ddG.ptm: PDB Model and Change in Stability of a Modified Protein

In ptm: Analyses of Protein Post-Translational Modifications

PDB Model and Change in Stability of a Modified Protein

Description

Builds a PDB model of the modified protein and computes the corresponding change in stability.

Usage

ddG.ptm(pdb, ch, pos, ptm, dir = 'f', pH = 7)

Arguments

pdb	the 4-letter identifier of a PDB structure or the path to a PDB file.
ch	a letter identifying the chain of interest.
pos	the position, in the primary structure, of the residue to be modified.
ptm	the post-translational modification to be considered. It should be one among: 'pSer', 'pThr', 'pTyr', 'MetO-Q', 'MetO-T'.
dir	indicates the direction of the PTM reaction: either forward ('f'), or backward ('b').
pH	a numeric value between 0 and 14.

Details

The current function uses FoldX to build the model of the modified protein. Currently, FoldX does not allow to change Met by MetO, so we use glutamine (Q) or threonine (T) to mimic MetO.

Value

The function computes and returns the DDG (kcal/mol) for the requested modification, defined as DDG = DGmodified - DGunmodified, where DG is the Gibbs free energy for the folding of the protein from its unfolded state. Thus, a positive value means a destabilizing effect, and vice versa. A PDB model containing the modified target is saved in the current directory.

Author(s)

Juan Carlos Aledo

References

Schymkowitz et al (2005) Nucl. Ac. Res. 33:W382-W388.

See Also

imutant(), foldx.mut(), ddG.profile()

Examples

## Not run: ddG.ptm('./1u8f_Repair.pdb', 'O', pos = 246, ptm = 'pThr')

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