Wheat, Barley and Rye are grasses.
Wheat, Barley and Rye plants produce seeds that primarily contain starch and protein. The proteins are chains of amino acids linked by peptide bonds. There are twenty amino acids, each with different shape, size and electical charge distribution. The nature of a protein is determined by the sequence of the amino acids - their order of occurrence - in the chains. The way the amino acids can rotate at the peptide bonds and these shape factors control how the long chains fold, and how the folded chains fold again, ultimately into structures with definite shape and utility to the life that creates them.
For the grass plant, the proteins serve as a storage reservoir to support growth of the embryonic plant when the seed begins to grow.
For animals, seeds represent a potential source of food - usable nourishment. The risks of eating any particular plant seed mostly revolve around the evolution of the plant in relation to animals that serve or thwart the plant's survival needs. Some plants depend on having their fruits eaten in order to disperse seeds that pass through the animal's digestive tract unharmed and are released at a distance. Other plants have evolved means of discouraging animals from eating their seeds. Apple seeds contain a substance that under some conditions turns into Hydrogen Cyanide. Seeds of the Castor Bean contain a protein that is extrmely toxic to mammals.
Considering animal protein as a food source, there is an expectation that the amino acid sequences will be compatible with other animals needs. There is no necessary expectation that plant proteins will be compatible with mammalian life. Animal proteins do not include all the amino acids. Plant proteins may include some amino acids that are not normally found in animal proteins.
One difference between these grass plant proteins and typical animal proteins, is that the plants have included the amino acid proline in their proteins. Proline has the character of providing peptide bonding sites that cause a kink in the chain of amino acids. While most of the other amino acids allow for smooth long chains, proline puts a corner bend into a chain. When two prolines occur near each other in a protein, human digestive enzymes are unable to obtain a good hold to break the peptide bonds. This allows peptide connected sequences instead of just separated amino acids to pass along the small intestine where they can meet immune system cells or even be absorbed to circulate in the bloodstream.
It is the immune response to the proline-containing peptides
that cause many people trouble. There are other effects of the circulating peptides
that can affect other people. Science is still learning a great deal about the mechanisms
of action on humans, although many early reports have guided current work.
Certain combinations of amino acids in gluten proteins prevent human digestive enzymes from separating some parts of the protein into individual amino acids. The intestinal epithelium transports some of the undigested protein into the bloodstream. Pieces of wheat gluten protein trigger an immune system response of the same type that fights off infections.
Due to an unfortunate accident of inheritance, some human immune systems have HLA marker types that are similar to the bits of gluten protein. The immune system, in attacking these bits of protein, employs a form of fuzzy logic, making tiny random changes to the antigen recognition pattern programmed into antibodies made by B and T cells. Since there is a similarity between the HLA patterns and the gluten protein fragments, the gradual shift of target pattern will randomly accidentally match the HLA, resulting in a full scale attack by the immune system on that specific tissue that is normally protected by the HLA pattern.