The surface of a protein is not at all like a ball of yarn, even though they are both one long string. This has profound implications for the immune system. Look at any solved protein structure. The backbone bobs and weaves taking water hating (hydrophobic) amino acids into the center of the protein, and putting water loving (hydrophilic) amino acids on the surface. So even though the peptide backbone is continuous, only discontinuous patches of it are displayed on the protein surface.
Which is a big problem for the immune system which wants to recognize the surface of the protein (which is all it first gets to see with an invading bug). Now we know that foreign proteins are ingested by the cell, chopped up by the proteasome, and fragments loaded on to immune molecules (class I Major Histocompatibility Complex antigens) and displayed on the cell surface so the immune system can learn what it looks like and react to it. The peptides aren’t very long — under 11 or so amino acids, but they are continuous.
What if the really distinct part of the protein surface (e.g. the immunogen) is made of two distinct patches from the backbone? A fascinating paper shows how the immune system might still recognize it. Chop the protein up into fragments by the proteasome, and then have the fragments from adjacent patches put back together. You know that any enzyme can be run in reverse, so if the proteasome can split peptide bonds apart it can also join them together.
This is exactly what was found in a recent paper — Science vol. 354 pp. 354 – 358 ’16. The small peptides (containing at most 11 amino acids) finding their way to the cell surface were analyzed in a technical tour de force. In aggregate they go by the fancy name of immunopeptidome. They found that the proteasome IS actually splicing peptide fragments together. This is called Proteasome Catalyzed Peptide Splicing (PCPS). The present work shows that it accounts for 1/3 of the class I immunopeptidome in terms of diversity and 1/4 in terms of abundance. One-third of self antigens are represented on the cell surface of the immune cell line they studied (GR-LCL the GR-lymphoblastoid cell line) ONLY by spliced peptides. The ordering of the spliced peptide was the same as the parent protein in only half. There was no preference for the length of the protein skipped by the splice.
The work has huge implications for immunology, not least autoimmune disease.
So today I wrote the author the following
Terrific paper ! Do you have any evidence for the spliced peptides being spatially contiguous on the surface of the parent protein. Have you looked?
This makes a lot of sense, because the immune system should ‘want’ to recognize protein conformations as they exist in the living cell, rather than stretches of amino acid sequence in the parent protein. Also, with few exceptions the surface of a given protein in vivo is a collection of discontinuous peptide sequences of the parent protein. I’ve always wondered how the immune system did this, and perhaps your paper explains things.
and got this back almost immediately
Interesting idea. We shall have a look for few examples where the crystallography structure or the parental protein is disclosed already.
It doesn’t get any better than this. Tomorrow I will be exactly 78 years and 6 months old. It shows I can still think (on occasion).