Spectral properties unique to the myoglobins lacking the usual distal histidine residue

Control of distal lysine coordination in a monomeric hemoglobin: A role for heme peripheral interactions

THB1 is a monomeric truncated hemoglobin (TrHb) found in the cytoplasm of the green alga Chlamydomonas reinhardtii. The canonical heme coordination scheme in hemoglobins is a proximal histidine ligand and an open distal site. In THB1, the latter site is occupied by Lys53, which is likely to facilitate Fe(II)/Fe(III) redox cycling but hinders dioxygen binding, two features inherent to the NO dioxygenase activity of the protein. TrHb surveys show that a lysine at a position aligning with Lys53 is an insufficient determinant of coordination, and in this study, we sought to identify factors controlling lysine affinity for the heme iron. We solved the "Lys-off" X-ray structure of THB1, represented by the cyanide adduct of the Fe(III) protein, and hypothesized that interactions that differ between the known "Lys-on" structure and the Lys-off structure participate in the control of Lys53 affinity for the heme iron. We applied an experimental approach (site-directed mutagenesis, heme modification, pH titrations in the Fe(III) and Fe(II) states) and a computational approach (MD simulations in the Fe(II) state) to assess the role of heme propionate-protein interactions, distal helix capping, and the composition of the distal pocket. All THB1 modifications resulted in a weakening of lysine affinity and affected the coupling between Lys53 proton binding and heme redox potential. The results supported the importance of specific heme peripheral interactions for the pH stability of iron coordination and the ability of the protein to undergo redox reactions.

Replacement of the heme axial lysine as a test of conformational adaptability in the truncated hemoglobin THB1

Amino acid replacement is a useful strategy to assess the roles of axial heme ligands in the function of native heme proteins. THB1, the protein product of the Chlamydomonas reinhardtii THB1 gene, is a group 1 truncated hemoglobin that uses a lysine residue in the E helix (Lys53, at position E10 by reference to myoglobin) as an iron ligand at neutral pH. Phylogenetic evidence shows that many homologous proteins have a histidine, methionine or arginine at the same position. In THB1, these amino acids would each be expected to convey distinct reactive properties if replacing the native lysine as an axial ligand. To explore the ability of the group 1 truncated Hb fold to support alternative ligation schemes and distal pocket conformations, the properties of the THB1 variants K53A as a control, K53H, K53M, and K53R were investigated by electronic absorption, EPR, and NMR spectroscopies. We found that His53 is capable of heme ligation in both the Fe(III) and Fe(II) states, that Met53 can coordinate only in the Fe(II) state, and that Arg53 stabilizes a hydroxide ligand in the Fe(III) state. The data illustrate that the group 1 truncated Hb fold can tolerate diverse rearrangement of the heme environment and has a strong tendency to use two protein side chains as iron ligands despite accompanying structural perturbations. Access to various redox pairs and different responses to pH make this protein an excellent test case for energetic and dynamic studies of heme ligation.

Autoxidation of giant extracellular hemoglobin of Glossoscolex paulistus: molecular mechanism and oligomeric implications

Giant extracellular hemoglobins present high redox stability due to their supramolecular architecture, high number of polypeptide chains and great compaction of protein subunits. The oligomeric assembly and the changes in the polypeptidic structure can influence the autoxidation rate of the heme proteins, being that different nucleophiles can act in this process due to pH alterations. In the present work, we have studied the autoxidation rate of whole Glossoscolex paulistus (HbGp) giant extracellular hemoglobin, as well as the autoxidation rate of the isolated d monomer of HbGp studied regarding pH variations. The kinetic decay behavior is dependent on pH, presenting mono-exponential or bi-exponential character, depending on the oligomeric state of the protein. Thus, the oligomeric dissociation in specific pH values demonstrated a bi-exponential kinetic decay. A mono-exponential kinetic behavior was verified in the pH range of 5.9-7.3, which is assigned to the native whole protein. In alkaline medium, the presence of hydroxide ions leads the autoxidation of whole hemoglobin to a complex behavior, which is described by the combination of two first-order kinetics. The slow process occurs due to the d monomer autoxidation. At pH 7.0, the kinetic is mono-exponential, indicating a highly conserved oligomeric structure. In acid medium, the proton-catalyzed autoxidation occurs both on the whole hemoglobin and in the d monomer. It has been found that proximal and distal histidines develop determinant roles regarding the autoxidation rate, being that the distal histidine controls the contact of ligands with the ferrous center through a very interesting "swinging door" mechanism. Despite the significant sensitivity of the distal histidine to the presence of protons, water molecules and anions, the influence of chemical changes around the heme, such as pH changes, is much more effective in hemoproteins without this amino acid as distal residue. This fact denotes the ability of HbGp to adapt to environmental disturbances caused by the presence of the distal histidine, which is responsible for the great redox and oligomeric stabilities encountered in HbGp.

Structure-Function Relationships in Unusual Nonvertebrate Globins

Based on the literature and our own results, this review summarizes the most recent state of nonvertebrate myoglobin (Mb) and hemoglobin (Hb) research, not as a general survey of the subject but as a case study. For this purpose, we have selected here four typical globins to discuss their unique structures and properties in detail. These include Aplysia myoglobin, which served as a prototype for the unusual globins lacking the distal histidine residue; midge larval hemoglobin showing a high degree of polymorphism; Tetrahymena hemoglobin evolved with a truncated structure; and yeast flavohemoglobin carrying an enigmatic two-domain structure. These proteins are not grouped by any common features other than the fact they have globin domains and heme groups. As a matter of course, various biochemical functions other than the conventional oxygen transport or storage have been proposed so far to these primitive or ancient hemoglobins or myoglobins, but the precise in vivo activity is still unclear. In this review, special emphasis is placed on the stability properties of the heme-bound O2. Whatever the possible roles of nonvertebrate myoglobins and hemoglobins may be (or might have been), the binding of molecular oxygen to iron(II) must be the primary event to manifest their physiological functions in vivo. However, the reversible and stable binding of O2 to iron(II) is not a simple process, since the oxygenated form of Mb or Hb is oxidized easily to its ferric met-form with the generation of superoxide anion. The metmyoglobin or methemoglobin thus produced cannot bind molecular oxygen and is therefore physiologically inactive. In this respect, protozoan ciliate myoglobin and yeast flavohemoglobin are of particular interest in their very unique structures. Indeed, both proteins have been found to have completely different strategies for overcoming many difficulties in the reversible and stable binding of molecular oxygen, as opposed to the irreversible oxidation of heme iron(II). Such comparative studies of the stability of MbO2 or HbO2 are of primary importance, not only for a full understanding of the globin evolution, but also for planning new molecular designs for synthetic oxygen carriers that may be able to function in aqueous solution and at physiological temperature.

An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control

A commonly observed coupling of sensory domains to GGDEF-class diguanylate cyclases and EAL-class phosphodiesterases has long suggested that c-di-GMP synthesizing and degrading enzymes sense environmental signals. Nevertheless, relatively few signal ligands have been identified for these sensors, and even fewer instances of in vitro switching by ligand have been demonstrated. Here we describe an Escherichia coli two-gene operon, dosCP, for control of c-di-GMP by oxygen. In this operon, the gene encoding the oxygen-sensing c-di-GMP phosphodiesterase Ec Dos (here renamed Ec DosP) follows and is translationally coupled to a gene encoding a diguanylate cyclase, here designated DosC. We present the first characterizations of DosC and a detailed study of the ligand-dose response of DosP. Our results show that DosC is a globin-coupled sensor with an apolar but accessible heme pocket that binds oxygen with a K(d) of 20 microM. The response of DosP activation to increasing oxygen concentration is a complex function of its ligand saturation such that over 80% of the activation occurs in solutions that exceed 30% of air saturation (oxygen >75 microM). Finally, we find that DosP and DosC associate into a functional complex. We conclude that the dosCP operon encodes two oxygen sensors that cooperate in the controlled production and removal of c-di-GMP.

N-terminal labeling of proteins by the Pictet-Spengler reaction

The Pictet-Spengler reaction was applied to the N-terminal labeling of horse heart myoglobin. This was performed in the following two steps: (1) conversion of the N-terminal glycine residue to an alpha-keto aldehyde by a transamination reaction and (2) condensation of the resulting activated myoglobin with tryptamine analogues by the Pictet-Spengler reaction. Ultraviolet (UV)/visible (vis) absorption and circular dichroism (CD) spectral data revealed that the tertiary structure of myoglobin was not altered by the Pictet-Spengler reaction.

Functional and structural characterization of the myoglobin from the polychaete Ophelia bicornis

The myoglobin of the polychaete annelid Ophelia bicornis was isolated, purified to homogeneity and characterized. The primary structure, obtained from cDNA and protein sequencing, consists of 139 amino acid residues. The alignment with other globin sequences showed that O. bicornis myoglobin misses the pre-A helix and the first six residues of the A helix. The presence of a PheB10-GlnE7 haem distal residue pair is in agreement with the measured oxygen affinity (P50=0.85 mmHg; 1 mmHg=0.133 kPa) and the only slightly higher autoxidation rate constant (0.28 h(-1)) with respect to that of the sperm whale myoglobin mutant E7 His-->Gln (0.21 h(-1)) and to elephant myoglobin (0.1 h(-1)). Oxygen-binding co-operativity was found to be absent under all the examined experimental conditions. The resistance of O. bicornis myoglobin towards autoxidation seems to confirm the important role of part of the A helix in the stability of the globin. The higher pKa of the acid-alkaline ferric transition of O. bicornis with respect to Asian elephant myoglobin, as well as the higher absorbance ratio of its ferric form to the oxy form measured in the Soret region (gammamet/gammaoxy) with respect to that of the African elephant myoglobin, suggested a stronger interaction between the distal glutamine and the water molecule at the sixth co-ordinate position.

Nature of the FeO2 bonding in myoglobin and hemoglobin: A new molecular paradigm

The iron(II)-dioxygen bond in myoglobin and hemoglobin is a subject of wide interest. Studies range from examinations of physical-chemical properties dependent on its electronic structure, to investigations of the stability as a function of oxygen supply. Among these, stability properties are of particular importance in vivo. Like all known dioxygen carriers synthesized so far with transition metals, the oxygenated forms of myoglobin and hemoglobin are known to be oxidized easily to their ferric met-forms, which cannot bind molecular oxygen and are therefore physiologically inactive. The mechanistic details of this autoxidation reaction, which are of clinical, as well as of physical-chemical, interest, have long been investigated by a number of authors, but a full understanding of the heme oxidation has not been reached so far. Recent kinetic and thermodynamic studies of the stability of oxymyoglobin (MbO2) and oxyhemoglobin (HbO2) have revealed new features in the FeO2 bonding. In vivo, the iron center is always subject to a nucleophilic attack of the water molecule or hydroxyl ion, which can enter the heme pocket from the surrounding solvent and thereby irreversibly displace the bound dioxygen from MbO2 or HbO2 in the form of O2- so that the iron is converted to the ferric met-form. Since the autoxidation reaction of MbO2 or HbO2 proceeds through a nucleophilic displacement following one-electron transfer from iron(II) to the bound O2, this reaction may be viewed as a meeting point of the stabilization and the activation of molecular oxygen performed by hemoproteins. Along with these lines of evidence, we finally discuss the stability property of human HbO2 and provide with the most recent state of hemoglobin research. The HbA molecule contains two types of alphabeta contacts and seems to differentiate them quite properly for its functional properties. The alpha1beta2 or alpha2beta1 contact is associated with the cooperative oxygen binding, whereas the alpha1beta1 or alpha2beta2 contact is used for controlling the stability of the bound O2. We can thus form a unified picture for hemoglobin function by closely integrating the cooperative and the stable binding of molecular oxygen with iron(II) in aqueous solvent. These new views on the nature of FeO2 bonding and the possible role of globin moiety in stabilizing MbO2 and HbO2 are of primary importance, not only for a full understanding of various hemoprotein reactions with O2, but also for planning new molecular designs for synthetic oxygen carriers which may be able to function in aqueous solvent and at physiological temperature.

The effect of acid and alkali unfolding and subsequent refolding on the pro-oxidative activity of trout hemoglobin

The pro-oxidative activity of trout hemoglobin was significantly increased at low pH (2.5-3.5) in a washed fish muscle (WFM) system. It was found that the more unfolded the hemoglobin was the more exposed its heme group was, which increased its pro-oxidative activity. The amount of oxidation products produced (TBARS) were, however, lower at low pH vs neutral pH. At pH 10.5-11, the pro-oxidative activity of hemoglobin was greatly suppressed. The conformation of hemoglobin was significantly more stable at high pH as compared to pH 7 as judged by its visible absorption spectrum. Hemoglobin readjusted from low pH to pH 7 had a higher pro-oxidative activity (i.e., more rapid oxidation) in WFM than native hemoglobin at pH 7, even though TBARS values were lower than in the untreated sample at pH 7. The results suggest that the WFM becomes slightly more susceptible to oxidation after low pH treatment but also produces less TBARS. The increased pro-oxidative activity after pH readjustment correlated well with an incomplete recovery in the native structure on pH readjustment. A longer unfolding time and a lower pH led to a less refolded hemoglobin with increased pro-oxidative activity. Hemoglobin was less pro-oxidative at low pH in the presence of 500 mM NaCl. The presence of salt did, however, increase the pro-oxidative properties of hemoglobin after readjustment to pH 7. The treatment of washed fish muscle at alkaline pH followed by adjustment to pH 7 led to a slight delay in hemoglobin-mediated lipid oxidation in WFM as compared to native hemoglobin at pH 7. The results suggest that WFM becomes less susceptible toward oxidation after pH readjustment from alkaline pH. These results clearly show that for muscle protein extraction/isolation processes requiring highly alkaline or acidic conditions, alkaline conditions are preferred if the lipid oxidation originating from hemoglobin is to be minimized.

The swinging movement of the distal histidine residue and the autoxidation reaction for midge larval hemoglobins

Some insects have a globin exclusively in their fast-growing larval stage. This is the case in the 4th-instar larva of Tokunagayusurika akamusi, a common midge found in Japan. In the polymorphic hemoglobin comprised of 11 separable components, hemoglobin VII (Ta-VII Hb) was of particular interest. When its ferric met-form was exposed to pH 5.0 from 7.2, the distal histidine was found to swing away from the E7 position. As a result, the iron(III) was converted from a hexacoordinate to a pentacoordinate form by a concomitant loss of the axial water ligand. The corresponding spectral changes in the Soret band were therefore followed by stopped-flow and rapid-scan techniques, and the observed first-order rate constants of k(out) = 25 s(-1) and kin = 128 s(-1) were obtained for the outward and inward movements, respectively, of the distal histidine residue in 0.1 m buffer at 25 degrees C. For O2 affinity, Ta-VII Hb showed a value of P50 = 1.7 Torr at pH 7.4, accompanied with a remarkable Bohr effect (deltaH+ = -0.58) almost equal to that of mammalian hemoglobins. We have also investigated the stability property of Ta-VII HbO2 in terms of the autoxidation rate over a wide range of pH from 4 to 11. The resulting pH-dependence curve was compared with those of another component Ta-V HbO2 and sperm whale MbO2, and described based on a nucleophilic displacement mechanism. In light of the O2 binding affinity, Bohr effect and considerable stability of the bound O2 against acidic autoxidation, we conclude that T. akamusi Hb VII can play an important role in O2 transport and storage as the major component in the larval hemolymph.

Yeast flavohemoglobin from Candida norvegensis. Its structural, spectral, and stability properties

Flavohemoglobin was isolated directly from the yeast Candida norvegensis and studied on its structural, spectral, and stability properties. In Candida flavohemoglobin, the 155 N-terminal residues make a heme-containing domain, while the remaining 234 C-terminal residues serve as a FAD-containing reductase domain. A pair of His-95 and Gln-63 was assigned to the proximal and distal residues, respectively. In purification procedure FAD was partially dissociated on a Butyl-Toyopearl column, so that FAD-lacking flavohemoglobin was also obtainable. In this ferric species, the Soret and charge-transfer bands were all characteristic of a penta-coordinate form. Compared with the recombinant heme domain expressed in Escherichia coli, we have measured the autoxidation rate over a wide pH range. The resulting pH dependence curves were then analyzed in terms of a nucleophilic displacement mechanism. As a result, the heme domain was found to be extremely susceptible to autoxidation, its rate being more than 100 times higher than that of sperm whale MbO2. However, this inherently high oxidation rate was dramatically suppressed in Candida flavohemoglobin to an extent almost comparable to the stability of mammalian myoglobins. These new findings lead us to conclude that Candida flavohemoglobin, differently from bacterial flavohemoglobins, can serve as an oxygen storage protein in aerobic conditions.

Nonvertebrate hemoglobins: functions and molecular adaptations

Hemoglobin (Hb) occurs in all the kingdoms of living organisms. Its distribution is episodic among the nonvertebrate groups in contrast to vertebrates. Nonvertebrate Hbs range from single-chain globins found in bacteria, algae, protozoa, and plants to large, multisubunit, multidomain Hbs found in nematodes, molluscs and crustaceans, and the giant annelid and vestimentiferan Hbs comprised of globin and nonglobin subunits. Chimeric hemoglobins have been found recently in bacteria and fungi. Hb occurs intracellularly in specific tissues and in circulating red blood cells (RBCs) and freely dissolved in various body fluids. In addition to transporting and storing O(2) and facilitating its diffusion, several novel Hb functions have emerged, including control of nitric oxide (NO) levels in microorganisms, use of NO to control the level of O(2) in nematodes, binding and transport of sulfide in endosymbiont-harboring species and protection against sulfide, scavenging of O(2 )in symbiotic leguminous plants, O(2 )sensing in bacteria and archaebacteria, and dehaloperoxidase activity useful in detoxification of chlorinated materials. This review focuses on the extensive variation in the functional properties of nonvertebrate Hbs, their O(2 )binding affinities, their homotropic interactions (cooperativity), and the sensitivities of these parameters to temperature and heterotropic effectors such as protons and cations. Whenever possible, it attempts to relate the ligand binding properties to the known molecular structures. The divergent and convergent evolutionary trends evident in the structures and functions of nonvertebrate Hbs appear to be adaptive in extending the inhabitable environment available to Hb-containing organisms.

A primitive myoglobin from Tetrahymena pyriformis: its heme environment, autoxidizability, and genomic DNA structure

A myoglobin-like protein isolated from Tetrahymena pyriformis is composed of 121 amino acid residues. This is much smaller than sperm whale myoglobin by 32 residues, suggesting a distinct origin from the common globin gene. We have therefore examined this unique protein for its structural, spectral and stability properties. As a result, the rate of autoxidation of Tetrahymena oxymyoglobin (MbO(2)) was found to be almost comparable to that of sperm whale MbO(2) over a wide range of pH 4-12 in 0.1 M buffer at 25 degrees C. Moreover, both pH profiles exhibited the remarkable proton-assisted process, which can be performed in sperm whale myoglobin by the distal (E7) histidine as its catalytic residue. These kinetic observations are also in full accord with spectral examinations for the presence of a distal histidine in ciliated protozoa myoglobin. At the same time, we have isolated the globin genes both from T. pyriformis and Tetrahymena thermophila, and found that there is no intron in their genomic structures. This is in sharp contrast to previous reports on the homologous globin genes from Paramecium caudatum and Chlamydomonas eugametos. Rather, the Tetrahymena genes seemed to be related to the cyanobacterial globin gene from Nostoc commune. These contracted or truncated globins thus have a marked diversity in the cDNA, protein, and genomic structures.

Dual nature of the distal histidine residue in the autoxidation reaction of myoglobin and hemoglobin comparison of the H64 mutants

The oxygenated form of myoglobin or hemoglobin is oxidized easily to the ferric met-form with generation of the superoxide anion. To make clear the possible role(s) of the distal histidine (H64) residue in the reaction, we have carried out detailed pH-dependence studies of the autoxidation rate, using some typical H64 mutants of sperm whale myoglobin, over the wide range of pH 5-12 in 0.1 M buffer at 25 degrees C. Each mutation caused a dramatic increase in the autoxidation rate with the trend H64V >/= H64G >/= H64L >> H64Q > H64 (wild-type) at pH 7.0, whereas each mutant protein showed a characteristic pH-profile which is essentially different from that of the wild-type or native sperm whale MbO2. In particular, all the mutants have lost the acid-catalyzed process that can play a dominant role in the autoxidation reaction of most mammalian myoglobins or hemoglobins. Kinetic analyses of various types of pH-profiles lead us to conclude that the distal histidine residue can play a dual role in the nucleophilic displacement of O2- from MbO2 or HbO2 in protic, aqueous solution. One is in a proton-relay mechanism via its imidazole ring, and the other is in the maximum protection of the FeO2 center against a water molecule or an hydroxyl ion that can enter the heme pocket from the surrounding solvent.

Cloning, overexpression and characterization of micro-myoglobin, a minimal heme-binding fragment

We report the cloning and expression of micro-myoglobin, a 78-amino-acid fragment containing residues 29-105 of sperm whale myoglobin, and spanning the region from mid-helix B to mid-helix G of the globin fold. In contrast to full-length myoglobin and to mini-myoglobin (residues 32-129), the micro-myoglobin apoprotein is almost unfolded. However, circular dichroism and absorption spectroscopy data indicate that this fragment is capable of folding into a functional heme-binding unit forming a complex with the prosthetic group with characteristics similar to native myoglobin. Therefore, this case represents a new example of cofactor-assisted folding. The experimental data suggest independence between myoglobin subdomains.

Hydrogen bonding interaction of the amide group of Asn and Gln at distal E7 of bovine myoglobin with bound-ligand and its functional consequences

Asn and Gln with an amide group at gamma- and delta-positions, respectively, were substituted for distal His-E7 of bovine myoglobin to establish a system where hydrogen bonding interaction between the distal residue and bound-ligand can be altered by changing donor-acceptor distance. Two mutant myoglobins showed nearly identical (1)H-NMR spectral pattern for resolved heme peripheral side-chain and amino acid proton signals and similar two-dimensional NMR connectivities irrespective of cyanide-bound and -unbound states, indicating that the heme electronic structure and the molecular structure of the active site are not affected by a difference in one methylene group at the E7 position. Chemical exchange rate of Asn-E7 N(delta)H proton in met-cyano myoglobin is larger than that of Gln-E7 N(epsilon)H proton by at least two orders of magnitude, suggesting a considerable difference in the strength of hydrogen bond between the E7 side-chain and bound-ligand, due to the differential donor-acceptor distance between the two mutants. Thus a comparative study between the two proteins provides an ideal system to delineate a relationship between the stabilization of bound-ligand by the hydrogen bond and myoglobin's ligand affinity. The Asn-mutant showed a faster dissociation of cyano ion from met-myoglobin than the Gln-mutant by over 30-fold. Similarly, oxygen dissociation is faster in the Asn-mutant than in the Gln-mutant by approximately 100-fold. Association of cyanide anion to the mutant met-myoglobin was accelerated by changing Gln to Asn by a 4-fold. Likewise, oxygen binding was accelerated by approximately 2-fold by the above substitution. The present findings confirm that hydrogen bonding with the distal residue is a dominant factor for determining the ligand dissociation rate, whereas steric hindrance exerted by the distal residue is a primary determinant for the ligand association.

A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties

The glbN gene of the cyanobacterium Nostoc commune UTEX 584 encodes a hemoprotein, named cyanoglobin, that has high oxygen affinity. The basis for the high oxygen affinity of cyanoglobin was investigated through kinetic studies that utilized stopped-flow spectrophotometry and flash photolysis. Association and dissociation rate constants were measured at 20 degrees C for oxygen, carbon monoxide, nitric oxide, and methyl and ethyl isocyanides. The association rate constants for the binding of these five ligands to cyanoglobin are the highest reported for any naturally occurring hemoglobin, suggesting an unhindered and apolar ligand binding pocket. Cyanoglobin also shows high rates of autoxidation and hemin loss, indicating that the prosthetic group is readily accessible to solvent. The ligand binding behavior of cyanoglobin was more similar to that of leghemoglobin a than to that of sperm whale myoglobin. Collectively, the data support the model of cyanoglobin function described by Hill et al. [(1996) J. Bacteriol. 178, 6587-6598], in which cyanoglobin sequesters oxygen, and presents it to, or is a part of, a terminal cytochrome oxidase complex in Nostoc commune UTEX 584 under microaerobic conditions, when nitrogen fixation, and thus ATP demand, is maximal.

African elephant myoglobin with an unusual autoxidation behavior: comparison with the H64Q mutant of sperm whale myoglobin

Elephant myoglobins both from Asian and African species have a glutamine in place of the usual distal (E7) histidine at position 64. We have isolated native oxymyoglobin directly from the skeletal muscle of African elephant (Loxodonta africana), and examined the autoxidation rate of oxymyoglobin (MbO2) to metmyoglobin (metMb) as a function of pH in 0.1 M buffer at 25 degreesC. As a result, African elephant MbO2 was found to be equally resistant to autoxidation as sperm whale myoglobin. However, the elephant myoglobin exhibited a distinct rate saturation below pH 6. Kinetic analysis of the pH profiles for the autoxidation rate has disclosed that African elephant MbO2 does not show any proton-catalyzed process, such as the one that can play a dominant role in the autoxidation reaction of sperm whale myoglobin by involving the distal histidine as its catalytic residue. Such a greater stability of African elephant MbO2 at low pH could be explained almost completely by the single H64Q mutation of sperm whale myoglobin. In African elephant aqua-metmyoglobin the Soret band was considerably broadened so as to produce another peak in the pentacoordinate 395 nm region. This unique spectral feature was therefore analyzed to show that the myoglobin is in equilibrium between two species, depending upon the presence or absence of a water molecule at the sixth coordinate position.

Imidazole is a sensitive probe of steric hindrance in the distal pockets of oxygen-binding heme proteins

The FixL heme-based sensor, despite its low affinity for oxygen, is much more reactive than myoglobin toward the large polar ligand imidazole. To determine which features of a myoglobin heme pocket favor binding of imidazole, we have measured binding of this ligand to the FixL heme domain, elephant myoglobin, wild-type sperm whale myoglobin, and sperm whale myoglobins having alanine, valine, threonine, glutamine, leucine, phenylalanine, or tryptophan substitutions of the distal (E7) histidine residue. Except for histidine, the association rate constants dropped more than 3000-fold as the volume of the E7 side chain, at position 64, was expanded from alanine (10(6) M-1 s-1) to phenylalanine (10(3) M-1 s-1). There was inhibition of imidazole binding due to displacement of coordinated water from H64 and H64Q sperm whale myoglobins, where the E7 side chain hydrogen bonds directly to the bound ligand. The imidazole dissociation rate constants varied less dramatically and less consistently with any single factor, though they were measurably decreased by hydrogen bonding to an E7 glutamine or histidine. On the whole, the results for the sperm whale myoglobin E7 substitutions show that the rate constants for imidazole binding are useful and sensitive indicators of steric hindrance and polar interactions in the distal pockets of myoglobins. The combined effects of the glutamine 64 and phenylalanine 29 in elephant myoglobin largely account for its increased imidazole association and dissociation rate constants, respectively, compared to those of sperm whale myoglobin. An unhindered distal pocket not competent to stabilize positive poles is indicated by the large imidazole association (>/=10(4) M-1 s-1) and dissociation (>/=50 s-1) rate constants, parameters that are characteristic of FixL.

1H NMR study of dynamics and thermodynamics of acid-alkaline transition in ferric hemoglobin of a midge larva (Tokunagayusurika akamusi)

One of the components of hemoglobin from the larval hemolyph of Tokunagayusurika akamusi possesses naturally occurring substitution at the E7 helical position (Leu E7) [M. Fukuda, T. Takagi, K. Shikama, Biochim. Biophys. Acta 1157 (1993) 185-191]. Its oxygen affinity is almost comparable to those of mammalian myoglobins and it exhibits Bohr effect. Both acidic and alkaline forms of the ferric hemoglobin have been investigated using 1H NMR in order to gain insight into molecular mechanisms for relatively high oxygen affinity and Bohr effect of this protein. The NMR data indicated that the acidic form of the protein possesses pentacoordinated heme, and that the alkaline form possessing OH- appears with increasing the pH value. pH titration yielded a pK value of 7.2 for the acid-alkaline transition, and this value is the lowest among the values reported so far for various myoglobins and hemoglobins. The kinetic measurements of the transition revealed that the activation energy for the dissociation of the Fe-bound OH-, as well as the dissociation and association rates, decrease with increasing the pH value. These pH dependence properties are likely to be related to the Bohr effect of this protein.

Recombinant [Phe(beta)63]hemoglobin shows rapid oxidation of the beta chains and low-affinity, non-cooperative oxygen binding to the alpha subunits

We have engineered alpha2beta2 [Phe63]hemoglobin by changing the highly conserved distal histidine of the beta chains to a phenylalanine. The mutant tetramer binds four high-affinity ligands, such as CO or NO, to the ferrous form, or CN to the oxidized iron; however, it binds only two low-affinity ligands, oxygen and azide. The absorption spectrum of the ferrous deoxy or ferric forms are not normal, displaying an enhanced absorption of the visible band near 560 nm. Half of the autooxidation process, attributed to the mutated beta subunits, is over 1000-fold faster than for Hb A. The mutant Hb exhibits non-cooperative binding of two oxygens with an affinity about fivefold lower than those of HbA valency hybrids (alpha met beta)2. Functional properties of this mutant Hb resemble those of Hb Saskatoon ([Tyr63]Hb) [Suzuki, T., Hayashi, A., Shimizu, A. & Yamamura, Y. (1966) Biochim. Biophys. Acta 127, 280-282]. Flash-photolysis experiments also indicate non-cooperative behaviour: the CO-recombination kinetics were independent of the fraction dissociated. Furthermore, the amplitude of the CO bimolecular phase was the same for the (alpha(CO)metbeta)2 valency hybrid or the (alphaCO betaCO)2 form, suggesting mainly geminate CO-recombination kinetics to the beta chains. EPR and Resonance Raman spectra did not show evidence for a hemichrome, normally considered as a six-coordinated iron with low-spin character. The EPR and resonance Raman spectra for the mutated beta subunits demonstrate the presence of a high-spin compound in the ferric and deoxy ferrous forms. In particular, the ferrous mutated beta subunits are penta-coordinated. The abnormal absorption spectra are possibly due to an interaction between the porphyrin and the phenyl ring in the distal position rather than to direct binding to the iron.

Nonsteric factors dominate binding of nitric oxide, azide, imidazole, cyanide, and fluoride to the rhizobial heme-based oxygen sensor FixL

BACKGROUND

The FixL protein is a heme-based sensor. Binding of oxygen to a unique heme domain inhibits a kinase domain of the type found in two-component regulators. Oxygen association is slow, but the dissociation rate is comparable to that of myoglobins. We have probed the size and chemistry of the FixL heme pocket by measuring the affinites, on rates and off rates for a wide variety of ferric heme ligands. Cyanide, but not fluoride, regulates the kinase activity. To examine how the sensory heme domain interacts with the kinase, we asked how the presence of the kinase domain affects ligand binding.

RESULTS

The affinities of ferric FixL for heme ligands follow the same trend as their pKa values: cyanide > 4-methyl imidazole > imidazole > fluoride > azide >> thiocyanate. The association rates follow the reverse trend. Striking differences from myoglobin include a 6-fold greater affinity for, and faster binding to, the bulky ligand imidazole, a 14-fold faster on rate for nitric oxide, a 2 800-fold lower affinity for azide, and a complete failure to bind thiocyanate. The presence of the kinase domain does not alter the affinity or binding kinetics of the high-spin ligand fluoride, but affects the off rates of other ligands. The EPR spectrum shows a characteristic pentacoordinate nitrosyl heme, indicating that the Fe-His bond in FixL is strained.

CONCLUSIONS

The importance of ligand deprotonation to the on rates and the fact that large ligands bind readily indicate that the heme pocket is open and apolar. Ligand basicity strongly influences the strength of binding. The destabilization of inhibitory ligands by the presence of the kinase domain is consistent with a 'load' imposed by coupling to the inactivating mechanism.

The unique structures of protozoan myoglobin and yeast hemoglobin: an evolutionary diversity

A hemoglobin-like protein is found in some of the single-celled organisms, but its structure is quite different from that of mammalian myoglobin or hemoglobin. For instance, a protozoan myoglobin isolated from Paramecium caudatum consists of 116 amino acid residues, so that this contracted form is nearly two thirds of sperm whale myoglobin. Yeast hemoglobin from Candida norvegensis, on the other hand, is composed of a single polypeptide chain with 387 amino acid residues, but of two distinct domains carrying different functions; that is the N-terminal, heme-containing region and the C-terminal, FAD-containing reductase domain. The very unique structures of these ancient hemoproteins tell us their own strategies to overcome many difficulties in the reversible and stable binding of molecular oxygen, a very strong oxidizing agent, to the heme iron(II) in aqueous solutions.

The pH-dependent swinging-out of the distal histidine residue in ferric hemoglobin of a midge larva (Tokunagayusurika akamusi)

Hemoglobin VII (TaVII) is a major component in the larval hemolymph of Tokunagayusurika akamusi, a common midge (Diptera) found in Japan. This protein contains 150 amino-acid residues including the usual distal histidine at position 64. When the aquomet-form was placed in acidic pH range, its Soret peak was considerably blue-shifted and accompanied by a marked decrease in intensity, indicative of the protein being converted into a structure quite similar to that of Aplysia myoglobin lacking the distal histidine residue. The pH-dependent magnetic circular dichroism spectra in the Soret region have also revealed that TaVII hemoglobin is in an equilibrium between a hexacoordinate and a pentacoordinate structure for its ferric heme iron. We attribute this to a transition from an iron-ligated water molecule that is hydrogen-bonded to the distal histidine, to a water-free iron with the histidine swung-out of the heme pocket. Furthermore, this process was described by the involvement of a single dissociable group with pKa = 6.3 in 0.1 M KCl at 25 degrees C.

Heme-based sensors, exemplified by the kinase FixL, are a new class of heme protein with distinctive ligand binding and autoxidation

FixL's are chimeric heme protein kinases from symbiotic nitrogen-fixing Rhizobia. We have overexpressed three FixL variants in Escherichia coli. Bradyrhizobium japonicum FixL, a soluble dimeric protein, is the first full-length FixL to be purified. The other two proteins are soluble truncations of Rhizobium meliloti FixL, which is a membrane protein. One contains both heme and kinase domains and is dimeric; the other has only the heme domain and is monomeric. We find that all the FixL's bind oxygen and carbon monoxide non-cooperatively, with very low affinities due entirely to slow association rates. FixL P50's for oxygen are 17-76 mmHg. FixL's may sense nitric oxide and carbon monoxide in addition to oxygen, especially at the low oxygen pressures encountered in vivo. Autoxidation rates are about 50 times faster than that of sperm whale myoglobin. The carbon monoxide affinity of FixL's is about 300 times lower than that of myoglobin, resulting in the unusually low values of 7.5-17 for the partition constant, M = P50(O2)/P50(CO), between carbon monoxide and oxygen. Met-FixL's have their Soret absorption maximum at 395 nm instead of the typical 408 nm and a steep hydroxymet transition at pH > or = 9.3; these properties indicate a pentacoordinated high-spin ferric heme and suggest a sterically hindered hydrophobic heme pocket lacking a distal (E7) histidine. FixL is the first member of a new class of heme proteins, the heme-based sensors, distinct from the oxygen carriers and electron transporters. We expect that some of the novel properties of FixL will be characteristic of the class.

Polymorphic hemoglobin from a midge larva (Tokunagayusurika akamusi) can be divided into two different types

The hemoglobin from the 4th-instar larva of Tokunagayusurika akamusi, a common midge found in eutrophic lakes in Japan, was composed of as many as 11 separable components (IA, IB, II, III, IV, V, VIA, VIB, VII, VIII, IX) on a DEAE-cellulose column. However, we have found that these components can be divided into two groups on the basis of their spectroscopic properties, one being named as the normal type (N-type) and the other being referred to as the low type (L-type). Since the major difference between them seemed to be the presence or absence of the distal (E7) histidine residue, which plays an important role in the stability properties of the bound dioxygen, the complete amino acid sequence was then determined for each typical component, namely, VII (N-type) and V (L-type): the former hemoglobin contained the usual distal histidine residue at position 64, whereas the latter one replaced it by isoleucine at position 66. The homology test for 40 N-terminal amino acid residues of all components also demonstrates that T. akamusi hemoglobin is composed of two different clusters showing a very early separation in the phylogenetic tree.

Ligand affinities in mutant metmyoglobins

Ligand binding to the wild-type and a series of mutant porcine myoglobins, expressed and purified from Escherichia coli cells, has been studied using UV-VIS absorption spectroscopy. The proximal pocket mutation, F7 Ser-->Leu (F7), causes an increased affinity for OH- and N3- binding to metmyoglobin. A hydrogen bond between the F7 serine residue and the imidazole side-chain of the proximal histidine has been removed by this mutation. It is suggested that this allows the imidazole group to reorientate, reducing the steric clash between itself and the haem pyrrole nitrogen atoms and leading to a shortening of the bond between the proximal histidine and the haem iron. Other conformational changes further away from the haem pocket have also been induced, but the mutant still crystallizes under the same conditions as for the wild-type protein. A series of distal pocket mutants, E11 Val-->Thr (VT), E7 His-->Val (HV) and a mutant with both of these substitutions (M2) all have greatly reduced the OH- and N3- binding affinity. These effects have been interpreted by considering several factors: the changed stability of the aquometmyoglobin form, hydrogen-bond formation between the ligand and the E7 residue, and electrostatic repulsion between the ligand and the E11 threonine residue.

The Soret magnetic circular dichroism of ferric high-spin myoglobins. A probe for the distal histidine residue

To find a simple criterion for the presence of the distal (E7) histidine residue in myoglobins and hemoglobins, the Soret magnetic-circular-dichroic spectra were examined for ferric metmyoglobins from various species. A distinct and symmetric dispersion-type curve was obtained for myoglobins containing the distal histidine, whereas a relatively weak and unsymmetric pattern was observed for myoglobins lacking this residue, such as those from three kinds of gastropodic sea molluscs, a shark and the African elephant. The magnetic-circular-dichroic spectra obtained would thus be a direct reflection of the presence or absence of a water molecule at the sixth coordinate position of the heme iron(III), this axial water ligand being stabilized by hydrogen-bond formation to the distal histidine residue. On the basis of these Soret magnetic-circular-dichroic signals, we also examined the structure of a protozoan myoglobin (or a monomeric hemoglobin) from Paramecium caudatum of particular interest for the evolution of these proteins from protozoa to higher animals.

Spectroscopic studies of an insect hemoglobin from the backswimmer Buenoa margaritacea (Hemiptera:Notonectidae)

Hemoglobin (Hb) isolated from the backswimmer Buenoa margaritacea has been analyzed spectroscopically. The met form at pH less than 6 shows a 30nm red shift in the Qv and Qo bands and a 5nm red shift in the Soret band compared to mammalian Hb, while only minor differences are seen in the spectra of the CO and O2 adducts of Hb from Buenoa and mammals. EPR spectra of the metHb show a superposition of signals; at low pH they are mainly of axial high-spin character, while at high pH a low-spin signal predominates with an O-type g-tensor (2.54, 2.61, 1.85) comparable to that of hydroxy myoglobin. Infrared spectra of Hb12C-16O at pH 8.2 reveal two major absorption bands at 1934 cm-1 and 1967 cm-1, which shift to 1892 cm-1 and 1923 cm-1, respectively, for Hb12C-18O. As isolated the Buenoa Hb consists of several isozymes, all of which have a histidine as the proximal ligand of the heme iron.

A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex

To gain insight into the folding mechanism of the cytochrome c complex, we prepared a complete set of homologous and hybrid two-fragment ferric complexes of four different types and related complexes from horse, tuna, yeast iso-l, and Candida cytochromes c. The complexes were characterized for structural properties. Apparent equilibrium constants of the complexes were determined to calculate delta G0 for binding. The results have allowed us to assign four core domains of the complex. A core domain is a structural region containing a hydrophobic core and the surrounding shell which folds and unfolds as a unit. Core domain 1 folds by itself and consists essentially of the right channel structure, found by R. E. Dickerson and colleagues, and a part of the heme. Core domains 2, 3, and 4, respectively, are assigned based on the cores located on the left (the Fe-S bond) and right sides and at the bottom of heme. Evidence of the core domain-domain interaction to stabilize the Fe-S bond, combined with the kinetic studies by G. R. Parr and H. Taniuchi, has led to a model of two alternative folding orders of the core domains for the horse type I complex: domain 1----3----2----4 or 1----2----3----4. Furthermore, delta G0 variation between the complexes has shown non-additive behavior, indicating the existence of a residue-residue interaction between the heme- and apofragments in the complex. Evidence suggests that this interaction in most cases occurs within or through the core groups of the ordered interface between the heme- and the apo-fragments formed by folding of core domains 1, 2, and 3. Evidence also suggests that such core group interaction manifests itself in the interaction to stabilize the Fe-S bond and may be manifested in the core domain-domain interaction.

Protozoan myoglobin from Paramecium caudatum. Its autoxidation reaction and hemichrome formation

Native oxymyoglobin (MbO2) was isolated directly from the cells of Paramecium caudatum with complete separation from metmyoglobin (metMb) on a DEAE-cellulose column. It was examined for its spectral and stability properties. When compared with sperm whale MbO2 used as a reference, Paramecium MbO2 was found to be much more susceptible to autoxidation over a wide range of pH (4-11) in 0.1 M buffer at 25 degrees C. Kinetic analysis has revealed that a proton-catalyzed displacement of O2- from MbO2 by an entering water molecule can play a dominant role in the autoxidation reaction of Paramecium MbO2 to metMb, as in the case of sperm whale MbO2 involving the distal histidine as its catalytic residue. At pH values higher than 9.5, however, Paramecium MbO2 was found to be oxidized to yield a hemichrome. The spontaneous formation of hemichromes is at variance with the other known myoglobins and is therefore discussed in relation to the unusual amino acid sequence of Paramecium myoglobin having a large number of deletion.