Effects of 2,4,6-trinitrotoluene in a holistic environmental exposure regime on a terrestrial salamander, Ambystoma tigrinum

2,4,6-Trinitrotoluene (TNT) is a defense-related environmental contaminant present at high concentrations in soil at some military installations. Tiger salamanders (Ambystoma tigrinum, family Ambystomatidae) were exposed to TNT in a soil matrix and fed earthworms that had also been exposed to TNT via contaminated soil. Such exposure was previously shown to result in significant accumulation of both TNT and TNT metabolites by salamanders. Following 14 days of combined oral and dermal exposures, salamanders were evaluated for signs of toxicity. Control and TNT-exposed salamanders gained weight (p < 0.025). In addition, organ to body weight ratios (kidney, liver, and spleen) were not affected by treatment. The function of splenic phagocytic cells was evaluated because these cells are sensitive to certain environmental chemical exposures. Neither the chemiluminescence response (H2O2 production) nor the phagocytic capacity of such cells were different between controls and treatment groups. In like manner, no changes were seen in the peripheral hematologic parameters investigated. Histopathologic evaluations were inconclusive, yet the liver revealed the presence of heavily pigmented iron-rich phagocytes (melanomacrophages). This investigation presents a realistic approach and preliminary data for investigating the effects of xenobiotic exposure in a soil matrix on a terrestrial vertebrate.

Environmental effects of radionuclides--observations on natural ecosystems

To better quantify risk to non-human species from exposure to environmental radioactivity, understanding of the behaviour of radionuclides in the biosphere needs to be increased. This study outlines current thinking on ecological risk assessment (ERA) methodology and applies the indicator species or critical groups approach to biota inhabiting a semi-natural coniferous woodland contaminated with the radionuclides 137Cs, 238Pu, 239+240Pu and 241Am. The majority of these radionuclides originate from routine aerial emissions from the nuclear fuel reprocessing plant at BNFL, Sellafield, Cumbria, UK. Radionuclide activity concentrations have been determined in biota from the woodland and estimates of absorbed dose rates (mGy d(-1)) have been calculated using the dosimetric models outlined. Dose rates to the key indicator species, Oniscus asellus, Carabus violaceous and Apodemus sylvaticus (detritivorous invertebrate, predatory invertebrate and the granivorous wood mouse) have been determined at 3.0 x 10(-3) mGy d(-1), 2.2 x 10(-3) mGy d(-1) and 1.0 x 10(-3) mGy d(-1) respectively. The values are at least three orders of magnitude lower than the 1 mGy d(-1) level below which no observable effects on populations in a terrestrial ecosystem are thought to occur. Limitations of this approach are discussed.

When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families

ATP is a ligand common to many proteins, yet it is unclear whether common recognition patterns do exist among the many different folds that bind ATP. Previously, it was shown that cAMP-dependent protein kinase, D-Ala:D-Ala ligase and the alpha-subunit of the alpha 2 beta 2 ribonucleotide reductase do share extensive common structural elements for ATP recognition although their folds are different. Here, we have made a survey of structures that bind ATP and compared them with the key features seen in these three proteins. Our survey shows that 12 different fold types share a specific recognition pattern for the adenine moiety, and 8 of these folds have a common structural framework for recognition of the AMP moiety of the ligand. The common framework consists of a tripeptide segment plus three additional residues, which provides similar polar and hydrophobic interactions between the protein and mononucleotide. Consensus interactions are represented by four key hydrogen bonds present in each fold type. Two of these four hydrogen bonds, together with three aliphatic residues, form a specific recognition pattern for the adenine moiety in all 12 folds. These similarities point to a structural-functional requirement shared by these different mononucleotide-binding proteins that represent at this time 28% of the adenine mononucleotide complexes found in the Brookhaven Protein Data Bank.

Local delivery of nadroparin via hydrogel-coated angioplasty balloon: effect on platelet deposition and smooth muscle cell proliferation--an experimental study

PURPOSE

To assess the feasibility of intravascular delivery of nadroparin, a low-molecular-weight heparin, via hydrogel-coated angioplasty balloons, and the effects of nadroparin delivered in this manner on platelet deposition and smooth muscle cell (SMC) proliferation.

MATERIALS AND METHODS

Tritiated nadroparin was used to determine the nadroparin-carrying capacity of the hydrogel-coating, kinetics of release from the balloons, and, in four pigs, delivery of the nadroparin to the iliac arterial wall. Platelet deposition in nadroparin-treated iliac arteries versus contralateral iliac arteries dilated with saline-loaded, hydrogel-coated balloons was quantified in seven pigs using 111Indium-labeled platelets. Smooth muscle cell proliferation in nadroparin and saline-treated iliac arteries in 10 pigs was evaluated 7 days after angioplasty with use of proliferating cell nuclear antigen.

RESULTS

Approximately 98 international units of nadroparin were delivered by the hydrogel-coated balloon, the majority to the angioplasty site and distal vessel. There was a trend toward decreased platelet deposition in nadroparin-treated arteries, but statistical significance was not achieved (P = .1563). Medial SMC proliferation was decreased in the nadroparin-treated arteries in nine of 10 pigs (P = .0137).

CONCLUSIONS

Hydrogel-coated balloons may be used to deliver nadroparin to the arterial wall, with measurable levels of the drug delivered to the site of angioplasty, and with resultant decrease in SMC proliferation.

Serious and fatal firearm injuries among children and adolescents in Alaska: 1991-1997

STUDY OBJECTIVE

To describe demographics, causal factors, intent, and incident locations of serious and fatal firearm injuries among children and adolescents in Alaska, for the years 1991 through 1997.

METHODS

Data from the Alaska Trauma Registry plus Vital Statistics death certificates were reviewed for a seven-year period (1991-1997). Data elements included are: intent (ICD 9-CM E-Codes and narratives); age group; region of incident; place of occurrence; alcohol or drug involvement; type of firearm used; and perpetrator.

RESULTS

During the seven-year study period, 222 children and adolescents ages 0-19 years were admitted to a hospital for a non-fatal firearm injury, plus 165 others received fatal firearm injuries. Of these 387 serious and fatal injuries, 34.9% (135) were determined to be unintentional, 36.4% (141) were suicides or suicide attempts, 23.3% (90) were homicide/assaults, 0.5% (2) were legal intervention, and for 4.9% (19) intent was unknown. Rates of serious and fatal firearm injuries per 100,000 youth for the six-year study period ranged from 14 in the Fairbanks North Star Borough and the Kenai Peninsula Borough to 105 in the Yukon-Kuskokwim Region. The statewide average for this period was 27.1 per 100,000 children and adolescents.

CONCLUSIONS

Firearm injuries are a leading cause of serious and fatal injuries to children and youth in Alaska. This study suggests that many children and adolescents in Alaska who were injured by firearms, or who caused injury to other children or youth by firearms, had easy access to them. Efforts should be made to convince adults not to let children or at risk teenagers have unsupervised access to firearms, and to promote safe storage of firearms.

Differential recognition of Toxoplasma gondii recombinant nucleoside triphosphate hydrolase isoforms by naturally infected human sera

Toxoplasma gondii possesses a highly active nucleoside triphosphate hydrolase, which has been shown to be an immunodominant antigen in mice and humans. Two isoforms (I and II) which exhibit different activities with respect to hydrolysis of ATP exist. Past studies suggest that all strains of T. gondii contain the less active nucleoside triphosphate hydrolase II, whilst only virulent strains contain the nucleoside triphosphate hydrolase I isoform. In order to further investigate the correlation between nucleoside triphosphate hydrolase isoform and biological significance, we cloned and expressed as glutathione S-transferase fusion proteins the full-length nucleoside triphosphate hydrolase I and II isoforms and two truncations of the nucleoside triphosphate hydrolase I isoform in Escherichia coli. We then used ELISAs with the full-length recombinant nucleoside triphosphate hydrolases as antigens to examine 188 naturally infected T. gondii-positive sera and 83 T. gondii-negative sera for antibody reactivity. All positive sera reacted to T. gondii whole tachyzoite lysate antigen, 31 sera reacted to both nucleoside triphosphate hydrolase isoforms, three sera reacted specifically to nucleoside triphosphate hydrolase I and two sera reacted to only nucleoside triphosphate hydrolase II. Immunoblot analysis of the five sera reacting to either nucleoside triphosphate hydrolase I or II revealed both quantitative and qualitative differences in reactivity to the two isoforms. Comparative immunoblot analysis using the truncations of the nucleoside triphosphate hydrolase I isoform, and one of these positive sera identified a presumptive differential epitope between the nucleoside triphosphate hydrolase I and II isoforms within an 81 amino acid region (amino acids 445-526) at the C-terminus of the nucleoside triphosphate hydrolase I isoform. This differential reactivity was further localised to the 12-residue region of greatest variability between the two isoforms (residues 488-499) using synthetic peptides. This is the first report where naturally infected human sera have been used to identify a differential epitope. Because this region is essential for substrate binding, an antibody response to this region may play some role in inhibition of this highly active enzyme.

Protein kinase C isoforms in pituitary cells displaying differential sensitivity to phorbol ester

Investigations with protein kinase C (PKC) isoform-specific antisera, revealed distinct profiles of PKC isoform content amongst pituitary tissues. Western analysis revealed the alpha, beta, delta, epsilon, zeta and theta isoforms of PKC are present in rat anterior and posterior pituitary tissue as well as in the GH3 somatomammotrophic cell line. AtT-20/D16-V corticotrophic and alphaT3-1 gonadotrophic murine cell lines contained no PKC-delta. The gamma or eta isoforms were undetected in any pituitary tissue. PKC activity measurements revealed Ca2+-independent PKCs in alphaT3-1 and GH3 cells which were more sensitive to activation by phorbol-dibutyrate (PDBu) than the corresponding PKC activity found in COS cells. However, Ca2+-dependent PKC activities were of similar sensitivity to PDBu in GH5, alphaT3-1 and COS cells, indicating that functional differences observed in PDBu-sensitivity in these cells may be due to differential activation of Ca2+-independent PKC isoforms. Moreover, substrate-specificity of these PKCs were also compared indicating that the amount of Ca2+-dependency of the observed PKC activity from the same pituitary tissue is dependent upon the substrate utilized by the PKC isotypes present. These findings explain differential sensitivities of PKC-mediated actions that have previously been observed in a range of pituitary cells.

Aerotaxis and other energy-sensing behavior in bacteria

Energy taxis is widespread in motile bacteria and in some species is the only known behavioral response. The bacteria monitor their cellular energy levels and respond to a decrease in energy by swimming to a microenvironment that reenergizes the cells. This is in contrast to classical Escherichia coli chemotaxis in which sensing of stimuli is independent of cellular metabolism. Energy taxis encompasses aerotaxis (taxis to oxygen), phototaxis, redox taxis, taxis to alternative electron acceptors, and chemotaxis to a carbon source. All of these responses share a common signal transduction pathway. An environmental stimulus, such as oxygen concentration or light intensity, modulates the flow of reducing equivalents through the electron transport system. A transducer senses the change in electron transport, or possibly a related parameter such as proton motive force, and initiates a signal that alters the direction of swimming. The Aer and Tsr proteins in E. coli are newly recognized transducers for energy taxis. Aer is homologous to E. coli chemoreceptors but unique in having a PAS domain and a flavin-adenine dinucleotide cofactor that is postulated to interact with a component of the electron transport system. PAS domains are energy-sensing modules that are found in proteins from archaea to humans. Tsr, the serine chemoreceptor, is an independent transducer for energy taxis, but its sensory mechanism is unknown. Energy taxis has a significant ecological role in vertical stratification of microorganisms in microbial mats and water columns. It plays a central role in the behavior of magnetotactic bacteria and also appears to be important in plant-microbe interactions.

"RKKH" peptides from the snake venom metalloproteinase of Bothrops jararaca bind near the metal ion-dependent adhesion site of the human integrin alpha(2) I-domain

Integrin alpha(1)beta(1) and alpha(2)beta(1) are the major cellular receptors for collagen, and collagens bind to these integrins at the inserted I-domain in their alpha subunit. We have previously shown that a cyclic peptide derived from the metalloproteinase domain of the snake venom protein jararhagin blocks the collagen-binding function of the alpha(2) I-domain. Here, we have optimized the structure of the peptide and identified the site where the peptide binds to the alpha(2) I-domain. The peptide sequence Arg-Lys-Lys-His is critical for recognition by the I-domain, and five negatively charged residues surrounding the "metal ion-dependent adhesion site" (MIDAS) of the I-domain, when mutated, show significantly impaired binding of the peptide. Removal of helix alphaC, located along one side of the MIDAS and suggested to be involved in collagen-binding in these I-domains, does not affect peptide binding. This study supports the notion that the metalloproteinase initially binds to the alpha(2) I-domain at a location distant from the active site of the protease, thus blocking collagen binding to the adhesion molecule in the vicinity of the MIDAS, while at the same time leaving the active site free to degrade nearby proteins, the closest being the beta(1) subunit of the alpha(2)beta(1) cell-surface integrin itself.

Physician use of diagnostic codes for child and adult abuse

OBJECTIVE

To report on physician use of diagnostic codes for child and adult abuse according to national medical care utilization data.

METHODS

Secondary data analysis was performed on the National Ambulatory Medical Care Survey (NAMCS) of office-based physician visits and the National Hospital Ambulatory Medical Care Survey (NHAMCS) of visits to hospital emergency and outpatient departments for 1993 to 1996. Both databases describe physician, patient, and visit characteristics, and variables include up to three diagnoses per visit.

RESULTS

Only 93 diagnoses of child or adult abuse were coded for 351,359 patient visits during the four years. As we would expect, child abuse was diagnosed more often than adult abuse (67 v 26), and the majority of cases (n = 57) were visits to emergency departments.

CONCLUSION

Diagnostic codes for abuse are not often used. Because these codes represent an important tool for reporting the prevalence and incidence of abuse, such documentation could lead to greater support for health care policies and resource allocation for victims of abuse. Lack of awareness about the diagnostic codes for abuse may be one explanation for underuse, but other barriers are also discussed.

Radionuclide behaviour and transport in a coniferous woodland ecosystem: vegetation, invertebrates and wood mice, Apodemus sylvaticus

Activity concentrations of radionuclides (134Cs, 137Cs, 238Pu, 239 + 240Pu and 241Am) were measured in vegetation, invertebrates and wood mice, Apodemus sylvaticus, collected in Lady Wood, a coniferous woodland in the vicinity of the British Nuclear Fuels reprocessing plant at Sellafield, Cumbria, UK. Vegetation was of low diversity and biomass with activity concentrations ranging from 1 to 5 Bq kg-1 (134Cs), 0.3-0.5 Bq kg-1 (238Pu), 0.8-8 Bq kg-1 (239 + 240Pu), and 0.6-16 Bq kg-1 (241Am), dry wt. Caesium-137 activity concentrations were high compared to the reference site in Cheshire, varying between 65 and 280 Bq kg-1. Marked inter-specific and temporal differences in radionuclide activity concentrations were recorded for invertebrate populations. Caesium-137, 238Pu, 239 + 240Pu and 241Am activity concentrations in detritivorous invertebrates were consistently higher than in all other invertebrate groups reflecting contamination of the leaf litter. The activity concentrations in detritivores increased during the autumn and winter, reflecting changes in diet as food sources varied throughout the year. Activity concentrations in invertebrates caught in Lady Wood were generally an order of magnitude higher than for the reference site. Activity concentrations in wood mice varied between 7 and 150 Bq kg-1 (137Cs), 0.1-0.3 Bq kg-1 (238Pu), 0.1-0.6 Bq kg-1 (239 + 240Pu) and 0.2-0.4 Bq kg-1 (241Am). There were clear differences in the activity concentration of 137Cs (P < 0.01), 239 + 240Pu (P < 0.05) and 241Am (P < 0.05) in animals caught in Lady Wood compared to the reference site. However, the activity concentrations for 238Pu were similar at both sites, reflecting a low gastrointestinal transfer. Seasonal variation in activity concentrations was observed for 137Cs, 238Pu and 241Am. This variation is attributed to changes in the age structure of the population and diet throughout the year.

Tunneled jugular small-bore central catheters as an alternative to peripherally inserted central catheters for intermediate-term venous access in patients with hemodialysis and chronic renal insufficiency

In 34 patients with chronic renal insufficiency or failure, 43 small-bore central catheters were placed via the internal or external jugular veins: right internal jugular vein, 28; left internal jugular vein, 14; right external jugular vein, one. Central venous access was achieved in all patients (mean catheter dwell time, 28 days; range, 3-99 days), with two minor complications (arterial puncture and catheter damage during suturing). Tunneled jugular small-bore central catheters are a vein-preserving alternative to peripherally inserted central catheters in this population.

Hemodialysis graft: use as access for upper and lower extremity arteriography and interventional procedures--initial experience

Functioning hemodialysis grafts were used as access sites for peripheral vascular arteriography and interventional procedures. In 11 patients with end-stage renal disease and ischemia, upper extremity (n = 8) or lower extremity (n = 3) arteriography was performed successfully. Angioplasty and other interventional procedures were performed via the same route in two of the patients. No bleeding complications occurred, and all patients were ambulatory immediately after the procedure.

Three-dimensional models of alpha(2A)-adrenergic receptor complexes provide a structural explanation for ligand binding

We have compared bacteriorhodopsin-based (alpha(2A)-AR(BR)) and rhodopsin-based (alpha(2A)-AR(R)) models of the human alpha(2A)-adrenengic receptor (alpha(2A)-AR) using both docking simulations and experimental receptor alkylation studies with chloroethylclonidine and 2-aminoethyl methanethiosulfonate hydrobromide. The results indicate that the alpha(2A)-AR(R) model provides a better explanation for ligand binding than does our alpha(2A)-AR(BR) model. Thus, we have made an extensive analysis of ligand binding to alpha(2A)-AR(R) and engineered mutant receptors using clonidine, para-aminoclonidine, oxymetazoline, 5-bromo-N-(4, 5-dihydro-1H-imidazol-2-yl)-6-quinoxalinamine (UK14,304), and norepinephrine as ligands. The representative docked ligand conformation was chosen using extensive docking simulations coupled with the identification of favorable interaction sites for chemical groups in the receptor. These ligand-protein complex studies provide a rational explanation at the atomic level for the experimentally observed binding affinities of each of these ligands to the alpha(2A)-adrenergic receptor.

Chloroethylclonidine and 2-aminoethyl methanethiosulfonate recognize two different conformations of the human alpha(2A)-adrenergic receptor

The substituted cysteine-accessibility method and two sulfhydryl-specific reagents, the methane-thiosulfonate derivative 2-aminoethyl methanethiosulfonate (MTSEA) and the alpha(2)-adrenergic receptor (alpha(2)-AR) agonist chloroethylclonidine (CEC), were used to determine the relative accessibility of engineered cysteines in the fifth transmembrane domain of the human alpha(2A)-AR (Halpha2A). The second-order rate constants for the reaction of the receptor with MTSEA and CEC were determined with the wild type Halpha2A (cysteine at position 201) and receptor mutants containing accessible cysteines at other positions within the binding-site crevice (positions 197, 200, and 204). The rate of reaction of CEC was similar to that of MTSEA at residues Cys-197, Cys-201, and Cys-204. The rate of reaction of CEC with Cys-200, however, was more than 5 times that of MTSEA, suggesting that these compounds may interact with two different receptor conformations. MTSEA, having no recognition specificity for the receptor, likely reacts with the predominant inactive receptor conformation (R), whereas the agonist CEC may stabilize and react preferentially with the active receptor conformation (R*). This hypothesis was consistent with three-dimensional receptor-ligand models, which further suggest that alpha(2A)-AR activation may involve the clockwise rotation of transmembrane domain 5.

Production, crystallization and preliminary X-ray analysis of the human integrin alpha1 I domain

Integrin alpha1beta1 is one of the main collagen receptors in many cell types. A fast large-scale production, purification and crystallization method for the integrin alpha1 I domain is reported here. The alpha1 I domain was crystallized using the vapour-diffusion method with a reservoir solution containing a mixture of PEG 4000, sodium acetate, glycerol and Tris-HCl buffer. The crystals belong to the C2 space group, with unit-cell parameters a = 74.5, b = 81.9, c = 37.3 A, alpha = gamma = 90.0, beta = 90.8 degrees. The crystals diffract to 2.0 A and a 94.2% complete data set to 2.2 A has been collected from a single crystal with an Rmerge of 5.8%.

A dimeric ternary complex of FGFR [correction of FGFR1], heparin and FGF-1 leads to an 'electrostatic sandwich' model for heparin binding

BACKGROUND

Fibroblastic growth factors (FGFs) are a family of cytokines involved in regulation of cell growth, differentiation and chemotaxis in a variety of tissue types. High-affinity FGF receptors (FGFRs) are transmembrane proteins that consist of three extracellular immunoglobulin-like domains, a transmembrane helix and an intracellular protein tyrosine kinase signalling domain. FGFRs are activated through ligand-dependent dimerization that allows trans-autophosphorylation of the tyrosine kinase domains. Heparin or heparin-like molecules, such as heparan sulphate proteoglycans, bind to both FGFs and FGFRs and are required for FGF signal transduction. At present no structure of the ternary complex for FGFR, FGF and heparin exists.

RESULTS

We have used the type-1 interleukin-1 receptor-interleukin-1 beta complex crystal structure, in which both the ligand and the receptor are homologous to those of the FGF-FGFR pair, to identify potential interactions in the FGFR-heparin-FGF ternary complex. A key feature of the modelled complex is the 'electrostatic sandwich' that is formed between the positively charged surfaces of FGF and the receptor, with the negatively charged heparin captured in between. The ternary complex places limits on the range of likely modes of receptor dimerization: one of five different dimeric receptor complexes built from the ternary complex correlates best with the experimental data.

CONCLUSIONS

The ternary complex of FGFR, FGF and heparin, derived on the basis of the homologous interleukin-1 receptor complex, is in agreement with much of the published experimental data, as is the dimeric receptor complex (FGFR-heparin-FGF)2. This work suggests that the FGF interactions seen in crystal structures, which have previously been used to predict the mode of FGF dimerization, might not be relevant to the biologically active dimeric FGFR-heparin-FGF complex.

Scavenger receptor class B type I in the rat ovary: possible role in high density lipoprotein cholesterol uptake and in the recognition of apoptotic granulosa cells

Scavenger receptor class B type I (SR-BI) mediates the selective uptake of high density lipoprotein cholesterol. SR-BI is expressed at high levels in the ovary, indicating that it plays a role in the delivery of cholesterol as substrate for steroid hormone production. However, SR-BI also binds anionic phospholipids with high affinity and could therefore be involved in the recognition of apoptotic cells. In this study we have characterized the expression of SR-BI in rat ovarian follicles undergoing atresia. Atretic follicles with cells undergoing apoptosis were identified by in situ DNA end labeling, and SR-BI expression was determined by in situ hybridization and immunohistochemistry. SR-BI was expressed in thecal cells at all stages of follicular development, including atretic follicles, and in corpus luteum. Isolated apoptotic granulosa cells (but not viable granulosa cells) bound annexin V, indicating that they display anionic phospholipids on the cell surface. Transfection of COS-7 cells with an expression vector carrying the rat SR-BI complementary DNA resulted in increased binding to apoptotic granulosa cells (46 +/- 2% of the SR-BI-expressing cells bound at least one granulosa cell compared with 24 +/- 3% for the mock-transfected cells; P < 0.0001), whereas the binding to viable granulosa cells was unchanged. Apoptotic granulosa cells also bound to isolated thecal shells. We conclude that thecal cells of both nonatretic and atretic follicles express SR-BI. The location of SR-BI expression in the ovary supports a role of this receptor in the uptake of high density lipoprotein cholesterol. In addition, our data suggest that SR-BI mediates the recognition of apoptotic granulosa cells by the surrounding thecal cells and that it therefore may play a role in the remodeling of atretic follicles to secondary interstitial cells.

Technique for construction of an in vivo model of simulated pulmonary metastases

RATIONALE AND OBJECTIVES

Existing methods used to simulate pulmonary metastases are unsatisfactory. The aim of this study was to create a simple in vivo model of pulmonary metastases by endobronchial deployment of small high-density beads in anesthetized dogs.

METHODS

Commercially available decorative beads measuring 2 and 4 mm in diameter and of high density (600 to 1200 Hounsfield units) were deployed in the peripheral airways of anesthetized dogs using catheter and guide wire manipulations through an endotracheal tube.

RESULTS

A total of 65 beads were placed in five dogs. Computed tomography demonstrated that 41 (63%) were satisfactorily located in the lung periphery, 9 (14%) were unsatisfactorily located in large airways, and 15 (23%) were not visible.

CONCLUSIONS

The endobronchial deployment of small high-density beads in the peripheral airways of anesthetized dogs is a novel and effective technique for creation of an in vivo model of pulmonary metastases.

Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes

A detailed comparison of the structures of aspartate aminotransferase, alanine race-mase, the beta subunit of tryptophan synthase, D-amino acid aminotransferase and glycogen phosphorylase has revealed more extensive structural similarities among pyridoxal phosphate (PLP)-binding domains in these enzymes than was observed previously. These similarities consist of seven common structural segments of the polypeptide chain, which form an extensive common structural organization of the backbone chain responsible for the appropriate disposition of key residues, some from the aligned fragments and some from variable loops joined to these fragments, interacting with PLPs in these enzymes. This common structural organization contains an analogous hydrophobic minicore formed from four amino acid side chains present in the two most conserved structural elements. In addition, equivalent alpha-beta-alpha-beta supersecondary structures are formed by these seven fragments in three of the five structures: alanine racemase, tryptophan synthase and glycogen phosphorylase. Despite these similarities, it is generally accepted that these proteins do not share a common heritage, but have arisen on five separate occasions. The common and contiguous alpha-beta-alpha-beta structure accounts for only 28 residues and all five enzymes differ greatly in both the orientation of the PLP pyridoxal rings and their contacts with residues close to the common structural elements.

Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm

We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.

A peptide inhibiting the collagen binding function of integrin alpha2I domain

Integrin alpha2 subunit forms in the complex with the beta1 subunit a cell surface receptor binding extracellular matrix molecules, such as collagens and laminin-1. It is a receptor for echovirus-1, as well. Ligands are recognized by the special "inserted" domain (I domain) in the integrin alpha2 subunit. Venom from a pit viper, Bothrops jararaca, has been shown to inhibit the interaction of platelet alpha2beta1 integrin with collagen because of the action of a disintegrin/metalloproteinase named jararhagin. The finding that crude B. jararaca venom could prevent the binding of human recombinant ralpha2I domain to type I collagen led us to study jararhagin further. Synthetic peptides representing hydrophilic and charged sequences of jararhagin, including the RSECD sequence replacing the well known RGD motif in the disintegrin-like domain, were synthesized. Although the disintegrin-like domain derived peptides failed to inhibit ralpha2I domain binding to collagen, a basic peptide from the metalloproteinase domain proved to be functional. In an in vitro assay, the cyclic peptide, CTRKKHDNAQC, was shown to bind strongly to human recombinant alpha2I domain and to prevent its binding to type I and IV collagens and to laminin-1. Mutational analysis indicated that a sequence of three amino acids, arginine-lysine-lysine (RKK), is essential for ralpha2I domain binding, whereas the mutation of the other amino acids in the peptide had little if any effect on its binding function. Importantly, the peptide was functional only in the cyclic conformation and its affinity was strictly dependent on the size of the cysteine-constrained loop. Furthermore, the peptide could not bind to alpha2I domain in the absence of Mg2+, suggesting that the conformation of the I domain was critical, as well. Cells could attach to the peptide only if they expressed alpha2beta1 integrin, and the attachment was inhibited by anti-integrin antibodies.

Structural model of the catalytic domain of an enzyme with cell adhesion activity: human vascular adhesion protein-1 (HVAP-1) D4 domain is an amine oxidase

Human vascular adhesion protein-1 (HVAP-1) is a multifunctional protein having at least two different cellular roles, functioning both as a lymphocyte-endothelial cell adhesion protein and as an enzyme with monoamine oxidase activity. HVAP-1 is a 180 kDa homodimeric glycoprotein consisting of a membrane-spanning domain and three predicted extracellular copper-containing amine oxidase domains. In HVAP-1 the extracellular domains are composed of a large domain D4, containing the active site and forming the interface of the dimer, while the smaller D2 and D3 domains surround the D4 dimer near the entrance to the active site. The structural model of the catalytic D4 domain of HVAP-1 reveals that all components necessary for enzymatic monoamine oxidase activity are indeed present within the HVAP-1 and pinpoints residues that may be key to substrate entry through a channel to the active site and residues likely to be involved in substrate specificity as well as structural features critical to dimer formation. Proper glycosylation is required for the cell adhesion function of HVAP-1 and the predicted location of the sugar units at the solvent-exposed surface suits this function well.