Showing papers by "Laboratory of Molecular Biology published in 1994"
TL;DR: The crystal structure of bovine mitochondrial F1-ATPase determined at 2.8 Å resolution supports a catalytic mechanism in intact ATP synthase in which the three catalytic subunits are in different states of the catalytic cycle at any instant.
Abstract: In the crystal structure of bovine mitochondrial F1-ATPase determined at 2.8 A resolution, the three catalytic beta-subunits differ in conformation and in the bound nucleotide. The structure supports a catalytic mechanism in intact ATP synthase in which the three catalytic subunits are in different states of the catalytic cycle at any instant. Interconversion of the states may be achieved by rotation of the alpha 3 beta 3 subassembly relative to an alpha-helical domain of the gamma-subunit.
2,878 citations
TL;DR: The nucleotide sequence of a contiguous 2,181,032 base pairs in the central gene cluster of chromosome III is completed, and comparison with the public sequence databases reveals similarities to previously known genes for about one gene in three.
Abstract: As part of our effort to sequence the 100-megabase (Mb) genome of the nematode Caenorhabditis elegans, we have completed the nucleotide sequence of a contiguous 2,181,032 base pairs in the central gene cluster of chromosome III. Analysis of the finished sequence has indicated an average density of about one gene per five kilobases; comparison with the public sequence databases reveals similarities to previously known genes for about one gene in three. In addition, the genomic sequence contains several intriguing features, including putative gene duplications and a variety of other repeats with potential evolutionary implications.
1,612 citations
TL;DR: Fusion proteins formed after chromosomal translocations are common in a range of tumour types; these are unique tumour antigens and are therefore potential targets for therapy design.
Abstract: Chromosomal abnormalities in tumours were recognized at the end of the last century but their significance has only recently become clear. Distinct translocations in leukaemias and in solid tumours lead to the activation of proto-oncogene products or, more commonly, creation of tumour-specific fusion proteins. The proteins in both categories are often transcription factors and thus disruption of transcriptional control plays a major role in the aetiology of cancer. Fusion proteins formed after chromosomal translocations are common in a range of tumour types; these are unique tumour antigens and are therefore potential targets for therapy design.
1,498 citations
TL;DR: Molecular modeling followed by optical, electron, and x-ray diffraction studies of a synthetic poly(L-glutamine) shows that it forms beta-sheets strongly held together by hydrogen bonds.
Abstract: Four inherited neurodegenerative diseases are linked to abnormally expanded repeats of glutamine residues in the affected proteins. Molecular modeling followed by optical, electron, and x-ray diffraction studies of a synthetic poly(L-glutamine) shows that it forms beta-sheets strongly held together by hydrogen bonds. Glutamine repeats may function as polar zippers, for example, by joining specific transcription factors bound to separate DNA segments. Their extension may cause disease either by increased, nonspecific affinity between such factors or by gradual precipitation of the affected proteins in neurons.
1,049 citations
TL;DR: Two abundant proteins of 140 and 134 amino acids were purified and sequenced from human brain and identified through their reactivity on immunoblots with a partially characterised monoclonal antibody that recognises tau protein in a phosphorylation‐dependent manner, defining a family of human brain synucleins.
1,028 citations
TL;DR: This work describes a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family, called 'covariance models'.
Abstract: We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family. We call these models 'covariance models'. A covariance model of tRNA sequences is an extremely sensitive and discriminative tool for searching for additional tRNAs and tRNA-related sequences in sequence databases. A model can be built automatically from an existing sequence alignment. We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information. Models trained on unaligned tRNA examples correctly predict tRNA secondary structure and produce high-quality multiple alignments. The approach may be applied to any family of small RNA sequences.
853 citations
TL;DR: The crystal structure of the RNA-binding domain of the small nuclear ribonucleoprotein U1A bound to a 21-nucleotide RNA hairpin has been determined and reveals the stereochemical basis for sequence-specific RNA recognition by the RNP domain.
Abstract: The crystal structure of the RNA-binding domain of the small nuclear ribonucleoprotein U1A bound to a 21-nucleotide RNA hairpin has been determined at 1.92 A resolution. The ten-nucleotide RNA loop binds to the surface of the β-sheet as an open structure, and the AUUGCAC sequence of the loop interacts extensively with the conserved RNP1 and RNP2 motifs and the C-terminal extension of the RNP domain. These interactions include stacking of RNA bases with aromatic side chains of proteins and many direct and water-mediated hydrogen bonds. The structure reveals the stereochemical basis for sequence-specific RNA recognition by the RNP domain.
845 citations
TL;DR: The crystal structure of the catalytically active core domain of HIV-1 integrase was determined and it is revealed that this domain of integrase belongs to a superfamily of polynucleotidyl transferases that includes ribonuclease H and the Holliday junction resolvase RuvC.
Abstract: HIV integrase is the enzyme responsible for inserting the viral DNA into the host chromosome; it is essential for HIV replication. The crystal structure of the catalytically active core domain (residues 50 to 212) of HIV-1 integrase was determined at 2.5 A resolution. The central feature of the structure is a five-stranded beta sheet flanked by helical regions. The overall topology reveals that this domain of integrase belongs to a superfamily of polynucleotidyl transferases that includes ribonuclease H and the Holliday junction resolvase RuvC. The active site region is identified by the position of two of the conserved carboxylate residues essential for catalysis, which are located at similar positions in ribonuclease H. In the crystal, two molecules form a dimer with a extensive solvent-inaccessible interface of 1300 A2 per monomer.
796 citations
TL;DR: The mscL nucleotide sequence predicts a unique protein of only 136 amino acids, with a highly hydrophobic core and very different from porins or other known proteins.
Abstract: All cellular organisms respond to vibration, touch, gravity or changes in osmolarity, although the molecules on which such mechanosensations depend are unknown. Candidates include certain channels that gate in response to membrane stretch. Patch-clamp experiments with Escherichia coli envelope have revealed a mechanosensitive channel with very large conductance (MscL) and one with a smaller conductance (MscS) which may be important in osmoregulation. Here we have solubilized and fractionated the envelope, reconstituted the MscL activity in vitro, and traced it to a small protein, whose gene, mscL, we then cloned. Insertional disruption of mscL removes the channel activity, whereas re-expression of mscL borne on an expression plasmid restores it. MscL-channel activities were observed in material from a cell-free expression system with mscL as the only template. The mscL nucleotide sequence predicts a unique protein of only 136 amino acids, with a highly hydrophobic core and very different from porins or other known proteins.
693 citations
TL;DR: In vitro differentiation of yolk sac tissue from homozygous mutant mice and sequentially targeted double-mutant ES cells demonstrates a block to erythroid development, which shows a pivotal role for a LIM domain protein in lineage specification during mammalian development and suggests that RBTN2 and GATA-1 are critical at similar stages of erystroid differentiation.
619 citations
TL;DR: The exceptionally high density of the protein interior shown here implies that packing forces play a more important role in protein stability than has been believed hitherto.
TL;DR: The specific expression of the GFAP-lacZ transgene means that it is now possible to target expression of other heterologous genes to astrocytes in vivo, and to study the mechanisms for reactive gliosis at the DNA level.
Abstract: Glial fibrillary acidic protein (GFAP) is an intermediate-filament protein expressed abundantly and almost exclusively in astrocytes of the CNS. We are studying transcriptional regulation of the GFAP gene to gain insight into astrocyte function and also to develop an astrocyte-specific expression system for manipulating brain physiology. In this work, we have produced transgenic mice carrying the bacterial lacZ reporter gene linked to a 2.2 kilobase 5'-flanking sequence derived from the human GFAP gene that previously was shown to direct astrocyte-specific transcription in cultured cells. We report that this promoter directs expression to astrocytes in the CNS. In addition, the upregulation of GFAP gene activity that follows injury to the brain was mimicked by the transgene. One of the transgenes was found to be X-linked and appeared to undergo the usual random inactivation that achieves gene dosage compensation in females. The brains of hemizygous females stained uniformly rather than displaying mosaic patches, indicating that astrocytes intermingle following their formation. The specific expression of the GFAP-lacZ transgene means that it is now possible to target expression of other heterologous genes to astrocytes in vivo, and to study the mechanisms for reactive gliosis at the DNA level.
TL;DR: Human hepatitis B virus core protein expressed in E. coli assembles into two sizes of particle, each containing 240 and 180 protein subunits, and their three-dimensional structures are determined by electron cryomicroscopy and image processing.
TL;DR: The three-dimensional structure of pentameric human serum amyloid P component at high resolution, the first reported for a pentraxin, reveals that the tertiary fold is remarkably similar to that of the legume lectins.
Abstract: The three-dimensional structure of pentameric human serum amyloid P component at high resolution, the first reported for a pentraxin, reveals that the tertiary fold is remarkably similar to that of the legume lectins. Carboxylate and phosphate compounds bind directly to two calcium ions; interactions with a carboxyethylidene ring are mediated by Asn 59 and Gln 148 ligands of the calcium ions. These X-ray results indicate the probable modes of binding of the biologically important ligands, DNA and amyloid fibrils.
TL;DR: Using the structures of telokin, and variable domains from antibodies, CD4 and CD8, a profile is constructed that describes the sequence characteristics of the structural core common to those proteins that form the cell adhesion molecules and surface receptors.
TL;DR: It is shown that PHF‐1 recognizes τ peptides containing either individually phosphorylated Ser396 or Ser404, but that there is a >10‐fold increase in the sensitivity of detection of τ peptide by PHF•1 when both serines are phosphorylate.
Abstract: The microtubule-associated protein tau is hyperphosphorylated in the paired helical filaments (PHFs) of Alzheimer's disease. Immunological and direct chemical studies have identified Ser396 and Ser404 as two of the phosphorylated sites. Previously, we have demonstrated, using synthetic tau peptides containing phosphorylated Ser396, that this site is recognized by the monoclonal antibody PHF-1. The present study extends this observation by showing that PHF-1 recognizes tau peptides containing either individually phosphorylated Ser396 or Ser404, but that there is a > 10-fold increase in the sensitivity of detection of tau peptides by PHF-1 when both serines are phosphorylated. The recognition of singly or doubly phosphorylated Ser396 and Ser404 in tau by PHF-1 can also be demonstrated in Chinese hamster ovary cells transfected with full-length wild-type tau constructs or mutant constructs with Ala substituted for Ser396 or Ser404. We conclude that the PHF-1 epitope contains both phosphorylated Ser396 and Ser404.
TL;DR: Comparison with 236 rearranged sequences revealed that no more than 24 of these germ‐line sequences could be assigned rearranged counterparts, that some of these were rarely used, and that only about 11 sequences are used frequently, suggesting that the expressed Vχ repertoire is mainly derived from a limited number of segments.
Abstract: From the genomic DNA of a single individual, we have amplified, cloned and sequenced 37 human germ-line V kappa segments. Four of these segments were new. We then compiled a comprehensive directory of all germ-line V kappa segments and identified 50 different sequences with open reading frames. Comparison with 236 rearranged sequences revealed that no more than 24 of these germ-line sequences could be assigned rearranged counterparts, that some of these were rarely used, and that only about 11 sequences are used frequently. This suggests that the expressed V kappa repertoire is mainly derived from a limited number of segments. Most surprisingly, the J kappa-distal region of the locus appears to be rarely used: we could unambiguously assign 162 rearranged sequences to V kappa segments of the J kappa-proximal region, but only 5 to segments of the J kappa-distal region.
TL;DR: A large number of receptor sequences have now been determined and detailed analysis of these has provided structural information about the receptors that can be examined in conjunction with the structural information from sequence analysis and the rhodopsin map.
TL;DR: Kainate-preferring receptors are a subclass of ionotropic glutamate receptors that might play a role in brain development and all genes undergo a peak in their expression in the late embryonic/early postnatal period, and GluR-5 expression during development shows the most interesting features because the changes are qualitative.
Abstract: Kainate-preferring receptors are a subclass of ionotropic glutamate receptors that might play a role in brain development. The expression of the five known genes encoding kainate receptor subunits (GluR-5, -6, -7, KA-1, and KA-2) was studied by in situ hybridization during pre- and postnatal development of the rat brain. We compared the combined expression patterns of these genes with autoradiography using 3H-kainate in the developing brain from embryonic day 12 (E12) through to adult. Although mRNAs for the receptor subunits (except KA-1) can be detected at stage E12, 3H-kainic acid binding (as an index of receptor protein) is not found at this stage. However, by E14 high-affinity kainate sites are found throughout the gray matter, but particularly in spinal cord, primordial cerebellum, and ventral forebrain structures. All genes undergo a peak in their expression in the late embryonic/early postnatal period. GluR-5 expression during development shows the most interesting features because the changes are qualitative. The GluR-5 gene shows peaks of expression around the period of birth in the sensory cortex (layers II, III, and IV), in CA1 hippocampal interneurons in the stratum oriens, in the septum, and in the thalamus. GluR-6 shows a prenatal expression peak in the cingulate gyrus of the neocortex. KA-1 transcripts appear with the development of the hippocampus and remain largely confined to discrete areas such as the CA3 region, the dentate gyrus, and subiculum. KA-2 transcripts are found throughout the CNS from as early as E12 and remain constant until adulthood. The GluR-5 and GluR-6 genes are coexpressed in multiple peripheral ganglia (e.g., cranial nerve ganglia, dorsal root ganglia, and mural ganglia) at E14.
TL;DR: The results show that full hypermutation depends on multiple elements, removal of some of which may drastically impair but not totally abolish the process.
TL;DR: How a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets, and a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions are described.
Abstract: We have used two selection techniques to study sequence-specific DNA recognition by the zinc finger, a small, modular DNA-binding minidomain. We have chosen zinc fingers because they bind as independent modules and so can be linked together in a peptide designed to bind a predetermined DNA site. In this paper, we describe how a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets. The amino acid sequences of selected fingers which bind the same triplet are compared to examine how sequence-specific DNA recognition occurs. Our results can be rationalized in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few alpha-helical positions. In the paper following this one, we describe a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions.
TL;DR: This work characterize the two novel phosphorylation-dependent anti-tau antibodies AT270 and AT180 and identify their epitopes as containing phosphorylated Thr-181 and Thr-231 respectively, and shows that these two threonine residues are partiallyosphorylated in fetal and adult tau and almost fully phosphorylate in PHF tau.
Abstract: Tau is a neuronal phosphoprotein the expression of which is developmentally regulated. A single tau isoform is expressed in fetal human brain but six isoforms are expressed in adult human brain, with the fetal isoform corresponding to the shortest adult isoform. Phosphorylation is also developmentally regulated, as fetal tau is phosphorylated at more sites than adult tau. In Alzheimer's disease, the six adult tau isoforms become hyperphosphorylated and form the paired helical filament (PHF), the major fibrous component of the neurofibrillary lesions. One way to identify phosphorylated sites in tau is to use antibodies that recognize phosphorylated residues within a specific amino acid sequence. We here characterize the two novel phosphorylation-dependent anti-tau antibodies AT270 and AT180 and identify their epitopes as containing phosphorylated Thr-181 and Thr-231 respectively. With these antibodies we show that these two threonine residues are partially phosphorylated in fetal and adult tau and almost fully phosphorylated in PHF tau. This result contrasts with previous studies of Ser-202 and Ser-396 which are partially phosphorylated in fetal tau, unphosphorylated in adult tau but almost fully phosphorylated in PHF tau.
TL;DR: It is discovered that ClpA, the ATPase component of the ATP-dependent ClpAP protease, is a molecular chaperone, and it is shown thatClpA targets RepA for degradation by ClpP, demonstrating a direct link between the protein unfolding function of chaperones and proteolysis.
Abstract: The two major molecular chaperone families that mediate ATP-dependent protein folding and refolding are the heat shock proteins Hsp60s (GroEL) and Hsp70s (DnaK). Clp proteins, like chaperones, are highly conserved, present in all organisms, and contain ATP and polypeptide binding sites. We discovered that ClpA, the ATPase component of the ATP-dependent ClpAP protease, is a molecular chaperone. ClpA performs the ATP-dependent chaperone function of DnaK and DnaJ in the in vitro activation of the plasmid P1 RepA replication initiator protein. RepA is activated by the conversion of dimers to monomers. We show that ClpA targets RepA for degradation by ClpP, demonstrating a direct link between the protein unfolding function of chaperones and proteolysis. In another chaperone assay, ClpA protects luciferase from irreversible heat inactivation but is unable to reactivate luciferase.
TL;DR: Vascular endothelial growth factor seems to be an appropriate candidate for mediating retinal diabetic neovascularization as well as other angiogenic growth factors identified so far in the literature.
Abstract: Objective: To study the involvement of eight angiogenic growth factors that have been identified so far in the literature, especially vascular endothelial growth factor, in proliferative diabetic retinopathy. Methods: Samples of neovascular membranes were obtained from diabetic patients; these samples, excised at vitrectomy, were used to study the expression of messenger RNA of the angiogenic factors by using the method of the reverse transcription-polymerase chain reaction. Vitreous aspirates that were taken from diabetic and control patients were used to quantify vascular endothelial growth factor-like activity with a competitive radioreceptor assay. Results: Of the eight angiogenic factors studied, vascular endothelial growth factor was the only one that was always expressed in the samples of neovascular membranes. Furthermore, vascular endothelial growth factor receptor-binding activity was greater in vitreous aspirates that were obtained from diabetic patients than in samples that were taken from control patients (P Conclusion: Vascular endothelial growth factor seems to be an appropriate candidate for mediating retinal diabetic neovascularization.
TL;DR: The conformation of the two forms of antithrombin demonstrates the extraordinary mobility of the reactive loop in the serpins and provides insights into the folding of the loop required for inhibitory activity together with the potential modification of this by heparin.
TL;DR: It is inferred that in most instances, sequence-specific binding of zinc fingers to DNA can be achieved by using a small set of amino acid-nucleotide base contacts amenable to a code.
Abstract: In the preceding paper [Choo, Y. & Klug, A. (1994) Proc. Natl. Acad. Sci. USA 91, 11163-11167], we showed how selections from a library of zinc fingers displayed on phage yielded fingers able to bind to a number of DNA triplets. Here, we describe a technique to deal efficiently with the converse problem--namely, the selection of a DNA binding site for a given zinc finger. This is done by screening against libraries of DNA triplet binding sites randomized in two positions but having one base fixed in the third position. The technique is applied here to determine the specificity of fingers previously selected by phage display. We find that some of these fingers are able to specify a unique base in each position of the cognate triplet. This is further illustrated by examples of fingers which can discriminate between closely related triplets as measured by their respective equilibrium dissociation constants. Comparing the amino acid sequences of fingers which specify a particular base in a triplet, we infer that in most instances, sequence-specific binding of zinc fingers to DNA can be achieved by using a small set of amino acid-nucleotide base contacts amenable to a code.
TL;DR: In this paper, a new family of proteins has been described that carries a novel cysteine-rich zinc-binding domain called the LIM domain, which is present in mammals, amphibians, flies, worms and plants.
TL;DR: A DNA-binding peptide comprising three zinc-fingers has been engineered to bind specifically to a unique nine-base-pair region of a BCRABL fusion oncogene in preference to the parent genomic sequences.
Abstract: A DNA-binding peptide comprising three zinc-fingers has been engineered to bind specifically to a unique nine-base-pair region of a BCR–ABL fusion oncogene in preference to the parent genomic sequences. Binding to the target oncogene in chromosomal DNA is possible in transformed cells in culture, and results in blockage of transcription. Consequently, murine cells rendered independent of growth factors by the action of the oncogene revert to factor dependence upon transient transfection with a vector expressing the peptide.
TL;DR: It is concluded that the rapid release of IL‐10 during endotoxemia is a natural antiinflammatory response controlling cytokine production and LPS toxicity.
Abstract: Interleukin-10 (IL-10) is a potent inhibitor of lipopolysaccharide (LPS)-induced tumor necrosis factor (TNF) production and has been shown to protect mice from endotoxin shock. As IFN-gamma is another important mediator of LPS toxicity, we studied the effects of IL-10 on LPS-induced IFN-gamma synthesis in vitro and in vivo. First, we found that the addition of recombinant human IL-10 (rhIL-10) (10 U/ml) to human whole blood markedly suppressed LPS-induced IFN-gamma release while neutralization of endogenously synthesized IL-10 resulted in increased IFN-gamma levels. The ability of rIL-10 to inhibit LPS-induced IFN-gamma synthesis was also observed in vivo in mice. Indeed, administration of 1000 U recombinant mouse IL-10 (rmIL-10) 30 min before and 3 h after challenge of BALB/c mice with 100 micrograms LPS resulted in a threefold decrease in peak IFN-gamma serum levels. We then examined the production and the role of IL-10 during murine endotoxemia. We found that LPS injection causes the rapid release of IL-10, peak IL-10 serum levels being observed 90 min after LPS challenge. Neutralization of endogenously produced IL-10 by administration of 2 mg JES5-2A5 anti-IL-10 monoclonal antibody (mAb) 2 h before LPS challenge resulted in a marked increase in both TNF and IFN-gamma serum levels while irrelevant isotype-matched mAb had no effect. The enhanced production of inflammatory cytokines in anti-IL-10 mAb-treated mice was associated with a 60% lethality after injection of 500 micrograms LPS, while all mice pretreated with control mAb survived. We conclude that the rapid release of IL-10 during endotoxemia is a natural antiinflammatory response controlling cytokine production and LPS toxicity.