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.

Overview of nucleic acid analysis programs.

We outline the mathematical distinctions among seven of the most popular computer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into three basic categories on the basis of their definitions of rotational parameters: matrix-based, projection-based, and combined matrix- and projection-based. The approaches also define and construct base and base-pair coordinate frames in a variety of ways. Despite these mathematical distinctions, the computed parameters from some programs are strongly correlated and directly comparable. By contrast, other programs which use identical methodologies sometimes yield very different results. The choice of reference frame rather than the mathematical formulation has the greater effect on calculated parameters. Any factor which influences the reference frame, such as fitting or not fitting standard bases to the experimentally derived coordinates, will have a noticeable effect on both complementary base pair and dimer step parameters.

Flexing and folding double helical DNA.

DNA base sequence, once thought to be interesting only as a carrier of the genetic blueprint, is now recognized as playing a structural role in modulating the biological activity of genes. Primary sequences of nucleic acid bases describe real three-dimensional structures with properties reflecting those structures. Moreover, the structures are base sequence dependent with individual residues adopting characteristic spatial forms. As a consequence, the double helix can fold into tertiary arrangements, although the deformation is much more gradual and spread over a larger molecular scale than in proteins. As part of an effort to understand how local structural irregularities are translated at the macromolecular level in DNA and recognized by proteins, a series of calculations probing the structure and properties of the double helix have been performed. By combining several computational techniques, complementary information as well as a series of built-in checks and balances for assessing the significance of the findings are obtained. The known sequence dependent bending, twisting, and translation of simple dimeric fragments have been incorporated into computer models of long open DNAs of varying length and chemical composition as well as in closed double helical circles and loops. The extent to which the double helix can be forced to bend and twist is monitored with newly parameterized base sequence dependent elastic energy potentials based on the observed configurations of adjacent base pairs in the B-DNA crystallographic literature.

Expression and purification of recombinant cynomolgus monkey cholesteryl ester transfer protein from Chinese hamster ovary cells.

Cholesteryl ester transfer protein (CETP) mediates the transfer of cholesteryl ester from high- and low-density lipoproteins to triglyceride-rich lipoproteins, and reciprocally mediates triglyceride transfer. The gene for cynomolgus monkey CETP was expressed in serum-free CHO culture with 2 micrograms/ml insulin as its only exogenous protein supplement. Cell growth was facilitated by immobilizing the CHO cells in alginate beads. Recombinant CETP (rCETP) was purified 176-fold with a three-step protocol resulting in a 60% final yield as measured by a fluorescent CETP activity assay. Typically, 3.4 mg of rCETP was purified from 1700 ml of media by affinity-gel chromatography involving Reactive Red 120 (RR120) followed by concanavalin A Sepharose 4B and rechromatography on RR120. SDS-PAGE shows a single broad band of M(r) ranging from 68,000 to 74,000 which immunoreacts in Western blot analysis. Amino acid analysis and protein sequencing of the purified protein agree with the theoretical amino acid composition and sequence of cynomolgus CETP.

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

Analyzing nucleic acid structures in a comparable manner has become increasingly important as the number of solved structures has increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Mathematical definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original physical intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple physical model (net rotation at constant angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical definitions are symmetrical with the property that a 5 degrees tilt is the same as a 5 degrees roll and a 5 degrees twist, except that the rotations take place about different axes. In other approaches, a 5 degrees tilt can mean a different amount of net rotation than a 5 degrees roll or a 5 degrees twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as mathematically induced artifacts in other approaches. This paper, together with the statistical analysis in the companion paper for determining the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures.

The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters.

This paper critically examines the methodologies used to analyze nucleic acid three-dimensional structure based on guidelines set at a 1988 EMBO workshop. The implications of these analyses cannot be fully understood without a thorough knowledge of how the numbers are calculated. This paper addresses one aspect of the calculations, namely the observed correlations between various parameters. These correlations are addressed in the mathematics by explicitly incorporating the concept of a pivot point, which is the point about which a base rotates as it buckles, propeller twists and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters found in other approaches. The correlations that are reduced or eliminated are actually artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. The mathematics we have developed, including the mathematics of pivot points, are presented in the companion paper. Here, we explain how some of the observed correlations occur as a by-product of the method of calculation, while others are truly structural, and we show how optimum pivot points can be determined to minimize artifactual correlations. The observation that experimental bases often rotate about the long axis in a "propeller" motion as well as rotate about the Z-axis of each base, "opening" into the major groove, is evident in the location of the optimum region for the pivot point as determined in this study. We consider locating a pivot point as a calibration step to increase the agreement between physical intuition and the mathematics of our program.

Nucleic acid structure analysis: a users guide to a collection of new analysis programs.

Common nomenclature describing the geometry of nucleic acid structures was established at a 1988 EMBO Workshop on DNA Curvature and Bending (Diekmann, S. (1988) J. Mol. Biol. 208, 787-791; Diekmann, S. (1989) The EMBO Journal 8, 1-4; Sarma, R.H. (1988) J. Biomol. Structure & Dynamics 6, 391-395; Dickerson, R.E. (1989) J. Biomol. Structure & Dynamics 6, 627-634; Dickerson, R.E. et al. (1989) Nuc. Acids Res. 17, 1979-1803). We have subsequently developed and incorporated sophisticated mathematics in a computer program to calculate the parameters described by the guidelines. The program calculates all the local parameters relating complementary bases and neighboring base and base pairs in both Cartesian and helical coordinate frames. In addition, the main mathematical property requested by the EMBO guidelines--that the magnitude of the parameters be independent of strand or direction of measurement--is accomplished without the use of a midway coordinate frame for the rotational parameters. The mathematics preserve the physical intuition used in defining the parameters; in particular, the rotational parameters are true rotations based on a simple physical model (rotation at constant angular velocity for a unit amount of time), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical equations are symmetric with the property that a 5 degrees tilt is the same as a 5 degrees roll or a 5 degrees twist, except that the rotations take place about different axes. In other approaches, a 5 degrees tilt can mean a different amount of net rotation from a 5 degrees roll or a 5 degrees twist. In addition, a great deal of flexibility is built into the program so that the user has control over the analysis, including the input format, the coordinate frame used for the base pairing relationship, the point about which the rotations are performed, and which geometric relationships are analyzed. While there is a great deal of flexibility, the program is easy to use. Interactive queries and user accessible files make the options in the program very convenient to tailor to individual needs. In addition, there is also a program that calculates bond lengths, valence angles, and torsion angles along the nucleic acid backbone, and within the sugar and base rings. Another program 'learns' the identities of the bond lengths, valence angles, and torsion angles that the user would like to determine.(ABSTRACT TRUNCATED AT 400 WORDS)

Comparative properties of untreated and N-nitrosobenzylmethyl-amine-transformed rat esophageal epithelial cell lines.

A culture system utilizing rat esophageal epithelial cells has been developed. Four normal and eight N-nitrosobenzylmethylamine-treated lines were compared with respect to chromosome number, anchorage-independent growth in agarose, and tumorigenic potential in syngeneic rats. All cell lines were aneuploid with nine in the near-tetraploid range and three in the near-diploid range. No relation between tumorigenic potential and chromosome number or structure was apparent. Similarly, anchorage-independent growth in agarose did not correlate with tumorigenic potential. Three of the 12 immortalized lines (two carcinogen-treated and 1 untreated) induced well-differentiated squamous cell carcinomas in syngeneic rats. These tumors had weak metastatic potentials suggesting that tumorigenic potential and metastatic ability are separately controlled. These cell lines will be useful for the investigation of factors involved in the conversion of immortalized rat esophageal epithelial cell lines to lines of high metastatic potential.

An unusually compact retrotransposon in maize.

Unlike any other known plant transposon, the maize transposable element Bs1 is similar to the retrotransposons previously described in yeast and Drosophila. Bs1 is bounded by 302 bp identical long terminal repeats (LTRs), and it contains open reading frames with apparent amino acid sequence similarity to reverse transcriptase and other retroviral pol gene enzymes. Bs1 is 3203 bp long, very short for a retrotransposon, and the apparent organization of its genetic information is significantly different from any previously described element. Although transcription of Bs1 has not been observed, it is probably an active transposon, since it was observed to transpose in a maize line that contains only two sequences hybridizing to Bs1 probes. Both of these sequences share 35 restriction sites with the cloned Bs1 element, and thus must be very similar or identical with it.

Ellagic acid toxicity and interaction with benzo[a]pyrene and benzo[a]pyrene 7,8-dihydrodiol in human bronchial epithelial cells.

Ellagic acid, a plant phenol present in various foods consumed by humans, has been reported to have both anti-mutagenic and anti-carcinogenic potential. To evaluate the potential anti-carcinogenic property of ellagic acid, we tested its effects on the toxicity of benzo[a]pyrene and benzo[a]pyrene, 7,8-dihydrodiol and binding of benzo[a]pyrene to DNA in cultured human bronchial epithelial cells. The toxicity of ellagic acid itself for human bronchial epithelial cells was also determined. Using a colony-forming efficiency assay, it was found that a nontoxic concentration of ellagic acid (5 micrograms/ml) enhanced the toxicity of benzo[a]pyrene 7,8-dihydrodiol in human bronchial epithelial cells. In contrast, ellagic acid at concentrations of 1.5 and 3.0 micrograms/ml inhibited binding of benzo[a]pyrene metabolites to DNA in these cells. An explanation for the potentiating effect of ellagic acid on the toxicity of benzo[a]pyrene, 7,8-dihydrodiol will require further investigation into the possible mechanisms of interaction between these two compounds.

Nucleotide sequence and molecular evolution of two tomato genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase.

We have isolated and sequenced two cDNA clones (LESS5 and LESS17) encoding the small subunit of ribulose-1,5-bisphosphate carboxylase of tomato (Lycopersicon esculentum). At the nucleotide level, the protein-coding regions of these genes are 85% conserved, while the untranslated 3' regions are only 55% conserved. Comparison with rbcS genes from other species of Solanaceae suggests that the tomato LESS5 gene, the Nicotiana tabacum NTSS23 gene and the Petunia hybrida SSU8 gene are orthologous members of the rbcS gene family. In addition, the tomato gene LESS17, and the Petunia hybrida gene SSU611, may also be orthologous, since their untranslated 3' regions are related. There is a large difference between the two tomato rbcS genes in the frequency of the CG dinucleotide. This difference may reflect different levels of methylation, and therefore expression, of the tomato genes. Many of the differences involving the CG dinucleotide can be represented as transitions between C and T on the noncoding strand. Such changes are consistent with observations that methylated cytosines are hot-spots for transitions.

Benzo(alpha)pyrene metabolism and DNA-binding in cultured explants of human bronchus and in monolayer cultures of human bronchial epithelial cells treated with ellagic acid.

Ellagic acid, a plant phenolic compound present in certain foods eaten by humans, has been reported to possess antimutagenic and anticarcinogenic properties. To evaluate the potential anticarcinogenic effect of ellagic acid in humans, we investigated the effect of nontoxic concentrations of ellagic acid on the metabolism of benzo(alpha)pyrene and binding of benzo(alpha)pyrene metabolites to DNA in cultured explants of human bronchus and in human bronchial epithelial cell cultures. Ellagic acid at concentrations of 10, 25, or 50 microM did not significantly alter the metabolism of benzo(alpha)pyrene in the bronchial explant cultures and in only one of four bronchial cell cultures. However, binding of metabolites of benzo(alpha)pyrene to DNA was inhibited in all explant and cell cultures of human bronchus by 26 to 77%. These results support the work of other investigators and suggest that ellagic acid may be an inhibitor of polycyclic aromatic hydrocarbon-induced carcinogenesis in humans.

Clonal growth and serial propagation of rat esophageal epithelial cells.

The clonal growth and serial propagation of rat esophageal epithelial cells in low serum-containing medium has been achieved without feeder layers or conditioned medium. To date, a total of four lines have been developed and maintained for as many as 40 passages in culture. Growth of the cells was possible only after modifying the culture medium (PFMR-4) by reducing the calcium concentration from 1 to 0.1 mM, and by adding low levels of dialyzed fetal bovine serum and seven growth factors; i.e. epidermal growth factor, hydrocortisone, ethanolamine, phosphoethanolamine, insulin, transferrin, and cholera toxin. Cell lines have been developed from both explant outgrowths and enzyme dissociated esophagi. The epithelial nature of the cells was confirmed by electron microscopy and immunological methods. Clonal growth studies revealed that optimal cell growth occurred in medium containing 2.4% dialyzed fetal bovine serum and 0.1 mM calcium. Calcium levels of 0.3 mM or higher caused the cells to stratify and undergo terminal differentiation. Coating the culture dishes with collagen, or a combination of collagen, fibronectin, and bovine serum albumin, increased both the cell growth rate and the colony forming efficiency. The successful long term culture of rat esophageal epithelial cells permits their use as models in studies concerned with esophageal differentiation and carcinogenesis.

In vitro transformation of rat esophageal epithelial cells with N-nitrosobenzylmethylamine.

Using an explant/cell culture system, rat esophageal epithelial cells were transformed in vitro by exposure to N-nitroso-N-benzyl-N-methylamine (BMNA). Twelve esophageal explant cultures per group were exposed twice (at days 1 and 7) to 0.0, 2.5, 5.0 or 10.0 micrograms BMNA/ml of medium. After incubation for 60-90 days, epithelial cells in primary cultures treated with all three concentrations of BMNA could be subcultured and cell lines were developed. The number of primary cultures and the number of subsequently developed epithelial cell lines was carcinogen-dose-dependent. Cell lines could only be established from carcinogen treated explants. Electron microscopy revealed that the BMNA-treated cell lines contained morphological markers of esophageal epithelial cells; i.e., numerous tonofilaments and junctional complexes, even after prolonged subculture. By immunofluorescence, the cells reacted positively with antibodies prepared to mouse skin prekeratins (K1 and K2). Two cell lines (from the 5 micrograms BMNA/ml group) were able to grow in soft agar and produce palpable tumors upon injection into syngeneic recipients. These tumors possessed the histological features of squamous cell carcinomas.

Chromosomal analysis of human prostatic adenocarcinoma cell lines.

Although detailed cytogenetic analysis has been carried out in many types of cancer, there is little information on the chromosomal makeup of prostatic cancer cells. Karyological analyses of cell lines derived from both metastatic and primary prostatic carcinoma have been carried out by Q-, C-, and sequential banding techniques. The metastatic line, PC-3, isolated from a bone marrow specimen, is an established epithelial line which is tumorigenic in nude, athymic mice and forms colonies in semisolid agar suspension. A subline, PC-3/M, was isolated from a PC-3-induced mouse tumor. Karyotypic analysis of PC-3 by Q- and C-banding showed the cells to be aneuploid at all culture passage levels. The modal chromosome number shifted from 62 to 55 between the 5th and 50th passages. PC-3 has a unique karyotype. Chromosomes 2, 3, 5, 15, and Y were always absent. At least 11 different marker chromosomes were observed. The subline, PC-3/M, had a similar karyotype and retained the parental PC-3 markers. PC-3/M had a more restricted chromosomal frequency distribution range. Nearly 73% of the PC-3/M cells examined had 60 or 61 chromosomes in contrast to the wide distribution seen in PC-3. Silver staining for nucleolus organizer regions indicated that the number of functional nucleolus organizer regions in PC-3 was proportional to the number of acrocentric chromosomes. Banding analysis of PC-5-PI isolated from primary prostatic adenocarcinoma indicated that this line also had a characteristic karyotype with 28% pseudodiploid and 72% pseudotetraploid components. All metaphases examined were partially trisomic in chromosome 9 and lacked a demonstrable Y chromosome.

Replicative epithelial cell cultures from normal human prostate gland.

Epithelial cell cultures of the normal human prostate gland were established. The subculturing of these cultures was accomplished with a novel nonenzymatic technique. These cultures were defined as normal epithelial cells on the basis of ultrastructure, karyotype, and inability to grow in soft agar.

Monolayer cultures of human prostatic cells.

The objective of this study was to isolate, characterize, and preserve normal prostatic epithelial and carcinoma cell lines. To date, four specimens have been acquired from patients with benign prostatic hypertrophy. Culture attempts have been successful, yielding a total of 32 cell lines. Three of these lines have been examined thus far and were found to have clearly demonstrable tartrate-inhibitable acid phosphatase granules by histochemical techniques. Several problem areas emerge from these preliminary studies. These involve the difficulty of (a) characterization of the cells as originating from prostatic epithelium, (b) identification of prostatic carcinoma cells, and (c) possible senescence in culture of cell lines.