the glyco world the glyco world saccharides, glycosides & glycans saccharides, glycosides &...

The Glyco WorldThe Glyco Worldsaccharides, glycosides & glycanssaccharides, glycosides & glycans


• What’s the (sugar) buzz?What’s the (sugar) buzz?• Carbohydrates: The language of glycoscienceCarbohydrates: The language of glycoscience• The glycosidic bond and glycan nomenclatureThe glycosidic bond and glycan nomenclature• Major carbohydrate classes: sugars, polysaccharides, Major carbohydrate classes: sugars, polysaccharides,

oligosaccharides and glycoconjugates oligosaccharides and glycoconjugates • Definitions and resourcesDefinitions and resources



http://www.youtube.com/watch?v=v9j-g0qspdk

““Understanding the structures Understanding the structures and functions of glycans is and functions of glycans is central to understanding biology.” central to understanding biology.”

“… “… Glycoscience researchers have Glycoscience researchers have developed a knowledge base that developed a knowledge base that can be used to address many of can be used to address many of today’s major research problems. today’s major research problems. When combined with current tools, When combined with current tools, it is a powerful resource to better it is a powerful resource to better understand human, plant, and understand human, plant, and microbial biology..” microbial biology..”

National Academies Press (2012)

Scanning electron microscopy of C. neoformans yeast cells.Van Duin et al. (2004) Antimicrobial Agents and Chemotherapy 48:2014

Light microscopy micrograph of Cryptococcus neoformans

Steenbergen et al. (2003) Microbes and Infection 5:667

What if a MAJOR cell component was invisible by standard microscopy?

Light microscopy micrograph of Cryptococcus neoformans capsule delineated by India ink. The inner circle represents the fungal cell, with the wide outer circle being the capsule.Steenbergen et al. (2003) Microbes and Infection 5:667

Electron microscopic thin section ofEscherichia coli K1Amako et al. (1988) J Bacteriol 170:4960

Unique to yeast – NO!

Electron microscopic thin section ofKlebsiella pneumoniaeAmako et al. (1988) J Bacteriol 170:4960

The Eukaryotic Cell SurfaceThe Eukaryotic Cell Surface

Tiny sugar “decorations”..added as an afterthought

Lodish, et al. (1995) Molecular Cell Biology 3rd ed.Lodish, et al. (1995) Molecular Cell Biology 3rd ed.

??

The “glycocalyx” surrounding a fibroblast – glycans stained blackThe “glycocalyx” surrounding a fibroblast – glycans stained black

lipid bilayerlipid bilayer

fibroblastfibroblast

extracellularextracellular

intracellularintracellular

Martinez-Palomo, A., et al. Cancer Res. 29, 925-937, 1969

Eukaryotic cell surfaceEukaryotic cell surface

““Evolution has failed to generate a [single] Evolution has failed to generate a [single] living cell devoid of surface glycosylation” living cell devoid of surface glycosylation” - -

A. VarkiA. Varki

““Every eukaryotic cell is covered with a dense and complex array Every eukaryotic cell is covered with a dense and complex array of glycans, which also feature prominently in extracellular matrix of glycans, which also feature prominently in extracellular matrix and secreted soluble molecules.” … in fact…and secreted soluble molecules.” … in fact…

Ajit Varki, “Perspectives on the Future of Glycobiology,” Athens, GA, 14-Mar-2011

Tropical Forest

Canopy

Tropical Forest

Canopy

Cohen & Varki (2010) OMICS 4:455

Ajit Varki, “Perspectives on the Future of Glycobiology,” Athens, GA, 14-Mar-2011

fibroblastfibroblast

Martinez-Palomo, A., et al. Cancer Res. 29, 925-937, 1969

The Cell SurfaceThe Cell Surface

Textbook image Real imageTextbook image Real image

Rosetta Stone, British MuseumRosetta Stone, British Museum


Glycobiology = Language (semiotics)Glycobiology = Language (semiotics)

Carbohydrates – the building blocks of Glycobiology

(CH2O)n = “carbo” “hydrate”

Generalized KetoseGeneralized Ketose

Generalized AldoseGeneralized Aldose

glucoseglucose fructosefructose

Generalized KetoseGeneralized KetoseGeneralized AldoseGeneralized Aldose


GlycoaldehydeGlycoaldehyde

Enantiomers: Enantiomers: mirror images of each other that are not superimposable.mirror images of each other that are not superimposable.

Diastereomers: Diastereomers: stereoisomers that are not enantiomers. stereoisomers that are not enantiomers.


Fischer projectionFischer projection

D-glyceraldehyde

L-glyceraldehydeD-glyceraldehyde

EnantiomersEnantiomers

* *

* Highest numbered asymmetric carbon = reference carbon

DiasteriomersDiasteriomers


* *

Enantiomers & DiasteriomersEnantiomers & Diasteriomers


* *

**

carbonsasymmetric

carbons

diaster-

iomers

diasteriomers &

enantiomers

3 1 0 2

4 2 2 4

5 3 4 8

6 4 8 16

Essentials of Glycobiology Second Edition

* *

** * *

* epimers: differ in only stereogenic center

Monosaccharides equilibrate between open chain and ring forms.Monosaccharides equilibrate between open chain and ring forms.Two ring forms (anomeric configurations) are possible, Two ring forms (anomeric configurations) are possible, αα and and ββ

Taylor & Drickamer (2011) Introduction to Glycobiology, 3rd edition

Lee & Lee (1999) J Chinese Chem Soc 46:283-291

C

C

C

C

H

HH

H

O

O O

O

O

CH OH

C

O

CHO H

C

Anomeric

carbon

Ring oxygen

Same direction as reference carbon = αDifferent direction from reference carbon = β

Determining anomeric configurationDetermining anomeric configuration

[PDB]

Monosaccharide conformation – Chair configuationsMonosaccharide conformation – Chair configuations

Taylor & Drickamer (2006) Introduction to Glycobiology, 2nd edition

Seven eukaryotic sugars and their relationship to glucoseSeven eukaryotic sugars and their relationship to glucose


Two important terminal eukaryotic sugarsTwo important terminal eukaryotic sugars


Glycan properties for molecular recognition and binding energyGlycan properties for molecular recognition and binding energyGlycan properties for molecular recognition and binding energyGlycan properties for molecular recognition and binding energy

Glucose Galactose

Sialic Acid

Mannose


When a glycosidic bond is formed the anomeric configuration is “locked”When a glycosidic bond is formed the anomeric configuration is “locked”

Glycosidic bonds link sugars togetherGlycosidic bonds link sugars together


(lactose) CCRC

http://glycam.ccrc.uga.edu/ccrc/pages/3dspt.html

Nomenclature:Nomenclature:

-Name the non-reducing (left-most) sugar (Gal)-Name the non-reducing (left-most) sugar (Gal) -Name the anomeric configuration ( -Name the anomeric configuration (ββ)) -Name the anomeric carbon number (1) -Name the anomeric carbon number (1) -Name the substituted carbon number (4) -Name the substituted carbon number (4) -Name the substituted sugar (Glc) -Name the substituted sugar (Glc)

RESULT: Gal RESULT: Gal ββ1-4 Glc1-4 Glc


NeuAc NeuAc α2-α2-3 Gal 3 Gal β1-β1-4 (Fuc 4 (Fuc α1-α1-3) GlcNAc3) GlcNAc

Nomenclature: Branches are placed in parenthesesNomenclature: Branches are placed in parentheses

Varki et al. (2009) Proteomics. 9:5398

Sugars, polysaccharides, Sugars, polysaccharides, oligosaccharides and glycoconjugatesoligosaccharides and glycoconjugates

Sugars, polysaccharides, Sugars, polysaccharides, oligosaccharides and glycoconjugatesoligosaccharides and glycoconjugates

• Simple mono- or disaccharides: often from plants or Simple mono- or disaccharides: often from plants or breakdown products of plant polysaccharides. breakdown products of plant polysaccharides. – Examples: glucose, sucrose (glucose Examples: glucose, sucrose (glucose αα1-1-22 fructose), maltose fructose), maltose

(Glc (Glc αα1-4 Glc), lactose (Gal 1-4 Glc), lactose (Gal ββ1-4 Glc).1-4 Glc).

• Polysaccharides: long polymers (linear or branched) of Polysaccharides: long polymers (linear or branched) of a single monosaccharidea single monosaccharide– Examples: Cellulose, amylose (starch), glycogen, chitinExamples: Cellulose, amylose (starch), glycogen, chitin

• Oligosaccharides: groups of monosaccharides (e.g. 3 Oligosaccharides: groups of monosaccharides (e.g. 3 or more) in linear or branched glycosidic linkageor more) in linear or branched glycosidic linkage– Examples: Sugars groups bound to proteins or lipids to form Examples: Sugars groups bound to proteins or lipids to form

glycoconjugates (see below)glycoconjugates (see below)

• GlycoconjugatesGlycoconjugates– Examples: Glycoproteins, glycolipids, proteoglycansExamples: Glycoproteins, glycolipids, proteoglycans

• Simple mono- or disaccharides: often from plants or Simple mono- or disaccharides: often from plants or breakdown products of plant polysaccharides. breakdown products of plant polysaccharides. – Examples: glucose, sucrose (glucose Examples: glucose, sucrose (glucose αα1-1-22 fructose), maltose fructose), maltose

(Glc (Glc αα1-4 Glc), lactose (Gal 1-4 Glc), lactose (Gal ββ1-4 Glc).1-4 Glc).

• Polysaccharides: long polymers (linear or branched) of Polysaccharides: long polymers (linear or branched) of a single monosaccharidea single monosaccharide– Examples: Cellulose, amylose (starch), glycogen, chitinExamples: Cellulose, amylose (starch), glycogen, chitin

• Oligosaccharides: groups of monosaccharides (e.g. 3 Oligosaccharides: groups of monosaccharides (e.g. 3 or more) in linear or branched glycosidic linkageor more) in linear or branched glycosidic linkage– Examples: Sugars groups bound to proteins or lipids to form Examples: Sugars groups bound to proteins or lipids to form

glycoconjugates (see below)glycoconjugates (see below)

• GlycoconjugatesGlycoconjugates– Examples: Glycoproteins, glycolipids, proteoglycansExamples: Glycoproteins, glycolipids, proteoglycans

Examples of polysaccharides: CelluloseExamples of polysaccharides: CelluloseExamples of polysaccharides: CelluloseExamples of polysaccharides: Cellulose

((ββ1-4 Glc 1-4 Glc ββ1-4 Glc)1-4 Glc)nn

Most abundant organic Most abundant organic compound on Earth. ~90% of compound on Earth. ~90% of cotton fiber, 50% of wood, cotton fiber, 50% of wood, 33% of all plant matter.33% of all plant matter.

Intra- and inter-strand hydrogen Intra- and inter-strand hydrogen bonding provides strengthbonding provides strength

http://en.wikipedia.org/wiki/Cellulose

Material sciences

Examples of polysaccharides: AmyloseExamples of polysaccharides: AmyloseExamples of polysaccharides: AmyloseExamples of polysaccharides: AmyloseLinear (amylose) and Linear (amylose) and branched (amylopectin) forms branched (amylopectin) forms are the carbohydrates of are the carbohydrates of starch. This major food source starch. This major food source is enzymatically broken down is enzymatically broken down to glucose during digestion…to glucose during digestion…

http://en.wikipedia.org/wiki/Amylopectin

((αα1-4 Glc 1-4 Glc αα1-4 Glc)1-4 Glc)nn

α1-6 Glc branches

…and during ethanol production

Examples of polysaccharides: GlycogenExamples of polysaccharides: GlycogenExamples of polysaccharides: GlycogenExamples of polysaccharides: Glycogen

http://en.wikipedia.org/wiki/Glycogen

Tissue storage form of Tissue storage form of glucose (primarily in the liver & glucose (primarily in the liver & muscle). “Animal Starch” – muscle). “Animal Starch” – same general structure as same general structure as plant starch, but more plant starch, but more branched & compact. Broken branched & compact. Broken down to glucose at need to down to glucose at need to quickly increase blood glucose quickly increase blood glucose levels.levels.

((αα1-4 Glc 1-4 Glc αα1-4 Glc)1-4 Glc)nn

α1-6 Glc branches

Examples of polysaccharides: ChitinExamples of polysaccharides: ChitinExamples of polysaccharides: ChitinExamples of polysaccharides: Chitin

((ββ1-4 GlcNAc 1-4 GlcNAc ββ1-4 GlcNAc)1-4 GlcNAc)nn

Among the most abundant of Among the most abundant of organic molecules on Earth, it organic molecules on Earth, it is the main component of the is the main component of the cell walls of fungi, the cell walls of fungi, the exoskeletons of arthropods exoskeletons of arthropods such as insects and such as insects and crustaceans (e.g., crabs, crustaceans (e.g., crabs, lobsters and shrimps).lobsters and shrimps).

http://en.wikipedia.org/wiki/Chitin

Rosetta Stone, British MuseumRosetta Stone, British Museum


Glycobiology = Language (semiotics)Glycobiology = Language (semiotics)

Oligosaccharides: Molecular diversity of glycansOligosaccharides: Molecular diversity of glycans

PolypeptidesPolypeptides GlycansGlycans

Building blocksBuilding blocks amino acidsamino acids monosaccharidesmonosaccharides

Number of different monomersNumber of different monomers 20 common20 common 9 common9 common

Linkage sites per monomerLinkage sites per monomer 11 3-43-4

Possible linkage configurationsPossible linkage configurations 11 22

Possible homodimer structuresPossible homodimer structures 11 6-86-8

Linkage modesLinkage modes linearlinear linear or branchedlinear or branched

HO

HO

O

HO

O

GalHO

OHO

HO

O

HO

O

GalHO

O

H2N C

Ala

OH

OH2N C

Ala

OH

O

Three different amino acids (Ala, Ser, Tyr) – 6 structuresThree different amino acids (Ala, Ser, Tyr) – 6 structures

Ala-Ser-TyrAla-Ser-TyrAla-Tyr-SerAla-Tyr-SerSer-Ala-TyrSer-Ala-TyrSer-Tyr-AlaSer-Tyr-AlaTyr-Ala-SerTyr-Ala-SerTyr-Ser-AlaTyr-Ser-Ala

Three different sugars (Glc, Gal, Man) – 1,056 structures …Three different sugars (Glc, Gal, Man) – 1,056 structures …

Man a1-4 Gal a1-3 Glc b1Man a1-6 Gal a1-3 Glc b1Man b1-2 Gal a1-3 Glc b1Man b1-3 Gal a1-3 Glc b1Man b1-4 Gal a1-3 Glc b1Man b1-6 Gal a1-3 Glc b1Man a1-2 Gal a1-4 Glc b1Man a1-3 Gal a1-4 Glc b1Man a1-4 Gal a1-4 Glc b1Man a1-6 Gal a1-4 Glc b1Man b1-2 Gal a1-4 Glc b1Man b1-3 Gal a1-4 Glc b1Man b1-4 Gal a1-4 Glc b1Man b1-6 Gal a1-4 Glc b1Man a1-2 Gal a1-6 Glc b1Man a1-3 Gal a1-6 Glc b1

Major Glycoconjugates of EukaryotesMajor Glycoconjugates of Eukaryotes

• GlycoproteinsGlycoproteins

• GlycolipidsGlycolipids

• ProteoglycansProteoglycans

What are:What are:

Glycobiology?Glycobiology?Glycosciences?Glycosciences?

Glycomics?Glycomics?

What are:What are:

Glycobiology?Glycobiology?Glycosciences?Glycosciences?

Glycomics?Glycomics?

GlycobiologyGlycobiologyThe study of the biological functions, structures, The study of the biological functions, structures, recognition and biosynthesis of recognition and biosynthesis of glycansglycans (sugar (sugar chains, saccharides) in the context of the chains, saccharides) in the context of the biological scaffolds to which they are attached biological scaffolds to which they are attached (e.g. glycolipids & glycoproteins).(e.g. glycolipids & glycoproteins).

GlycobiologyGlycobiologyThe study of the biological functions, structures, The study of the biological functions, structures, recognition and biosynthesis of recognition and biosynthesis of glycansglycans (sugar (sugar chains, saccharides) in the context of the chains, saccharides) in the context of the biological scaffolds to which they are attached biological scaffolds to which they are attached (e.g. glycolipids & glycoproteins).(e.g. glycolipids & glycoproteins).

GlycosciencesGlycosciencesGlycobiology & Glycochemistry, including…Glycobiology & Glycochemistry, including…

-Chemical synthesis-Chemical synthesis -Chemoenzymatic synthesis -Chemoenzymatic synthesis -Metabolic engineering -Metabolic engineering -Glycomimetics -Glycomimetics -Glycan conformation and structure -Glycan conformation and structure -Material Sciences -Material Sciences -Plant and bacterial polysaccharides -Plant and bacterial polysaccharides

GlycosciencesGlycosciencesGlycobiology & Glycochemistry, including…Glycobiology & Glycochemistry, including…

-Chemical synthesis-Chemical synthesis -Chemoenzymatic synthesis -Chemoenzymatic synthesis -Metabolic engineering -Metabolic engineering -Glycomimetics -Glycomimetics -Glycan conformation and structure -Glycan conformation and structure -Material Sciences -Material Sciences -Plant and bacterial polysaccharides -Plant and bacterial polysaccharides

GlycomicsGlycomics- Analytical glycosciences- Analytical glycosciences -Glycan bioinformatics -Glycan bioinformatics

““Glycome” – The total complement of glycansGlycome” – The total complement of glycans in a cell or organism in a cell or organism

GlycomicsGlycomics- Analytical glycosciences- Analytical glycosciences -Glycan bioinformatics -Glycan bioinformatics

““Glycome” – The total complement of glycansGlycome” – The total complement of glycans in a cell or organism in a cell or organism

Glycobiology resourcesGlycobiology resourcesGlycobiology resourcesGlycobiology resources

Oxford University Press, New YorkOxford University Press, New York Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. Content freely available at: Content freely available at: http://www.ncbi.nlm.nih.gov/books/NBK1908http://www.ncbi.nlm.nih.gov/books/NBK1908

http://glycam.ccrc.uga.edu/ccrc/pages/3dspt.html

the glyco world the glyco world saccharides, glycosides & glycans saccharides, glycosides &...

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