VMD-L Mailing List

From: Kyle Billings (krb_at_udel.edu)
Date: Mon Mar 25 2024 - 12:28:59 CDT

Hello Users,

  I am working on creating a psf/pdb using Psfgen to model an ester between
the Gly77-Tyr78 of KcsA (PDB:4MSW). I found parameters to modify the ester
linkage published from Li. et. al (https://urldefense.com/v3/__https://doi.org/10.1073/pnas.1706983114__;!!DZ3fjg!7NANVEnRX4o-lm715IR1fjoNBdHcy2zDmDRJcMQkTp89tzO1zO6hT5uQmDGsXeAEciouaoaTomL06g$ )
and the file should be attached to this post. When applying the patch, the
positions ester oxygen and the alpha carbon hydrogen atom of Tyr78 fail to
be set. I was wondering if there is a flaw in my methodology that I am not
seeing? I am sorry for the length of this message in advance.

 The current method is to convert manually the TYF 78 to TYR 78, because
4MSW already has the ester in the structure. This is to comply atom naming
from the patch for each monomer of 4MSW.
-----------------------------------------------------------------------------------------------
for {set i 0} { $i < 4 } { incr i } {
        puts $i
        # load the ##_*.pdb
        mol load pdb 4MSW/${i}_4msw.pdb2.pdb
# # select the atoms that we need to make
        [atomselect top "resname TYF and name C1 " ] set name C
        [atomselect top "resname TYF and name O1" ] set name O
        [atomselect top "resname TYF and name N" ] set type NH1
        [atomselect top "resname TYF and name C2" ] set name CA
        [atomselect top "resname TYF and name C3 " ] set name CB
        [atomselect top "resname TYF and name C4 " ] set name CG
        [atomselect top "resname TYF and name C5 " ] set name CD1
        [atomselect top "resname TYF and name C6 " ] set name CE1
        [atomselect top "resname TYF and name C7 " ] set name CZ
        [atomselect top "resname TYF and name C8 " ] set name CE2
        [atomselect top "resname TYF and name C9 " ] set name CD2
        [atomselect top "resname TYF and name O3"] set name OH
        [atomselect top "resname TYF "] set resname TYR
        [atomselect top "not (resname HOH TIP3 OH2 SOL DGA K)" ] writepdb
parts/TEMP_fixed_${i}.pdb
}
-----------------------------------------------------------------------------------------------

  From there we can the newly made monomer pdb's to build the psf. I apply
the pdbalias as stated in the Membrane Proteins Tutorial (Advanced), and
load in the CHARMM36 topologies. After the adding the additional topology
for the amide to ester mutation I build the psf/pdb a follows.
-----------------------------------------------------------------------------------------------
topology toppar/toppar_all36_amide_to_ester.str

foreach i {0 1 2 3} {
        # make the segment
        segment PRO$i {
                pdb parts/fixed_${i}.pdb
        }
        # coord pdb
        coordpdb parts/fixed_${i}.pdb PRO$i
        regenerate angles dihedrals
}
regenerate angles dihedrals
writepdb KcsA_ester.pdb
writepsf KcsA_ester.psf
-----------------------------------------------------------------------------------------------

  The resulting pdb has both the OE atom and the HA atom of the Tyr78-Gly77
ester are failed to be guessed. My current solution to fix the atoms OE
position it so move the atom using scripting is to move that atom to the
crystal structure atom position. I am worried that this is will induce
artifacts however. My only other thought is build a separate top file for
TYF residue in 4MSW from the protein topology/parameters and the top of the
patch. Any advice is welcome, and thanks for your time.

Kyle
Post Doc. at University of Delaware