Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Azurin”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 775 records · Page 43Linked to original sources
PubMed2005

Underlying hydrophobic sequence periodicity of protein tertiary structure.

Hydropathy plots or window averages over local stretches of the sequence of residue hydrophobicity have revealed patterns related to various protein tertiary structural features. This has enabled identification of regions of the sequence that are at the surface or within the interior of globular soluble proteins, regions located within the lipid bilayer of transmembrane proteins, portions of the sequence that characterize repeating motifs, as well as motifs that usefully characterize different protein structural families. This, therefore, provides one example of the generally expressed maxim that "sequence determines structure". On the other hand, a number of previous investigations have shown the rapidly varying values of residue hydrophobicity along the sequence to be distributed approximately randomly. So one might question just how much of the sequence actually determines structure. It is, therefore, of interest to extract that part of this rapidly varying distribution of residue hydrophobicity that is responsible for the longer wavelength variations that correlate with protein tertiary structural features and to determine their prevalence within the entire distribution. This is accomplished by a finite Fourier analysis of the sequence of residue hydrophobicity and of a new measure of residue distance from the protein interior. Calculations are performed on a number of globins, immunoglobulins, cuprodoxins, and papain-like structures. The spectral power of the Fourier amplitudes of the frequencies extracted, whose inverse transforms underlie the windowed values of residue hydrophobicity is shown to be a small fraction of the total power of the hydrophobicity distribution and thereby consistent with a distribution that might appear to be predominantly random. The wide range of sequence identity between proteins having the same fold, all exhibiting similar small fractions of power amplitude that correlate with the longer wavelength inside-to-outside excursions of the amino acid residues, supports the general contention that close sequence identity is an expression of a close evolutionary relationship rather than an expression of structural similarity. Practical implications of the present analysis for protein structure prediction and engineering are also described.

Amino Acid Sequence↗
PubMed2007

Conserved water molecular dynamics of the different X-ray structures of rusticyanin: an unique aquation potentiality of the ligand bonded Cu++ center.

The invariant water molecular interaction involving in the Rusticyanin of Thiobacillus ferrooxidans is thought to be important for its molecular complexation with other proteins at differential acidophilic situation. The comparative analysis of the different x-ray, energy minimized, and auto solvated structures of Rusticyanin revealed the presence of five specific invariant bound water molecules (among the approximately 150 water molecules per monomer) in the crystals. The five W 205, W 206, W 112, W 214, and W 221 water molecules (in Rusticyanin PDB code: 1RCY) were seem to be invariant in all the seven structures (PDB codes: 1RCY, 1A3Z, 1A8Z, 1E3O, 1GY1, 1GY2, 2CAL). Among the five conserved water molecules the W 221 (of 1 RCY or the equivalent water molecules in the other oxidized form of Rusticyanin structures) had endowed an interesting coordination potentiality to Cu(+2) ion during the energy minimization. The W 221 was observed to approach toward the tetrahedrally bonded Cu(+2) ion through the opposite (or trans) route of metal-bonded Met 148. This direct water molecular coordination affected the tetrahedral geometry of Cu(+2) to trigonal bipyramidal. Presumably this structural dynamics at the Cu(+2) center could involve in the electron transport process during protein-protein complexation.

Azurin↗
PubMed1996

The amino acid sequence of the spinach basic cupredoxin plantacyanin.

We describe the amino acid sequence of plantacyanin isolated from spinach leaves. This small basic copper-binding plant cupredoxin contains 91 amino acids (accession no. S70746) and its theoretical average mass of 9788.2 Da was confirmed by electrospray ionization mass spectrometry. When compared to the sequences of other plant cupredoxins, the most similar homologs were cucumber basic blue protein and stellacyanin from Laquer tree with 44-58% identical residues. Other known plant cupredoxins were significantly less similar which may allow to divide the plant cupredoxins into two subgroups, the single-domain cupredoxins (plantacyanin, cucumber basic blue protein and stellacyanin) and the two-domain, hydroxyproline-containing cupredoxins (cucumber peeling cupredoxin, basic blue protein from Arabidopsis thaliana and horseradish umecyanin).

Amino Acid Sequence↗
PubMed1997

Complications of laparoscopic cholecystectomy: the experience of a university-affiliated teaching hospital.

BACKGROUND: In most published reports on laparoscopic cholecystectomy, the cases have been accrued from small community hospitals in a multicenter fashion. The purpose of this study was to compare the rate of complication following laparoscopic cholecystectomy performed at a single university-affiliated teaching hospital to those quoted in the literature. STUDY DESIGN: A retrospective review of the first 1300 laparoscopic cholecystectomies performed at the Videoscopic Surgery Center at Pennsylvania Hospital from May 1990 through January 1994 was undertaken. Complications were classified as those related to creation of the initial pneumoperitoneum and those related to cholecystectomy. RESULTS: A 3% conversion rate to open cholecystectomy (n = 40) was noted due to the presence of dense adhesions, gangrenous cholecystitis, or difficult anatomic relationships. There were 18 complications (1.4%) related to creation of the initial pneumoperitoneum and 14 complications (1.1%) related to cholecystectomy. Complications related to laparoscopy included bleeding from the abdominal wall (n = 2), trocar site hernia (n = 11), hollow viscus injury (n = 1), and wound infection (n = 4). Complications related to cholecystectomy included unanticipated retained CBD stone (n = 5), symptomatic bile leak (n = 6), hollow viscus injury (n = 1), intraabdominal abscess (n = 1), and a retained portion of gallbladder (n = 1). There were no perioperative deaths related to laparoscopic cholecystectomy, and the overall morbidity was 2.4%. Long-term follow-up revealed no cases of benign biliary strictures. CONCLUSIONS: With attention to anatomy, technique, and meticulous dissection, laparoscopic cholecystectomy can be safely performed in a university-affiliated teaching hospital setting.

Adolescent↗
PubMed1997

Endoscopic preperitoneal herniorrhaphy in professional athletes with groin pain.

INTRODUCTION: Surgical exploration of the groin with subsequent herniorrhaphy has been recommended for obscure groin pain in athletes. The purpose of this study was to evaluate the efficacy of endoscopic preperitoneal herniorrhaphy and, if indicated, contralateral groin exploration in professional athletes with groin pain. PATIENTS AND METHODS: Eight professional athletes presented with groin pain and underwent endoscopic preperitoneal herniorrhaphy between February 1994 and May 1996. All athletes were male with a median age of 25.1 years (range: 22-30). Seven of the athletes complained of unilateral groin pain while one patient had bilateral pain. Seven had undergone previous conservative treatment without success. Despite multiple examinations, only two patients had been diagnosed with hernias prior to referral to the surgeon. Of the remaining six patients, all were found to have small inguinal hernias in the symptomatic groin. Seven of the patients were noted to have bilateral pathology. RESULTS: Operative time averaged 55.3 min. All patients were ambulatory without significant difficulty within the first 24 h, discontinued oral narcotic use within 72 h of surgery, and were back to recreational activities within 1 week. Aerobic conditioning was resumed within a maximum of 2 weeks. Full conditioning and/or return to full competition occurred within a 2- to 3-week period. At the time of 4 week follow-up, all athletes reported no more than minimal postexertional discomfort, with near total relief of early postoperative symptoms. No athletes noted any impairment in their ability to perform at peak levels. CONCLUSIONS: Groin pain in athletes is a difficult problem requiring a multidisciplinary approach to diagnosis and treatment planning. Endoscopic preperitoneal herniorrhaphy is an effective treatment for obscure groin pain when the pain is associated with an inguinal hernia and allows for a short recovery time back to full athletic activity.

Adult↗
PubMed1995

Bile leak following laparoscopic cholecystectomy.

The incidence and significance of bile leak after open cholecystectomy have been studied. The purpose of this study was to determine the incidence and significance of postoperative bile leak associated with both emergent and elective laparoscopic cholecystectomies. One thousand four hundred patients undergoing laparoscopic cholecystectomy from July 1990 to January 1995 were retrospectively reviewed. Twenty-seven percent of laparoscopic cholecystectomies were performed urgently for acute cholecystitis. Diisopropyl-iminodiacetic acid (DISIDA) scan was used to determine the presence of a bile leak or obstruction. Also, a subgroup of 63 patients from March to May of 1992 was studied in a nonblinded prospective fashion to determine the rate of asymptomatic bile leak. The incidence of bile leak in the subgroup of 63 patients was 4.7% (n = 3). All of these bile leaks were asymptomatic and of no clinical significance. The incidence of bile leak in the remaining 1337 was 0.14% (n = 2). These bile leaks were discovered by DISIDA scan following a workup of atypical abdominal pain following laparoscopic cholecystectomy. Both of these patients underwent ERCP with papillotomy. There were no ductal injuries in the entire series. Symptomatic bile leaks following laparoscopic cholecystectomy are rare. Asymptomatic bile leaks occur infrequently and are of no clinical significance.

Bile Ducts↗
PubMed1995

Small bowel obstruction following endoscopic extraperitoneal-preperitoneal herniorrhaphy.

Laparoscopic hernia repair has a number of unique potential complications. These include complications of pneumoperitoneum, general anesthesia, trocar injuries and complications of small bowel obstruction related to trocar site fascial defects, intraabdominal adhesions, and reaction with the synthetic mesh. A totally extraperitoneal approach should, in theory, eliminate postoperative small bowel obstruction in that the peritoneal space is never entered. A case of small bowel obstruction following totally extraperitoneal-preperitoneal herniorrhaphy is presented.

Anesthesia, Epidural↗
PubMed1996

The efficacy of epidural anesthesia for endoscopic preperitoneal herniorrhaphy: a prospective study.

Laparoscopic herniorrhaphy has been criticized because of the need for general anesthesia. The endoscopic preperitoneal approach allows the use of epidural anesthesia, obviating the potential complications and side effects seen with general anesthesia. The purpose of this study was to determine the efficacy of epidural anesthesia for preperitoneal herniorrhaphy. Fifty-two patients underwent repair of a total of 80 hernias over a 6-month period. Thirty-six patients underwent their repairs with the use of epidural anesthesia with the goal of a T-4 sensory level. A tension-free prosthetic repair was performed in all patients. Seventeen patients had unilateral repairs and nineteen had bilateral repairs under epidural, while seven patients had unilateral repairs and nine patients had bilateral repairs under general anesthesia. There were no significant differences in patient demographics. All herniorrhaphies were electively performed on an outpatient basis by a single surgeon (A.L.S.) in a teaching setting. There were no significant differences for unilateral and bilateral repairs when type of anesthesia was compared. There was only one conversion from epidural to general anesthesia, secondary to poor sensory blockade first noticed during creation of the preperitoneal space (97% success rate). Seven patients receiving epidural anesthesia experienced pneumoperitoneum during the procedure. This did not effect the ability to perform the hernia repair successfully. There were no complications related to the epidural anesthetic. Endoscopic preperitoneal herniorrhaphy can be performed effectively under epidural anesthesia, obviating the need for general anesthesia.

Adult↗
PubMed1989

A fast and sensitive multiple sequence alignment algorithm.

A two-step multiple alignment strategy is presented that allows rapid alignment of a set of homologous sequences and comparison of pre-aligned groups of sequences. Examples are given demonstrating the improvement in the quality of alignments when comparing entire groups instead of single sequences. The modular design of computer programs based on this algorithm allows for storage of aligned sequences and successive alignment of any number of sequences.

Algorithms↗
PubMed1999

Site-directed mutagenesis of a possible type 1 copper ligand of bilirubin oxidase; a Met467Gln mutant shows stellacyanin-like properties.

In our previous paper, we reported a mutant of recombinant Myrothecium verrucaria bilirubin oxidase, in which the Met467 residue was replaced by Gly [Shimizu, A. et al. (1999) Biochemistry 38, 3034-3042]. This mutant displayed a remarkable reduction in enzymatic activity and an evident decrease in the intensity of the absorption band around 600 nm (type 1 charge transfer transition). In this study, we report the preparation of three Met467 mutants (Met467Gln, Met467His, and Met467Arg) and characterize their enzymatic activities, midpoint potentials, and absorption and ESR spectra. Met467His and Met467Arg show no enzymatic activity and a great reduction in the intensity of the absorption band around 600 nm. Furthermore, their ESR spectra show no type 1 copper signal, but only a type 2 copper signal; however, oxidation by ferricyanide caused the type 1 copper signal to appear. On the other hand, Met467Gln as expressed shows both type 1 and type 2 copper signals in its ESR spectrum, the type 1 copper atom parameters being very different from usual blue copper proteins but very similar to those of stellacyanin. The enzymatic activity of the Met467Gln mutant for bilirubin is quite low (0.3%), but the activity for potassium ferrocyanide is similar (130%) to that of the wild type enzyme. These results indicate that Met467 is important for characterizing the features of the type 1 copper of bilirubin oxidase.

Amino Acid Sequence↗
PubMed1993

Crystallization and preliminary X-ray studies on pseudoazurin from Achromobacter cycloclastes IAM1013.

New crystals of a blue copper protein, pseudoazurin from denitrifier Achromobacter cycloclastes IAM1013, have been obtained by means of vapor diffusion with ammonium sulfate as a precipitant at pH 6.0 and 4 degrees C. The crystals belong to the orthorhombic system, space group P2(1)2(1)2(1), with unit cell dimensions of a = 56.69(2), b = 61.53(2), and c = 30.20(1) A. The asymmetric unit includes one molecule of pseudoazurin with a Vm value of 2.04 A3/Da. The crystals are so stable against X-ray irradiation that a complete data set up to 1.54 A has been collected using a single native crystal. Solution of the structure was performed by means of the Patterson search techniques, and the current crystallographic R-factor is 17.5% at 3.0 A resolution. Refinement at higher resolution is in progress.

Alcaligenes↗
PubMed1994

Extracellular transport of pseudoazurin of Alcaligenes faecalis in Escherichia coli using the COOH-terminal domain of Serratia marcescens serine protease.

A large COOH-terminal domain of Serratia marcescens serine protease (SSP) is essentially required for the excretion of the mature protease region through the outer membrane in Escherichia coli. For investigation of the possibility of transporting foreign periplasmic proteins by utilizing the function of the COOH-terminal domain of SSP, the pseudoazurin (PA) gene of Alcaligenes faecalis was fused to three different lengths of the COOH-terminal domain via a BglII linker sequence (AGATCT) which would be translated into Arg-Ser, one of the cleavage sequences of the OmpT protease. The outer membrane fractions of E. coli JM105 harboring each of the fused genes on a multicopy plasmid was found to contain the PA-SSP hybrid protein without the signal sequence as well as the COOH-terminal domain of SSP processed at the Arg-Ser sequence. Trypsin-treatment of intact and cold osmotically shocked cells suggested that the COOH-terminal domain of SSP in the hybrid protein was rigidly integrated in the outer membrane, while the PA part of the hybrid protein was exposed on the cell surface. The localization of the PA part was confirmed by immunolabelling of intact cells with the anti-PA antibody. Furthermore, exogenous addition of purified SSP to the intact E. coli cells containing the hybrid protein liberated the PA part from the cells into the medium, probably by cleavage at or very near the site processed during the normal secretion of intact SSP.(ABSTRACT TRUNCATED AT 250 WORDS)

Alcaligenes↗
PubMed1999

Homology modeling of the multicopper oxidase Fet3 gives new insights in the mechanism of iron transport in yeast.

Fet3, the multicopper oxidase of yeast, oxidizes extracellular ferrous iron which is then transported into the cell through the permease Ftr1. A three-dimensional model structure of Fet3 has been derived by homology modeling. Fet3 consists of three cupredoxin domains joined by a trinuclear copper cluster which is connected to the blue copper site located in the third domain. Close to this site, which is the primary electron acceptor from the substrate, residues for a potential iron binding site could be identified. The surface disposition of negatively charged residues suggests that Fet3 can translocate Fe(3+) to the permease Ftr1 through a pathway under electrostatic guidance.

Amino Acid Sequence↗
PubMed1999

Analysis and prediction of inter-strand packing distances between beta-sheets of globular proteins.

Any two beta-strands belonging to two different beta-sheets in a protein structure are considered to pack interactively if each beta-strand has at least one residue that undergoes a loss of one tenth or more of its solvent contact surface area upon packing. A data set of protein 3-D structures (determined at 2.5 A resolution or better), corresponding to 428 protein chains, contains 1986 non-identical pairs of beta-strands involved in interactive packing. The inter-axial distance between these is significantly correlated to the weighted sum of the volumes of the interacting residues at the packing interface. This correlation can be used to predict the changes in the inter-sheet distances in equivalent beta-sheets in homologous proteins and, therefore, is of value in comparative modelling of proteins.

Amino Acids↗
PubMed1992

Site-directed mutagenesis of pseudoazurin from Alcaligenes faecalis S-6; Pro80Ala mutant exhibits marked increase in reduction potential.

Pseudoazurin (a blue copper protein or cupredoxin) of a denitrifying bacterium Alcaligenes faecalis S-6 is a direct electron carrier for a Cu-containing nitrite reductase (NIR) of the same organism. Site-directed mutagenesis of the pseudoazurin was carried out using an Escherichia coli expression system. Replacement of Tyr74 by Phe to remove an internal hydrogen bond in the beta-barrel caused a slight decrease in heat stability as well as a requirement for a higher concentration of Cu2+ for production in the E. coli host. Exchange of Ala for Pro80 adjacent to His81, one of the four ligands binding a type I Cu atom, caused a marked increase in reduction potential by 139 mV without change in the optical absorption spectrum. The ability of the pseudoazurin to transfer electrons to NIR was markedly diminished but the apparent Km of NIR for pseudoazurin was not affected by the mutation. X-ray diffraction data collected on the oxidized and reduced forms of the Pro80Ala mutant show that a water molecule occupies the pocket created by the absent side chain. This observation suggests that the increase in reduction potential may be caused due to the increased solvent accessibility to the Cu atom. The electron density difference maps on these structures (at 2.0 A) show that this water moves during the change in oxidation state, and that there are small, but localized, conformational changes greater than 6.5 A from the copper site, as well as movement of both the Cu2+ and the cysteinate sulfur.

Alcaligenes↗
PubMed1993

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure.

A 3-D model of a protein can be constructed from its amino acid sequence and the 3-D structures of one or more homologues by annealing three sets of fragments: the structurally conserved regions, structurally variable regions and the side chains. The method encoded in the computer program COMPOSER was assessed by generating 3-D models of eight proteins whose crystal structures are already known and for which 3-D structures of homologues are available. In the structurally conserved regions, differences between modelled and X-ray structures are smaller than the differences between the X-ray structures of the modelled protein and the homologues used to build the model. When several homologues are used, the contributions of the known structures are weighted, preferably by the square of sequence similarity; this is especially important when the similarities of the homologues to the modelled structure differ greatly. The 'collar' extension approach, in which a similar region of different length in a homologue is used to extend the framework, can result in a more accurate model. If known homologues comprise more than one related group of proteins and they are both distantly related to the unknown, then alignment of the sequence to be modelled with each group of homologues facilitates identification of structurally conserved regions of the unknown and leads to an improved model. Models have root mean square differences (r.m.s.d.s) with the structures defined by X-ray analysis of between 0.73 and 1.56 A for all C alpha atoms, for seven the eight models. For the model of mucor pepsin, where the closest homologue has 33% sequence identity and 20% of the residues are in structurally variable regions, the r.m.s.d. for the framework region is 1.71 A and the r.m.s.d. for all C alpha atoms is 3.47 A.

Amino Acid Sequence↗
PubMed1995

A reliable sequence alignment method based on probabilities of residue correspondences.

Probabilities of all possible correspondences of residues in aligning two proteins are evaluated by assuming that the statistical weight of each alignment is proportional to the exponent of its total similarity score. Based on such probabilities, a probability alignment that includes the most probable correspondences is proposed. In the case of highly similar sequence pairs, the probability alignments agree with the maximum similarity alignments that correspond to the alignments with the maximum similarity score. Significant correspondences in the probability alignments are those whose probabilities are > 0.5. The probability alignment method is applied to a few protein pairs, and results indicate that such highly probable correspondences in the probability alignments are probably correct correspondences that agree with the structural alignments and that incorrect correspondences in the maximum similarity alignments are usually insignificant correspondences in the probability alignments. The root mean square deviations in superimposition of corresponding residues tend to be smaller for significant correspondences in the probability alignments than for all correspondences in the maximum similarity alignments, indicating that incorrect correspondences in the maximum similarity alignments tend to be insignificant correspondences in probability alignments. This fact is also confirmed in 109 protein pairs that are similar to each other with sequence identities between 90 and 35%. In addition, the probability alignment method may better predict correct correspondences than the maximum similarity alignment method. Probability alignments do, of course, depend on a scoring scheme but are less sensitive to the value of parameters such as gap penalties. The present probability alignment method is useful for constructing reliable alignments based on the probabilities of correspondences and can be used with any scoring scheme.

Amino Acid Sequence↗
PubMed1995

Identification of interaction site of pseudoazurin with its redox partner, copper-containing nitrite reductase from Alcaligenes faecalis S-6.

Pseudoazurin, a low molecular weight protein containing a single type I copper, functions as an electron donor to a copper-containing nitrite reductase (NIR) in a denitrifying bacterium Alcaligenes faecalis S-6. To elucidate the protein-protein interaction between these two copper-containing proteins, each of nine out of 13 lysine residues on the surface of pseudoazurin were independently replaced by alanine or aspartate, and the effects of the mutations on the interaction with NIR, as well as the physicochemical properties of pseudoazurin, were analyzed. All of the mutated pseudoazurins showed optical spectra and oxidation-reduction potentials almost identical to those of wild-type pseudoazurin, suggesting that none of the replacements of these lysine residues affected the environment around the type I copper site. Kinetic analysis of electron transfer between mutated pseudoazurins and NIR reveals that the lysine mutations have very little effect on the rate of electron transfer to NIR, but substitution at residues 10, 38, 57 and 77, all close to the copper site, substantially decreases the affinity of pseudoazurin for NIR. This suggests that pseudoazurin interacts with NIR through the region close to the type I copper site. The refined X-ray structures of Lys38Asp and Lys10Asp/Lys38Asp show that the molecular structure has indeed changed little. A new space group is observed for the Lys109Ala mutant crystal. Crystal packing interactions change for the Lys10Asp/Lys38Asp mutant but remain the same for Lys38Asp and Lys59Ala mutants.

Alanine↗