Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes

The hepatitis C virus NS3 protein contains a serine protease domain with a chymotrypsin-like fold, which is a target for development of therapeutics. We report the crystal structures of this domain complexed with NS4A cofactor and with two potent, reversible covalent inhibitors spanning the P1-P4 residues. Both inhibitors bind in an extended backbone conformation, forming an anti-parallel beta-sheet with one enzyme beta-strand. The P1 residue contributes most to the binding energy, whereas P2-P4 side chains are partially solvent exposed. The structures do not show notable rearrangements of the active site upon inhibitor binding. These results are significant for the development of antivirals.

Crystal structure of delta-chymotrypsin bound to a peptidyl chloromethyl ketone inhibitor

Chymotrypsin is a member of the trypsin family of serine proteases and is one of the first proteins successfully studied by X-ray crystallography. It is secreted into the intestine as the inactive precursor chymotrypsinogen; four sequential cleavages of the peptide bonds following residues 13, 15, 146 and 148 occur to generate the active pi, delta, kappa and alpha forms of chymotrypsin. (13)C NMR has shown [O'Connell & Malthouse (1995). Biochem. J. 307, 353-359] that when the delta form of chymotrypsin is inhibited by 2-(13)C-enriched benzyloxycarbonylglycylglycylphenylalanyl chloromethane, a tetrahedral adduct is formed which is thought to be analogous to the tetrahedral intermediate formed during catalysis. This inhibitor complex has been crystallized as a dimer in space group P4(1)2(1)2. The structure has been refined at 2.14 A resolution to an R value of 21.2% (free R = 25.2%). Conformational differences between delta-chymotrypsin and chymotrypsinogen in the region of the flexible autolysis loop (residues 145-150) were observed. This is the first crystal structure of delta-chymotrypsin and includes two residues which are disordered in previous crystal structures of active chymotrypsin. A difference of 11.3 A(2) between the average B values of the monomers within the asymmetric unit is caused by lattice-disordering effects approximating to rotation of the molecules about a crystallographic screw axis. The substrate-binding mode of the inhibitor was similar to other chymotrypsin peptidyl inhibitor complexes, but this is the first published chymotrypsin structure in which the tetrahedral chloromethyl ketone transition-state analogue is observed. This structure is compared with that of a similar tetrahedral transition-state analogue which does not alkylate the active-site histidine residue.

Head and neck schwannomas--a 10 year review

Schwannomas of the head and neck are uncommon tumours that arise from any peripheral, cranial or autonomic nerve. Twenty-five to 45 per cent of extracranial schwannomas occur in the head and neck region and thus are usually in the domain of the otolaryngologist. They usually present insidiously and thus are often diagnosed incorrectly or after lengthy delays, however, better imaging and cytological techniques have lessened this to some degree more recently. For benign lesions conservative surgical excision is the treatment of choice bearing in mind possible vagal or sympathetic chain injury. Malignant schwannomas are best treated with wide excision where possible. The role of adjuvant therapy remains uncertain and irrespective of treatment modality prognosis is poor with an overall survival of 15 per cent. However, recent advances in ras oncogene inhibitors may hold hope for the future.

MAD data collection - current trends

The multiwavelength anomalous dispersion (MAD) method of protein structure determination is becoming a routine technique in protein crystallography. The increased number of wavelength-tuneable synchrotron beamlines capable of performing challenging MAD experiments, coupled with the widespread availability of charge-coupled device (CCD) based X-ray detectors with fast read-out times have brought MAD structure determination to a new exciting level. Ultrafast MAD data collection is now possible and, with the widespread use of selenium in the form of selenomethionine for phase determination, the method is growing in popularity. Recent developments in crystallographic software are complementing the above advances, paving the way for rapid protein structure determination. An overview of a typical MAD experiment is described, with emphasis on the rates and quality of data acquisition now achievable at third-generation synchrotron sources.

The Westaby T-Y tracheobronchial stent in otolaryngology

The Westaby T-Y tracheobronchial silicone stent can be used for the relief of upper airway obstruction beyond the limit of a standard tracheostomy tube. We report on our experience in the use of the Westaby tube in 10 patients over a five-year period. The general features of the tube, indications for its use, and its method of insertion are described. The versatility and advantages over other stents are discussed. Two cases reports are described and the clinical course and outcomes of the individual patients are outlined.

Sinogenic brain abscess

The otolaryngological contribution to the combined treatment of intracranial suppuration secondary to sinusitis can vary from observation to external approach sinus exploration. Limited surgical intervention using the endoscopic approach, in conjunction with neurosurgical drainage, has recently been adopted at our department as the initial therapeutic strategy in the management of such cases. A retrospective analysis of the otolaryngological input into the treatment of 16 patients with sinogenic brain abscess at the Department of Otolaryngology/Head and Neck Surgery, Beaumont Hospital, Dublin, Ireland is presented. This study reveals that it is generally a disease of young adult males without an antecedent history of sinus disease and that Strep. Milleri is the most common causative organism. It is demonstrated that there is a lack of a consistent approach to the management in the acute phase and that there is an inadequate initial radiologic evaluation of the paranasal sinuses. There are two forms of presentation: 1) an ENT complaint with development of an abscess, and 2) an idiopathic abscess with subsequent identification of a paranasal sinus infective source. Extensive initial intervention seems to be associated with an increased incidence of revision surgery, thus suggesting that a limited endoscopic approach combined with neurosurgical drainage is the optimal course in the first-line management of sinogenic abscess.

Taking MAD to the extreme: ultrafast protein structure determination

Multiwavelength anomalous diffraction data were measured in 23 min from a 16 kDa selenomethionyl substituted protein, producing experimental phases to 2.25 A resolution. The data were collected on a mosaic 3 x 3 charge-coupled device using undulator radiation from the Structural Biology Center 19ID beamline at the Argonne National Laboratory's Advanced Photon Source. The phases were independently obtained semiautomatically by two crystallographic program suites, CCP4 and CNS. The quality and speed of this data acquisition exemplify the opportunities at third-generation synchrotron sources for high-throughput protein crystal structure determination.

Structure of a new crystal form of human Hsp70 ATPase domain

Hsp70 proteins are highly conserved proteins induced by heat shock and other stress conditions. An ATP-binding domain of human Hsp70 protein has been crystallized in two major morphological forms at pH 7.0 in the presence of PEG 8000 and CaCl2. Both crystal forms belong to the orthorhombic space group P212121, but show no resemblance in unit-cell parameters. Analysis of the crystal structures for both forms shows a 1-2 A shift of one of the subdomains of the protein. This conformational change could reflect a 'natural' flexibility of the protein which might be relevant to ATP binding and may facilitate the interaction of other proteins with Hsp70 protein.

Crystallization and preliminary crystallographic analysis of an NADH oxidase that functions in peroxide reduction in Thermus aquaticus YT-1

NADH oxidase from Thermus aquaticus is a thermostable flavoenzyme that is similar in amino-acid sequence and other properties to the flavoenzyme component of the NADH peroxidase systems from Salmonella typhimurium and Amphibacillus xylanus. The enzyme has been isolated from T. aquaticus and crystallized using the hanging-drop method of vapour diffusion with sodium citrate as a precipitant at pH 8.5. The crystals belong to the hexagonal space group P622 with unit-cell dimensions a = b = 89.9, c = 491.6 A, and diffract to 2.5 A resolution.

X-ray crystal structure of the Desulfovibrio vulgaris (Hildenborough) apoflavodoxin-riboflavin complex

The apoprotein of flavodoxin from Desulfovibrio vulgaris forms a complex with riboflavin. The ability to bind riboflavin distinguishes this flavodoxin from other short-chain flavodoxins which require the phosphate of FMN for flavin binding. The redox potential of the semiquinone/hydroquinone couple of the bound riboflavin is 180 mV less negative than the corresponding complex with FMN. To elucidate the binding of riboflavin, the complex has been crystallized and the crystal structure solved by molecular replacement using native flavodoxin as a search model to a resolution of 0.183 nm. Compared to the FMN complex, the hydrogen-bonding network at the isoalloxazine sub-site of the riboflavin complex is severely disrupted by movement of the loop residues Ser58-Ile64 (60-loop) which contact the isoalloxazine by over 0.35 nm, and by a small displacement of the isoalloxazine moiety. The 60-loop movement away from the flavin increases the solvent exposure of the flavin-binding site. The conformation of the site at which 5'-phosphate of FMN normally binds is similar in the two complexes, but in the riboflavin complex a sulphate or phosphate ion from the crystallization buffer occupies the space. This causes small structural perturbations in the phosphate-binding site. The flexibility of the 60-loop in D. vulgaris flavodoxin appears to be a contributing factor to the binding of riboflavin by the apoprotein, and a feature that distinguishes the protein from other 'short chain' flavodoxins. In the absence of the terminal phosphate group, free movement at the 5'-OH group of the ribityl chain can occur. Thus, the 5'-phosphate of FMN secures the cofactor at the binding site and positions it optimally. The structural changes which occur in the 60-loop in the riboflavin complex probably account for most of the positive shift that is observed in the midpoint potential of the semiquinone/hydroquinone couple of the riboflavin complex compared to that of the FMN complex.

Refinement of triclinic hen egg-white lysozyme at atomic resolution

X-ray diffraction data have been collected at both low (120 K) and room temperature from triclinic crystals of hen egg-white lysozyme to 0.925 and 0.950 A resolution, respectively, using synchrotron radiation. Data from one crystal were sufficient for the low-temperature study, whereas three crystals were required at room temperature. Refinement was carried out using the programs PROLSQ, ARP and SHELXL to give final conventional R factors of 8.98 and 10.48% for data with F > 4sigma(F) for the low- and room-temperature structures, respectively. The estimated r.m.s. coordinate error is 0.032 A for protein atoms, 0.050 A for all atoms in the low-temperature study, and 0.038 A for protein atoms and 0.049 A for all atoms in the room-temperature case, as estimated from inversion of the blocked least-squares matrix. The low-temperature study revealed that the side chains of 24 amino acids had multiple conformations. A total of 250 waters, six nitrate ions and three acetate ions, two of which were modelled with alternate orientations were located in the electron-density maps. Three sections of the main chain were modelled in alternate conformations. The room-temperature study produced a model with multiple conformations for eight side chains and a total of 139 water molecules, six nitrate but no acetate ions. The occupancies of the water molecules were refined in both structures and this step was shown to be meaningful when assessed by use of the free R factor. A detailed description and comparison of the structures is made with reference to the previously reported structure refined at 2.0 A resolution.

Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants

Mutants of the electron-transfer protein flavodoxin from Desulfovibrio vulgaris were made by site-directed mutagenesis to investigate the role of glycine-61 in stabilizing the semiquinone of FMN by the protein and in controlling the flavin redox potentials. The spectroscopic properties, oxidation-reduction potentials, and flavin-binding properties of the mutant proteins, G61A/N/V and L, were compared with those of wild-type flavodoxin. The affinities of all of the mutant apoproteins for FMN and riboflavin were less than that of the wild-type apoprotein, and the redox potentials of the two 1-electron steps in the reduction of the complex with FMN were also affected by the mutations. Values for the dissociation constants of the complexes of the apoprotein with the semiquinone and hydroquinone forms of FMN were calculated from the redox potentials and the dissociation constant of the oxidized complex and used to derive the free energies of binding of the FMN in its three oxidation states. These showed that the semiquinone is destabilized in all of the mutants, and that the extent of destabilization tends to increase with increasing bulkiness of the side chain at residue 61. It is concluded that the hydrogen bond between the carbonyl of glycine-61 and N(5)H of FMN semiquinone in wild-type flavodoxin is either absent or severely impaired in the mutants. X-ray crystal structure analysis of the oxidized forms of the four mutant proteins shows that the protein loop that contains residue 61 is moved away from the flavin by 5-6 A. The hydrogen bond formed between the backbone nitrogen of aspartate-62 and O(4) of the dimethylisoalloxazine of the flavin in wild-type flavodoxin is absent in the mutants. Reliable structural information was not obtained for the reduced forms of the mutant proteins, but if the mutants change conformation when the flavin is reduced to the semiquinone, to facilitate hydrogen bonding between N(5)H and the carbonyl of residue 61, then the change must be different from that known to occur in wild-type flavodoxin.

Crystallization and preliminary X-ray crystallographic analysis of the electron-transferring flavoprotein from Megasphaera elsdenii

Electron-transferring flavoprotein from the rumen bacterium Megasphaera elsdenii is a heterodimer (M(r) = 75 kDa) containing FAD as cofactor and functioning solely to mediate electron transfer between the prosthetic groups of other proteins. The enzyme was crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 4000 as precipitant. The crystals obtained belong to the space group P2(1)2(1)2(1) with unit-cell dimensions of a = 58.75, b = 61.77 and c = 122.27 A. Interestingly the crystals exhibit a low solvent content. Crystals diffracted to beyond 2.5 A using synchrotron radiation.

Recurrent laryngeal nerve dysfunction following carotid endarterectomy

Recurrent laryngeal nerve dysfunction is a significant complication of carotid endarterectomy and vocal cord paralysis is a major source of morbidity. This study prospectively assessed patients undergoing carotid endarterectomy to determine the nature and frequency of vocal cord damage and attempt to identify avoidable factors. Fifty consecutive patients undergoing carotid endarterectomy for symptomatic disease were studied. A standardized surgical technique was used emphasizing identification of the vagus nerve and minimal disturbance of the surrounding tissues. All patients underwent pre-operative and post-operative (day 2) indirect laryngoscopy and videostroboscopy. Pre-operative assessment found asymptomatic compensated vocal cord paralysis in one patient who had previously had a stroke. Post-operative laryngoscopy revealed asymptomatic impaired vocal cord mobility in three patients (6%) all of whom recovered completely. In addition six patients (12%) developed post-operative hoarseness of whom five have fully recovered. The remaining patient (2%) developed vocal cord paralysis which is permanent to date. This prospective study demonstrates that recurrent laryngeal nerve dysfunction is a common but often transient complication of carotid endarterectomy. The incidence of vocal cord paralysis in this group was less than many of the reported series. This could be due to the technique of minimal dissection which may prevent disturbance of the vagal segmental blood supply. Pre-operative vocal cord assessment is essential in all patients undergoing carotid endarterectomy.

Oral terbutaline after parenteral tocolysis: a randomized, double-blind, placebo-controlled trial

OBJECTIVE

Our purpose was to determine whether oral terbutaline, used after successful intravenous tocolysis, will prolong pregnancy and prevent recurrent preterm labor.

STUDY DESIGN

After successful intravenous tocolysis, 203 women with preterm labor at 24 weeks' to 34 weeks 6 days' gestation were randomized to terbutaline (5 mg orally, every 4 hours) or placebo until 37 weeks' gestation. Women with recurrent preterm labor were treated with intravenous magnesium sulfate; if tocolysis was successful, they continued with the initial study medication. The primary outcome was the percentage delivered of their infants within 1 week of beginning oral tocolytic therapy. Latency, recurrent preterm labor, and maternal and neonatal outcomes were also assessed.

RESULTS

Pregnancy outcome data were available in 200 women. There were no differences seen between the two groups in the incidence of delivery at 1 week (18% vs 24%, 95% confidence interval 0.44 to 1.29). In addition, there were no differences regarding median latency, mean gestational age at delivery, or the incidence of recurrent preterm labor (20% vs 16%, 95% confidence interval 0.64 to 2.71). Post hoc evaluation of 96 women enrolled before 32 weeks' gestation suggested pregnancy prolongation with maintenance oral terbutaline (p < 0.01).

CONCLUSIONS

Maintenance oral terbutaline therapy initiated at 24 weeks' to 34 weeks 6 days' gestation after successful parenteral tocolysis is not associated with pregnancy prolongation or a reduction in the incidence of recurrent preterm labor.

Examining the ear: clinical teaching

Although otolaryngology represents up to 20% of the workload of general practitioners, the time allocated in the undergraduate medical curriculum to clinical teaching of ENT disorders is disproportionately small. Many GPs have indicated a desire for further training in ENT, particularly in small groups. This study was carried out on a group of 27 GPs who wished to revise their diagnostic skills in otoscopy by attending a 2-hour teaching session on basic examination of the ear and the recognition and management of common otological conditions. The GPs skill in otoscopy before and after the course was assessed subjectively by means of a self-administered questionnaire and scored objectively by ENT surgeons. Aspects of otoscopy chosen for assessment were technique of examination of the external ear, choosing correct speculum size, techniques of holding the otoscope and pinna, tympanic membrane description and diagnostic ability. An improvement between the objective pre- and post-workshop scores was found for assessment of the external ear, choice of speculum size, description of the tympanic membrane and diagnostic ability. No significant differences in the pre- and post-workshop scores was found for the techniques of holding the otoscope or holding the pinna. The majority of the GPs found the workshop beneficial. Postgraduate teaching of specialist diagnostic skills such as otoscopy to GPs is useful. An improvement in such skills should enable the GPs to manage ENT problems more confidently and refer patients appropriately to the ENT outpatients.

Cervicofacial actinomycosis: an unusual cause of submandibular swelling

Two cases of cervicofacial actinomycosis, resulting in submandibular swelling, are presented. How actinomycosis may present under the guise of malignancy is well demonstrated. Factors predisposing to the condition, difficulties with diagnosis, isolation methods of the causative organism and treatment of the disease, are discussed.

Bacteriology of tonsil and adenoid and sampling techniques of adenoidal bacteriology

The value of pernasal swabs and direct adenoid swabs in chronic adenoid and adenotonsillar disease was assessed in 175 patients. Prior to adenoidectomy (53 patients) or adenotonsillectomy (122 patients), pernasal and direct adenoid swabs were taken. Adenoid currettings and tonsil tissue were cultured. Haemophilus influenzae was the bacterium most frequently isolated from adenoid currettings and from the centre (core) of the resected tonsil. There was a close relationship between the bacteriology of the pernasal swab and the adenoid tissue and tonsil core in 72 and 71% of patients, respectively. There was an identical profile of pathogens in 52 and 49%, respectively. We suggest that in children with adenoiditis or adenotonsillitis and hypertrophy of the adenoid, a pernasal swab should be used in preference to a throat swab in selecting appropriate antimicrobial therapy. Penicillin and ampicillin are not appropriate blind therapy in chronic adenoid and adenotonsillar infections because of the prevalence of beta-lactamase-producing aerobes (40%) in adenoid and tonsil core in these conditions.

Post-tonsillectomy bacteraemia

Post-tonsillectomy bacteraemia is a well recognized aetiological factor in streptococcal endocarditis. Prophylactic penicillin has been recommended to reduce its incidence in susceptible patients undergoing tonsillectomy. Recent studies have shown a change in the microflora and an increase in the number of penicillin resistant organisms in the tonsils of patients undergoing tonsillectomy. The aim of this study has been to assess the incidence of post-tonsillectomy bacteraemia, identify the organisms associated with it and review the suitability of penicillin in prophylactic regimens. Of the 32 patients included in the study, 11 (34.4%) had positive post-tonsillectomy blood cultures. We were surprised at this low incidence of bacteraemia and have postulated a possible reason. Haemophilus influenzae was isolated from 4 (36.4%) of the positive cultures and Streptococcus viridans in only 1 (9%). Rather than using penicillin for prophylaxis a beta-lactamase stable antibiotic would be more appropriate.

Amplitude rise time and the perception of the voiceless affricate/fricative distinction

Variation of amplitude envelope at stimulus onset has been considered to be of primary importance for distinguishing voiceless affricates from fricatives (e.g., [symbol: see text]). In earlier perceptual experiments, however, variation in amplitude rise time was confounded with variation in frication duration. In two experiments, these variables were independently manipulated, and their individual and combined effects for perception of magnitude of [symbol: see text] were examined. Variation in amplitude rise time alone was not sufficient to signal the voiceless affricate/fricative contrast in these experiments, but variation in frication duration alone was sufficient.