B.1.8 PARAM2 – Modification of PARAM1 for CO and Heme

PARAM2 has new parameters added pertaining to carbon monoxide binding to heme proteins.

B.1.8.1 Bonds

CM-OM

carbon monoxide stretch, see Caughey et al (Biochemical and Clinical Aspects of Hemoglobin Abnormalities).

FE-CM

Iron-carbon monoxide stretch, see Kroeker et al (J. Chem. Phys. 72: 4846, 1980) Values for the chemisorption of CO onto Fe matrix, data based on tunnelling spectroscopy; no data for proteins

FE-NR

Fe-proximal histidine N epsilon stretch, see K. Nagai et al (J. Mol. Biol. 136: 271, 1980); Kincaid et al (Proc. Nat. Acad. Sci. USA 76: 549, 1979) No change in equilibrium bond distance from that in Gelin's thesis.

B.1.8.2 Angles

FE-CM-OM

Iron carbon monoxide bend, see Kroeker et al (vide supra)

NP-FE-CM

Porphyrin nitrogen Fe carbon monoxide bend. No data available, values selected to be consistent with that for proximal histidine (5th ligand) nitrogen Fe porphyrin nitrogen bend.

B.1.8.3 Dihedrals

X-FE-CM-X

no data available, values selected to be consistent with that for X-FE-NR-X (i.e. just as the heme can rotate without great hindrance about the Iron-proximal histidine bond so can the CO rotate freely about the Iron-carbon bond)

B.1.8.4 Polarizabilities Etc.

The values for CM same as that for carbonyl carbon, and the values for OM same as that for carbonyl oxygen.