Linker Subunits Research Articles

Sequencing of the Lumbricus terrestris genome reveals degeneracy in its erythrocruorin genes

The erythrocruorin of Lumbricus terrestris (LtEc) is a relatively large macromolecular assembly that consists of at least four different hemoglobin subunits (A, B, C, and D) and four linker subunits (L1, L2, L3, and L4). The complexity and stability of this large structure make LtEc an attractive hemoglobin-based oxygen carrier that could potentially be used as a substitute for donated red blood cells. However, the sequences of the LtEc subunit sequences must be determined before a scalable recombinant expression platform can be developed. The goal of this study was to sequence the L. terrestris genome to identify the complete sequences of the LtEc subunit genes. Our results revealed multiple homologous genes for each subunit (e.g., two homologous A globin genes; A1 and A2), with the exception of the L4 linker. Some of the homologous genes encoded identical peptide sequences (C1 and C2, L1a and L1b), while cDNA and mass spectrometry experiments revealed that some of the homologs are not expressed (e.g., A2). In contrast, multiple sequences for the B, D, L2, and L4 subunits were detected in LtEc samples. These observations reveal novel degeneracy in LtEc and other annelids, along with some new revisions to its previously published peptide sequences.

Insight into Viral Hijacking of CRL4 Ubiquitin Ligase through Structural Analysis of the pUL145-DDB1 Complex.

Viruses evolve mechanisms to exploit cellular pathways that increase viral fitness, e.g., enhance viral replication or evade the host cell immune response. The ubiquitin-proteosome system, a fundamental pathway-regulating protein fate in eukaryotes, is hijacked by all seven classes of viruses. Members of the Cullin-RING family of ubiquitin (Ub) ligases are frequently co-opted by divergent viruses because they can target a broad array of substrates by forming multisubunit assemblies comprised of a variety of adapters and substrate receptors. For example, the linker subunit DDB1 in the cullin 4-RING (CRL4)-DDB1 Ub ligase (CRL4DDB1) interacts with an H-box motif found in several unrelated viral proteins, including the V protein of simian virus 5 (SV5-V), the HBx protein of hepatitis B virus (HBV), and the recently identified pUL145 protein of human cytomegalovirus (HCMV). In HCMV-infected cells, pUL145 repurposes CRL4DDB1 to target STAT2, a protein vital to the antiviral immune response. However, the details of how these divergent viral sequences hijack DDB1 is not well understood. Here, we use a combination of binding assays, X-ray crystallography, alanine scanning, cell-based assays, and computational analysis to reveal that viral H-box motifs appear to bind to DDB1 with a higher affinity than the H-box motifs from host proteins DCAF1 and DDB2. This analysis reveals that viruses maintain native hot-spot residues in the H-box motif of host DCAFs and also acquire favorable interactions at neighboring residues within the H-box. Overall, these studies reveal how viruses evolve strategies to produce high-affinity binding and quality interactions with DDB1 to repurpose its Ub ligase machinery. IMPORTANCE Many different viruses modulate the protein machinery required for ubiquitination to enhance viral fitness. Specifically, several viruses hijack the cullin-RING ligase CRL4DDB1 to degrade host resistance factors. Human cytomegalovirus (HCMV) encodes pUL145 that redirects CRL4DDB1 to evade the immune system through the targeted degradation of the antiviral immune response protein STAT2. However, it is unclear why several viruses bind specific surfaces on ubiquitin ligases to repurpose their activity. We demonstrate that viruses have optimized H-box motifs that bind DDB1 with higher affinity than the H-box of native binders. For viral H-boxes, native interactions are maintained, but additional interactions that are absent in host cell H-boxes are formed, indicating that rewiring CRL4DDB1 creates a selective advantage for the virus. The DDB1-pUL145 peptide structure reveals that water-mediated interactions are critical to the higher affinity. Together, our data present an interesting example of how viral evolution can exploit a weakness in the ubiquitination machinery.

Scaffold subunits support associated subunit assembly in the Chlamydomonas ciliary nexin–dynein regulatory complex

The nexin-dynein regulatory complex (N-DRC) in motile cilia and flagella functions as a linker between neighboring doublet microtubules, acts to stabilize the axonemal core structure, and serves as a central hub for the regulation of ciliary motility. Although the N-DRC has been studied extensively using genetic, biochemical, and structural approaches, the precise arrangement of the 11 (or more) N-DRC subunits remains unknown. Here, using cryo-electron tomography, we have compared the structure of Chlamydomonas wild-type flagella to that of strains with specific DRC subunit deletions or rescued strains with tagged DRC subunits. Our results show that DRC7 is a central linker subunit that helps connect the N-DRC to the outer dynein arms. DRC11 is required for the assembly of DRC8, and DRC8/11 form a subcomplex in the proximal lobe of the linker domain that is required to form stable contacts to the neighboring B-tubule. Gold labeling of tagged subunits determines the precise locations of the previously ambiguous N terminus of DRC4 and C terminus of DRC5. DRC4 is now shown to contribute to the core scaffold of the N-DRC. Our results reveal the overall architecture of N-DRC, with the 3 subunits DRC1/2/4 forming a core complex that serves as the scaffold for the assembly of the "functional subunits," namely DRC3/5-8/11. These findings shed light on N-DRC assembly and its role in regulating flagellar beating.

A Colorful Pallet of B-Phycoerythrin Proteoforms Exposed by a Multimodal Mass Spectrometry Approach

Summary Cyanobacteria and red algae represent some of the oldest lifeforms on the planet. During billions of years of evolution, they have fine-tuned the structural details of their light-harvesting antenna, called phycobilisomes, which represents one of the most efficient systems for light harvesting and energy transfer. Yet, the exact details of phycobilisome assembly and energy transfer are still under investigation. Here, we employed a multi-modal mass spectrometric approach to unravel the molecular heterogeneity within B-phycoerythrin, the major phycobiliprotein in the red algae P. cruentum. B-phycoerythrin consists of 12 subunits (αβ)12 arranged in a ring with the central cavity housing a linker (γ) subunit, which is crucial for stabilizing B-phycoerythrin within the phycobilisome. Using top-down MS, we unravel the heterogeneity in the γ proteoforms, characterizing the distinct γ chains and multiple isobaric chromophores they harbor. Our data highlight the key role γ plays in phycobilisome organization that enables optimal light transmission.

CRL4DCAF1 is required in activated oocytes for follicle maintenance and ovulation.

In mammals, oocytes within the primordial follicles require a number of essential factors to maintain their survival. However, the survival factors for activated oocytes have been poorly characterized. Recently we reported that damaged DNA binding protein-1 (DDB1), the linker subunit of the cullin ring-finger ubiquitin E3 ligase-4 (CRL4) complex, and its substrate adaptor, DDB1-CUL4 associated factor-1 (DCAF1), were essential for primordial follicle maintenance. In this study we specifically deleted these in the oocytes of growing follicles, to investigate if DDB1 and DCAF1 were also survival factors for activated oocytes. In the ovaries of Ddb1(fl/fl);Zp3-Cre mice, the primordial follicle pool was intact, but awakened oocytes and growing follicles beyond the primary stage were rapidly depleted. In the ovaries of Dcaf1(fl/fl);Pten(fl/fl);Gdf9-Cre and Ddb1(fl/fl);Pten(fl/fl);Gdf9-Cre mice, global primordial follicle activation was stimulated by enhanced PI3K signaling, but the awakened oocytes were rapidly lost due to no CRL4(DCAF1) activity. These mouse models provided original evidence that CRL4(DCAF1) was essential for maintaining oocyte survival, not only those in dormancy at the primordial follicle stage, but also naturally awakened oocytes and those awakened by hyper-activation of PI3K signaling. Interestingly, the oocyte-specific Ddb1 or Dcaf1 knockout mice had ovulation defects even before oocyte exhaustion. CRL4(DCAF1) within oocytes was required for cumulus expansion and ovulation-related somatic gene expression in a cell non-autonomous manner. Granulosa cells that surrounded these Ddb1 or Dcaf1-deleted oocytes exhibited increased rates of apoptosis and showed poor responses to ovulation signals. These results suggested that CRL4 in oocytes also regulated granulosa cell functions in a cell non-autonomous manner.

Structural Mechanism of SDS-Induced Enzyme Activity of Scorpion Hemocyanin Revealed by Electron Cryomicroscopy

Phenoloxidases (POs) occur in all organisms and are involved in skin and hair coloring in mammals, and initiating melanization in wound healing. Mutation or overexpression of PO can cause albinism or melanoma, respectively. SDS can convert inactive PO and the oxygen carrier hemocyanin (Hc) into enzymatically active PO. Here we present single-particle cryo-EM maps at subnanometer resolution and pseudoatomic models of the 24-oligomeric Hc from scorpion Pandinus imperator in resting and SDS-activated states. Our structural analyses led to a plausible mechanism of Hc enzyme PO activation: upon SDS activation, the intrinsically flexible Hc domain I twists away from domains II and III in each subunit, exposing the entrance to the active site; this movement is stabilized by enhanced interhexamer and interdodecamer interactions, particularly in the central linker subunits. This mechanism could be applicable to other type 3 copper proteins, as the active site is highly conserved.

Low Resolution Crystal Structure of Arenicola Erythrocruorin: Influence of Coiled Coils on the Architecture of a Megadalton Respiratory Protein

Annelid erythrocruorins are extracellular respiratory complexes assembled from 180 subunits into hexagonal bilayers. Cryo-electron microscopic experiments have identified two different architectural classes. In one, designated type I, the vertices of the two hexagonal layers are partially staggered, with one hexagonal layer rotated by about 16° relative to the other layer, whereas in the other class, termed type II, the vertices are essentially eclipsed. We report here the first crystal structure of a type II erythrocruorin, that from Arenicola marina, at 6.2 Å resolution. The structure reveals the presence of long continuous triple-stranded coiled-coil “spokes” projecting towards the molecular center from each one-twelfth unit; interdigitation of these spokes provides the only contacts between the two hexagonal layers of the complex. This arrangement contrasts with that of a type I erythrocruorin from Lumbricus terrestris in which the spokes are broken into two triple-stranded coiled coils with a disjointed connection. The disjointed connection allows formation of a more compact structure in the type I architecture, with the two hexagonal layers closer together and additional extensive contacts between the layers. Comparison of sequences of the coiled-coil regions of various linker subunits shows that the linker subunits from type II erythrocruorins possess continuous heptad repeats, whereas a sequence gap places these repeats out of register in the type I linker subunits, consistent with a disjointed coiled-coil arrangement.

Lumbricus Erythrocruorin at 3.5 Å Resolution: Architecture of a Megadalton Respiratory Complex

Annelid erythrocruorins are highly cooperative extracellular respiratory proteins with molecular masses on the order of 3.6 million Daltons. We report here the 3.5 A crystal structure of erythrocruorin from the earthworm Lumbricus terrestris. This structure reveals details of symmetrical and quasi-symmetrical interactions that dictate the self-limited assembly of 144 hemoglobin and 36 linker subunits. The linker subunits assemble into a core complex with D(6) symmetry onto which 12 hemoglobin dodecamers bind to form the entire complex. Although the three unique linker subunits share structural similarity, their interactions with each other and the hemoglobin subunits display striking diversity. The observed diversity includes design features that have been incorporated into the linker subunits and may be critical for efficient assembly of large quantities of this complex respiratory protein.

Novel dissociation mechanism of a polychaetous annelid extracellular haemoglobin

The extracellular haemoglobin of the marine polychaete, Arenicola marina, is a hexagonal bilayer haemoglobin of approximately 3600 kDa, formed by the covalent and noncovalent association of many copies of both globin subunits (monomer and trimer) and nonglobin or 'linker' subunits. In order to analyse the interactions between globin and linker subunits, dissociation and reassociation experiments were carried out under whereby Arenicola hexagonal bilayer haemoglobin was exposed to urea and alkaline pH and the effect was followed by gel filtration, SDS/PAGE, UV-visible spectrophotometry, electrospray-ionization MS, multiangle laser light scattering and transmission electron microscopy. The analysis of Arenicola haemoglobin dissociation indicates a novel and complex mechanism of dissociation compared with other annelid extracellular haemoglobins studied to date. Even though the chemically induced dissociation triggers partial degradation of some subunits, spontaneous reassociation was observed, to some extent. Parallel dissociation of Lumbricus haemoglobin under similar conditions shows striking differences that allow us to propose a hypothesis on the nature of the intersubunit contacts that are essential to form and to hold such a complex quaternary structure.

The stoichiometry of the four linker subunits of Lumbricus terrestris hemoglobin suggests an asymmetric distribution

The extracellular, giant (∼3.6 MDa) hexagonal bilayer hemoglobin of the earthworm Lumbricus terrestris consists of 12 dodecamers of globin chains tethered to a central complex of 36 non-globin, linker chains (24–32 kDa). Four types of linker chains L1–L4 have been detected by electrospray ionization (ESI) and by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) and isolated by reversed phase high pressure liquid chromatography (HPLC). Deconvolution of the HPLC elution profile and of the MS spectra provided the following individual linker contents, expressed as percent of the sum of the four linker peak areas: HPLC-21% L1, 37% L2, 23% L3 and 19% L4, MALDI-47% L1, 29% L2, 16% L3 and 8% L4; ESI-24% L1, 16% L2, 40% L3 and 20% L4; respectively. Comparison with electrophoretic results revealed a surprising lack of overall agreement between all the methods. The calculated mean values of the available linker contents were found to be 32±12% L1, 28±9% L2, 27±10% L3 and 13±7% L4, suggesting the following relative stoichiometry: L1: L2: L3: L4 ≈1: 1: 1: 0.5. With a total of 36 linkers, a hexagonally symmetric distribution of each of the four linker chains is impossible. Thus, the asymmetric linker distribution provides an explanation for the existence of a large dipole moment of Lumbricus terrestris hemoglobin, 17300±2300 Da ( Takashima et al., 1999).

X-ray photoelectron spectroscopy as a probe of intermolecular interactions in porphyrin polymer thin films.

High-resolution X-ray photoelectron spectroscopy (XPS) has been applied to a series of free-base and Zn-porphyrin polymers in which the macrocycles are separated by oligo(phenylene vinylene) units (OPV) of different, controllable lengths. Neat films of all the Zn-porphyrin polymers unexpectedly reveal two peaks in the N 1s XPS region ( approximately 400 eV). The peak areas vary with the length of the OPV bridge, suggesting an intermolecular interaction between the porphyrin and linker subunits. A series of XPS analyses were performed to identify the different interactions taking place in these thin films. To inhibit interpolymer interactions, one of the polymers was incorporated into a nonconjugated PMMA matrix, collapsing the N1s spectrum to a single peak at 398.0 eV, relative to the neat film signals at 397.8 and 400.1 eV. In a conjugated matrix of OPV, two peaks remain at 401.7 and 399.5 eV. Extensive vacuum drying of the neat film leads to a single peak at 398.3 eV, suggesting loss of trapped solvent molecules. Ultimately, we attribute the lower energy signal of the neat films to solvent ligation, and the higher energy peak is attributed to interactions between the porphyrins and conjugated bridges on nearby polymer chains. This interpretation is successfully applied to the N 1s XPS data from a previously reported Zn-porphyrin oligomer-based multilayer array.

Structural hierarchy in erythrocruorin, the giant respiratory assemblage of annelids.

Many annelids, including the earthworm Lumbricus terrestris, have giant cooperative respiratory proteins (molecular masses greater than 3.5 million Da) freely dissolved in the blood, rather than packaged in cells. These complexes, termed either erythrocruorins or hemoglobins, are assembled from many copies of both hemoglobin subunits and nonhemoglobin or "linker" subunits. In this paper, we present the crystal structure of Lumbricus erythrocruorin at 5.5-A resolution, which reveals a remarkable hierarchical organization of 144 oxygen-binding hemoglobin subunits and 36 nonhemoglobin linker subunits. The hemoglobin chains arrange in novel dodecameric substructures. Twelve trimeric linker complexes project triple-stranded helical coiled-coil "spokes" toward the center of the complex; interdigitation of these spokes appears crucial for stabilization. The resulting complex of linker chains forms a scaffold on which twelve hemoglobin dodecamers assemble. This structure specifies the unique, self-limited assemblage of a highly cooperative single molecule.

Subunit distribution of calcium-binding sites in Lumbricus terrestris hemoglobin.

The giant, approximately 3.6-MDa hexagonal bilayer hemoglobin (Hb) of Lumbricus terrestris consist of twelve 213-kDa globin subassemblies, each comprised of three disulfide-bonded trimers and three monomer globin chains, tethered to a central scaffolding of 36-42 linkers L1-L4 (24-32 kDa). It is known to contain 50-80 Ca and 2-4 Cu and Zn; the latter are thought to be responsible for the superoxide dismutase activity of the Hb. Total reflection X-ray fluorescence spectrometry was used to determine the Ca, Cu, and Zn contents of the Hb dissociated at pH approximately 2.2, the globin dodecamer subassembly, and linker subunits L2 and L4. Although the dissociated Hb retained 20 Ca2+ and all the Cu and Zn, the globin subassembly had 0.4 to approximately 3 Ca2+, depending on the method of isolation, and only traces of Cu and Zn. The linkers L2 and L4, isolated by reversed-phase high-pressure liquid chromatography at pH approximately 2.2, had 1 Ca per mole and very little Cu and Zn. Electrospray ionization mass spectrometry of linker L3 at pH approximately 2.2 and at neutral pH demonstrated avid binding of 1 Ca2+ and additional weaker binding of 7 Ca2+ in the presence of added Ca2+. Based on these and previous results which document the heterogeneous nature of the Ca2+-binding sites in Lumbricus Hb, we propose three classes of Ca2+-binding sites with affinities increasing in the following order: (i) a large number of sites (>100) with affinities lower than EDTA associated with linker L3 and dodecamer subassembly, (ii) approximately 30 sites with affinities higher than EDTA occurring within the cysteine-rich domains of linker L3 and dodecamer subassembly, and (iii) approximately 25 very high affinity sites associated with the linker subunits L1, L2, and L4. It is likely that the low-affinity type (i) sites are the ones involved in the effects of 1-100 mM Group IIA cations on Lumbricus Hb structure and function, namely increased stability of its quaternary structure and increased affinity and cooperativity of its oxygen binding.

The apparently symmetrical hexagonal bilayer hemoglobin from Lumbricus terrestris has a large dipole moment

The giant ∼3.6 MDa hexagonal bilayer hemoglobin (HBL Hb) from Lumbricus terrestris consists of 12 213-kDa dodecamers of four globin chains ([b+a+c] 3[d] 3) tethered to a central scaffold of ∼36 non-globin, linker subunits L1–L4 (24–32 kDa). Three-dimensional reconstructions obtained by electron cryomicroscopy showed it to have a D 6 point-group symmetry, with the two layers rotated ∼16° relative to each other. Measurement of the dielectric constants of the Hb and the dodecamer over the frequency range 5–100 kHz indicated relaxation frequencies occurring at 20–40 and 300 kHz, respectively, substantially lower than the 700–800 kHz in HbA. The dipole moments calculated using Oncley's equation were 17 300±2300 D and 1400 D for the Hb and dodecamer, respectively. The approximately threefold higher dipole moment of the dodecamer relative to HbA is consistent with an asymmetric shape in solution suggested by small-angle X-ray scattering. Although a two-term Debye equation and a prolate ellipsoid of revolution model provided a good fit to the experimental dielectric dispersion of the dodecamer, a three-term Debye equation based on an oblate ellipsoid of revolution model was required to fit the asymmetric dielectric dispersion curve of the Hb: the required additional term may represent either an induced dipole moment or a substructure which rotates independently of the main permanent dipole component of the Hb. The D 6 point-group symmetry implies that the dipole moments of the dodecamers cancel out. Thus, in addition to a possible contribution from fluctuations of the proton distribution, the large dipole moment of the Hb may be due to an asymmetric distribution of the heterogeneous linker subunits.

Deletion of the PB-loop in the L(CM) subunit does not affect phycobilisome assembly or energy transfer functions in the cyanobacterium Synechocystis sp. PCC6714.

In cyanobacteria, light energy is mainly harvested for photosynthesis by the phycobilisome (PBS): a large pigment-protein complex. This complex is composed of heterodimeric phycobiliproteins that are assembled with the aid of linker polypeptides in order to optimize light-energy absorbance and transfer to photosystem II. The core membrane linker subunit (L(CM)) is a fascinating multifunctional polypeptide that participates in the PBS structure, function and anchoring to the photosynthetic membrane. Sequence analysis has defined several domains within the L(CM) polypeptide. The C-terminal portion contains two to four repeated domains that are similar to the conserved domains of linker polypeptides and are believed to play the same role. The N-terminal portion is similar to phycobiliproteins (PB-domain) and carries, like phycobiliproteins, a covalently linked phycobilin chromophore. This domain is interrupted by a so-called PB-loop insertion. The PB-domain of the L(CM) is thus regarded as one of the core subunits, with its PB-loop protruding towards the photosynthetic membrane. The PB-loop was thought to be involved in the attachment of the PBS to the photosynthetic membrane. We generated an apcE gene (encoding L(CM)), in which we deleted the sequence encoding 54 amino acids of the PB-loop domain. The modified gene was expressed in a Synechocystis PCC6714 strain in which the apcE gene had been inactivated. The truncated polypeptide was functionally equivalent to the wild-type L(CM); PBSs were assembled and functioned as in the wild-type. The PB-loop of the L(CM) seems thus dispensable for the PBS biogenesis and function.

Quaternary structure of the extracellular haemoglobin of the lugworm Arenicola marina: a multi-angle-laser-light-scattering and electrospray-ionisation-mass-spectrometry analysis.

To elucidate the quaternary structure of the extracellular haemoglobin (Hb) of the marine polychaete Arenicola marina (lugworm) it was subjected to multi-angle laser-light scattering (MALLS) and to electrospray-ionisation mass spectrometry (ESI-MS). It was also subjected to SDS/PAGE analysis for comparative purposes. MALLS analysis gave a molecular mass of 3648 +/- 24 kDa and a gyration radius of 11.3 +/- 1.7 nm. Maximum entropy analysis of the multiply charged electrospray spectra of the native, dehaemed, reduced and carbamidomethylated Hb forms, provided its complete polypeptide chain and subunit composition. We found, in the reduced condition, eight globin chains of molecular masses 15952.5 Da (a1), 15974.8 Da (a2), 15920.9 Da (b1), 16020.1 Da (b2), 16036.2 Da (b3), 16664.8 Da (c), 16983.2 Da (d1), 17033.1 Da (d2) and two linker chains L1, 25174.1 Da, and L2, 26829.7 Da. In the native Hb, chains b, c, d occur as five disulphide-bonded trimer subunits T with masses of 49560.4 Da (T1), 49613.9 Da (T2), 49658.6 Da (T3), 49706.8 Da (T4), 49724.5 Da (T5). Linker chains L1 and L2 occur as one disulphide-bonded homodimer 2L1 (D1) of 50323.1 Da and one disulphide-bonded heterodimer L1-L2 (D2) of 51 981.5 Da. Polypeptide chains a and d possess one free cysteine residue and chains d possess an unusual total of five cysteine residues. Semi-quantitative analysis of ESI-MS data allowed us to propose the following model for the one-twelfth protomer: [(3a1)(3a2)2T] (T corresponding to either T3, T4 or T5). From electron micrograph data T1 and T2 are probably located at the centre of the molecule as mentioned in previous studies. The Hb would thus be composed of 198 polypeptide chains with 156 globin chains and 42 linker chains, each twelfth being in contact with 3.5 linker subunits, providing a total mass of 3682 kDa including haems in agreement with the experimental molecular mass determined by MALLS. From ESI-MS relative intensities and the model proposed above, the globin/linker ratio gave 0.71:0.29 and 0.73:0.27, respectively. The estimation of haem content by pyridine haemochromogen and by cyanmethaemoglobin (HiCN) methods also support the globin chain number provided by ESI-MS.

Superoxide Dismutase Activity in the Giant Hemoglobin of the Earthworm,Lumbricus terrestris

The giant hemoglobin, which occurs in free solution in the blood of earthworms, contains copper and zinc and exhibits superoxide dismutase activity as assessed by competition assays using cytochrome c or nitroblue tetrazolium. On a molar basis, the activity of this hemoglobin was approximately 10% that of the mammalian copper, zinc superoxide dismutase. The dodecamer, which contains the globin chains but lacks the linker subunits, had very little activity when compared to the complete native molecule. This suggests that the superoxide dismutase activity resides in one of the linker subunits. This is the first report of a superoxide dismutase bound to a respiratory pigment.

The Multi-hemoglobin System of the Hydrothermal Vent Tube Worm Riftia pachyptila: II. COMPLETE POLYPEPTIDE CHAIN COMPOSITION INVESTIGATED BY MAXIMUM ENTROPY ANALYSIS OF MASS SPECTRA

The deep-sea tube worm Riftia pachyptila Jones possesses a complex of three extracellular Hbs: two in the vascular compartment, V1 (approximately 3500 kDa) and V2 (approximately 400 kDa), and one in the coelomic cavity, C1 (approximately 400 kDa). These native Hbs, their dissociation products and derivatives were subjected to electrospray ionization mass spectrometry (ESI-MS). The data were analyzed by the maximum entropy deconvolution system. We identified three groups of peaks for V1 Hb, at approximately 16, 23 27, and 30 kDa, corresponding to (i) two monomeric globin chains, b (Mr 16,133.5) and c (Mr 16,805.9); (ii) four linker subunits, L1 L4 (Mr 23,505.2, 23,851.4, 26,342.4, and 27,425.8, respectively); and (iii) one disulfide-bonded dimer D1 (Mr 31,720.7) composed of globin chains d (Mr 15,578.5) and e (Mr 16, 148.3). V2 and C1 Hbs had no linkers and contained a glycosylated monomeric globin chain, a (Mr 15,933.4) and a second dimer D2 (Mr 32,511.7) composed of chains e and f (Mr 16,368.1). The dimer D1 was absent from C1 Hb, clearly differentiating V2 and C1 Hbs. These Hbs were also subjected to SDS-PAGE analysis for comparative purposes. The following models are proposed ((cD1)(bD1)3) for the one-twelfth protomer of V1 Hb, ((cD)(bD)6(aD)) (D corresponding to either D1 or D2) for V2 and C1 Hbs. HBL V1 Hb would be composed of 180 polypeptide chains with 144 globin chains and 36 linker chains, each twelfth being in contact with three linker subunits, providing a total molecular mass = 3285 kDa. V2 and C1 would be composed of 24 globin chains providing a total molecular mass = 403 kDa and 406 kDa, respectively. These results are in excellent agreement with experimental Mr determined by STEM mass mapping and MALLS.

Mass Spectrometric Composition and Molecular Mass of Lumbricus terrestrisHemoglobin: A Refined Model of its Quaternary Structure

Sedimentation equilibrium measurements and scanning transmission electron microscopy (STEM) mass mapping of the extracellular, hexagonal bilayer hemoglobin (HBL Hb) of the earthworm Lumbricus terrestrisprovided masses of 3.41 to 3.66 MDa and 3.56 (±0.13) MDa, respectively. The Hb also contains 57.2 (±6.0) moles of tightly bound Ca per mole of protein. The Hb and its subunits obtained by dissociation, in native, dehemed and reduced carbamidomethylated forms, were subjected to electrospray ionization mass spectroscopy (ESI-MS). Maximum entropy deconvolution identified three groups of peaks, at ∼6 kDa, 24 to 32 kDa and ∼53 kDa corresponding to the monomer subunit M (globin chain d), four linker subunits and the disulfide-bonded trimer T (globin chains a+ b+ c). Subunit M consisted of three components, d1(15, 992.4), d2(15, 978.0) and d3(15, 962.1) (±1.0 Da), with relative intensities 1.0:0.5:0.3, respectively. Subunit T consisted of four major components, T1 (52, 922.6), T2 (52, 760.0), T3 (52, 598.5) and T4 (52, 435.4) (±4.0 Da), with relative intensities 0.6:1.0:0.2:0.7, respectively. ESI-MS of carbamidomethylated T, demonstrated that, unlike chains b(16, 254.4) and c(17, 289.2), chain aexists as a series of four, hexose-connected, glycosylated isoforms, a1 to a4 (19, 389.9, 19, 227.4, 19, 065.3 and 18, 902.9) (±1.0 Da). The mass differences between the deglycosylated chain a(17, 524.0) and a1 to a4 correspond to glycan side-chains (GlcNAc) 2(Man) n ( n=6 to 9). Four groups of peaks were observed in the 24 to 32 kDa region. Linkers L1a(27, 540.8) and L1b(27, 702.4) (±2.0 Da) are isoforms of L1(25, 837.5 in N-deglycosylated Hb) with glycan side-chains (GlcNAc) 2(Man) n ( n=8,9). Linkers L2(32, 104.3 (±5.0) Da) and L3(24, 912.9 (±2.0) Da) occur as single species. Linkers L4ato L4c(24, 019.0, 24, 102.3 and 24, 169.9) (±2.0 Da) with relative intensities 1.0:0.8:0.8, have not been identified previously. From ESI-MS relative intensities, L1:L2:L3:L4=0.6:0.4:1.0:0.5 and globin linker=0.78:0.22. HPLC of LumbricusHb provided a globin linker=0.73:0.27 (±0.02) and a heme content of 2.52 (±0.14) wt%. A model is proposed for the HBL structure, wherein 12 213.4 kDa dodecamers (144 globin chains, 2561 kDa) decorate a hexagonal framework of 36 linker chains (12 L1+ 6 L2+ 12 L3+ 6 L4) to provide a total mass of 3.531 MDa, each dodecamer being in contact with three linker subunits.

Electrospray Ionization Mass Spectrometric Determination of the Complete Polypeptide Chain Composition of Tylorrhynchus heterochaetus Hemoglobin

Electrospray ionization mass spectrometry (ESI-MS) of the native, reduced, and carbamidomethylated forms of the extracellular, 3.38-MDa hemoglobin from the marine polychaete Tylorrhynchus heterochaetus, when combined with a maximum entropy (MaxEnt) analysis, provided a complete description of the polypeptide chain composition. This hemoglobin, a hetero-multimeric complex of approximately 180 polypeptide chains, consisting of globin and linker subunits in an approximately 3:1 mass ratio, is among the largest protein complexes investigated by ESI-MS. The globin subunits consist of a monomer subunit (chain I, 15575.4 Da) and a disulfide-bonded trimer subunit, 50068.4 Da, consisting of globin chains IIA (16601.9 Da), IIB (16680.4 Da), and IIC (16,794.0 Da). Linker subunits L1-L5, 23233.8, 24835.4, 25326.9, 28202.2, and 26317.2 Da, respectively, were found together with a disulfide-bonded dimer of L2, 52609.4 Da. Using the exact masses of the subunits, a plausible model of the hemoglobin consisting of 144 globin chains (36 monomers and 36 trimers) and 36 linker chains provides a calculated mass of 3.42 MDa.