Sperm Whale Myoglobin Research Articles

Solution Structure and Backbone Dynamics of Component IV Glycera dibranchiata Monomeric Hemoglobin−CO,

The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.

Folding of Deoxymyoglobin Triggered by Electron Transfer

The met and deoxy forms of sperm whale myoglobin (Mb) can be unfolded by guanidine hydrochloride (GuHCl). Electronic absorption and circular dichroism spectroscopic measurements show that folded deoxyMb is more stable than the folded met protein. Laser excitation of NADH generates species that rapidly reduce unfolded metMb, triggering the formation of folded deoxyMb in less than 10 ms (pH 7.0, 2.5 to 3 M GuHCl, 20 °C). At comparable reaction driving forces (∼10 kJ/mol), deoxyMb folds much faster than reduced cytochrome c.

Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors

Protein structures are flexible both in solution and in the solid state. X-ray crystallographically determined thermal factors monitor the flexibility of protein atoms. A method utilizing such factors is proposed to delineate protein regions through which a ligand can exchange between binding site and bulk solvent. It is based on the assumption that thermally excited protein regions are excellent candidates for opening a ligand channel. Computationally simple and inexpensive, the method analyzes directions from which thermal factors can propagate within the protein, resulting in thermal motion paths (TMPs). Applications to engineered T4 lysozymes, where an artificial internal cavity can host hydrophobic molecules, and to sperm whale myoglobins, where the active site is completely buried, yielded results in agreement with other independent structural observations and with previous hypotheses. Further new features could also be suggested. The proposed TMP analysis could aid molecular dynamics simulation studies as well as time-resolved and site-directed mutagenesis experimental studies, especially given its modest computational expense and its direct roots in experimental results based on thermal factors determined in high-resolution crystallographic studies.

Solution and Crystal Structures of a Sperm Whale Myoglobin Triple Mutant That Mimics the Sulfide-binding Hemoglobin fromLucina pectinata

The bivalve mollusc Lucina pectinata harbors sulfide-oxidizing chemoautotrophic bacteria and expresses a monomeric hemoglobin I, HbI, with normal O2, but extraordinarily high sulfide affinity. The crystal structure of aquomet Lucina HbI has revealed an active site with three residues not commonly found in vertebrate globins: Phe(B10), Gln(E7), and Phe(E11) (Rizzi, M., Wittenberg, J. B., Coda, A., Fasano, M., Ascenzi, P., and Bolognesi, M. (1994) J. Mol. Biol. 244, 86-89). Engineering these three residues into sperm whale myoglobin results in a triple mutant with approximately 700-fold higher sulfide affinity than for wild-type. The single crystal x-ray structure of the aquomet derivative of the myoglobin triple mutant and the solution 1H NMR active site structures of the cyanomet derivatives of both the myoglobin mutant and Lucina HbI have been determined to examine further the structural origin of their unusually high sulfide affinities. The major differences in the distal pocket is that in the aquomet form the carbonyl of Gln64(E7) serves as a H-bond acceptor, whereas in the cyanomet form the amido group acts as H-bond donor to the bound ligand. Phe68(E11) is rotated approximately 90 degrees about chi2 and located approximately 1-2 A closer to the iron atom in the myoglobin triple mutant relative to its conformation in Lucina HbI. The change in orientation potentially eliminates the stabilizing interaction with sulfide and, together with the decrease in size of the distal pocket, accounts for the 7-fold lower sulfide affinity of the myoglobin mutant compared with that of Lucina HbI.

Tritium planigraphy: from the accessible surface to the spatial structure of a protein.

The method of tritium planigraphy, which provides comprehensive information on the accessible surface of macromolecules, allows an attempt at reconstructing the three-dimensional structure of a protein from the experimental data on residue accessibility for labeling. The semiempirical algorithm proposed for globular proteins involves (i) predicting theoretically the secondary structure elements (SSEs), (ii) experimentally determining the residue-accessibility profile by bombarding the whole protein with a beam of hot tritium atoms, (iii) generating the residue-accessibility profiles for isolated SSEs by computer simulation, (iv) locating the contacts between SSEs by collating the experimental and simulated accessibility profiles, and (v) assembling the SSEs into a compact model via these contact regions in accordance with certain rules. For sperm whale myoglobin, carp and pike parvalbumins, the lambda cro repressor, and hen egg lysozyme, this algorithm yields the most realistic models when SSEs are assembled sequentially from the amino to the carboxyl end of the protein chain.

Photodissociation and Rebinding of H2O to Ferrous Sperm Whale Myoglobin

Photodissociation and Rebinding of H₂O to Ferrous Sperm Whale Myoglobin

Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry

The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 angstroms resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112 degrees. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the N(epsilon) atom of histidine64 is located 2.8 angstroms away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold.

From metmyoglobin to deoxy myoglobin: relaxations of an intermediate state.

Metmyoglobin has been reduced at low temperature (below 100 K) using x-rays or by excitation of tris(2,2,bipyridine)ruthenium(II) chloride with visible light. Upon reduction, an intermediate state is formed where the structure of the protein is very similar to that of metmyoglobin with the water molecule still bound to the heme iron, but the iron is II low spin. The nature of the intermediate state has been investigated with optical spectroscopy. The Q(O) and Q(V) bands of the intermediate state are split, suggesting that the protoporphyrin is distorted. The intermediate state undergoes a relaxation observed by a shifting of the Soret band at temperatures above 80 K. Above 140 K, the protein begins to relax to the deoxy conformation. The relaxation kinetics of the protein have been monitored optically as a function of time and temperature from minutes to several hours and from 150 K to 190 K. By measuring the entire visible spectrum, we are able to distinguish between electron transfer processes and the protein relaxation from the intermediate state to deoxy myoglobin. The relaxation has been measured in both horse myoglobin and sperm whale myoglobin with the relaxation occurring on faster time scales in horse myoglobin. Both the reduction kinetics and the relaxation show non-exponential behavior. The reduction kinetics can be fit well to a stretched exponential. The structural relaxation from the intermediate state to the deoxy conformation shows a more complex, dynamical behavior and the reaction is most likely affected by the relaxation of the protein within the intermediate state.

Solution 1H NMR Study of the Electronic Structure and Magnetic Properties of High-Spin Ferrous or Deoxy Myoglobins

Solution 1D and 2D NMR, together with limited isotope labeling, have led to the assignment of the heme, axial His, and numerous heme contact residues in sperm whale, horse, and human deoxy myoglobin. The paramagnetic relaxivity leads to increased line widths and shorter T1s with little compensation in increased dispersion due to dipolar shifts. Hence only limited, but crucial F helix standard backbone sequence specific assignment could be made for heme cavity residues. Numerous other residues with significant dipolar shifts could be assigned from the characteristic scalar connectivities and dipolar contacts to the heme predicted by the crystal structure. It is concluded that the complete and unambiguous assignment of the heme pyrrole substituent signals is not attainable by 2D NMR alone without either partial deuterium labeling of the heme or parallel assignment of key residues in dipolar contact with the heme; hence the present study revises some earlier assignments. The resulting dipolar shifts for nonligated residues, together with the crystal coordinates of deoxy myoglobin, were used to determine the orientation relative to the heme and the anisotropy of the paramagnetic susceptibility tensor. The significant anisotropy, |Δχ| ∼1 × 10-9 m3/mol, however, is shown to result in dipolar shift with reciprocal square, rather than just reciprocal, absolute temperature dependence, which is indicative of large zero field splitting rather than g-tensor anisotropy. The appropriate equation for a 5B2 ground state allows an estimate of the zero-field splitting, D ∼−10 cm-1, which is in good agreement with earlier results. The present NMR data favor a spin-only magnetic moment with S = 2 and D ∼−10 cm-1 over a ground state with S < 2 and significant orbital contribution (Hendrich and Debrunner, 1989).

Computer Simulations of Carbon Monoxide Photodissociation in Myoglobin: Structural Interpretation of the B States

The early diffusion processes of a photodissociated ligand (carbon monoxide) in sperm whale myoglobin and its Phe 29 mutant are studied computationally. An explicit solvent model is employed in which the protein is embedded in a box of at least 2300 water molecules. Electrostatic interactions are accounted for by using the particle mesh Ewald. Two hundred seventy molecular dynamics trajectories are computed for 10 ps. Different models of solvation and the ligand, and their influence on the diffusion are examined. The two B states of the CO are identified as “docking” sites in the heme pocket. The sites have a similar angle with respect to the heme normal, but differ in the orientation in the plane. The computational detection of the B states is stable under a reasonable variation of simulation conditions. However, in some trajectories only one of the states is observed. It is therefore necessary to use extensive simulation data to probe these states. Comparison to diffraction experiments and spectroscopy is performed. The shape of the experimental infrared spectra is computed. The overall linewidth is in an agreement with experiment. The contributions to the linewidth (van der Waals and electrostatic interactions) are discussed.

B-Cell Activation In Vitro by Helper T Cells Specific to a Protein Region that is Recognized Both by T Cells and by Antibodies

This laboratory had previously mapped the regions of T and B cell recognition on sperm whale myoglobin (Mb). Mb has five regions (E1-E5) that are recognized by both T cells and B cells (i.e. antibodies, Abs) and an additional region (E6) that is recognized exclusively by T cells (i.e., TE6) and to which no Abs are detectable. The responses to the site are each under separate genetic control. Recently, we showed in an H-2d haplotype that TE6 cells preferentially activated Mb-primed B cells (BMb) that made Abs against sites within E3 and E4 on the same protein. In the present work, we established, from Mb-primed SJL mice, an E4-specific T cell line (TE4) by passage in vitro with synthetic peptide E4. At relatively low numbers, these T cells activated syngeneic BMb cells in vitro to produce anti-Mb Abs that recognized each of the antigenic sites within regions E1, E2, E3, E4 and E5. We confirmed the ability of TE4 to activate B cells that produce Abs against each of these regions by allowing TE4 to activate in vitro syngeneic B cells that had been primed with E1, E2, E3, E4 or E5. The helper activity of TE4 cells was dependent on the in vitro concentration of the challenge Ag (intact Mb or peptide E4). Thus, T cells against an epitope may provide help restricted to B cells that make Abs against selected antigenic sites or they may activate B cells that make Abs against all the antigenic sites of a protein. This might depend on the site-specificity of the T cell and/or on the host.

Effects of the arrangement of a distal histidine on regioselectivity of the coupled oxidation of sperm whale myoglobin mutants

The arrangement of a distal histidine of sperm whale myoglobin alters the regioselectivity of the heme degradation by coupled oxidation.

The tautomeric state of histidines in myoglobin

1H-15N HMQC spectra were collected on 15N-labeled sperm whale myoglobin (Mb) to determine the tautomeric state of its histidines in the neutral form. By analyzing metaquoMb and metcyanoMb data sets collected at various pH values, cross-peaks were assigned to the imidazole rings and their patterns interpreted. Of the nine histidines not interacting with the heme in sperm whale myoglobin, it was found that seven (His-12, His-48, His-81, His-82, His-113, His-116, and His-119) are predominantly in the N epsilon2H form with varying degrees of contribution from the Ndelta1 H form. The eighth, His-24, is in the Ndelta1H state as expected from the solid state structure. 13C correlation spectra were collected to probe the state of the ninth residue (His-36). Tentative interpretation of the data through comparison with horse Mb suggested that this ring is predominantly in the Ndelta1H state. In addition, signals were observed from the histidines associated with the heme (His-64, His-93, and His-97) in the 1H-15N HMQC spectra of the metcyano form. In several cases, the tautomeric state of the imidazole ring could not be derived from inspection of the solid state structure. It was noted that hydrogen bonding of the ring was not unambiguously reflected in the nitrogen chemical shift. With the experimentally determined tautomeric state composition in solution, it will be possible to broaden the scope of other studies focused on the electrostatic contribution of histidines to the thermodynamic properties of myoglobin.

A 1H NMR comparative study of the structure of the critical packing interfaces between helix and non-helical region in various ligation states of sperm whale myoglobin

NMR signals arising from HisB5 N δ H and HisEF5 N ε H protons in sperm whale met-aquo, met-azido, met-imidazole and deoxy myoglobins have been assigned. HisB5 N δ H proton and N ε atom are hydrogen-bonded to peptide carbonyl oxygen of AspB1 and HisGH1 N ε H proton, respectively. This unique triad hydrogen bond stabilizes the interface between the B helix and the GH corner, which is critical to the stability of its protein folding. HisEF5 N ε H proton is hydrogen-bonded to one of the side-chain carboxyl oxygen atoms of AspH18 and this internal hydrogen bond stabilizes the orientation of the EF corner, the hinge region between the heme binding E and F helices, relative to the H helix. The assigned His NH proton signals were used as probes to investigate possible structural differences of these critical interfaces among various ligation states of myoglobin. Shift differences of the signals among the proteins strongly suggested that the AspB1-HisB5-HisGH1 and HisEF5-AspH18 hydrogen bonds are affected by heme ligation. The present study demonstrates the presence of a structural correlation between the active site and the critical interfaces in myoglobin.

Therapeutic vaccination of woodchucks against chronic woodchuck hepatitis virus infection

Background/Aims: Therapeutic vaccination is a new approach to treat patients with chronic hepatitis B virus infection. We have used the woodchuck model to examine the efficacy and safety of this approach. Methods: Seven woodchucks chronically infected with woodchuck hepatitis virus were immunized with surface antigen from this virus, purified from plasma, in conjunction with a peptide named FIS (encompassing amino acids 106–118: FISEAIIHVLHSR from sperm whale myoglobin), which is recognized by T helper lymphocytes. As controls, two woodchucks chronically infected with woodchuck hepatitis virus were immunized: one with FIS only and the other with surface antigen only. Results: Co-immunization with surface antigen and FIS, but not with FIS or surface antigen alone, induced anti-surface antibodies in 7 7 immunized woodchucks. In the two woodchucks in which the highest titer of anti-surface antibody was elicited, severe liver damage was observed: one died of fulminant hepatitis and the other became seriously ill with hepatic injury and had to be sacrificed. Conclusions: Co-immunization of chronically infected woodchucks with surface antigen and a peptide recognized by T helper cells produces a good anti-surface antibody response. However, this strategy needs to be optimized before its implementation in humans. Although our experiments are not strictly comparable to vaccination of chronically hepatitis B virus-infected patients with recombinant or plasma-derived vaccines, we believe that precautions should be taken to avoid the risk of severe liver injury when immunizing hepatitis B virus carriers.

Ligand migration in sperm whale myoglobin.

Geminate oxygen rebinding to myoglobin was followed from a few nanoseconds to a few microseconds after photolysis for more than 25 different oxymyoglobin point mutants in the presence and absence of 12 atm of xenon. In all cases, two relaxations were observed: an initial fast phase (half-time 20 ns) and a slower, smaller phase (half-time 0.5-2 micros). Generally, xenon accelerates the fast reaction but slows the slower reaction and diminishes its amplitude. The rates and proportions of the two components and the effects of xenon on them vary widely for different mutants. The locations of specific xenon binding sites [Tilton, R. F., Kuntz, I. D. Jr., and Petsko, G. A. (1984) Biochemistry 23, 2849-2857], the effects of point mutations on the geminate reactions, and molecular dynamics simulations were used to suggest locations in the protein interior occupied by ligands on the nanosecond to microsecond time scale. Photodissociated ligands may occupy xenon site 4 in the distal pocket and xenon site 1 below the plane of the heme. Rebinding from these positions corresponds to the slower geminate phase for O2 rebinding. The rapid geminate component is determined by competition between rebinding from a position closer to the iron atom and escape to solvent or more distant locations in the protein.

Reaction of variant sperm-whale myoglobins with hydrogen peroxide: the effects of mutating a histidine residue in the haem distal pocket.

The reaction of hydrogen peroxide with a number of variants of sperm-whale myoglobin in which the distal pocket histidine residue (His64) had been mutated was studied with a combination of stopped-flow spectroscopy and freeze-quench EPR. The rate of the initial bimolecular reaction with hydrogen peroxide in all the proteins studied was found to depend on the polarity of the amino acid side chain at position 64. In wild-type myoglobin there were no significant optical changes subsequent to this reaction, suggesting the rapid formation of the well-characterized oxyferryl species. This conclusion was supported by freeze-quench EPR data, which were consistent with the pattern of reactivity previously reported [King and Winfield (1963) J. Biol. Chem. 238, 1520-1528]. In those myoglobins bearing a mutation at position 64, the initial bimolecular reaction with hydrogen peroxide yielded an intermediate species that subsequently decayed via a second hydrogen peroxide-dependent step leading to modification or destruction of the haem. In the mutant His64-->Gln the calculated electronic absorption spectrum of the intermediate was not that of an oxyferryl species but seemed to be that of a low-spin ferric haem. Freeze-quench EPR studies of this mutant and the apolar mutant (His64-->Val) revealed the accumulation of a novel intermediate after the first hydrogen peroxide-dependent reaction. The unusual EPR characteristics of this species are provisionally assigned to a low-spin ferric haem with bound peroxide as the distal ligand. These results are interpreted in terms of a reaction scheme in which the polarity of the distal pocket governs the rate of binding of hydrogen peroxide to the haem iron and the residue at position 64 governs both the rate of heterolytic oxygen scission and the stability of the oxyferryl product.

Lymphocyte reactivity to hepatitis C virus (HCV) antigens shows evidence for exposure to HCV in HCV-seronegative spouses of HCV-infected patients.

Lymphocyte reactivity against hepatitis C virus (HCV) antigens was studied in 20 couples in which 1 member had chronic hepatitis C. This was done to investigate the possibility of HCV transmission between spouses that was not followed by seroconversion. Twenty healthy subjects without any risk factors for HCV transmission served as negative controls. All the patients' spouses and the healthy controls were negative for HCV RNA and for anti-HCV antibody. Lymphocytes were cultured with recombinant HCV core and nonstructural antigens (c22, c33, c100, c200, and NS5) and with control antigens (sperm whale myoglobin, chicken lysozyme, and superoxide dismutase). Lymphocytes from 10 patients and 4 seronegative spouses proliferated in the presence of at least one HCV antigen. No proliferation was shown with nonspecific antigens or in the control group. This study gives evidence for possible in vivo priming with HCV antigens that did not lead to seroconversion in spouses of HCV-positive patients.

A myoglobin mutant designed to mimic the oxygen-avid Ascaris suum hemoglobin: elucidation of the distal hydrogen bonding network by solution NMR

The solution 1H NMR structure of the active site and ligand dissociation rate for the cyanomet complex have been determined for a sperm whale myoglobin triple mutant Leu29(B10)-->Tyr, His64(E7)-->Gln, Thr67(E10)-->Arg that mimics the distal residue configuration of the oxygen-avid hemoglobin from Ascaris suum. A double mutant that retains Leu29(B10) was similarly investigated. Two-dimensional NMR analysis of the iron-induced dipolar shifts, together with the conserved proximal side structure for the two mutants, allowed the determination of the orientations of the paramagnetic susceptibility tensor for each complex. The resulting magnetic axes, together with paramagnetic relaxation and steady-state NOEs, led to a quantitative description of the distal residue orientations. The distal Tyr29(B10) in the triple mutant provides a strong hydrogen bond to the bound cyanide comparable to that provided by His64(E7) in wild-type myoglobin. The distal Gln64(E7) in the triple mutant is sufficiently close to the bound cyanide to severe as a hydrogen bond donor, but the angle is not consistent with a strong hydrogen bond. Dipolar contacts between the Arg67(E10) guanidinium group and the Gln64(E7) side chain in both mutants support a hydrogen-bond to the Gln64(E7) carbonyl group. The much lower oxygen affinity of this triple mutant relative to that of Ascaris hemoglobin is concluded to arise from side-chain orientations that do not allow hydrogen bonds between the Gln64(E7) side-chain NHs and both the ligand and Tyr29(B10) hydroxyl oxygen. Cyanide dissociation rates for the reduced cyanide complexes are virtually unaffected by the mutations and are consistent with a model of the rate-determining step as the intrinsically slow Fe-C bond breaking that is largely independent of any hydrogen bonds to the cyanide nitrogen.

Trehalose prevents myoglobin collapse and preserves its internal mobility.

A quantitative model, which involves diffusion on a temperature-dependent potential, is utilized to analyze the time-dependence of geminate CO recombination to sperm whale myoglobin in a trehalose glass and the accompanying spectral shifts. Most of the recombination is inhomogeneous. This is due to higher geminate reactivity rather than slower protein relaxation. A fraction of the hemes undergoes relaxation with a concomitant increase in the barrier height for recombination. The activation energy for conformational diffusion (relaxation) is considerably lower than in glycerol/water. "Protein collapse", manifested in glycerol/water by a decrease in the equilibrium conformational separation between the bound and deoxy states, is completely prevented in trehalose. We postulate that the high internal viscosity in glycerol/water is due to dehydration of the heme pocket. Trehalose prevents the escape of the few vital internal water molecules and thus preserves the internal lability of the protein. This might be important in understanding the ability of trehalose to protect against the adverse effects of dehydration.