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Biomedical subjects

B F Edwards

Publications and source records attributed to B F Edwards.

At least 19 recordsLinked to original sources
PubMed2001

Critical wavelength for river meandering.

A fully nonlinear modal analysis identifies a critical centerline wave number q(c) for river meandering that separates long-wavelength bends, which grow to cutoff, from short-wavelength bends, which decay. Exact, numerical, and approximate analytical results for q(c) rely on the Ikeda, Parker, and Sawai [J. Fluid Mech. 112, 363 (1981)] model, supplemented by dynamical equations that govern the river migration and length. Predictions also include upvalley bend migration at long times and a peak in lateral migration rates at intermediate times. Experimental tests are suggested.

Journal Article↗
PubMed2001

Postoperative renal insufficiency.

The poor clinical outcomes associated with postoperative HARI necessitate increased vigilance for HARI detection and intervention to minimize the progression to dialysis dependency. Patient survival significantly worsens if HARI requires the initiation of dialysis. Postoperative changes, including intravascular volume expansion, SIRS, and reduced lean body mass, frequently confound the detection of HARI. Serum creatinine levels frequently do not reflect the decreased renal function because creatinine production rate is decreased with reduced lean body mass, and the serum creatinine concentration is reduced by increased intravascular volume expansion and increased volume of distribution associated with anasarca. Additional indices of renal function must be used postoperatively, including urine output, net volume status, urinalysis with microscopic examination of the spun pellet, and corrected estimations of creatinine clearance. Few therapeutic interventions currently exist to reverse HARI other than optimization of renal perfusion and limitation of nephrotoxin exposure. Dialysis remains a cornerstone of maintenance therapy for refractory and severe HARI. Selection of dialysis modality continues to be based on modality availability and patient stability.

Blood Volume↗
PubMed2001

Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme.

BACKGROUND: In Escherichia coli bearing the plasmid R773, resistance to arsenite, arsenate, antimonite, and tellurite is conferred by the arsRDABC plasmid operon that codes for an ATP-dependent anion pump. The product of the arsC gene, arsenate reductase (ArsC), is required to efficiently catalyze the reduction of arsenate to arsenite prior to extrusion. RESULTS: Here, we report the first X-ray crystal structures of ArsC at 1.65 A and of ArsC complexed with arsenate and arsenite at 1.26 A resolution. The overall fold is unique. The native structure shows sulfate and sulfite ions binding in the active site as analogs of arsenate and arsenite. The covalent adduct of arsenate with Cys-12 in the active site of ArsC, which was analyzed in a difference map, shows tetrahedral geometry with a sulfur-arsenic distance of 2.18 A. However, the corresponding adduct with arsenite binds as a hitherto unseen thiarsahydroxy adduct. Finally, the number of bound waters (385) in this highly ordered crystal structure approaches twice the number expected at this resolution for a structure of 138 ordered residues. CONCLUSIONS: Structural information from the adduct of ArsC with its substrate (arsenate) and with its product (arsenite) together with functional information from mutational and biochemical studies on ArsC suggest a plausible mechanism for the reaction. The exceptionally well-defined water structure indicates that this crystal system has precise long-range order within the crystal and that the upper limit for the number of bound waters in crystal structures is underestimated by the structures in the Protein Data Bank.

Arsenates↗
PubMed1999

Topographic distribution of bcl-2 protein in feline tissues in health and neoplasia.

The bcl-2 family of genes encodes proteins that influence apoptosis. In the present immunohistochemical study, the topographic distribution of bcl-2 protein was examined in healthy feline fetal, neonatal, and adult tissues, a feline renal cell line, and feline tumors obtained from a veterinary hospital. The topographic distribution of bcl-2 in healthy tissues was similar to that described in human tissues. In lymphoid tissues, follicular mantle cells strongly expressed bcl-2. In complex and differentiating epithelium, bcl-2 expression was detected in stem cell and proliferation zones. Bcl-2 expression was also detected in lower crypts of the intestine and in skin basal layers. The feline Crandell kidney cells expressed bcl-2 diffusely throughout the cytoplasm. Of 180 tumors examined, bcl-2 was expressed almost uniformly in cutaneous basal cell tumors, thyroid adenomas, and mammary carcinomas and in 50% of the lymphomas examined. Bcl-2 may play a role in blocking apoptotic cell death in a broad range of normal feline tissues, whereas dysregulated bcl-2 may extend the life of certain tumors or render certain tumors resistant to therapy because most chemotherapeutic and radiotherapeutic agents eliminate tumor cells by triggering apoptosis.

Animals↗
PubMed1999

Crotalase, a fibrinogen-clotting snake venom enzyme: primary structure and evidence for a fibrinogen recognition exosite different from thrombin.

Crotalase, a fibrinogen-clotting enzyme isolated from the venom of Crotalus adamanteus, and its overlapping fragments were subjected to Edman degradation. The resulting amino acid sequence [see text] characteristic of a serine proteinase. Comparison with thrombin, the physiological fibrinogen-clotting enzyme, showed that thrombin's fibrinogen-recognition exosite (FRE) is poorly represented in crotalase. Hirudin, a FRE-dependent inhibitor, had no effect on crotalase. Spatial modeling of crotalase yielded a possible alternative fibrinogen-recognition site comprised of Arg 60F, Lys 85, Lys 87, and Arg 107 (underlined in the sequence above). Crotalase also lacks thrombin's YPPW loop, as well as its functionally important ETW 146-148, and its heparin-binding site. The enzyme contains a single asparagine-linked glycosylation site, NFT, bearing neutral and amino sugars that account for 8.3% of the enzyme's total molecular weight of 29,027. The calculated absorbance of crotalase at 280 nm, 1%, cm(-1) is 15.2.

Amino Acid Sequence↗
PubMed1999

Preclinical study in cats of the pro-photosensitizer 5-aminolevulinic acid.

OBJECTIVE: To determine whether feline cells were able to convert 5-aminolevulinic acid (ALA) to protoporphyrin IX (PpIX) in vivo and in vitro, whether i.v. administration of ALA to healthy cats resulted in adverse effects, and whether PpIX accumulated in a squamous cell carcinoma (SCC) of a cat. ANIMALS: 4 healthy adult cats and 1 adult cat with a cutaneous SCC. PROCEDURE: In vitro production of PpIX was determined by incubating Crandell feline kidney cells with ALA. Effects of ALA administration and in vivo production of PpIX were determined by administering ALA (100, 200, or 400 mg/kg of body weight) to healthy cats and collecting skin biopsy specimens for up to 24 hours after drug administration. Blood samples were collected for CBC and serum biochemical analyses, and necropsies were performed. Accumulation of PpIX in a SCC was determined by treating a cat with a facial SCC with ALA and collecting specimens of the tumor and adjacent grossly normal skin. RESULTS: Incubation of ALA with feline cells resulted in time- and dose-dependent cytoplasmic accumulation of PpIX in vitro. After i.v. ALA administration, PpIX was detected in all tissues examined, with the highest fluorescence intensity in epithelia and in squamous cell carcinoma. The tumor-to-skin fluorescence intensity ratio was 5. All cats developed hepatotoxicoses. CONCLUSIONS AND CLINICAL RELEVANCE: Results from this limited number of cats suggest that ALA may be a useful photosensitizer in cats, but that doses > 100 mg/kg, i.v., may not be safe.

Aminolevulinic Acid↗
PubMed1998

Templates for design of inhibitors for serine proteases: application of the program DOCK to the discovery of novel inhibitors for thrombin.

The program DOCK was used to search for novel inhibitors for alpha-thrombin. Four among the top twelve best scoring compounds from the Cambridge Structural Data Base inhibited this enzyme, and three of them inhibited alpha-thrombin in a competitive mode. These molecules are expected to serve as general templates for structural elaboration in targeting diverse serine proteases for selective inhibition.

Binding Sites↗
PubMed1997

New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK.

BACKGROUND: The conversion of prothrombin to thrombin by factor Xa is the penultimate step in the blood clotting cascade. In vivo, where the conversion occurs primarily on activated platelets in association with factor Va and Ca2+ ions, meizothrombin is the major intermediate of the two step reaction. Meizothrombin rapidly loses the fragment 1 domain (F1) by autolysis to become meizothrombin des F1 (mzTBN-F1). The physiological properties of mzTBN-F1 differ dramatically from those of thrombin due to the presence of prothrombin fragment 2 (F2), which remains covalently attached to the activated thrombin domain in mzTBN-F1. RESULTS: The crystal structure of mzTBN-F1 has been determined at 3.1 A resolution by molecular replacement, using only the thrombin domain, and refined to R and Rfree values of 0.205 and 0.242, respectively. The protease active site was inhibited with D-Phe-Pro-Arg-chloromethylketone (PPACK) to reduce autolysis. The mobile linker chain connecting the so-called kringle and thrombin domains and the first two N-acetylglucosamine residues attached to the latter were seen in electron-density maps improved with the program SQUASH. Previously these regions had only been modeled. CONCLUSIONS: The F2 kringle domain in mzTBN-F1 is bound to the electropositive heparin-binding site on thrombin in an orientation that is systematically shifted and has significantly more interdomain contacts compared to a noncovalent complex of free F2 and free thrombin. F2 in mzTBN-F1 forms novel hydrogen bonds to the carbohydrate chain of thrombin and perhaps stabilizes a unique, rigid conformation of the gamma-autolysis loop through non-local effects. The F2 linker chain, which does not interfere with the active site or fibrinogen-recognition site, is arranged so that the two sites cleaved by factor Xa are separated by 36 A. The two mzTBN-F1 molecules in the asymmetric unit share a tight 'dimer' contact in which the active site of one molecule is partially blocked by the F2 kringle domain of its partner. This interaction suggests a new model for prothrombin organization.

Acetylglucosamine↗
PubMed1997

Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16.

A peptide containing residues 1-50 of the Aalpha-chain of fibrinogen, expressed as a fusion peptide with beta-galactosidase, is rapidly cleaved by thrombin at Arg-16, similarly to whole fibrinogen. When Phe-8, which is highly conserved, is replaced with tyrosine (F8Y), the cleavage is slowed drastically [Lord, Byrd, Hede, Wei and Colby (1990) J. Biol. Chem. 265, 838-843]. To examine the structural basis for this result, we have determined the crystal structure of bovine thrombin complexed with a synthetic peptide containing residues 1-23 of fibrinogen Aalpha and the F8Y mutation. The crystals are in space group P43212, with unit-cell dimensions of a = 88.3 A (1 A = 0.1 nm), c = 195.5 A and two complexes in the asymmetric unit. The final R factor is 0.183 for 2sigma data from 7.0 to 2.5 A resolution. There is continuous density for the five residues in the P3, P2, P1, P1' and P2' positions of the peptide (Gly-14f to Pro-18f) at the active site of thrombin, and isolated but well-defined density for Tyr-8f at position P9 in the hydrophobic pocket of thrombin. The tyrosine residue is shifted relative to phenylalanine in the native peptide because the phenol side chain is larger and makes a novel, intrapeptide hydrogen bond with Gly-14f. Adjacent peptide residues cannot form the hydrogen bonds that stabilize the secondary structure of the native peptide. Consequently, the 'reaction'geometry at the scissile bond, eight residues from the mutation, is perturbed and the peptide is mostly uncleaved in the crystal structure.

Animals↗
PubMed1997

The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence.

alpha-Chemokines comprise a family of cytokines that are chemotactic for neutrophils and have a structure similar to platelet factor 4 (PF4), in which the first two cysteine residues are separated by one residue (Cys-X-Cys). The two alpha-chemokines, connective tissue activating peptide-III (CTAP-III) and neutrophil activating peptide-2 (NAP-2), are carboxyl-terminal fragments of platelet basic protein (PBP) that are generated by monocyte-derived proteases. NAP-2 strongly stimulates neutrophils that are present during inflammation whereas its precursors, PBP and CTAP-III, are inactive, although they also possess the highly conserved, amino-terminal sequence, Glu-Leu-Arg (ELR), that is critical for receptor binding. To resolve this conundrum, we have determined the crystal structure of recombinant Asp-CTAP, which has ten fewer amino-terminal residues than CTAP-III but five more than NAP-2. The space group is P2(1)with unit cell dimensions a = 43.8 A, b = 76.8 A, c = 43.8 A, and beta =97.0 degrees, and a tetramer in the asymmetric unit. The molecular replacement method, with the NAP-2 tetramer as a starting model, was used to determine the initial phase information. The final R-factor is 0.196 (Rfree = 0.251) for 2sigma data from 7.0 to 1.75 A resolution. This high-resolution model of Asp-CTAP is the longest defined structure of an alpha-chemokine to date. The electron density map shows an over-all structure for Asp-CTAP that is very similar to that of NAP-2, but with the additional five amino-terminal residues folding back through a type-II turn, thereby stabilizing the oligomeric "inactive" state, and masking the critical ELR receptor binding region that is exposed in the structure of NAP-2.

Amino Acid Sequence↗
PubMed1997

Crystal structure of a class I ubiquitin conjugating enzyme (Ubc7) from Saccharomyces cerevisiae at 2.9 angstroms resolution.

Ubiquitin-conjugating enzymes are a family of related proteins that participate in the ubiquitination of proteins. Previous studies on the crystal structures of Saccharomyces cerevisiae Ubc4 and Arabidopsis thaliana Ubc1 indicated that the smallest enzymes (class I), which consist entirely of the conserved core domain, share a common tertiary fold. Here we report the three-dimensional structure of the S. cerevisiae class I enzyme encoded by the UBC7 gene. The crystal structure has been solved using molecular replacement techniques and refined by simulated annealing to an R-factor of 0.183 at 2.93 A resolution. Bond lengths and angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 2.3 degrees, respectively. Ubc7 is an alpha/beta protein with four alpha-helices and a four-stranded antiparallel beta-sheet. With the exception of two regions where extra residues are present, the tertiary folding of Ubc7 is similar to those of the other two enzymes. The ubiquitin-accepting cysteine is located in a cleft between two loops. One of these loops is nonconserved, as this region of the Ubc7 molecule differs from the other two enzymes by having 13 extra residues. There is also a second single amino acid insertion that alters the orientation of the turn between the first two beta-strands. Analysis of the 13 ubiquitin-conjugating enzyme sequences in S. cerevisiae indicates that there may be two other regions where extra residues could be inserted into the common tertiary fold. Both of these other regions exhibit significant deviations in the superposition of the three structures and, like the two insertion regions in Ubc7, may represent hypervariable regions within a common tertiary fold. As ubiquitin-conjugating enzymes interact with different substrates or other accessory proteins in the ubiquitination pathway, these variable surface regions may confer distinct specificity to individual enzymes.

Amino Acid Sequence↗
PubMed1997

Photodynamic therapy of facial squamous cell carcinoma in cats using a new photosensitizer.

BACKGROUND AND OBJECTIVE: Photodynamic therapy has been shown to be an effective treatment modality for surface-oriented neoplasms of the skin, respiratory, gastrointestinal, and urogenital systems. The purpose of this study was to assess the safety and efficacy of photodynamic therapy using a new photosensitizer in the treatment of squamous cell carcinomas of the feline facial skin. STUDY DESIGN/MATERIALS AND METHODS: Cats with naturally occurring squamous cell carcinomas of the facial skin were entered into the study. Tumors were staged using a modification of the World Health Organization (WHO) system for classification of feline tumors of epidermal origin. Photodynamic therapy was delivered to the tumors using an argon-pumped dye laser 24 hours after the administration of the photosensitizer pyropheophorbide-alpha-hexyl-ether (HPPH-23). Following treatment, tumors were evaluated for complete response rates and local control durations. RESULTS: Fifteen tumors were staged T1a (< 1.5 cm diameter, noninvasive), 18 T1b (< 1.5 cm, invasive), and 28 T2B (> 1.5 cm, invasive). Complete response rates as well as local control durations were significantly (P < 0.05) related to stage. Complete response was achieved in 100% of T1a tumors, 56% of T1b tumors, and 18% of T2b tumors. One-year local control rates were 100% for T1a tumors and 53% for T1b tumors; overall 1-year local control rate for all treated tumors was 62%. Clinical, hematological, and biochemical evidence of toxicity was not seen in any cat following drug administration. However, morbidity was observed following treatment of large, invasive tumors of the nasal plane. CONCLUSION: Photodynamic therapy with the photosensitizer HPPH-23 was safe and effective in treating early stage squamous cell carcinomas of the feline nasal plane and facial skin. However, toxicity was encountered following treatment of large neoplasms.

Animals↗
PubMed1997

The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding.

Unliganded bovine alpha-thrombin and prethrombin-2 have been co-crystallized, in space group P21212, using either ammonium sulfate or polyethylene glycol 2000 (PEG2K), and their structures determined at 2.2 A and 2.3 A, respectively. Initial phases were determined by molecular replacement and refined using XPLOR to final R factors of 0.187 (Rfree = 0.255) and 0.190 (Rfree = 0.282) for the salt and PEG2K models, respectively. The apo-enzyme form of bovine alpha-thrombin shows dramatic shifts in placement for the Tyr-Pro-Pro-Trp segment, for Glu-192, and for the catalytic residues His-57 and Ser-195, when compared to 4 thrombin complexes representing different states of catalysis, namely (1) the Michaelis complex (residues 7-19 of fibrinogen A alpha with a non-cleavable scissile bond), (2) enzyme-inhibitor complex (D-Phe-Pro-Arg chloromethylketone), (3) enzyme product complex (residues 7-16 of fibrinopeptide A), and (4) the exosite complex (residues 53-64 of hirudin). The structures of bovine and human prethrombin-2 are generally similar to one another (RMS deviation of 0.68 A) but differ significantly in the Arg-15/Ile-16 cleavage region and in the three activation domains, which are disordered in bovine prethrombin-2, analogous to that seen for trypsinogen.

Animals↗
PubMed1996

Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1', P2', and P3' substrate residues.

The crystal structure of the noncovalent complex of bovine thrombin and a fibrinogen-A alpha tridecapeptide substrate analog, G17 psi, in which the scissile bond amide nitrogen of Gly-17f has been replaced by a methylene carbon, has been determined at 2.3 A resolution with an R factor of 17.1%. The geometry of the active site indicates that the crystal structure is a close model of the true Michaelis complex. The three independently determined thrombin/G17 psi complexes in the crystal asymmetric unit reveal novel interactions for the P2' and P3' residues-Pro-18f and Arg-19f, respectively-on the carboxyl-terminal side of the scissile bond and confirm previously observed interactions of the P1 (Arg-16f) through P10 (Asp-7f) positions on the amino-terminal side. The thrombin S2' binding site for Pro-18f, as observed in all three complexes, differs from that predicted by modeling studies and is notable for including two carbonyl oxygens of the thrombin main chain. Arg-19f occupies two binding sites on thrombin, S3'A and S3'B, which have dramatically different placements for the arginyl side chain and carboxyl terminus.

Animals↗
PubMed1996

Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement.

Crystals of the bovine thrombin-hirudins(51-65) complex have space group P6(1)22 with cell constants a = 116.4, and c = 200.6 A and two thrombin molecules in the asymmetric unit. Only one thrombin molecule could be located by generalized molecular replacement; the second was fit visually as a rigid body to an improved electron-density difference map. The structure was refined to R = 0.192 with two B values per residue (main chain and side chain) at 3.2 A. The polar interactions of the peptides with the exosite of thrombin show differences consistent with the known flexibility in the interactions of the C-terminal peptide of hirudin with thrombin. The hirudin peptide in complex 2 has a higher temperature factor as compared with peptide 1 which may be correlated partly with a larger number of short-range electrostatic interactions between peptide 1 and thrombin and partly with the fact that thrombin 2 is epsilon-thrombin which is cleaved at Thr149A near the peptide binding site. Later, using this structure as a test case, it was shown that the position for the second thrombin could also be determined by a novel modification of the molecular-replacement method in which the contribution of the known molecule is subtracted from the structure factors. This approach is facile and applicable to any crystal containing two or more macromolecules in the asymmetric unit in which some but not all of the molecules can be determined by molecular replacement.

Journal Article↗
PubMed1996

Molecular symmetry of the dodecamer subunit of Lumbricus terrestris hemoglobin.

The principal functional subunit of the approximately 3500 kDa extracellular Lumbricus terrestris hemoglobin is a 213 kDa dodecamer of four chemically distinct globin chains, consisting of a non-covalent complex of three trimer submits (disulfide-bonded chains a, b and c) and three monomer subunits (chain d). X-ray diffraction of crystals of the dodecamer grown at neutral pH, were found to be monoclinic, with the unit cell dimensions: a = 112.3 A, b = 190.0 A, c = 69.6 A, beta = 102.0 degrees with h + k + l = 2n + 1 absent, characteristic of space group I121. In addition, these crystals exhibit a pseudo trigonal P321 symmetry with unit cell dimensions a = 190.5 A, b = 190.5 A, c = 69.5 A, gamma = 120.0 degrees. Assuming that the assymetric unit contains an entire dodecamer, a model of the latter was constructed that satisfies the symmetry of the trigonal pseudo cell and is consistent with the symmetry of the I121 crystallographic cell. The resulting model has strong implications concerning the hexagonal bilayer structure of the native hemoglobin.

Animals↗