Legal aspects of conserving native oysters in Scotland.

Native oysters (Ostrea edulis) historically supported valuable fisheries in Scotland, but are now absent from areas of former abundance on the east coast and occur mainly in isolated populations in west coast sea lochs. The main contemporary threat is from unauthorized gathering. In most places, the exclusive right to gather is retained by the Crown, as a remnant of the feudal system, but in some areas the right has been acquired by individuals or institutions. A temporary right to gather oysters may be obtained by permit from the proprietor, or through a Several or Regulating Order made under shellfish fisheries legislation. The right to gather oysters is separate from ownership of the foreshore or sea bed on which they are located. To receive the maximum legal protection, oyster beds must be marked out, or the rights to them otherwise adequately made known. Wild or formerly-cultivated oyster beds may not meet this criterion and, in any case, enforcement is difficult in remote locations. It has been proposed that there should be a statutory public right to gather oysters. Were this to be created, then strong conservation measures would need to be implemented to protect native oysters from eradication by uncontrolled gathering.

Photochemistry of the pi-extended 9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracene system: generation and characterisation of the radical cation, dication, and derived products.

Flash photolysis of bis[4.5-di(methylsulfanyl) 1,3-dithiol-2-ylidene]-9,10(-dihydroanthracene (1) in chloroform leads to formation of the transient radical cation species 1.+ which has a diagnostic broad absorption band at lambdamax approximately 650 nm. This band decays to half its original intensity over a period of about 80 micros. Species 1.+ has also been characterised by resonance Raman spectroscopy. In degassed solution 1.+ disproportionates to give the dication 1(2+), whereas in aerated solutions the photodegradation product is the 10-[4,5-di(methylsulfanyl) 1,3-dithiol-2-ylidene]anthracene-9(10 H)one (2). The dication 1(2+) has been characterised by a spectroelectrochemical study [lambdamax (CH2Cl2) = 377, 392, 419, 479 nm] and by an X-ray crystal structure of the salt 1(2-) (ClO4)2, which was obtained by electrocrystallisation. The planar anthracene and 1,3-dithiolium rings in the dication form a dihedral angle of 77.2 degrees; this conformation is strikingly different from the saddle-shaped structure of neutral 1 reported previously.

Electrochemical evidence for electronic interactions through the para-carborane skeleton in the novel tricluster [(Co2C2(SiMe3)(CO)4(dppm))2(mu-CB10H10C)].

The electrochemical properties of the title compound reveal electronic interactions between two dicobalt-dicarbon clusters via a 1,12-para-carborane cage.

Synthesis and structure of the cluster ion pair [Ru3(CO)9[mu-P(NPri2)2]3][Ru6(CO)15(mu 6-C)[mu-P(NPri2)2]]. A theoretical overview of M3(mu-PR2)3 frameworks.

The compound [Ru3(CO)9[mu-P(NPri2)2]3][Ru6(CO)15(mu 6-C)[mu-P(NPri2)2]] (1), obtained via the addition of PCl(NPri2)2 to K2[Ru4(CO)13], crystallizes in the monoclinic space group P2l/c with a = 15.537(8) A, b = 36.151(16) A, c = 19.407(5) A, beta = 91.14(2) degrees, Z = 4, and R = 0.069 for 8006 observed reflections. The unit cell is unusual in that it contains both a typical octahedral Ru6 cluster anion (1a), featuring an encapsulated carbide, and a symmetrical phosphido bridge, in addition to a 50-electron trinuclear cluster cation [Ru3(CO)9[mu-P(NPri2)2]3]+ (1c). The latter, with approximate D3h symmetry, exhibits long Ru-Ru distances (> or = 3.15 A). Among the family of clusters with M3(mu-PR2)3 cores and different numbers of both electrons (TEC) and terminal ligands (LxLyLz), 1c is unique in that it is a 333 stereotype with 50 valence electrons. MO calculations permit us to predict the existence of redox congeners of 1c clusters and related 48e Re3 clusters. This work also presents a summary of the relationships between the electronic and the geometric structures for all known M3LxLyLz(mu-PR2)3 species. The basic stereochemical features are influenced by the total-electron count and, hence, by the degree of M-M bonding, as well as the remarkable flexibility of the phosphido bridging ligands. The mu-PR2 ligands need not necessarily lie in the M3 plane, and a wide range of M-P-M angles (as small as 72 degrees or as large as 133 degrees) have been observed.

Active sites in complement components C5 and C3 identified by proximity to indels in the C3/4/5 protein family.

We recently suggested that sites of length polymorphisms in protein families (indels) might serve as useful guides for locating protein:protein interaction sites. This report describes additional site-specific mutagenesis and synthetic peptide inhibition studies aimed at testing this idea for the paralogous complement C3, C4, and C5 proteins. A series of C5 mutants was constructed by altering the C5 sequence at each of the 27 indels in this protein family. Mutants were expressed in COS cells and were assayed for hemolytic activity and protease sensitivity. Mutants at five indels showed relatively normal expression but substantially reduced sp. act., indicating that the mutations damaged sites important for C5 function. Twenty-three synthetic peptides with C5 sequences and 10 with C3 sequences were also tested for the ability to inhibit C hemolytic activity. Three of the C5 peptides and one of the C3 peptides showed 50% inhibition of both C hemolytic and bactericidal activities at a concentration of 100 microM. In several cases both the mutational and peptide methods implicated the same indel site. Overall, the results suggest that regions important for function of both C3 and C5 lie proximal to residues 150-200 and 1600-1620 in the precursor sequences. Additional sites potentially important for C5 function are near residue 500 in the beta-chain and at two or three sites between the N-terminus of the alpha'-chain and the C5d fragment. One of the latter sites, near residue 865, appears to be important for proteolytic activation of C5.

Binding kinetics of engineered mutants provide insight about the pathway for entering and exiting the intestinal fatty acid binding protein.

To better understand the mechanism by which fatty acids bind to and dissociate from the binding cavities of fatty acid binding proteins (FABPs), we constructed 31 single amino acid mutants of the intestinal FABP (I-FABP) and determined the rate constants for binding and dissociation, primarily for long-chain fatty acids (FA). FA dissociation from these proteins was measured both by the ADIFAB method and by the change in tryptophan fluorescence of the FABPs. Rate constants for binding (kon) were calculated from the rate constants for dissociation (koff) and the equilibrium binding affinities. Amino acid substitutions were made at locations within the binding cavity, in the region of the gap between the betaD- and betaE-strands, and within the "portal" region of the protein. The koff values for the mutant proteins ranged from about 20-fold slower to 4-fold faster than the wild-type (WT) protein. Values for kon were as much as 20-fold slower than the WT protein, but in no case was kon significantly faster than the WT. Mutants with slower and faster koff values were generally those involving sites within the binding cavity and, relative to the WT protein, revealed higher and lower affinities, respectively. Reduced rates of binding were generally, but not exclusively, associated with sites within the portal region. For example, for F68A which is located closer to the opposite end of the protein from the portal region, the kon is more than 10-fold slower than WT. Even for these distal sites, however, the evidence is consistent with reductions in kon being due to alterations of the portal region. Binding affinities and rate constants measured as a function of ionic strength also suggest that the FA initially binds, through an electrostatic interaction, to Arg-56 on the surface of the protein, before inserting into the binding cavity. Thus, the results of this study are consistent with FA binding to I-FABP involving an initial interaction with Arg-56 followed by insertion of the FA, through the portal region, into the binding cavity and with a reversal of these steps for the dissociation reaction.

Active sites in complement component C3 mapped by mutations at indels.

Engineered mutants of human complement component C3 were used to test the idea that sites of length polymorphisms in protein families (indels) can guide a search for protein:protein interaction sites. Sequence changes were introduced at each of the 27 indels in the C3/4/5 protein family, and mutants at 26 indels were expressed by transiently transfected COS cells. Expressed proteins were assayed 1) for concentration, by ELISA and by autoradiography of radiolabeled protein; 2) for classical pathway hemolytic activity; 3) for susceptibility to proteolytic activation by the alternative pathway and cobra venom factor C3 convertases; and 4) for susceptibility to complement factor I in the presence of factor H. Most of the mutations did not appreciably alter expression or activity relative to wild-type C3, consistent with the idea that most indels occur at the protein surface. Mutations at four indels severely damaged C3 functional activity, but did not affect the stability or structure of the protein, as assessed by their effects on expression by COS cells and on susceptibility to cleavage by C3 convertases and factor I. These indels are therefore near functionally important amino acid residues; they represent good candidates for sites of protein:protein interactions. Mutation of the sequence at a fifth indel altered the equilibrium between the latent and reacted C3 conformations, and mutations at 4 other indels substantially decreased both protein activity and expression. The mutants provided an overview of the structural and functional roles played by different parts of C3.

Thermodynamics of fatty acid binding to engineered mutants of the adipocyte and intestinal fatty acid-binding proteins.

We constructed 18 single amino acid mutants of the adipocyte fatty acid-binding protein (A-FABP) and 17 of the intestinal fatty acid-binding protein (I-FABP), at locations in the fatty acid (FA) binding sites. For each mutant protein, we measured thermodynamic parameters that characterize FA binding. Binding affinities ranged from about 200-fold smaller to 30-fold larger than the wild type (WT) proteins. Thermodynamic parameters revealed that binding affinities often inaccurately reported changes in protein-FA interactions because changes in the binding entropy and enthalpy were usually compensatory and larger than the binding free energy. FA-FABP interactions were quite different for I-FABP and A-FABP proteins. Binding affinities were larger and decreased to a greater degree with increasing FA solubility for most of the I-FABP as compared with the A-FABP proteins, consistent with a more hydrophobic binding site for the I-FABP proteins. In A-FABP, Ala substitutions for Arg106 and Arg126, which interact with the FA carboxylate, reduce affinities by about 100-fold, but in I-FABP, R106A increases affinities up to 30-fold. Moreover, in A-FABP, the thermodynamic parameters predict that the FA carboxylate location switches from the 126-position in R106A to the 106 position in R126A. Finally, the A-FABP proteins, in contrast to the I-FABP proteins, reveal significant heat capacity changes (DeltaCp) upon FA binding, and substitutions at residues Arg106 and Arg126 reduce the magnitude of DeltaCp.

Mutants of rat intestinal fatty acid-binding protein illustrate the critical role played by enthalpy-entropy compensation in ligand binding.

Site-specific variants of rat intestinal fatty acid-binding protein were constructed to identify the molecular interactions that are important for binding to fatty acids (FAs). Several variants displayed affinities that appeared incompatible with the crystal structure of the protein-FA complex. Thermodynamic measurements provided an explanation for these apparent inconsistencies and revealed that binding affinities often inaccurately reported changes in protein-FA interactions because changes in the binding entropy and enthalpy were usually compensatory. These results demonstrate that understanding the effects of amino acid replacements on ligand binding requires measurements of enthalpy and entropy, in addition to affinity.

Complement-inhibiting peptides identified by proximity to indels in the C3/4/5 protein family.

To find protein-protein interactive sites in complement component C3, we examined regions of C3 that are proximal to sites of length polymorphism or indels in the C345 protein family. We reasoned that indels probably mark protein interactive sites because they usually involve residues at protein surfaces. To test for the involvement of individual indels, we examined the effects on complement function of synthetic peptides corresponding to indel-proximal segments of C3. We inferred that if such a segment made direct contact with a C3 binding protein, then the corresponding peptide might also bind to that protein and inhibit binding to C3. Twenty-one peptides were tested; four of these inhibited complement-mediated erythrocyte lysis at < or =100 microM and complement-mediated killing of Escherichia coli at about threefold higher levels. These results indicate that the four peptides act as specific inhibitors of complement. They also suggest that indels can be effective guides for locating interactive sites in C3 and in any protein that is a member of a protein family. Because only a linear sequence is required, a focus on indels may be particularly useful for identifying interactive sites in proteins for which a three-dimensional structure is unavailable.

Complement component C5: engineering of a mutant that is specifically cleaved by the C4-specific C1s protease.

Previous studies showed that simply inserting or substituting a few amino acid residues immediately downstream of the proteolytic activation site in C component C3 renders that site susceptible to the C4-specific C1s protease. This report describes the results of extending those studies to the closely related component C5. We found that small changes, similar to those that made C3 susceptible to C1s, were insufficient to render C5 C1s-sensitive; and neither more extensive substitution downstream of the cleavage site with a 14 residue long segment from C4, nor upstream substitution with an 8 residue long C4 segment gave C1s cleavage. However, substitution of both the upstream and downstream segments gave a hybrid C5 protein, designated ASC4, which was cleaved by C1s. The protease sensitivity of ASC4 was curious, however, in that C1s was more active against the secreted extracellular biosynthetic precursor, pro-ASC4(E) than mature ASC4, whereas a C5-specific convertase cleaved the mature protein but not the precursor. In contrast, both mature and precursor forms of wild-type C5 were cleaved by the C5 convertase, but neither of course is recognized by C1s. These results demonstrate that a mutant C5 molecule can be constructed that is cleaved at the activation site by both C1s and C5 convertase. This suggests that the structures necessary for specific recognition by the two proteases have little or no overlap and that recognition by C5 convertase involves residues that are distant from the activation site itself.

Substrate specificities of the protease of mouse serum Ra-reactive factor.

Ra-reactive factor (RaRF) is a serum bactericidal factor whose function seems to be to activate C in a manner similar to that of C1, but with activation triggered by binding to bacterial polysaccharides instead of to immune complexes. It is composed of multiple polysaccharide-binding subunits associated with a novel serine protease, and its overall structural organization is similar to that of C1. This similarity extends to the serine protease component, which shares a similar modular construction and about 40% sequence identity with the C1r and C1s subcomponents of C1. In this study, we examined the substrate specificity of mouse RaRF by assaying its ability to cleave C components C3, C4, and C5, and its activity against the murine C4 isotype, sex-limited protein. Our results revealed that RaRF preferentially cleaves the C4 alpha-chain with specific activities 20- to 100-fold greater than either human or murine C1s, and that RaRF also cleaves the C3 alpha-chain, but with a lower efficiency than C4 alpha. We also found that RaRF is much less sensitive than C1s to mutations near the proteolytic site and that the two proteases show different reactivities against synthetic substrates. Hence, although the RaRF protease and C1s have similar structures and play similar roles in C activation, they also display clear differences in substrate range and in the details of their substrate recognition mechanisms. Finally, we found that RaRF does not cleave sex-limited protein even at a level 100-fold higher than necessary for C4 cleavage.

Substrate specificities of murine C1s.

An early step in the initiation of the classical C pathway is the proteolytic activation of component C4 by subcomponent C1-s. We have examined the substrate specificity of murine C1-s (mC1-s) by measuring its proteolytic activity on human and murine C4, and on the murine C4 isotype designated sex-limited protein (Slp). The latter substrate was examined because previous studies have demonstrated that Slp is not cleaved by C1-s, and hence Slp has been assumed to be nonfunctional in the C pathways. Those earlier studies used human, not murine, C1-s, however; a recent report has suggested that Slp is an essential component of a novel complement activation pathway and that the previous failure to observe cleavage of Slp is probably the result of a species incompatibility between Slp and the heterologous human C1-s (hC1-s). The present studies do not support this idea, as we found no evidence of cleavage of Slp by homologous murine C1-s even at enzyme concentrations 10-fold higher than that necessary for 50% cleavage of murine C4 (mC4). We did find a species-specific affect in the cleavage of mC4, where mC1-s is about 10-fold more effective than heterologous hC1-s in cleaving mC4, but mC1-s itself does not distinguish between human and murine C4, cleaving both equally well. Hence mC1-s does not exhibit the species specificity previously found for hC1-s, which shows a several hundred-fold preference for homologous human C4 over murine C4.