The uniqueness of protein sequences: molecular territoriality

The number of tripeptides which do not occur and which occur only a small number of times in the existing data bank of protein sequences is much larger than that expected on the basis of random selection (from Monte Carlo analyses). Forty tripeptides are not found in the data bank of 289 500 amino acids while the value expected on the basis of random selection is 8.0 +/- 3.1. Seventy-one tripeptides occur only once with an expected value of 37.1 +/- 6.1. These results suggest that some peptides not found in certain species are reserved for use only in other species. The proposal is made that small peptides serve as species specific markers and function as signals in the recognition process for activation of the immune response.