Ligand-apomyoglobin interactions. Configurational adaptability of the haem-binding site.

1. The interaction of the haem-binding region of apomyoglobin with different ligands was examined by ultrafiltration, equilibrium dialysis and spectrophotometry, to study unspecific features of protein-ligand interactions such as they occur in, for example, serum albumin binding. 2. Apomyoglobin, in contrast with metmyoglobin, binds at pH 7, with a high affinity, one molecule of Bromophenol Blue, bilirubin and protoporphyrin IX, two molecules of n-dodecanoate and n-decyl sulphate and four molecules of n-dodecyl sulphate and n-tetradecyl sulphate. 3. The number of high-affinity sites and/or association constants for the alkyl sulphates are enhanced by an increase of hydrocarbon length, indicating hydrophobic interactions with the protein. 4. Measurements of the temperature-dependence of the association constants of the high-affinity sites imply that the binding processes are largely entropy-driven. 5. Binding studies in the presence of two ligands show that bilirubin plus Bromophenol Blue and dodecanoate plus Bromophenol Blue can be simultaneously bound by apomyoglobin, but with decreased affinities. By contrast, the apomyoglobin-protoporphyrin IX complex does not react with Bromophenol Blue. 6. Optical-rotatory-dispersion measurements show that the laevorotation of apomyoglobin is increased towards that of metmyglobin in the presence of haemin and protoporphyrin IX. Small changes in the optical-rotatory-dispersion spectrum of apomyoglobin are observed in the presence of the other ligands. 7. It is concluded that the binding sites on apomyoglobin probably do not pre-exist but appear to be moulded from predominantly non-polar amino acid residues by reaction with hydrophobic ligands. 8. Comparison with data in the literature indicates that apomyoglobin on a weight basis has a larger hydrophobic area avaialble for binding of ligands than has human serum albumin. On the other hand, the association constants of serum for the ligands used in this study are generally somewhat larger than those of apomyoglobin.     

Biochemical properties of the heme oxygenase inhibitor, Sn-protoporphyrin. Interactions with apomyoglobin and human serum albumin

Sn-protoporphyrin is a strong competitive inhibitor of heme oxygenase and a potential pharmacological agent for the treatment of neonatal hyperbilirubinemia. Little is otherwise known about the biochemistry of tin porphyrins. We have investigated aspects of the chemistry of tin-protoporphyrin in aqueous solution and of its interactions with heme-binding proteins other than heme oxygenase, specifically apomyoglobin and human serum albumin. In the pH region 7-10, Soret region absorption studies of unbound Sn-protoporphyrin demonstrate a pH-dependent monomer-dimer equilibrium (KD congruent to 10(6) M-1 at pH 7) with little higher aggregation. Dissociation of the dimer is relatively slow at neutral pH, permitting interaction of protein ligands with monomeric and dimeric species to be distinguished and providing insights into kinetic mechanisms of porphyrin binding by heme-binding proteins. In the present study, the kinetics of interaction of Sn-protoporphyrin with apomyoglobin are presented as novel evidence that this binding proceeds by an induced fit mechanism. Binding of Sn-protoporphyrin to both apomyoglobin and serum albumin is unexpectedly weak. Between pH 7 and 9, the apparent affinity of Sn-protoporphyrin for apomyoglobin is less than 1/200 that of heme and, at pH 9, is also significantly less than that of protoporphyrin. The apparent affinity of Sn-protoporphyrin for human serum albumin is less than 1/1000 that of heme and 1/30 to 1/100 that of protoporphyrin. Competition studies between heme and Sn-protoporphyrin and between bilirubin and Sn-protoporphyrin indicate that Sn-protoporphyrin distributes differently among porphyrin-binding sites on serum albumin than does heme and that it is also not an effective competitor with bilirubin for bilirubin-binding sites. These results argue that Sn-protoporphyrin should not significantly alter normal mechanisms for the binding and transport of heme or of preformed bilirubin by serum albumin. From a more general perspective, the results indicate potentially unusual binding site selectivity by tin chelates; possible origins of this selectivity are discussed.     

Investigation of apomyoglobin stability depending on urea and temperature at two different pH values

Equilibrium unfolding of apomyoglobin by urea was investigated in the temperature range from 5 to 25 degrees C at two pH values. The thermodynamic parameters of the apomyoglobin native-unfolded state transition were determined. Conformational changes in the protein structure were monitored by tryptophan fluorescence and far UV circular dichroism. Apomyoglobin preserves its native conformation at pH 5.7 and 6.2 in the temperature range used. It was shown that the apomyoglobin stability and its unfolding cooperativity are substantially lower at 5 degrees C than at other temperatures. This fact should be taken in account at the investigation of apomyoglobin.     

Molten globule versus variety of intermediates: influence of anions on pH-denatured apomyoglobin.

The molten globule state was shown to be the third thermodynamic state of protein molecules in addition to their native and unfolded states. On the other hand, it was reported that optical and hydrodynamic properties of pH-denatured apomyoglobin depend on the nature of anions added to the protein solution. This observation was used to conclude that there are many 'partly folded' intermediates between the native and unfolded states rather than one distinct molten globule state. However, little is known on the structures of pH-denatured apomyoglobin in the presence of different anions. Two tyrosine residues in horse apomyoglobin have been successively modified by the reaction with tetranitromethane. This approach was employed to measure the distances between tryptophans and modified tyrosines in different states of apomyoglobin by the method of direct energy transfer. Experimental data show that the distance between the middle of the A-helix and the beginning of the G-helix and/or the end of the H-helix in 'anion-induced' states are very close to those in the native holo- and apomyoglobins. This suggests that the AGH helical complex, being the most structured part of apomyoglobin in the molten globule state, exists also in pH-denatured apomyoglobin in the presence of different anions. Consequently, all non-native forms of apomyoglobin studied so far share the common important feature of its native structure.     

Interactions of apomyoglobin with membranes: mechanisms and effects on heme uptake

The last step of the folding reaction of myoglobin is the incorporation of a prosthetic group. In cells, myoglobin is soluble, while heme resides in the mitochondrial membrane. We report here an exhaustive study of the interactions of apomyoglobin with lipid vesicles. We show that apomyoglobin interacts with large unilamellar vesicles under acidic conditions, and that this requires the presence of negatively charged phospholipids. The pH dependence of apomyoglobin interactions with membranes is a two-step process, and involves a partially folded state stabilized at acidic pH. An evident role for the interaction of apomyoglobin with lipid bilayers would be to facilitate the uptake of heme from the outer mitochondrial membrane. However, heme binding to apomyoglobin is observed at neutral pH when the protein remains in solution, and slows down as the pH becomes more favorable to membrane interactions. The effective incorporation of soluble heme into apomyoglobin at neutral pH suggests that the interaction of apomyoglobin with membranes is not necessary for the heme uptake from the lipid bilayer. In vivo, however, the ability of apomyoglobin to interact with membrane may facilitate its localization in the vicinity of the mitochondrial membranes, and so may increase the yield of heme uptake. Moreover, the behavior of apomyoglobin in the presence of membranes shows striking similarities with that of other proteins with a globin fold. This suggests that the globin fold is well adapted for soluble proteins whose functions require interactions with membranes.     

Non-covalent modification of the heme-pocket of apomyoglobin by a 1,10-phenanthroline derivative

To expand the repertoire of artificial enzymes that are constructed by replacing the natural prosthetic group of hemoproteins with non-natural cofactors, we examined incorporation of a non-porphyrinic ligand (1) into the heme-pocket of apomyoglobin in a non-covalent fashion. Ligand 1 is a highly conjugated 1,10-phenanthroline derivative, which shares some structural features with protoporphyrin IX; for example, molecular size and arrangement of hydrophobic and anionic parts. Addition of apomyoglobin to a solution of 1 induces clear changes in the absorption spectrum of 1, suggesting one-to-one incorporation of 1 into the heme cavity of apomyoglobin with an affinity of 6.3 x 10(6)M(-1). We found that the hydrolytic activity of apomyoglobin toward p-nitrophenyl hexanoate was greatly suppressed because of the incorporation of 1 into the heme-pocket.     

Copper(II) Schiff-base complexes and apoglobin stability.

N,N'-Propylene-bis-(N-salicylidene)copper(II) (Cu(Salprn)) explicitly stabilizes apomyoglobin. The optical spectrum of this copper(II) Schiff-base complex of apomyoglobin arises from the electronic excitations of pi *-O-Salprn-->dx2-y2 and N-Salprn-->dx2-y2. Shifts of these transitions with respect to those of the parent complex may be a consequence of hydrophobic solvatochromism or binding of an additional ligand. ESR parameters imply no change in the identity of the first coordination sphere around the copper, while hydrophobic solvatochromism cannot be excluded. Combination of copper(II) Schiff-base complex with apomyoglobin does not inhibit the ability of apomyoglobin to extract hemin from the main component of Glycera dibranchiata hemoglobin. Hemin replaces the copper complex, and the value of the apparent first-order rate constant varies with time. The mechanism involves dissociative and associative interchange pathways. Values of rate constants for transfer of hemin to copper(II) Schiff-base apomyoglobin complex, as well as the change of concentration with time are evaluated.     

Conformational changes in sperm-whale metmyoglobin due to combination with antibodies to apomyoglobin

1. No ferrihaem was detected in the precipitate formed by metmyoglobin with an antiserum to apomyoglobin and the extinction at 410mmu of metmyoglobin, due to ferrihaem, was decreased by the univalent fragments of apomyoglobin antibodies. It was concluded that the combination of apomyoglobin antibodies with metmyoglobin caused the release of ferrihaem. As the removal of ferrihaem from metmyoglobin is accompanied by a conformational change, it was concluded that the conformation of metmyoglobin was altered by the apomyoglobin antibodies. 2. Antisera to metmyoglobin were divided into two groups; antisera of the first group revealed differences between the immunological reactivities of metmyoglobin and apomyoglobin, whereas no differences were detected with antisera of the second group. 3. Metmyoglobin was only partially re-formed by adding haematin to the precipitate produced by apomyoglobin with an antiserum of the first group, whereas complete re-formation of metmyoglobin was achieved in the presence of antisera of the second group. No metmyoglobin was formed on the addition of haematin to the precipitates produced by either metmyoglobin or apomyoglobin with the anti-apomyoglobin serum. 4. Immune precipitates formed by antisera to metmyoglobin dissociated at pH1.8, whereas those formed by the anti-apomyoglobin serum did not dissociate. 5. These results suggest that apomyoglobin possessed different conformations when combined with metmyoglobin antibodies and apomyoglobin antibodies.     

Solvent accessibility of the heme pocket in tuna myoglobin

The accessibility of the heme binding site of two apomyoglobins, i.e. tuna and sperm whale apomyoglobin, has been evaluated by quenching the fluorescence of their ANS-conjugates. The quenching pattern obtained by using charged and uncharged quenchers revealed that the heme pocket of tuna apomyoglobin is more accessible than that of sperm whale. Moreover, a larger number of positively charged groups is present in the heme pocket of tuna apomyoglobin as indicated by comparing the extent of quenching produced by iodide and cesium ion. The relaxation time of ANS bound to tuna apomyoglobin is lower than that of the same chromophore bound to sperm whale globin thus indicating that there is some localized flexibility in the tuna globin.     

Defining the interacting regions between apomyoglobin and lipid membrane by hydrogen/deuterium exchange coupled to mass spectrometry

Sperm whale myoglobin can be considered as the model protein of the globin family. The pH-dependence of the interactions of apomyoglobin with lipid bilayers shares some similarities with the behavior of pore-forming domains of bacterial toxins belonging also to the globin family. Two different states of apomyoglobin bound to a lipid bilayer have been characterized by using hydrogen/deuterium exchange experiments and mass spectrometry. When bound to the membrane at pH 5.5, apomyoglobin remains mostly native-like and interacts through alpha-helix A. At pH 4, the binding is related to the stabilization of a partially folded state. In that case, alpha-helices A and G are involved in the interaction. At this pH, alpha-helix G, which is the most hydrophobic region of apomyoglobin, is available for interaction with the lipid bilayer because of the loss of the tertiary structure. Our results show the feasibility of such experiments and their potential for the characterization of various membrane-bound states of amphitropic proteins such as pore-forming domains of bacterial toxins. This is not possible with other high-resolution methods, because these proteins are usually in partially folded states when interacting with membranes.     

Intermediate states of apomyoglobin: Are they parts of the same area of conformations diagram?

Several research teams have reported detection and characterization of various apomyoglobin intermediate states different in their accumulation mode, thus putting a natural question as to proportions of these intermediates. The current report presents spectral properties of sperm whale apomyoglobin studied over a wide range of conditions with the use of circular dichroism and fluorescence techniques. Based on the experimental data, a diagram of apomyoglobin conformational states has been constructed. It shows that though induced by various denaturants, all the observed intermediates belong to one and the same area in the diagram.     

Quench-flow experiments combined with mass spectrometry show apomyoglobin folds through and obligatory intermediate

Folding of apomyoglobin is characterized by formation of a compact intermediate that contains substantial helicity. To determine whether this intermediate is obligatory or whether the protein can fold directly into the native state via an alternate parallel pathway, we have combined quench-flow hydrogen-exchange pulse labeling techniques with electrospray ionization mass spectrometry. The mass spectra of apomyoglobin obtained at various refolding times suggest that apomyoglobin indeed folds through a single pathway containing an obligatory intermediate with a significant hydrogen-bonded secondary structure content.     

Proof of nanosecond timescale relaxation in apomyoglobin by phase fluorometry

Apomyoglobin was labeled with the fluorescent probe 2-p-toluidinylnaphthalene-6-sulfonic acid (TNS). Apparent phase shift and demodulation lifetimes of bound TNS were measured at various emission wavelengths. The lifetimes increased with increasing wavelength. Similar results were obtained for TNS in the viscous solvent glycerol at 10°C but not for TNS in vitrified or fluid solvent. The wavelength-dependent lifetimes suggest apomyoglobin is relaxing around the TNS molecule during its fluorescent lifetime. Importantly, the apparent phase lifetimes exceeded the apparent modulation lifetimes on the long wavelength side of the emission for TNS in apomyoglobin at 3°C and for TNS in glycerol at 10°C. This result proves the increasing lifetimes are a result of an excited state reaction during the lifetime of the excited state and are not a result of heterogeneity in the fluorescence emission. From the lifetimes on the short wavelength side of the emission the relaxation time of apomyoglobin was estimated to be 18 nsec.     

Origin of the anomalous circular dichroism spectra of many apomyoglobin mutants

Several authors have reported that many sperm whale apomyoglobin mutants show anomalous circular dichroism spectra. These mutants have a low molar ellipticity compared to the wild-type protein but in several cases have the same stability of unfolding. A model in which native apomyoglobin is not folded in the same manner as that in other proteins and in which mutants show progressive reductions in their degree of folding has been suggested to explain this phenomenon. However, nuclear magnetic resonance of the native apomyoglobin conformation has shown that this state is folded and compact, raising the possibility that the anomalous circular dichroism spectra could have another explanation. We studied several mutants with anomalous circular dichroism spectra and found that these proteins were all contaminated with nucleic acid that contributed to the ultraviolet absorption and caused uncertainty in the determination of protein concentration. The resulting overestimation of the concentration of apomyoglobin explains the phenomenon of anomalous circular dichroism spectra. We describe a procedure to remove the contaminant nucleic acid which yields accurate protein concentration measurements and provides the normal circular dichroism spectra. Our findings support a well-structured native conformation for apomyoglobin and may also be of the interest to scientists working with the purification of recombinant proteins.     

Protein adsorption onto organically modified silica glass leads to a different structure than sol-gel encapsulation

The secondary structures of two proteins were examined by circular dichroism spectroscopy after adsorption onto a series of organically modified silica glasses. The glasses were prepared by the sol-gel technique and were varied in hydrophobicity by incorporation of 5% methyl, propyl, trifluoropropyl, or n-hexyl silane. Both cytochrome c and apomyoglobin were found to lose secondary structure after adsorption onto the modified glasses. In the case of apomyoglobin, the α-helical content of the adsorbed protein ranged from 21% to 28%, well below the 62% helix found in solution. In contrast, these same glasses led to a striking increase in apomyoglobin structure when the protein was encapsulated within the pores during sol-gel processing: the helical content of apomyoglobin increased with increasing hydrophobicity from 18% in an unmodified glass to 67% in a 5% hexyl-modified glass. We propose that proteins preferentially adsorb onto unmodified regions of the silica surface, whereas encapsulated proteins are more susceptible to changes in surface hydration due to the proximity of the alkyl chain groups.     

Preparation and spectral characterization of the heme d1.apomyoglobin complex: an unusual protein environment for the substrate-binding heme of Pseudomonas cytochrome oxidase

The heme d1 prosthetic group isolated from Pseudomonas cytochrome oxidase combines with apomyoglobin to form a stable, optically well-defined complex. Addition of ferric heme d1 quenches apomyoglobin tryptophan fluorescence suggesting association in a 1:1 molar ratio. Optical absorption maxima for heme d1.apomyoglobin are at 629 and 429 nm before, and 632 and 458 nm after dithionite reduction; they are distinct from those of heme d1 in aqueous solution but more similar to those unobscured by heme c in Pseudomonas cytochrome oxidase. Cyanide, carbon monoxide and imidazole alter the spectrum of heme d1.apomyoglobin demonstrating axial coordination to heme d1 by exogeneous ligands. The cyanide-induced optical difference spectra exhibit isosbestic points, and a Scatchard-like analysis yields a linear plot with an apparent dissociation constant of 4.2 X 10(-5) M. However, carbon monoxide induces two absorption spectra with Soret maxima at 454 or 467 nm, and this duplicity, along with a shoulder that correlates with the latter before binding, suggests multiple carbon monoxide and possibly heme d1 orientations within the globin. The 50-fold reduction in cyanide affinity over myoglobin is more consistent with altered heme pocket interactions than the intrinsic electronic differences between the two hemes. However, stability of the heme d1.apomyoglobin complex is verified further by the inability to separate heme d1 from globin during dialysis and column chromatography in excess cyanide or imidazole. This stability, together with a comparison between spectra of ligand-free and -bound derivatives of heme d1-apomyoglobin and heme d1 in solution, implies that the prosthetic group is coordinated in the heme pocket through a protein-donated, strong-field ligand. Furthermore, the visible spectrum of heme d1.apomyoglobin varies minimally with ligand exchange, in contrast to the Soret, which suggests that much spectral information concerning heme d1 coordination in the oxidase is lost by interference from heme c absorption bands. A comparison of the absorption spectra of heme d1.apomyoglobin and Pseudomonas cytochrome oxidase, together with a critical examination of the previous axial ligand assignments from magnetic resonance techniques in the latter, implies that it is premature to accept the assignment of bishistidine heme d1 coordination in oxidized, ligand-free oxidase and other iron-isobacteriochlorin-containing enzymes.     

Structural characterization of unfolded states of apomyoglobin using residual dipolar couplings

The conformational propensities of unfolded states of apomyoglobin have been investigated by measurement of residual dipolar couplings between (15)N and (1)H in backbone amide groups. Weak alignment of apomyoglobin in acid and urea-unfolded states was induced with both stretched and compressed polyacrylamide gels. In 8 M urea solution at pH 2.3, conditions under which apomyoglobin contains no detectable secondary or tertiary structure, significant residual dipolar couplings of uniform sign were observed for all residues. At pH 2.3 in the absence of urea, a change in the magnitude and/or sign of the residual dipolar couplings occurs in local regions of the polypeptide where there is a high propensity for helical secondary structure. These results are interpreted on the basis of the statistical properties of the unfolded polypeptide chain, viewed as a polymer of statistical segments. For a folded protein, the magnitude and sign of the residual dipolar couplings depend on the orientation of each bond vector relative to the alignment tensor of the entire molecule, which reorients as a single entity. For unfolded proteins, there is no global alignment tensor; instead, residual dipolar couplings are attributed to alignment of the statistical segments or of transient elements of secondary structure. For apomyoglobin in 8 M urea, the backbone is highly extended, with phi and psi dihedral angles favoring the beta or P(II) regions. Each statistical segment has a highly anisotropic shape, with the N-H bond vectors approximately perpendicular to the long axis, and becomes weakly aligned in the anisotropic environment of the strained acrylamide gels. Local regions of enhanced flexibility or chain compaction are characterized by a decrease in the magnitude of the residual dipolar couplings. The formation of a small population of helical structure in the acid-denatured state of apomyoglobin leads to a change in sign of the residual dipolar couplings in local regions of the polypeptide; the population of helix estimated from the residual dipolar couplings is in excellent agreement with that determined from chemical shifts. The alignment model described here for apomyoglobin can also explain the pattern of residual dipolar couplings reported previously for denatured states of staphylococcal nuclease and other proteins. In conjunction with other NMR experiments, residual dipolar couplings can provide valuable insights into the dynamic conformational propensities of unfolded and partly folded states of proteins and thereby help to chart the upper reaches of the folding landscape.     

How strong are side chain interactions in the folding intermediate?

Influence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH‐induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15–50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.     

Sequence determinants of a protein folding pathway

Local hydrophobic collapse of the polypeptide chain and transient long-range interactions in unfolded states of apomyoglobin appear to occur in regions of the amino acid sequence which, upon folding, bury an above-average area of hydrophobic surface. To explore the role of these interactions in protein folding, we prepared and characterized apomyoglobins with compensating point mutations designed to change the average buried surface area in local regions of the sequence, while conserving as much as possible the constitution of the hydrophobic core. The behavior of the mutants in quench-flow experiments to determine the folding pathway was exactly as predicted by the changes in the buried surface area parameter calculated from the amino acid sequence. In addition, spin label experiments with acid-unfolded mutant apomyoglobin showed that the transient long-range contacts that occur in the wild-type protein are abolished in the mutant, while new contacts are observed between areas that now have above-average buried surface area. We conclude that specific groupings of amino acid side-chains, which can be predicted from the sequence, are responsible for early hydrophobic interactions in the first phase of folding in apomyoglobin, and that these early interactions determine the subsequent course of the folding process.     

The immunological activity of some of the chymotryptic peptides of sperm-whale myoglobin

1. Sperm-whale apomyoglobin was digested with chymotrypsin in a dialysis sac. The ultrafiltrate contained incompletely hydrolysed fragments which partially inhibited the precipitation of metmyoglobin and apomyoglobin by some antisera produced against metmyoglobin. The inhibitory activity was stable to heating at 100 degrees and depended on the peptide structure. 2. The fragments were fractionated according to molecular size and were purified by ion-exchange chromatography. Six pure peptides and two peptides which contained a minor impurity were isolated. Their amino acid compositions and N-terminal amino acid sequences were determined and their entire amino acid sequences deduced from the known amino acid sequence of sperm-whale myoglobin. 3. The peptides formed no detectable precipitates with the antisera. Five of the eight peptides partially inhibited the precipitation of apomyoglobin and/or metmyoglobin by one antiserum. Six of the peptides inhibited the precipitation of apomyoglobin by one or other of two antisera; at least two of these peptides inhibited both antisera. One peptide failed to inhibit the precipitation of either antigen by either antiserum. Two of the peptides possessed the same serological specificity. 4. The molar ratios of inhibitors to antigen for 50% of the maximum inhibition decreased as the molecular size of the inhibitor increased. With one antiserum and with apomyoglobin as the antigen, molar ratios 12 and 80 were obtained for peptides with molecular weights 2051 and 793 respectively. 5. The size and structure of an antigenic site is discussed in relation to the known steric configuration of myoglobin.