(Table A1) Chemical composition of abyssal peridotites from ODP Hole 153-920

The compatibility of vanadium (V) during mantle melting is a function of oxygen fugacity (fO2): at high fO2's, V becomes more incompatible. The prospects and limitations of using the V content of peridotites as a proxy for paleo-fO2 at the time of melt extraction were investigated here by assessing the uncertainties in V measurements and the sensitivity of V as a function of degree of melt extracted and fO2. V-MgO and V-Al2O3 systematics were found to be sensitive to fO2 variations, but consideration of the uncertainties in measurements and model parameters indicates that V is sensitive only to relative fO2 differences greater than ~2 log units. Post-Archean oceanic mantle peridotites, as represented by abyssal peridotites and obducted massif peridotites, have V-MgO and -Al2O3 systematics that can be modeled by 1.5 GPa melting between FMQ - 3 and FMQ - 1. This is consistent with fO2's of the mantle source for mid-ocean ridge basalts (MORBs) as determined by the Fe3+ activity of peridotitic minerals and basaltic glasses. Some arc-related peridotites have slightly lower V for a given degree of melting than oceanic mantle peridotites, and can be modeled by 1.5 GPa melting at fO2's as high as FMQ. However, the majority of arc-related peridotites have V-MgO systematics overlapping that of oceanic mantle peridotites, suggesting that although some arc mantle may melt under slightly oxidizing conditions, most arc mantle does not. The fact that thermobarometrically determined fO2's in arc peridotites and lavas can be significantly higher than that inferred from V systematics, suggests that V retains a record of the fO2 during partial melting, whereas the activity of Fe3+ in arc peridotitic minerals and lavas reflect subsequent metasomatic overprints and magmatic differentiation/emplacement processes, respectively. Peridotites associated with middle to late Archean cratonic mantle are characterized by highly variable V-MgO systematics. Tanzanian cratonic peridotites have V systematics indistinguishable from post-Archean oceanic mantle and can be modeled by 3 GPa partial melting at ~FMQ - 3. In contrast, many South African and Siberian cratonic peridotites have much lower V contents for a given degree of melting, suggesting at first glance that partial melting occurred at high fO2's. More likely, however, their unusually low V contents for a given degree of melting may be artifacts of excess orthopyroxene, a feature that pervades many South African and Siberian peridotites but not the Tanzanian peridotites. This is indicated by the fact that the V contents of South African and Siberian peridotites are correlated with increases in SiO2 content, generating data arrays that cannot be modeled by partial melting but can instead be generated by the addition of orthopyroxene through processes unrelated to primary melt depletion. Correction for orthopyroxene addition suggests that the South African and Siberian peridotites have V-MgO systematics similar to those of Tanzanian peridotites. Thus, if the Tanzanian peridotites represent the original partial melting residues, and if the South African and Siberian peridotites have been modified by orthopyroxene addition, then there is no indication that Archean cratonic mantle formed under fO2's significantly greater than that of modern oceanic mantle. Instead, the fO2's inferred from the V systematics in these three cratonic peridotite suites are within range of modern oceanic mantle. This also suggests that the transition from a highly reducing mantle in equilibrium with a metallic core to the present oxidized state must have occurred by late Archean times.

Chemical and isotopic compositions of rocks and minerals from the Ashadze and Logachev hydrothermal fields, Mid-Atlantic Ridge

This study was aimed at reconstructing a sequence of events in the magmatic and metamorphic evolution of peridotites, gabbroids, and trondhjemites from internal oceanic complexes of the Ashadze and Logachev hydrothermal vent fields. Collections of plutonic rocks from Cruises 22 and 26 of R/V "Professor Logachev", Cruise 41 of R/V "Akademik Mstislav Keldysh", and from the Serpentine Russian-French expedition aboard R/V "Pourquoi pas?" were objects of this study. Data reported here suggest that the internal oceanic complexes of the Ashadze and Logachev fields formed via the same scenario in these two regions of the Mid-Atlantic Ridge. On the other hand, an analysis of petrological and geochemical characteristics of the rocks indicated that the internal oceanic complexes of the MAR axial zone between 12°58'N and 14°45'N show pronounced petrological and geochemical heterogeneity manifested in variations in degree of depletion of mantle residues and in Nd isotopic compositions of rocks from the gabbro-peridotite association. Trondhjemites from the Ashadze hydrothermal field can be considered as partial melting products of gabbroids under influence of hydrothermal fluids. It was supposed that presence of trondhjemites in internal oceanic complexes of MAR can be used as a marker for the highest temperature deep-rooted hydrothermal systems. Perhaps, the region of the MAR axial zone, in which petrologically and geochemically contrasting internal oceanic complexes are spatially superimposed, serves as an area for development of large hydrothermal clusters with considerable ore-forming potential.

Structural basis for chemical inhibition of human blood coagulation factor Xa

Factor Xa, the converting enzyme of prothrombin to thrombin, has emerged as an alternative (to thrombin) target for drug discovery for thromboembolic diseases. An inhibitor has been synthesized and the crystal structure of the complex between Des[1–44] factor Xa and the inhibitor has been determined by crystallographic methods in two different crystal forms to 2.3- and 2.4-Å resolution. The racemic mixture of inhibitor FX-2212, (2RS)-(3′-amidino-3-biphenylyl)-5-(4-pyridylamino)pentanoic acid, inhibits factor Xa activity by 50% at 272 nM in vitro. The S-isomer of FX-2212 (FX-2212a) was found to bind to the active site of factor Xa in both crystal forms. The biphenylamidine of FX-2212a occupies the S1-pocket, and the pyridine ring makes hydrophobic interactions with the factor Xa aryl-binding site. Several water molecules meditate inhibitor binding to residues in the active site. In contrast to the earlier crystal structures of factor Xa, such as those of apo-Des[1–45] factor Xa and Des[1–44] factor Xa in complex with a naphthyl inhibitor DX-9065a, two epidermal growth factor-like domains of factor Xa are well ordered in both our crystal forms as well as the region between the two domains, which recently was found to be the binding site of the effector cell protease receptor-1. This structure provides a basis for designing next generation inhibitors of factor Xa.

Chemical synthesis of the precursor molecule of the Aequorea green fluorescent protein, subsequent folding, and development of fluorescence

The present paper describes the total chemical synthesis of the precursor molecule of the Aequorea green fluorescent protein (GFP). The molecule is made up of 238 amino acid residues in a single polypeptide chain and is nonfluorescent. To carry out the synthesis, a procedure, first described in 1981 for the synthesis of complex peptides, was used. The procedure is based on performing segment condensation reactions in solution while providing maximum protection to the segment. The effectiveness of the procedure has been demonstrated by the synthesis of various biologically active peptides and small proteins, such as human angiogenin, a 123-residue protein analogue of ribonuclease A, human midkine, a 121-residue protein, and pleiotrophin, a 136-residue protein analogue of midkine. The GFP precursor molecule was synthesized from 26 fully protected segments in solution, and the final 238-residue peptide was treated with anhydrous hydrogen fluoride to obtain the precursor molecule of GFP containing two Cys(acetamidomethyl) residues. After removal of the acetamidomethyl groups, the product was dissolved in 0.1 M Tris⋅HCl buffer (pH 8.0) in the presence of DTT. After several hours at room temperature, the solution began to emit a green fluorescence (λmax = 509 nm) under near-UV light. Both fluorescence excitation and fluorescence emission spectra were measured and were found to have the same shape and maxima as those reported for native GFP. The present results demonstrate the utility of the segment condensation procedure in synthesizing large protein molecules such as GFP. The result also provides evidence that the formation of the chromophore in GFP is not dependent on any external cofactor.

Interaction of two arginine residues in lactate oxidase with the enzyme flavin: Conversion of FMN to 8-formyl-FMN

Two arginine residues, Arg-181 and Arg-268, are conserved throughout the known family of FMN-containing enzymes that catalyze the oxidation of α-hydroxyacids. In the lactate oxidase from Aerococcus viridans, these residues have been changed to lysine in two single mutations and in a double mutant form. In addition, Arg-181 has been replaced by methionine to determine the effect of removing the positive charge on the residue. The effects of these replacements on the kinetic and thermodynamic properties are reported. With all mutant forms, there are only small effects on the reactivity of the reduced flavin with oxygen. On the other hand, the efficiency of reduction of the oxidized flavin by l-lactate is greatly reduced, particularly with the R268K mutant forms. The results demonstrate the importance of the two arginine residues in the binding of substrate and its interaction with the flavin, and are consistent with a previous hypothesis that they also play a role of charge neutralization in the transition state of substrate dehydrogenation. The replacement of Arg-268 by lysine also results in a slow conversion of the 8-CH3- substituent of FMN to yield 8-formyl-FMN, still tightly bound to the enzyme, and with significantly different physical and chemical properties from those of the FMN-enzyme.

Mapping the σ70 subunit contact sites on Escherichia coli RNA polymerase with a σ70-conjugated chemical protease

The core enzyme of Escherichia coli RNA polymerase acquires essential promoter recognition and transcription initiation activities by binding one of several σ subunits. To characterize the proximity between σ70, the major σ for transcription of the growth-related genes, and the core enzyme subunits (α2ββ′), we analyzed the protein-cutting patterns produced by a set of covalently tethered FeEDTA probes [FeBABE: Fe (S)-1-(p-bromoacetamidobenzyl)EDTA]. The probes were positioned in or near conserved regions of σ70 by using seven mutants, each carrying a single cysteine residue at position 132, 376, 396, 422, 496, 517, or 581. Each FeBABE-conjugated σ70 was bound to the core enzyme, which led to cleavage of nearby sites on the β and β′ subunits (but not α). Unlike the results of random cleavage [Greiner, D. P., Hughes, K. A., Gunasekera, A. H. & Meares, C. F. (1996) Proc. Natl. Acad. Sci. USA 93, 71–75], the cut sites from different probe-modified σ70 proteins are clustered in distinct regions of the subunits. On the β subunit, cleavage is observed in two regions, one between residues 383 and 554, including the conserved C and Rif regions; and the other between 854 and 1022, including conserved region G, regions of ppGpp sensitivity, and one of the segments forming the catalytic center of RNA polymerase. On the β′ subunit, the cleavage was identified within the sequence 228–461, including β′ conserved regions C and D (which comprise part of the catalytic center).

Site-directed spin labeling and chemical crosslinking demonstrate that helix V is close to helices VII and VIII in the lactose permease of Escherichia coli.

Site-directed chemical cleavage of lactose permease indicates that helix V is in close proximity to helices VII and VIII. To test this conclusion further, permease containing a biotin-acceptor domain and paired Cys residues at positions 148 (helix V) and 228 (helix VII), 148 and 226 (helix VII), or 148 and 275 (helix VIII) was affinity purified and labeled with a sulfhydryl-specific nitroxide spin label. Spin-spin interactions are observed with the 148/228 and 148/275 pairs, indicating close proximity between appropriate faces of helix V and helices VII and VIII. Little or no interaction is evident with the 148/226 pair, in all likelihood because position 226 is on the opposite face of helix VII from position 228. Broadening of the electron paramagnetic resonance spectra in the frozen state was used to estimate distance between the 148/228 and the 148/275 pairs. The nitroxides at positions 148 and 228 or 148 and 275 are within approximately 13-15 A. Finally, Cys residues at positions 148 and 228 are crosslinked by dibromobimane, a bifunctional crosslinker that is approximately 5 A. long, while no crosslinking is detected between Cys residues at positions 148 and 275 or 148 and 226. The results provide strong support for a structure in which helix V is in close proximity to both helices VII and VIII and is oriented in such a fashion that Cys-148 is closer to helix VII.

The determination of trace residues on metal surfaces /

"U.S. Atomic Energy Commission Contract AT(29-1)-1106."

Chemical and functional identification and characterization of novel sulfated alpha-conotoxins from the cone snail Conus anemone

An LC/MS analysis with diagnostic screening for the detection of peptides with posttranslational modifications revealed the presence of novel sulfated peptides within the -conotoxin molecular mass range in Conus anemone crude venom. A functional assay of the extract showed activity at several neuronal nicotinic acetylcholine receptors (nAChRs). Three sulfated alpha-conotoxins (AnIA, AnIB, and AnIC) were identified by LC/MS and assay-directed fractionation and sequenced after purification. The most active of these, alpha-AnIB, was further characterized and used to investigate the influence of posttranslational modifications on affinity. Synthetic AnIB exhibited subnanomolar potency at the rat alpha3/beta2 nAChR (IC50 0.3 nM) and was 200-fold less active on the rat alpha7 nAChR (IC50 76 nM). The unsulfated peptide [Tyr(16)]AnIB showed a 2-fold and 10-fold decrease in activities at alpha3beta2 (IC50 0.6 nM) and alpha7(IC50 836 nM) nAChR, respectively. Likewise, removal of the C-terminal amide had a greater influence on potency at the alpha7 (IC50 367 nM) than at the alpha3beta2 nAChR (IC50 0.5 nM). Stepwise removal of two N-terminal glycine residues revealed that these residues affect the binding kinetics of the peptide. Comparison with similar 4/7-alpha-conotoxin sequences suggests that residue 11 (alanine or glycine) and residue 14 (glutamine) constitute important determinants for alpha3beta2 selectivity, whereas the C-terminal amidation and sulfation at tyrosine-16 favor alpha7 affinity.

Novel natriuretic peptides from the venom of the inland taipan (Oxyuranus microlepidotus): isolation, chemical and biological characterisation

Three natriuretic-like peptides (TNP-a, TNP-b, and TNP-c) were isolated from the venom of Oxyuranus microlepidotus (inland taipan) and were also present in the venoms of Oxyuranus scutellatus canni (New Guinea taipan) and Oxyuranus scutellatus scutellatus (coastal taipan). They were isolated by HPLC, characterised by mass spectrometry and Edman analysis, and consist of 35-39 amino acid residues. These molecules differ from ANP/BNP through replacement of invariant residues within the 17-membered ring structure and by inclusion of proline residues in the C-terminal tail. TNP-c was equipotent to ANP in specific GC-A assays or aortic ring assays whereas TNP-a and TNP-b were either inactive (GC-A over-expressing cells and endothelium-denuded aortic rings) or weakly active (endothelium-in tact aortic rings). TNP-a and TNP-b were also unable to competitively inhibit the binding of TNP-c in endothelium-denuded aortae (GC-A) or endothelium-in tact aortae (NPR-C). Thus, these naturally occurring isoforms provide a new platform for further investigation of structure-function relationships of natriuretic peptides. (C) 2004 Elsevier Inc. All rights reserved.

Chemical synthesis and structure elucidation of bovine kappa-casein (1-44)

The caseins (alpha(s1), alpha(s2), beta, and kappa) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine K-casein, the protein which maintains the micellar structure of the caseins. K-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro(8) to Arg(34). This is the first report which demonstrates extensive secondary structure within the casein class of proteins. (c) 2006 Elsevier Inc. All rights reserved.

Phytotoxicity of surface waters of the Thames and Brisbane River Estuaries: A combined chemical analysis and bioassay approach for the comparison of two systems

The Thames Estuary, UK, and the Brisbane River, Australia, are comparable in size and catchment area. Both are representative of the large and growing number of the world's estuaries associated with major cities. Principle differences between the two systems relate to climate and human population pressures. In order to assess the potential phytotoxic impact of herbicide residues in the estuaries, surface waters were analysed with a PAM fluorometry-based bioassay that employs the photosynthetic efficiency (photosystem II quantum yield) of laboratory cultured microalgae, as an endpoint measure of phytotoxicity. In addition, surface waters were chemically analysed for a limited number of herbicides. Diuron atrazine and simazine were detected in both systems at comparable concentrations. In contrast, bioassay results revealed that whilst detected herbicides accounted for the observed phytotoxicity of Brisbane River extracts with great accuracy, they consistently explained only around 50% of the phytotoxicity induced by Thames Estuary extracts. Unaccounted for phytotoxicity in Thames surface waters is indicative of unidentified phytotoxins. The greatest phytotoxic response was measured at Charing Cross, Thames Estuary, and corresponded to a diuron equivalent concentration of 180 ng L-1. The study employs relative potencies (REP) of PSII impacting herbicides and demonstrates that chemical analysis alone is prone to omission of valuable information. Results of the study provide support for the incorporation of bioassays into routine monitoring programs where bioassay data may be used to predict and verify chemical contamination data, alert to unidentified compounds and provide the user with information regarding cumulative toxicity of complex mixtures. (c) 2005 Elsevier B.V. All rights reserved.

Predicting the solvent accessibility of transmembrane residues from protein sequence

In this study, we propose a novel method to predict the solvent accessible surface areas of transmembrane residues. For both transmembrane alpha-helix and beta-barrel residues, the correlation coefficients between the predicted and observed accessible surface areas are around 0.65. On the basis of predicted accessible surface areas, residues exposed to the lipid environment or buried inside a protein can be identified by using certain cutoff thresholds. We have extensively examined our approach based on different definitions of accessible surface areas and a variety of sets of control parameters. Given that experimentally determining the structures of membrane proteins is very difficult and membrane proteins are actually abundant in nature, our approach is useful for theoretically modeling membrane protein tertiary structures, particularly for modeling the assembly of transmembrane domains. This approach can be used to annotate the membrane proteins in proteomes to provide extra structural and functional information.