NMR, IR, Mössbauer and quantum chemical investigations of metalloporphyrins and metalloproteins

Crystallographic and Spectroscopic Studies of Peroxide-derived Myoglobin Compound II and Occurrence of Protonated FeIV–O

High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (<1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mössbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.

ATCUN-like metal-binding motifs in proteins: identification and characterization by crystal structure and sequence analysis

The amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motif is a small metal-binding site found in the N-terminus of many naturally occurring proteins. The ATCUN motif has been implicated in DNA cleavage and has been shown to have antitumor activity. In proteins, the ATCUN motif is formed from a histidine in the third position, its preceding residue and the free N-terminus. Four nitrogen atoms from these three residues act as metal ligands. Knowledge of metal-binding geometry helps in the design of metal-binding peptides and in understanding of the mechanisms of metal-mediated functions. Since the N-terminus region of ATCUN-containing proteins is highly disordered, no geometrical features can be derived from the protein structures. However, the crystal structure of a small metal-bound ATCUN peptide shows that the nitrogen ligands form a distorted square planar geometry. Distance constraints derived from this designed peptide were used to search 1949 polypeptide chains to find ATCUN-like motifs in any position along the polypeptide chain. Only approximately 1.9% and approximately 0.3% of histidines are involved in partial and full ATCUN-like geometric features, respectively. These two datasets were compared with the dataset of all histidines. None of the ATCUN-like motifs occur in the middle of an alpha-helix or a beta-strand. Further sequence analysis revealed total conservation of ATCUN histidines in four proteins including the transcription factor TBX3, implicated in Ulnar-Mammary Syndrome. Our analysis suggests that the ATCUN-like motif in TBX3 is a potential metal-binding site, although a structural role was not completely ruled out. Metal-binding activity in TBX3, if confirmed, will help us to understand the role of metals in transcriptional regulation and is likely to cast light on the causes of some serious genetic disorders. A conformational role is suggested for ATCUN-like motifs in other proteins.

Nuclear magnetic resonance shifts in paramagnetic metalloporphyrins and metalloproteins

We report the first detailed investigation of the (1)H, (13)C, (15)N, and (19)F nuclear magnetic resonance (NMR) spectroscopic shifts in paramagnetic metalloprotein and metalloporphyrin systems. The >3500 ppm range in experimentally observed hyperfine shifts can be well predicted by using density functional theory (DFT) methods. Using spin-unrestricted methods together with large, locally dense basis sets, we obtain very good correlations between experimental and theoretical results: R(2) = 0.941 (N = 37, p < 0.0001) when using the pure BPW91 functional and R(2) = 0.981 (N = 37, p < 0.0001) when using the hybrid functional, B3LYP. The correlations are even better for C(alpha) and C(beta) shifts alone: C(alpha), R(2) = 0.996 (N = 8, p < 0.0001, B3LYP); C(beta), R(2) = 0.995 (N = 8, p < 0.0001, B3LYP), but are worse for C(meso), in part because of the small range in C(meso) shifts. The results of these theoretical calculations also lead to a revision of previous heme and proximal histidine residue (13)C NMR assignments in deoxymyoglobin which are confirmed by new quantitative NMR measurements. Molecular orbital (MO) analyses of the resulting wave functions provide a graphical representation of the spin density distribution in the [Fe(TPP)(CN)(2)](-) (TPP = 5,10,15,20-tetraphenylporphyrinato) system (S = (1)/(2)), where the spin density is shown to be localized primarily in the d(xz) (or d(yz)) orbital, together with an analysis of the frontier MOs in Fe(TPP)Cl (S = (5)/(2)), Mn(TPP)Cl (S = 2), and a deoxymyoglobin model (S = 2). The ability to now begin to predict essentially all heavy atom NMR hyperfine shifts in paramagnetic metalloporphyrins and metalloproteins using quantum chemical methods should open up new areas of research aimed at structure prediction and refinement in paramagnetic systems in much the same way that DFT methods have been used successfully in the past to predict/refine elements of diamagnetic heme protein structures.

Theoretical study of the discrimination between O(2) and CO by myoglobin

Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.