Tryptophan, sugars, inflammation

Tryptophan binds basic amino acids, sugars and alkaloids. Examples of tryptophan binding include glycosidase, importins, arginine transporters and cytokine receptors. Molecules that mimic and interfere with these interactions are important drugs.

I have always been interested in nuts, bolts and mechanisms. That has progressed from Erector sets and Lincoln Logs, to chemistry sets and microscopes, and ultimately to computational models. So when I think about inflammation and disease, I think in terms of how molecules interact to produce the symptoms of disease. I seek the molecular basis of inflammation, and how proteins and small molecules interact to make people sick. In most of the interactions that I study, that means how proteins bind to carbohydrates, e.g. heparin, and how alkaloids, e.g. curcumin from turmeric, disrupt those interactions.

Enzymes bind to sugars and catalyze particular biochemical changes in the sugars through amino acids on the surface of the enzyme. Examination of the surface of the enzyme would show pits or clefts with exposed tryptophan residues. The tryptophan does not hydrogen bond with water, i.e. it is hydrophobic. Similarly the top and bottom faces of sugar, such as glucose, are hydrophobic. If a sugar crashes into a tryptophan, as a result of thermal motion, the sugar will stick, because exposing the hydrophobic of both surfaces to water is a higher energy state; the sugar is bonded to the tryptophan.

I have taken a mathematical model of a sugar-binding protein and highlighted the surface of the protein, the helical twists of the protein backbone, the yellow tryptophan and the red and white sugar. You can see that the faces of the sugar and the tryptophan are touching.

I have explored hundreds of protein structures derived by X-ray crystallography and NMR. Sugar-binding enzymes, such as glycosidases, glycanases, lectins, etc., usually have tryptophans to bind the sugars. Examination of enzymes that bind long chains of sugars have a series of tryptophan stepping stones that are spaced and oriented to bind the faces of the sugars.

Some of the structures that molecules display are just amazing. Glucose chains are very long in the polysaccharides that we are familiar with as starch. Small lengths up to about a dozen sugars would be call dextrins. If these dextrins are connected end to end, they become cyclodextrins. The cyclodextrins can be of different sizes, but instead of being bracelets for different sized wrists, the cyclodextrins bind to molecules of different sizes. Since the inner surface of the cyclodextrins is hydrophobic, other small hydrophobic molecules that can slip into the rings, will get stuck. These bound molecules, which would otherwise interact with your senses to produce smells, are odorless. Thus, cyclodextrins can eliminate odors and that is just what they do in the product called Febreze.

Cyclodextrins and short dextrins can also be visualized as they bind to an enzyme, amylase, that would normally hydrolyze starch to dextrins. I have highlighted the structures of an amylase mathematical model derived by X-ray crystalography, to show how the cyclodextrin on the upper left surrounds an aromatic amino acid (in this case tyrosine) and the dextrin binds to a series of aromatic amino acids in the enzymes active site with several orange tyrosines to the right.

Sugars and tryptophans also bind to the hydrophobic arms of the basic amino acids, arginine and lysine. I have illustrated this in the case of a disaccharide bound between tryptophan (yellow) and arginine (blue) in the binding site of a lectin, a protein that binds to specific sugars.

Polysaccharide, such as heparin, that have bulky hydrogen-bonding sulfates bound to one face can still bind a tryptophan to unobstructed faces, and a basic amino acid to the other face. The basic amino acids bind in a two step process. The positively charged nitrogen at the end of the amino acid first binds to the negatively charged oxygens of the sulfates and then subsequently the nitrogen forms hydrogen bonds with the sulfates and hydrophobic interactions as the arm of the amino acid lies across the surface of the sugar.

Alkaloids, aromatic molecules with positively charged nitrogens and other negatively charged plant molecules interact with the aromatic amino acids and polysaccharides and alter human physiology. Berberine, from Barberries, has been used to treat arthritis, but it also binds and makes heparin fluorescent. Thus, berberine can be used as a fluorescent dye to visualize mast cells, which are the source of heparin. I have used berberine to stain heparan sulfate proteoglycans on cartilage producing chondrocytes in cell culture. Quinine is also similar in structure to berberine and college students should know that quinine in tonic water fluoresces in black light (UV). Putting the two together, I successfully stained my chondrocytes with tonic water!

The significance of these investigations is the potential to explain how traditional herbal remedies work and to develop new approaches for the prevention and treatment of inflammation based diseases.