Showing papers by "Laboratory of Molecular Biology published in 1984"
TL;DR: The complete (172,282 base pairs) nucleotide sequence of the B95-8 strain of Epstein–Barr virus has been established using the dideoxynucleotide/M13 sequencing procedure.
Abstract: The complete (172,282 base pairs) nucleotide sequence of the B95-8 strain of Epstein-Barr virus has been established using the dideoxynucleotide/M13 sequencing procedure. Many RNA polymerase II promoters have been mapped and the mRNAs from these promoters have been assigned to the latent or early/late productive virus cycles. Likely protein-coding regions have been identified and three of these have been shown to encode a ribonucleotide reductase, a DNA polymerase and two surface glycoproteins.
2,016 citations
TL;DR: The crystal structure of the nucleosome core particle has been solved to 7 A resolution as discussed by the authors, and the right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within.
Abstract: The crystal structure of the nucleosome core particle has been solved to 7 A resolution. The right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within. The central turn of superhelix and H3 . H4 tetramer have dyad symmetry, but the H2A . H2B dimers show departures due to interparticle associations.
863 citations
TL;DR: Cell lines have been established that secrete hapten-specific antibodies in which the Fc portion has been replaced either with an active enzyme moiety or with polypeptide displaying c-myc antigenic determinants.
Abstract: The introduction into lymphocytes of immunoglobulin-gene DNA that has been manipulated in vitro allows the production of novel antibodies. In this way, cell lines have been established that secrete hapten-specific antibodies in which the Fc portion has been replaced either with an active enzyme moiety or with polypeptide displaying c-myc antigenic determinants.
718 citations
TL;DR: The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences.
Abstract: This paper describes computer methods for locating signals in nucleic acid sequences The signals include ribosome binding sites, promoter sequences and splice junctions The methods are of use both to those trying to interpret the function of newly determined sequences and to those studying the molecular mechanisms involved in the recognition of these special signal sequences
647 citations
TL;DR: An analytical formula has been derived for the calculation of the solvent accessible surface area of a protein molecule or equivalently the surface area exterior to an arbitrary number of overlapping spheres, which was motivated by the need for a computationally feasible simulation of the hydrophobic effect in proteins.
633 citations
TL;DR: The structure of human deoxyhaemoglobin was refined at 1.74 A resolution using data collected on film at room temperature from a synchrotron X-ray source and the effects of intermolecular contacts on the structure were investigated.
621 citations
TL;DR: The structure of this pleiotropic activator of gene transcription in bacteria and its interaction sites at promoter DNA's as well as the role of this protein in the RNA polymerase-promoter interactions are reviewed.
Abstract: The structure of this pleiotropic activator of gene transcription in bacteria and its interaction sites at promoter DNA's as well as the role of this protein in the RNA polymerase-promoter interactions are reviewed.
577 citations
TL;DR: By making mutants of the Pro51 enzyme at two residues that make hydrogen bonds to the ATP substrate, it is shown that Pro51 greatly improves the strength of one of these contacts.
555 citations
TL;DR: Most continuous antigenic determinants of tobacco mosaic virus protein, myoglobin and lysozyme correspond to those surface regions in the protein structure, as determined by X-ray crystallography, which possess a run of high-temperature factors along the polypeptide backbone, that is, a high segmental mobility.
Abstract: Most continuous antigenic determinants of tobacco mosaic virus protein (TMVP), myoglobin and lysozyme correspond to those surface regions in the protein structure, as determined by X-ray crystallography, which possess a run of high-temperature factors along the polypeptide backbone, that is, a high segmental mobility. The mobility of an antigenic determinant may make it easier to adjust to a pre-existing antibody site not fashioned to fit the exact geometry of a protein. The correlation found between temperature factors and antigenicity is better than that between hydrophilicity and antigenicity.
550 citations
TL;DR: It is concluded that somatic mutation of germ-line encoded genes plays a major role in the generation of antibodies with increased affinity for oxazolone with time after immunization.
Abstract: Studies on the development of the immune response suggest that the repertoire of expressed antibody specificities is strongly influenced by antigen (reviewed in ref. 1). One way in which this influence is manifested is by a progressive increase in the affinity of antibody for antigen with time after immunization. This phenomenon, termed the 'maturation' of the immune response, must be due to a change in the structure of the antibody being synthesized. However, the precise nature of the changes involved and the genetic mechanisms used to produce them have not been clearly defined. We have now investigated the maturation of the immune response to the hapten 2-phenyloxazolone by mRNA sequencing of specific hybridomas. We conclude that somatic mutation of germ-line encoded genes plays a major role in the generation of antibodies with increased affinity for oxazolone with time after immunization.
514 citations
TL;DR: The structure of form II crystals of bovine pancreatic trypsin inhibitor has been investigated by joint refinement of X-ray and neutron data and eleven amide hydrogens were found to be protected from exchange after three months of soaking the crystals in deuterated mother liquor at pH 8·2.
TL;DR: This work inserted the sequence Ile-Glu-Gly-Arg between the 31 amino-terminal residues of λ cII protein and Val 1 of human β-globin, and produced this hybrid in high yield in E. coli, and cleaved the hybrid specifically at the single arginine, using blood coagulation factor Xa and thus liberated the authentic β- globin chain.
Abstract: High-level expression of many eukaryotic genes has proved difficult to achieve even when a strong promoter and the ribosome binding sequence from highly expressed Escherichia coli genes have been placed in front of the coding sequences. To overcome this problem, many eukaryotic proteins have been efficiently produced as hybrids after fusion of their genes with a coding sequence of E. coli genes. However, such hybrid proteins are not suitable for functional studies or clinical use unless the authentic protein sequence can be released by specific cleavage. Here, we have inserted the sequence Ile-Glu-Gly-Arg between the 31 amino-terminal residues of lambda cII protein and Val 1 of human beta-globin, and produced this hybrid in high yield in E. coli. We then cleaved the hybrid specifically at the single arginine, using blood coagulation factor Xa and thus liberated the authentic beta-globin chain. As factor Xa is specific for the tetrapeptide Ile-Glu-Gly-Arg, which is rare in protein sequences, our expression/cleavage system is applicable to the efficient production of many eukaryotic proteins.
TL;DR: Examining at single-bond resolution the interactions of three commonly used nucleases with a DNA of natural origin, the 160 bp tyrT promoter, explains how sequence zones of a certain base composition, or purine-pyrimidine asymmetry, can influence the recognition of DNA by protein molecules.
TL;DR: A sequence from the Ubx 5' exon in the bithorax complex of Drosophila melanogaster was expressed as a fusion protein in bacteria that was used to raise rabbit antisera and monoclonal antibodies.
TL;DR: An interactive computer program (ANALYSEQ) that is used from a simple graphics terminal to determine the function of nucleic acid sequences and contains methods to locate genes by looking for the effects that coding for a protein has on the coding sequence.
Abstract: We describe an interactive computer program (ANALYSEQ) that is used from a simple graphics terminal. The main purpose of the program is to determine the function of nucleic acid sequences but it also offers the simpler listing, searching and counting options. It contains methods to locate genes by looking for the effects that coding for a protein has on the coding sequence, to locate tRNA genes by looking for secondary structure and conserved bases, and methods to locate signals such as promoters. Techniques to identify unusual regions of sequence and to search for potential Z DNA-forming regions are also included. Most of the routines produce graphical output which gives ease of interpretation and allows superposition of several independent forms of analysis.
TL;DR: Asters in the mutant embryos at the nonpermissive temperature contained only short microtubules suggesting that the morphology of the asters is important for directing the movement of the pronuclei.
TL;DR: The recently discovered similarity between the human epidermal growth factor (EGF) receptor and the avian erythroblastosis virus v-erb-B protein1 supports the hypothesis that viral oncogenes share a common evolutionary origin with genes encoding growth-regulating cell-surface receptors.
Abstract: The recently discovered similarity between the human epidermal growth factor (EGF) receptor and the avian erythroblastosis virus v-erb-B protein1 supports the hypothesis that viral oncogenes share a common evolutionary origin with genes encoding growth-regulating cell-surface receptors. To elucidate the relationship between receptors and malignant transformation, we have now used a fragment of v-erb-B as a probe to screen a cDNA library of mRNA from A431 human carcinoma cells, which possess a large number of EGF receptors2. Of the six clones isolated, the largest (pE7) contains an insert of 2.4 kilobase pairs (kbp) whose deduced amino acid sequence is homologous to the v-erb-B protein and identical to reported EGF receptor peptide sequences1. This pE7 cDNA hybridized to three prominent RNAs of ∼10, 5.6 and 2.9 kilobases (kb), and to three minor species of 6.3, 4.6 and 3.3 kb. All were present in elevated levels in A431 cells. The prominent 2.9-kb RNA was homologous only to the 5′ portion of the pE7 insert. This result raises the possibility that differential RNA processing is used by A431 cells to generate a variety of RNAs.
TL;DR: The unique information available about the formation and stabilities of the disulphides during refolding of reduced bovine pancreatic trypsin inhibitor provides a useful description of the way in which numerous weak interactions within a protein co-operate to produce a stable folded conformation.
TL;DR: Most mammalian cells, such as fibroblasts, continuously internalize part of their surface membrane by endocytosis, and then later return it to the cell surface, a cyclical process initiated by coated pits in the plasma membrane.
Abstract: Most mammalian cells, such as fibroblasts, continuously internalize part of their surface membrane by endocytosis, and then later return it to the cell surface This cyclical process is initiated by coated pits in the plasma membrane These pits collect specific receptors plus lipid for internalization, but exclude other proteins On a motile cell, the sites of endocytosis (randomly located on the cell) and those of membrane return (located at the front of the cell) are not coincident This causes a bulk flow of lipid plus receptors in the plasma membrane, away from the front of the cell Large objects on the cell surface are swept to the rear of the cell by this flow, a process called capping Cells may use this polarized endocytic cycle to move
TL;DR: Analyses of the product with RNAase T1 revealed that pairing initiates at or near the 5' end of RNA I and propagates toward its 3' end, which facilitates complete pairing along the entire length ofRNA I that initiates from the 5'-end region.
TL;DR: It is shown here that DNA replication is required for the onset of repression, which is necessary for the repression of silent mating type loci in yeast.
Abstract: A putative origin of DNA replication is associated with the DNA sequences necessary for the repression of silent mating type loci in yeast. These sequences lie about a kilobase away from the affected promoters, so the repression must act at a distance. We show here that DNA replication is required for the onset of repression.
TL;DR: Five commonly used nucleases were surveyed for their ability to distinguish among several different DNA backbone configurations and only micrococcal nuclease is demonstrably base-specific, with a strong preference for T, A over C, G in any structural context.
TL;DR: This paper describes how these coding effects can be measured and used to detect protein coding regions.
Abstract: Protein genes can be found either by searching the DNA sequence for signals such as ribosome binding sites or by looking for the effects that coding for a protein has on the coding sequence. This paper describes how these coding effects can be measured and used to detect protein coding regions.
TL;DR: The results support a model in which c-myc oncogene activation in Burkitt's lymphoma occurs by disruption of a normal transcriptional control mechanism in which the c- myc protein is itself involved.
Abstract: Our previous studies of a translocated c-myc gene in the Raji Burkitt's lymphoma cell showed somatic mutations in exons 1 and 2. We have extended these observations to two other translocated c-myc genes and find a common occurrence of mutation in the noncoding exon 1. We also found that in Raji cells, unlike other Burkitt's lymphoma cell lines, the normal allele of the c-myc gene is transcribed as well as the translocated gene. These results support a model in which c-myc oncogene activation in Burkitt's lymphoma occurs by disruption of a normal transcriptional control mechanism in which the c-myc protein is itself involved.
TL;DR: In vivo, RNA I controls plasmid copy number and incompatibility and inhibits expression of a galK gene fused to the primer promoter and can be explained by alteration of the binding of RNA I to RNA II by the Rom protein.
TL;DR: The characterization of cDNA and genomic clones encoding human T-cell receptor β-chain genes shows strong evolutionary conservation of the dual Cβ gene system in these two species.
Abstract: Immune systems of vertebrates function via two types of effector cells, B and T cells, which are capable of antigen-specific recognition. The immunoglobulins, which serve as antigen receptors on B cells, have been well characterized with respect to gene structure, unlike the T-cell receptors. Recently, cDNA clones thought to correspond to the beta-chain locus of the human and mouse T-cell receptor have been described. The presumptive beta-chain clones detect gene rearrangement specifically in T-cell DNA and show homology with immunoglobulin light chains. The similarity of the T-cell beta-chain gene system to the immunoglobulin genes has been further demonstrated by the recent observation of variable- and constant-region gene segments as well as joining segments and putative diversity segments. We report here the characterization of cDNA and genomic clones encoding human T-cell receptor beta-chain genes. There are two constant-region genes (C beta 1 and C beta 2), each capable of rearrangement and expression as RNA. The gene arrangement, analogous to that of mouse beta-chain genes, shows strong evolutionary conservation of the dual C beta gene system in these two species.
TL;DR: A fifth postulate is proposed, namely that of the coupling unit, to the four existing postulates of 'delocalized protonic coupling' and it is shown that, with this postulate, protono-coupling can again account for most experimental observations.
TL;DR: The dnaA protein appears not to be essential for the replication of either plasmid; therefore, the function of the sequence in P1 and F may be regulatory.
TL;DR: It has been shown that fem-1(+) is part of the sex-determination pathway and has two distinct functions: in the soma it prevents the action of tra-1, thereby allowing male development to occur, and in the germline it is necessary for spermatogenesis in both sexes.