The primary structure of myohemerythrin

Klippenstein, Gerald L.; Cote, Joseph L.; Ludlam, Suzanne E.

doi:10.1021/bi00650a027

Cited by 50 publications

(20 citation statements)

References 26 publications

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“…The transformation matrix in this program is calculated by the Kabsch (20) algorithm. This superposition shows that previous sequence alignments ( [21][22][23] that placed the deletion between residues 90 and 96 were misaligned by 1 residue. cur as monomers (myohemerythrin), dimers, trimers, tetramers, and octamers.…”

mentioning

confidence: 68%

Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins.

Sheriff¹,

Hendrickson²,

Stenkamp³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

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Thermal factor parameters (B values) have been compared from the refined crystal structures of the myohemerythrin from Themiste zostericola and of the octameric hemerythrin from Themiste dyscrita. These B values, which are directly related to atomic mobilities, are found to correlate rather closely with the solvent accessible areas within the respective crystals. Although protomeric units of the two molecules have exceptionally similar three-dimensional structures, there are marked differences between the patterns of relative atomic mobilities along the polypeptide chains. The differences correspond to lattice and oligomer contacts. An adjustment of the B values based on the fraction of accessible area occluded by contacts yields values that correlate well between the independent subunits and that should pertain more closely to those for the protomer free in solution.That proteins are internally dynamic molecules is demonstrated by various spectroscopic experiments (1-3), by reaction kinetics (4, 5), by theoretical simulations (6, 7), and by crystal diffraction studies (8)(9)(10)(11). This investigation of mobility in hemerythrins is based on standard crystallographic experiments. These provide a comprehensive, albeit averaged, picture as the diffraction data are sensitive to all of the individual atomic mobilities. Detailed refinements yield relatively accurate positional coordinates and a measure of the distribution of atomic displacements about each atomic centroid. In isotropic analyses this measure is the B value, or "thermal parameter," which is simply related by B = 8ir27 to the unidirectional mean-square displacement, 7, averaged over the measurement time and the entire lattice. These displacements reflect mobility due to harmonic thermal vibrations, dynamic disordering between discrete conformers, and static variations frozen into the crystal lattice.We have analyzed the B values in our well-refined structures of myohemerythrin and an octameric hemerythrin and find strong correlations with solvent-accessible area (12) in the crystal. Even turns of a-helices are readily distinguished by variation in B values between internal and external surfaces. However, the patterns of relative mobilities along the polypeptide chains of these two similar molecules differ markedly. Differences arise especially at lattice and oligomer contacts. We have devised a procedure that relates hindrance of mobility to the occlusion of surface accessibility caused by intermolecular contacts. Thus, we "correct" B values to ones that might pertain to hemerythrin protomers free in solution.Hemerythrins are a class of oxygen carriers found in four invertebrate phyla. These proteins bind oxygen and certain other anionic ligands at a dimeric iron center coordinated directly by functional side chains (13,14). Hemerythrins oc- (20) algorithm. This superposition shows that previous sequence alignments ( [21][22][23] that placed the deletion between residues 90 and 96 were misaligned by 1 residue. cur as monomers (myohemerythrin),...

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mentioning

confidence: 68%

Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins.

Sheriff¹,

Hendrickson²,

Stenkamp³

et al. 1985

Proc. Natl. Acad. Sci. U.S.A.

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“…low methionine and arginine contents (Nejmeddine et al, 1988) and the apparent high resemblance observed previously (Demuynck et al, 1991 j between the N-terminal region of the MP I1 and the myohemerythrin of Themiste zostericola (Klippenstein et al, 1976) misidentified by the authors as Themiste pyroides according to Hendrickson and Ward (1 977). Cyanogen bromide cleavagc of the nativc protein followed by RP-HPLC scparation resulted in the isolation and subsequently sequencing of two fragments, MI and M2 (see Fig.…”

Section: Sequencing Of the Proteolytic Fragments From The Mp I1mentioning

confidence: 85%

“…In fact, among the 119 amino acids of the MP 11, the sequence comparison revealed 97 and 76 identical amino acid positions with Lhe myohcmcrythrin reported in the Fame species N. diversicolor (Takagi and Cox. (Takagi and Cox, 1991) and 7: zostericolu (Klippenstein et al, 1976). 4, 5 and 6. hemerythrins subunits of 7: pyroides (Ferrell and Kitto, 1971).…”

Section: Discussionmentioning

confidence: 99%

“…Enclosed amino acids represent identical amino acids positions to that of MP 11. 1991), and the myohemerythrin of Z zostericola (Klippenstein et al, 1976) respectively, against 56 positions with the hemerythrins subunits of T pyroides (Ferrell and Kitto,197 1 ) and Phascolopsis gouldii (Klippenstein, 1972) and only 53 positions with that of Themistc dyscritum (Loehr et al, 1978). It is interesting to note that MP I1 possesses a cysteine residue located at the same position as that of the sipunculid myohemerythrin but not represented in the Newis myohemerythrin (Takagi and Cox, 1991).…”

Section: Discussionmentioning

confidence: 99%

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Amino acid sequence of the small cadmium‐binding protein (MP II) from Nereis diversicolor (annelida, polychaeta)

Demuynck¹,

Li²,

Schors³

et al. 1993

European Journal of Biochemistry

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The primary sequence of the low-molecular-mass cadmium-binding protein metalloprotein I I of Nereis diversicolor (Hediste diversicolor, recent denomination) has been determined. This protein is composed of 119 amino acids and has 80.8% identity with the Lett. 285,[25][26][27]. The fact that iron, which normally binds to myohemerythrin, is not found to be associated with the cadmium-binding protein metalloprotein I1 in cadmium-exposed animals could be the result of the complete abolition of the iron-binding capacity of the protein due to the binding of cadmium.In the animal kingdom, exposition to cadmium leads to the uptake of the metal and its binding to low-molecularmass-proteins. In vertebrates, Cd is bound mainly to the metallothionein that is characterized by a high cysteinc content and the absence of aromatic amino acids. The metallothionein binds not only Cd but also metals such as zinc, copper and mercury. This is possible through the formation of metalthiolate clusters (Kay et a]., 1991).In invertebrates, two main types of low-molecular-mass Cd-binding proteins (Cd-BP) have been reported (Stone and Overnell, 1985). The first group consists of metallothioneinlike proteins that have structural identities with mammalian metallothioneins (Lerch et a]., 1982;Nemer et al., 1985;Brouwer et al., 1989;Roesijadi et al., 1989;Slice et al., 1990). The second group of low-molecular-mass Cd-BP is represented by the non-metallothionein-like proteins that have a low cysteine content and often possess aromatic amino acids (Dohi et al., 1983;Fowler and Megginson, 1986: Stone et a]., 1986; Bauer-Hilty et al.. 1989).In the case of annelids, few studies have been performed on the Cd-BP, although the animals rcpresent an important part of the endofauna largely distributed over terrestrial, freshwater and marine ecosystems that are, in many instances, subjected to strong toxic-metal contamination. In the Cor-respondenre m S. Demuynck,

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“…Peptide homologs of the MHr C helix (14), and the omission-series peptides used to identify antigenic sites (see below), were made by a method of simultaneous multiple peptide synthesis in which the peptide resins were contained in individual solvent-permeable packets (15). Crude peptides were purified to >90% homogeneity by reverse-phase highperformance liquid chromatography (16).…”

Section: Methodsmentioning

confidence: 99%

Influence of protein flexibility and peptide conformation on reactivity of monoclonal anti-peptide antibodies with a protein alpha-helix.

Fieser

Tainer

Geysen

et al. 1987

Proc. Natl. Acad. Sci. U.S.A.

144

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Monoclonal antibodies against an a-helical region of the iron-containing, oxygen-binding protein myohemerythrin were isolated following immunization of mice with either the whole protein or a peptide homolog of the helix. Three distinct epitopes within the myohemerythrin helix were identified. The individual residues within two of these epitopes that were essential for antibody binding were determined by measuring antibody binding to a set of peptides in which each amino acid of the epitope was replaced in turn by each of the other 19 amino acids. Hydrophilic residues that are exposed in the native conformation and buried, hydrophobic residues were both shown to be irreplaceable, suggesting their direct involvement in antibody binding. The influence of antigen conformation on antibody binding to these amphipathic epitopes was assessed by measuring the relative affinities of the antibodies for peptides, intact protein, and apoprotein. All of the antibodies bound to apoprotein better than to native protein, indicating that relaxation of the native structure by removal of the iron center increases antibody affinity for myohemerythrin. However, not all of the antibodies tested bound to peptides better than to protein, suggesting that increased antigen flexibility is not always sufficient to maximize antibody binding. Antibody binding to peptides appeared to also be influenced by the ability of the peptides to attain secondary structure at the epitopes, either alone or due to carrier influences.Successful binding of anti-peptide antibodies to native proteins has been correlated with hydrophilicity (1) and surface exposure (2, 3) of protein antigenic determinants. Antigenic crossreactivity between peptides and their homologous sequences on proteins may also depend on their conformational similarity. On one hand, areas of an intact protein that react with anti-peptide antibodies correspond with areas of greater than average atomic mobility, or flexibility (4,5). This "segmental motion" at the antigenic site allows it to resemble the more flexible peptide. On the other hand, the range of conformations adopted by immunogenic peptides may also be restricted, possibly by interactions between the peptide and its protein carrier (6,7). Also, certain free peptides can adopt conformational preferences in aqueous solution (8-10). Therefore, peptide/protein crossreactivity may be greatest at sites that are flexible in the native protein but have a high propensity for a particular structure in the free peptide.A previous study (11) of the antigenicity of the iron-containing, oxygen-binding protein myohemerythrin (MHr) identified nine separate sites bound by polyclonal anti-protein antisera. Eight of these nine sites were shown to include both highly exposed and buried residues in the native MHr, with each type directly involved in binding to antibodies. To extend these earlier results, we have raised monoclonal anti-peptide and anti-protein antibodies reactive with one ofthe four a-helices of MHr. Whereas polyclonal antis...

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The primary structure of myohemerythrin

Cited by 50 publications

References 26 publications

Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins.

Influence of solvent accessibility and intermolecular contacts on atomic mobilities in hemerythrins.

Amino acid sequence of the small cadmium‐binding protein (MP II) from Nereis diversicolor (annelida, polychaeta)

Influence of protein flexibility and peptide conformation on reactivity of monoclonal anti-peptide antibodies with a protein alpha-helix.

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