CIS peptides

Lothar Esser esser at CHOP.SWMED.EDU
Wed Mar 27 12:33:43 EST 1996


On Wed, 27 Mar 1996, Ashley Buckle wrote:

> We are trying to refine a CIS peptide bond (not Pro) by first patching 
> it as CISP (as in the manual), but without success - XPLOR flips it to 
> trans every time and we dont really understand how to solve this. Has 
> anyone actually refined a protein structure with a CIS (non-Pro) 
> peptide bond?

  I made the same observation that x-plor changed a cis-peptide bond (in 
my case ASN) to trans. In my parameter file there is the statement :

dihe X    C    NH1  X  1250.0       1       0.0    ! always trans

which apparently forces all peptides to be in the cis configuration 
except for PRO because ATOM N is of TYPE N ( not NH1) . 

Because I also have "normal" trans-ASN I defined a new residue name (CAS) 
for the residue with a cis-peptide bond. Note that a new atom type has 
been assigned to ATOM N in CAS : ATOM N TYPE=NH4  
This worked for me just fine. 
Here is what I changed in the parameter and topology files :

{ =================================
    These are the changes I made in 
        parhcsdx_ace.pro 
  ================================= }

bond C    NH4  3020.408  1.329 ! 0.014
bond CH1E NH4  1639.889  1.458 ! 0.019
bond H    NH4    405.0  0.98 !*

  ! LE:  ANGLE CH1E C    NH4     20.0 117.5
angle CH1E C    NH4   485.856  116.200 !2.0

  ! LE: CAS  ANGLE NH4  C    O       65.0 121.0
angle NH4  C    O     759.150  123.000 !1.6

  ! LE : CAS ANGLE C    CH1E NH4
angle C    CH1E NH4   247.886  111.200 !2.8
angle CH1E CH1E NH4   672.465  111.500 !1.7 *

  ! LE: ANGLE CH2E CH1E NH4     65.0 110.0
angle CH2E CH1E NH4   672.465  110.500 !1.7

  ! LE: CAS  ANGLE C    NH4  CH1E    77.5 120.0
angle C    NH4  CH1E  599.823  121.700 !1.8
angle C    NH4  H       30.0 120.0 !* LE: CAS 
angle CH1E NH4  H       35.0 120.0 !* LE: CAS 

  ! LE: dihedrals and improper 
dihe X    C    NH4  X   1250.0    2 180.0    ! LE: CAS double minimum CIS ! 
dihe X    CH1E NH4  X      0.9    3   0.0    ! LE: CAS
impr C    X    X    NH4  300.0    0   0.0    ! LE: CAS
impr NH4  X    X    H    135.0    0   0.0    ! LE: CAS            
impr NH4  X    X    NH4   75.0    0   0.0    ! LE: CAS (for CAS-CAS )
impr NH4  X    X    NR    75.0    0   0.0    ! LE: CAS (for CAS-X ) 

NONBonded  NH4     0.2384   2.8509      0.2384   2.8509 ! LE: CAS

{ ===============================
  These are the changes I made in 
        tophcsdx_ace.pro
  =============================== }

MASS   NH4   14.00670! LE: Atom type definition for CIS ASN (CAS)

!---------------------------- LE: CIS ASN --------------------------------
! Changes : 2-10-96  ATOM N TYPE=NH1 ->  ATOM N TYPE NH4
!-------------------------------------------------------------------------
RESIdue CAS
 GROUp
  ATOM N    TYPE=NH4   CHARge=-0.35   END
  ATOM H    TYPE=H     CHARge= 0.25   END
  ATOM CA   TYPE=CH1E  CHARge= 0.10   END
  ATOM CB   TYPE=CH2E  CHARge= 0.00   END
  ATOM CG   TYPE=C     CHARge= 0.55   END  !#
  ATOM OD1  TYPE=O     CHARge=-0.55   END  !#
  ATOM ND2  TYPE=NH2   CHARge=-0.60   END  !#
  ATOM HD21 TYPE=H     CHARge= 0.30   END  !#
  ATOM HD22 TYPE=H     CHARge= 0.30   END  !#
  ATOM C    TYPE=C     CHARge= 0.55   END  !#
  ATOM O    TYPE=O     CHARge=-0.55   END  !#
  BOND N    CA
  BOND CA   C
  BOND C    O
  BOND N    H
  BOND CA   CB
  BOND CB   CG
  BOND CG   OD1
  BOND CG   ND2
  BOND ND2  HD21
  BOND ND2  HD22

  DIHEdral N    CA   CB   CG
  DIHEdral CA   CB   CG   OD1
  DIHEdral CB   CG   ND2  HD21

  IMPRoper CA   N    C    CB  !tetrahedral CA
  IMPRoper CG   OD1  ND2  CB  !planar CG
  IMPRoper ND2  HD21 HD22 CG  !planar ND2

  DONOr H    N
  DONOr HD21 ND2
  DONOr HD22 ND2
  ACCEptor OD1 CG
  ACCEptor O C

END {CAS}

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


Hope that helps. 

  Lothar Esser

-------------------------------------------------------------------
Dr. Lothar Esser 
Howard Hughes Medical Institute 
5323 Harry Hines Blvd.
Dallas Texas 75235-9050

e-mail : esser at chop.swmed.edu




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