Hello,
I have read the email correspondences about incorporating MTSL into
proteins and the aberrant display with some visualization software. I
have noticed this also, but I think (although I am a novice) that the
problem is deep rooted.
I have used a spin label as a paramagnetic relaxation enhancer to
obtain distance constraints. I found the instructions for
incorporating the CYSP residue and all worked fine. However, in every
structure calculation I find that the nitroxide side chain is in a
completely extended conformation. ALL dihedrals are 180. For MTSL
X1=-60, X2=-60 and X3(CB-1SG-2SG-CL1) =+/-90 for at least a start
(these are from many crystal structures from the Hubbell group)
The cysp.top file refers to the sulfurs as SG1 and SG2
------------------------------
residue CYSP
group
...
atom SG1 type=S charge=-0.19 end
atom SG2 type=S charge=-0.19 end
...
----------------------------
...but in CHARMm these are defined as 1SG and 2SG for the disulfide
residue in the protein topology file "top_all27_prot_na.rtf" from a
recent (c31b1) version of the CHARMM forcefield and following that is
form the xplor topallhdg.pro file
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
! use in a patch statement
! follow with AUTOgenerate ANGLes DIHEdrals command
GROUP
ATOM 1CB CT2 -0.10 !
ATOM 1SG SM -0.08 ! 2SG--2CB--
GROUP ! /
ATOM 2SG SM - 0.08 ! -1CB--1SG
ATOM 2CB CT2 -0.10 !
DELETE ATOM 1HG1
DELETE ATOM 2HG1
BOND 1SG 2SG
IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
presidue DISU ! disulfide bridge ...CYS - DISU - CYS...
group
delete atom 1HG end
modify atom 1CB charge= 0.20 end
modify atom 1SG charge=-0.20 end
group
delete atom 2HG end
modify atom 2CB charge= 0.20 end
modify atom 2SG charge=-0.20 end
add bond 1SG 2SG
add angle 1CB 1SG 2SG
add angle 1SG 2SG 2CB
add ic 1CA 1CB 1SG 2SG 0.0 0.0 180.0 0.0 0.0
add ic 1CB 1SG 2SG 2CB 0.0 0.0 180.0 0.0 0.0
add ic 1SG 2SG 2CB 2CA 0.0 0.0 180.0 0.0 0.0
end
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Could the sulfur notation be an issue? Also if you notice the CHARMm
file has the 90 degree dihedral, but the xplor file has it noted as
180. Am I missing anything here?
Any advice or info would be appreciated.
Thanks,
Linda
--
Linda Columbus
The Scripps Research Institute
10550 N.Torrey Pines Road, SP30-101
La Jolla, CA 92037
Phone: (858) 784-1000 x43288
Fax: (858) 784-7443
