Large-scale purification of human BACE expressed in mammalian cells and removal of the prosegment with HIV-1 protease to improve crystal diffraction.

BACE, or beta-secretase, is an attractive target in the treatment of Alzheimer's Disease because of its involvement in the generation of amyloid beta peptides. BACE is a type I transmembrane aspartyl protease composed of pre-, pro-, catalytic, transmembrane and cytoplasmic domains. For the present study, the coding sequence was truncated just before the transmembrane domain and the resulting construct was extended with the C-terminal addition of a (His)(6) and expressed in several mammalian host cells. The enzyme expressed in CHO cells had the best crystallographic behavior and was purified in large quantities in a three step procedure. The purified BACE was comprised of two forms, namely the full length proBACE construct beginning with Thr(1), and a derivative missing the first 24 amino acids beginning with E(25). These BACE precursors co-crystallized in the presence of inhibitors yielding structures to 3.2 A resolution. HIV-1 protease treatment of this mixture resulted in complete cleavage of the F(39)-V(40) bond, leaving the V(40)EM...ES(432) (His)(6) derivative that was purified yielding an enzyme that was no more active than untreated BACE but co-crystallized with inhibitors producing well shaped, bipyramidal co-crystals diffracting to 2.6 A resolution.

High yield expression of human BACE constructs in Eschericia coli for refolding, purification, and high resolution diffracting crystal forms.

BACE (beta-site APP cleaving enzyme) or beta-secretase, the enzyme responsible for processing APP to give the N-terminal portion of the Abeta peptide, is a membrane bound aspartyl protease consisting of an ectodomain catalytic unit, a C-terminal transmembrane segment and a cytoplasmic domain. Three BACE constructs, pET11a-BACE, pQE80L-BACE, and pQE70-BACE were designed to terminate at a position just before the transmembrane domain (Ser(432)) and are described schematically below. (1) pET11a-T7.Tag-G-S-M-(A-8GV......QTDES(432)), (2) pQE80L-Met-R-G-S-(His)(6)-G-S-I-E-T-D-(T(1)QH...QTDES(432)), and (3) pQE70-Met-BACE (R(36)GSFVEMG....PQTDES(432) (His) (6)) Each construct was over-expressed in Escherichia coli as inclusion bodies. The inclusion body proteins were solubilized in urea and refolded by dilution in water to yield active enzyme. Maximal activity for pET11a-BACE and pQE80L-BACE was usually reached at day 3 to 4, while construct pQE70-BACE required about 21 days. Active BACE was purified to homogeneity by anion-exchange chromatography and affinity chromatography over a column of immobilized peptide inhibitor. The process, easily scalable to 60 liters of cell culture, yielded in excess of 400 mg of active enzyme for crystallographic analysis. Highly purified pET11a-BACE and pQE70-BACE formed complexes with various inhibitors, the latter protein giving crystals diffracting up to 1.45 A resolution. In addition, a crystal form that does not require the presence of an inhibitor has been obtained for pQE70-BACE. This ligand-free crystal form has proven useful for the preparation of BACE-inhibitor complexes in soaking experiments.

High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.

BACKGROUND: Zinc fingers of the Cys2-His2 class comprise one of the largest families of eukaryotic DNA-binding motifs and recognize a diverse set of DNA sequences. These proteins have a relatively simple modular structure and key base contacts are typically made by a few residues from each finger. These features make the zinc finger motif an attractive system for designing novel DNA-binding proteins and for exploring fundamental principles of protein-DNA recognition. RESULTS: Here we report the X-ray crystal structures of zinc finger-DNA complexes involving three variants of Zif268, with multiple changes in the recognition helix of finger one. We describe the structure of each of these three-finger peptides bound to its corresponding target site. To help elucidate the differential basis for site-specific recognition, the structures of four other complexes containing various combinations of these peptides with alternative binding sites have also been determined. CONCLUSIONS: The protein-DNA contacts observed in these complexes reveal the basis for the specificity demonstrated by these Zif268 variants. Many, but not all, of the contacts can be rationalized in terms of a recognition code, but the predictive value of such a code is limited. The structures illustrate how modest changes in the docking arrangement accommodate the new sidechain-base and sidechain-phosphate interactions. Such adaptations help explain the versatility of naturally occurring zinc finger proteins and their utility in design.

The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls.

BACKGROUND: The repeating disaccharide and pentapeptide units of the bacterial peptidoglycan layer are connected by a lactyl ether bridge biosynthesized from UDP-N-acetylglucosamine and phosphoenolpyruvate in sequential enol ether transfer and reduction steps catalyzed by MurA and MurB respectively. Knowledge of the structure and mechanism of the MurB enzyme will permit analysis of this unusual enol ether reduction reaction and may facilitate the design of inhibitors as candidate next-generation antimicrobial agents. RESULTS: The crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase, MurB, has been solved at 3.0 A and compared with our previously reported structure of MurB complexed with its substrate enolpyruvyl-UDP-N- acetylglucosamine. Comparison of the liganded structure of MurB with this unliganded form reveals that the binding of substrate induces a substantial movement of domain 3 (residues 219-319) of the enzyme and a significant rearrangement of a loop within this domain. These ligand induced changes disrupt a stacking interaction between two tyrosines (Tyr190 and Tyr254) which lie at the side of the channel leading to the active site of the free enzyme. CONCLUSIONS: The conformational change induced by enolpyruvyl-UDP-N- acetylglucosamine binding to MurB results in the closure of the substrate-binding channel over the substrate. Tyr190 swings over the channel opening and establishes a hydrogen bond with an oxygen of the alpha-phosphate of the sugar nucleotide substrate which is critical to substrate binding.

The versatility of phosphoenolpyruvate and its vinyl ether products in biosynthesis.

The diverse enzymes that use phosphoenolpyruvate as a substrate lie at the heart of cellular energy metabolism, as well as a number of critical biosynthetic pathways. The versatility of the enol ether linkage is reflected not only in the rich chemistry and enzymology of PEP, but also in the variety of metabolites in which the high-energy enol ether linkage is preserved.

Crystallization and preliminary X-ray crystallographic studies of UDP-N-acetylenolpyruvylglucosamine reductase.

The overexpression and purification of the second enzyme in Escherichia coli peptidoglycan biosynthesis, UDP-N-acetylenolpyruvylglucosamine reductase (MurB), provided sufficient protein to undertake crystallization and X-ray crystallographic studies of the enzyme. MurB crystallizes in 14-20% PEG 8000, 100 mM sodium cacodylate, pH 8.0, and 200 mM calcium acetate in the presence of its substrate UDP-N-acetylglucosamine enolpyruvate. Crystals of MurB belong to the tetragonal space group P4(1)2(1)2 with a = b = 49.6 A, c = 263.2 A, and alpha = beta = gamma = 90 degrees at -160 degrees C and diffract to at least 2.5 A. Screening for heavy atom derivatives has yielded a single site that is reactive with both methylmercury nitrate and Thimerosal.

Synapses formed by olivocochlear axon branches in the mouse cochlear nucleus.

Cochlear nucleus branches of thick olivocochlear axons were labeled by injections of horseradish peroxidase into the spiral ganglion of the cochlear basal turn in mice. Six labeled axons were traced by light microscopy, and selected portions of seven branches were sectioned serially for electron microscopic examination. Axonal branches most frequently terminated near certain granule cell regions of the ventral cochlear nucleus. This article describes terminals, synapses, and postsynaptic elements of these olivocochlear branches. The olivocochlear branches had both terminal and en passant boutons that contained round vesicles and made asymmetric synapses with other neuronal processes. About a quarter of the synapses also possessed additional specializations, postsynaptic, or subjunctional bodies. Mossy terminals, a multisynaptic type of terminal commonly found in granule cell regions, were not found arising from any of the labeled branches. No somatic synapses were found, although contacts with cell bodies were occasionally observed. The predominant synaptic target of olivocochlear branches were what appeared to be dendrites of large diameter. At least some of these large dendrites received multiple synapses from a single labeled olivocochlear branch. The morphological characteristics of reconstructed dendrites suggest that multipolar cells might be predominant targets for the medial olivocochlear system in the cochlear nucleus. This was demonstrated in one case in which a large dendrite was followed to its cell body of origin.

Projection of septal organ receptor neurons to the main olfactory bulb in rats.

The septal organ of Masera is a distinct patch of olfactory epithelium on the septal wall of the nasal cavity. It lies ventral to the main olfactory receptor sheet. Central projections of the septal organ to the main and/or accessory olfactory bulb were studied with punctate HRP injections into the posterior dorsomedial olfactory bulb of rat pups. Injection sites encompassed 2-8% of the main olfactory bulb glomeruli and some injection sites were confined to the accessory olfactory bulb glomeruli. The distribution of receptor neurons in the septal organ that were labeled as a result of retrograde transport from the injection sites was determined. Olfactory receptor neurons were labeled in septal organs of those animals with injection sites confined to the main olfactory bulb. Subsequent to the posterior dorsomedial bulbar injections of this study, labeled receptor neurons were preferentially located in the posterior portion of the septal organ and were clustered about a plane dorsal to the plane bisecting the organ. Injections confined to the accessory olfactory bulb only labeled vomeronasal organ receptor neurons. Thus it is likely that the main olfactory bulb and not the accessory olfactory bulb is the bulbar terminus of septal organ receptor neurons. To date, experimental evidence suggests that the septal organ system may comprise an anatomically and functionally unique chemosensory pathway for odor detection.

Synapses from medial olivocochlear branches in the inferior vestibular nucleus.

Olivocochlear neurons are auditory efferent neurons that convey information from the brainstem to the auditory periphery. With light and electron microscopy, using mice, we studied the central branches of medial olivocochlear neurons that are given off to the inferior vestibular nucleus. At the level of the electron microscope, the branches form synapses. The synapses are asymmetric with round vesicles, suggesting that they are excitatory. The synapses are formed mainly onto neuronal dendrites. These dendrites have a large range of diameters, and they may emanate from several types of target neurons. These results indicate that the inferior vestibular nucleus is an integrating center for vestibular, auditory, and other types of information, but the results do not fit with current theories about the function of the olivocochlear system.

Transneuronal labeling of cochlear nucleus neurons by HRP-labeled auditory nerve fibers and olivocochlear branches in mice.

Auditory nerve fibers were labeled by extracellular injections of horseradish peroxidase into the spiral ganglion in mice. The labeled fibers were traced in an anterograde direction through the auditory nerve into the cochlear nucleus. In almost half of the injections, the labeled endings of auditory nerve fibers contacted cochlear nucleus neurons that were also labeled with horseradish peroxidase and were presumably transneuronally labeled. Only darkly labeled endings were associated with transneuronally labeled neurons, but not all darkly labeled endings had targets that were transneuronally labeled. Transneuronal labeling occurred almost exclusively in the ventral cochlear nucleus, often between endbulbs and bushy cells. Both "modified" endbulbs and the larger endbulbs of Held transneuronally labeled the bushy cells that they contacted. At the ultrastructural level, transneuronal labeling was evident as a darkening of ribosomes and the membrane surfaces of mitochondria, endoplasmic reticulum, and the nucleus. Transneuronal labeling occurred rarely in octopus, small, and stellate cells, and in neurons of the dorsal cochlear nucleus. Spiral ganglion injections also label olivocochlear fibers, efferent fibers that pass through the ganglion en route to the hair cells. These fibers give off branches to the cochlear nucleus that were rarely associated with transneuronal labeling. In eight instances, the targets of olivocochlear branches were stellate cells or small cells. We suggest that in our mouse preparation, horseradish peroxidase is effective as a transneuronal marker because the short distance from injection site to the cochlear nucleus results in a high concentration of horseradish peroxidase in the endings of the auditory nerve fibers.

Synaptic input to cochlear nucleus dendrites that receive medial olivocochlear synapses.

Axons of olivocochlear neurons originate in the superior olivary complex and project to the cochlea. Along their course, medial olivocochlear axons give off branches to the cochlear nucleus. We labeled these branches with horseradish peroxidase and used electron microscopy to determine their target dendrites. Target dendrites were of two classes: "large" dendrites and "varicose" dendrites. Using serial sections, we reconstructed the dendrites and, in addition to the labeled olivocochlear input, we determined the synaptic profile of unlabeled inputs onto the dendrites. We classified the terminals on the basis of the shape and size of their synaptic vesicles. On large dendrites, the predominant type of unlabeled terminal had small round (SmRnd) vesicles. These terminals are likely to be excitatory, and some of them may originate from unlabeled medial olivocochlear branches. On varicose dendrites, the predominant type of terminal had pleomorphic vesicles. These terminals are likely to be inhibitory. They may be from descending inputs that arise in higher centers. A final type of terminal onto large dendrites exhibited signs of neuronal degeneration, possibly because the cell body of origin was damaged during the injection procedure. These terminals often had long, perforated synaptic densities and may originate from type II primary afferents. Thus, medial olivocochlear efferents and type II afferents, which both contact outer hair cells in the periphery, appear to synapse onto the same targets in the cochlear nucleus. In contrast, where examined, the target dendrites did not receive terminals with large vesicles from afferents that contact inner hair cells. Thus, target neurons appear to function in a neural circuit associated more closely with outer than with inner hair cells.

Brainstem branches from olivocochlear axons in cats and rodents.

Horseradish peroxidase was used to label axons of olivocochlear (OC) neurons by intracellular injections in cats and extracellular injections in rodents. These axons arise from cell bodies in the superior olivary complex and project to the cochlea. En route to the cochlea, the thick axons (greater than 0.7 micron diam.) of medial olivocochlear (MOC) neurons formed collaterals that terminated in the ventral cochlear nucleus, the interstitial nucleus of the vestibular nerve (in cats), and the inferior vestibular nucleus (in rodents). The thin axons (less than 0.7 micron diam.), presumed to arise from lateral olivocochlear (LOC) neurons, did not branch near the CN. Within the CN, the MOC collaterals tended to ramify in and near regions with high densities of granule cells, regions also associated with the terminals of type II afferent axons (Brown et al.: J. Comp. Neurol. 278:581-590, '88). These results suggest that those fibers associated peripherally with outer hair cells (MOC efferents and type II afferents) are associated centrally with regions containing granule cells, whereas those fibers associated with inner hair cells peripherally (LOC efferents and type I afferents) are not.

Unmyelinated axons of the auditory nerve in cats.

This paper describes some central terminations of type II spiral ganglion neurons as labeled by extracellular injections of horseradish peroxidase (HRP) into the auditory nerve of cats. After histological processing with diaminobenzidine, both thick (2-4 microns) and thin (0.5 microns) fibers of the auditory nerve were stained. Whenever traced, thick fibers always originated from type I spiral ganglion neurons and thin fibers always from type II ganglion neurons. Because the labeling of type II axons faded as fibers projected into the cochlear nucleus, this report is limited to regions of the ventral cochlear nucleus near the auditory nerve root. The central axons of type II neurons are unmyelinated, have simple yet variable branching patterns in the cochlear nucleus, and form both en passant and terminal swellings. Under the light microscope, most swellings are located in the neuropil but they are also found in the vicinity of cell bodies, nodes of Ranvier of type I axons, and blood vessels. Eighteen en passant swellings in the neuropil were located by light microscopy and resectioned for electron microscopy; two of these swellings exhibited ultrastructural features characteristic of chemical synapses. The data indicate that inputs from outer hair cells might be able to influence auditory processing in the cochlear nucleus through type II primary neurons.

Neuron labeling by extracellular delivery of horseradish peroxidase in vivo: a method for studying the local circuitry of projection and interneurons at physiologically characterized sites.

An anatomical method is described that yields individual neurons with continuously labeled dendrites and axons following the extracellular deposition of horseradish peroxidase (HRP) at neurophysiological recording sites in vivo. The method is a logical evolution of previous methods for iontophoretic delivery of HRP: Parameters critical to the ultimate concentration of HRP at the labeling site are reduced by an order of magnitude relative to standard practice. In successful cases one neuron or two in the immediate vicinity (50 microns) of recording sites is/are labeled. Labeling of other processes traversing the injection site, if any, is subliminal at highest light microscopic magnification. Due to the labeling of so few cells and the absence of other labeled processes, dendritic trees and local axonal arbors can be reconstructed without ambiguity. In addition to recovering neurons at sites characterized with physiological (e.g., sensory) stimuli, the method offers the further advantage of being fully compatible with subsequent electron microscopy. Both large (> 20 microns) and small (approximately 8 microns) neuron types and glia have been labeled.

High-resolution 2-deoxyglucose autoradiography in quick-frozen slabs of neonatal rat olfactory bulb.

We have used rapid freezing and freeze-substitution fixation to permit electron microscopic study of [3H]2-deoxyglucose autoradiographs. The techniques minimize diffusion of label into processing fluids and, by inference, migration of label within tissue. Slabs of olfactory bulbs from 12-day-old rats were quick-frozen after one hour of exposure to physiological olfactory stimuli. In light microscopic autoradiographs at low magnification, the neuropil of individual olfactory glomeruli appeared uniformly labeled with different levels of labeling in different glomeruli. At higher magnification, glomerular neuropil labeling consisted of small unlabeled regions surrounded by label clusters, suggesting greater deoxyglucose uptake by olfactory nerve terminals as compared with their postsynaptic dendrites. Periglomerular neurons were labeled differentially. Some microglia and glia precursor cells were heavily labeled in all bulbar laminae. The ultrastructure of cells and neuropil in all bulbar laminae was well-preserved. Cell processes and organelles could be identified in both stained sections and unstained electron microscopic autoradiographs. These experiments demonstrate the feasibility of combining quick-freezing with freeze substitution, in order to extend the resolution of studies using diffusable tracers such as 2-deoxyglucose. The results suggest that this is a promising method for assessing several controversies concerning deoxyglucose incorporation and neuronal and glial metabolism.

Synapses from labeled type II axons in the mouse cochlear nucleus.

This study investigates the ultrastructure and central targets in the cochlear nucleus of axonal swellings of type II primary afferent neurons. Type II axons comprise only 5-10% of the axons of the auditory nerve of mammals, but they alone provide the afferent innervation of the outer hair cells. In this study, type II axons were labeled with horseradish peroxidase, and serial-section electron microscopy was used to examine their swellings in: (1) the granule-cell lamina at its boundary with posteroventral cochlear nucleus, (2) the rostral anteroventral cochlear nucleus, and (3) the auditory nerve root. Only some (18%) of the type II terminal and en-passant swellings formed synapses. The synapses were asymmetric and contained clear round synaptic vesicles, suggesting that they are excitatory. Type II synapses were compared to those from type I fibers providing the afferent innervation of the inner hair cells. Type II synapses tended to have slightly smaller and fewer synaptic vesicles, had a greater proportion of the membrane apposition accompanied by a postsynaptic density, and often had densities that were discontinuous or 'perforated'. In all cochlear nucleus regions examined, the postsynaptic targets of type II synapses had characteristics of dendrites; in most cases these dendrites could not be traced to their cell bodies of origin. Some evidence suggests, however, that targets may include granule cells, spherical cells, and other cells in the nerve root. These results suggest afferent information from outer hair cells reaches diverse regions and targets within the cochlear nucleus.

Cytotoxic testing for food allergy: evaluation of reproducibility and correlation.

Cytotoxic food tests still present conflicting opinions concerning their validity. Nine atopic patients with or without a history of food allergy were studied along with 5 nonatopic patients. All tests were conducted in a double-blind fashion with 6 determinations for each of 10 food antigens. Reproducibility of the test (5/6 positive or negative) was demonstrated with wheat, milk, yeast, chocolate, and orange. In the nonatopic group, reproducible results were obtained for wheat, egg, yeast, chocolate, and chicken. Clinical correlation with 11 foods in 7 patients was demonstrated. However, there were 46 positive tests without correlation and 2 negative tests with positive histories. Therefore, there appears to be reproducibility of the tests to only 3 foods but no apparent correlation with clinical symptoms. At the present time, cytotoxic tests offer no reliable help in establishing the diagnosis of food allergy.

Effects of sensory deprivation on the developing mouse olfactory system: a light and electron microscopic, morphometric analysis.

Closure of the nostril by electrocauterization on postnatal day (PN) 1 or 2 was used to study effects of olfactory deprivation on developing olfactory epithelium (OE) and bulb (OB) in CD-1 mice. No damage was observed in OE sections 1 or 3 days after closure, and at PN 30 no difference was found in the number of OE receptors between closed and open sides. Odor deprivation and a decrease in functional activity in experimental bulbs was evident from deoxyglucose autoradiographs at PN 21 and PN 30. At PN 30 deprived bulbs appeared smaller than nondeprived bulbs. Nissl stains revealed normal cytoarchitecture, but a protargol stain demonstrated fewer intraglomerular dendrites in deprived bulbs. At PN 30, volumes of deprived bulbs were 26% smaller than nondeprived bulbs. The volume of each bulbar lamina was 13 to 35% smaller than the comparable nondeprived lamina except for the ventricular/subependymal zone which was not significantly different between bulbs. Volumes of bulbs contralateral to the closed naris and the volumes of their laminae were not significantly different from control bulbs, suggesting no hypertrophy of nondeprived laminae. Deprivation did not affect the number of mitral cells seen at PN 30, their nuclear size, or their number of nucleoli. Lateral olfactory tract cross-sectional area was also unaffected by deprivation. Mitral cell perikaryal size, however, was smaller in deprived bulbs. Soma surface areal density of deprived mitral-to-granule cell synapses in deprived bulbs was 65% of the nondeprived density, while the density of granule-to-mitral cell synapses was only 46% of the nondeprived density. It is concluded that neonatal naris closure brings about a functional deprivation of the OB without receptor degeneration. Neonatal olfactory deprivation affects the perikaryal surface area but not the number of mitral cells. Also, deprivation markedly affects the reciprocal synapses between mitral and granule cells. Olfactory sensation thus appears necessary for normal development of OB neurons and synapses.

Kinetic characterization of wild-type and S229A mutant MurB: evidence for the role of Ser 229 as a general acid.

X-ray derived structural data predicted that serine 229 was positioned to act as a proton donor to the developing C2 carbanion during the reduction of enolpyruvyl-UDP-N-acetylglucosamine catalyzed by the bacterial peptidoglycan biosynthetic flavoenzyme MurB. To investigate this effect, a mutant where serine 229 was replaced by alanine was constructed and purified. Kinetic analysis of the two half-reactions for the mutant enzyme revealed a 9-fold decrease in the reduction of EFlox by NADPH and a dramatic 10(7)-fold decrease in the reoxidation of EFlred with the enolpyruvyl substrate. In addition, studies of S229A with the substrate analog, (E)-enolbutyryl-UDP-N-acetylglucosamine, showed a striking bias of the partitioning toward formation of the (Z) geometric isomer as opposed to formation of the reduced product UDP-methylmuramic acid, which was the predominant product in wild-type MurB. These studies provide evidence for the proposed role of this active-site serine as a general acid catalyst.

X-ray crystal structures of the S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine at 1.8-A resolution.

MurB catalyzes the second committed step in the synthesis of peptidoglycan, a key component of the bacterial cell wall. The crystal structures of both a S229A mutant and wild-type MurB in the presence of the substrate enolpyruvyl-UDP-N-acetylglucosamine were solved and refined at 1.8 A resolution. The single point mutation of residue 229 from serine to alanine eliminated a hydroxyl group which has previously been proposed to play a critical role as a proton donor during the second half-reaction of MurB, namely, reoxidation of FADH2 and reduction of the enolpyruvyl substrate. The mutation also resulted in the loss of the water molecule-hydrogen bonded to the serine hydroxyl in the wild-type structure changing the hydrogen-bonding network with in the active site. Comparison of the wild-type and S229A mutant structures confirms that the dramatic kinetic defect of an approximately 10(7)-fold decrease observed for the Ser 229 Ala mutant in the second half-reaction [Benson, T.E., Walsh, C.T., & Massey, V. (1997) Biochemistry 36, 796-805] is a direct result of the loss of the serine hydroxyl moiety rather than other nonspecific active-site changes or general structural defects.