sluv - Calculate Volume and Other Properties from Sequence

Calculate molecular weight the partial specific volume and the molecular extinction coefficient of proteins (and glycoproteins) from their residue composition.

Key references and sources of data are:

• S. J. Perkins (1986). Protein volumes and hydration effects: The calculations of partial specific volumes, neutron scattering matchpoints and 280-nm absorption coefficients for proteins and glycoproteins from amino acid sequences. Eur. J. Biochem. 157, 169-180

• S. J. Perkins (2001). X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and model fits. Biophysical Chemistry 93, 129-139

Useage:

Run using the command:

sluv < INPUT_FILE

INPUT_FILE is a specifically formated file containing residue frequencies (see Notes).

Notes:

The input file for sluv contains residue frequencies in a particular order and should be generated from the input template, all lines must be retained but edited as follows:

• "Template 0" can be replaced with any title
• Delete each 3-letter code amino acid/glycan code and replace it by the frequency of that residue in the sequence

Output:

The program spews a lot of data out to stdout (it may well be adviseable to pipe this to a file for future reference). The most important parameters are found in the secton titled:

************* TOTAL GLYCOPROTEIN ********************************************

Important values provided include:

MOLECULAR WEIGHT
EXTINCTION COEFF (280 NM)

and the values in the CON85 columns (the consensus values from Perkins 1986) for

VOLUME
SPECIFIC VOLUMES