Increasing the conformational stability by replacement of heme axial ligand in c-type cytochrome

To investigate the role of the heme axial ligand in the conformational stability of c-type cytochrome, we constructed M58C and M58H mutants of the red alga Porphyra yezoensis cytochrome c(6) in which the sixth heme iron ligand (Met58) was replaced with Cys and His residues, respectively. The Gibbs free energy change for unfolding of the M58H mutant in water (DeltaG degrees (unf)=1.48 kcal/mol) was lower than that of the wild-type (2.43 kcal/mol), possibly due to the steric effects of the mutation on the apoprotein structure. On the other hand, the M58C mutant exhibited a DeltaG degrees (unf) of 5.45 kcal/mol, a significant increase by 3.02 kcal/mol compared with that of wild-type. This increase was possibly responsible for the sixth heme axial bond of M58C mutant being more stable than that of wild-type according to the heme-bound denaturation curve. Based on these observations, we propose that the sixth heme axial ligand is an important key to determine the conformational stability of c-type cytochromes, and the sixth Cys heme ligand will give stabilizing effects.     

Covalent heme attachment to the protein in human heme oxygenase-1 with selenocysteine replacing the His25 proximal iron ligand

To characterize heme oxygenase with a selenocysteine (SeCys) as the proximal iron ligand, we have expressed truncated human heme oxygenase-1 (hHO-1) His25Cys, in which Cys-25 is the only cysteine, in the Escherichia coli cysteine auxotroph strain BL21(DE3)cys. Selenocysteine incorporation into the protein was demonstrated by both intact protein mass measurement and mass spectrometric identification of the selenocysteine-containing tryptic peptide. One selenocysteine was incorporated into approximately 95% of the expressed protein. Formation of an adduct with Ellman’s reagent (DTNB) indicated that the selenocysteine in the expressed protein was in the reduced state. The heme-His25SeCys hHO-1 complex could be prepared by either (a) supplementing the overexpression medium with heme, or (b) reconstituting the purified apoprotein with heme. Under reducing conditions in the presence of imidazole, a covalent bond is formed by addition of the selenocysteine residue to one of the heme vinyl groups. No covalent bond is formed when the heme is replaced by mesoheme, in which the vinyls are replaced by ethyl groups. These results, together with our earlier demonstration that external selenolate ligands can transfer an electron to the iron [Y. Jiang, P.R. Ortiz de Montellano, Inorg. Chem. 47 (2008) 3480-3482 ], indicate that a selenyl radical is formed in the hHO-1 His25SeCys mutant that adds to a heme vinyl group.     

When an amide is more like histidine than imidazole: the role of axial ligands in heme catalysis

 Of the many subtle protein-cofactor interactions which facilitate oxidative catalysis by heme enzymes, the role of the axial ligand has for some time appeared to be fairly well understood. Recent studies from several laboratories, however, have provided good reason to reemphasize the importance of secondary interactions between the axial ligand and protein, as the results suggest that simple ligand identity is neither necessary nor sufficient for function. It has been widely proposed that the strong hydrogen bond between a proximal carboxylate and the histidine ligand of peroxidases assists O–O bond heterolysis and stabilizes the Fe(IV)=O center that is produced. Recent replacements of the axial ligand in a number of heme proteins have produced a few surprises, suggesting that the subtle interactions between the ligand and protein may in some cases be more important than the actual identity of the ligand. Received and accepted: 7 May 1996     

Differential steric effects in the axial ligation of pyridine and imidazole to α- and β-alkylcobinamides

One subclass of B₁₂-requiring enzymes is now known to bind their B₁₂ coenzymes “base-off,” with a histidine residue from the protein supplying an imidazole ligand to the cobalt center. Recent results from Sirovatka and Finke (J.M. Sirovatka and R.G. Finke, J.Am. Chem. Soc. 119, (1997) 3057) show that imidazole has an extraordinary trans effect on the mode of carbon–cobalt bond cleavage in coenzyme B₁₂ analogs, compared to pyridine or the natural 5,6-dimethylbenzimidazole ligand, and it was suggested that a differential steric effect could, in part, account for the uniqueness of the imidazole ligand. Such a differential steric effect for imidazole and pyridine is now demonstrated by studies of the thermodynamics of ligation of these ligands to the α and β diastereomers of two alkylcobinamides (RCbi⁺s, derivatives of cobalamins which lack the normal axial nucleotide) based on the known differences in steric crowding of the α (“lower”) and β (“upper”) axial ligand positions of cobalt corrinoids. Imidazole binds more tightly than pyridine to both diastereomers of NCCH₂Cbi⁺ and CF₃Cbi⁺, in all cases due to a more favorable entropy change, which is the result of lowered steric interference with corrin side chain thermal motions.     

Leghaemoglobin: a model for the investigation of haem protein axial ligation

The structural identity of the axial ligands is one of the major determinants of haem protein function and properties. In this work, the mobile distal histidine residue of soybean leghaemoglobin a has been replaced with a non-coordinating alanine residue (H61A variant) and the H61A variant has been characterised using a range of spectroscopic methods. These experiments provide a useful experimental framework for the examination of haem axial ligation and structure-function relationships.     

Phospholipid assisted folding of a denatured heme protein: effect of phosphatidylethanolamine

The role of the aminophospholipid, phosphatidylethanolamine (PE), has been well established to act as a non-protein molecular chaperone in the folding and assembly of polytopic membrane proteins. However, such studies with soluble proteins have not been done so far and in particular with the heme proteins. We have used the heme enzyme, horseradish peroxidase (HRP), as the model heme protein and studied the effect of different phospholipids on its refolding from denatured state. Dimyristoylphosphatidylethanolamine (DMPE), a bilayer-forming PE, was able to increase the reactivation yield of denatured HRP upon 30min refolding at 25 degrees C. However, dioleoylphosphatidylethanolamine (DOPE), containing one double bond in the fatty acid chains, which does not favour bilayer organization, did not support proper refolding. The phospholipids with N-methylated head groups, phosphatidylcholines, e.g., DMPC and DOPC showed differential effects when DMPC remained mostly non-supportive while DOPC on the contrary led to inhibition of the refolding of the denatured heme enzyme. Fluorescence spectroscopic studies also indicated changes in the microenvironments of the heme moiety and the single tryptophan residue of HRP in presence of the aminophospholipid.     

CFP: a web-server for constructing sequence-based protein conformational flexibility profiles

Many proteins contain conformationally flexible segments that undergo significant changes in the backbone conformation or completely lack a well­defined conformation. Previously, we have developed the generalized local propensity (GLP), a quantitative sequence-based measure of the protein backbone flexibility. In this paper, we present the CFP (Conformational Flexibility Profile) web­server that constructs the GLP flexibility profile for a user­submitted sequence and uses this profile to identify segments with high backbone flexibility. The statistical significance of a flexible sequence segment is assessed using the discrete scan statistics based on the density of flexible residues observed in this segment.

Availability

CFP is publicly available at http://cfp.rit.albany.edu     

Low frequency spectral density of ferrous heme: perturbations induced by axial ligation and protein insertion

Femtosecond coherence spectroscopy is used to probe low frequency (20-400 cm⁻¹) modes of the ferrous heme group in solution, with and without 2-methyl imidazole (2MeIm) as an axial ligand. The results are compared to heme proteins (CPO, P450_cam, HRP, Mb) where insertion of the heme into the protein results in redistribution of the low frequency spectral density and in (∼60%) longer damping times for the coherent signals. The major effect of imidazole ligation to the ferrous heme is the “softening” of the low frequency force constants by a factor of ∼0.6 ± 0.1. The functional consequences of imidazole ligation are assessed and it is found that the enthalpic CO rebinding barrier is increased significantly when imidazole is bound. The force constant softening analysis, combined with the kinetics results, indicates that the iron is displaced by only ∼0.2 Å from the heme plane in the absence of the imidazole ligand, whereas it is displaced by ∼0.4 Å when imidazole (histidine) is present. This suggests that binding of imidazole (histidine) as an axial ligand, and the concomitant softening of the force constants, leads to an anharmonic distortion of the heme group that has significant functional consequences.     

Perturbed heme binding is responsible for the blistering phenotype associated with mutations in the Caenorhabditis elegans dual oxidase 1 (DUOX1) peroxidase domain

Dual oxidase (DUOX) enzymes support a wide variety of essential reactions, from cellular signaling to thyroid hormone biosynthesis. In Caenorhabditis elegans, the DUOX system (CeDUOX1/2) plays a crucial role in innate immunity and in stabilizing the cuticle by forming tyrosine cross-links. The current model suggests that superoxide generated by CeDUOX1 at the C-terminal NADPH oxidase domain is rapidly converted to H(2)O(2). The H(2)O(2) is then utilized by the N-terminal peroxidase-like domain to cross-link tyrosines. We have now created a series of mutations in the isolated peroxidase domain, CeDUOX1(1-589). One set of mutations investigate the roles of a putative distal tyrosine (Tyr(105)) and Glu(238), a proposed covalent heme-binding residue. The results confirm that Glu(238) covalently binds to the heme group. A second set of mutations (G246D and D392N) responsible for a C. elegans blistering cuticle phenotype was also investigated. Surprisingly, although not among the catalytic residues, both mutations affected heme co-factor binding. The G246D mutant bound less total heme than the wild type, but a higher fraction of it was covalently bound. In contrast, the D392N mutant appears to fold normally but does not bind heme. Molecular dynamics simulations of a CeDUOX1(1-589) homology model implicate displacements of the proximal histidine residue as the likely cause. Both enzymes are structurally stable and through altered heme interactions exhibit partial or complete loss of tyrosine cross-linking activity, explaining the blistering phenotype. This result argues that the CeDUOX peroxidase domain is primarily responsible for tyrosine cross-linking.     

The occurrence of leghemoglobin protein in the uninfected interstitial cells of soybean root nodules

The distribution of leghemoglobin (Lb) in resin-embedded root nodules of soybean (Glycine max (L.) Merr.) was investigated using immunogold labeling. Using anti-Lb immunoglobulin G and protein A-gold, Lb or its apoprotein was detected both in cells infected by Bradyrhizobium japonicum and in uninfected interstitial cells. Leghemoglobin was present in the cytoplasm, exclusive of the organelles, and in the nuclei of both cell types. In a comparison of the density of labeling in adjacent pairs of infected and uninfected cells, Lb was found to be about four times more concentrated in infected cells. This is the first report of Lb in uninfected cells of any legume nodule; it raises the possibility that this important nodule-specific protein may participate in mediating oxygen flow to host plant organelles throughout the infected region of the nodule.Abbreviations BSA bovine serum albumin - IgG immunoglobulin G - kDA kilodalton - Lb leghemoglobin - TBST Tris-buffered saline plus Tween 20     

Heme controls the regulation of protein tyrosine kinases Jak2 and Src

Protein tyrosine kinases play key roles in many molecular and cellular processes in diverse living organisms. Their proper functioning is crucial for the normal growth, development, and health in humans, whereas their dysfunction can cause serious diseases, including various cancers. As such, intense studies have been performed to understand the molecular mechanisms by which the activities of protein tyrosine kinases are regulated in mammalian cells. Particularly, small molecules that can modulate the activity of tyrosine kinases are of great importance for discovering therapeutic drug candidates for numerous diseases. Notably, heme cannot only serve as a prosthetic group for hemoglobins and enzymes, but it also is a small signaling molecule that can control the activity of diverse signaling and regulatory proteins. Using a computational search, we found that a group of non-membrane spanning tyrosine kinases contains one or more CP motifs that can potentially bind to heme and mediate heme regulation. We then used experimental approaches to determine whether heme can affect the activity of any of these tyrosine kinases. We found that heme indeed affects the phosphorylation of key tyrosine residues in Jak2 and Src, and is therefore able to modulate Jak2 and Src activity. Further experiments showed that Jak2 and Src bind to heme and that the presence of heme alters the sensitivity of Jak2 and Src to trypsin digestion. These results suggest that heme actively interacts with Jak2 and Src and alters their conformation.     

Effects of reduction and ligation of heme iron on the thermal stability of heme-hemopexin complexes

Hemopexin has two homologous domains (N- and C-terminal domains), binds 1 mole of heme per mole with high affinity (K_d < 1 pM) in a low-spin bis-histidyl complex, and acts as a transporter for the heme. Transport is accomplished via endocytosis without degradation of the protein. Factors that affect stability of the heme coordination complex and potentially heme release in vivo were examined. The effects of temperature on hemopexin, its N-terminal domain, and their respective ferri-, ferro-, and CO-ferro-heme complexes were studied using absorbance and circular dichroism (CD) spectroscopy. As monitored with second-derivative absorbance spectra, the higher order structure of apo-hemopexin unfolds with a T_m of 52°C in 50 mM sodium phosphate buffer and is stabilized by 150 mM NaCl (T_m 63°C). Bis-histidyl heme coordination by hemopexin, observed by Soret absorbance, is substantially weakened by reduction of ferri-heme-hemopexin (T_m 55.5°C) to the ferro-heme form (T_m 48°C), and NaCl stabilizes both complexes by 10-15°C. CO binding to ferro-heme-hemopexin restores complex stability (T_m 67°C). Upon cooling, unfolded apo- and ferri-heme-hemopexin extensively refold and recover substantial heme-binding activity, but the characteristic ellipticity of the native protein (UV region) and heme complex (Soret region) are not regained, indicating that altered refolded forms are produced. Lowering the pH from 7.4 to 6.5 has little effect on the stability of the apo-protein but increases the T_m of heme complexes by 5-12°C. The stability of the apo-N-terminal domain (T_m 53°C) is similar to that of intact hemopexin, and the ferri-, ferro-, and CO-ferro-heme complexes of the N-terminal domain have T_m values of 53°C, 33°C, and 75°C, respectively.     

Solution structure of cyanoferricytochrome c: ligand-controlled conformational flexibility and electronic structure of the heme moiety

The solution structure of cyanoferricytochrome c has been determined using NMR spectroscopy. As a result of including additional constraints derived from pseudocontact shifts, a high-resolution NMR structure was obtained with high accuracy. In order to study the conformational transition between the native protein and its ligand adducts, the present structure was compared with the solution structures of the wild-type cytochrome c and the imidazole-cytochrome c complex. Like the solution structure of imidazole-cytochrome c, the heme crevice is widened by the swinging out of residues 77-85 and a noticeable shift of the 50s helix. However, unlike imidazole, cyanide exerts less significant perturbation on the conformation of the heme cavity, which is revealed by a more compact residue package in the distal pocket. Furthermore, comparison of the solution structure of CN-iso-1Met80Ala cytochrome c with the structure of cyanoferricytochrome c indicated that the binding of cyanide has a different impact on the distal cavity conformation in the two proteins. In addition, the magnetic properties of the present system are discussed and a comprehensive study of the electronic structure of ligand-cytochrome c complexes and the native protein is also described. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00775-001-0334-y.     

A simple method for the determination of reduction potentials in heme proteins

We describe a simple method for the determination of heme protein reduction potentials. We use the method to determine the reduction potentials for the PAS-A domains of the regulatory heme proteins human NPAS2 (E_m = −115 mV ± 2 mV, pH 7.0) and human CLOCK (E_m = −111 mV ± 2 mV, pH 7.0). We suggest that the method can be easily and routinely applied to the determination of reduction potentials across the family of heme proteins.     

Rapid synthesis of DNA-cysteine conjugates for expressed protein ligation

We report a rapid method for the covalent modification of commercially available amino-modified DNA oligonucleotides with a cysteine moiety. The resulting DNA-cysteine conjugates are versatile reagents for the efficient preparation of covalent DNA-protein conjugates by means of expressed protein ligation (EPL). The EPL method allows for the site-specific coupling of cysteine-modified DNA oligomers with recombinant intein-fusion proteins, the latter of which contain a C-terminal thioester enabling the mild and highly specific reaction with N-terminal cysteine compounds. We prepared a cysteine-modifier reagent in a single-step reaction which allows for the rapid and near quantitative synthesis of cysteine-DNA conjugates. The latter were ligated with the green fluorescent protein mutant EYFP, recombinantly expressed as an intein-fusion protein, allowing for the mild and selective formation of EYFP-DNA conjugates in high yields of about 60%. We anticipate many applications of our approach, ranging from protein microarrays to the arising field of nanobiotechnology.     

Replacement of the axial histidine heme ligand with cysteine in nitrophorin 1: spectroscopic and crystallographic characterization

To evaluate the potential of using heme-containing lipocalin nitrophorin 1 (NP1) as a template for protein engineering, we have replaced the native axial heme-coordinating histidine residue with glycine, alanine, and cysteine. We report here the characterization of the cysteine mutant H60C_NP1 by spectroscopic and crystallographic methods. The UV/vis, resonance Raman, and magnetic circular dichroism spectra suggest weak thiolate coordination of the ferric heme in the H60C_NP1 mutant. Reduction to the ferrous state resulted in loss of cysteine coordination, while addition of exogenous imidazole ligands gave coordination changes that varied with the ligand. Depending on the substitution of the imidazole, we could distinguish three heme coordination states: five-coordinate monoimidazole, six-coordinate bisimidazole, and six-coordinate imidazole/thiolate. Ligand binding affinities were measured and found to be generally 2–3 orders of magnitude lower for the H60C mutant relative to NP1. Two crystal structures of the H60C_NP1 in complex with imidazole and histamine were solved to 1.7- and 1.96-Å resolution, respectively. Both structures show that the H60C mutation is well tolerated by the protein scaffold and suggest that heme–thiolate coordination in H60C_NP1 requires some movement of the heme within its binding cavity. This adjustment may be responsible for the ease with which the engineered heme–thiolate coordination can be displaced by exogenous ligands.     

Evidence for the hydrophobic cavity of heme oxygenase-1 to be a CO-trapping site

Carbon monoxide (CO) is produced during the heme catabolism by heme oxygenase. In brain or blood vessels, CO functions as a neurotransmitter or an endothelial-derived relaxing factor. To verify whether crystallographically proposed CO-trapping sites of rat and cyanobacterial heme oxygenase-1 really work, heme catabolism by heme oxygenase-1 from rat and cyanobacterial Synechocystis sp. PCC 6803 has been scrutinized in the presence of 2-propanol. If 2-propanol occupies the trapping sites, formation of CO-bound verdoheme should be enhanced. Although effects of 2-propanol on the rat heme oxygenase-1 reaction were obscure, the reaction of cyanobacterial enzyme in the presence of NADPH/ferredoxin reductase/ferredoxin was apparently affected. Relative amount of CO-verdoheme versus CO-free verdoheme detected by optical absorption spectra increased as the equivalent of 2-propanol increased, thereby supporting indirectly that the hydrophobic cavity in cyanobacterial enzyme traps CO to reduce CO inhibition of verdoheme degradation.     

Attachment of a histidine tag to the minimal zinc finger protein of the Aspergillus nidulans gene regulatory protein AreA causes a conformational change at the DNA-binding site

Histidine (His) tags are one of the most popular fusion tags for the isolation of proteins via metal affinity chromatography. The fusion tag is routinely left attached to the protein when carrying out experiments, with the assumption that the addition has no effect on structure or function. In the present study, we have prepared four proteins of the gene regulatory protein AreA from Aspergillus nidulans for crystallization experiments: a 91-amino acid peptide encompassing the minimal DNA-binding region, both with and without the His-tag (HZFB and ZFB, respectively), and a 155-amino acid protein previously proposed to be the entire DNA-binding domain for AreA, both with and without the His-tag (HG1b and G1b, respectively). To test the integrity of the four AreA proteins, urea denaturation experiments and DNA-binding studies were performed using fluorescence spectroscopy. The DNA-binding data showed similar dissociation constants for all proteins, with Kd values in the nanomolar range. The urea denaturation data, however, clearly indicated that the HZFB protein exhibited a completely different denaturation profile when compared to the ZFB, HG1b, and G1b proteins. The HZFB protein showed a profile indicative of the presence of an altered conformation around the sole tryptophan, whereas the other proteins showed a transition point between 3 and 4 M urea concentration. These data show that, although function was not altered for any of the proteins studied, the structure of one of the His-tagged proteins was different from the native form of that protein.     

Effect of the axial ligands on the structure and reactivity of tin verdoheme in the ring opening process

Conversion of tin(IV) verdoheme complex to tin(IV) biliverdin complex in the presence of hydroxide ion as a nucleophile and various axial ligands has been investigated using the B3LYP method. Our calculations show that in the six coordinate tin(IV) verdoheme complex with imidazole and hydroxyl axial ligands, conversion of tin(IV) verdoheme to open chain macrocycle is favorable thermodynamically but not kinetically. It has been determined that ring opening is prevented through a ligand-centered mechanism. Whereas, in other six coordinate complexes, formation of open chain macrocycles is favorable from both thermodynamics and kinetics point of views. On the contrary, in the five and four coordinate verdoheme complexes of tin(IV) binding of hydroxide to tin terminates the reaction at verdoheme stage and the ring opening is blocked. In fact, in the two latter coordination states, metal-centered inhibition is the proposed mechanism for blocking the ring opening. NBO analysis has shown that in the six coordinate verdoheme complexes internal hydrogen bonding has a key role in inhibition or facilitation of ring opening. These key findings have been confirmed with the results obtained from MO analysis. The presented results could be a hint for the possible implications or coordination for the competitive inhibition of degradation of verdoheme to biliverdin by hydrolysis reaction.     

The effect of protein conformational flexibility on the electronic properties of a chromophore

In this paper we address the question of how a protein environment can modulate the absorption spectrum of a chromophore during a molecular dynamics simulation. The effect of the protein is modeled as an external field acting on the unperturbed eigenstates of the chromophore. Using a first-principles method recently developed in our group, we calculated the perturbed electronic energies for each frame and the corresponding wavelength absorption during the simulation. We apply this method to a nanosencond timescale molecular dynamics simulation of the light-harvesting peridinin-chlorophyll-protein complex from Amphidinium carterae, where chlorophyll was selected among the chromophores of the complex for the calculation. The combination of this quantum-classical calculation with the analysis of the large amplitude motions of the protein makes it possible to point out the relationship between the conformational flexibility of the environment and the excitation wavelength of the chromophore. Results support the idea of the existence of a correlation between protein conformational flexibility and chlorophyll electronic transitions induced by light.