Peace on Earth

By Iddo on January 29th, 2009

Credit: Wikimedia Commons; image in Public Domain.

Here is a little trick I performed as a first year grad student a while ago and which I would like to share. My PhD adviser, Hanah Margalit was supposed to give a talk at a joint Israeli-Palestinian meeting. (Hopefully, such days will be back soon and permanently!) The audience was rather broad, and included many non-scientists. So how do we show how cool bioinformatics is to such a heterogeneous crowd, in a space of 30 minutes, without losing their attention or going over their heads? Ron Unger from Bar Ilan university suggested we do what most of us always try to do: search for peace. Or rather, PEACE: Proline, Glutamate, Alanine, Cysteine, Glutamate, a representation of a short peptide in one-letter amino acid code.

So, I ran BLAST on PEACE against the nr database, which contains a non-redundant comprehensive set of most proteins that have been deposited in public databases. Too many results. OK, I tried again, this time against the human genome only. (Or rather against the known human proteins in SwissProt, we did not have the whole genome yet). Here’s what I came up with, and it is still the top hit today in the human protein sequences:

>
sp|P53785.1|ZP3_MACRA  RecName: Full=Zona pellucida sperm-binding protein 3; AltName:
Full=Zona pellucida glycoprotein ZP3; Short=Zona pellucida
protein C; AltName: Full=Sperm receptor; Contains: RecName:
Full=Processed zona pellucida sperm-binding protein 3; Flags:
Precursor
Length=424

 Score = 20.2 bits (40),  Expect =   578
 Identities = 5/5 (100%), Positives = 5/5 (100%), Gaps = 0/5 (0%)

Query  1   PEACE  5
           PEACE
Sbjct  75  PEACE  79

The zona pellucida sperm binding protein. From the RefSeq summary:

"The protein encoded by this gene is a structural component of the zona
pellucida and functions in primary binding and induction of the sperm
acrosome reaction".

FYI, the zona pellucida (Latin: “transparent zone”) is the outer membrane surrounding the oocyte. This is the first protein that binds the sperm, the first step in creating a new life.

The obvious conclusion? Make Love, not War.

[Applause].

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