Ruffling in a Series of Nickel(II) meso-Tetrasubstituted Porphyrins as a Model for the Conserved Ruffling of the Heme of Cytochromes c

Molecular structures and magnetic resonance spectroscopic investigations of highly distorted six-coordinate low-spin iron(III) porphyrinate complexes

Three bis-axially ligated complexes of iron(III) octaethyltetraphenylporphyrin, (OETPP)Fe(III), have been prepared, which are low-spin complexes, each with two axial nitrogen-donor ligands (N-methylimidazole (N-MeIm), 4-(dimethylamino)pyridine (4-NMe(2)Py), and 2-methylimidazole (2-MeImH)). The crystal and molecular structure of the bis-(2-MeImH) complex shows the macrocycle to be in a saddled conformation, with the ligands in perpendicular planes aligned at 14 degrees to the porphyrin nitrogens so as to relieve the steric interaction between the 2-methyl groups and the porphyrin. The Fe-N(por) bond lengths are typical of nonplanar six-coordinate low-spin Fe(III) complexes, while the axial Fe-N(ax) bond lengths are substantially longer than those of [(TPP)Fe(2-MeImH)(2)](+) (2.09(2) A as compared to 2.015(4) and 2.010(4) A). The crystal and molecular structure of the bis-(4-NMe(2)Py) complex also shows the macrocycle to be in a mainly saddled conformation, but with a significant ruffled component. As a result, the average Fe-N(por) bonds are significantly shorter (1.951 A as compared to 1.974 A) than those of the bis-(2-MeImH) complex. One ligand is aligned at 9 degrees to two trans porphyrin nitrogens, while the other is at 79 degrees to the same porphyrin nitrogens, producing a dihedral angle of 70 degrees between the ligand planes. The EPR spectrum of this complex, like that of the bis-(2-MeImH) complex, is of the "large g(max)" type, with g(max) = 3.29 and 3.26, respectively. However, in frozen CD(2)Cl(2), [(OETPP)Fe(N-MeIm)(2)](+) exhibits both "large g(max)" and normal rhombic signals, suggesting the presence of both "perpendicular" and "parallel" ligand orientations. The 1- and 2D (1)H NMR spectra of each of these complexes, as well as the chloroiron(III) starting material, were investigated as a function of temperature. The COSY and NOESY/EXSY spectra of the chloride complex are consistent with the expected J-coupling and saddle inversion dynamics, respectively. Complete spectral assignments for the bis-(N-MeIm) and -(4-NMe(2)Py) complexes have been made using 2D (1)H NMR techniques. In each case, the number of resonances due to methylene (two) and phenyl protons (one each) is consistent with D(2)(d)() symmetry, and therefore an effective perpendicular orientation of the axial ligands on the time scale of the NMR experiments. The temperature dependences of the (1)H resonances of these complexes show significant deviations from Curie behavior, and also evidence of extensive ligand exchange and rotation. Spectral assignment of the eight methylene resonances of the bis-(2-MeImH) complex to the four ethyl groups was possible through the use of 2D (1)H NMR techniques. The complex is fluxional, even at -90 degrees C, and ROESY data suggest that the predominant process is saddle inversion accompanied by simultaneous rotation of the axial ligands. Saddle inversion becomes slow on the 2D NMR time scale as the temperature is lowered in the ligand order of N-MeIm > 4-NMe(2)Py > 2-MeImH, probably due mainly to progressive destabilization of the ground state rather than progressive stabilization of the transition state of the increasingly "hindered" bis-ligand complexes.

Factors affecting the electronic ground state of low-spin iron(III) porphyrin complexes

To determine the factors affecting the ground-state electron configuration of low-spin Fe(III) porphyrin complexes, we have examined the (1)H NMR, (13)C NMR, and EPR spectra of a series of low-spin bis-ligated Fe(III) porphyrin complexes [Fe(Por)L(2)](+/-), in which the positions of porphyrin substituents and the coordination ability of axial ligands are different. The seven porphyrins used in this study are meso-tetraalkylporphyrins (TRP: R is propyl, cyclopropyl, or isopropyl), meso-tetraphenylporphyrin (TPP), meso-tetrakis(2,3,4,5,6-pentafluorophenyl)porphyrin, and 5,10,15,20-tetraphenyl-2,3,7,8,12,13,17,18-octaalkylporphyrins (ORTPP: R is methyl or ethyl). The porphyrin cores of TRP are more or less S(4)-ruffled depending on the bulkiness of the alkyl substituents, while those of ORTPP are highly S(4)-saddled. Three types of axial ligands are examined which have the following characteristics in ligand field theory: they are (i) strong sigma-donating imidazole (HIm), (ii) strong sigma-donating and weak pi-accepting cyanide (CN(-)), and (iii) weak sigma-donating and strong pi-accepting tert-butyl isocyanide ((t)BuNC). In the case of the bis(HIm) complexes, only the isopropyl complex, [Fe(T(i)PrP)(HIm)(2)](+), has shown the less common (d(xz), d(yz))(4)(d(xy))(1) ground state; the other six complexes have exhibited the common (d(xy))(2)(d(xz), d(yz))(3) ground state. When the axial imidazole is replaced by cyanide, even the propyl and cyclopropyl complexes have shown the (d(xz), d(yz))(4)(d(xy))(1) ground state; the TPP and ORTPP complexes have still maintained the common (d(xy))(2)(d(xz), d(yz))(3) ground state. In the case of the bis((t)()BuNC) complexes, all the complexes have shown the (d(xz), d(yz))(4)(d(xy))(1) ground state. However, the contribution of the (d(xz), d(yz))(4)(d(xy))(1) state to the electronic ground state differs from complex to complex; the (d(xz), d(yz))(4)(d(xy))(1) contribution is the largest in [Fe(T(i)PrP)((t)()BuNC)(2)](+) and the smallest in [Fe(OETPPP)((t)BuNC)(2)](+). We have then examined the electronic ground state of low-spin [Fe(OEP)((t)BuNC)(2)](+) and [Fe(ProtoIXMe(2))((t)BuNC)(2)](+); OEP and ProtoIXMe(2) represent 2,3,7,8,12,13,17,18-octaethylporphyrin and protoporphyrin-IX dimethyl ester, respectively. These porphyrins have a(1u) HOMO in contrast to the other seven porphyrins that have a(2u) HOMO. The (13)C NMR and EPR studies have revealed that the contribution of the (d(xz), d(yz))(4)(d(xy))(1) state in these complexes is as small as that in [Fe(OETPP)((t)BuNC)(2)](+). On the basis of these results, we have concluded that the low-spin iron(III) porphyrins that have (i) strong axial ligands, (ii) highly saddle shaped porphyrin rings, (iii) porphyrins with a(1u) HOMO, and (iv) electron withdrawing substituents at the meso positions tend to maintain the common (d(xy))(2)(d(xz), d(yz))(3) ground state.

Calcium-dependent conformation of a heme and fingerprint peptide of the diheme cytochrome c peroxidase from Paracoccus pantotrophus

The structural changes in the heme macrocycle and substituents caused by binding of Ca(2+) to the diheme cytochrome c peroxidase from Paracoccus pantotrophus were clarified by resonance Raman spectroscopy of the inactive fully oxidized form of the enzyme. The changes in the macrocycle vibrational modes are consistent with a Ca(2+)-dependent increase in the out-of-plane distortion of the low-potential heme, the proposed peroxidatic heme. Most of the increase in out-of-plane distortion occurs when the high-affinity site I is occupied, but a small further increase in distortion occurs when site II is also occupied by Ca(2+) or Mg(2+). This increase in the heme distortion explains the red shift in the Soret absorption band that occurs upon Ca(2+) binding. Changes also occur in the low-frequency substituent modes of the heme, indicating that a structural change in the covalently attached fingerprint pentapeptide of the LP heme occurs upon Ca(2+) binding to site I. These structural changes may lead to loss of the sixth ligand at the peroxidatic heme in the semireduced form of the enzyme and activation.

On the negligible impact of ruffling on the electronic spectra of porphine, tetramethylporphyrin, and perfluoroalkylporphyrins

In the first part of this paper, the syntheses, structural characterization, molecular modeling, and electronic spectra for planar and nonplanar perfluoroalkylated porphyrins, (R(f))(4)P's, are reported. These studies demonstrate that the intrinsic substituent effect of the perfluoroalkyl group on the long-wavelength electronic spectrum of porphyrins is substantial, and similar (in magnitude) to that of a phenyl ring. Moreover, it is shown that out-of-plane distortion of (R(f))(4)P's has a negligible impact on their electronic spectra. These data bolster the findings of our earlier work and demonstrate that nonplanarity of (R(f))(4)P's does not result in a red-shift in their optical spectra. In the second part of this paper, time-dependent density functional spectral calculations (B3LYP/6-311G/TD) for porphine, 5,10,15,20-tetrakis(trifluoromethyl)porphyrin, and 5,10,15,20-tetramethylporphyrin in a variety of ruffled conformations are reported. The results of these studies indicate that (1) substantial ruffling of porphyrins has a negligible effect upon their electronic spectra, (2) similarly small effects upon electronic spectra are predicted if electron-withdrawing or electron-releasing groups decorate the porphyrin periphery, (3) for sterically encumbered porphyrins, ruffling can actually result in hypsochromic shifts in various absorption bands, and (4) the bulk of the red-shift commonly thought to be due to nonplanar distortion actually arises from other substituent effects. These results pose serious challenges to previous theoretical and empirical studies that have sought to find a cause-and-effect relationship between nonplanarity and electronic spectra in porphyrins.

Structure and Photophysics of β-Octafluoro-meso-tetraarylporphyrins

The structure of THF-coordinated [2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetraphenylporphinato]zinc, Zn(F(8)TPP).THF, and photophysical studies of 2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetraphenylporphyrin, F(8)TPP, Zn(F(8)TPP), 2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetrakis(pentafluorophenyl)porphyrin, F(28)TPP, and [2,3,7,8,12,13,17,18-octafluoro-5,10,15,20-tetrakis(pentafluorophenyl)porphinato]zinc, Zn(F(28)TPP), in benzonitrile, are reported. A key point from these studies is that the octafluorinated F(8)TPP and perfluorinated F(28)TPP porphyrins possess similar absorption spectra, but dissimilar X-ray crystal structures and disparate photophysical characteristics. These data cannot be easily accommodated within currently accepted theories which relate macrocycle distortion and optoelectronic properties.

Carbonmonoxy horseradish peroxidase as a function of pH and substrate: influence of local electric fields on the optical and infrared spectra

Infrared and optical spectra of carbonmonoxy horseradish peroxidase were monitored as a function of pH and substrate binding. The analyses of experimental results together with semiempirical calculations show that the CO-porphyrin complex is sensitive to environmental changes. The electronic Q(0,0) band of the porphyrin and the CO stretching mode respond to external perturbations with different symmetry dependencies. In this way, the complex is nonisotropic, and the combined spectral analyses constitute a valuable tool for the investigation of structure. In the absence of substrate and at pH 6.0, the low-spin heme optical Q(0,0) absorption band is a single peak that narrows as the temperature decreases. Under these conditions, the CO vibrational stretch frequency is at 1903 cm(-1). Addition of the substrates benzohydroxamic acid or naphthohydroxamic acid produces a split of approximately 320 cm(-1) in the Q(0,0) absorption band that is clearly evident at < 100 K and shifts the CO absorption to 1916 cm(-1). Increasing the pH to 9.3 also causes a split in the Q(0,0) optical band and elicits a shift in nu(CO) to a higher frequency (1936 cm(-1)). The splitting of the Q(0,0) band and the shifts in the IR spectra are both consistent with changes in the local electric field produced by the proximity of the electronegative carbonyl of the substrate near the heme or the protonation and/or deprotonation of the distal histidine, although other effects are also considered. The larger effect on the Q(0,0) band with substrate at low pH and the shift of nu(CO) at high pH can be rationalized by the directionality of the field and the orientation dependence of dipolar interactions.

Atom transfer reactions of (TTP)Ti(eta 2-3-hexyne): synthesis and molecular structure of trans-(TTP)Ti[OP(Oct)3]2

Atom and group transfer reactions were found to occur between heterocumulenes and (TTP)Ti(eta 2-3-hexyne), 1 (TTP = meso-5,10,15,20-tetra-p-tolylporphyrinato dianion). The imido derivatives (TTP)Ti=NR (R = iPr, 2; tBu, 3) were produced upon treatment of complex 1 with iPrN=C=NiPr, iPrNCO, or tBuNCO. Reactions between complex 1 and CS2, tBuNCS, or tBuNCSe afforded the chalcogenido complexes, (TTP)Ti=Ch (Ch = Se, 4; S, 5). Treatment of complex 1 with 2 equiv of PEt3 yielded the bis(phosphine) complex, (TTP)Ti(PEt3)2, 6. Although (TTP)Ti(eta 2-3-hexyne) readily abstracts oxygen from epoxides and sulfoxides, the reaction between 1 and O=P(Oct)3 did not result in oxygen atom transfer. Instead, the paramagnetic titanium(II) derivative (TTP)Ti[O=P(Oct)3]2, 7, was formed. The molecular structure of complex 7 was determined by single-crystal X-ray diffraction: Ti-O distance 2.080(2) A and Ti-O-P angle of 138.43(10) degrees. Estimates of Ti=O, Ti=S, Ti=Se, and Ti=NR bond strengths are discussed.

Syntheses and structural characterization of the (OCnOPor) capped porphyrins: Co(OC2OPor).CH2Cl2, Co(OC2OPor)(NO)out.0.46CHCl3, Co(OC3OPor).CHCl3, and Co(OC3OPor)(MeIm).3C7H8

The compounds Co(OC2OPor).CH2Cl2 (1), Co(OC2OPor)(NO)out.0.46CHCl3 (2), Co(OC3OPor).CHCl3 (3), and Co(OC3OPor)(MeIm).3C7H8 (4) (OC2OPor = 5,10,15,20-(benzene-1,2,4,5- tetrakis(2-phenyloxy)ethoxy)-2',2",2"',2""-tetraylporphyrinato dianion; OC3OPor = 5,10,15,20-(benzene-1,2,4,5-tetrakis(2- phenyloxy)propoxy)-2',2",2"',2""-tetraylporphyrinato dianion; MeIm = 1-methylimidazole), have been synthesized, and their structures have been determined by single-crystal X-ray diffraction methods at T = -120 degrees C: 1, a = 8.824(1) A, b = 16.674(1) A, c = 16.836(1) A, alpha = 104.453(1) degrees, beta = 92.752(1) degrees, gamma = 90.983(1) degrees, P1, Z = 2; 2, a = 9.019(1) A, b = 16.588(2) A, c = 16.909(2) A, alpha = 103.923(2) degrees, beta = 92.082(2) degrees, gamma = 93.583(2) degrees, P1, Z = 2; 3, a = 13.484(3) A, b = 14.404(3) A, c = 14.570(3) A, alpha = 105.508(3) degrees, beta = 100.678(3) degrees, gamma = 93.509(4) degrees, P1, Z = 2; 4, a = 16.490(1) A, b = 22.324(2) A, c = 17.257(1) A, b = 92.437(1) degrees, P2(1)/n, Z = 4. These compounds are the first structurally characterized Co-bound members of the OCnOPor ligand system. The NO ligand in 2 and the MeIm ligand in 4 bind asymmetrically and lead to several metrical changes in these porphyrins, e.g., variations in average porphyrin deviations and Co atom displacements relative to the porphyrinato N atoms and the mean porphyrin planes.

Database of C-glycosylporphyrins in Web fashion

The aim of this work was to organize chemical data in a client-server environment using Database Management System and Web fashion for the client interface. To solve this ancient problem (for us) merging text data, reaction schemes, tridimensional structures, and NMR, CD, and UV spectra images, we have based our implementation on a few fundamental points: no cost for the user, availability of data via the Internet, standard and freeware software, and a Web browser for the database inquiry. These functions are delivered in a platform-independent manner via the Internet and are used by computational experts and nonexperts alike. C-Glycosylporphyrins is the class of compounds chosen to test our applications. These results can be exportable for many other classes of chemical compounds.

A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling

The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 A. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.

Addition and metathesis reactions of zirconium and hafnium imido complexes

The zirconium and hafnium imido metalloporphyrin complexes (TTP)M = NArtPr (TTP = meso-5,10,15,20-tetra-p-tolylporphyrinato dianion; M = Zr (1), Hf; AriPr = 2,6-diisopropylphenyl) were used to mediate addition reactions of carbonyl species and metathesis of nitroso compounds. The imido complexes react in a stepwise manner in the presence of 2 equiv of pinacolone to form the enediolate products (TTP)M[OC(tBu)CHC(tBu)(Me)O] (M = Zr (2), Hf (3)), with elimination of H2NAriPr. The bis(mu-oxo) complex [(TTP)ZrO]2 (4) is formed upon reaction of (TTP)Zr = NAriPr with PhNO. Treatment of compound 4 with water or treatment of compound 2 with acetone produced the (mu-oxo)bis(mu-hydroxo)-bridged dimer [(TTP)Zr]2(mu-O)(mu-OH)2 (5). Compounds 2, 4, and 5 were structurally characterized by single-crystal X-ray diffraction.

Porphyrin interactions with wild-type and mutant mouse ferrochelatase

Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the heme biosynthetic pathway, catalyzes Fe(2+) chelation into protoporphyrin IX. Resonance Raman and UV-vis absorption spectroscopies of wild-type and engineered variants of murine ferrochelatase were used to examine the proposed structural mechanism for iron insertion into porphyrin. The recombinant variants (i.e., H207N and E287Q) are enzymes in which the conserved amino acids histidine-207 and glutamate-287 of murine ferrochelatase were substituted with asparagine and glutamine, respectively. Both of these residues are at the active site of the enzyme as deduced from the Bacillus subtilis ferrochelatase three-dimensional structure. On the basis of changes in the UV-vis absorption spectrum, addition of free-base or metalated porphyrins to wild-type ferrochelatase and H207N variant yields a 1:1 complex, most likely a monomeric protein-bound species at the active site. In contrast, the addition of porphyrin (either free base or metalated) to E287Q is substoichiometric, as this variant retains bound porphyrin in the active site during isolation and purification. The specificity of porphyrin binding is confirmed by the narrowing of the structure-sensitive lines and the vinyl vibrational mode in the resonance Raman spectra. Shifts in the resonance Raman lines of free-base and metalated porphyrins bound to the wild-type ferrochelatase indicate a nonplanar distortion of the porphyrin macrocycle. However, the magnitude of the distortion cannot be determined without first defining the specific type of deformation. Significantly, the extent of the nonplanar distortion varies in the case of H207N- and E287Q-bound porphyrins. In fact, resonance Raman spectral decompositions indicate a homogeneous ruffled deformation for the nickel protoporphyrin bound to the wild-type ferrochelatase, whereas both planar and ruffled conformations are present for the H207N-bound porphyrin. Perhaps more revealing is the unusual resonance Raman spectrum of the endogenous E287Q-bound porphyrin, which has the structure-sensitive lines greatly upshifted relative to those of the free-base protoporphyrin in solution. This could be interpreted as an equilibrium between protein conformers, one of which favors a highly distorted porphyrin macrocycle. Taken together, these findings suggest that distortion occurs in murine ferrochelatase for some porphyrins, even without metal binding, which is apparently required for the yeast ferrochelatase.

Synthesis and Electrochemical Studies of a Series of Fluorinated Dodecaphenylporphyrins

Dodecaphenylporphyrins with varying degrees of fluorination of the peripheral phenyl rings (F(x)()DPPs) were synthesized as model compounds for studying electronic effects in nonplanar porphyrins, and detailed electrochemical studies of the chloroiron(III) complexes of these compounds were undertaken. The series of porphyrins, represented as FeDPPCl and as FeF(x)()DPPCl where x = 4, 8 (two isomers), 12, 20, 28, or 36, could be reversibly oxidized by two successive one-electron transfer steps in dichloromethane to give pi-cation radicals and pi-dications, respectively. All of the compounds investigated could also be reduced by three electrons in benzonitrile or pyridine. In benzonitrile, three reversible reductions were observed for the unfluorinated compound FeDPPCl, whereas the FeF(x)()DPPCl complexes generally exhibited irreversible first and second reductions which were coupled to chemical reactions. The chemical reaction associated with the first reduction involved a loss of the chloride ion after generation of [Fe(II)F(x)()DPPCl](-). The second chemical reaction involved a conversion between the initially generated Fe(II) porphyrin pi-anion radical and the final Fe(I) porphyrin reduction product. In pyridine, three reversible one-electron reductions were observed with the second reduction affording stable Fe(II) porphyrin pi-anion radicals for all of the complexes investigated.

Nickel(II) and Zinc(II) meso-Tetracyclohexylporphyrins. Structural and Electronic Effects Induced by meso-Cyclohexyl Substitution in Metalloporphyrins

The synthesis and X-ray structures of the zinc(II) and nickel(II) complexes of meso-tetracyclohexylporphyrin H(2)(TCHP) are described. The nonplanarity of the meso substituents results in steric crowding at the porphyrin periphery. In the solid state, the nickel(II) complex Ni(TCHP) has a ruffled porphyrin conformation while Zn(TCHP) exhibits a stepped distortion of the macrocycle. In chloroform solution, fast rotation of the cyclohexyl groups on the NMR time scale is observed at room temperature for both complexes. Temperature-dependent (1)H NMR spectra showed that the (-g,g,-g,g) conformer of Zn(TCHP) and Ni(TCHP) is prevalent in solution at low temperatures and gave an estimate for the rotation barrier of the cyclohexyl groups (DeltaG(c)() = 10-12 kcal mol(-)(1)). In both complexes, the porphyrin ring is easier to oxidize and harder to reduce than in their tetraphenylporphyrin M(TPP) congeners, in agreement with the stronger electron-donating effect of the cyclohexyl group. The magnitude of the potential shift is larger for the first oxidation than for the first reduction, reflecting a smaller HOMO-LUMO energy gap and a greater degree of macrocycle distortion than in the M(TPP) derivatives. This information is of importance to understanding the protein regulation of electron-transfer processes by cytochrome c and other redox active proteins. Crystal data: Ni(TCHP).CHCl(3).CH(3)CN, monoclinic, C2/c, a = 27.405(12), b = 10.004(21), c = 32.877(24) Å, beta = 107.71(3) degrees at 127 K, Z = 8. Zn(TCHP), monoclinic, P2(1)/a, a = 11.159(15), b = 11.992(7), c = 13.465(20) Å, beta = 102.85(16) degrees at 127 K, Z = 2.

High-Spin (meso-Tetraalkylporphyrinato)iron(III) Complexes As Studied by X-ray Crystallography, EPR, and Dynamic NMR Spectroscopies

1H NMR spectra of a series of high-spin (meso-tetraalkylporphyrinato)iron(III) chlorides, [Fe(TRP)Cl] where R = Me, Et, Pr, or (i)Pr, have been measured at various temperatures in CD(2)Cl(2) solution. In the case of the Et, Pr, and (i)Pr complexes, either the methyl or the methylene signal split into two signals with equal integral intensities at low temperature. In contrast, the Me complex did not show any splitting even at -100 degrees C. The results have been ascribed to the hindered rotation of the meso-alkyl groups about C(meso)-C(alpha) bonds. The activation free energies for rotation have been determined as 8.0 (-72 degrees C), 8.5 (-60 degrees C), and 8.9 (-62 degrees C) kcal.mol(-1) for the Et, Pr, and (i)Pr complexes, respectively, at coalescence temperatures given in parentheses. The small activation free energy for rotation of the isopropyl groups observed in the present system is explained in terms of the nonplanarity of the porphyrin ring, which has been verified both by the X-ray crystallographic analysis and by the EPR spectrum taken in a frozen CH(2)Cl(2)-toluene solution. The success in observing the hindered rotation of less bulky primary alkyl groups such as ethyl and propyl groups at an easily accessible temperature range is attributed to the large difference in chemical shifts of the mutually exchanging protons, ca. 3500 Hz in the case of the Et complex, caused by the paramagnetism of the five-coordinated ferric porphyrin complexes.

Resonance Raman investigation of nickel microperoxidase-11

Resonance Raman and UV-visible absorption spectra show that nickel(II) microperoxidase-11 (NiMP-11) is four-coordinate in aqueous solution in the pH range from 1.0 to 13.0. In aqueous solutions of NiMP-11 in the absence of cetyltrimethylammonium bromide (CTAB), NiMP-11 is aggregated. In CTAB micellar solutions, where aggregation of NiMP-11 does not occur, the Raman spectra of NiMP-11 are similar to that of nickel(II) cytochrome c (NiCyt-c). The presence of the peptide segment shifts the equilibrium heavily in favor of the nonplanar form, just as does the entire protein component in the case of NiCyt-c. This further elucidates the structural mechanism by which the protein segment ruffles the heme, most likely modulating the redox potential as indicated for the cytochromes c3 [Ma, J.-G., et al. (1998) Biochemistry 37, 12431-12442]. Furthermore, the hydrophobic environment that is provided by the CTAB micelle is found to be crucial to the native folding of the pentapeptide and formation of two hydrogen bonds in the peptide backbone. These two H-bonds act to contract the peptide segment exerting the force on the macrocycle that causes the ruffling and makes the redox potential more negative than if the heme were to remain planar. The structure of the heme and pentapeptide may also be associated with redox-linked triggering of the formation and release of cytochrome-protein complexes.

Distinct structures and environments for the three hemes of the cytochrome bc1 complex from Rhodospirillum rubrum. A resonance Raman study using B-band excitations

The B-band excited resonance Raman (RR) spectra (100-1700 cm-1) of the bacterial cytochrome bc1 complex purified from Rhodospirillum rubrum are reported. Four redox states, i.e., the persulfate-oxidized, "as prepared", and ascorbate- and dithionite-reduced states of the complex, were investigated with the laser excitations at 406.7, 413.1, and 441.6 nm. Following the different absorption properties of the b- and c-type hemes and the different resonance enhancements of the vibrational modes of oxidized and reduced hemes, RR contributions from the b- and c-type hemes were characterized. For the nu2, nu10, and nu8 porphyrin vibrational modes, individual contributions of hemes c1, bH, and bL were determined. The data show that the macrocycle conformation of the three hemes of the cytochrome bc1 complex is different. In particular, the frequencies assigned to ferrous heme bL (1580, 1610, and 352 cm-1, respectively) reveal that its porphyrin is more strongly distorted than that of ferrous heme bH (1584, 1614, and 344 cm-1, respectively). The frequencies of the nu11 modes (1543, 1536, and 1526 cm-1 for ferrous heme c1, heme bH, and heme bL, respectively) confirm that the axial histidylimidazole ligands of heme bL have a marked anionic character. Strong differences in the peripheral interactions of the three hemes with the proteins were also detected through the frequency differences of the nu5, nu13, nu14, and nu42 modes. Considering that hemes bH and bL are inserted into a four-helice bundle, the RR data are interpreted in the frame of a strong protein constraint on heme bL.

Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein

BACKGROUND

Because of its ability to spontaneously generate its own fluorophore, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria is used extensively as a fluorescent marker in molecular and cell biology. The yellow fluorescent proteins (YFPs) have the longest wavelength emissions of all GFP variants examined to date. This shift in the spectrum is the result of a T203Y substitution (single-letter amino acid code), a mutation rationally designed on the basis of the X-ray structure of GFP S65T.

RESULTS

We have determined the crystal structures of YFP T203Y/S65G/V68L/S72A and YFP H148G to 2.5 and 2.6 A resolution, respectively. Both structures show clear electron density for nearly coplanar pi-pi stacking between Tyr203 and the chromophore. The chromophore has been displaced by nearly 1 A in comparison to other available structures. Although the H148G mutation results in the generation of a solvent channel to the chromophore cavity, intense fluorescence is maintained. The chromophore in the intact protein can be titrated, and the two variants have pKa values of 7.0 (YFP) and 8.0 (YFP H148G).

CONCLUSIONS

The observed red shift of the T203Y YFP variant is proposed to be mainly due to the additional polarizability of the pi-stacked Tyr203. The altered location of the chromophore suggests that the exact positions of nearby residues are not crucial for the chemistry of chromophore formation. The YFPs significantly extend the pH range over which GFPs may be employed as pH indicators in live cells.

The structural origin of nonplanar heme distortions in tetraheme ferricytochromes c3

Resonance Raman (RR) spectroscopy, molecular mechanics (MM) calculations, and normal-coordinate structural decomposition (NSD) have been used to investigate the conformational differences in the hemes in ferricytochromes c3. NSD analyses of heme structures obtained from X-ray crystallography and MM calculations of heme-peptide fragments of the cytochromes c3 indicate that the nonplanarity of the hemes is largely controlled by a fingerprint peptide segment consisting of two heme-linked cysteines, the amino acids between the cysteines, and the proximal histidine ligand. Additional interactions between the heme and the distal histidine ligand and between the heme propionates and the protein also influence the heme conformation, but to a lesser extent than the fingerprint peptide segment. In addition, factors that influence the folding pattern of the fingerprint peptide segment may have an effect on the heme conformation. Large heme structural differences between the baculatum cytochromes c3 and the other proteins are uncovered by the NSD procedure [Jentzen, W., Ma, J.-G., and Shelnutt, J. A. (1998) Biophys. J. 74, 753-763]. These heme differences are mainly associated with the deletion of two residues in the covalently linked segment of hemes 4 for the baculatum proteins. Furthermore, some of these structural differences are reflected in the RR spectra. For example, the frequencies of the structure-sensitive lines (nu4, nu3, and nu2) in the high-frequency region of the RR spectra are lower for the Desulfomicrobium baculatum cytochromes c3 (Norway 4 and 9974) than for the Desulfovibrio (D.) gigas, D. vulgaris, and D. desulfuricans strains, consistent with a more ruffled heme. Spectral decompositions of the nu3 and nu10 lines allow the assignment of the sublines to individual hemes and show that ruffling, not saddling, is the dominant factor influencing the frequencies of the structure-sensitive Raman lines. The distinctive spectra of the baculatum strains investigated are a consequence of hemes 2 and 4 being more ruffled than is typical of the other proteins.

Axial Coordination and Conformational Heterogeneity of Nickel(II) Tetraphenylporphyrin Complexes with Nitrogenous Bases

Axial ligation of nickel(II) 5,10,15,20-tetraphenylporphyrin (NiTPP) with pyrrolidine or piperidine has been investigated using X-ray crystallography, UV-visible spectroscopy, resonance Raman spectroscopy, and molecular mechanics (MM) calculations. By varying the pyrrolidine concentration in dichloromethane, distinct nu(4) Raman lines are found for the four-, five-, and six-coordinate species of NiTPP. The equilibrium constants for addition of the first and second pyrrolidine axial ligands are 1.1 and 3.8 M(-)(1), respectively. The axial ligands and their orientations influence the type and magnitude of the calculated nonplanar distortion. The differences in the calculated energies of the conformers having different ligand rotational angles are small so they may coexist in solution. Because of the similarity in macrocyclic structural parameters of these conformers and the free rotation of the axial ligands, narrow and symmetric nu(2) and nu(8) Raman lines are observed. Nonetheless, the normal-coordinate structural-decomposition analysis of the nonplanar distortions of the calculated structures and the crystal structure of the bis(piperidine) complex reveals a relationship between the orientations of axial ligand(s) and the macrocyclic distortions. For the five-coordinate complex with the plane of the axial ligand bisecting the Ni-N(pyrrole) bonds, a primarily ruffled deformation results. With the ligand plane eclipsing the Ni-N(pyrrole) bonds, a mainly saddled deformation occurs. With the addition of the second axial ligand, the small doming of the five-coordinate complexes disappears, and ruffling or saddling deformations change depending on the relative orientation of the two axial ligands. The crystal structure of the NiTPP bis(piperidine) complex shows a macrocycle distortion composed of wav(x) and wav(y) symmetric deformations, but no ruffling, saddling, or doming. The difference in the calculated and observed distortions results partly from the phenyl group orientation imposed by crystal packing forces. MM calculations predict three stable conformers (ruf, sad, and planar) for four-coordinate NiTPP, and resonance Raman evidence for these conformers was given previously.

Synthesis and Electrochemical Reactivity of sigma-Bonded and N-Substituted Cobalt Porphycenes

The first synthesis and characterization of sigma-bonded and N-substituted cobalt porphycenes is reported. The investigated compounds are represented as (Pc)Co(R) and (N-CH(3)OEPc)CoCl, where R is CH(3) or C(6)H(5), Pc is the dianion of 2,3,6,7,12,13,16,17-octaethylporphycene (OEPc), 2,7,12,17-tetrapropylporphycene (TPrPc), or 2,7,12,17-tetraethyl-3,6,13,16-tetramethylporphycene (EtioPc), N-CH(3)OEPc is the monoanion of N-methyl-2,3,6,7,12,13,16,17-octaethylporphycene. Each sigma-bonded (Pc)Co(R) derivative can be reversibly reduced or oxidized by two electrons, but a slow migration of the sigma-bonded R group occurs following electrogeneration of [(Pc)Co(R)](+)()(*)() leading, as a final product, to an N-substituted cobalt(II) porphycene which is also electroactive and undergoes two reductions in PhCN. The singly reduced product of this reaction is formulated as a Co(II) pi-anion radical which undergoes a slow "back-migration" of the CH(3) group to regenerate (OEPc)Co(CH(3)).

Reconstitution of the B800 bacteriochlorophylls in the peripheral light harvesting complex B800-850 of rhodobacter sphaeroides 2.4.1 with BChl a and modified (bacterio-)chlorophylls

A method is described for reversibly removing bacteriochlorophyll from the B800-site of the B850-850 antenna complex from Rhodobacter sphaeroides. This method uses the oligosaccharidic detergent Triton BG-10, together with an incubation at pH 5.0. Reconstitution at the B800-site has been successfully achieved for a range of modified bacteriochlorophylls. Copyright 1998 Elsevier Science B.V. All rights reserved.

Substituent-Induced Perturbation Symmetries and Distortions of meso-tert-Butylporphyrins

The out-of-plane and in-plane distortions of a series of nickel(II) meso-substituted porphyrins with 0, 1, 2, or 4 tert-butyl groups [nickel(II) porphine (NiP), nickel(II) mono-tert-butylporphyrin (NiMtBuP), nickel(II) di-tert-butylporphyrin (NiDtBuP), and nickel(II) tetra-tert-butylporphyrin (NiTtBuP)] are investigated using molecular mechanics (MM) calculations, X-ray crystallography, UV-visible absorption spectroscopy, and resonance Raman spectroscopy. MM calculations are used to predict the stable conformations for this series of porphyrins. The out-of-plane distortions are then analyzed in terms of displacements along the normal coordinates of the porphyrin macrocycle using a new normal-coordinate structural decomposition method. As expected, the distortions are found to occur primarily along the lowest-frequency normal coordinate of each symmetry type and the distortions could be adequately simulated using only the lowest-frequency normal coordinates as a basis (the minimal basis). However, the distortions could be simulated significantly more accurately by extending the minimal basis by including the second-lowest-frequency normal coordinate of all symmetries. Using the extended basis is most important for the in-plane distortions. Detailed analysis of the types of distortion revealed that both the out-of-plane and the in-plane distortions depend on the perturbation symmetry of the peripheral substituents. The symmetry primarily depends on the pattern of substitution (number and positions of substituents) and the orientations of substituents. Often the perturbation symmetry can be predicted for a given porphyrin simply from the possible orientations of the substituents. Then, the main type(s) of symmetric deformation occurring for each possible molecular symmetry can be readily predicted from a D(4)(h)() correlation table. The stable conformers predicted by MM for the series of tert-butyl-substituted porphyrins confirm this simple but informative approach. Experimental verification of the calculated contributions of the symmetric deformations is provided by normal-coordinate structural decomposition of the available X-ray crystal structures of NiP, NiMtBuP, and NiDtBuP. The solid-state results are also supported by the resonance Raman and UV-visible absorption spectroscopic characterization of the porphyrins in solutions. The X-ray crystal structure of NiMtBuP is reported here for the first time.

Protein-induced changes in nonplanarity of the porphyrin in nickel cytochrome c probed by resonance Raman spectroscopy

The influence of the protein on the nonplanarity of the macrocycle for nickel(II)-reconstituted cytochrome c (NiCyt-c) has been investigated with pH-dependent resonance Raman and UV-visible absorption spectroscopy and molecular mechanics calculations. The spectra reveal that NiCyt-c near neutral pH has axially coordinated Ni, but below pH 3 and above pH 12, four-coordinate species predominate. The shape of the structure-sensitive Raman line nu10 of NiCyt-c is asymmetric and broad and it changes with pH. This broad line can be decomposed well into at least two sublines, a low-frequency line that results from a nonplanar conformer and a high-frequency line that arises from a nearly planar conformer. Upon lowering the pH from 3.0 to 1.0, the amount of the nonplanar conformer decreases relative to that of the planar conformer. The decreased nonplanarity can be accounted for in terms of the disruption of a hydrogen-bonding network in the peptide backbone upon lowering the pH. Molecular mechanics (MM) calculations on iron(III) and nickel(II) microperoxidase 5 (MP-5) as well as some model heme derivatives have been carried out in order to locate the part of the protein that causes the heme distortion observed in the X-ray crystal structures of cytochromes c. The energy-optimized structures of MP-5 and the model compounds were analyzed using the normal-coordinate structural decomposition method to specify and quantify the out-of-plane macrocyclic distortions. MM calculations for MP-5 show that two hydrogen bonds formed between the amide groups in the peptide backbone are important in maintaining the ruffled deformation of the macrocycle. All evidence presented supports the hypothesis that the nonplanar distortion of the porphyrin of cytochromes c is largely maintained by a relatively small protein segment including the cysteines, the amino acids between the cysteines, and the adjacent histidine ligand. Hydrogen bonding within the backbone of this segment is important in maintaining the conformation of the peptide that induces the porphyrin distortion.