sluv2 - Calculate Volume and Other Properties from Sequence

Calculate the scattering length per unit volume for a protein or glycoprotein from its amino acid and carbohydrate composition.

This is a reimplementation of the sluv tool originally created by Stephen J. Perkins in 1979. Documentation of the methods used can be found in:

• Perkins, S. J. (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

• Perkins, S. J. (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:

sluv2.py [-h] -i [INPUT_FILE] [-t {fas,pdb,yml}] [-o [OUTPUT_FILE]]
                [-m {classic,model,auc,project}]

Arguments:

  -h, --help            show this help message and exit
  -i [INPUT_FILE], --input_file [INPUT_FILE]
                        Path to the input composition file
  -t {fas,pdb,yml}, --input_type {fas,pdb,yml}
                        Input file format (pdb, fasta or sluv yaml)
  -o [OUTPUT_FILE], --output_file [OUTPUT_FILE]
                        Path to the output file
  -m {classic,model,auc,project}, --mode {classic,model,auc,project}
                        Type of analysis to run

Notes:

Whilst the PDB and FASTA file formats are external standards the sluv YAML format contains simple residue name and frequency pairs using the YAML format. An input template is provided with number of each residue set to 0, replace this value for your system of interest or use sctget_sequence.py_ to generate the YAML file.

Output:

'auc' mode selected:

Molecular Weight:
Absorption Coefficient x 1.03:
Specific Volume (Perkins 1986 - Consensus):

'model' mode selected:

Volume (Perkins 1986 - Amino Acid Crystals):
Estimated Hydrated Volume:

The estimated hydrated volume comes from assuming that 0.3 g of water is added for each g of protein.

'project' mode selected:

The output from both 'auc' and 'model' is produced.

'classic' mode selected:

The program spews out a lot of data (it is adviseable to set an output file so this is stored 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 PER85 columns (the values taken from crystal structures in Perkins 1986) for

VOLUME
SPECIFIC VOLUMES