[Covalent structure of horse myoglobin]

Molecular charge and electrophoretic mobility in cetacean myoglobins of known sequence

Fourteen myoglobins of known sequence were examined by polyacrylamide gel electrophoresis at five pH values. Gels at each pH divided the sequences into six to eight distinct classes, while the combination of the results of three gels at different pH levels distinguished 13 of 14, or 93%, of the sequences. The relative mobility of the myoglobins in the gels is significantly correlated with the charges of the proteins calculated from the pK values of the ionized groups. Major differences in mobility corresponded to expected differences in charge due to the amino acid substitutions between sequences. In addition to sequences differing in the total number of acidic and basic residues, those differing from each other in the total number of histidines were distinguished on low-pH gels. One pair of sequences differing by the exchange of lysine for arginine was separated on high-pH gels, as predicted from the differences in ionization of these two amino acids. On gels at pH 10.4, there was greater deviation of electrophoretic mobility from charge than on other gels, possibly due to the influence of amino acid substitutions in the neighborhood of lysine residues. Manipulation of the concentration and composition of the gels did not change the separation of the sequences from each other. Examination of myoglobins by gel electrophoresis at a wide range of pH values allows discrimination of nearly all amino acid substitutions and demonstrates the close relationship between titration and relative electrophoretic mobility.

High performance gel permeation chromatography of proteins. Application to embryonic inducing factors

Proteins in the molecular weight range of 10 000-170 000 were separated by high performance gel permeation chromatography. Silica particles with 30 nm or 50 nm pores were derivatized with glycidoxypropyltrimethoxysilane and used as support. The proteins were eluted with 50% formic acid. A protein fraction which induces endodermal and mesodermal tissues in amphibian gastrula ectoderm was purified by this method.

Genetic control of the immune response to myoglobin. VII. Antibody responses to myoglobin variants reveal that gene restriction of the antibody responses to myoglobin antigenic sites is dependent on the chemical properties of the sites

Previously it has been shown that the immune responses to sperm-whale myoglobin are under H-2-linked Ir-gene control. More importantly the responses to the synthetic antigenic sites are each under separate genetic control. In the present studies we investigated the genetic control of the antibody response to four different myoglobins of known structure, to determine whether this genetic control is influenced by changes in the properties of the sites. The results suggest that genetic control of the responses to individual antigenic sites on a protein antigen is not only determined by the genetic constitution of the host species but also by the chemical properties of the individual sites. It appears that the H-2 subregions mapping the responses to given antigenic sites can also recognize other sites, which were previously unrecognizable in a homologous protein, if their chemical properties are suitably altered.

The antibody response to myoglobin is independent of the immunized species. Analysis in terms of replacements in the antigenic sites and in environmental residues of the cross-reactions of fifteen myoglobins with sperm-whale myoglobin antisera raised in different species

The recent determination of the entire antigenic structure of sperm-whale myoglobin with rabbit and goat antisera has permitted the examination of whether the antigenic structure recognized by antibodies depends on the species in which the antisera are raised. Also, by knowledge of the antigenic structure, the molecular factors that determine and influence antigenicity can be better understood in terms of the effects of amino acid substitutions occurring in the antigenic sites and in the environmental residues of the sites. In the present work, the myoglobins from finback whale, killer whale, horse, chimpanzee, sheep, goat, bovine, echidna, viscacha, rabbit, dog, cape fox, mouse and chicken were examined for their ability to cross-react with antisera to sperm-whale myoglobin. By immunoadsorbent titration studies with radioiodinated antibodies, each of these myoglobins was able to bind antibodies to sperm-whale myoglobin raised in goat, rabbit, chicken, cat, pig and outbred mouse. It was found that the extent of cross-reaction of a given myoglobin was not dependent on the species in which the antisera were raised. This indicated that the antibody response to sperm-whale myoglobin (i.e. its antigenic structure) is independent of the species in which the antisera are raised and is not directed to regions of sequence differences between the injected myoglobin and the myoglobin of the immunized host. Indeed, in each antiserum from a given species examined, that antiserum reacted with the myoglobin of that species. The extent of this auto-reactivity for a given myoglobin was comparable with the general extent of cross-reactivity shown by that myoglobin with antisera raised in other species. The cross-reactivities and auto-reactivities (both of which are of similar extents for a given myoglobin) can be reasonably rationalized in terms of the effects of amino acid substitutions within the antigenic sites and within the residues close to these sites. These findings confirm that the antigenicity of the sites is inherent in their three-dimensional locations.

Complete amino acid sequence of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris

The complete primary structure of the major component myoglobin from the goose-beaked whale, Ziphius cavirostris, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three peptides resulting from the cleavage of the apomyoglobin at its two methionine residues with cyanogen bromide along with the four peptides resulting from the cleavage with trypsin of the citraconylated apomyoglobin at its three arginine residues. Further digestion of the central cyanogen bromide peptide with S. aureus strain V8 protease and the 1,2-cyclohexanedione-treated central cyanogen bromide peptide with trypsin enabled the determination of the remainder of the covalent structure. This myoglobin differs from the cetacean myoglobins determined to date at 12 to 17 positions. These large sequence differences reflect the distant taxonomic relationships between the goose-beaked whale and the other species of Cetacea the myoglobin sequences of which have previously been determined.

Evolution of the amino acid substitution in the mammalian myoglobin gene

Multivariate statistical analyses were applied to 16 physical and chemical properties of amino acids. Four of these properties; volume, polarity, isoelectric point (charge), and hydrophobicity were found to explain adequately 96% of the total variance of amino acid attributes. Using these four quantitative measures of amino acid properties, a structural discriminate function in the form of a weighted difference sum of squares equation was developed. The discriminate function is weighted by the location of each particular residue within a given tertiary structure and yields a numerical discriminate or difference value for the replacement of these residues by different amino acids. This resulting discriminate value represents an expression of the perturbation in the local positional environment of a protein when an amino acid substitution occurs. With the use of this structural discriminate function, a residue by residue comparison of the known mammalian myoglobin sequences was carried out in an attempt to elucidate the positions of possible deviations from the known tertiary structure of sperm whale myoglobin. Only 11 of the 153 residue positions in myoglobin demonstrated possible structural deviations. From this analysis, indices of difference were calculated for all amino acid exchanges between the various myoglobins. All comparisons yielded indices of difference that were considerably lower than would be expected if mutations had been fixed at random, even if the organization of the genetic code is taken into consideration. On the basis of these results, it is inferred that some form of selection has acted in the evolution of mammalian myoglobins to favor amino acid substitutions that are compatible with the retention of the original conformation of the protein.

On the evolution of myoglobin

In previous studies, particularly of primates, a high degree of concordance was obtained between an evolutionary pattern based on comparative anatomy and another based on a reconstruction of the possible pathway of evolution of the myoglobin molecule. Accordingly, in extending our studies, we included species of uncertain evolutionary kinship, such as the tree shrew, and also increased the representation of species within the mammalian orders already studied, in the hope that it would be possible to resolve some contended issues and to establish the sequence of branching and pattern of relationship between those orders. As a first step, the phylogenetic pattern within each of the mammalian orders was constrained on zoological grounds according to generally accepted kinship based on the evidence of comparative anatomy and the fossil record. Eight phylogenetic patterns reflecting different possible kinship between the orders were chosen for detailed investigation and for each of these the most economical (parsimonious) pathway which could be obtained for the evolution of myoglobin was reconstructed. The uncertainties which are inherent in such reconstruction were increased by a high incidence of parallel substitutions. Although the eight phylogenetic patterns were widely different from one another it was found that none of the solutions had a An amino acid difference matrix is of special interest because it carries information which is more comparable with that obtained by immunological methods, where access to sequence information has not usually been available. Several different clustering procedures were applied to the amino acid difference matrix for myoglobin. As would be expected from the different assumptions on which each is based, the procedures resulted in different branching patterns which varied in their degree of zoological acceptability. Clustering of the harbour seal with the Cetacea suggested that there might be functional reasons, perhaps associated with diving, for several substitutions acquired in parallel by the myoglobins of these mammals. Repeated clustering of the horse with the sportive lemur, and a tendency for the opossum to join the primates, is associated with a high proportion of parallel substitutions. This tends to undermine confidence in phylogenetic inferences which might be drawn from the repeated clustering of the tree shrew (and often the hedgehog) among the primates. If we assume that there is an overall resemblance of the three-dimensional structure of all myoglobins, and use the crystallographic model of sperm whale myoglobin as a basis, the availability of over 30 vertebrate myoglobin sequences (and that of the mollusc Aplysia ) has provided an opportunity to consider the functional relevance of certain positions at which the nature of the amino acid residue appears to have remained unchanged, or to have changed only conservatively, during several hundred million years of evolution. Part of this conservation is attributable to the maintenance of the monomeric nature of the molecule, and it seems likely that much of the conservatism can be attributed to functional needs in initiating the folding of the molecule and in the maintenance of its tertiary structure. Concomitantly, consideration is given to the likely functional consequence of some of the substitutions which have been accepted. Atassi and his co-workers have carried out extensive immunological studies on myoglobin using antisera prepared in rabbit and goat. The availability of the amino acid sequences of rabbit and sheep (in lieu of goat) has made it possible to investigate the relation between amino acid sequence difference and the distance as measured by immunological criteria. It has not been possible to confirm Reichlin’s hypothesis that the myoglobin antigenic reactive regions of Atassi are particularly variable compared with the rest of the molecule; on the contrary it appears that differences in the immunological reactive regions occur approximately in proportion to those occurring in the molecule as a whole. Estimates of the rate of molecular evolution are of interest because its supposed constancy has been a major argument in favour of the hypothesis that a high proportion of fixed mutations are neutral, or nearly so, as far as selection is concerned. F urthermore, a near constant rate of molecular evolution holds promise for a molecular clock which might be used for dating evolutionary events. However, there is considerable variation in the rate of molecular evolution as evidenced by differences in the number of nucleotide substitutions (‘hits’) in lineages arising from the same phylogenetic branching point or by the examination of the changes at the amino acid level. In order to investigate absolute rates of evolution we sought to establish the best estimate of the date of divergence between the ancestors of the living species included in this study. These dates are based on direct fossil evidence and must be regarded as minimum dates because we have not indulged in open-ended speculations about fossils which have not yet been found. The combination of these dates with the evidence of our cladograms leads us to reaffirm our earlier finding that there are considerable differences in the amount of change in different lineages. For example, whereas one lineage (to gibbon) appears to have accepted no mutations during the past 20 Ma, another lineage (to ox) seems to have fixed seven mutations during the last 18 Ma. Goodman and others have drawn attention to the apparently low rate of molecular evolution among higher primates; a similar observation applies to the myoglobin of the Old World monkeys so far studied, but neither the myoglobins of New World monkeys nor the prosimian myoglobins share this feature. After their divergence from one another the two bird lineages included in this study appear to have fixed mutations at rates comparable with those found among mammals during the past 79 Ma. However, the number of differences between the bird and mammal ancestral stems appears to be remarkably low bearing in mind the date of divergence of their ancestors, about 293 Ma ago. Recognizing that this could be an artefact resulting from multiple changes at the same site, from undetectable back mutations and from isosemantic mutations accumulating during a long period of evolution, various procedures were adopted to transform the data in order to estimate the number of such events. None of these procedures, however, eliminated the phenomenon that during the first 214 Ma since their separation the ancestral stems leading eventually to birds and mammals seem to have fixed mutations in their myoglobin at a lower rate than the average rate prevailing during the past 79 Ma, the latter being approximately one mutation in 4 Ma. It is to be expected that sampling error will produce some fluctuations in rate, but even over the relatively long period of 79 Ma the fastest rate of fixation of mutations is about three times the slowest rate and so we are inclined to discard the molecular clock as unreliable for dating divergences, at least within this span of time. On integrating the various sections of this study we see that the changes in myoglobin have not been at random throughout the molecule. Given the constraints demanded by the functional morphology of the molecule itself and the constraints of the genetic code, it is to be expected that both will contribute to parallel change in different lineages. In the reconstructed pathways of evolution of myoglobin about 50 % of the changes were found in parallel in other lineages. There is an indication, provided by the larger number of arginine residues present in aquatic forms, that some of these parallel changes may be correlated with mode of life. The adaptive significance of the several parallel changes between the cetaceans and the pinnipeds certainly deserves physiological investigation. Regardless of the causes of parallel evolution at the molecular level this phenomenon has contributed to unexpected similarities between myoglobins and has led to difficulties in phylogenetic reconstruction of a nature already familiar to comparative anatomists.

Applications of gas-liquid chromatography in protein chemistry. II. Determination of amide residues in nanomolar amounts of proteins

A method for the quantitative determination of amide residues in nanomolar amounts of proteins is described, based on dilute acid hydrolysis at 100 degrees, followed by isothermal gas-liquid chromatography of the ammonia released by on-column neutralisation of the hydrolysate and quantitation by means of a conductometric detector. Amide contents are given for twenty well characterised proteins, as well as for asparagine and glutamine.

The myoglobin of the fruit-bat (Rousettus aegyptiacus)

The myoglobin of the fruit-bat (Rousettus aegyptiacus) has been investigated. It has 153 amino acid residues. When the possible therian ancestral myoglobin is taken into consideration, the myoglobin of the fruit-bat resembles most closely that of the hedgehog.

Comparison of the amino acid sequence of pig heart myoglobin with other ungulate myoglobins

The primary structure of pig heart myoglobin has been established by study of the tryptic peptides of whole globin and by analysis of the fragments obtained by CNBr cleavage. Thermolysin and chymotrypsin digestion were used to determine the sequence of the M fragment (56-131). Automatic Edman degradation of whole globin and of the M fragment completed the sequence of pig myoglobin. Comparison with other ungulates shows that pig myoglobin is far from other artiodactyls previously studied (ox and sheep) and close to the eutherian ancestral chain.

[Specificity of thermolysin action on dog myoglobin]

The proteolytic specificity of thermolysin has been studied by quantitative analysis of an enzymic digest of dog myoglobin. Results confirm main specificities of thermolysin towards Phenylalanine, Isoleucine, Leucine or Tyrosine bonds; the influence of neighbourhood was also determined and the conclusions are in a good agreement with the known structure of the active site of thermolysin.

[Tryptic hydrolysis extended to the level of aspartyl bonds]

A quantitative modification of free carboxyl groups in peptides and proteins can be obtained, under mild conditions, by reacting them with ethylenediamine in the presence of N-ethyl-N'-(3-dimethylaminopropyl)-Carbodimide. Aminoethylasparagine and aminoethylglutamine side chains are thus generated in place of the corresponding carboxylic ones. The first kind of residue because of its structure closer to that of lysine, is a point of greater potential trypsic cleavage than the second one. The specificity and yields of this enzymatic cleavage reaction and its possible application in sequence studies are discussed.

Fluroescence of proteins in 6-M guanidine hydrochloride. A method for the quantitative determination of tryptophan

To determine the tryptophan content in proteins,an analytical ultraviolet fluroescence method is proposed based on making uniform the environment of aromatic chromophores in 6-7 M guanidine hydrochloride. The fluorescence intensity scale is calibrated using standard solutions of free tryptophan. A correlation coefficient between the fluorescence of protein tryptophanyl residues and of free tryptophan was estimated in testing 17 well characterized proteins. This method is particularly suited to proteins carrying groups absorbing in the 290-370 nm region, such as flavin, heme and pyridoxal phosphate and in the presence of substances such as 2-mercaptoethanol which prohibit the use of the spectroscopic or magnetic circular dichroism methods. It is less time-consuming than techniques requiring hydrolysis or chemical reactions.

The covalent structure of dog myoglobin

The primary structure of the myoglobin of the domestic dog (German shepherd) was studied. Tryptic and thermolytic peptides were compared with the sequence of other known myoglobins; the stepwise automatic Edman's degradation of the whole globin and also the chymotryptic digestion of the median fragment obtained by CNBr cleavage completed this sequence. Comparison of the established dog myoglobin structure with those from other carnivora shows 16 differences versus badger, 20 versus harbour seal and 15 versus California sea lion.

Comparison of the myoglobin of the zebra (Equus burchelli) with that of the horse (Equus caballus)

The tryptic and peptic peptides from the myoglobin of the zebra (Equus burchelli) have been compared with those obtained from the myoglobin of the horse (Equus caballus). No differences in the myoglobin were found between these two species.

The primary sequence of chicken myoglobin (Gallus gallus)

After enzymatic digestion of chicken myoglobin by trypsin, chymotrypsin or thermolysin, the separation of peptides was performed by column chromatography on various ion exchange resins. Each peptide was purified by high-voltage paper electrophoresis or by chromatography either on paper or on ion-exchange resin, and its complete amino acid sequence was then determined by the combined dansyl-Edman procedure and by endopeptidase digestions. The whole globin was submitted to automatic Edman degradation using the Beckman sequencer. Residues have been positioned from overlaps of sequence data between tryptic (T), chymotryptic (C) and thermolysin (Th) peptides. The stepwise degradation of the whole globin confirmed the alignment of the N-terminal third of the molecule. The combination of these different approaches has led to the complete determination of the 153 residues sequence forming the polypeptide chain of chicken myoglobin. Comparison of the established chicken myoglobin structure with those from other species shows a conservation of structure, although the avian protein exhibits more variations in its amino acid sequence than has been found between other known myoglobins which all belong to mammalian species.

Electrostatic effects in myoglobin. Application of the modified Tanford-Kirkwood theory to myoglobins from horse, California grey whale, harbor seal, and California sea lion

The modified Tanford-Kirkwood electrostatic theory (Shire et al., 1974a) was applied to ferrimyoglobins from the following animal species: sperm whale (Physeter catodon), horse, California grey whale (Eschrichtius gibbosus), harbor seal (Phoca vitulina), and California sea lion (Zalophus californianus). Computations were made of the overall hydrogen ion titration curves of the proteins, and of pH and ionic strength variations of ionization equilibria for individual groups in the protein, with particular reference to the hemic acid ionization of the iron bound water molecule. Coordinates and static solvent accessibility were estimated in terms of the sperm whale myoglobin structure. Where possible, theoretical results and experimental data are compared. Some comparative features of charge and ionization properties among the various myoglobins are presented.

Kinetic and equilibrium studies of the ligand binding reactions of eight electrophoretic components of sperm whale ferrimyoglobin

The reactions of eight electrophoretic components of sperm whale ferrimyoglobin with fluoride, azide, and cyanide have been studied. There do not appear to be significant differences in rate constants or equilibrium constants among the various components. We conclude that at pH 7.0 in 0.05 M potassium phosphate these ligand binding kinetics and equilibria are insensitive to the net charge on the protein. The variation of the azide equilibrium constant with ionic strength from mu 0.01 M to 0.11 M is not in accord with the predictions of the Debye-Hückel theory. On the other hand, azide association kinetic and equilibrium constants are respectively six- and threefold greater for beef ferrimyoglobin than for the isoelectric whale ferrimyoglobin (band V). An examination of the data for whale, horse, and beef myoglobins reveals that large differences in azide (but not CO) association rate constants are associated with amino acid substitutions at residues 45 and 99 in the heme cavity.