No human protein is exempt from bacterial motifs, not even one.

The hypothesis that mimicry between a self and a microbial peptide antigen is strictly related to autoimmune pathology remains a debated concept in autoimmunity research. Clear evidence for a causal link between molecular mimicry and autoimmunity is still lacking. In recent studies we have demonstrated that viruses and bacteria share amino acid sequences with the human proteome at such a high extent that the molecular mimicry hypothesis becomes questionable as a causal factor in autoimmunity.

The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.

Background: We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousands of times), whereas some are quite rare, and a small number do not appear at all. To understand the physico-chemical-biological basis underlying peptide usage at the proteomic level, in this study we analyse the energetic costs for the synthesis of rare and never-expressed versus frequent pentapeptides.

Codon number shapes peptide redundancy in the universal proteome composition.

The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers occur more than 50,000 times.

Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools.

Background: Peptides derived from endogenous antigens can bind to MHC class I molecules. Those which bind with high affinity can invoke a CD8+ immune response, resulting in the destruction of infected cells. Much work in immunoinformatics has involved the algorithmic prediction of peptide binding affinity to various MHC-I alleles.

BoLA class I allele diversity and polymorphism in a herd of cattle.

Major histocompatibility complex class I genes are among the most polymorphic genes characterized. The high level of polymorphism is essential for generating host immune responses. In humans, three distinct genomic loci encode human leukocyte antigen (HLA) class I genes, allowing individuals to express up to six different HLA class I molecules.