[Genome] questions about PI distribution

[Fan Hsu]

Hi I-Hui,

Here is the answer from the proteome expert who originally conceived of our
Proteome Browser:

Our bimodal peak distribution refers to proteins encoded by the nuclear
genome.  There are too few proteins encoded by the mitochondrial genome
alone to determine a meaningful statistical distribution or to influence the
nuclear distribution.  The internal pH of the mitochondrion may differ from
that of the cytoplasm.  There are a fair number of nuclear encloded proteins
that are targeted to the mitochondrion.  The graph we provide also does not
separate out proteins exported out of the cell nor integral membrane
proteins nor those ending in specialized compartments like the peroxisome.
So it would be better to stratify the pI distribution by using cell
location.  That release of known genes had several thousand erroneous gene
models as well.  However it appears that cytoplasmic proteins dominate the
statistics so the distribution hasn't changed much from what a twenty year
old textbook might show.

Insoluble proteins are generally not functional and rapidly degraded by
various pathways.  For this reason there is presumably selective pressure
against otherwise innocent surface charge changes that much push a protein
into a region where it is not adequately soluble.  We might predict that the
pI might be stable for a given protein from the comparative genomics
standpoint as there appears to be a substantial unfavorable barrier to
passage from acid to basic.

Fan.
-----Original Message-----
From: genome-bounces at soe.ucsc.edu [mailto:genome-bounces at soe.ucsc.edu]On
Behalf Of s58881139 at yahoo.com.tw
Sent: Tuesday, June 05, 2007 6:55 PM
To: genome at soe.ucsc.edu
Subject: [Genome] questions about PI distribution


Hi!

  May I ask one question about PI distribution ?

  As I know, typical PI distribution in eukaryocyte is a  typical trimodial
distribution ( represent the peak in the near-neutral pI region).

  I read the note from UCSC proteome browser user's guide :
  "
  The mammalian pI distribution seems adequately modeled by an acidic
Gaussian centered on pH 5.8, a pronounced trough at pH 7.4, and an alkaline
Gaussian centered on pH 8.8. The near-neutral pI region has presumably been
depleted by selective pressure -- cytoplasmic proteins are least soluble at
their isoelectric point.  "


  Why I read a report the pI distribution in human mitochondrial proteome is
a typical trimodial distribution ( represent the peak in the near-neutral pI
region)?

  What is the selective pressure?

  Thank you for your help.

  Have a nice day.

                                                                   I-HUI

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