Heme proteins conformation

Apart from the unusual temperature dependence of the Fe Mossbauer quadrupole splitting, which can be rationalized on the basis of heme/protein conformational dynamics, the diamagnetism of oxyMb/Hb originally reported by Pauling and Coryell in 1936 has held up to scrutiny remarkably well. The reported O—O distances of bound O2 in oxyHb and oxyMb range from... 

Tian, W.D. Sage, J.T. Champion. P.M. Chien, E. Sligar. S.G. Probing heme protein conformational equilibration rates with kinetic selection. Biochemistry 1996. 35. 3487 3502. 

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

Tab. 3.3 Main structural data defining the optimized heme-CO complex for each protein conformation l-V. The last row corresponds to the results obtained for the heme-CO isolated model (Section 3.3.1). 

Tab. 3.4 Shift of the C-O and Fe-C stretch frequencies relative to the isolated heme-CO system for each of the protein conformations l-V. Hydrogen bond energies are also listed. Distances are given in A, frequencies in cm-1 and energies in kcal mol-1.

The low reactivity of both Cyt111 and Cyt11 toward NO can be attributed to occupation of the heme iron axial coordination sites by an imidazole nitrogen and by a methionine sulfur of the protein (28). Thus, unlike other heme proteins where one axial site is empty or occupied by H20, formation of the nitrosyl complex not only involves ligand displacement but also significant protein conformational changes which inhibit the reaction with NO. However, the protein does not always inhibit reactivity given that Cat and nNOS are more reactive toward NO than is the model complex Fem(TPPS)(H20)2 (Table II). Conversely, the koS values... 

Measurements of the proximal histidine-iron stretching frequency by Resonance Raman spectroscopy revealed that this bond is very weak in relation to other heme protein systems (vFe.His = 204 cm-1) (130). Formation of the sGC-NO complex labilizes this ligand resulting in the formation of a 5-coordinate high spin iron(II) complex, and the conformational change responsible for the several hundred-fold increase in catalytic activity (126,129,130). 

It is quite evident that the ferrous complexes of porphyrins, both natural and synthetic, have extremely high affinities towards NO. A series of iron (II) porphyrin nitrosyls have been synthesized and their structural data [11, 27] revealed non-axial symmetry and the bent form of the Fe-N=0 moiety [112-116]. It has been found that the structure of the Fe-N-O unit in model porphyrin complexes is different from those observed in heme proteins [117]. The heme prosthetic group is chemically very similar, hence the conformational diversity was thought to arise from the steric and electronic interaction of NO with the protein residue. In order to resolve this issue femtosecond infrared polarization spectroscopy was used [118]. The results also provided evidence for the first time that a significant fraction (35%) of NO recombines with the heme-Fe(II) within the first 5 ps after the photolysis, making myoglobin an efficient N O scavenger. 

There is currently much interest in electron transfer processes in metal complexes and biological material (1-16, 35). Experimental data for electron transfer rates over long distances in proteins are scarce, however, and the semi-metheme-rythrin disproportionation system appears to be a rare authentic example of slow electron transfer over distances of about 2.8 nm. Iron site and conformational changes may also attend this process and the tunneling distances from iron-coordinated histidine edges to similar positions in the adjacent irons may be reduced from the 3.0 nm value. The first-order rate constant is some 5-8 orders of magnitude smaller than those for electron transfer involving some heme proteins for which reaction distances of 1.5-2.0 nm appear established (35). 

The biphasic reaction with CO points to the existence of multiple heme-hemopexin conformers, and this is borne out by spectral analyses. The absorbance spectra of rabbit ferri-, ferro-, and CO-ferro-mesoheme-hemopexin are entirely analogous to those of other bis-histidyl heme proteins such as cytochrome 65 142), but the CD spectra exhibit unusual features (Fig. 11). Of particular interest are the weak signal of the ferro complex and the bisignate signal of the CO-ferro complex (also seen in the NO-ferro-mesoheme-hemopexin complex (140) and in human ferri-protoheme—hemopexin (139)). 

The ferro-complex CD spectrum shows that reduction of the heme iron alters the heme environment. Redox-induced protein conformation changes could alter the S5unmetry in the heme pocket or produce two binding modes for the reduced complex whose asymmetries nearly cancel each other. Redox-linked conformational changes are especially interesting in view of recent findings of oxido-reductase activity associated with the heme-hemopexin-receptor interaction (89). 

Fig. 12. Schematic views of bis-histidyl ferri-, ferro-, and CO-ferro-heme-hemopexin. Unlike myoglobin with one open distal site, heme bound to hemopexin is coordinated to two strong field ligands, either of which a priori may be displaced by CO. This may well produce coupled changes in protein conformation like the Perutz mechanism for 02-binding by hemoglobin (143). The environment of heme bound to hemopexin and to the N-domain may be influenced by changes in the interactions of porphyrin-ring orbitals with those of aromatic residues in the heme binding site upon reduction and subsequent CO binding.

Probing Metalloproteins Electronic absorption spectroscopy of copper proteins, 226, 1 electronic absorption spectroscopy of nonheme iron proteins, 226, 33 cobalt as probe and label of proteins, 226, 52 biochemical and spectroscopic probes of mercury(ii) coordination environments in proteins, 226, 71 low-temperature optical spectroscopy metalloprotein structure and dynamics, 226, 97 nanosecond transient absorption spectroscopy, 226, 119 nanosecond time-resolved absorption and polarization dichroism spectroscopies, 226, 147 real-time spectroscopic techniques for probing conformational dynamics of heme proteins, 226, 177 variable-temperature magnetic circular dichroism, 226, 199 linear dichroism, 226, 232 infrared spectroscopy, 226, 259 Fourier transform infrared spectroscopy, 226, 289 infrared circular dichroism, 226, 306 Raman and resonance Raman spectroscopy, 226, 319 protein structure from ultraviolet resonance Raman spectroscopy, 226, 374 single-crystal micro-Raman spectroscopy, 226, 397 nanosecond time-resolved resonance Raman spectroscopy, 226, 409 techniques for obtaining resonance Raman spectra of metalloproteins, 226, 431 Raman optical activity, 226, 470 surface-enhanced resonance Raman scattering, 226, 482 luminescence... 

Ye, X., lonascu, D., Gruia, R, Yu, A., Benabbas, A., and Champion, P. M. 2007. Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates. Proc. Nat. Acad. Sci. USA 104 14682-87. 

Castro, C. E., and E. W. Bartnicki, Conformational isomerism and effective redox geometry in the oxidation of heme proteins by alkyl halides, cytochrome C, and cytochrome oxidase , Biochem., 14,498-503 (1975). 

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