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1.
 The effect of axial ligand nodal plane orientation on the contact and pseudocontact shifts of a symmetrical low-spin octamethylferriheme center has been calculated as a function of the angle of the axial ligand. Simple Hückel techniques have been used to estimate the contact contribution, and values obtained from model hemes, together with counter-rotation of the g-tensor, have been used to estimate the pseudocontact contribution, for the eight β-pyrrole methyl and four meso-H positions. It is found that the maximum and minimum contact shifts occur when the axial ligand is aligned at an angle of ±15° to the meso-H axes of the heme, rather than when the axial ligand plane lies along the porphyrin nitrogens, as assumed previously by some investigators. For systems having one planar axial ligand or two ligands in parallel planes, the contact and pseudocontact contributions at the meso-H positions are comparable in size (at least on the basis of simple Hückel estimates), while the contact contribution clearly dominates the isotropic shifts of the heme methyls. Allowing for the substituent effect of the 2,4-vinyls of protohemin, or the 2,4-thioethers of hemin c, as well as the average diamagnetic shifts of the heme methyls and meso-H, plots of the predicted shifts as a function of axial ligand nodal plane orientation have been constructed for hemin b- and c-containing proteins. Excellent agreement in the order of shifts, and reasonable agreement in the sizes of the observed shifts, is observed in the majority of the ferriheme proteins for which the methyl and meso-H resonances have been assigned and proton shifts reported. Plots have also been constructed for hemin c-containing proteins having the two axial ligand nodal planes oriented at relative angles of 40°, 70°, and 80°. Excellent agreement in the order of shifts, and reasonable agreement in the magnitudes of the observed shifts, is observed in all cases of bacterial cytochromes which do not fit the plots that assume the ligands are in parallel planes, except one – the cytochrome c-552 of Nitrosomonas europae. Except for this case, where the order of the predicted methyl shifts at any angle of the axial ligands disagrees with the observed, the reasons can usually be attributed to a large dihedral angle between two axial ligand nodal planes, to strong H-bonding interactions involving His and/or CN ligands, or to off-axis binding of one (or both) axial ligand(s). Ruffling of the porphyrin ring may also contribute to the contact shift in as yet undefined ways. Hence, despite the simplicity of the calculations, the agreement with observed data is highly satisfying and the concept of the importance of axial ligand plane orientation on the observed proton shifts of heme proteins is fully confirmed. Received: 15 June 1998 / Accepted: 6 August 1998  相似文献   

2.
Experimental magnetic susceptibility tensors are reported for eight haems c with bis-His coordination. These data, obtained by fitting the dipolar shifts of backbone protons in the tetrahaem cytochromes c 3 from Desulfovibrio vulgaris and D. gigas, are analysed together with published values for other haem proteins. The x and y axes are found to rotate in the opposite sense to the axial ligands and are also counter-rotated with respect to the frontier molecular orbitals of the haem. The magnetic z-axis is close to the normal to the haem plane in each case. The magnitudes of the magnetic anisotropies are used to derive crystal field parameters and the rhombic splitting, V, is correlated with the dihedral angle between the axial ligands. Hence, it is apparent that the axial ligands are the dominant factor in determining the variation in magnetic properties between haems, and it is confirmed that “high g max” EPR signals are a reliable indicator of near-perpendicular ligands. These results are in full agreement with the analysis of non-Curie effects and electronic structure in the His-Met coordinated cytochromes c and c 551. Collectively, they show that the orientations of axial ligands to the haem may be estimated from single-crystal EPR data, from 13C NMR shifts of the haem substituents, or from NMR dipolar shifts of the polypeptide. Received: 3 September 1999 / Accepted: 10 December 1999  相似文献   

3.
Neuroglobin, a new member of hemoprotein family, can reversibly bind oxygen and take part in many biological processes such as enzymatic reaction, signal transduction and the mitochondria function. Different from myoglobin and hemoglobin, it has a hexacoordinated heme environment, with histidyl imidazole of proximal His96(F8) and distal His64(E7) directly bound to the metal ion. In the present work, solution 1H NMR spectroscopy was employed to investigate the electronic structure of heme center of wild-type met-human neuroglobin. The resonances of heme protons and key residues in the heme pocket were assigned. Two heme orientations resulting from a 180° rotation about the α-γ-meso axis with a population ratio about 2:1 were observed. Then the 1H NMR chemical shifts of the ferriheme methyl groups were used to predict orientations of the axial ligand. The obtained axial ligand plane angle φ is consistent with that from the molecular dynamics simulation but not with those from the crystal data. Compared with mouse neuroglobin, the obtained average ligand orientation of human neuroglobin reflects the changeability of heme environment for the Ngb family.  相似文献   

4.
b and c with His, Met, and cyanide ligands. Variations in the electronic structure of the haem and the magnetic susceptibility tensors have been shown to depend primarily on the axial ligand geometry, and the shifts of haem substituents have been used to obtain the first structural information for several cytochromes. Recently, the database of assigned spectra for bis-His haems has been extended sufficiently for an empirical equation to be produced for treating 1H NMR data from haem methyl groups at 298 K. However, the database used contains large systematic deviations and the form of the equation leads to systematic errors in the ligand geometries. This article describes the link with the semi-empirical methods used previously and provides a set of corrected empirical parameters as well as an improved equation. The possibilities for generalising the empirical method to account for ligands other than His and temperatures other than 298 K are discussed. Received: 19 October 1999 / Accepted: 21 February 2000  相似文献   

5.
The 1H NMR chemical shifts of the heme methyl groups of the ferriheme complex of metneuroglobin (Du et al. in J. Am. Chem. Soc. 125:8080–8081, 2003) predict orientations of the axial histidine ligands (Shokhirev and Walker in J. Biol. Inorg. Chem. 3:581–594, 1998) that are not consistent with the X-ray data (Vallone et al. in Proteins Struct. Funct. Bioinf. 56:85–94, 2004), and the EPR spectrum (Vinck et al. in J. Am. Chem. Soc. 126:4516–4517, 2004) is only marginally consistent with these data. The reasons for these inconsistencies appear to be rooted in the high degree of aqueous solution exposure of the heme group and the fact that there are no strong hydrogen-bond acceptors for the histidine imidazole N–H protons provided by the protein. Similar inconsistencies may exist for other water-soluble heme proteins, and 1H NMR spectroscopy provides a simple means to verify whether the solution structure of the heme center is the same as or different from that in the crystalline state.  相似文献   

6.
The recombinant product of the hemoglobin gene of the cyanobacterium Synechocystis sp. PCC 6803 forms spontaneously a covalent bond linking one of the heme vinyl groups to a histidine located in the C-terminal helix (His117, or H16). The present report describes the 1H, 15N, and 13C NMR spectroscopy experiments demonstrating that the recombinant hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002, a protein sharing 59% identity with Synechocystis hemoglobin, undergoes the same facile heme adduct formation. The observation that the extraordinary linkage is not unique to Synechocystis hemoglobin suggests that it constitutes a noteworthy feature of hemoglobin in non-N2-fixing cyanobacteria, along with the previously documented bis-histidine coordination of the heme iron. A qualitative analysis of the hyperfine chemical shifts of the ferric proteins indicated that the cross-link had modest repercussions on axial histidine ligation and heme electronic structure. In Synechocystis hemoglobin, the unreacted His117 imidazole had a normal pK a whereas the protonation of the modified residue took place at lower pH. Optical experiments revealed that the cross-link stabilized the protein with respect to thermal and acid denaturation. Replacement of His117 with an alanine yielded a species inert to adduct formation, but inspection of the heme chemical shifts and ligand binding properties of the variant identified position 117 as important in seating the cofactor in its site and modifying the dynamic properties of the protein. A role for bis-histidine coordination and covalent adduct formation in heme retention is proposed.Electronic Supplementary Material Supplementary material is available in the online version of this article at Abbreviations DQF-COSY double-quantum-filtered correlated spectroscopy - GlbN cyanoglobin - Hb hemoglobin - hx hexacoordinate - MALDI matrix-assisted laser desorption ionization - NOE nuclear Overhauser effect - NOESY two-dimensional nuclear Overhauser effect spectroscopy - rHb recombinant hemoglobin - rHb-A recombinant hemoglobin with covalently attached heme - rHb-R recombinant heme-reconstituted hemoglobin - S6803 Synechocystis sp. PCC 6803 - S7002 Synechococcus sp. PCC 7002 - TOCSY totally correlated two-dimensional spectroscopy - TPPI time-proportional phase incrementation - trHb truncated hemoglobin - WATERGATE water suppression by gradient-tailored excitation - WEFT water elimination Fourier transform  相似文献   

7.
The chemical shifts of the methyl protons of protoporphyrin IX, which are readily assigned, are related to the structural features of the axial histidine ligands in heme proteins with bis-His or His-CN axial coordination (Bertini I, Luchinat C, Parigi G, Walker FA (1999) JBIC 4:515-519). In the present paper, a module is developed which transforms the chemical shifts into a pseudo-potential energy that is a function of the dihedral angles defining the orientation of the axial ligand planes. Minimization of this pseudo-potential energy, together with the energetic contributions provided by the other constraints, yields structures consistent with the heme methyl chemical shifts. Oxidized cytochrome b(5) from rat and the cyanide derivative of the M80A mutant of yeast cytochrome c are used for test calculations. In the case of scarcity of NOEs for the axial ligands, owing to the presence of the paramagnetic center, the above structural constraints are shown to be quite precious. The newly refined structures are deposited in the PDB.  相似文献   

8.
 The paramagnetic 1H NMR spectra of the Co(II) and Ni(II) substituted forms of the type 1 blue copper protein (cupredoxin) amicyanin have been assigned. This is the first such analysis of a cupredoxin, which has a distorted tetrahedral active site with the ligands provided by two histidines, a cysteine and a methionine. The isotropic shifts of the resonances in these spectra are compared with those of Co(II) and Ni(II) azurin. A number of interesting similarities and differences are found. The coordination of the metal by the two equatorial histidine ligands is very similar in both proteins. The interaction between the introduced metal and the thiolate sulfur of the equatorial cysteine ligand is enhanced in the amicyanin derivatives. Resonances belonging to the weak axial methionine ligand exhibit much larger shifts in the amicyanin derivatives, indicative of shorter M(II)-S(Met) distances. The presence of shorter axial M(II)-S(Met) and equatorial M(II)-S(Cys) distances in both Co(II) and Ni(II) amicyanin is ascribed to the absence of a second axially interacting amino acid at the active site of this cupredoxin. Received: 2 February 1999 / Accepted: 19 May 1999  相似文献   

9.
Nitrophorin 3 (NP3) is the only one of the four major NO-binding heme proteins found in the saliva of the blood-sucking insect Rhodnius prolixus (also called the Kissing Bug) for which it has not been possible to obtain crystals of diffraction quality for structure determination by X-ray crystallography. Thus we have used NMR spectroscopy, mainly of the hyperfine-shifted ferriheme substituent resonances, to learn about the similarities and differences in the heme pocket and the iron active site of NP3 as compared to NP2, which has previously been well-characterized by both X-ray crystallography and NMR spectroscopy. Only one residue in the heme pocket differs between the two, F27 of NP2 is Y27 for NP3; in both cases this residue is expected to interact strongly with the 2-vinyl side chain of the B heme rotational isomer or the 4-vinyl of the A heme rotational isomer. Both the high-spin (S = 5/2) aquo complex, NP3-H2O, and the low-spin (S = 1/2) N-methylimidazole (NMeIm) complex of NP3 have been studied. It is found that the chemical shifts of the protons of both forms are similar to those of the corresponding NP2 complexes, but with minor differences that indicate a slightly different angle for the proximal histidine (H57) ligand plane. The B heme rotational isomer is preferred by both NP3 and NP2 in both spin states, but to a greater extent when phenylalanine is present at position 27 (A:B = 1:8 for NP2, 1:6 for NP3-Y27F, 1:4 for NP3, and 1:3 for NP2-F27Y). Careful analysis of the 5Me and 8Me shifts of the A and B isomers of the two high-spin nitrophorins leads to the conclusion that the heme environment for the two isomers differs in some way that cannot be explained at the present time. The kinetics of deprotonation of the aquo ligand of the high-spin complexes of NP2 and NP3 are very different, with NP2 giving well-resolved high-spin aquo and “low-spin” hydroxo proton NMR spectra until close to the end of the titration, while NP3 exhibits broadened 1H NMR spectra indicative of an intermediate-rate of exchange on the NMR timescale between the two forms throughout the titration. The heme methyl shifts of NP2-OH are similar in magnitude and spread to those of NP2-CN, while those of metmyoglobin-hydroxo complexes are much larger in magnitude but not spread. It is concluded that the hydroxo complex of NP2 is likely S = 1/2 with a mixed(dxy)2(dxz, dyz)3/(dxy)1(dxz, dyz)4 electron configuration, while those of metMb-OH are likely S = 1/2,3/2 mixed spin systems.  相似文献   

10.
Cytochrome c′′ from Methylophilus methylotrophus contains a single haem with bis-histidine coordination which couples electron and proton transfer by reversible detachment of one of the axial ligands on reduction. 13C NMR of the haem substituents is now used to determine the orientations of the two histidine ligands of the ferricytochrome. The relative orientation of the ligands is found to be nearly perpendicular (an angle of 85±2° between the histidine planes was obtained), which is consistent with the near-axial g-tensor determined by EPR. Although the absolute orientation of the axial ligands is not well defined in the presence of near-axial symmetry, 13C NMR is found to be a useful complement to EPR for obtaining quantitative information for systems of this type. Received: 13 May 1996 / Accepted: 10 July 1996  相似文献   

11.
 The reduction potentials of blue copper sites vary between 180 and about 1000 mV. It has been suggested that the reason for this variation is that the proteins constrain the distance between the copper ion and its axial ligands to different values. We have tested this suggestion by performing density functional B3LYP calculations on realistic models of the blue copper proteins, including solvent effects by the polarizable continuum method. Constraining the Cu-SMet bond length to values between 245 and 310 pm (the range encountered in crystal structures) change the reduction potential by less than 70 mV. Similarly, we have studied five typical blue copper proteins spanning the whole range of reduction potentials: stellacyanin, plastocyanin, azurin, rusticyanin, and ceruloplasmin. These studies included the methionine (or glutamine) ligand as well as the back-bone carbonyl oxygen group that is a ligand in azurin and is found at larger distances in the other proteins. The active-site models of these proteins show a variation in the reduction potential of about 140 mV, i.e., only a minor part of the range observed experimentally (800 mV). Consequently, we can conclude that the axial ligands have a small influence on the reduction potentials of the blue copper proteins. Instead, the large variation in the reduction potentials seems to arise mainly from variations in the solvent accessibility of the copper site and in the orientation of protein dipoles around the copper site. Received: 7 April 1999 / Accepted: 26 July 1999  相似文献   

12.
The amino acid at position 51 in the cytochrome c 6 family is responsible for modulating over 100 mV of heme midpoint redox potential. As part of the present work, the X-ray structure of the imidazole adduct of the photosynthetic cytochrome c 6 Q51V variant from Phormidium laminosum has been determined. The structure reveals the axial Met ligand is dissociated from the heme iron but remains inside the heme pocket and the Ω-loop housing the Met ligand is stabilized through polar interactions with the imidazole and heme propionate-6. The latter is possible owing to a 180° rotation of both heme propionates upon imidazole binding. From equilibrium and kinetic studies, a Val residue at position 51 increases the stability of the Fe–S(Met) interaction and also affects the dynamics associated with imidazole binding. In this respect, the k obs for imidazole binding to Arabidopsis thaliana cytochrome c 6A, which has a Val at the position equivalent to position 51 in photosynthetic cytochrome c 6, was found to be independent of imidazole concentration, indicating that the binding process is limited by the Met dissociation rate constant (about 1 s−1). For the cytochrome c 6 Q51V variant, imidazole binding was suppressed in comparison with the wild-type protein and the V52Q variant of cytochrome c 6A was found to bind imidazole readily. We conclude that the residue type at position 51/52 in the cytochrome c 6 family is additionally responsible for tuning the stability of the heme iron–Met bond and the dynamic properties of the ferric protein fold associated with endogenous ligand binding.  相似文献   

13.
Liquid-state NMR spectroscopy is a powerful technique to elucidate binding properties of ligands on proteins. Ligands binding in hydrophobic pockets are often in close proximity to methyl groups and binding can lead to subtle displacements of methyl containing side chains to accommodate the ligand. To establish whether pseudocontact shifts can be used to characterize ligand binding and the effects on methyl groups, the N-terminal domain of HSP90 was tagged with caged lanthanoid NMR probe 5 at three positions and titrated with a ligand. Binding was monitored using the resonances of leucine and valine methyl groups. The pseudocontact shifts (PCS) caused by ytterbium result in enhanced dispersion of the methyl spectrum, allowing more resonances to be observed. The effects of tag attachment on the spectrum and ligand binding are small. Significant changes in PCS were observed upon ligand binding, indicating displacements of several methyl groups. By determining the cross-section of PCS iso-surfaces generated by two or three paramagnetic centers, the new position of a methyl group can be estimated, showing displacements in the range of 1–3 Å for methyl groups in the binding site. The information about such subtle but significant changes may be used to improve docking studies and can find application in fragment-based drug discovery.  相似文献   

14.
In the genome of the untypical cyanobacterium Gloeobacter violaceus PCC 7421 two potential cytochrome b 6 proteins PetB1 and PetB2 are encoded. Such a situation has not been observed in cyanobacteria, algae and higher plants before, and both proteins are not characterized at all yet. Here, we show that both apo-proteins bind heme with high affinity and the spectroscopic characteristics of both holo-proteins are distinctive for cytochrome b 6 proteins. However, while in PetB2 one histidine residue, which corresponds to H100 and serves as an axial ligand for heme b H in PetB1, is mutated, both PetB proteins bind two heme molecules with different midpoint potentials. To recreate the canonical heme b H binding cavity in PetB2 we introduced a histidine residue at the position corresponding to H100 in PetB1 and subsequently characterized the generated protein variant. The presented data indicate that two bona fide cytochrome b 6 proteins are encoded in Gloeobacter violaceus. Furthermore, the two petB genes of Gloeobacter violaceus are each organized in an operon together with a petD gene. Potential causes and consequences of the petB and petD gene heterogeneity are discussed.  相似文献   

15.
The role of glycosylation on voltage-dependent channel gating for the cloned human cardiac sodium channel (hH1a) and the adult rat skeletal muscle isoform (μl) was investigated in HEK293 cells transiently transfected with either hH1a or μl cDNA. The contribution of sugar residues to channel gating was examined in transfected cells pretreated with various glycosidase and enzyme inhibitors to deglycosylate channel proteins. Pretreating transfected cells with enzyme inhibitors castanospermine and swainsonine, or exo-glycosidase neuroaminidase caused 7 to 9 mV depolarizing shifts of V 1/2 for steady-state activation of hH1a, while deglycosylation with corresponding drugs elicited about the same amount of depolarizing shifts (8 to 9 mV) of V 1/2 for steady-state activation of μl. Elevated concentrations of extracellular Mg2+ significantly masked the castanospermine-elicited depolarizing shifts of V 1/2 for steady-state activation in both transfected hH1a and μl. For steady-state activation, deglycosylation induced depolarizing shifts of V 1/2 for hH1a (10.6 to 12 mV), but hyperpolarizing shifts for μl (3.6 to 4.4 mV). Pretreatment with neuraminidase had no significant effects on single-channel conductance, the mean open time, and the open probability. These data suggest that glycosylation differentially regulates Na channel function in heart and skeletal muscle myocytes. Received: 8 April 1999/Revised: 18 June 1999  相似文献   

16.
17.
The oxygenase domains of nitric oxide synthases are unusual in that they contain at least three ligand binding sites; these correspond to the axial heme ligand position, the substrate binding site, and the pterin binding site. Ligands can occupy portions of a site or extend into regions of adjacent sites. Depending on the size, shape, and binding mode of ligands to these positions, cooperative and anticooperative interactions mediated conformationally and by binding domain overlap can be observed. In the present study we describe competition between arginine and imidazole at the axial heme ligand position; a second imidazole, which occupies part of the arginine site in some crystal structures, is too weak to contribute to the equilibria. All spectroscopic titrations using imidazole competition depend on displacement of the heme axial imidazole ligand, which drives the ferriheme low spin. Aminoguanidine, a partial arginine analog, has multiple binding modes. It is somewhat competitive with arginine; a ternary complex forms, but the K(d) for arginine increases from 1 to 15 microM in the presence of saturating aminoguanidine. Aminoguanidine competition with imidazole is very weak, amounting to approximately a factor of two increase in K(d). This implies that aminoguanidine has multiple binding modes and is not well described as an arginine analog. The major binding mode occupies part of the binding site but does not extend into the imidazole axial ligand binding domain and probably corresponds to the crystal structure. The other binding mode is not significantly overlapped with the arginine site.  相似文献   

18.
Transient electric dichroism has been measured for the ferriheme–poly(L -lysine)[(Lys)n], ferroheme–(Lys)n, and ferroheme–(Lys)n–carbon monoxide (CO) solutions at pH 9–12. The Soret absorption maximum in electronic spectrum (λ), the reduced linear dichroism (ρ) at complete orientation and the calculated angle (?) between the porphyrin plane of a bound heme and the oriented polymer axis are determined for the following complexes: a ferriheme–(Lys)n complex at pH 9.5–10.5 (λ = 420 nm, ρ = 0.50, and ? = 19°), a ferroheme–(Lys)n complex at pH 9.5–10.2 (λ = 432 nm, ρ = 0.77, and ? = 0°), and a ferroheme–(Lys)n–CO complex at pH 9.25 (λ = 430 nm, ρ = 0.38, and ? = 24°). Based on the above data, the validity of the structures of heme–(Lys)n complexes proposed by other investigators is discussed.  相似文献   

19.
The proton NMR spectra of the bis-4-substituted pyridinates of ferric tetrapheylporphyrin and octaethylporphyrin complexes have been recorded and analyzed fort he purpose of ascertaining the influence of variable axial lignad basicity on the bonding and magnetic properties of the iron. Under the conditions of slow ligand exhange where the bis stoichiometry can be established, all complexes exist exlusively in the low-spin, S = 12, state. The hyperfine shifts at ?60° C for both the porphyrins and axial ligands are shown to be very sensitive to the basicity of the substituted pyridine, as measured by its pKa. For the tetraphenylporphyrin complexes, we illustrate that the pattern of the meso-phenyl hyperfine shifts permits a quantitative separation of the contact and dipolar contributions to these shifts. This separation reveals that the shift variations with pyridine pKa are dominated by changes in the magnetic susceptibility anisotropy (dipolar shift), which decreases markedly upon lowering the pyridine basicity; ESR data support this conclusion in the few samples investigated. However, this trend in magnetic anisotropy with ligand basicity is not valid when comparing pyridines with other ligands such as imidazoles. The important change in the contact shift reflects a decrease in porphyrin → iron π change transfer as the ligand basicity is lowered. A correlation between increase in proton NMR linewidth and magnetic anisotrophy of the iron suggests that electron spin relaxation occurs via a process which couples the same levels that control the magnetic anisotropy.  相似文献   

20.
After transformation of the vinyl groups in hemin into H, CH2CH3 and COCH3, the propionic acid side chains were converted into esters and amides using (-)-menthol, (-)-2-methylbutanol and (-)-1-phenylethylamine. By introducing the CS ligand into the apical position, square pyramidal complexes were obtained, differing only in the Fe configuration, which could not be separated. However, the two diastereomers with different Fe configuration, having optically active 1-phenylethylisonitrile and pyridine (or 4-methylpyridine) as ligands in the axial positions, at −20°C exhibit different chemical shifts demonstrating configurational stability at the Fe atom on the 1H NMR time scale. At room temperature epimerization at the Fe atom occurs by ligand exchange reactions.  相似文献   

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