Interesting biological figures

[Frank]

I am still in awe that the complexity of the human body can be reached with just ~25,000 genes. Makes me imagine that it will someday be possible to design a totally new organism. Here are some interesting figures to ponder:

Human figures:
Genome size: ~25,000
Proteome size: Estimates range from 23,000 to 120,000, with an average estimate of 50,000 (Harrison et al. 2002)

Figures of the entire protein universe:
Number of different protein folds: Estimates range from ~1,000 to ~10,000 (Grant et al. 2004). SCOP currently contains ~1,000
Number of different protein-protein interaction types: ~10,000 (of which 2000 are currently known) (Aloy et al. 2004)

It would be interesting to know how many biological functions there are in human. Does anyone know?
And do you know how many different folds are present in the human proteome? C. elegans has 600 (Qiana et al. 2001)

References:
Paul M. Harrison, Anuj Kumar, Ning Lang, Michael Snyder and Mark Gerstein A question of size: the eukaryotic proteome and the problems in defining it
Nucleic Acids Research, 2002, Vol. 30, No. 5 1083-1090

Alastair Grant, David Lee, and Christine Orengo. Progress towards mapping the universe of protein folds Genome Biol. 2004; 5(5): 107.

P. Aloy and R.B. Russell, Ten thousand interactions for the molecular biologist, Nat Biotechnol 22 (2004), pp. 1317–1321.

Jiang Qiana, Nicholas M. Luscombea, and Mark Gerstein Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model Journal of Molecular Biology Volume 313, Issue 4 , 2 November 2001, Pages 673-681

[oBWhat]

Very interesting figures and numbers!

I am sure those numbers are also on the low side. With post-translational modifications, splice variants, the number of "biologically unique" (different functional) proteins is going to be very high.

Also, there are many genes that are missed also many are pseudogenes as well.



Thanks for posting that information Frank!

[Frank]

Originally Posted by oBWhat

I am sure those numbers are also on the low side. With post-translational modifications, splice variants, the number of "biologically unique" (different functional) proteins is going to be very high.

The estimates for the proteome size have taken splice variants into account. But not post-translational modifications, which can indeed be numerous. However do these in general lead to a different function? Or are they mostly used as an "on/off switch"?

[admin]

Yeah that is an interesting question.

The thing is a protein phosphorylated at one site may bind to one protein, whereas a protein with unphosphorylated residue may be enzymatically active.

Now when it binds to the other protein it acts as a inhibitor of that protein.

Is that defined as two functions?

In biology anything is possible.

[Frank]

Yes I would classify that as two functions.

I don't expect the number of different functions (the "functionome") is much larger than the proteome. I expect it will obey a power-law just like many other biological (and non-biological) phenomena, such as the number of domains in a protein (Koonin et al. 2002). Meaning the great majority of proteins has only 1 function, and the number of proteins with increasing numbers of functions decreases exponentially.

Eugene V. Koonin, Yuri I. Wolf and Georgy P. Karev The structure of the protein universe and genome evolution Nature 420, 218-223 (14 November 2002)

[Frank]

Doesn't 10,000 protein protein interactions seem like a small number, if you take into account the proteome size?