IUBio GIL .. BIOSCI/Bionet News .. Biosequences .. Software .. FTP

PATCH statement

Yoram Puius puius at aecom.yu.edu
Tue Mar 31 22:21:41 EST 1998

eiichi tsuji wrote:

> i have some question about 'PATCH' statement.
> we have a small inhibitor covalently bound to our protein
> and would specify the attachment of the inhibitior to a
> cysteine residue.
> But i could not generate covalent bond between inhibitor
> and cysteine.
> i've prepared parameter and topology file for inhibitor,
> but are unsure of the 'PATCH' we need to specify the bonds.
> how do i generate covalent bond between inhibitor and protein?

You need to define a PRESidue which specifies what the linkage is.  A
good place
to start is the disulfide patch from the tophcsdx.pro file:

PRESidue DISU       { disulfide bridge  ...CYS      CYS...
                                              \DISU/            }
  MODIfy ATOM 1CB           CHARge= 0.19  END
  MODIfy ATOM 1SG  TYPE=S   CHARge=-0.19  END
  MODIfy ATOM 2CB           CHARge= 0.19  END
  MODIfy ATOM 2SG  TYPE=S   CHARge=-0.19  END



 ADD DIHEdral   1CA 1CB 1SG 2SG
 ADD DIHEdral   1CB 1SG 2SG 2CB
 ADD DIHEdral   1SG 2SG 2CB 2CA


So, the atoms from the first cysteine are prefixed by a "1" and from the
second by a "2"
(this is important for non-symmetric linkages such as the one you want).

Changing charges may be irrelevant for your purposes, but what you *do *
have to do is
to specify the new bond you create between the two residus and *all* of
bond angles (three atoms) and dihedral angles (four atoms) which
result.  You may get
errors if you don't define these.

So you'll have lines like

ADD BOND 1SG 2O1   ! bond from Cys to inhibitor oxygen called O1
ADD ANGLE 1CB 1SG 2O1  ! angle across Cys sulfur
ADD ANGLE 1SG 2O1 2C2  ! angle from Cys sulfur, across inhibtor O1, to
next atom C2

A subsequent problem you might get would be that your inhibitor has
funny atoms in it,
where you've created new atom types -- you sometimes get OX1, CX2 atom
types after
using XPLO2D.  The problem is, you need constants for the bonds and bond
in your parameter file to take these into account!

If you are hooking up your Cys sulfur to a user-defined oxygen type
called OX1, you'd
have to add a new parameter file which includes lines something like

bond S    OX1    2410.110  2.030 ! new bond between cys and inhibitor
angle CH2E S    OX1     599.823  103.800 ! angle between cys
beta-carbon, sulfur, and inhibitor atom

You would also need angle parameters for the angle between S, OX1, and
any atoms bound
to the OX1.

After these are all debugged, you can invoke a patch from generate like
the examples with
the disulfide, except your new patch residue will have some other name.

Hope this helped.  Please feel free to ask for clairifications of this

    - 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

More information about the X-plor mailing list

Send comments to us at archive@iubioarchive.bio.net