Sulfoxide Refinement

[Yoram Puius]

Tristan J. Fiedler M.Sc. wrote:
> 
> XPLOR question:
> 
> I am trying to create topology/param files for a cysteine which appears
> to be oxidized with a terminal oxygen into a sulfoxide.  Could you
> please provide any info. as to creating/finding these files.
> 
> Thank you..
> 
> Tristan Fiedler

I used info at HIC-up http://alpha2.bmc.uu.se/hicup/ to cobble together
these files:




remarks file par_cysox.pro  (7/13/98 Y. Puius)
REMARKS Patch for oxidized cysteine.
REMARKS Parameters taken from cso.par at HIC-up

! This is a parameter for the CYS SG to OXY OD bond
! Source:  generated by XPLO2D server from CYO residues
! from PDB files:  1DMP, 1JOA, 1QBS, 1SBI
! Ignored overly long bonds in: 1PRX, 2ORA


BOND SM  OH1    200.0  1.573 ! Nobs =    6 ... Range =  1.457 1.614

ANGLe CH2E  SM  OH1     200.0   106.23 ! Nobs =    6 ... Range =   
98.32  115.38
                                       ! CB-SG-OD for CysOX

angle CH1E CH2E SM  367.377  114.400   !2.3 CA-CB-SG for CysOX,
                                       ! stolen from Cys in parhcsdx.pro

DIHEdral CH1E CH2E SH1E OH1 750.0 3 0.0 ! useless, for now




remarks file top_cysox.pro  (7/13/98 Y. Puius)
REMARKS Patch for oxidized cysteine.

RESIDUE OXY  ! Single hydroxyl group floating out in nowhere
             ! Called OD because bound to Cys SG

  GROUp
    ATOM OD  TYPE=OH1  CHARge=-0.65   END

END {OXY}


!------------------------------------------------------------------


PRESidue CYSO   ! Patch to change reduced Cys to oxidized
                ! 1=CYS, 2=OXY
  GROUP
   MODIFY ATOM 1SG  TYPE=SM    CHARge=-0.12   END

  ADD BOND 1SG 2OD
  ADD ANGLe 1CB 1SG 2OD
  ADD DIHEdral  1CA 1CB 1SG 2OD

END {CYSO}





To implement, read in the relevant files, and in generate.inp add
something like

PATCH CYSO
   reference=1=(resid 235)
   reference=2=(resid 1235)
END

where 235 is the CYS and 1235 is a single oxygen atom in a residue
called
OXY with an atom named OD.

The parameters themselves are really approximate, and you might be
able to get better ones form the Cambridge database or a good
friend who'll run a Gaussian job for you.  Use these parameters at
you own risk, or you can guess your own from other structures
at HIC-up.  No warranty express or implied, yadda yadda yadda...

Have fun,
	Yoram



-- 
_______________________________________________________________________
Yoram A. Puius                Albert Einstein College of Medicine
6th year M.D.-Ph.D.           Department of Biochemistry
mailto:puius at aecom.yu.edu     1300 Morris Park Avenue, Bronx, NY  10461
        http://www.geocities.com/Athens/Forum/7504
_______________________________________________________________________
    "As a child, I was an imaginary playmate." - Tom Robbins