Dear Emboss team,
could you please add a feature to pepstats? It would be fantastic to have
the specific partial volume of the protein in the list of the properties.
Calculation is easy: Just take the average of the specific partial volumes
of the amino acids. Since pepstats already gives the Mole% of all amino
acids, it would only need three addional steps:
1) Calculate the Mole%-value times the specific partial volume for each
amino acid.
2) add all up
3) divide by 100
Ideally, the value could be given as list line of the summary, e. g.,
[...]
Probability of expression in inclusion bodies = 0.520
Specific partial volume = 0.736
Here are the specific partial volumes of the amino acids:
A = Ala 0.74
B = Asx 0.61
C = Cys 0.63
D = Asp 0.60
E = Glu 0.66
F = Phe 0.77
G = Gly 0.64
H = His 0.67
I = Ile 0.90
K = Lys 0.82
L = Leu 0.90
M = Met 0.75
N = Asn 0.62
P = Pro 0.76
Q = Gln 0.67
R = Arg 0.70
S = Ser 0.63
T = Thr 0.70
V = Val 0.86
W = Trp 0.74
X = Xaa 0.724
Y = Tyr 0.71
Z = Glx 0.665
The calculation is correct within +/- 20%. The reference for these values
is:
Scott C. Schuyler, David Pellman: "Analysis of the size and shape of
protein complexes from yeast" Chapter 8 (pages 150-168) in: Methods in
Enzymology 351: Guide to Yeast Genetics and Molecular and Cell Biology:
Part C Eds.: Christine Guthrie,
Gerald R. Fink, 2002
and references therein.
Background info
I am interested in the hydrodynamic properties of proteins. A good
introduction to this topic is this publication:
Erickson HP. Size and shape of protein molecules at the nanometer level
determined by sedimentation, gel filtration, and electron microscopy. Biol
Proced Online. 2009 May 15;11:32-51. doi: 10.1007/s12575-009-9008-x.
PubMed PMID: 19495910; PubMed Central PMCID: PMC3055910.
One of the key parameters for the hydrodynamic calculations is the partial
specific volume of the proteins (v2 in Erickson's publication). For
proteins, this value can be anything between 0.7 and 0.75 cm3/g. While a
good first approximation of the partial specific volume is 0.73 cm3/g, I
would like to calculate the protein specific value using the numbers
above. Since pepstats is my favourite program to calculate amino acid
composition, extinction coefficient and other parameters, it would be
great if pepstats also would calculate the specifc partial volume.
As far as I know, there is no program available does this kind of
calculation.
Best regards, Daniel
--
Daniel Schlieper
Biochemische Pflanzenphysiologie
Heinrich-Heine-Universitaet
40204 Duesseldorf, Germany
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