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Biomedical subjects

P F Johnson

Publications and source records attributed to P F Johnson.

At least 55 records · Page 3Linked to original sources
PubMed1993

Identification of C/EBP basic region residues involved in DNA sequence recognition and half-site spacing preference.

C/EBP and GCN4 are basic region-leucine zipper (bZIP) DNA-binding proteins that recognize the dyad-symmetric sequences ATTGCGCAAT and ATGAGTCAT, respectively. The sequence specificities of these and other bZIP proteins are determined by their alpha-helical basic regions, which are related at the primary sequence level. To identify amino acids that are responsible for the different DNA sequence specificities of C/EBP and GCN4, two kinds of hybrid proteins were constructed: GCN4-C/EBP chimeras fused at various positions in the basic region and substitution mutants in which GCN4 basic region amino acids were replaced by the corresponding residues from C/EBP. On the basis of the DNA-binding characteristics of these hybrid proteins, three residues that contribute significantly to the differences in C/EBP and GCN4 binding specificity were defined. These residues are clustered along one face of the basic region alpha helix. Two of these specificity residues were not identified as DNA-contacting amino acids in a recently reported crystal structure of a GCN4-DNA complex, suggesting that the residues used by C/EBP and GCN4 to make base contacts are not identical. A random binding site selection procedure also was used to define the optimal recognition sequences for three of the GCN4-C/EBP fusion proteins. These experiments identify an element spanning the hinge region between the basic region and leucine zipper domains that dictates optimal half-site spacing (either directly abutted for C/EBP or overlapping by one base pair for GCN4) in high-affinity binding sites for these two proteins.

Amino Acid Sequence↗
PubMed1992

Racial norms: esthetic and prosthodontic implications.

A review of the orthodontic literature reveals that different races have different cephalometric norms. This has great implications in the placement and arrangement of teeth and in the evaluation of esthetics in people of dissimilar ethnic origins. In the diverse American society, prosthodontists and restorative dentists need to be concerned with the phylogenetic characteristics of their patients. The resultant esthetic differences can have significant importance in the function and design of prostheses.

Denture Design↗
PubMed1991

A family of C/EBP-related proteins capable of forming covalently linked leucine zipper dimers in vitro.

Mouse and rat genomic DNA libraries were screened by reduced stringency hybridization with the DNA-binding domain of the c/ebp gene as a probe. Three genes were isolated that encode bZIP DNA-binding proteins (designated CRP1, CRP2, and CRP3) with strong amino acid sequence similarities to the C/EBP-binding domain. CRP2 is identical to the protein described recently by other groups as NF-IL6, LAP, IL-6DBP, and AGP/EBP, whereas CRP1 and CRP3 represent novel proteins. Several lines of evidence indicate that these three proteins, along with C/EBP, comprise a functional family. Each bacterially expressed polypeptide binds to DNA as a dimer with recognition properties that are virtually identical to those of C/EBP. Every member also bears a conserved cysteine residue at or near the carboxyl terminus, immediately following the leucine zipper, that at least in vitro allows efficient disulfide cross-linking between paired zipper helices. We developed a gel assay for covalent dimers to assess leucine zipper specificities among the family members. The results demonstrate that all pairwise combinations of dimer interactions are possible. To the extent that we have examined them, the same heterodimeric complexes can be detected intracellularly following cotransfection of the appropriate pair of genes into recipient cells. All members are also capable of activating in vivo transcription from promoters that contain a C/EBP-binding site. Our findings indicate that a set of potentially interacting C/EBP-like proteins exists, whose complexity is comparable to that of other bZIP protein subfamilies such as Jun, Fos, and ATF/CREB.

Amino Acid Sequence↗
PubMed1989

Cognate DNA binding specificity retained after leucine zipper exchange between GCN4 and C/EBP.

Both C/EBP and GCN4 are sequence-specific DNA binding proteins that control gene expression. Recent evidence implicates C/EBP as a transcriptional regulator of genes involved in lipid and carbohydrate metabolism. The C/EBP protein binds avidly to the dyad symmetric sequence 5'-ATTGCGCAAT-3'; GCN4 regulates the transcription of genes that control amino acid biosynthesis in yeast, and binds avidly to the dyad symmetric sequence 5'-ATGA(G/C)TCAT-3'. Both C/EBP and GCN4 bind DNA via the same structural motif. This motif has been predicted to be bipartite, consisting of a dimerization interface termed the "leucine zipper" and a DNA contact surface termed the "basic region." Specificity of DNA binding has been predicted to be imparted by the basic region. As a test of this hypothesis, recombinant proteins were created wherein the basic regions and leucine zippers of GCN4 and C/EBP were reciprocally exchanged. In both of the recombinant polypeptides, DNA binding specificity is shown to track with the basic region.

Amino Acid Sequence↗
PubMed1989

The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite.

C/EBP is a rat liver nuclear protein capable of sequence-specific interaction with DNA. The DNA sequences to which C/EBP binds in vitro have been implicated in the control of messenger RNA synthesis. It has therefore been predicted that C/EBP will play a role in regulating gene expression in mammalian cells. The region of the C/EBP polypeptide required for direct interaction with DNA has been identified and shown to bear amino acid sequence relatedness with the product of the myc, fos, and jun proto-oncogenes. The arrangement of these related amino acid sequences led to the prediction of a new structural motif, termed the "leucine zipper," that plays a role in facilitating sequence-specific interaction between protein and DNA. Experimental tests now provide support for the leucine zipper hypothesis.

Amino Acid Sequence↗
PubMed1988

The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins.

A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins.

Binding Sites↗
PubMed1988

Isolation of a recombinant copy of the gene encoding C/EBP.

In two previous studies we described the properties of a heat-stable DNA-binding protein present in rat liver nuclei. This protein, hereafter termed C/EBP, is capable of selective binding to the CCAAT homology of several viral promoters (Graves et al. 1986), as well as the core homology common to many viral enhancers (Johnson et al. 1987). We now report the isolation of a recombinant clone of the gene that encodes C/EBP. Expression of the clone in bacterial cells yields a protein that binds in vitro to both the CCAAT homology and the enhancer core homology, providing conclusive evidence that a single gene product accounts for both binding activities. By examining the properties of protease-derived fragments of C/EBP, we have localized its DNA-binding domain to a 14-kD fragment. A 60-amino-acid segment located within the DNA-binding domain of C/EBP bears sequence similarity to the products of the myc and fos oncogenes.

Amino Acid Sequence↗
PubMed1988

In situ detection of sequence-specific DNA binding activity specified by a recombinant bacteriophage.

We have used a recombinant bacteriophage that expresses the DNA-binding domain of C/EBP to optimize conditions for a screening technique that may facilitate the cloning of genes that encode sequence-specific DNA-binding proteins. The method relies on the expression of cDNA inserts in bacteriophage lambda gt11. Fusion protein adsorbed onto nitrocellulose filters is probed with radioactive, double-stranded DNA as a ligand. Two procedures greatly increase the level of binding between ligand and recombinant fusion protein. First, nitrocellulose filters are processed through a denaturation/renaturation regimen using 6 M guanidine hydrochloride. Second, synthetic DNA corresponding to the specific binding site is catenated extensively using DNA ligase. The combination of these procedures leads to remarkably strong detection signals. Specific DNA-binding signals can be detected on duplicate filters, and filters can be washed and reused by repeating the cycle of denaturation/renaturation.

Animals↗
PubMed1987

Bond strength of a luting composite to dentin with different bonding systems.

This study evaluated the tensile bond strength of Conclude luting composite to dentin under different environmental conditions with Scotchbond dental adhesive, the FNP system, and unfilled BIS-GMA resin used as bonding agents. Although the bonding systems reportedly yield high tensile bond values to enamel, large differences were observed in this study for bond values to dentin. Only the FNP bonding system produced consistently high tensile load values to dentin under the three environmental conditions tested.

Adhesives↗
PubMed1987

Identification of a rat liver nuclear protein that binds to the enhancer core element of three animal viruses.

This report describes the identification and purification of a nuclear protein from rat liver that binds selectively to DNA sequences associated with several animal virus enhancers. The binding activity was tracked by direct DNase I footprinting through four steps of biochemical fractionation. These procedures led to the identification of a polypeptide species exhibiting an apparent molecular weight of 20 kD that accounts for enhancer binding activity. DNase I and dimethyl sulfate footprinting assays were used to examine the manner in which the purified protein binds to enhancer elements associated with SV40, murine sarcoma virus, and polyoma virus. The results of these assays indicate that the initial interaction established between the 20-kD protein and each viral enhancer occurs via a common DNA sequence known as the enhancer core homology.

Animals↗
PubMed1986

Homologous recognition of a promoter domain common to the MSV LTR and the HSV tk gene.

We have partially purified, from rat liver, a nuclear protein fraction with sequence-specific affinity to a promoter domain shared by the herpesvirus tk gene and the Moloney murine sarcoma virus LTR. For both promoters, the protein-binding domain occurs roughly 80 bp upstream of the mRNA cap site and harbors the pentanucleotide sequence 5'-CCAAT-3'. The MSV LTR pentanucleotide occurs on the coding strand in an orientation pointing toward the retroviral transcription unit. The HSV tk pentanucleotide occurs on the noncoding strand in an orientation pointing away from the gene. Assays in microinjected frog oocytes and transfected mouse L cells indicate that equivalent point mutations, introduced at each residue of the CAT pentanucleotide of each promoter, lead to similar changes in promoter activity. Furthermore, they similarly alter binding of the nuclear protein fraction. Surprisingly, a C to G transversion at the first residue of the CAT pentanucleotide, which severely impairs the activity of both promoters, appears to increase affinity of the CAT binding protein.

Binding Sites↗
PubMed1986

Cast connectors: an alternative to soldering base metal alloys.

A solderless technique has been described for correcting an unstable framework of a base metal fixed partial denture. This technique has been used without failure since 1981 for cast joints with porcelain-fused-to-metal fixed partial dentures.

Acrylic Resins↗