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

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/ddG.R

Description

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

Usage

1
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

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

ptm documentation built on May 24, 2021, 9:06 a.m.

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