NMR chemical shift assignment of the C-terminal region of the Menangle virus phosphoprotein.

Menangle virus is a bat-borne paramyxovirus with zoonotic potential. The single-stranded RNA genome of the virus is encapsidated in a helical nucleocapsid which is the template for both transcription and genome replication. Each of these operations is performed by the viral RNA polymerase. The phosphoprotein is the non-catalytic subunit of the polymerase, and its C-terminal region enables the polymerase to engage with the nucleocapsid. Here, we report the 1H, 15N, and 13C chemical shift assignments of the C-terminal region (amino acids 267-388) of the Menangle virus phosphoprotein. This region has a bipartite character, with a highly flexible and structurally disordered sequence preceding a structured nucleocapsid-binding domain. NMR chemical shift assignment will enable the detailed characterization of the dynamic behavior of the phosphoprotein, and its functional linkage with polymerase translocation.

The structure of truncated recombinant human bile salt-stimulated lipase reveals bile salt-independent conformational flexibility at the active-site loop and provides insights into heparin binding.

Human bile salt-stimulated lipase (BSSL), which is secreted from the pancreas into the digestive tract and from the lactating mammary gland into human milk, is important for the effective absorption of dietary lipids. The dependence of BSSL on bile acids for activity with water-insoluble substrates differentiates it from other lipases. We have determined the crystal structure of a truncated variant of human BSSL (residues 1-5.8) and refined it at 2.60 A resolution, to an R-factor of 0.238 and R(free) of 0.275. This variant lacks the C-terminal alpha-helix and tandem C-terminal repeat region of native BSSL, but retains full catalytic activity. A short loop (residues 115-126) capable of occluding the active-site (the active site loop) is highly mobile and exists in two conformations, the most predominant of which leaves the active-site open for interactions with substrate. The bile salt analogue 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonic acid (CHAPS) was present in the crystallisation medium, but was not observed bound to the enzyme. However, the structure reveals a sulfonate group from the buffer piperizine ethane sulfonic acid (PIPES), making interactions with Arg63 and His115. His115 is part of the active-site loop, indicating that the loop could participate in the binding of a sulphate group from either the glycosaminoglycan heparin (known to bind BSSL) or a bile acid such as deoxycholate. Opening of the 115-126 active-site loop may be cooperatively linked to a sulphate anion binding at this site. The helix bundle domain of BSSL (residues 319-398) exhibits weak electron density and high temperature factors, indicating considerable structural mobility. This domain contains an unusual Asp:Glu pair buried in a hydrophobic pocket between helices alpha(H) and alpha(K) that may be functionally important. We have also solved the structure of full-length glycosylated human BSSL at 4.1 A resolution, using the refined coordinates of the truncated molecule as a search model. This structure reveals the position of the C-terminal helix, missing in the truncated variant, and also shows the active-site loop to be in a closed conformation.

Characterization of Rous sarcoma virus Gag particles assembled in vitro.

Purified retrovirus Gag proteins or Gag protein fragments are able to assemble into virus-like particles (VLPs) in vitro in the presence of RNA. We have examined the role of nucleic acid and of the NC domain in assembly of VLPs from a Rous sarcoma virus (RSV) Gag protein and have characterized these VLPs using transmission electron microscopy (TEM), scanning TEM (STEM), and cryoelectron microscopy (cryo-EM). RNAs of diverse sizes, single-stranded DNA oligonucleotides as small as 22 nucleotides, double-stranded DNA, and heparin all promoted efficient assembly. The percentages of nucleic acid by mass, in the VLPs varied from 5 to 8%. The mean mass of VLPs, as determined by STEM, was 6.5 x 10(7) Da for both RNA-containing and DNA oligonucleotide-containing particles, corresponding to a stoichiometry of about 1,200 protein molecules per VLP, slightly lower than the 1,500 Gag molecules estimated previously for infectious RSV. By cryo-EM, the VLPs showed the characteristic morphology of immature retroviruses, with discernible regions of high density corresponding to the two domains of the CA protein. In spherically averaged density distributions, the mean radial distance to the density corresponding to the C-terminal domain of CA was 33 nm, considerably smaller than that of equivalent human immunodeficiency virus type 1 particles. Deletions of the distal portion of NC, including the second Zn-binding motif, had little effect on assembly, but deletions including the charged residues between the two Zn-binding motifs abrogated assembly. Mutation of the cysteine and histidine residues in the first Zn-binding motif to alanine did not affect assembly, but mutation of the basic residues between the two Zn-binding motifs, or of the basic residues in the N-terminal portion of NC, abrogated assembly. Together, these findings establish VLPs as a good model for immature virions and establish a foundation for dissection of the interactions that lead to assembly.

Locating the anomalous scatterers within a crystal using dual-wavelength X-ray diffraction measurements.

A simple algebraic expression is used to calculate the structure-factor amplitudes of the anomalous scatterers within a protein crystal, using X-ray diffraction measurements made at two wavelengths and given a single type of anomalous scatterer within the crystal. The expression is exact and is readily derived from the standard algebraic equations for analyzing multi-wavelength anomalous diffraction data. Evaluation of the expression requires estimates for (lambda)f' and (lambda)f", the real and imaginary components of the anomalous scattering, respectively. When these are not known at the wavelengths in question, a statistical procedure is suggested, applicable when the crystal space group has centrosymmetric projections, which allows the expression to be used regardless. The method may provide a useful alternative to existing procedures when (lambda)f' and (lambda)f" are unknown or when data have been measured at a limited number of wavelengths.

The organization of mature Rous sarcoma virus as studied by cryoelectron microscopy.

We have studied the organization of mature infectious Rous sarcoma virus (RSV), suspended in vitreous ice, using transmission electron microscopy. The enveloped virions are spherical in shape, have a mean diameter of 127 nm, and vary significantly in size. Image processing reveals the presence of the viral matrix protein underlying the lipid bilayer and the viral envelope proteins external to the lipid bilayer. In the interior of the virus, the characteristic mature retroviral core is clearly imaged. In contrast to lentiviruses, such as human immunodeficiency virus, the core of RSV is essentially isometric. The capsid, or external shell of the core, has a faceted, almost polygonal appearance in electron micrographs, but many capsids also exhibit continuous surface curvature. Cores are not uniform in size or shape. Serrations observed along the projected faces of the core suggest a repetitive molecular structure. Some isolated cores were observed in the sample, confirming that cores are at least transiently stable in the absence of the viral envelope. Using an approach grounded in geometric probability, we estimate the size of the viral core from the projection data. We show that the size of the core is not tightly controlled and that core size and virion size are positively correlated. From estimates of RNA packing density we conclude that either the RNA within the core is loosely packed or, more probably, that it does not fill the core.

Structure and self-association of the Rous sarcoma virus capsid protein.

BACKGROUND: The capsid protein (CA) of retroviruses, such as Rous sarcoma virus (RSV), consists of two independently folded domains. CA functions as part of a polyprotein during particle assembly and budding and, in addition, forms a shell encapsidating the genomic RNA in the mature, infectious virus. RESULTS: The structures of the N- and C-terminal domains of RSV CA have been determined by X-ray crystallography and solution nuclear magnetic resonance (NMR) spectroscopy, respectively. The N-terminal domain comprises seven alpha helices and a short beta hairpin at the N terminus. The N-terminal domain associates through a small, tightly packed, twofold symmetric interface within the crystal, different from those previously described for other retroviral CAs. The C-terminal domain is a compact bundle of four alpha helices, although the last few residues are disordered. In dilute solution, RSV CA is predominantly monomeric. We show, however, using electron microscopy, that intact RSV CA can assemble in vitro to form both tubular structures constructed from toroidal oligomers and planar monolayers. Both modes of assembly occur under similar solution conditions, and both sheets and tubes exhibit long-range order. CONCLUSIONS: The tertiary structure of CA is conserved across the major retroviral genera, yet sequence variations are sufficient to cause change in associative behavior. CA forms the exterior shell of the viral core in all mature retroviruses. However, the core morphology differs between viruses. Consistent with this observation, we find that the capsid proteins of RSV and human immunodeficiency virus type 1 exhibit different associative behavior in dilute solution and assemble in vitro into different structures.

Crystallization and preliminary X-ray analysis of native and recombinant human bile-salt dependent lipase: strategies for improvement of diffraction quality.

Human bile-salt dependent lipase (BSDL), secreted into both the digestive tract and human milk, is integral to the effective absorption of dietary lipids. In attempts to obtain crystals suitable for high-resolution X-ray crystallographic studies, various forms of the enzyme have been crystallized, including native and desialidated human milk BSDL and both intact recombinant BSDL and a truncated form lacking the heavily glycosylated C-terminal repeat region. Trigonal crystals of native BSDL, with unit-cell parameters a = b = 90.0, c = 156.1 A, were obtained using 15-20%(w/v) PEG 8000 as precipitant. These crystals diffract to 3.5 A along the unique axis, but to only 5-7 A in orthogonal directions. Crystals of recombinant truncated BSDL grown from 15-20%(w/v) PEG 6000 are orthorhombic, space group P2(1)2(1)2(1), with unit-cell parameters a = 59.2, b = 90.0, c = 107.7 A, and diffract to 2.6 A resolution. These are suitable for structural analysis by X-ray crystallography.

Chlorpyrifos: a ten-year US poison center exposure experience.

We performed a retrospective review of data based on poison center exposure inquiries related to chlorpyrifos (CP) and the corresponding poison center-determined medical outcomes reported to the Toxic Exposure Surveillance System (TESS) of the American Association of Poison Control Centers. Ten y (1985-1994) of TESS data were obtained. Medical outcomes representing all inquiries, accidental/unintentional inquiries, and intentional/suicidal inquiries were tabulated. Published TESS data was also tabulated to allow comparison of CP exposure inquiries to all non-pharmaceutical and insecticides/pesticides exposure inquiries for like time periods. Frequency of antidote use, product sales data, CP-related fatality reports, and pertinent issues related to telephone derived surveillance data were also reviewed; 36, 183 CP exposure inquiries were identified. Of all CP exposure inquiries, 27, 473 (75.9%) were assessed as having no significant health consequences; 4,511 (12.5%) outcomes were judged unrelated and 2,980 (8.2%) were unable to be followed. Reported significant medical outcomes for the remaining exposure inquiries were moderate 1,092 (3.0%), major 119 (0.3%) and death 8 (0.02%). Considering only calls with outcomes judged causally related to CP, where a given level of effect could reasonably be determined, 95.8% (27,473/28,692) of these calls resulted in no significant health effects. Use of antidotes specific to organophosphates were infrequent [atropine, 1.0% (385) and 2-PAM, 0.5% (177) of all cases respectively]. Despite the number of reported CP exposure inquiries, relatively few resulted in outcomes of consequence. TESS data suggested that the majority of patients undergoing medical evaluation and/or treatment after a suspected CP exposure do not require specific antidotes. TESS data serves as a useful first step in evaluating product safety. Assessment of product toxicity requires additional investigation of reported adverse effects and circumstances related to the incident.

On the molecular-replacement problem in the presence of merohedral twinning: structure of the N-terminal half-molecule of human lactoferrin.

The structure of a hemihedrally twinned protein crystal with two molecules in the asymmetric unit was solved by molecular replacement. The protein, a site-specific mutant of the N-terminal half-molecule of human lactoferrin, is able to undergo an internal rigid-body domain motion. Therefore, determining the structure required the independent positioning of four protein domains. The molecular-replacement solutions were obtained using a conventional real-space rotation function, and a translation function based on the linear correlation coefficient. Once the molecules were positioned, it was necessary to assign them to the appropriate twin domain. Several methods for doing this are described, one of which leads to a determination of the volume of each twin domain. In the appendix to the paper we discuss the interpretation of the self-rotation function in the presence of merohedral twinning.

The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP.

BACKGROUND: The organism Zymomonas mobilis occurs naturally in sugar-rich environments. To protect the bacterium against osmotic shock, the periplasmic enzyme glucose-fructose oxidoreductase (GFOR) produces the compatible, solute sorbitol by reduction of fructose, coupled with the oxidation of glucose to gluconolactone. Hence, Z mobilis can tolerate high concentrations of sugars and this property may be useful in the development of an efficient microbial process for ethanol production. Each enzyme subunit contains tightly associated NADP which is not released during the catalytic cycle. RESULTS: The structure of GFOR was determined by X-ray crystallography at 2.7 A resolution. Each subunit of the tetrameric enzyme comprises two domains, a classical dinucleotide-binding domain, and a C-terminal domain based on a predominantly antiparallel nine-stranded beta sheet. In the tetramer, the subunits associate to form two extended 18-stranded beta sheets, which pack against each other in a face to face fashion, creating an extensive interface at the core of the tetramer. An N-terminal arm from each subunit wraps around the dinucleotide-binding domain of an adjacent subunit, covering the adenine ring of NADP. CONCLUSIONS: In GFOR, the NADP is found associated with a classical dinucleotide-binding domain in a conventional fashion. The NADP is effectively buried in the protein-subunit interior as a result of interactions with the N-terminal arm from an adjacent subunit in the tetramer, and with a short helix from the C-terminal domain of the protein. This accounts for NADP's inability to dissociate. The N-terminal arm may also contribute to stabilization of the tetramer. The enzyme has an unexpected structural similarity with the cytoplasmic enzyme glucose-6-phosphate dehydrogenase (G6PD). We hypothesize that both enzymes have diverged from a common ancestor. The mechanism of catalysis is still unclear, but we have identified a conserved structural motif (Glu-Lys-Pro) in the active site of GFOR and G6PD that may be important for catalysis.

Search designs for protein crystallization based on orthogonal arrays.

In protein crystallography, the initial experimental problem is the identification of physical and chemical conditions that will support nucleation and crystal growth. Ideally, experiments to search for such conditions would be based on a full-factorial structure, with variation in the temperature and solution composition. However, consideration of even a moderate number of possibilities for the composition of the system will result in factorial experiments which may be prohibitively large. In this paper it is proposed that search experiments for protein crystallization might be based on orthogonal arrays. These are subsets of full-factorial experiments which possess a great deal of symmetry, such that a uniform distribution of points throughout the experimental region is preserved. Such experiments have reasonable size, explore the proposed experimental region in a systematic fashion, and form a logical basis for a sequential approach to the search for crystallization conditions. Examples of such initial search experiments are given, and their application to some recent protein crystallization problems in this laboratory is described briefly. The relationship of this approach to other protein crystallization search procedures is also discussed.

Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution.

The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 A resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0-1.8 A. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO(4)(2-) ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 A from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 A were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0-2.2 A. The final model of 1954 protein atoms, 264 water molecules, two SO(4)(2-) ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 A from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 A in reduced azurin to 1.24 A in oxidized azurin and 1.16 A in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.

Clinical observations and medical outcome in 149 cases of arsenate ant killer ingestion.

One hundred forty-nine (149) consecutive cases of arsenate-containing ant killer reported to the Minnesota Regional Poison Center over 4 1/2 months were retrospectively reviewed with a follow-up (1 week to 3 months) completed in 132 (89%) of the population studied. One hundred and forty eight (99%) of the ingestions were accidental. The majority of cases involved children 3 years of age and younger. Only three patients accidentally ingesting the product were symptomatic (mild episodes of vomiting and diarrhea which cleared in all patients within 12 hours). No patient was referred to a medical center for treatment and no patient reached on follow-up reported any additional ill effects as a result of the exposure. In addition to the 149 patients in this series, we describe two representative patients who accidentally ingested similar amounts of sodium arsenate-containing ant killer, resulting in urine arsenic of 3500 micrograms/24 h and 5819 micrograms/24 h. They required no chelation treatment and had no evident sequelae during 4-6 months of medical follow-up. This experience supports poison center directed home management for the majority of single, acute, and accidental ingestions of small quantities (< 5 mL) of arsenate-containing ant killers as a safe alternative to medical center referral and adverse reactions to chelation.

Activation of aldehyde dehydrogenase at physiological temperatures.

The release of NADH from the enzyme.NADH complexes was rate limiting at 37 degrees, for the oxidation of propionaldehyde by sheep liver cytosolic aldehyde dehydrogenase. Marked substrate activation was observed at this temperature as was activation by p-(chloromercuri)benzoate. Activation of enzymic activity may be of importance in vivo.

Comprehensive pharmaceutical services for a state correctional facility.

A contractual model for comprehensive pharmaceutical services involving a major medical center pharmacy, a university, and a state department of corrections is described. Project goals and methods for the provision of services are described. These include areas of formulary development, inventory management, drug distribution, on-site placement of pharmacy operations, and educational development. Impact of the program was assessed over a 30-month period. Development of policies and procedures for drug use in a correctional setting enabled implementation of a strict patient population-specific drug formulary. Procedural changes resulted in an 83% decrease in on-site drug inventories and a 62% decrease in quarterly drug expenditures. A one-time saving of more than $26,500 resulted from the decrease in on-site inventory, and an annual saving of $44,000 is projected for decreased drug expenditures. All but five controlled substances were removed from the formulary, and only 13 nonprescription items remained in the formulary. An educational course on health care in correctional settings provided exposure for pharmacy students to this new area of institutional practice. The contractual model proved both cost-effective and functional for the department of corrections.