The pseudocontact shifts of NMR signals, which arise from the magnetic susceptibility anisotropy of paramagnetic molecules, have been used as structural constraints under the form of a pseudopotential in the SANDER module of the AMBER 4.1 molecular dynamics software package. With this procedure, restrained energy minimization (REM) and restrained molecular dynamics (RMD) calculations can be performed on structural models by using pseudocontact shifts. The structure of the cyanide adduct of the Met80Ala mutant of the yeast iso-1-cytochrome c has been used for successfully testing the calculations. For this protein, a family of structures is available, which was obtained by using NOE and pseudocontact shifts as constraints in a distance geometry program. The structures obtained by REM and RMD calculations with the inclusion of pseudocontact shifts are analyzed.

The DelPhi program package has been used to confirm that the span in reduction potentials among high-potential Fe(4)S(4) ferredoxins must be mainly ascribed to the net protein charges arising from acidic and basic residues. Subsequently, the order of the individual reduction potentials of the iron ions in Fe(2)S(2) ferredoxins as found from NMR spectroscopy was explained mainly on the basis of different solvation contributions to the electrostatic potential. The individual reduction potentials of the iron ions in high-potential Fe(4)S(4) ferredoxins, again available from NMR spectroscopy, are only qualitatively reproduced. It is proposed that the protein triggers a distortion in the cluster which would be a further contribution to the electrochemical inequivalence of the individual iron ions.

Molecular dynamics (MD) calculations are performed on cytochrome c peroxidase (CcP) and on horseradish peroxidase, isoenzyme C (HRP), and its substrate adduct with p-cresol. For CcP, a refinement in solution of the X-ray structure is obtained which indicates that in solution the protein structure is very similar to that in the crystal. For HRP, the X-ray structure is not available. We have generated a model of this protein based on the recently reported structure of the similar lignin peroxidase (LiP) protein. This model involves the entire system as all the amino acid residues match the sequence. This HRP model was refined through energy minimization and MD calculations. A refined structural model for HRP, for the first time involving the entire protein, is therefore now available. The tertiary structure of HRP is close to that of LiP, and also the active site in the two proteins has significantly similar structures. The well-ordered water molecules and the extensive H-bond network present in the X-ray structure of CcP is maintained in the dynamics without any constraints, indicating that the active site residues produce a field strong enough to make all these interactions quite stable. Interestingly, also in HRP a network of ordered water molecules and H-bonds is present, again without constraints. This is consistent with the similarities of the active sites in the two proteins. Finally, we have calculated the MD structure of the adduct of HRP and a substrate molecule, p-cresol. This structural model is compared with the NMR data, which are in fairly good agreement. The binding site and the protein-substrate interactions are discussed.

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