Amino acid sequence of myoglobin from the mollusc Dolabella auricularia

Heme protein identified from scaly-foot gastropod can synthesize pyrite (FeS2) nanoparticles

The scaly-foot gastropod (Chrysomallon squamiferum), which lives in the deep-sea zone of oceans around thermal vents, has a black shell and scales on the foot. Both the black shell and scales contain iron sulfide minerals such as greigite (Fe₃S₄) and pyrite (FeS₂). Although pyrite nanoparticles can be used as materials for solar panels, it is difficult to synthesize stable and spherical nanoparticles in vitro. In this study, we extracted organic molecules that interact with nano-pyrite from the shell of the scaly-foot gastropod to develop a low-cost, eco-friendly method for pyrite nanoparticles synthesis. Myoglobin (csMG), a heme protein, was identified in the iron sulfide layer of the shell. We purified recombinant csMG (r-csMG) and demonstrated that r-csMG helped in the conversion of ferric ions, sulfide ions and sulfur into spherical shaped pyrite nanoparticles at 80°C. To reduce the effort and cost of production, we showed that commercially available myoglobin from Equus caballus (ecMG) also induced the in vitro synthesis of pyrite nanoparticles. Using structure-function experiments with digested peptides, we highlighted that the amino acid sequence of r-csMG peptides controlled the spherical shape of the nanoparticle while the hemin molecules, which the peptides interacted with, maintained the size of nanoparticles. Synthesized pyrite nanoparticles exhibited strong photoluminescence in the visible wavelength region, suggesting its potential application as a photovoltaic solar cell material. These results suggest that materials for solar cells can be produced at low cost and energy under eco-friendly conditions. STATEMENT OF SIGNIFICANCE: Pyrite is a highly promising material for photovoltaic devices because of its excellent optical, electrical, magnetic, and transport properties and high optical absorption coefficient. Almost all current pyrite synthesis methods use organic solvents at high temperature and pressure under reducing conditions. Synthesized pyrite nanoparticles are unstable and are difficult to use in devices. The scaly-foot gastropod can synthesize pyrite nanoparticles in vivo, meaning that pyrite nanoparticles can be generated in an aqueous environment at low temperature. In this study, we demonstrated the synthesis of pyrite nanoparticles using a heme protein identified in the iron sulfide layer of the scaly-foot gastropod shell. These results exemplify how natural products in organisms can inspire the innovation of new technology.

Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets

The globular dioxygen binding heme protein myoglobin (Mb) is present in several species. Its interactions with the simple nitrogen oxides, namely, nitric oxide (NO) and nitrite, have been known for decades, but the physiological relevance has only recently become more fully appreciated. We previously reported the O-nitrito mode of binding of nitrite to ferric horse heart wild-type (wt) MbIII and human hemoglobin. We have expanded on this work and report the interactions of nitrite with wt sperm whale (sw) MbIII and its H64A, H64Q, and V68A/I107Y mutants whose dissociation constants increase in the following order: H64Q < wt < V68A/I107Y < H64A. We also report their X-ray crystal structures that reveal the O-nitrito mode of binding of nitrite to these derivatives. The MbII-mediated reductions of nitrite to NO and structural data for the wt and mutant MbII-NOs are described. We show that their FeNO orientations vary with distal pocket identity, with the FeNO moieties pointing toward the hydrophobic interiors when the His64 residue is present but toward the hydrophilic exterior when this His64 residue is absent in this set of mutants. This correlates with the nature of H-bonding to the bound NO ligand (nitrosyl O vs N atom). Quantum mechanics and hybrid quantum mechanics and molecular mechanics calculations help elucidate the origin of the experimentally preferred NO orientations. In a few cases, the calculations reproduce the experimentally observed orientations only when the whole protein is taken into consideration.

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.

Bacterial expression and characterization of molluscan IDO-like myoglobin

The indoleamine 2,3-dioxygenase (IDO)-like myoglobin (Mb) is a unique type of Mb isolated from the buccal mass of several archgastropod species. Here, we expressed Sulculus diversicolor IDO-like Mb as a GST-fusion protein in bacteria. The visible spectrum of GST-fusion IDO-like Mb shows characteristic alpha- and beta-peaks, indicating that it binds oxygen. To identify residues important in heme and oxygen binding, we constructed site-directed mutants. We initially replaced each of the 7 histidines of S. diversicolor IDO-like Mb with alanine. The spectra of three mutants (H74A, H288A, and H332A) revealed a remarkable loss of absorbance around 414 nm, indicating that they cannot bind heme. His(74), His(288), and His(332) were also replaced by arginine or tyrosine. Neither H332R nor H332Y contains heme, suggesting that His(332) is the proximal ligand of IDO-like Mb. In contrast, both H74R and H288Y mutants were isolated in the heme-binding oxy-form. The autoxidation rates of these two mutants showed that they can bind oxygen as stably as wild-type. His(74) and His(288) might be partially associated with heme-binding, but do not act as the distal ligand. The S. diversicolor IDO-like Mb seems to stably bind oxygen in a different manner from normal myoglobins.

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.

Preparation of artificial 2-, 3-, 4- and 8-domain myoglobins and comparison of their autoxidation rates

Although most hemoglobins and myoglobins consist of 15-kDa single-domain subunits, structurally unusual hemoglobins, such as Artemia 9-domain and Barbatia 2-domain hemoglobins, occur naturally in several invertebrates. These hemoglobins appear to be the result of gene duplication and fusion. Using cDNA coding for the open reading frame of Aplysia kurodai myoglobin, artificial cDNA inserts corresponding to contiguous dimer, trimer, tetramer and octamer myoglobins (2-, 3-, 4- and 8-domain myoglobins) were prepared and cloned into pMAL or pQE plasmids. These artificial myoglobins and wild-type single-domain myoglobins were successfully expressed in Escherichia coli in the heme-attached, oxygenated form. Myoglobin was purified partially by ammonium sulfate fractionation and gel filtration, and autoxidation rates were examined. The autoxidation rates of recombinant wild-type myoglobins with MBP or hexameric His tag were comparable to those of native myoglobin, suggesting that the recombinant proteins appear to be properly folded and that the N-terminal MBP or His tag does not have an affect on the rate. On the other hand, the rates were significantly decreased in the 2- and 3-domain myoglobins (50% and 30% of the single-domain myoglobins, respectively). The rates for 4- and 8-domain myoglobins were similar to those for 3-domain myoglobin. These results indicate that the artificial poly-domain structure of myoglobin is more stable than the usual single-domain myoglobin from the viewpoint of storage of bound dioxygen.

1H-NMR study of dynamics and thermodynamics of Cl− binding to ferric hemoglobin of a midge larva (Tokunagayusurika akamusi)

The functional properties of the Arg residue at the E10 helical position in myoglobin and hemoglobin lacking the highly conserved His residue at the E7 position have received considerable interest as to the structure-function relationship of the oxygen-binding hemoproteins, because Arg E10 in such proteins has been shown to play similar roles to those His E7 plays in ordinary proteins. One of the components of hemoglobin from the larval hemolyph of Tokunagayusurika akamusi is also a naturally occurring E7 genetic variant with Ile E7 and Arg E10. This study demonstrated, for the first time, that the positively charged, elongated, and flexible side-chain of Arg E10 in T.akamusi hemoglobin contributes to stabilization of the coordination of biologically relevant Cl(-) to heme iron. Determination of the dynamics of the Cl(-) binding to T. akamusi ferric hemoglobin involving paramagnetic 1H-NMR indicated that the Cl(-) affinity increases with decreasing pH as a result of the fact that the binding rate increases with decreasing pH, whereas the dissociation rate is almost completely independent of pH. The pH-dependent character of the Cl(-) binding rate correlated well with the ionization state of heme peripheral side-chain propionate groups, which was clearly manifested in the pH-dependent shift changes of heme methyl proton signals, suggesting that negative charges of heme propionate groups constitute a kinetic barrier for Cl(-) entry into the heme pocket. These findings provide an insight into the pH-dependent ligand binding properties of T. akamusi hemoglobin.

Evidence of met-form myoglobin from Theliostyla albicilla radular muscle

Gastropod mollusc myoglobins provide interesting clues to the evolution of this family of proteins. In addition to conventional monomeric myoglobins, this group also has dimeric and unusual indoleamine dioxygenase-like myoglobins. We isolated myoglobin from the radular muscle of living gastropod mollusc Theliostyla albicilla. The myoglobin appeared to be present in an oxidized met-form, a physiologically inactive form that is not capable of binding oxygen. Under the same extraction conditions, myoglobins mainly of the physiologically active oxy-form have been isolated from other molluscs. The complete amino acid sequence of 157 residues of Theliostyla myoglobin shows that it has a long N-terminal extension of seven residues and contains three functional key residues: CD1-Phe, E7-His, and F8-His. The metmyoglobin can easily be reduced to a ferrous state with Na(2)S(2)O(4). The autoxidation rate of the oxy-form was comparable to other molluscan myoglobins over a wide pH range, and Theliostyla myoglobin was shown to be stable as an oxygen-binding protein. Thus, the predominantly met-form of myoglobin in Theliostyla can be attributed to the incomplete functioning of the myoglobin reduction system in the radular muscle. Although the function of Theliostyla myoglobin is unclear, it may be a scavenger of H(2)O(2).

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.

Solution (1)H NMR study of the influence of distal hydrogen bonding and N terminus acetylation on the active site electronic and molecular structure of Aplysia limacina cyanomet myoglobin

The sea hare Aplysia limacina possesses a myoglobin in which a distal H-bond is provided by Arg E10 rather than the common His E7. Solution (1)H NMR studies of the cyanomet complexes of true wild-type (WT), recombinant wild-type (rWT), and the V(E7)H/R(E10)T and V(E7)H mutants of Aplysia Mb designed to mimic the mammalian Mb heme pocket reveal that the distal His in the mutants is rotated out of the heme pocket and is unable to provide a stabilizing H-bond to bound ligand and that WT and rWT differ both in the thermodynamics of heme orientational disorder and in heme contact shift pattern. The mean of the four heme methyl shifts is shown to serve as a sensitive indicator of variations in distal H-bonding among a set of mutant cyanomet globins. The heme pocket perturbations in rWT relative to WT were traced to the absence of the N-terminal acetyl group in rWT that participates in an H-bond to the EF corner in WT. Analysis of dipolar contacts between heme and axial His and between heme and the protein matrix reveal a small approximately 2 degrees rotation of the axial His in rWT relative to true WT and a approximately 3 degrees rotation of the heme in the double mutant relative to rWT Mb. It is demonstrated that both the direction and magnitude of the rotation of the axial His relative to the heme can be determined from the change in the pattern of the contact-dominated heme methyl shift and from the dipolar-dominated heme meso-H shift. However, only NOE data can determine whether it is the His or heme that actually rotates in the protein matrix.

A myoglobin evolved from indoleamine 2,3-dioxygenase, a tryptophan-degrading enzyme

The distribution, isolation, spectral and oxygen-binding properties, stability of ferrous state (autoxidation), amino acid sequence and gene structure of indoleamine 2,3-dioxygenase (IDO)-like myoglobins are summarized, and their evolution is discussed. Although it has long been thought that all hemoglobins and myoglobins have evolved from a common ancestral gene encoding a 14-16 kDa polypeptide, the discovery of IDO-like myoglobin from several gastropod molluscs clearly indicates that there was an alternative pathway for myoglobin evolution.

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.

cDNA cloning and predicted primary structure of scallop sarcoplasmic reticulum Ca(2+)-ATPase

Sarcoplasmic reticulum (SR) Ca(2+)-ATPase of the scallop cross-striated adductor muscle was purified with deoxycholate and digested with lysyl endopeptidase for sequencing of the digested fragments. Overlapping cDNA clones of the ATPase were isolated by screening the cDNA library with an RT-PCR product as a hybridization probe, which encodes the partial amino acid sequence of the ATPase. The predicted amino acid sequence of the ATPase contained all the partial sequences determined with the proteolytic fragments and consisted of the 993 residues with approximately 70% overall sequence similarity to those of the SR ATPases from rabbit fast-twitch and slow-twitch muscles. An outline of the structure of the scallop ATPase molecule is predicted to mainly consist of ten transmembrane and five 'stalk' domains with two large cytoplasmic regions as observed with the rabbit ATPase molecules. The sequence relationship between scallop and other sarco/endoplasmic reticulum-type Ca(2+)-ATPases is discussed.

Convergent evolution. The gene structure of Sulculus 41 kDa myoglobin is homologous with that of human indoleamine dioxygenase

The abalone Sulculus diversicolor contains abundant myoglobin in its buccal mass. The myoglobin consists of 377 amino acid residues and has a molecular mass of 41 000 Da, 2.5 times larger than that of other myoglobins. Sulculus myoglobin can bind oxygen reversibly, and the P50 was determined to be 3.8 mmHg at 20 degrees C and pH 7.4, showing that the oxygen affinity of Sulculus myoglobin is lower than those of vertebrate and invertebrate myoglobins. The cDNA-derived amino acid sequence showed no significant homology with those of any other invertebrate myoglobins and hemoglobins, but surprisingly showed 35% homology with a vertebrate tryptophan-degrading enzyme, indoleamine dioxygenase (IDO). The structure of the Sulculus myoglobin gene has been determined to consist of 14 exons and 13 introns (15.3 kbp). Compared with the gene of human IDO (10 exon-9 intron structure), the splice junctions of 7 introns were exactly conserved between the two genes, suggesting that these introns have been conserved for at least 600 million years. The Sulculus gene has 5 additional introns, one of which is located outside the coding region. From these results we conclude that Sulculus myoglobin evolved from an IDO gene and represents a typical case of functional convergence. Comparison of the amino acid sequence of each exon of Sulculus myoglobin with those of usual globin sequences showed that there is no significant evolutionary relationship between them. The IDO-like myoglobin is unexpectedly widely distributed among gastropodic molluscs, such as Sulculus, Nordotis, Battilus, Omphalius and Chlorostoma.

The cDNA-derived amino acid sequence of chain II of the heterodimeric hemoglobin from the blood clam Barbatia virescens

The blood clam Barbatia virescens expresses a unique heterodimeric hemoglobin consisting of chains I and II in erythrocytes. This is in sharp contrast to the tetrameric (alpha 2 beta 2) and polymeric two-domain hemoglobins of the congeneric species Barbatia reeveana and Barbatia lima. The 3' and 5' parts of the cDNA of B. virescens chain II have been amplified separately by polymerase chain reaction (PCR), and the complete nucleotide sequence of 690 bp was determined. The open reading frame is 477 nucleotides in length and encodes a protein with 158 amino acid residues, of which 120 amino acids were identified directly by the protein sequencing of the peptides obtained from digestions with trypsin, S. aureus V8 protease and pepsin. The mature protein begins with the blocked Ser, and thus the N-terminal Met is cleaved away. The molecular mass for the protein was calculated to be 17605 Da. The cDNA-derived amino acid sequence of B. virescens heterodimeric chain II shows the highest homology (42%) with that of B. virescens chain I, but shows lower homology (32-35%) with those of tetrameric alpha and beta chains of B. lima. This indicates that B. virescens chains I and II do not correspond to B. lima alpha and beta chains, namely the heterodimeric hemoglobin is a unique gene product expressed only in B. virescens.

1H-NMR and EPR studies on met-azido and met-imidazole Dolabella auricularia myoglobin

Met-azido and met-imidazole forms of the myoglobin from the mollusc Dolabella auricularia have been studied by 1H-NMR and EPR spectroscopy. In the mollusc myoglobin, in which His-E7 is replaced by Val, the guanidino group of Arg-E10 serves as an alternative hydrogen-bond donor to the bound ligand. Therefore, the guanidino group of Arg-E10 plays similar roles in ligand stabilization to that the His-E7 imidazole does in most vertebrate myoglobins. Differences in both the structural and electronic properties between Arg and His side chains largely affect the stability of met-azido and met-imidazole forms of the protein. Due to a weak stabilization by Arg-E10, the bound-N3- ligand is replaced by OH- at higher pH, although it is stable at neutral and acidic pH. In the absence of the hydrogen-bonding interaction, Fe-bound imidazole in met-imidazole Dolabella myoglobin is only stable at neutral pH and is removed at acidic pH and replaced by OH- at basic pH. The temperature study also revealed that the bound imidazole is replaced by OH- at higher temperature. These results confirm that the presence of steric hindrance between these bulky ligands and the long and bulky side chain of Arg-E10 in the distal pocket of the mollusc myoglobin. Thus steric effects contribute significantly to the stability of exogenous ligand in the distal pocket of myoglobin.

Dynamics and thermodynamics of acid-alkaline transitions in metmyoglobins lacking the usual distal histidine residue

The kinetics of the acid-alkaline transition in the ferric myoglobins from the gastropodic mollusc Dolabella auricularia and the shark Mustelus japonicus, which possess the distal Val E7 and Gln E7, respectively, has been investigated using the paramagnetic 1H-NMR saturation transfer measurements in order to gain insight into functional properties of these non-His distal residues. Both myoglobins possess the penta-coordinated heme below the pK of the transition (7.8 and 10.0 for Dolabella and Mustelus myoglobins, respectively) and bind OH- above the pK. The pH dependence of the transition rates and the relatively high activation barrier (58 +/- 9 kJ/mol) for the dissociation of the Fe-bound OH- in Dolabella myoglobin indicate a strong interaction between the bound ligand and the guanidino NH proton of the Arg E10 in Dolabella myoglobin. Such a strong interaction between Fe-bound OH- and the Arg E10 side-chain in Dolabella myoglobin is also manifested in the EPR spectra. For Mustelus myoglobin, the pH and temperature dependence studies on the kinetics strongly suggest that the distal Gln E7 in this myoglobin does not contribute significantly to stabilize the Fe-bound ligand.

Nemoglobins: Divergent nematode globins

Globins are proteins commonly associated with oxygen transport in vertebrate blood, but the invertebrate phyla display a wide variety of globin types that reflect their disparate life styles and evolutionary history. It has been known for over 100 years that parasitic nematodes contain globins, but recent molecular investigations are only now beginning to shed some light on their curious properties. Mark Blaxter here describes the diversity of the different globins found in nematodes, and reviews emerging data on their evolution and function.

Adventitious variability? The amino acid sequences of nonvertebrate globins

1. The more than 140 amino acid sequences of non-vertebrate hemoglobins (Hbs) and myoglobins (Mbs) that are known at present, can be divided into several distinct groups: (1) single-chain globins, containing one heme-binding domain; (2) truncated, single-chain, one-domain globins; (3) chimeric, one-domain globins; (4) chimeric, two-domain globins; and (5) chimeric multi-domain globins. 2. The crystal structures of eight nonvertebrate Hbs and Mbs are known, all of them monomeric, one-domain globin chains. Although these molecules represent plants, prokaryotes and several metazoan groups, and although the inter-subunit interactions in the dimeric and tetrameric molecules differ from the ones observed in vertebrate Hbs, the secondary structures of all seven one-domain globins retain the characteristic vertebrate "myoglobin fold". No crystal structures of globins representing the other four groups have been determined. 3. Furthermore, a number of the one-, two- and multi-domain globin chains participate in a broad variety of quaternary structures, ranging from homo- and heterodimers to highly complex, multisubunit aggregates with M(r) > 3000 kDa (S. N. Vinogradov, Comp. Biochem. Physiol. 82B, 1-15, 1985). 4. (1) The single-chain, single-domain globins are comparable in size to the vertebrate globins and exhibit the widest distribution. (A) Intracellular Hbs include: (i) the monomeric and polymeric Hbs of the polychaete Glycera; (ii) the tetrameric Hb of the echiuran Urechis; (iii) the dimeric Hbs of echinoderms such as Paracaudina and Caudina; and (iv) the dimeric and tetrameric Hbs of molluscs, the bivalves Scapharca, Anadara, Barbatia and Calyptogena. (B) Extracellular Hbs include: (i) the multiple monomeric and dimeric Hbs of the larva of the insect Chironomus; (ii) the Hbs of nematodes such as Trichostrongylus and Caenorhabditis; (iii) the globin chains forming tetramers and dodecamers and comprising approximately 2/3 of the giant (approximately 3600 kDa), hexagonal bilayer (HBL) Hbs of annelids, e.g. the oligochaete Lumbricus and the polychaete Tylorrhynchus and of the vestimentiferan Lamellibrachia; and (iv) the globin chains comprising the ca 400 kDa Hbs of Lamellibrachia and the pogonophoran Oligobrachia. (C) Cytoplasmic Hbs include: (i) the Mbs of molluscs, the gastropods Aplysia, Bursatella, Cerithedea, Nassa and Dolabella and the chiton Liolophura; (ii) the three Hb of the symbiont-harboring bivalve Lucina; (iii) the dimeric Hb of the bacterium Vitreoscilla; and (iv) plant Hbs, including the Hbs of symbiont-containing legumes (Lgbs), the Hbs of symbiont-containing non-leguminous plants and the Hbs in the roots of symbiont-free plants.(ABSTRACT TRUNCATED AT 400 WORDS)

NMR study of the molecular and electronic structure of the heme cavity in Dolabella met-cyano myoglobin

The molecular and electronic structure of the active site of the cyanide-ligated ferric complex of the myoglobin from the mollusc Dolabella auricularia has been investigated using NMR. Analysis of nuclear Overhauser effects has revealed that the correlation times for the internal motion of the heme propionate alpha-CH2 and beta-CH2 groups at ambient temperature are about 5 and 4 ns, respectively. These correlation times indicate that the terminal carboxylate groups of both the heme propionates are not bound to the protein via salt bridges. Although the absence of the propionate-protein interaction does not influence the equilibrium population of the two heme orientational isomers involving rotation about the alpha,gamma-meso axis, it allows the heme to rotate about the iron-His bond in the active site of the myoglobin. Such rotational motion of the heme resulted in an anomalous temperature-dependence of the heme methyl-proton hyperfine shift. Thus the present myoglobin studies provide the first example demonstrating the rotation of the heme about the iron-His bond in native myoglobin.

The amino acid sequence of hemoglobin III from the symbiont-harboring clam Lucina pectinata

The cytoplasmic hemoglobin III from the gill of the symbiont-harboring clam Lucina pectinata consists of 152 amino acid residues, has a calculated Mm of 18,068, including heme, and has N-acetyl-serine as the N-terminal residue. Based on the alignment of its sequence with other vertebrate and nonvertebrate globins, it retains the invariant residues Phe45 at position CD1 and His98 at the proximal position F8, as well as the highly conserved Trp16 and Pro39 at positions A12 and C2, respectively. The most likely candidate for the distal residue at position E7 is Gln66. Lucina hemoglobin III shares 95 identical residues with hemoglobin II (J. D. Hockenhull-Johnson et al., J. Prot. Chem. 10, 609-622, 1991), including Tyr at position B10, which has been shown to be capable of entering the distal heme cavity and placing its hydroxyl group within a 2.8 A of the water molecule occupying the distal ligand position, by modeling the hemoglobin II sequence using the crystal structure of sperm whale metmyoglobin. The amino acid sequences of the two Lucina globins are compared in detail with the known sequences of mollusc globins, including seven cytoplasmic and 11 intracellular globins. Relative to 75% homology between the two Lucina globins (counting identical and conserved residues), both sequences have percent homology scores ranging from 36-49% when compared to the two groups of mollusc globins. The highest homology appears to exist between the Lucina globins and the cytoplasmic hemoglobin of Busycon canaliculatum.

Amino-acid sequence of the cooperative dimeric myoglobin from the radular muscles of the marine gastropod Nassa mutabilis

The complete amino-acid sequence of the dimeric and cooperative myoglobin from the radular muscles of Nassa mutabilis, a common edible gastropod mollusc on the Italian coast, has been determined. The molecule is a homodimer. The monomer is composed of 147 amino-acid residues, with a molecular mass of 15,760 Da. Its sequence is homologous with those of the dimeric myoglobins of the gastropod molluscs of the Prosobranchia subclass Busycon canaliculatum (63% conserved residues) and Cerithidea rhizophorarum (46% conserved residues). The rate of autoxidation to met-myoglobin of N. mutabilis oxymyoglobin at 25 degrees C is strongly pH-dependent with relative minimal rate values in the pH range 7 to 8.

Amino acid sequence of myoglobin from the chiton Liolophura japonica and a phylogenetic tree for molluscan globins

Myoglobin was isolated from the radular muscle of the chiton Liolophura japonica, a primitive archigastropodic mollusc. Liolophura contains three monomeric myoglobins (I, II, and III), and the complete amino acid sequence of myoglobin I has been determined. It is composed of 145 amino acid residues, and the molecular mass was calculated to be 16,070 D. The E7 distal histidine, which is replaced by valine or glutamine in several molluscan globins, is conserved in Liolophura myoglobin. The autoxidation rate at physiological conditions indicated that Liolophura oxymyoglobin is fairly stable when compared with other molluscan myoglobins. The amino acid sequence of Liolophura myoglobin shows low homology (11-21%) with molluscan dimeric myoglobins and hemoglobins, but shows higher homology (26-29%) with monomeric myoglobins from the gastropodic molluscs Aplysia, Dolabella, and Bursatella. A phylogenetic tree was constructed from 19 molluscan globin sequences. The tree separated them into two distinct clusters, a cluster for muscle myoglobins and a cluster for erythrocyte or gill hemoglobins. The myoglobin cluster is divided further into two subclusters, corresponding to monomeric and dimeric myoglobins, respectively. Liolophura myoglobin was placed on the branch of monomeric myoglobin lineage, showing that it diverged earlier from other monomeric myoglobins. The hemoglobin cluster is also divided into two subclusters. One cluster contains homodimeric, heterodimeric, tetrameric, and didomain chains of erythrocyte hemoglobins of the blood clams Anadara, Scapharca, and Barbatia. Of special interest is the other subcluster. It consists of three hemoglobin chains derived from the bacterial symbiontharboring clams Calyptogena and Lucina, in which hemoglobins are supposed to play an important role in maintaining the symbiosis with sulfide bacteria.

Primary structure of chain I of the heterodimeric hemoglobin from the blood clam Barbatia virescens

The blood clam Barbatia virescens has a heterodimeric hemoglobin in erythrocytes. Interestingly, the congeneric clams B. reeveana and B. lima contain quite different hemoglobins: tetramer and polymeric hemoglobin consisting of unusual didomain chain. The complete amino acid sequence of chain I of B. virescens has been determined. The sequence was mainly determined from CNBr peptides and their subpeptides, and the alignment of the peptides was confirmed by sequencing of PCR-amplified cDNA for B. virescens chain I. The cDNA-derived amino acid sequence matched completely with the sequence proposed from protein sequencing. B. virescens chain I is composed of 156 amino acid residues, and the molecular mass was calculated to be 18,387 D, including a heme group. The sequence of B. virescens chain I showed 35-42% sequence identity with those of the related clam Anadara trapezia and the congeneric clam B. reeveana. An evolutionary tree for Anadara and Barbatia chains clearly indicates that all of the chains are evolved from one ancestral globin gene, and that the divergence of chains has occurred in each clam after the speciation. The evolutionary rate for clam hemoglobins was estimated to be about four times faster than that of vertebrate hemoglobin. We suggest that blood clam hemoglobin is a physiologically less important molecule when compared with vertebrate hemoglobins, and so it evolved rapidly and resulted in a remarkable diversity in quaternary and subunit structure within a relatively short period.

Molecular mechanism for ligand stabilization in the mollusc myoglobin possessing the distal Val residue

Myoglobin extracted from the triturative stomach of Dolabella auricularia, a common mollusc found on the Japanese coast, possesses naturally occurring substitution at the distal E7 position (Val-E7) and its oxygen affinity is only slightly lower than those of the common mammalian myoglobins possessing the usual His-E7. 1H nuclear magnetic resonance studies of Dolabella met-cyano myoglobin have revealed that a guanidino NH proton of Arg-E10 is hydrogen-bonded to the Fe-bound CN-. The role of Arg-E10 as a hydrogen-bond donor for Fe-bound ligand in the present myoglobin appears to be responsible for its relatively high ligand affinity.

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.

Kinetic characterization of the acid-alkaline transition in Dolabella auricularia ferric myoglobin using 1H-NMR saturation transfer experiments

The acid-alkaline transition in ferric myoglobin of the mollusc, Dolabella auricularia, exerts the changes in both the coordination and spin states of the heme iron. Slower transition rate, compared to the NMR time scale, in this myoglobin allowed the observation of separate signals arising from the two forms, and pH titration yielded a pK value of 7.8. 1H-NMR saturation transfer experiments have been successfully used not only to provide the first signal assignments for the heme methyl proton resonances of the Met-hydroxyl form of the myoglobin, but also to determine the kinetics of the transition.

The amino acid sequence of hemoglobin II from the symbiont-harboring clam Lucina pectinata

The cytoplasmic hemoglobin II from the gill of the clam Lucina pectinata consists of 150 amino acid residues, has a calculated Mm of 17,476, including heme and an acetylated N-terminal residue. It retains the invariant residues Phe 44 at position CD1 and His 65 at the proximal position F8, as well as the highly conserved Trp 15 at position A12 and Pro 38 at position C2. The most likely candidate for the distal residue at position E7, based on the alignment with other globins, is Gln 65. However, optical and EPR spectroscopic studies of the ferri Hb II (Kraus, D. W., Wittenberg, J. B., Lu, J. F., and Peisach, J., J. Biol. Chem. 265, 16054-16059, 1990) have implicated a tyrosinate oxygen as the distal ligand. Modeling of the Lucina Hb II sequence, using the crystal structure of sperm whale aquometmyoglobin, showed that Tyr 30 substituting for the Leu located at position B10 can place its oxygen within 2.8 A of the water molecule occupying the distal ligand position. This structural alteration is facilitated by the coordinate mutation of the residue at position CD4, from Phe 46 in the sperm whale myoglobin sequence to Leu 47 in Lucina Hb II.

Amino acid sequence of myoglobin from the mollusc Bursatella leachii

The complete amino acid sequence of myoglobin from the triturative stomach of gastropodic mollusc Bursatella leachii has been determined. It is composed of 146 amino acid residues, is acetylated at the N-terminus, and contains a single histidine residue at position 95 which corresponds to the heme-binding proximal histidine. The E7 distal histidine, which is conserved widely in myoglobins and hemoglobins, is replaced by valine in Bursatella myoglobin. The amino acid sequence of Bursatella myoglobin shows strong homology (73-84%) with those of Aplysia and Dolabella myoglobins.

Amino acid sequence of the dimeric hemoglobin (Hb I) from the deep-sea cold-seep clam Calyptogena soyoae and the phylogenetic relationship with other molluscan globins

The deep-sea cold-seep clam Calyptogena soyoae has two homodimeric hemoglobins (Hbs I and II) in erythrocytes. The complete amino acid sequence of Hb I has been determined. It is composed of 144 amino acid residues, has a high content of hydrophobic residues, and a calculated molecular weight of 16,350 including a heme group. The sequence of Calyptogena Hb I showed high homology (42% identity) with that of Calyptogena Hb II (Suzuki, T., Takagi T. and Ohta, S. (1989) Biochem. J. 260, 177-182), although it has a long insertion of seven residues in the C-terminal region compared with Hb II. On the other hand, it showed low homology (12-20% identity) with other molluscan globins. As well as Hb II, Calyptogena Hb I lacked the N-terminal extension of 7-9 residues characteristic of molluscan intracellular hemoglobins, and the distal (E7) histidine was replaced by glutamine. A phylogenetic tree was constructed from 13 molluscan globins belonging to the five families Aplysiidae, Galeodidae, Potamididae, Arcidae and Vesicomyidae. The globin sequences of Calyptogena (Vesicomyidae) were found to be rather distant from other globin sequences, suggesting that they might conserve a primitive form of molluscan globins.

Amino acid sequence of a major globin from the sea cucumber Paracaudina chilensis

The sea cucumber Paracaudina chilensis (Echinodermata) contains three major globins I, II and III in coelomic cells. The complete amino acid sequence of globin I has been determined. It is composed of 157 amino acid residues, is acetylated at the N-terminus, and has a characteristic N-terminal extension of 9-10 residues when compared with vertebrate globins. The sequence of Paracaudina globin I showed slightly higher homology with human alpha globin (25%) rather than with the invertebrate Anadara alpha globin (22%). Paracaudina globin I also showed strong homology (59%) with globin D from another sea cucumber, Molpadia arenicola (Mauri, F.C. (1985) Ph.D. dissertation, University of Texas). The globin sequences from the phylum Echinodermata have an important position in the molecular evolution of the globins, because they are the invertebrate group most closely related to the vertebrates.

The ear-shell (Sulculus diversicolor aquatilis) myoglobin is composed of an unusual 39 kDA polypeptide chain

An unusual myoglobin was isolated from the buccal mass of the ear-shell Sulculus diversicolor aquatilis. The myoglobin consists of a 39 kDa polypeptide chain which is about double the size of the usual myoglobin subunit, contains one heme per molecule, and has an unusual spectral property ion the oxy-form. On the basis of these properties and partial amino acid sequencing, we propose that Sulculus myoglobin has a didomain structure, and that one of the two domains does not function as an oxygen-binding domain. So far, a myoglobin of this type has not been described in molluscs.

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

Myoglobins can be divided into two groups. One group contains the usual myoglobins that have histidine at the distal (E7) position, and the other contains a few, but interesting myoglobins that lack the usual distal histidine residue. Spectroscopic examinations have shown that there is a remarkable difference in the Soret band between the two types of myoglobin, and an absorbance ratio of the Soret peak of the acidic met-form to that of the oxy-form seems to be very useful as a simple criterion for predicting whether or not a myoglobin has the usual distal histidine residue.

Aplysia limacina myoglobin. Crystallographic analysis at 1.6 A resolution

The crystal structure of the ferric form of myoglobin from the mollusc Aplysia limacina has been refined at 1.6 A resolution, by restrained crystallographic refinement methods. The crystallographic R-factor is 0.19. The tertiary structure of the molecule conforms to the common globin fold, consisting of eight alpha-helices. The N-terminal helix A and helix G deviate significantly from linearity. The distal residue is recognized as Val63 (E7), which, however, does not contact the heme directly. Moreover the sixth (distal) co-ordination position of heme iron is not occupied by a water molecule at neutrality, i.e. below the acid-alkaline transition point of A. limacina myoglobin. The heme group sits in its crevice in the conventional orientation and no signs of heme isomerism are evident. The iron atom is 0.26 A out of the porphyrin plane, with a mean Fe-N (porphyrin) distance of 2.01 A. The co-ordination bond to the proximal histidine has a length of 2.05 A, and forms an angle of 4 degrees with the heme normal. A plane containing the imidazole ring of the proximal His intersects the heme at an angle of 29 degrees with the (porphyrin) 4N-2N direction. Inspection of the structure of pH 9.0 indicates that a hydroxyl ion is bound to the Fe sixth co-ordination position.

An evolutionary tree for invertebrate globin sequences

A phylogenetic tree was constructed from 245 globin amino acid sequences. Of the six plant globins, five represented the Leguminosae and one the Ulmaceae. Among the invertebrate sequences, 7 represented the phylum Annelida, 13 represented Insecta and Crustacea of the phylum Arthropoda, and 6 represented the phylum Mollusca. Of the vertebrate globins, 4 represented the Agnatha and 209 represented the Gnathostomata. A common alignment was achieved for the 245 sequences using the parsimony principle, and a matrix of minimum mutational distances was constructed. The most parsimonious phylogenetic tree, i.e., the one having the lowest number of nucleotide substitutions that cause amino acid replacements, was obtained employing clustering and branch-swapping algorithms. Based on the available fossil record, the earliest split in the ancestral metazoan lineage was placed at 680 million years before present (Myr BP), the origin of vertebrates was placed at 510 Myr BP, and the separation of the Chondrichthyes and the Osteichthyes was placed at 425 Myr BP. Local "molecular clock" calculations were used to date the branch points on the descending branches of the various lineages within the plant and invertebrate portions of the tree. The tree divided the 245 sequences into five distinct clades that corresponded exactly to the five groups plants, annelids, arthropods, molluscs, and vertebrates. Furthermore, the maximum parsimony tree, in contrast to the unweighted pair group and distance Wagner trees, was consistent with the available fossil record and supported the hypotheses that the primitive hemoglobin of metazoans was monomeric and that the multisubunit extracellular hemoglobins found among the Annelida and the Arthropoda represent independently derived states.

Autoxidation of oxymyoglobin with the distal (E7) glutamine

We reported previously that the distal(E7) histidine is replaced by glutamine in myoglobin from the shark, Galeorhinus japonicus. The amino-acid sequence of myoglobin from another shark, Heterodontus japonicus, has been determined. The myoglobin is composed of 148 residues, is acetylated at the N-terminus, and contains the distal(E7) histidine at position 59. Although the sequence homologies between G. japonicus, H. japonicus, and sperm-whale myoglobins were about 40-55%, their hydropathy profiles were very similar, indicating that they have a similar geometry in their globin folding. The autoxidation rates of the two shark oxymyoglobins were examined in 0.1 M buffer at 25 degrees C over pH range 4.5-11.5. The pH dependence for the autoxidation of H. japonicus myoglobin was very similar to that of sperm-whale myoglobin, although the rate was about 10-times higher over the pH range examined. In both myoglobins, autoxidation was largely accelerated by H+. On the other hand, the pH dependence of G. japonicus myoglobin, which has the distal glutamine in the place of histidine, was quite different from those of sperm-whale and H. japonicus myoglobins. One of the most remarkable features is the fact that the autoxidation rate is not enhanced with an increase in the concentration of H+ in the acidic range of pH, where the autoxidation of sperm-whale and H. japonicus myoglobins is most accelerated. This finding suggests that the distal(E7) histidine participates in the autoxidation reaction as a catalytic residue facilitating the movement of a catalytic proton.