Cytochrome P450 ferric heme parameters for GROMOS87

heme topology

Bonds:

Bond angles

Proper torsions

Improper torsions

Parameters of cysteine liganding to FE3+ of heme

atom number	atom name	GROMOS atom type	el. charge	charge group
1	N	N	-0.28000	1
2	H	H	0.28000	1
3	CA	CH1	0.00000	2
4	CB	CH2	-0.10000	3
5	SG	S	-0.50000	4
6	C	C	0.38000	5
7	O	O	-0.38000	5

Notes:

1. The GROMOS87 template heme was used as a starting point
2. All bond angles of the template were checked (many have wrong values !) and were corrected if necessary.
3. The bonded parameters for the covalently bound cysteine were modelled according to the X-ray structure of the P450cam:camphor complex (PDB identifier: 2cpp).
4. Improper dihedral parameters: various MD simulations were performed using the dihedral definitions of the GROMOS template. In these simulations, we observed that the heme unit bent considerably. In order to prevent these distortions, we added 32 additional improper dihedrals to make the heme more stiff.
   In simulations with this modified heme, the heme unit seems to keep enough flexibility. But when average structures are calculated from simulations, the heme plane is more or less flat and stays close to the crystal geometry.
5. In the template, FE does not have Lennard-Jones interactions. We assigned LJ-parameters according to [1] where they were used in MD simulations of cytochrome P450cam with the AMBER force field. The new GROMOS atom type is called 'FELJ'.
6. Electrostatic charges on the heme unit were assigned purely empirically. The charges on the propionate chains were assigned according to the ASP-residue in GROMOS87, the charge on the cysteine-sulfur was assigned as -0.5 e [1], and -0.1 e was assigned to the cysteine-CB. Therefore, the heme has a net charge of -1.4e in order to give a formal charge of -2.0e together with the cysteine ligand.
   In order to test+optimize the charges on FE/N and the ring system, we followed the procedure of Harris & Loew [2] : Short (10 ps) MD simulations were performed for the substrate-free crystal structure of P450cam (PDB identifier: 1phc) in which a water molecule is located at the position of the 6th FE-ligand.
   When the ab-initio derived charges of Jones [3] were used for FE and N, the distance between water oxygen and FE was too short (1.8 A compared to 2.3 A in the X-ray structure). We repeated the simulation with 5 different combinations of FE/N charges. The carbon atoms in the 5-membered rings were kept neutral, and low charges were assigned to the remaining carbon atoms (0.1e or 0.2e) so that the total charge on the heme adds up to -1.4e. The final values resulted in an average oxygen-Fe distance of 2.1 A.
7. Parameters are given in the format of sgm files for the ARGOS program. For the covalent attachment of the heme to the cysteine, the cysteine atoms are represented by negative atom numbers vis: -21 for the sulphur and -22 for the CB atom.