[EMBOSS] pepstats feature request

[Daniel Schlieper]

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