in signaling
4. Plant lectins, blood group determination, specificities, uses in diagnostics for blood types and cell surface antigens,
5. Bacterial lectins, Arthropod lectins
Bacterial carbohydrate cell surface polymers
a. peptidoglycan, related ß-lactam antibiotics, lysozymes, mutanolysins, biosynthesis
pathway including polyisoprenoid carriers.
b. lipopolysaccharides: Core structure, biosynthesis, endotoxin activity
c. bacterial diagnostics based on cell wall, catalytically disabled lysozymes
d. colominic acids, molecular mimicry of polysialic acids in developing brain,
meningitis,
e. N-acetyl heparosan, heparin analogs, hyaluronic acid, Sialyl-Lewis antigens,
f. bacterial mimicry of Homo sapiens structures.
g. dextran sucrase and streptococcal extracellular polymerization mechanisms - Relationship to tooth plaque.
h. Helicobacter pylorus, Campylobacter jejunum, cell surface receptor determinants, relation to gastric ulcers, campylobacter jejunum, duodenal ulcers, molecular mimicry.
Tuberculosis, Leprosy, mycobacterial anergic polysaccharides, Mycobacterial cell surfaces
a. phenolic glycolipids
b. lipoarabinomannan
c. cord factors, virulence factors in tuberculosis, leprosy
i. pathways of trehalose synthesis as potential targets of pharmacology.
Carbohydrate-specific protein receptors in biomedical systems
1. human urinary tract infections and the galactose determinant for e.coli binding:
2. porcine-human organ transplantation and the alpha-galactose determinant
(Swedish company cloning genetically altered pigs for human transplant
organs, describe evidence for human antibody to allograft determinants.)
4. Cholera toxin receptor and ganglioside structure
5. ganglioside binding proteins in myelin sheath, effects of knock out mice.
6. bacteriophage receptor sites and potential antibiotic therapy and diagnostics
(Is Arrowsmith therapy a current reality with modern technology?)
a. rhamnosidases
b. lysozymes
c. d-peptidases in carbohydrate polymer cross links
Plant Saccharide polymers:
Cellulose and non-cellulosic plant cell wall polymers,
hemicelluloses,
pectins,
biosynthesis, degradation by fungi and bacteria,
saccharide fragment signaling systems in plant pathogen resistance,
Fungal and arthropod polymers,.
a. chitin, glucans, cell wall structure, biosynthesis
b. Vibrio chitinoclastic system, strategy
c. fungal diagnostics systems based on cell wall (calcofluor, chitinase) patents,
applications to human fungal disease, “Eosinophilic Fungal RhinoSinusitis”Mayo Clinic
Human ABO blood groups, Lewis determinants, p blood types,
a. HEMPAS genetic disorder of carbohydrate transferases
b. En(a)- blood type,
c. MkMk blood type,
d. Glycophorins
e. Falciparum Malaria, carbohydrate and other receptors on human red cells,
mechanism of merozoite rophry invasion of red cell surface.
Phosphatidyl inositol carbohyhdrate protein anchors,, structure, biosynthesis
Genetic diseases of missing glycosylation enzymes.
a. Biosynthesis of N-linked glycoprotein saccharides,
b. O-linked N-acetylGlucosamines on intracellular proteins as signaling intermediates,
alternative sulfation of glycosylation sites
Knock-out mice for various glycosyl transferases, hydrolases, phenotypes
a. beta galNAc transferase and higher gangliosides knockout
b. Notch mutations in drosophila related to higher animal differentiation
c. Fringe mutations in drosophila
Seaweed polymers, agar-agar, alginates, structures, biosynthesis, degradation
Mammalian Connective Tissue and other Glycosaminoglycans
a. heparin, heparan sulfate
anticlotting active sites,
fibroblast growth factor control,
herpesvirus receptors.
E. Coli K12 and N-acetyl heparosan
b. dermatan sulfate, heparin cofactor II activity, structures
d. chondroitin sulfates, hyaluronic acid, structure of cartilage, link proteins,
e. bacterial polymers resembling polylactosamines in development,
f. erythrocyte cell surface structures,
g. fetal placental polysaccharide types,
h. effect on collagen binding in fibronectins, keratan sulfates
Molecular modelling of disaccharides and other oligosaccharides
Frontal affinity chromatography to find pharmacophores
Non Enzymatic Glycosylation - diabetes, aging
a. (Maillard reactions, cross link breakers) (
b. Alteon Corp, cross link inhibitors, cross link breakers, ALT711
Aminoglycoside antibiotics, function, structures, biosynthesis
Sweeteners, sugar receptor, sucralose (splenda), aspartame (equal), saccharins, sugar alcohols
Sugar Transport systems;
a. Glucose transport: Glut1-Glut9, mammals, bacteria. Mechanism, function, inhibitors (phloridzin)
b. Lac Permease, chitobiose permease
c. Phosphotransferase transporters
d. Transport of sugar nucleotides into Golgi for synthesis, genetic disorders of transport.
NOD system of receptors and chitin-oligosaccharide effectors for rhizobium nodulation of legumes
Carbohydrate-carbohydrate interactions, binding, recognition.
Influenza: Neuraminidase inhibitors (tamiflu), infectious cell binding (hemagglutinin, drugs in development)
Please make your requests by email for the various subjects, first come,
first choices, The Prof. will assign presentation dates. Each student will make
a number of presentations, depending on class size.
Class time and place may be changed by agreement of all students if some conflicts occur.
Grades will be based on quality of and effort spent on Student Presentations, questions, class discussions and the Final Exam.
FINAL EXAM:
The Final Exam will be a Research Proposal in NIH, USDA or NSF format. The first draft is due two weeks before scheduled final exam, reviewed within one week by Prof., and the adequately revised proposal after detailed critique will be due at the exam time on the published final exam date. These proposals will be based on any subject of “glycobiology”, based on any of the class presentations, or if on subjects not covered, topic to be discussed in advance with Prof. The proposal will be graded on the basis of originality, cogent research plan and significance.