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PubMed2004

FamClash: a method for ranking the activity of engineered enzymes.

This article introduces the computational procedure FamClash for analyzing incompatibilities in engineered protein hybrids by using protein family sequence data. All pairs of residue positions in the sequence alignment that conserve the property triplet of charge, volume, and hydrophobicity are first identified, and significant deviations are denoted as residue-residue clashes. This approach moves beyond earlier efforts aimed at solely classifying hybrids as functional or nonfunctional by correlating the rank ordering of these hybrids based on their activity levels. Experimental testing of this approach was performed in parallel to assess the predictive ability of FamClash. As a model system, single-crossover ITCHY (incremental truncation for the creation of hybrid enzymes) libraries were prepared from the Escherichia coli and Bacillus subtilis dihydrofolate reductases, and the activities of functional hybrids were determined. Comparisons of the predicted clash map as a function of crossover position revealed good agreement with activity data, reproducing the observed V shape and matching the location of a local peak in activity.

Bacillus subtilis↗
PubMed1987

Complete amino acid sequence and in vitro expression of rat NF-M, the middle molecular weight neurofilament protein.

A lambda gtII expression library was prepared from rat brain and screened with a polyclonal antiserum, which recognizes both NF-H and NF-M. An NF-M cDNA clone (pNF-M3C = 1.6 kb) was isolated and characterized. The fusion protein of NF-M3C, when used as an affinity matrix for the anti-neurofilament serum, isolated a subpopulation of antibodies specific for NF-M. Northern analysis demonstrates a single band of approximately 3000 nt and a constant message level for NF-M during postnatal development from postnatal day 0 (PO) to adulthood. Using pNF-M3C as a probe, a second cDNA clone was isolated from a lambda gtII rat brain expression library (pNF-M2D = 2.7 kb). The 2 clones were sequenced and pNF-M2D was found to encode the entire rat NF-M protein. The calculated molecular weight is 95,600, which is only 65% of the molecular weight determined by SDS-PAGE. The amino acid sequence of rat NF-M shows the conserved rod segment present in all intermediate filament proteins. The molecule also contains an unusual C-terminal extension with stretches of glutamic acid, which could contribute to the anomalous migration of this protein on SDS-PAGE and the fact that NF-M does not readily assemble into filaments. The pNF-M2D clone was transcribed and translated in vitro utilizing a rabbit reticulocyte lysate system. The resulting radiolabeled translation products were unexpectedly shown to comigrate with purified rat NF-M on 1- and 2-dimensional gels, even though the translated protein is not phosphorylated.

Amino Acid Sequence↗
PubMed2001

Searching sequence space for protein catalysts.

Genetic selection was used to explore the probability of finding enzymes in protein sequence space. Large degenerate libraries were prepared by replacing all secondary structure units in a dimeric, helical bundle chorismate mutase with simple binary-patterned modules based on a limited set of four polar and four nonpolar residues. Two-stage in vivo selection yielded catalytically active variants possessing biophysical and kinetic properties typical of the natural enzyme even though approximately 80% of the protein originates from the simplified modules and >90% of the protein consists of only eight different amino acids. This study provides a quantitative assessment of the number of sequences compatible with a given fold and implicates previously unidentified residues needed to form a functional active site. Given the extremely low incidence of enzymes in completely unbiased libraries, strategies that combine chemical information with genetic selection, like the one used here, may be generally useful in designing novel protein scaffolds with tailored activities.

Amino Acid Sequence↗
PubMed1992

Wheat Ec metallothionein genes. Like mammalian Zn2+ metallothionein genes, wheat Zn2+ metallothionein genes are conspicuously expressed during embryogenesis.

A cDNA library was prepared from the bulk mRNA of mature wheat embryos and screened with mixed 32P-labeled oligonucleotide probes that encoded parts of the partial amino-acid sequence for the Zn-containing Ec protein. Each DNA insert in 11 positives from a screen of 10(5) plaques encoded a 5' untranslated and a 3' untranslated region, in addition to an open reading frame (of 81 amino acids) which, in every case, corresponded to at least 56 of the 59 amino acids in the partial polypeptide sequence previously determined for the Ec protein. The three different mRNA sequences encoded in the cDNA probably correspond to single-copy genes in the A, B and D genomes of hexaploid wheat. A wheat genomic library was screened with 32P-labeled cDNA and gave a single positive in a screen of 5 x 10(5) plaques. A 3.1-kb genomic fragment (gf-3.1) was sequenced and a cap site for the encoded mRNA was determined by primer extension. The gf-3.1 sequence encodes an intronless mRNA for the Ec protein and contains appreciable amounts of 5' and 3' flanking sequences. In addition to a putative TATA box, two inverted-repeat sequences and one direct-repeat sequence, the 5' flank in gf-3.1 contains a sequence similar to the abscisic-acid-responsive element in other higher-plant genes but does not contain sequences similar to the metal-responsive elements in animal metallothionein genes. Consistent with these findings, RNA blotting shows that accumulation of Ec mRNA is abundant in immature embryos, undetectable in germinated embryos and can be induced by adding abscisic acid, but not by adding Zn2+ to the medium in which mature wheat embryos are germinated. The findings suggest that the wheat Ec metallothionein genes, like mammalian liver metallothionein genes, are conspicuously expressed during embryogenesis.

Amino Acid Sequence↗
PubMed2003

DNA sequence-based "bar codes" for tracking the origins of expressed sequence tags from a maize cDNA library constructed using multiple mRNA sources.

To enhance gene discovery, expressed sequence tag (EST) projects often make use of cDNA libraries produced using diverse mixtures of mRNAs. As such, expression data are lost because the origins of the resulting ESTs cannot be determined. Alternatively, multiple libraries can be prepared, each from a more restricted source of mRNAs. Although this approach allows the origins of ESTs to be determined, it requires the production of multiple libraries. A hybrid approach is reported here. A cDNA library was prepared using 21 different pools of maize (Zea mays) mRNAs. DNA sequence "bar codes" were added during first-strand cDNA synthesis to uniquely identify the mRNA source pool from which individual cDNAs were derived. Using a decoding algorithm that included error correction, it was possible to identify the source mRNA pool of more than 97% of the ESTs. The frequency at which a bar code is represented in an EST contig should be proportional to the abundance of the corresponding mRNA in the source pool. Consistent with this, all ESTs derived from several genes (zein and adh1) that are known to be exclusively expressed in kernels or preferentially expressed under anaerobic conditions, respectively, were exclusively tagged with bar codes associated with mRNA pools prepared from kernel and anaerobically treated seedlings, respectively. Hence, by allowing for the retention of expression data, the bar coding of cDNA libraries can enhance the value of EST projects.

Base Sequence↗
PubMed1993

Isolation of cosmids and fetal brain cDNAs from the proximal long arm of human chromosome 22.

The proximal portion of human chromosome 22q appears to carry genes implicated in the pathogenesis of various developmental disorders, including the cat eye syndrome (CES) and the DiGeorge syndrome (DGS). A cosmid library was prepared from a radiation hybrid selected for its content in chromosome 22 fragments. A large fraction of cosmids containing human DNA were found to derive from the juxtacentromeric region of chromosome 22, as shown by fluorescence in situ hybridization (FISH) performed using individual cosmids or cosmid pools as probes. Finer mapping was obtained for individual cosmids by hybridization to a somatic cell hybrid mapping panel which splits the long arm of the chromosome into 14 bins numbered 1 to 14 from the centromere to the telomere. Of the 10 cosmids mapped, eight belonged to group 1, the other two to group 14, in agreement with FISH data. Rare endonuclease sites and fragments conserved between species were searched in single cosmids, resulting in the selection of seven cosmid fragments which were used to screen a human fetal brain cDNA library. Three cDNAs were identified, encoded from two chromosome 22 genes which appeared to be novel, as determined from partial end sequence and comparison with the database entries. Fine localization of the 30.9 cDNA indicated that the corresponding gene was located in a segment of proximal 22q overlapping with the critical DGS region.

Animals↗
PubMed2003

Continuous flow techniques in organic synthesis.

As part of the dramatic changes associated with the need for preparing compound libraries in pharmaceutical and agrochemical research laboratories, the search for new technologies that allow automation of synthetic processes has become one of the main topics. Despite this strong trend for automation high-throughput chemistry is still carried out in batches, whereas flow-through processes are rather restricted to production processes. This is far from understandable because the main advantages of that approach are facile automation, reproducibility, safety, and process reliability, because constant reaction parameters can be assured. Indeed, methods and technologies are missing that allow rapid transfer from the research level to process development without time-consuming adaptation and optimization of methods from the laboratory scale to production plant scale. Continuous-flow processes are considered as a universal lever to overcome these restrictions and, only recently, joint efforts between synthetic and polymer chemists and chemical engineers have resulted in the first continuous-flow devices and microreactors; these allow rapid preparation of compounds with minimum workup. Many of these approaches use immobilized reagents and catalysts, which are embedded in a structured flow-through reactor. It is generally accepted, that for achieving best reaction and kinetic parameters for convective-flow processes monolithic materials are ideally suited as solid phases or polymer supports. In addition, immobilization techniques have to be developed that allow facile regeneration of the active species in the reactor.

Journal Article↗
PubMed1994

Identification and cloning of ELF-1, a developmentally expressed ligand for the Mek4 and Sek receptor tyrosine kinases.

Mek4 and Sek are tyrosine kinases with expression patterns in the mouse embryo that suggest important functions in early development. However, like all Eph family kinases, both were identified as orphan receptors without known ligands. We show that Mek4 and Sek soluble receptor-alkaline phosphatase fusion proteins can be used in a procedure termed RAP in situ to identify regions of ligand expression in the mouse embryo. Based on this spatial information, a cDNA expression library was prepared, and was screened with the fusion proteins to identify Eph ligand family-1 (ELF-1). In cell lines and embryos, ELF-1 is membrane bound by a phosphatidylinositol tail, a feature that may account for unique biological functions. Its sequence is homologous with B61, a ligand for the Eck kinase, defining a family of related ligands. The expression domains of ELF-1, Mek4 and Sek indicate potential roles in embryonic patterning.

Amino Acid Sequence↗
PubMed1992

Cloning and sequencing of cDNA encoding the putative insect plasma membrane V-ATPase subunit A.

For the first time a cDNA encoding subunit A of an invertebrate V-ATPase has been sequenced. The cDNA library was prepared from larval midgut of the tobacco hornworm, Manduca sexta, and screened with monoclonal antibodies to the midgut plasma membrane subunit A. From the cDNA sequence the insect subunit A is predicted to consist of 617 amino acids with a relative molecular mass of 68,162. The predicted primary structure is similar to that of the published eukaryotic subunit A proteins (Bos, Daucus, Saccharomyces and Neurospora); it most closely resembles the bovine amino acid sequences with which it has an 83% sequence identity.

Adenosine Triphosphatases↗
PubMed1991

Molecular cloning of transcripts that accumulate during the late G1 phase in cultured mouse cells.

To identify previously undetected genes that might be involved in later stages of the transition from a quiescent state (G0) to the DNA synthetic phase (S) of murine cells, we set out to isolate cDNA clones derived from mRNAs that appear late in G1 phase in serum-stimulated cells. A lambda-cDNA library was prepared using poly(A)+ RNA from chemically transformed Balb/c 3T3 cells (BP/A31) that had been brought to quiescence and subsequently stimulated for 12 h with serum. From the first screening of approximately 21,000 recombinant phage plaques, about 100 clones were isolated that hybridized to a single-stranded cDNA pool derived from stimulated-cell RNA but not to DNAs made from resting-cell RNA. Eventually, six different clones were identified. The mRNAs from five of these genes increased gradually during the G0 to S transition, in contrast to the "immediate-early" rise of c-myc mRNA or the later rise of thymidine kinase mRNA. These six clones were sequenced and compared to the GenBank database. Clones LG-80, LG-2, and LG-69 are highly homologous to beta-actin, lactate dehydrogenase, and alpha-tubulin. Clones LG-5, LG-61, and LG-74 had no significant homologies to known sequences. A subtractive cDNA library was used to isolate two additional clones, Sub-S1 and Sub-S2; these have homologies to enolase and ribosomal protein L32. Additional studies that examine the function and regulation of these newly identified "late response" genes in the pre-DNA synthesis pathway are in progress.

Amino Acid Sequence↗
PubMed1991

A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals.

A panel of human monoclonal antibody Fab fragments has been generated against the surface glycoprotein gp120 of type 1 human immunodeficiency virus (HIV) by antigen selection from a random combinatorial library expressed on the surface of filamentous phage. The library was prepared from 5 ml of bone marrow from an asymptomatic individual who has been HIV-positive for 6 years. The antibodies have high affinity for antigen (mostly with affinity constants of greater than 10(8) M-1) and notable sequence diversity. Given appropriate donor selection, the methods described should allow the generation of antibodies for the evaluation of passive immunization as a therapy for AIDS.

Amino Acid Sequence↗
PubMed2002

Serological identification of antigens associated with renal cell carcinoma.

Serological analysis of cDNA expression libraries (SEREX) is a technique designed for the identification of tumor specific antigens serologically recognized by the patient immune system. Application of SEREX to different types of tumor led to the identification of a wide range of tumor-associated antigens. Here we used SEREX to search for new antigens associated with renal cancer. The cDNA expression libraries were prepared from two renal cell carcinoma specimens and screened with the autologous patients sera. A total of 96 positive clones representing 66 different genes were isolated, including 18 genes with unknown function. All positive clones were further characterized by reactivity against a panel of sera from healthy donors and patients with renal cancer. As a result, we identified four antigens with a cancer-related serological profile, which may be used for the diagnostics of renal cancer.

Antibodies↗
PubMedDate not supplied

Isolation of a unique membrane protein from Naegleria fowleri.

Naegleria fowleri, an amoeboflagellate, is the causative agent of Primary Amoebic Meningoencephalitis, a fulminating disease of the central nervous system. In order to elucidate the mechanisms of pathogenicity of this amoeba, a cDNA expression library was prepared from N. fowleri RNA. A specific protein was found to be expressed from a cDNA clone designated Mp2CL5. Northern blot analysis showed that the Mp2CL5 mRNA was expressed in pathogenic N. fowleri but was not expressed in non-pathogenic Naegleria species nor in Acanthamoeba. Western blot analysis using anti-N. fowleri antiserum demonstrated that IPTG-induced Escherichia coli Mp2CL5 expressed a 23-kDa recombinant protein. The Mp2CL5 recombinant protein was histidine-tagged and purified to homogeneity from E. coli. A polyclonal rabbit antiserum was prepared against the purified Mp2CL5 recombinant protein. This antibody was used to further characterize the Mp2CL5 native protein expressed by N. fowleri. Western blot analysis in conjunction with immunofluorescence microscopy demonstrated the presence of a native protein of 17 kDa on the plasma membrane of N. fowleri trophozoites. The native N. fowleri protein was expressed in the logarithmic phase of trophozoite growth and the production of this protein increased through the stationary phase of growth. Studies are in progress to examine further its role as a virulence factor.

Amebiasis↗
PubMed2001

Directional cDNA library construction assisted by the in vitro recombination reaction.

We report here a new directional cDNA library construction method using an in vitro site-specific recombination reaction, based on the integrase-excisionase system of bacteriophage lambda. Preliminary experiments revealed that in vitro recombinational cloning (RC) provided important advantages over conventional ligation-assisted cloning: it eliminated restriction digestion for directional cloning, generated low levels of chimeric clones, reduced size bias and, in our hands, gave a higher cloning efficiency than conventional ligation reactions. In a cDNA cloning experiment using an in vitro synthesized long poly(A)(+) RNA (7.8 kb), the RC gave a higher full-length cDNA clone content and about 10 times more transformants than conventional ligation-assisted cloning. Furthermore, characterization of rat brain cDNA clones yielded by the RC method showed that the frequency of cDNA clones >2 kb having internal NotI sites was approximately 6%, whereas these cDNAs could not be cloned at all or could be isolated only in a truncated form by conventional methods. Taken together, these results indicate that the RC method makes it possible to prepare cDNA libraries better representing the entire population of cDNAs, without sacrificing the simplicity of current conventional ligation-assisted methods.

Animals↗
PubMed1992

Characterization of a paired box- and homeobox-containing quail gene (Pax-QNR) expressed in the neuroretina.

The retina is an integral part of the central nervous system, and consists of two layers, the outer pigmented layer and the inner sensory layer or neuroretina (NR). The NR layer contains several strata of cells (glial and neuronal) derived from proliferating neuroectodermal precursors that differentiate after terminal mitosis. In vitro, NR cells can differentiate not only into neuronal and glial types, but also into pigment and lens cells. Quail (Coturnix coturnix japonica) NR cells (QNR) infected with MC29 transforming retrovirus become pigmented after several passages in vitro. In order to characterize the genes expressed in these pigmented MC29 QNR, a cDNA library was prepared from these cells. After differential screening we have isolated a cDNA clone which identifies an RNA expressed in NR but not in the pigmented layer of the retina. This cDNA encodes a protein related to that of Drosophila, mouse and zebrafish paired box- and homeobox-containing segmentation genes and is called Pax-QNR. The expression of Pax-QNR in the NR is confined to the ganglionic cell layer and to the lower part of the inner nuclear layer containing the amacrine or correlation neurones.

Amino Acid Sequence↗
PubMed1989

Cloning and sequence analysis of cDNA for precursor of a crustacean hyperglycemic hormone.

Crustacean hyperglycemic hormone (CHH) from Carcinus maenas, a 72 amino acid neuropeptide, originates in neurosecretory perikarya in the eyestalk ganglia. Poly (A)RNA was isolated from these perikarya and a cDNA library was prepared. Screening of 20,000 clones with a 26-mer oligonucleotide, corresponding to a partial sequence of CHH, yielded one positive clone with an insert of approximately 2,000 bp, which contained the complete coding sequence for a pre-pro CHH. This precursor consists of a putative 26 amino acid signal sequence, a 38 amino acid peptide of unknown function (Peptide C), and the CHH sequence at the carboxyl end. The CHH-sequence is flanked N-terminally by a Lys-Arg cleavage site and C-terminally by the tetrapeptide Gly-Arg-Lys-Lys which is followed by the stop codon.

Amino Acid Sequence↗
PubMed1999

Covalent immobilization of recombinant human alphavbeta3 integrin on a solid support with retention of functionality.

Alphavbeta3 is the major receptor mediating the attachment of osteoclasts to bone surface and plays a critical role in bone resorption and remodeling. Interfering with alphavbeta3 binding inhibits osteoclast-mediated bone resorption, and thus demonstrates the potential utility of alphavbeta3 antagonists for therapy of osteoporosis. This report describes the generation of an alphavbeta3 affinity column which was created to enable screening of collections of large numbers of ligands, e.g., combinatorial libraries (previously prepared by us), to sort and identify ligands with the highest affinity for alphavbeta3. We demonstrate that covalent immobilization of the heterodimeric alphavbeta3 receptor can be achieved with retention of characteristic ligand binding properties. Human alphavbeta3 was isolated from human embryonic kidney cells (HEK 293) that stably express high levels of the recombinant receptor and then affinity purified to homogeneity. Purified alphavbeta3 receptor was linked covalently to activated CH-Sepharose 4B beads. Quantification of immobilized functional receptor was determined by Scatchard analysis. The immobilized functional receptor maintains binding properties similar to the membrane-embedded and soluble receptor. The immobilized receptor also can be used to select the highest affinity ligand from among a mixture of peptides which differ in their binding affinity, structure, and hydrophobicity, both when the peptides are loaded in equimolar concentrations in a mixture and when the concentration of the highest affinity ligand is reduced 10-fold. Liquid chromatography-mass spectrometry was utilized to confirm selective ligand binding and to demonstrate that preferential binding was not due to nonspecific hydrophobic interactions with immobilized alphavbeta3 receptor or the affinity column. This approach may be of general use for affinity-based screening of ligands for other integrins and should enable practical screening of combinatorial libraries containing large numbers of potential ligands for the human alphavbeta3 integrin receptor, including linear peptides, cyclic peptides, and peptidomimetics.

Binding, Competitive↗
PubMed1997

Restriction sites as identification tags for lymphocyte cDNAs.

A cDNA library was prepared from BW 5147 murine lymphoma cells in lambda ecc III phage and randomly partitioned into 291 sectors, each with 800-1000 recombinant phage plaques. One sector was chosen for further characterization in terms of sensitivity to restriction endonuclease cutting. Aliquots of DNA preparations from this sector were treated with XhoI, SmaI, NcoI, PvuII, PstI, HindIII, EcoRI, BamHI, and ApaLI before being used as templates in a cell-free expression system. The polypeptide products were separated by two-dimensional (2-D) gel electrophoresis and radiofluorographs of the gels were submitted to computer-aided image analysis. The matched patterns were inspected for the presence or absence of spots upon individual endonuclease treatments. Thereafter the results were integrated in a data matrix which served as a basis to construct "restriction tags" for all spots. These (restriction) tags are binary numbers termed "cut numbers" and are a representation of the set of recognition sequences which are (or are not) part of the coding sequence. From 493 sequences (visualized as 2-D gel spots), 12 were not cut by any of the nine enzymes, while 45 were cut by all of them. The percentages of sequences resistant to enzyme treatment ranged between 17% and 77% for NcoI and XhoI, respectively. The enzyme treatments led to the appearance of a certain portion of "new spots", probably products from truncated sequences. From 512 possible cut numbers, 136 were assigned to the 493 spots. Restriction tags are available to facilitate retrieval of cDNA clones from the (partitioned) cDNA library.

Animals↗