imutant: Compute Changes in Stability (DDG)

In ptm: Analyses of Protein Post-Translational Modifications

Compute Changes in Stability (DDG)

Description

Computes changes in the stability of a protein after a residue mutation using a machine-learning approach.

Usage

imutant(protein, ch = "_", pos, newres = "", pH = 7, Te = 25, timeout = 60)

Arguments

protein	either the 4-letter identifier of a PDB structure, or the amino acid sequence (one letter amino acid code) of a protein.
ch	a letter identifying the chain of interest.
pos	the position, in the primary structure, of the residue to be mutated.
newres	the one letter code of the residue to be incorporated. When a value is not entered for this parameter, then the function will compute DDG for the mutation to any possible amino acid.
pH	a numeric value between 0 and 14.
Te	a numeric value indicating the temperature in degrees Celsius.
timeout	maximum time to wait, in seconds, for a response from the I-Mutant server.

Details

This function implements the I-Mutant v2.0 tool, which is a fast method based on a support vector machine approach to predict protein stability changes upon single point mutations.

Value

The function computes and returns a dataframe containing the following variables:

• Position: Position in the primary structure of the mutated residue.

• WT: Amino acid found at that position in the wild-type protein.

• NW: New amino acid found in the mutated protein.

• DDG: Change in Gibbs free energy (kcal/mol), defined as DDG = DGmt - DGwt, where DG is the change in Gibbs free energy for the folding of the protein from its unfolded state. Thus, a positive value means a stabilizing effect, and vice versa.

• pH: -log H+]

• T: Temperature in Celsius degrees.

• RSA: Relative Solvent Accessible Area (Only if a PDB file has been provided).

Author(s)

Juan Carlos Aledo

References

Capriotti et al (2005) Nucl. Ac. Res. 33:W306-W310.

See Also

foldx.mut(), ddG.profile()

Examples

## Not run: imutant(protein = '1u8f', ch = 'O', pos = 46, newres = 'K')

ptm documentation built on Aug. 7, 2022, 5:05 p.m.