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T J Gibson

Publications and source records attributed to T J Gibson.

At least 19 recordsLinked to original sources
PubMed1991

Base sequence discrimination by zinc-finger DNA-binding domains.

Zinc fingers constitute important eukaryotic DNA-binding domains, being present in many transcription factors. The Cys2/His2 zinc-finger class has conserved motifs of 28-30 amino acids which are usually present as tandem repeats. The structure of a Cys2/His2 zinc finger has been determined by nuclear magnetic resonance, but details of its interaction with DNA were not established. Here we identify amino acids governing DNA-binding specificity using in vitro directed mutagenesis guided by similarities between the zinc fingers of transcription factors Sp1 and Krox-20. Krox-20 is a serum-inducible transcription activator which is possibly involved in the regulation of hindbrain development; it contains three zinc fingers similar to those of Sp1 and binds to a 9-base-pair target sequence which is related to that of Sp1. Our results show that each finger spans three nucleotides and indicate two positions in Krox-20 zinc fingers that are important for base-pair selectivity. Modelling with molecular graphics suggests that these residues could bind directly with the bases and that other amino acid-base contacts are also possible.

Amino Acid Sequence↗
PubMed1991

Proposed structure for the DNA-binding domain of the Myb oncoprotein based on model building and mutational analysis.

Myb-related proteins from plants to humans are characterized by a DNA-binding domain which contains two to three imperfect repeats of approximately 50 amino acids each. Based on the evolutionary conservation of specific residues, secondary structural predictions suggest an arrangement of alpha helices homologous to that seen in the homeodomains, members of the helix-turn-helix family of DNA-binding proteins. We have used molecular modelling in conjunction with site-directed mutagenesis to test the feasibility of this structure. We propose that each Myb repeat consists of three alpha helices packed over a hydrophobic core which is built around the three highly conserved tryptophan residues. The C-terminal helix forms part of the helix-turn-helix motif and can be positioned into the major groove of B-form DNA, allowing prediction of residues critical for specificity of interaction. Modelling also allowed positioning of adjacent repeats around the major groove over an 8 bp binding site.

Amino Acid Sequence↗
PubMed1990

Protruding domain of tomato bushy stunt virus coat protein is a hitherto unrecognized class of jellyroll conformation.

The capsid protein of tomato bushy stunt virus (TBSV) has two antiparallel beta-sheet domains with the so-called jellyroll conformation. Contrary to previous analyses, we note that these domains are non-superimposable topologies. The TBSV shell (S) domain topology is common to many other proteins but the protruding (P) domain is a unique conformation so far found in no other protein. The TBSV capsid P domain did not arise from the S domain by a gene duplication event as previously assumed. It is proposed instead that the P domain was acquired from an as yet unidentified cellular protein. The four possible unique jellyroll topologies that might occur in proteins are discussed and illustrated.

Capsid↗
PubMed1990

Metabolic complexity in the RNA world and implications for the origin of protein synthesis.

A model is presented for the evolution of metabolism and protein synthesis in a primitive, acellular RNA world. It has been argued previously that the ability to perform metabolic functions logically must have preceded the evolution of a message-dependent protein synthetic machinery and that considerable metabolic complexity was achieved by ribo-organisms (i.e., organisms in which both genome and enzymes are comprised of RNA). The model proposed here offers a mechanism to account for the gradual development of sophisticated metabolic activities by ribo-organisms and explains how such metabolic complexity would lead subsequently to the synthesis of genetically encoded polypeptides. RNA structures ancestral to modern ribosomes, here termed metabolosomes, are proposed to have functioned as organizing centers that coordinated, using base-pairing interactions, the order and nature of adaptor-mounted substrate/catalyst interactions in primitive metabolic pathways. In this way an ancient genetic code for metabolism is envisaged to have predated the specialized modern genetic code for protein synthesis. Thus, encoded amino acids initially would have been used, in conjunction with other encoded metabolites, as building blocks for biosynthetic pathways, a role that they retain in the metabolism of contemporary organisms. At a later stage the encoded amino acids would have been condensed together on similar RNA metabolosome structures to form the first genetically determined, and therefore biologically meaningful, polypeptides.(ABSTRACT TRUNCATED AT 250 WORDS)

Genetic Code↗
PubMed1990

Catalytic RNA and the origin of genetic systems.

The recent discovery of catalytic RNA molecules has provoked enormous interest in the origin of life and has given rise to new speculations about how living systems developed on the primitive earth. Here we outline why the discovery of catalytic RNA molecules has profound evolutionary implications, and then go on to discuss models for the emergence of metabolic complexity and protein synthesis in a primitive 'RNA world', emphasizing the constraints imposed on such models by genetical arguments.

Biological Evolution↗
PubMed1988

Chelation therapy.

Explore the source record for details and available documents.

Chelating Agents↗
PubMed1988

A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins.

Many eukaryotic transcriptional activator proteins, including the Xenopus 5S RNA gene activator protein TFIIIA and the HeLa cell protein Sp1, have an approximately 30 amino acid repeating motif which binds to short, specific DNA sequences. Over 150 of these sequences are now known. Based on the observed distribution of amino acid residues, a series of constraints and predictions can be proposed for the structure of the motif. A compatible three-dimensional structural model has been developed by a combination of interactive model building and refinement by molecular dynamics. The model structure consists of a two-stranded beta-hairpin stabilizing a C-terminal alpha-helix by both zinc ligands and hydrophobic interactions. Four of the residue positions on the helix N-terminus and exposed face are predicted to provide base specific ligands. Further implications of the model for DNA binding are discussed.

Amino Acid Sequence↗
PubMed1987

Lorist2, a cosmid with transcriptional terminators insulating vector genes from interference by promoters within the insert: effect on DNA yield and cloned insert frequency.

Transcription terminators have been included in a phage-lambda-replicon-based cosmid vector, Lorist2, to insulate vector genes against transcriptional interference from cloned insert DNA. DNA yields of recombinant clones containing Escherichia coli genomic DNA inserts are more even for Lorist2 than with its progenitor LoristB. However, the terminators provide only a partial reduction in the over-representation of r X DNA-containing clones generally observed in cosmid libraries of Caenorhabditis elegans DNA, suggesting that causes other than transcriptional readthrough into the vector contribute to this problem.

Animals↗
PubMed1987

Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression.

Four new features have been included in a phage-lambda-replicon-based cosmid vector, Lorist6. A ScaI restriction site allows insertion of blunt-ended DNA, partially digested with AluI or any other restriction enzyme which creates blunt ends after cleavage. NotI and BamHI sites enable construction of libraries using double digestion with NotI + Sau3AI. The promoter of the neo gene has been substituted by a promoter derived from the tet gene of pBR322, increasing expression of the resistance gene product. A transcriptional terminator has been placed downstream from the neo gene to prevent transcription into insert DNAs.

Cloning, Molecular↗
PubMed1986

Severity of injuries in road crashes. A comparison of injured occupants of forward control vehicles and conventional passenger cars.

Light vans are being used increasingly as substitutes for conventional passenger cars in Australia. These "forward control" vans are not required to meet the same safety standards as passenger cars. A study group of 258 injured occupants of light vans was identified from the records of the Motor Accidents Board of Victoria. A comparison group of 3468 injured occupants of conventional cars was also identified. Both groups had been injured in accidents occurring in Victoria between 1980 and 1983. The injuries received by the van occupants were compared with those received by the car occupants. Van occupants injured in frontal crashes were more likely to have sustained leg injury, and were more likely to have sustained serious injury than were car occupants who were injured in frontal crashes. Forward control vans were found to lack protection for occupants in frontal crashes.

Accidents, Traffic↗
PubMed1986

Coding content and expression of the EBV B95-8 genome in the region from base 62,248 to base 82,920.

The DNA sequence of a 20,672-base region of the EBV B95-8 genome from the BamHI site separating fragments BamHI-F and BamHI-Q to the EcoRI site separating fragments EcoRI-G2 and EcoR1-F has been determined. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for RNAs from this region. Five mRNAs have been identified and correlated with five open reading frames in the DNA sequence. Two of these open reading frames encode ribonucleotide reductase subunits. A further two open reading frames are present including one for a predicted protein of 340 kDa for which no transcript has yet been detected.

Base Sequence↗
PubMed1985

The BamHI F region of the B95-8 Epstein-Barr virus genome.

The BamHI F region of the B95-8 Epstein-Barr virus (EBV) genome has been sequenced and analysed for transcription signals and open reading frames. S1 mapping and northern blotting with probes from M13 recombinants have been used to search for mRNAs. Four rightward-reading frames encoding basic proteins appear to be expressed by 3'-coterminal early mRNAs. Two leftward-reading frames appear to be expressed by 3'-coterminal early mRNAs.

Base Sequence↗
PubMed1979

Treatment of cholelithiasis in patients with sickle cell anemia.

The incidence of cholelithiasis and surgical risk of cholecystectomy in patients with sickle cell anemia is reviewed. Records of all patients with sickle cell disease currently attending the Medical University of South Carolina Hematology Clinic were reviewed. An oral cholecystogram has been part of the initial evaluation for the past year. The records of 16 patients having cholecystectomy from 1968 to 1977 were reviewed with regard to diagnostic studies, preoperative preparation, morbidity, and mortality. When the status of the gallbladder is known, the incidence of cholelithiasis is 67%. The morbidity of elective cholecystectomy was high (37%); there was one death. Cholecystectomy is not recommended for the discovery of asymptomatic gallstones because of the relatively poor surgical risk and short life expectancy of these patients.

Adolescent↗
PubMed1975

Arthropathy, skin and bone lesions in pancreatic disease.

A patient with a history of alcoholism and pancreatic calcification, developed subcutaneous fat necrosis and an arthropathy, associated with a pancreatic pseudocyst and accompanied by an elevation of serum lipase and amylase. The illness was complicated by bacteremia and destructive bone lesions. A clinical distinction between osteomyelitis and medullary fat necrosis proved difficult. Infection of bone was demonstrated at one site but did not exclude medullary fat necrosis elsewhere.

Amylases↗