Biomedical subjects

A Coda

Publications and source records attributed to A Coda.

At least 19 recordsLinked to original sources

PubMed2004

Comparison of polypropylene and polyethylene terephthalate (Dacron) meshes for abdominal wall hernia repair: a chemical and morphological study.

For the first time, by scanning electron microscopy (SEM), polypropylene (PP) excised meshes (ethylene oxide sterilized) for abdominal wall hernia repair have been shown to be greatly damaged physically, independently of the implantation time, while the polyethylene terephthalate (PET), or Dacron, ones (gamma radiation sterilized), did not undergo alterations due to the sterilization process and were not damaged, even after long implantation periods. Fourier-Transform Infrared Spectroscopy (FTIR) study of PP and PET excised meshes, as well as of their extracts with cyclohexane, has shown the presence of species, such as squalene, palmitic and stearic acid, in some cases, cholesterol, transferred from the surrounding tissues to the polymer during the implantation period. In the case of PP meshes, these small organic molecules would reduce physical and mechanical properties of the material. A hypothesis is presented to account for the better behavior (not in the clinical sense) of PET meshes.

Adult↗

PubMed2002

Structural alterations of prosthetic meshes in humans.

The use of prosthetic mesh in abdominal wall hernia surgery is a well-accepted practice. What is not settled, however, is the type of prosthesis that best suits the purpose. The narrow choice today means a prosthesis of polyester or polypropylene. These are available in many designs, configuration of weave, thickness of weave and strand, and size of pore. There has been a pervasive feeling that these materials "shrink". To what extent they do has not been accurately defined. This study was designed to measure such "shrinkage". Interestingly, our measurements revealed that prosthetic meshes could "expand" as well as "shrink". The extent to which they do varies between -40% and 58.5%. Whereas it was felt that fibrocyte activity and its eventual scar formation accounted for the "shrinkage" of the mesh, we have discovered that structural alterations in the size of the mesh pores can be affected by distilled water, saline, blood, formalin, bleach, as well as in vivo implantation. Prosthetic meshes are, therefore, not the inert materials they are claimed to be and can expand as well as shrink. We have, unfortunately, not been able to correlate the degree or direction of change to any known parameter.

Adult↗

PubMed2001

Gasless laparoscopic-assisted ileostomy or colostomy closure using an abdominal wall-lifting device.

BACKGROUND: Restoration of intestinal continuity in patients with ileostomy after total colectomy or with colostomy after Hartmann's procedure is a major operation. Herein we illustrate the validity of gasless laparoscopically assisted reversal using abdominal wall lifting. METHODS: The operation was performed on 10 patients from February 1997 to May 1999. Seven of them had a left iliac stoma after a Hartmann resection, and three had an ileostomy after total colectomy. RESULTS: The laparoscopic reversal was completed in eight patients; the two others were converted to an open procedure. Three major complications occurred (30%). There were no deaths. The average operation time was 192 min (range, 125-265). Time of discharge from surgery averaged 9.5 days. Mean follow-up of these patients was 12 months and negative. CONCLUSIONS: Laparoscopically assisted ileo- or colorectal anastomosis without pneumoperitoneum and using a laparotenser can be considered for the reversal of patients with ileostomy or colostomy. Even taking the high rate of intraoperative or postoperative complications into consideration, the advantages that make such a laparoscopic approach suitable include reduced trauma related to a second major abdominal operation, reduced postoperative pain, and fewer cutaneous tissues exposed to bacterial contamination. Moreover, the use of a laparotenser makes it possible to operate on elderly patients with cardiovascular diseases. In the absence of pneumoperitoneum, it becomes possible to use traditional instruments, with a consequent reduction in costs.

Abdominal Muscles↗

PubMed2000

Cross-talk and ammonia channeling between active centers in the unexpected domain arrangement of glutamate synthase.

INTRODUCTION: The complex iron-sulfur flavoprotein glutamate synthase catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine, a reaction in the plant and bacterial pathway for ammonia assimilation. The enzyme functions through three distinct active centers carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor. RESULTS: The 3.0 A crystal structure of the dimeric 324 kDa core protein of a bacterial glutamate synthase was solved by the MAD method, using the very weak anomalous signal of the two 3Fe-4S clusters present in the asymmetric unit. The 1,472 amino acids of the monomer fold into a four-domain architecture. The two catalytic domains have canonical Ntn-amidotransferase and FMN binding (beta/alpha)8 barrel folds, respectively. The other two domains have an unusual "cut (beta/alpha)8 barrel" topology and an unexpected novel beta-helix structure. Channeling of the ammonia intermediate is brought about by an internal tunnel of 31 A length, which runs from the site of L-glutamine hydrolysis to the site of L-glutamate synthesis. CONCLUSIONS: The outstanding property of glutamate synthase is the ability to coordinate the activity of its various functional sites to avoid wasteful consumption of L-glutamine. The structure reveals two polypeptide segments that connect the catalytic centers and embed the ammonia tunnel, thus being ideally suited to function in interdomain signaling. Depending on the enzyme redox and ligation states, these signal-transducing elements may affect the active site geometry and control ammonia diffusion through a gating mechanism.

Ammonia↗

PubMed2000

Incisional hernia and fascial defect following laparoscopic surgery.

Complications involving the abdominal wall, particularly incisional hernias, were not expected when laparoscopic procedures were first introduced. With the increasing number of laparoscopies in abdominal surgery, more incisional hernias are observed. The authors report 13 cases of umbilical incisional hernia, which occurred late after laparoscopic cholecystectomy, and one case of omental procidentia through a lateral port, which occurred early after laparoscopic hernia repair with the transabdominal preperitoneal technique. There are 4 men and 10 women (mean age, 59.8 years; range, 40-74 years). Between March 1991 and December 1997, a total of 1,287 patients underwent laparoscopic operations at the Surgical Department of the Gradenigo Hospital in Turin, Italy. Incisional hernia incidence is 1%. Risk factors, such as chronic bronchitis or weight increase, which give rise to endoabdominal pressure, are present in some cases. Malnutrition may have a major role in many cases. Calculi larger than 15 mm are also seen frequently. Postlaparoscopy incisional hernia is generally a minor complication--only once did its occurrence cause a strangulated hernia. All precautions, including fascial suturing, must be taken to reduce the 1% incidence of postoperative incisional hernias.

Adult↗

PubMed2000

[Spigelian hernia: an up-to-date].

Nine cases of Spigelian hernia occurred and surgically treated in the years 1992-1997 are reported. Spigelian hernias were observed in 5 females and 3 males with mean age of 62.1 years (range 49-70). In 5 cases prosthetic repair has been done with preperitoneal mesh and a very good outcome. In a 61 years old obese female spigelian hernia was bilateral. Her left sided hernia needed an emergency operation for strangulation. Hernia has been repaired by simple suture and recurred early. For the diagnosis of Spigelian hernia it is essential to remember it inside the "Spigelian belt". The satisfactory results obtained at present by prosthetic repair are underlined.

Aged↗

PubMed1999

Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.

BACKGROUND: Given the vital role of NAD+ in cell metabolism, the enzymes involved in bacterial de novo NAD+ biosynthesis are possible targets for drug design against pathogenic bacteria. The first reaction in the pathway is catalysed by L-aspartate oxidase (LASPO), a flavoenzyme that converts aspartate to iminoaspartate using either molecular oxygen or fumarate as electron acceptors. LASPO has considerable sequence homology with the flavoprotein subunits of succinate dehydrogenase (SDH) and fumarate reductase (FRD). RESULTS: The crystal structure of the apoform of LASPO from Escherichia coli has been determined to 2.2 A resolution. The enzyme shows a novel fold for an FAD-dependent protein, comprising a three-domain structure: an FAD-binding domain with the dinucleotide-binding fold, a C-terminal three-helical bundle domain, and an alpha + beta capping domain, which is topologically similar to the small subunit of spinach ribulose-1,5-bisphosphate carboxylase/oxygenase. The interface between the FAD-binding and capping domains defines a cleft in which the active site is located. CONCLUSIONS: A number of strictly conserved residues present in all three domains indicate that LASPO, SDH and FRD share the same overall folding topology. Many of these conserved residues are in the FAD-binding site and active centre, suggesting a similar catalytic mechanism. Thus, LASPO, SDH and FRD form a class of functionally and structurally related oxidoreductases that are all able to reduce fumarate and to oxidise a dicarboxylate substrate.

Amino Acid Oxidoreductases↗

PubMed1999

A 30-angstrom-long U-shaped catalytic tunnel in the crystal structure of polyamine oxidase.

BACKGROUND: Polyamines are essential for cell growth and differentiation; compounds interfering with their metabolism are potential anticancer agents. Polyamine oxidase (PAO) plays a central role in polyamine homeostasis. The enzyme utilises an FAD cofactor to catalyse the oxidation of the secondary amino groups of spermine and spermidine. RESULTS: The first crystal structure of a polyamine oxidase has been determined to a resolution of 1.9 Angstroms. PAO from Zea mays contains two domains, which define a remarkable 30 Angstrom long U-shaped catalytic tunnel at their interface. The structure of PAO in complex with the inhibitor MDL72527 reveals the residues forming the catalytic machinery and unusual enzyme-inhibitor CH.O H bonds. A ring of glutamate and aspartate residues surrounding one of the two tunnel openings contributes to the steering of the substrate towards the inside of the tunnel. CONCLUSIONS: PAO specifically oxidizes substrates that have both primary and secondary amino groups. The complex with MDL72527 shows that the primary amino groups are essential for the proper alignment of the substrate with respect to the flavin. Conservation of an N-terminal sequence motif indicates that PAO is member of a novel family of flavoenzymes. Among these, monoamine oxidase displays significant sequence homology with PAO, suggesting a similar overall folding topology.

Amino Acid Sequence↗

PubMed1999

Incisional hernia and fascial defect following laparoscopic surgery.

Adult↗

PubMed1998

Structure of the mutant E92K of [2Fe-2S] ferredoxin I from Spinacia oleracea at 1.7 A resolution.

Ferredoxin I (Fd I) from Spinacia oleracea is composed of 97 amino-acid residues and a [2Fe-2S] cluster. The crystal structure of the E92K mutant of Fd I was solved by molecular replacement and refined to an R factor of 19.6% for 11755 reflections at 1.7 A resolution. The overall structure and the active centre of spinach Fd is highly conserved with respect to ferredoxins of known structure. The E92K mutation appears to disturb a hydrogen-bond network which stabilizes the loop bearing the [2Fe-2S] cluster. This observation provides a rationale for the reduced electron-transfer efficiency displayed by the E92K mutant. Inspection of the crystal packing reveals that the side chain of Lys92 is engaged in an intermolecular interaction with Asp26 of a symmetry-related molecule. This feature may explain why only the mutant E92K and not wild-type Fd I could be successfully crystallized.

Amino Acid Sequence↗

PubMed1998

Crystallization and preliminary X-ray analysis of polyamine oxidase from Zea mays L.

Polyamine oxidase catalyses the oxidation of the secondary amino group of spermine, spermidine and their acetyl derivatives. The enzyme plays an important role in the regulation of polyamine intracellular concentration and is a member of the family of flavin-containing amine oxidases. Crystals of maize polyamine oxidase have been grown by the hanging-drop vapour-diffusion technique. The crystals are in hexagonal space group P6122 (or P6522) with cell dimensions a = b = 184.6, c = 280.9 A. A native data set has been collected to 2.7 A resolution at a synchrotron radiation source.

Binding Sites↗

PubMed1998

A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure.

BACKGROUND: Nicotinamide adenine dinucleotide (NAD+) has a central role in life processes. The ubiquitous enzyme NAD+ synthetase catalyzes a key step in NAD+ biosynthesis, transforming deamido-NAD+ into NAD+ by a two-step reaction. NAD+ synthetase belongs to the amidotransferase family and has been recognized as a member of the family of N-type ATP pyrophosphatases. In order to investigate the mechanism of the reaction carried out by NAD+ synthetase we have determined a high-resolution three-dimensional structure of the Bacillus subtilis homodimeric NAD+ synthetase in complex with the trapped reaction intermediate NAD-adenylate. RESULTS: Two NAD-adenylate molecules and two pyrophosphate (PPi) molecules are observed in the 1.3 A resolution structure of the NAD+ synthetase-NAD-adenylate complex. Structural studies on the NAD+ synthetase-NAD-adenylate adduct and on the cation-binding sites reveal a new deamido-NAD+-binding site located at the subunit interface, locate a binuclear magnesium cluster at the ATP-binding site and, identify two monovalent cation sites, one of which may represent an ammonium-binding site. CONCLUSIONS: Our results suggest that two different catalytic strategies have been adopted by NAD+ synthetase in the two different steps of the reaction. During the adenylation step, no protein residues seem to be located properly to directly participate in catalysis, which is likely to be carried out with the fundamental assistance of an electron-withdrawing trimetallic constellation present in the active site. A different behavior is observed for the second step, in which an ammonium ion is the binding species. In this step, Asp173 is a key residue in both deprotonation of the primarily bound ammonium ion, and stabilization of the tetrahedral transition-state intermediate. Moreover, the structural data suggest that product release can take place only after all substrates are bound to the enzyme, and product release is ultimately controlled by the conformation adopted by two mobile loops.

Adenosine Diphosphate Ribose↗

PubMed1997

Crystal structures and inhibitor binding in the octameric flavoenzyme vanillyl-alcohol oxidase: the shape of the active-site cavity controls substrate specificity.

BACKGROUND: Lignin degradation leads to the formation of a broad spectrum of aromatic molecules that can be used by various fungal micro-organisms as their sole source of carbon. When grown on phenolic compounds, Penicillium simplicissimum induces the strong impression of a flavin-containing vanillyl-alcohol oxidase (VAO). The enzyme catalyses the oxidation of a vast array of substrates, ranging from aromatic amines to 4-alkyphenols. VAO is a member of a novel class of widely distributed oxidoreductases, which use flavin adenine dinucleotide (FAD) as a cofactor covalently bound to the protein. We have carried out the determination of the structure of VAO in order to shed light on the most interesting features of these novel oxidoreductases, such as the functional significance of covalent flavinylation and the mechanism of catalysis. RESULTS: The crystal structure of VAO has been determined in the native state and in complexes with four inhibitors. The enzyme is an octamer with 42 symmetry; the inhibitors bind in a hydrophobic, elongated cavity on the si side of the flavin molecule. Three residues, Tyr108, Tyr503 and Arg504 form an anion-binding subsite, which stabilises the phenolate form of the substrate. The structure of VAO complexed with the inhibitor 4-(1-heptenyl)phenol shows that the catalytic cavity is completely filled by the inhibitor, explaining why alkylphenols bearing aliphatic substituents longer than seven carbon atoms do not bind to the enzyme. CONCLUSIONS: The shape of the active-site cavity controls substrate specificity by providing a 'size exclusion mechanism'. Inside the cavity, the substrate aromatic ring is positioned at an angle of 18 degrees to the flavin ring. This arrangement is ideally suited for a hydride transfer reaction, which is further facilitated by substrate deprotonation. Burying the substrate beneath the protein surface is a recurrent strategy, common to many flavoenzymes that effect substrate oxidation or reduction via hydride transfer.

Alcohol Oxidoreductases↗

PubMed1997

Active site plasticity in D-amino acid oxidase: a crystallographic analysis.

D-Amino acid oxidase (DAAO) is the prototype of the flavin-containing oxidases. It catalyzes the oxidative deamination of various D-amino acids, ranging from D-Ala to D-Trp. We have carried out the X-ray analysis of reduced DAAO in complex with the reaction product imino tryptophan (iTrp) and of the covalent adduct generated by the photoinduced reaction of the flavin with 3-methyl-2-oxobutyric acid (kVal). These structures were solved by combination of 8-fold density averaging and least-squares refinement techniques. The FAD redox state of DAAO crystals was assessed by single-crystal polarized absorption microspectrophotometry. iTrp binds to the reduced enzyme with the N, C alpha, C, and C beta atoms positioned 3.8 A from the re side of the flavin. The indole side chain points away from the cofactor and is bound in the active site through a rotation of Tyr224. This residue plays a crucial role in that it adapts its conformation to the size of the active site ligand, providing the enzyme with the plasticity required for binding a broad range of substrates. The iTrp binding mode is fully consistent with the proposal, inferred from the analysis of the native DAAO structure, that substrate oxidation occurs via direct hydride transfer from the C alpha to the flavin N5 atom. In this regard, it is remarkable that, even in the presence of the bulky iTrp ligand, the active center is made solvent inaccessible by loop 216-228. This loop is thought to switch between the "closed" conformation observed in the crystal structures and an "open" state required for substrate binding and product release. Loop closure is likely to have a role in catalysis by increasing the hydrophobicity of the active site, thus making the hydride transfer reaction more effective. Binding of kVal leads to keto acid decarboxylation and formation of a covalent bond between the keto acid C alpha and the flavin N5 atoms. Formation of this acyl adduct results in a nonplanar flavin, characterized by a 22 degrees angle between the pyrimidine and benzene rings. Thus, in addition to an adaptable substrate binding site, DAAO has the ability to bind a highly distorted cofactor. This ability is relevant for the enzyme's function as a highly efficient oxidase.

Arginine↗

PubMed1997

Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp.

BACKGROUND: The first hemoglobin identified in bacteria was isolated from Vitreoscilla stercoraria (VtHb) as a homodimeric species. The wild-type protein has been reported to display medium oxygen affinity and cooperative ligand-binding properties. Moreover, VtHb can support aerobic growth in Escherichia coli with impaired terminal oxidase function. This ability of VtHb to improve the growth properties of E. coli has important applications in fermentation technology, assisting the overexpression of recombinant proteins and antibiotics. Oxygen binding heme domains have been identified in chimeric proteins from bacteria and yeast, where they are covalently linked to FAD- and NAD(P)H-binding domains. We investigate here the fold, the distal heme site structure and the quaternary assembly of a bacterial hemoglobin which does not bear the typical flavohemoglobin domain organization. RESULTS: The VtHb three-dimensional structure conforms to the well known globin fold. Nevertheless, the polypeptide segment connecting helices C and E is disordered, and residues E7-E10 (defined according to the standard globin fold nomenclature) do not adopt the usual alpha-helical conformation, thus locating Gln53(E7) out of the heme pocket. Binding of azide to the heme iron introduces substantial structural perturbations in the heme distal site residues, particularly Tyr29(B10) and Pro54(E8). The quaternary assembly of homodimeric VtHb, not observed before within the globin family, is based on a molecular interface defined by helices F and H of both subunits, the two heme iron atoms being 34 A apart. CONCLUSIONS: The unusual heme distal site structure observed shows that previously undescribed molecular mechanisms of ligand stabilization are operative in VtHb. The polypeptide chain disorder observed in the CE region indicates a potential site of interaction with the FAD/NADH reductase partner, in analogy with observations in the chimeric flavohemoglobin from Alcaligenes eutrophus.

Amino Acid Sequence↗

PubMed1997

Expression, purification, crystallization, and preliminary X-ray diffraction analysis of the homodimeric bacterial hemoglobin from Vitreoscilla stercoraria.

The recombinant homodimeric hemoglobin from the strictly aerobe gram-negative bacterium Vitreoscilla stercoraria has been expressed in Escherichia coli, purified to homogeneity, and crystallized by vapor diffusion techniques, using ammonium sulfate as precipitant. The crystals belong to the monoclinic space group P2(1) and diffract to HIGH resolution. The unit cell parameters are alpha = 62.9, b = 42.5, c = 63.2 A, beta = 106.6 degrees; the asymmetric unit contains the homodimeric hemoglobin, with a volume solvent content of 42%.

Bacillus subtilis↗

PubMed1997

Crystallization and preliminary X-ray analysis of the flavoenzyme vanillyl-alcohol oxidase from Penicillium simplicissimum.

Vanillyl-alcohol oxidase catalyses the oxidation of several 4-hydroxybenzyl alcohols by using 8-alpha-(N3-histidyl)-FAD as a covalently bound prosthetic group. Crystals of vanillyl-alcohol oxidase from Penicillium simplicissimum have been grown by using the vapor diffusion technique. The space group was found to be I, with cell dimensions a = b = 140.5 A, c = 132.9 A. Diffraction data have been recorded to 3.2 A resolution by using a laboratory source and to 2.5 A resolution on flash freezing the crystal at the ELETTRA Synchrotron X-ray diffraction beam line.

Alcohol Oxidoreductases↗

PubMed1997

[Prosthetic repair of inguino-crural hernia using Rives technique].

The authors report their experience with Rives procedure, a prosthetic repair of groin hernias using preperitoneal sutured mesh by parainguinal access. This operation is not technically easy to perform and is usually done out of necessity in cases with higher risk of recurrence because of systemic factors of chronic abdominal high pressure and/or of local factors of risk, when there are contraindications to operations like Stoppa procedure. Our series report 38 patients operated upon on 5 years, with incidence of 5.8% overall hernias repaired in the same period. 33 are males, 5 females, with average age of 60.5 years. Mean time required for the operation is 94 minutes (range 55'-130'). About postoperative complications we complain of one testicular atrophy, but none infections. Follow-up range is 9-50 months (average 23.2 months) for 30 patients operated more than one year ago. All but one were revisited after almost 12 months. No recurrences were detected.

Adult↗