The structure of annelid and mollusc hemoglobins.

The polypeptide chain composition and the chemical properties of several annelid hemoglobins and chlorocruorins are presented. In agreement with earlier studies on the hemoglobin from Arenicola cristata (Waxman, L. (1971) J. Biol. Chem. 246, 7318-7327), nearly all of the pigments which have been examined consist of one or more different disulfide-linked polypeptide chains of 13,000 to 16,000 daltons, and the heme-protein stoichiometry suggests that more than one polypeptide is associated with each heme. Except for the prosthetic group, there is no outstanding chemical difference between the chlorocruorins and the hemoglobins, nor is ther any apparent differnce between those hemoglobins which show cooperative oxygen binding properties and those which do not. The results suggest that all these hemoglobins have similar structures. On the other hand, the polypeptide chains of mollusc hemoglobins have molecular weights of greater than 220,000. Each polypeptide binds many heme groups. Thus, annelids use small polypeptide chains while molluscs use giant polypeptides to carry O2.     

Heterotypic complex formation between subunits of microtubule-associated proteins 1A and 1B is due to interaction of conserved domains

The microtubule-associated proteins MAP1A and MAP1B are related but distinct multi-subunit protein complexes that consist of heavy and light chains. The predominant forms of these complexes are homotypic, i.e. they consist of a MAP1A heavy chain associated with MAP1A light chains or a MAP1B heavy chain associated with MAP1B light chains, respectively. In addition, MAP1A and MAP1B can exchange subunits and form heterotypic complexes consisting of a MAP1A heavy chain associated with MAP1B light chains which might play a role in a transition period of neuronal differentiation. Here we extend previous findings by confirming that heterotypic MAP1B heavy chain-MAP1A light chain complexes also exist in the developing murine brain. We show that these complexes form through interaction of homologous domains conserved in heavy and light chains of MAP1A and MAP1B. Likewise, conserved domains of the MAP1A and MAP1B light chains account for formation of light chain heterodimers. By yeast 2-hybrid analysis we located the light chain binding domain on the heavy chain to amino acids 211-508, thereby defining a new functional subdomain.     

Embryonic hemoglobins of different animal species

Summary The existence of embryonic hemoglobins is demonstrated in sheep-, calf and pig embryos. The occurrence and disappearance of these hemoglobins is quantitatively determined by cellulose acetate gel electrophoresis; hemoglobins as well as the globin chains, dissociated in 8 molar urea were quantitated. Sedimentation and diffusion experiments in the analytical ultracentrifuge revealed a S₂₀ of 4.3 and a D₂₀ of 6.6 for the examined hemoglobins. Therefore it is concluded that all hemoglobins occurring at different stages of embryonic and fetal development consist of 4 polypeptide chains with a total molecular weight of 66,000. The subsequent formation of the different polypeptide chains during ontogenesis is shown: At first only -chains are formed as demonstrated by the existence of Hb Gower I, consisting of four identical -chains. Subsequently the -chain appears, which leads to Hb Gower 2 (₂₂). The third polypeptide chain formed during the ontogenesis the -chain results finally in the appearance of HbF.In addition the existence of a HbF pig is demonstrated by the fingerprint technique.     

Structure and hydrodynamic properties of plectin molecules

Plectin is a cytoskeletal, high molecular weight protein of widespread and abundant occurrence in cultured cells and tissues. To study its molecular structure, the protein was purified from rat glioma C6 cells and subjected to chemical and biophysical analyses. Plectin's polypeptide chains have an apparent molecular weight of 300,000, as shown by one-dimensional sodium dodecyl sulfate/polyacrylamide electrophoresis. Cross-linking of non-denatured plectin in solution with dimethyl suberimidate and electrophoretic analyses on sodium dodecyl sulfate/agarose gels revealed that the predominant soluble plectin species was a molecule of 1200 X 10(3) Mr consisting of four 300 X 10(3) Mr polypeptide chains. Hydrodynamic properties of plectin in solution were obtained by sedimentation velocity centrifugation and high-pressure liquid chromatography analysis yielding a sedimentation coefficient of 10 S and a Stokes radius of 27 nm. The high f/fmin ratio of 4.0 indicated a very elongated shape of plectin molecules and an axial ratio of about 50. Shadowing and negative staining electron microscopy of plectin molecules revealed multiple domains: a rigid rod of 184 nm in length and 2 nm in diameter, and two globular heads of 9 nm diameter at each end of the rod. Circular dichroism spectra suggested a composition of 30% alpha-helix, 9% beta-structure and 61% random coil or aperiodic structure. The rod-like shape, the alpha-helix content as well as the thermal transition within a midpoint of 45 degrees C and the transition enthalpy (168 kJ/mol) of secondary structure suggested a double-stranded, alpha-helical coiled coil rod domain. Based on the available data, we favor a model of native plectin as a dumb-bell-like association of four 300 X 10(3) Mr polypeptide chains. Electron microscopy and turbidity measurements showed that plectin molecules self-associate into various oligomeric states in solutions of nearly physiological ionic strength. These interactions apparently involved the globular end domains of the molecule. Given its rigidity and elongated shape, and its tendency towards self-association, plectin may well be an interlinking element of the cytoskeleton that may also form a network of its own.     

Structures of Invertebrate Hemoglobins

Hemoglobin is widely distributed among the invertebrates. Intracellularhemoglobins consist of relatively small molecules with mol wtsof 15–17,000 or dimeric, tetrameric or octameric aggregatesof 15–17,000 mol wt subunits. Sequence homology is presentbut not extensive in those pigments which have been studiedand the characteristic myoglobin fold of vertebrate hemoglobinoccurs in at least two invertebrate hemoglobins. The wide arrayof aggregation states among invertebrate hemoglobins providessome simple models for understanding homotropic functional propertiesexhibited by many of these pigments. Polymeric extracellularhemoglobins are present in annelids molluscs crustacean arthropodsand nematodes. Annelid extracellular hemoglobins and chlorocruorinsconsist of 3 x 10⁶ mol wt two-tiered hexagonal arrays of submultipleswhich in turn are based on polypeptide chain subunits of molwt 14–16 000. Molluscan extracellular hemoglobins areconstructed from a different subunit arrangement. In the planorbidsnail and clam extracellular hemoglobins the subunits appearto be 175 000 and 300 000 mol wt linear series of 15–17000 dalton oxygen binding domains respectively. Planorbid snailnative hemoglobin presents circular structures 200 Å indiameter in the electron microscope with 10-fold symmetry inat least one view, and clam extracellular hemoglobins are huge345 by 1200 Å rodlike structures. Crustacean extracellularhemoglobins are also polymeric pigments and at least in a fewspecies appear to have subunits which are tandemly linked oxygenbinding domains. The polymeric hemoglobins of nematodes havemolecular weights of about 330 000. The subunit molecular weightand heme content suggest a value of 40,000 daltons which setthe nematode pigments apart from all other hemoglobins so farstudied. An overview of invertebrate hemoglobin structures andsome of the questions they pose are presented in this paper.     

Native and subunit molecular mass and quarternary structure of the hemoglobin from the primitive branchiopod crustacean Triops cancriformis

Many branchiopod crustaceans are endowed with extracellular, high-molecular-weight hemoglobins whose exact structural characteristics have remained a matter of conjecture. By using a broad spectrum of techniques, we provide precise and coherent information on the hemoglobin of one of the phylogenetically 'oldest' extant branchiopods, the tadpole shrimp Triops cancriformis. The hemoglobin dissociated under reducing conditions into two subunits, designated TcHbA and TcHbB, with masses of 35,775+/-4 and 36,055+/-4 Da, respectively, determined by ESI-MS. Nonreducing conditions showed only two disulfide-bridged dimers, a homodimer of TcHbA, designated D1 (71,548+/-5 Da), and the heterodimer D2 (71,828+/-5 Da). Carbamidomethylation of free SH groups revealed the presence of three cysteines per subunit and indicated one intrasubunit and one intersubunit disulfide bridge. Ultracentrifugation and light-scattering experiments under nondenaturating conditions yielded mass estimates that suggested an uneven number of 17 subunits forming the native hemoglobin. This unrealistic number resulted from the presence of two size classes (16-mer and 18-mer), which were recognized by native PAGE and Ferguson plot analysis. ESI-MS revealed three hemoglobin isoforms with masses of 588.1 kDa, 662.0 kDa, and 665.0 kDa. The 16-mer and the smaller 18-mer species are supposed to be composed of TcHbA only, given the dominance of this subunit type in SDS/PAGE. Transmission electron microscopy of negatively stained specimens showed a population of compact molecules with geometrical extensions of 14, 16 and 9 nm. The proposed stoichiometric model of quarternary structure provides the missing link to achieve a mechanistic understanding of the structure-function relationships among the multimeric arthropodan hemoglobins.     

Principles of protein-protein interactions

In the postgenomic era, one of the most interesting and important challenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist independently. Thus experimental investigation of protein-protein interactions has been extensive, including recent large-scale screens using mass spectrometry. The role of computational research on protein-protein interactions encompasses not only prediction, but also understanding the nature of the interactions and their three-dimensional structures. I will discuss properties such as sequence conservation and co-regulation of genes and proteins involved in different types of physical interactions. Given that all proteins consist of their evolutionary units, the domains, all interactions occur between these domains. The interactions between domains belonging to different protein families will be the second topic of my talk.     

Artemia hemoglobins: Increase in net synthesis of the β-polypeptide (relative to the α-polypeptide) in hypoxia

Previous studies have shown that in the brine shrimp there are three dimeric hemoglobins with polypeptide composition α₂, αβ, β₂. Concentrations of the α- and β-polypeptides increase in hypoxia. We now report a two-dimensional electrophoretic method for assay of radiolabelled polypeptidesin each hemoglobin. Net synthesis (synthesis minus degradation) of the β-chain, relative to that of the α-chain, increases more than 3-fold (in male and female adults) within 3 days following a downshift in oxygen concentration from 0.2 to 0.1 mM in the culture medium. 3 days after downshift (2 days after in vivo incorporation of radiolabelled leucine), the β-homodimer contained 10–20% of the radiolabel in the three hemoglobins although β₂ was usually not detectable in the protein stain of an overloaded gel. The amount of radioactive leucine incorporated per unit amount of protein was more than 300-times greater in the β₂ homodimer than in the β-subunit of the heterodimer, suggesting that β₂ does not dissociate rapidly during electrophoresis on the first dimension non-denaturing gel. This evidence for stable association of the two β-monomers and the 5–8 heme-binding domains within each monomer (in vivo and during electrophoresis on non-denaturing gels) allows us to exclude one of two alternative interpretations of genetic data published previously. We present an independent line of evidence for the dimer model of the native hemoglobins (which states that each polypeptide has many heme-binding domains).     

Molecular mass of macromolecules and subunits and the quaternary structure of hemoglobin from the microcrustacean Daphnia magna

The molecular masses of macromolecules and subunits of the extracellular hemoglobin from the fresh-water crustacean Daphnia magna were determined by analytical ultracentrifugation, multiangle laser light scattering and electrospray ionization mass spectrometry. The hemoglobins from hypoxia-incubated, hemoglobin-rich and normoxia-incubated, hemoglobin-poor Daphnia magna were analyzed separately. The sedimentation coefficient of the macromolecule was 17.4 +/- 0.1 S, and its molecular mass was 583 kDa (hemoglobin-rich animals) determined by AUC and 590.4 +/- 11.1 kDa (hemoglobin-rich animals) and 597.5 +/- 49 kDa (hemoglobin-poor animals), respectively, determined by multiangle laser light scattering. Measurements of the hemoglobin subunit mass of hemoglobin-rich animals by electrospray ionization mass spectrometry revealed a significant peak at 36.482 +/- 0.0015 kDa, i.e. 37.715 kDa including two heme groups. The hemoglobin subunits are modified by O-linked glycosylation in the pre-A segments of domains 1. No evidence for phosphorylation of hemoglobin subunits was found. The subunit migration behavior during SDS/PAGE was shown to be influenced by the buffer system used (Tris versus phosphate). The subunit mass heterogeneity found using Tris buffering can be explained by glycosylation of hemoglobin subunits. Based on molecular mass information, Daphnia magna hemoglobin is demonstrated to consist of 16 subunits. The quaternary structure of the Daphnia magna hemoglobin macromolecule was assessed by three-dimensional reconstructions via single-particle analysis based on negatively stained electron microscopic specimens. It turned out to be much more complex than hitherto proposed: it displays D4 symmetry with a diameter of approximately 12 nm and a height of about 8 nm.     

Synthesis, self-assembly and characterization of a new glucoside-type hydrogel having a Schiff base on the aglycon

A new hydrogel based on a substituted phenyl glucoside with a Schiff base in the aglycon was synthesized, and the self-assembling characteristics was studied. FTIR spectra, UV-vis absorption spectra and X-ray diffraction (XRD) revealed that π-π interactions between the Schiff base moieties, hydrogen bonds, and the interdigitated interactions between hydrophobic chains had effects on the formation of the self-assembling hydrogel. Scanning electron microscopic (SEM) and transmission electron microscopic (TEM) observation showed that the three-dimensional hydrogel network was constructed from nanotubes with inner diameters of ca. 75 nm and wall of ca. 20 nm.     

Hemoglobin equilibrium analysis by the multiangle laser light-scattering method

Dimer-tetramer and monomer-dimer-tetramer equilibria of tetrameric hemoglobins and their single chains in the CO form, respectively, were evaluated using the microbatch multiangle light-scattering (MALS) analysis system. The molecular weights of human Hb A and Hb F in the CO form were dependent on concentration. The dissociation constants to dimers of Hb A and Hb F were 2.58 x 10(-6) and 0.66 x 10(-6), respectively. Equilibration of single globin chains, including alpha, beta, and gamma chains, was also evaluated by the same method. The dissociation constants of alpha-chain dimers to monomers, of beta-chain tetramers to monomers, and of gamma-chain tetramers to dimers were 14 x 10(-6), 25 x 10(-17), and 6.86 x 10(-6) M, respectively. These results indicate that the MALS analysis system can not only determine molecular weight but also characterize protein-protein interactions of multi-subunit proteins.     

Exploring embryonic germ line development in the water flea, Daphnia magna, by zinc-finger-containing VASA as a marker

VASA is an ATP-dependent RNA helicase belonging to the DEAD-box family that, in many organisms, is specifically expressed in germ line cells throughout the life cycle, making it a powerful molecular marker to study germ line development. To obtain further information on germ line development in crustaceans, we cloned VASA cDNAs from three branchiopod species: water fleas Daphnia magna and Moina macrocopa, and brine shrimp Artemia franciscana. RNA helicase domains in branchiopod VASA were highly conserved among arthropod classes. However, N-terminal RNA-binding domains in branchiopod VASA were highly diverged and, unlike other arthropod VASA reported so far, possessed repeats of retroviral-type zinc finger (CCHC) motifs. Raising specific antibodies against Daphnia VASA revealed that the primordial germ cells (PGCs) in this organism segregate at a very early cleavage stage of embryogenesis in parthenogenetic and sexual eggs. Clusters of PGCs then start to migrate inside the embryo and finally settle at both sides of the intestine, the site of future gonad development. RNA analyses suggested that maternally supplied vasa mRNA was responsible for early VASA expression, while zygotic expression started during blastodermal stage of development.     

Comparative studies on the structure and aggregative properties of the myosin molecule. I. The structure of the lobster myosin molecule.

Myosin purified from the abdominal flexor muscle of the lobster, Homarus americanus, has a number average length of 1559 +/- 218 A, a rod like tail 1335 A long and a globular head 225 X 45 A as determined from electron microscopic observations on platinum shadowed preparations. The mass of the molecule was determined to be ca. 486,000 daltons from high speed equilibrium centrifugation studies at neutral and alkaline pH, and by SDS-acrylamide gel electrophoresis. Both sedimentation equilibrium centrifuge studies at alkaline pH and SDS-acrylamide gel electrophoresis experiments, indicate that the molecule contains a heavy chain core (two polypeptide chains weighing ca. 210,000 daltons each) and ca. four light chains of two weight classes (ca. 16,000 and 20,000 daltons). The amino acid composition of the myosin was determined. The specific activities of the Mg2+ -activated, K+/EDTA-activated, and Ca2+ -activated ATPases of the myosin were determined. Kinetic analysis of the digestion of lobster myosin with trypsin suggests that lobster myosin contains three classes of lysine and arginine residues; slowly split (k = 2.07 +/- 0.31 X 10(-2) moles/min2), rapidly split (k = 11.0 +/- 1.83 X 10(-2) moles/min2) and trypsin insensitive. There are 187 +/- 22 slowly split residues, 280 +/- 35 rapidly split residues, and 144 +/- 41 trypsin insensitive bonds per molecule. Comparison of these molecular parameters with those for the vertebrate skeletal muscle myosin indicates that the two myosins are similar in terms of mass, shape and overall polypeptide chain composition but may be considerably different in terms of local polypeptide chain conformation or composition.     

Structural studies of a branchiopod crustacean (Lepidurus bilobatus) extracellular hemoglobin. Evidence for oxygen-binding domains.

The extracellular hemoglobin of the notostracan branchiopod Lepidurus bilobatus has an apparent molecular weight of 680,000 and may exist in a dissociation-association equilibrium dependent on pH and ligand state. The pigment contains one heme per 18,000 g protein. However, attempts to dissociate the hemoglobin by harsh denaturing conditions results in a 33-34,000 molecular weight polypeptide chain as well as traces of some 62-64,000 molecular weight material. Limited proteolysis of this hemoglobin with subtilisin produces 14,800 and 16,500 dalton heme-containing polypeptides (domains) which bind oxygen reversibly. These domains, isolated by column chromatography, have a heme content similar to the intact pigment. It is proposed that the intact 34,000 dalton subunit of Lepidurus hemoglobin consists of two linearly linked oxygen binding domains. Oxygen binding properties of the intact hemoglobin show a low oxygen affinity with a slight Bohr effect. In contrast, the isolated domains display a relatively high oxygen affinity and lack a Bohr effect between pH 7.0 and 8.0. It is apparent that the intact 34,000 dalton polypeptide is necessary for the expression of the heterotropic interactions of the native pigment.     

The hemoglobins of phoronopsis viridis, of the primitive invertebrate phylum phoronida: characterization and subunit structure.

The primitive invertebrate, Phoronopsis viridis, of the phylum Phoronida, has intra-cellular hemoglobins composed of four unique polypeptide chains, two of which associate to form hetero- and homodimers and two which do not associate at all. The CO-derivatives of the associating chains are completely dimeric; removal of the ligand does not result in further aggregation as it does in several other invertebrate hemoglobins. Oxidation of the associating hemoglobins is accompanied by dissociation to monomers, but the cyanide derivative of the methemoglobin is dimeric. The four polypeptide chains all have molecular weights of about 16,000 as determined by iron content and gel electrophoresis with sodium dodecyl sulfate. The two associating chains form three components with isoelectric points at pH 5.6, 5.9, and 6.9 whereas those for the two monomeric chains are at pH 6.2 and 7.9. The chains have been characterized by amino acid composition, tryptic peptide patterns, and the amino acid sequence of the NH₂-terminal segment. The oxygen equilibrium of a dimeric fraction has been determined at pH 7.5 and 20 °C; the pressure of half-saturation is 2.3 mm Hg.     

Purification and biochemical characterization of soluble methane monooxygenase hydroxylase from Methylosinus trichosporium IMV 3011

Methane monooxygenase hydroxylase was purified by chromatography and characterized by electrophoresis and spectroscopy. The molecular mass of hydroxylase was 201.3 KDa as determined by gel filtration, whereas the total molecular mass was 234 KDa as judged by SDS-PAGE. Structure study indicated that the enzyme is a homodimer structure, consisting of three subunits, designated alpha, beta, and gamma, with molecular masses of 58 KDa, 36 KDa, and 23 KDa respectively. IEF analysis indicated that the enzyme has a pI of 5.2. The UV-Vis spectrum of hydroxylase revealed an absorption peak near 281 nm and a weak shoulder peak around 395 nm-420 nm, and a fluorescence spectrum revealed an emission peak at 341.3 nm. Circular dichroism measurement indicated that hydroxylase mainly consists of alpha-helical regions. Finally, phylogenetic analysis indicated that this strain is very close to Methylosinus trichosporium OB3b.     

Crystal structure of RVV-X: an example of evolutionary gain of specificity by ADAM proteinases

Russell's viper venom factor X activator (RVV-X) is a heterotrimeric metalloproteinase with a mammalian ADAM-like heavy chain and two lectin-like light chains. The crystal structure of RVV-X has been determined at 2.9 A resolution and shows a hook-spanner-wrench-like architecture, in which the metalloproteinase/disintegrin region constitutes a hook, and the lectin-like domains constitute a handle. A 6.5nm separation between the catalytic site and a putative exosite suggests a docking model for factor X. The structure provides a typical example of the molecular evolution of multi-subunit proteins and insights into the molecular basis of target recognition and proteolysis by ADAM/adamalysin/reprolysin proteinases.     

Purification and characterization of putrescine synthase from cucumber seedlings. A multifunctional enzyme involved in putrescine biosynthesis

The multifunctional enzyme, putrescine synthase has been purified fromCucumis sativus and characterized. This enzyme harbours agmatine iminohydrolase, ornithine transcarbamylase, putrescine transcarbamylase and carbamate kinase activities, whose concerted action results in agmatine → putrescine conversion. The enzyme resolved into two aggregation forms, enzyme aggregated and enzyme monomer upon electrophoresis at pH 8.3. Evidence has been provided by two-dimensional gel electrophoresis that both enzyme aggregated and enzyme monomer comprise of identical polypeptide chains. Under non-reducing conditions on sodium dodecyl sulphate-polyacrylamide gel electrophoresis, the protein moves as a single 150 KDa polypeptide; however, in the presence of 2-mercaptoethanol on sodium dodecyl sulphate-polyacrylamide gel elec trophoresis, it migrates as 3 polypeptides of molecular weight 48,000, 44,000 and 15,000. The enzyme undergoes age-dependentin vivo proteolytic degradation from a 66 KDa polypeptide (primary translational product), through 48 KDa polypeptide to 44 KDa species and finally to small molecular weight peptides. Preliminary results of this work were presented at Golden Jubilee and Annual General Body Meetings of Society of Biological Chemists (India) and the Second Congress of Asian and Ocean Biochemists (1980) held at Bangalore, 1981,Indian J. Biochem. Biophys.,18, 113.     

Leukosialin, a major sialoglycoprotein on human leukocytes as differentiation antigens

Most blood cells derived from the bone-marrow are known to possess only a limited number of heavily sialylated glycoproteins. We have recently isolated a major sialoglycoprotein on leukocytes and found that this glycoprotein, termed leukosialin, is ubiquitously present on various human leukocytes, granulocytes, monocytes/macrophages and T- and B-lymphocytes. Our studies showed that leukosialin is significantly glycosylated by O-linked oligosaccharides (90 chains/molecule). The structures of those O-linked oligosaccharides are characteristic to each cell lineage and maturation stage. The polypeptide portion of these molecules are, however, apparently the same, with a molecular size of 52 KDa. So it will be interesting to explore the possibility that leukosialin expresses different functions by having different O-glycosylation in a variety of hematopoietic cells.     

Structure and oxygen equilibrium of the three coelomic cell hemoglobins of the echiuran worm Thalassema mellita (Conn)

1. The three coelomic cell hemoglobins from Thalassema mellita have been isolated to purity; the two major components have dimeric structure while the third minor component has monomeric structure. 2. Acid-urea Triton gel electrophoresis of the isolated hemoglobins identified three polypeptides among the three hemoglobins, one of the dimeric hemoglobins is a heterodimer (pI = 4.9) with one polypeptide sharing identity with the monomeric hemoglobin (pI = 6.3), while the other dimer is a homodimer (pI = 4.5) consisting of the third polypeptide. 3. SDS gel electrophoresis suggests that the two dimeric hemoglobins have interpolypeptide disulfide bonds. 4. Coelomic cell suspensions and lysed coelomic cells have PO2 at half saturation (P50) of 2.5-3.0 mmHg and cooperativity values (n) of 1.5-1.93. 5. All three isolated hemoglobins have higher oxygen affinities and lower cooperativity values (P50 = 1-2 mmHg, n = 1-1.3) than lysed coelomic cells suggesting some heterotrophic and homotrophic interactions.