Dear
Marilyn,
the study that
originally inspired the 'rule-of-thumb' that proteins with ~30%
sequence identity are likely to share similar folds is described in
one of the classic papers by Chothia and Lesk:
"How different amino
acid sequences determine similar protein structures: the structure and
evolutionary dynamics of the globins." J Mol Biol. 1980 Jan
25;136(3):225-70.
In that paper you
will also find a plot of r.m.s.d vs sequence identity which reveals that the 3
angs rmsd (which we generally take as an upper-boundary for structural
similarity) occurs at about 25-30% seq.id.
Best
wishes
Savvas
-------------------------------------------------------------------------------------------------------
Savvas N. Savvides
Professor of Structural Biology
Laboratory for Protein Biochemistry / Structural Biology Group
Ghent University
K.L.Ledeganckstraat 35, 7th floor
9000 Ghent, BELGIUM
Phone: +32-(0)9-264.51.24 ; +32-(0)472-92.85.19 ; FAX: +32-(0)9-264.53.38
Email: [EMAIL PROTECTED]
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-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yoder, Marilyn
Sent: woensdag 21 september 2005 23:44
To: CCP4 Bulletin Board
Subject: [ccp4bb]: sequence/structure homology
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Yoder, Marilyn
Sent: woensdag 21 september 2005 23:44
To: CCP4 Bulletin Board
Subject: [ccp4bb]: sequence/structure homology
My 'googling' skills
are failing me and thought perhaps someone here could point me in the right
direction.
I have two
questions.
1. It is often
stated that with ~30% sequence identity, protein folds will likely be
similar. I can't find a reference to this 'rule-of-thumb'. I suspect
there has been a systematic study showing this to be the case, but I can't put
my finger on it.
2. I'm looking
for examples where proteins of some size, at least 100 amino acids, have
sequence identity of ~30% but do not have similar folds. Again, I'm having
difficulties finding such and would appreciate any examples anyone can
provide. (Wasn't there a contest or something where investigators
were challenged to introduce the minimal sequence change that generated a
'different' structure?).
Many
thanks,
Marilyn
Yoder
Marilyn D. Yoder
Division of Cell Biology and
Biophysics
University of Missouri-Kansas
City
5007 Rockhill Rd.
Kansas City, MO
64110-2499
phone: 816-235-1986
fax: 816-235-1503
