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

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.

Protein and gene structure of a chlorocruorin chain of Eudistylia vancouverii

The polychaete annelid, Eudistylia vancouverii, contains as oxygen carrier a hexagonal bilayer (HBL) chlorocruorin. One of the globin chains, chain a1, has 142 amino acids (Mr 16,054.99) and its sequence deviates strongly from other nonvertebrate globin sequences. Unprecedented, it displays a Phe at the distal position E7 as well as at position B10, creating a very hydrophobic heme pocket probably responsible for the low oxygen affinity of the native molecule. Phylogenetic analysis of annelid globin chains clearly proves that globin chain a1 belongs to type I of globin chains having a pattern of 3 cysteine residues essential for the aggregation into a HBL structure. The gene coding for globin chain a1 is interrupted by 2 introns at the conserved positions B12.2 and G7.0. Based on protein and gene structure it can therefore be concluded that the globin chains of chlorocruorins are not fundamentally different from other annelid globin chains.

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.

1H NMR investigation of the distal hydrogen bonding network and ligand tilt in the cyanomet complex of oxygen-avid Ascaris suum hemoglobin

The O(2)-avid hemoglobin from the parasitic nematode Ascaris suum exhibits one of the slowest known O(2) off rates. Solution (1)H NMR has been used to investigate the electronic and molecular structural properties of the active site for the cyano-met derivative of the recombinant first domain of this protein. Assignment of the heme, axial His, and majority of the residues in contact with the heme reveals a molecular structure that is the same as reported in the A. suum HbO(2) crystal structure (Yang, J., Kloek, A., Goldberg, D. E., and Mathews, F. S. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 4224-4228) with the exception that the heme in solution is rotated by 180 degrees about the alpha,gamma-meso axis relative to that in the crystal. The observed dipolar shifts, together with the crystal coordinates of HbO(2), provide the orientation of the magnetic axes in the molecular framework. The major magnetic axis, which correlates with the Fe-CN vector, is found oriented approximately 30 degrees away from the heme normal and indicates significant steric tilt because of interaction with Tyr(30)(B10). The three side chain labile protons for the distal residues Tyr(30)(B10) and Gln(64)(E7) were identified, and their relaxation, dipolar shifts, and nuclear Overhauser effects to adjacent residues used to place them in the distal pocket. It is shown that these two distal residues exhibit the same orientations ideal for H bonding to the ligand and to each other, as found in the A. suum HbO(2) crystal. It is concluded that the ligated cyanide participates in the same distal H bonding network as ligated O(2). The combination of the strong steric tilt of the bound cyanide and slow ring reorientation of the Tyr(30)(B10) side chain supports a crowded and constrained distal pocket.

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 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.

Characterization of the myoglobin and its coding gene of the mollusc Biomphalaria glabrata

A cDNA clone isolated from a Biomphalaria glabrata (Mollusca, Gastropoda) neural cDNA library was identified as encoding a myoglobin-like protein of 148 amino acids with a single domain and a calculated mass of 16,049.29. Alignment with globin sequences with known tertiary structure confirms its overall globin nature. The expressed myoglobin was identified in the radular muscle and isolated. Oxygen equilibrium measurements on the protein reveal a high oxygen affinity. Val-B10 and Gln-E7, important residues for the determination of the oxygen affinity, are strikingly different from the standard molluscan pattern (Conti, E., Moser, C., Rizzi, M., Mattevi, A., Lionetti, C., Coda, A., Ascenzi, P., Brunori, M., Bolognesi, M. (1993) J. Mol. Biol. 233, 498-508). The single gene encoding the globin chain is interrupted by three introns at positions A3.2, B12.2, and G7.0. Comparison with other nonvertebrate globin genes reveals on the one hand conservation (B12.2 and G7.0) and on the other hand variability of the insertion positions (A3.2). The Biomphalaria myoglobin sequence was used together with all other molluscan globin sequences available to assess the origin and phylogeny of the phylum. Our results confirm the doubts raised about monophyletic origin of the Mollusca, which was first observed using SSU rRNA as a molecular marker.

Comparative studies of the indoleamine dioxygenase-like myoglobin from the abalone Sulculus diversicolor

The abalone Sulculus diversicolor contains abundant myoglobin in its buccal mass. The myoglobin is homodimeric and the molecular mass of the constituent polypeptide chain is 41,000 Da. The amino acid sequence and gene structure are highly homologous with those of a vertebrate tryptophan-degrading enzyme, indoleamine dioxygenase (IDO). Thus Sulculus myoglobin evolved from an IDO gene, and represents a typical case of functional convergence. The oxygen equilibrium properties of Sulculus myoglobin were examined and compared with those of myoglobins from other sources. It binds 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 significantly lower than those of usual 16 kDa myoglobins. It also displays no cooperativity (nmax: 1.02-1.06) and no alkaline Bohr effect between pH 7.0 and 7.9. The cDNA-derived amino acid sequences of vertebrate IDOs, molluscan IDO-like myoglobins and a homolog in the yeast Saccharomyces were aligned, and several amino acid residues were proposed as candidates for key residues to control the function of IDO or myoglobin.

Trematode myoglobins, functional molecules with a distal tyrosine

The myoglobins of two trematodes, Paramphistomum epiclitum and Isoparorchis hypselobagri, were isolated to homogeneity. The native molecules are monomeric with Mr 16,000-17,000 and pI 6.5-7.5. In each species, at least four different globin isoforms occur. Primary structure was determined at the protein level. The globin chains contain 147 amino acid residues. Although major determinants of the globin fold are conserved, characteristic substitutions are present. A Tyr residue occurs at the helical positions B10 and E7 (distal position). This is confirmed by NMR measurements (Zhang, W., Rashid, K. A., Haque, M., Siddiqi, A. H., Vinogradov, S. N., Moens, L. & La Mar, G. N. (1997) J. Biol. Chem. 272, 3000-3006). A distal Tyr normally provokes oxidation of the iron atom and the inability to bind oxygen, whereas a Tyr-B10 is indicative for a high oxygen affinity. In contrast, trematode myoglobins are functional molecules with a high oxygen affinity. Molecular modeling predicts two possible positions for the aromatic ring of Tyr-E7: one being outside the heme pocket making it freely accessible to the ligand and one within the heme pocket potentially able to form a second hydrogen bond with the iron-bound oxygen. A hydrogen bond between Tyr-B10 and the bound oxygen as in the Ascaris hemoglobin is predicted as well. The predicted structure may explain the high oxygen affinity of the trematode myoglobins.

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.

NMR study of the active site of shark met-cyano myoglobins

The myoglobins from the sharks Galeorhinus japonicus and Musterus japonicus possess a distal Gln-E7 instead of the usually found His-E7. The met-cyano form of these shark myoglobins has been studied by 1H- and 15N-NMR in order to gain insight into the functional properties of the Gln-E7. The analysis of paramagnetic relaxation has provided the assignment of the resonance arising from one of the Gln-E7 N epsilon H labile protons, whilst the rate of its chemical exchange has been analyzed in detail by using a saturation transfer method. The hydrogen-bonding interaction between this proton and Fe-bound-CN(-) has been clearly manifested in the hyperfine shift of the Gln-E7 N epsilon H proton resonance as well as its chemical exchange behavior. The resonances of the Gln-E7 side-chain non-labile protons have been partly assigned on a basis of both scalar and dipolar connectivities. The analysis of the dipolar connectivities among the side-chain protons and the iron-proton distances determined from their paramagnetic relaxation rate has revealed that the side chain adopts a conformation with its carbonyl oxygen oriented away from the heme. Although (1)H-NMR spectra of these two myoglobins are essentially similar, a relatively large difference in the shift of Gln-E7 N(epsilon)H proton and Fe-bound C15 N- resonances between the two has been observed which is attributed to a differential hydrogen-bonding interaction between these proteins. The present study demonstrates the sensitivity of NMR parameters to the hydrogen-bonding interaction between coordinated ligand and a distal amino-acid side chain in paramagnetic hemoproteins.

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.

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.

Crystal structure of a distal site double mutant of sperm whale myoglobin at 1.6 A resolution

The three-dimensional structure of sperm whale myoglobin His64(E7)-->Val,Thr67(E10)-->Arg double mutant has been studied by X-ray crystallography at 1.6 A resolution, and refined to a crystallographic R-factor of 0.197. The Arg67(E10) side chain is extended in the direction of the ligand binding site, and its NH1 atom is at a distance of 3.11 A from the NH1 atom of Arg45(CD3), which is also pointing towards the distal site. Both are kept in this position by hydrogen bonding and electrostatic interactions with a solvent sulfate ion, located amongst the two, on the protein surface. No liganded water molecule is present at the sixth coordination position of the Fe(III) heme.