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PubMed1997

Investigation by electrospray ionization mass spectrometry of the extracellular hemoglobin from the polychaete annelid Alvinella pompejana: an unusual hexagonal bilayer hemoglobin.

Alvinella pompejana inhabits deep-sea hydrothermal vent sites along the East-Pacific Rise, where it colonizes the walls of actively venting high-temperature chimneys. This worm is the most thermophilic metazoan known to date. In Alvinella, as in other alvinellids, oxygen transport is mainly achieved by an extracellular Hb dissolved in the vascular blood. This Hb has a molecular mass of 3833 +/- 14 kDa as revealed by multiangle laser light scattering (MALLS). Native and derivative Hb (reduced, carbamidomethylated, and deglycosylated) were analyzed by electrospray ionization mass spectrometry (ESI-MS). The data were processed by the maximum entropy deconvolution system (MaxEnt). We identified three groups of peaks for Alvinella Hb, at ca. 16, 23-26, and 50 kDa corresponding to (i) four monomeric globin chains, a1 (16 633.4), a2(16 532.4), a3 (16 419.6), and a4(16 348.9); (ii) four linker chains, L1-L4 (22 887. 1, 24 230.5, 26 233.6, and 25 974.4); and (iii) one disulfide-bonded trimer T (51 431.9) composed of globin chains b (16 477.5), c (16 916.1), and d (18 048.8). These Hbs were also subjected to SDS-PAGE analysis for comparative purposes. In addition, using the ESI-MS data we propose two alternative models for the quaternary structure of Alvinella's Hb.

Animals↗
PubMed1998

A hierarchy of disulfide-bonded subunits: the quaternary structure of Eudistylia chlorocruorin.

The quaternary structure of the cysteine-rich, approximately 3500-kDa chlorocruorin (Chl) from the marine polychaete Eudistylia vancouverii was investigated using maximum entropy deconvolution of the electrospray ionization mass spectra (ESIMS). The native Chl provided two groups of peaks, at approximately 25 and approximately 33 kDa, and one peak at approximately 66 kDa. ESIMS of the reduced and reduced and carbamidomethylated Chl and of its subunits obtained by HPLC provided the complete subunit composition of the Chl. Two groups of nonglobin linker chains were observed: L1a-f (25 000.4, 25 017.9, 25 039.6, 25 057.0, 25 074.4 and 25 096.8 Da) and L2a-d (25 402.7, 25 446.0, 25 461.6 and 25 478.3Da) (+/-2.5 Da), with relative intensities L1:L2 = 5:2. Six globin chains were found, a1, a2, and b1-4, with reduced masses of 16 051.5, 16 172.4, 16 853.5, 17 088.9, 17 161.2 and 17 103.6 (+/-1.0 Da) and relative intensities of 8:4:1:4:2:1, respectively. Disulfide-bonded dimers and a tetramer of globin chains were identified: D1 = a1 + b3 at 33 207.1; D2 at 33 374.1, which had a cysteinylated Cys (a2 + b2 + Cys); and D3 = a1 + b4 at 33 149.4 Da (+/-3.0 Da), with relative intensities D1:D2:D3 = 5:4:1 and T = a1 + a2 + b1 + b2 at 66 154.8 +/- 4.0 Da. A 206-kDa dodecamer subunit obtained by dissociation of the Chl in 4 M urea [Qabar, A. N., et al. (1991) J. Mol. Biol. 222, 1109-1129], was found to consist only of tetramers T. A model was proposed for the Chl, based on a dimer:tetramer ratio of 2:1: four 206-kDa dodecamers (trimer of tetramers) and 48 dimers tethered to a framework of 30 L1 and 12 L2 linker chains. The 144 globin chains (2480 kDa) and 42 linker chains (1059 kDa) provide a total mass of 3539 kDa, in good agreement with the 3480 +/- 225 kDa determined previously by STEM mass mapping. The hierarchy of disulfide-bonded globin subunits observed for Eudistylia Chl provides a built-in heterogeneity of hexagonal bilayer structures.

Animals↗
PubMed1998

Solution structure and backbone dynamics of component IV Glycera dibranchiata monomeric hemoglobin-CO.

The solution structure and backbone dynamics of the recombinant, ferrous CO-ligated form of component IV monomeric hemoglobin from Glycera dibranchiata (GMH4CO) have been characterized by NMR spectroscopy. Distance geometry and simulated annealing calculations utilizing a total of 2550 distance and torsion angle constraints yielded an ensemble of 29 structures with an overall average backbone rmsd of 0.48 A from the average structure. Differences between the solution structure and a related crystal structure are confined to regions of lower precision in either the NMR or X-ray structure, or in regions where the amino acid sequences differ. 15N relaxation measurements at 76.0 and 60.8 MHz were analyzed with an extended model-free approach, and revealed low-frequency motions in the vicinity of the heme, concentrated in the F helix. Amide proton protection factors were obtained from H-D amide exchange measurements on 15N-labeled protein. Patterns in the backbone dynamics and protection factors were shown to correlate with regions of heterogeneity and disorder in the ensemble of NMR structures and with large crystallographic B-factors in the X-ray structures. Surprisingly, while the backbone atoms of the F helix have higher rmsds and larger measures of dynamics on the microsecond to millisecond time scale than the other helices, amide protection factors for residues in the F helix were observed to be similar to those of the other helices. This contrasts with H-D amide exchange measurements on sperm whale myoglobin which indicated low protection for the F helix (S. N. Loh and B. F. Volkman, unpublished results). These results for GMH4 suggest a model in which the F helix undergoes collective motions as a relatively rigid hydrogen-bonded unit, possibly pivoting about a central position near residue Val87.

Amino Acid Sequence↗
PubMedDate not supplied

Traditional topological indices vs electronic, geometrical, and combined molecular descriptors in QSAR/QSPR research.

A comparison of the performance of molecular descriptors of different types was conducted. The study was concentrated on determining which descriptors are included in the best linear multivariate regression models constructed for modeling various physicochemical properties (melting point, boiling point, refractive index, molar volume, and density) and biological activities (anaesthetic activity, narcotic activity, sweetness intensity). A total of 84 molecular descriptors published over the past 2 decades was included in this study, plus some of their normalized and squared forms. It was shown that, for the estimation of physicochemical properties, the best small regression models with one to four parameters are mainly comprised of "classical" topological indices such as the Randić index, Wiener index, and molecular connectivity indices. For the correlation of biological activity, combinations of topological indices with geometrical descriptors produced regression models of the best quality. In-house developed software was used for generation of the molecular descriptors (the GROUND program) and for the statistical QSAR/QSPR analysis (the GROUNDSTAT program).

Anesthetics, Local↗
PubMed2002

Biotransformation of arsenate to the tetramethylarsonium ion in the marine polychaetes Nereis diversicolor and Nereis virens.

Arsenic compounds in aqueous extracts of the marine polychaetes Nereis diversicolor and Nereis virens were determined by HPLC-ICP-MS. Both polychaetes contained most of their water-soluble arsenic as arsenobetaine (approximately 60%), and the tetramethylarsonium ion was also a significant arsenic constituent (approximately 20% in N. diversicolor and approximately 30% in N. virens). Trimethylarsoniopropionate and arsenosugars were present in the Nereis species as minor constituents, and traces of arsenocholine, trimethylarsine oxide, and arsenate were also detected. When N. diversicolor and N. virens were exposed in laboratory experiments to different concentrations of arsenate in seawater (10, 50, 100, 500, and 1000 microg of As L(-1)), both species accumulated arsenic in a dose-dependent manner. Atthe highest exposure level, they achieved mean arsenic concentrations (dry mass) of approximately 70 mg of As kg(-1) (N. virens) and 90 mg of As kg(-1) (N. diversicolor), which represented about a 5-fold increase when compared with the control animals. The arsenic taken up by the polychaetes was readily methylated, and the major metabolite was the tetramethylarsonium ion (up to approximately 85% of the accumulated arsenic). Two other products of arsenic methylation, methylarsonate and trimethylarsine oxide, were also produced to a small extent; however, dimethylarsinate, another likely intermediate in the formation of the tetramethylarsonium ion, could not be detected in these experiments. The remaining accumulated arsenic was present as unchanged arsenate. This is the first report of significant biomethylation of arsenic to the tetramethyl stage and provides a ready explanation for the widespread occurrence of tetramethylarsonium ion in marine animals.

Animals↗
PubMed2004

Use of passive samplers to mimic uptake of polycyclic aromatic hydrocarbons by benthic polychaetes.

Experiments were conducted to test whether passive samplers made of low-density polyethylene (polyethylene devices, or PEDs) can estimate the extent of uptake of polycyclic aromatic hydrocarbons (PAHs) by benthic polychaetes (Nereis virens) in contaminated marine sediments. For a variety of PAHs, PEDs reached 90% equilibrium with sediment PAHs in 60 days or less. Using 60-day sediment bioaccumulation tests, we have demonstrated a significant relationship between PAH concentrations in the polychaetes and the PEDs (R2 = 0.67, p = 0.002), with the PEDs taking up less PAHs than the polychaetes. Because of this relationship, PEDs can potentially be used in a regulatory context to simulate uptake of bioavailable PAHs in contaminated marine sediments. The PED PAH concentrations were also used to calculate porewater PAH concentrations that allowed for the estimation of a linear free-energy relationship between the lipid-water distribution coefficient (Klip) and the octanol-water distribution coefficient (KOW) for PAH uptake in marine polychaetes (R2 = 0.94, p < 0.0001).

Animals↗
PubMed2005

Addition of activated carbon to sediments to reduce PCB bioaccumulation by a polychaete (Neanthes arenaceodentata) and an amphipod (Leptocheirus plumulosus).

This work examines the effects of adding coke or activated carbon on the bioavailability of polychlorinated biphenyls (PCBs) in contaminated sedimentfrom South Basin at Hunters Point, San Francisco Bay. We show with 28-day sediment exposure tests that PCB bioaccumulation in a polychaete (Neanthes arenaceodentata) is reduced by 82% following 1-month contact of sediment with activated carbon and by 87% following 6-months contact of sediment with activated carbon. PCB bioaccumulation in an amphipod (Leptocheirus plumulosus) is reduced by 70% following 1-month contact of sediment with activated carbon and by 75% after 6-months contact of sediment with activated carbon. Adding coke had a negligible effect on reducing PCB bioaccumulation, probably because of the low specific surface area and the slow kinetics of PCB diffusion intothe solid coke particles. Reductions in congener bioaccumulation with activated carbon were inversely related to congener Kow, suggesting that the efficacy of activated carbon is controlled by the mass-transfer rate of PCBs from sediment and into activated carbon. We find that reductions in aqueous PCB concentrations in equilibrium with the sediment were similar to reductions in PCB bioaccumulation. While no lethality was observed following activated carbon addition, growth rates were reduced by activated carbon for the polychaete, but not for the amphipod, suggesting the need for further study of the potential impacts of activated carbon on exposed communities. The study suggests that treatment of the biologically active layer of contaminated sediments with activated carbon may be a promising in-situ technique for reducing the bioavailability of sediment-associated PCBs and other hydrophobic organic compounds.

Amphipoda↗
PubMed2004

Commercially available chemicals that mimic a deposit feeder's (Arenicola marina) digestive solubilization of lipids.

To develop a simple and cost-effective bioavailability test for sediment-bound contaminants, the solubilization strengths of mixtures of four commercially available surfactants and four proteins were compared to that of digestive fluids from a deposit-feeding benthic polychaete Arenicola marina. Initial tests indicated that sodium taurocholate, a vertebrate bile salt, was the most accurate mimic of A. marina gut fluids' solubilization of individual polycyclic aromatic hydrocarbons (PAH). Further testing with nutritional lipids and other hydrophobic contaminants confirmed the similarities of these fluids. Bovine serum albumin (BSA) solubilization of PAH was the most efficient of all the proteins tested. A cocktail of sodium taurocholate and BSA was compared to A. marina's solubilization of 12 PAH from four different contaminated sediments (from Boston, Charleston, Jacksonville, and San Diego harbors). The two solutions released most PAH to similar extents; 40 of 48 PAH-sediment combinations were released at amounts within a factor of 2 in cocktail and gut fluid solutions. Therefore, the cocktail may serve as a surrogate for real gut fluids and allow easier adoption of the in vitro incubation approach to bioavailability testing.

Animals↗
PubMed2005

Biomimetic extraction of Bacillus thuringiensis insecticidal crystal proteins from soil based on invertebrate gut fluid chemistry.

Quantitative monitoring of Bacillus thuringiensis (Bt) insecticidal crystal proteins in soil has been hampered by the lack of efficient extraction/detection methods. A novel approach for simple and effective Bt protein extraction was explored by evaluating extraction solutions from invertebrate gut fluids. Marine worm gut fluids were identified as promising for extracting Bt protein from soil. An artificial gut fluid based on these marine worm gut fluids was developed using commercially available chemicals and was evaluated for its ability to extract Bt proteins from soil. On the basis of experiments with Cry1 proteins, the artificial gut fluid in combination with ELISA was highly effective for protein extraction and analysis in a variety of soil types and was well-correlated with bioassay results. Coupling of immunoassay with this extraction method provides, for the first time, an efficient, accurate, and quantitative assay for routine measurement of Bt protein residues in soil.

Animals↗
PubMed1999

Distribution of bromophenols in species of marine polychaetes and bryozoans from eastern Australia and the role of such animals in the flavor of edible ocean fish and prawns (shrimp).

Sixteen species (44 samples) of marine polychaetes and 10 species (14 samples) of bryozoans from eastern Australia were analyzed by GC/MS for the key seafood flavor components 2- and 4-bromophenol, 2, 4- and 2,6-dibromophenol, and 2,4,6-tribromophenol. All five bromophenols were found in 91% of polychaetes and 64% of bryozoans. The remaining samples all contained at least three bromophenols. 2,4, 6-Tribromophenol was found in all polychaetes and bryozoans and, with few exceptions, was present in the highest concentrations. The total bromophenol content determined on a wet-weight basis varied widely between species: for polychaetes, from 58 ng/g for Australonuphis teres to 8.3 million ng/g for Barantolla lepte, and for bryozoans, from 36 ng/g for Cladostephus spongiosus to 1668 ng/g for Amathia wilsoni. Species of polychaetes with the highest concentrations of bromophenols were all collected from muddy environments. The possible effects that dietary polychaetes and bryozoans have on the ocean-, brine-, or iodine-like flavors of certain seafoods are discussed.

Animals↗
PubMed2006

Hydrophobic distal pocket affects NO-heme geminate recombination dynamics in dehaloperoxidase and H64V myoglobin.

The recombination dynamics of NO with dehaloperoxidase (DHP) from Amphitrite ornata following photolysis were measured by femtosecond time-resolved absorption spectroscopy. Singular value decomposition (SVD) analysis reveals two important basis spectra. The first SVD basis spectrum reports on the population of photolyzed NO molecules and has the appearance of the equilibrium difference spectrum between the deoxy and NO forms of DHP. The first basis time course has two kinetic components with time constants of tau(11) approximately 9 ps and tau(12) approximately 50 ps that correspond to geminate recombination. The fast geminate process tau(11) arises from a contact pair with the heme iron in a bound state with S = 3/2 spin. The slow geminate process tau(12) corresponds to the recombination from a more remote docking site >3 A from the heme iron with the greater barrier corresponding to a S = 5/2 spin state. The second SVD basis spectrum represents a time-dependent Soret band shift indicative of heme photophysical processes and protein relaxation with time constants of tau(21) approximately 3 ps and tau(22) approximately 17 ps, respectively. A comparison between the more rapid rate constant of the slow geminate phase in DHP-NO and horse heart myoglobin (HHMbNO) or sperm whale myoglobin (SWMbNO) suggests that protein interactions with photolyzed NO are weaker in DHP than in the wild-type MbNOs, consistent with the hydrophobic distal pocket of DHP. The slower protein relaxation rate tau(22) in DHP-NO relative to HHMbNO implies less effective trapping in the docking site of the distal pocket and is consistent with a greater yield for the fast geminate process. The trends observed for DHP-NO also hold for the H64V mutant of SWMb (H64V MbNO), consistent with a more hydrophobic distal pocket for that protein as well. We examine the influence of solution viscosity on NO recombination by varying the glycerol content in the range from 0% to 90% (v/v). The dominant effect of increasing viscosity is the increase of the rate of the slow geminate process, tau(12), coupled with a population decrease of the slow geminate component. Both phenomena are similar to the effect of viscosity on wild-type Mb due to slowing of protein relaxation resulting from an increased solution viscosity and protein surface dehydration.

Amino Acid Substitution↗
PubMed2006

Spectroscopic study of substrate binding to the carbonmonoxy form of dehaloperoxidase from Amphitrite ornata.

Dehaloperoxidase (DHP) is a globular heme enzyme found in the marine worm Amphitrite ornata that can catalyze the dehalogenation of halophenols to the corresponding quinones by using hydrogen peroxide as a cosubstrate. Its three-dimensional fold is surprisingly similar to that of the oxygen storage protein myoglobin (Mb). A key structural feature common to both DHP and Mb is the existence of multiple conformations of the distal histidine. In DHP, the conformational flexibility may be involved in promotion of substrate and cosubstrate entry and exit. Here we have explored the dynamics of substrate binding in DHP using Fourier transform infrared spectroscopy and flash photolysis. A number of discrete conformations at the active site were identified from the appearance of multiple CO absorbance bands in the infrared region of the spectrum. Upon photolysis at cryogenic temperatures, the CO molecules are trapped at docking sites within the protein matrix, as inferred from the appearance of several photoproduct bands characteristic of each site. Substrate binding stabilizes the protein by approximately 20 kJ/mol. The low yield of substrate-bound DHP at ambient temperature points toward a steric inhibition of substrate binding by carbon monoxide.

Animals↗
PubMed2006

Exploring gradients of halogens and zinc in the surface and subsurface of Nereis jaws.

The outstanding mechanical properties of impact-bearing tissues, such as Nereis jaws, make their morphology and chemical composition a subject of particular interest. The complex structure of the jaw was recently reported to exhibit molecular gradients that were closely correlated with stiffness and hardness.(18) Accordingly, we have explored the spatial distribution and bonding chemistries of Zn and the halogens in the surface structure of the jaws. Using secondary ion mass spectrometry (SIMS) and scanning electron microscopy (SEM), we found that Cl, Br, and I distributions are enhanced in surface layers of the basal protected portion of the jaw but are shifted to greater depths toward the exposed jaw tip. There are thus two complementary halogen gradients in the jaw: one on the surface that decreases from the base to the tip, coupled to an increasing one in the subsurface layers. The outer surface coating appeared to have granular morphology, in contrast to the anisotropic, fibrous core that dominates the subarchitecture. Using X-ray photoelectron spectroscopy (XPS), we discovered that Zn, I, and Br in the jaws have single chemical environments whereas chlorine is present in two distinct modes (Cl-Zn and Cl-C). Given the inverse relationship between surface exposure and halogen abundance in the jaws, it is unlikely that the halogens contribute directly to mechanical properties such as wear and hardness.

Animal Structures↗
PubMed1998

Detailed NMR analysis of the heme-protein interactions in component IV Glycera dibranchiata monomeric hemoglobin-CO.

Complete 13C, 15N, and 1H resonance assignments have been obtained for the recombinant, ferrous CO-ligated from of component IV monomeric hemoglobin from Glycera dibranchiata. This 15642 Da myoglobin-like protein contains a large number of glycine and alanine residues (47) and a heme prosthetic group. Coupling constant information has allowed the determination of chi(1) and chi(2) torsion angles, backbone phi angles, as well as 43 of 81 possible assignments to H beta 2/beta 3 pairs. The 13C alpha, 13 beta, 13C', and 1H alpha assignments yield a consensus chemical shift index (CSI) that, in combination with NOE information and backbone torsion angles, defines seven distinct helical regions for the protein's global architecture. Discrepancies between the CSI and NOE/3JHNH alpha-based secondary structure definitions have been attributed to heme ring current shifts on the basis of calculations from a model structure [Alam et al. (1994) J. Protein Chem., 13, 151-164]. The agreement can be improved by correcting the 1H alpha chemical shifts for the ring current contributions. Because the holoprotein was assembled from isotopically enriched globin and natural isotope-abundance heme, data from 13C-filtered/13C-edited and 13C-filtered/13C-filtered 2D NOESY experiments could be used to determine complete heme proton assignments and to position the heme within the protein. The results confirm the unusual presence of Phe31 (B10) and Leu58 (E7) side chains near the heme ligand binding site which may alter the polarity and steric environment and thus the functional properties of this protein.

Amino Acid Sequence↗
PubMed1998

Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra.

A maximum likelihood (ML)-based approach has been established for the direct extraction of NMR parameters (e.g., frequency, amplitude, phase, and decay rate) simultaneously from all dimensions of a D-dimensional NMR spectrum. The approach, referred to here as HTFD-ML (hybrid time frequency domain maximum likelihood), constructs a time-domain model composed of a sum of exponentially-decaying sinusoidal signals. The apodized Fourier transform of this time-domain signal is a model spectrum that represents the 'best-fit' to the equivalent frequency-domain data spectrum. The desired amplitude and frequency parameters can be extracted directly from the signal model constructed by the HTFD-ML algorithm. The HTFD-ML approach presented here, as embodied in the software package CHIFIT, is designed to meet the challenges posed by model fitting of D-dimensional NMR data sets, where each consists of many data points (10(8) is not uncommon) encoding information about numerous signals (up to 10(5) for a protein of moderate size) that exhibit spectral overlap. The suitability of the approach is demonstrated by its application to the concerted analysis of a series of ten 2D 1H-15N HSQC experiments measuring 15N T1 relaxation. In addition to demonstrating the practicality of performing maximum likelihood analysis on large, multidimensional NMR spectra, the results demonstrate that this parametric model-fitting approach provides more accurate amplitude and frequency estimates than those obtained from conventional peak-based analysis of the FT spectrum. The improved performance of the model fitting approach derives from its ability to take into account the simultaneous contributions of all signals in a crowded spectral region (deconvolution) as well as to incorporate prior knowledge in constructing models to fit the data.

Algorithms↗
PubMed2001

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami bay and its phylogenetic analysis.

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.

Animals↗