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K R Williams

Publications and source records attributed to K R Williams.

At least 19 recordsLinked to original sources
PubMed1992

Identification of amino acid residues at the interface of a bacteriophage T4 regA protein-nucleic acid complex.

The bacteriophage T4 regA protein (M(r) = 14,6000) is a translational repressor of a group of T4 early mRNAs. To identify a domain of regA protein that is involved in nucleic acid binding, ultraviolet light was used to photochemically cross-link regA protein to [32P]p(dT)16. The cross-linked complex was subsequently digested with trypsin, and peptides were purified using anion exchange high performance liquid chromatography. Two tryptic peptides cross-linked to [32P]p(dT)16 were isolated. Gas-phase sequencing of the major cross-linked peptide yielded the following sequence: VISXKQKHEWK, which corresponds to residues 103-113 of regA protein. Phenylalanine 106 was identified as the site of cross-linking, thus placing this residue at the interface of the regA protein-p(dT)16 complex. The minor cross-linked peptide corresponded to residues 31-41, and the site of cross-linking in the peptide was tentatively assigned to Cys-36. The nucleic acid binding domain of regA protein was further examined by chemical cleavage of regA protein into six peptides using CNBr. Peptide CN6, which extends from residue 95 to 122, retains both the ability to be cross-linked to [32P]p(dT)16 and 70% of the nonspecific binding energy of the intact protein. However, peptide CN6 does not exhibit the binding specificity of the intact protein. Three of the other individual CNBr peptides have no measurable affinity for nucleic acid, as assayed by photo-cross-linking or gel mobility shifts.

Amino Acid Sequence↗
PubMed1992

Purification and characterization of an endo-exonuclease from adult flies of Drosophila melanogaster.

An endo-exonuclease (designated nuclease III) has been purified to near homogeneity from adult flies of Drosophila melanogaster. The enzyme degrades single- and double-stranded DNA and RNA. It has a sedimentation co-efficient of 3.1S and a strokes radius of 27A The native form of the purified enzyme appears to be a monomer of 33,600 dalton. It has a pH optimum of 7-8.5 and requires Mg2+ or Mn2+ but not Ca2+ or Co2+ for its activity. The enzyme activity on double-stranded DNA was inhibited 50% by 30 mM NaCl, while its activity on single-stranded DNA required 100 mM NaCl for 50% inhibition. Under the latter conditions, its activity on double-stranded DNA was inhibited approximately 98%. The enzyme degrades DNA to complete acid soluble products which are a mixture of mono- and oligonucleotides with 5'-P and 3'-OH termini. Supercoiled DNA was converted by the enzyme to nicked and subsequently to linear forms in a stepwise fashion under the condition in which the enzyme works optimally on single-stranded DNA. The amino acid composition and amino acid sequencing of tryptic peptides from purified nuclease III is also reported.

Amino Acid Sequence↗
PubMed1992

Shuffling of amino acid sequence: an important control in synthetic peptide studies of nucleic acid-binding domains. Binding properties of fragments of a conserved eukaryotic RNA binding motif.

We have used synthetic peptides to study a conserved RNA binding motif in yeast poly(A)-binding protein. Two peptides, 45 and 44 amino acids in length, corresponding to amino and carboxyl halves of a 90-amino acid RNA-binding domain in the protein were synthesized. While the amino-terminal peptide had no significant affinity for nucleic acids, the carboxyl-terminal peptide-bound nucleic acids with similar characteristics to that for the entire 577 residue yeast poly(A)-binding protein. In 100 mM NaCl, the latter peptide retained over 50% of the intrinsic binding free energy of the protein, as well as, similar RNA versus DNA binding specificity. However, shuffling of the sequence of this 44 residue peptide had surprisingly little effect on its nucleic acid binding properties suggesting the overriding importance of amino acid composition as opposed to primary sequence. Deletion studies on the 44 residue peptide with the "correct" sequence succeeded in identifying amino acids important for conferring RNA specificity and for increasing our understanding of the molecular basis for nucleic acid binding by synthetic peptides. The shuffled peptide study, however, clearly indicates that considerable caution must be exercised before extrapolating results of structure/function studies on synthetic peptide analogues to the parent protein.

Amino Acid Sequence↗
PubMed1992

Problems in alloplastic middle ear reconstruction.

Alloplastic materials have been used in middle ear reconstruction since 1952. Biologically, biomaterials and specifically ceramics can be defined as being bioinert, bioactive or biodegradable; these terms being descriptive of the biochemical response provoked by the material in the host tissue. Various ceramics, carbons and polymers and their reactions have been studied by the author and his colleagues over the past 5 years utilising animal implantation and fibroblast culture studies aligned with experience from clinical usage. The qualities of the ideal alloplastic implant namely: biocompatibility, stabilisation and incorporation, the consistency of the implant and bioactive bonding and the biofunctionality or mechanics, are applied to the materials currently available. No single alloplastic material fulfills all criteria, the problems encountered in relation to the biomaterials are reported. A better understanding of the microstresses, fatigue and microfractures is necessary, before the ideal alloplastic biomaterial becomes available.

Animals↗
PubMed1992

A dynamic and natural frequency analysis of the Fisch II spandrel using the finite element method.

The recent introduction of the Fisch II spandrel total ossicular replacement prosthesis (TORP), has provided impressive initial hearing benefits in patients. The design, based on a combination of soft plastic and a highly flexible metal shaft, has been analysed in terms of its sound collecting and conducting behaviour using the finite element method. The analysis has examined the mode shapes, displacements and natural frequencies of the prosthesis for a variety of material properties and geometries. The results indicate the optimum vibration characteristics are obtained with a Polycell elastic modulus of 100 N/mm2, with the natural frequency independent of modulus above this value. Furthermore, the diameter of the spandrel shaft is crucially important, with an increase in magnitude of the first natural frequency of 54% for a 25% increase in shaft diameter. At a Polycell membrane thickness of 0.07 mm and a shaft diameter of 0.12 mm, the tympanic membrane and Fisch II prosthesis have almost identical frequencies over the 1st to 6th frequency range. This fact, together with the flexibility of clinical procedures involved in its use, may be the reason for its success.

Animals↗
PubMed1992

The effects of wearing high heeled shoes on pedal pressure in women.

The purpose of this study was to investigate the effects of increased heel height in women's shoes on foot pressure during walking. An increase in heel height increased the maximum peak pressure under the metatarsal heads in the forefoot, decreased the time to maximum peak pressure under the metatarsal heads, and increased the rate of loading to the metatarsals during early support. The higher pressures noted with increased heel height were accompanied by a more uniform distribution of pressure beneath the forefoot. These findings may denote increased stress to the various tissues in the foot when walking in high heeled shoes, which may contribute to deleterious orthopaedic changes. Quantitative studies need to be conducted to determine whether orthopaedic changes occur with prolonged wearing of high heeled shoes.

Adult↗
PubMed1991

Expression of the gene encoded by a family of macronuclear chromosomes generated by alternative DNA processing in Oxytricha fallax.

Hypotrichous ciliated protozoa, such as Oxytricha fallax, produce tiny chromosomes during generation of the transcriptionally active macronucleus. The 81-MAC family of macronuclear chromosomes is produced by alternative DNA processing, such that the chromosomes share a common region of 1.6 kbp. Transcription of a 1.3 kb mRNA from the common region has been analyzed. Transcription starts very near the telomere (34 bp), in a 23 bp region of pure A + T DNA. Polyadenylation sites are very near the other telomere (26 bp), also in a region of nearly pure A + T DNA. Three introns are clustered in the first third of the gene. Intron removal can follow polyadenylation, and the order of removal is not fixed. All three known sequence versions of the 81-MAC chromosomes are represented in the mRNA pool, with no evidence of any further versions. The A + T sequences surrounding the transcription starts and polyadenylation sites are conserved among versions. Introns have conserved 5' and 3' ends and a putative branch-point sequence (YYRAT), but otherwise are highly diverged and are AT-rich. A single long open reading frame, interrupted by the three introns, encodes a homolog of known mitochondrial solute carriers, and contains the codon TAA, which does not encode 'stop,' but a conserved glutamine; TAG appears also to encode glutamine. The results significantly enlarge the small data set of transcription start and polyadenylation sites, of intron features, and of translation signals for hypotrichs.

Animals↗
PubMed1991

A retrovirus-like zinc domain is essential for translational repression of bacteriophage T4 gene 32.

Gene 32 protein (gp32), a single-stranded DNA-binding protein from bacteriophage T4, contains a zinc-binding subdomain with sequence homologies to the 3-cysteine/1-histidine zinc-binding motif found in a variety of retroviruses and plant viruses. In vitro studies suggest that autoregulation of gp32 occurs at the level of translation by gp32 specifically binding gene 32 mRNA at an unusual stem-loop structure that can be modeled as an RNA pseudoknot. Nucleation of gp32 binding via this pseudoknot is thought to be needed to facilitate cooperative binding of gp32 through a largely unstructured region that overlaps the ribosome binding site (McPheeters, D. S., Stormo, G. D., and Gold, L. (1988) J. Mol. Biol. 201, 517-535). Removal of Zn(II) from gp32 results in a protein that retains the ability to bind single-stranded RNA with high affinity but is unable to specifically autoregulate itself at the level of translation. Deletion of the pseudoknot sequences from the gene 32 autoregulatory region results in an mRNA that cannot be repressed by gp32. These results suggest that the zinc-binding subdomain of gp32 plays an essential role in autoregulation by providing a critical element necessary for nucleating cooperative binding at the gene 32 mRNA pseudoknot.

Amino Acid Sequence↗
PubMed1991

Interactions of the A1 heterogeneous nuclear ribonucleoprotein and its proteolytic derivative, UP1, with RNA and DNA: evidence for multiple RNA binding domains and salt-dependent binding mode transitions.

The 319-residue A1 heterogeneous nuclear ribonucleoprotein is the best studied of the group of major or core mammalian hnRNP proteins that bind pre-mRNA immediately following transcription. Circular dichroism studies suggest that binding of A1 and its proteolytic fragment, UP1 (residues 1-195), to nucleic acids results in an unstacking of the bases of poly(A). On the basis of poly[d(A-T)] and poly[r(A-U)] melting studies, both A1 and UP1 are helix-destabilizing proteins. Titrations of A1 and UP1 with poly(A), poly(U), and poly[d(T)] suggest that these two proteins do not bind with significant base specificity. A previous study indicated that A1, which contains a glycine-rich COOH terminus (residues 196-319) not present in UP1, binds cooperatively to polynucleotides while UP1 does not [Cobianchi et al. (1988) J. Biol. Chem. 263, 1063-1071]. Here we confirm this latter finding and demonstrate that the cooperativity parameter for A1 binding, which has a value of about 35 for binding to both single-stranded RNA and DNA, is insensitive to the NaCl concentration at least up to 0.4 M. In contrast to the cooperativity parameter, the occluded site size for A1 binding to RNA is salt dependent and increases from about 14 to 28 upon increasing the NaCl concentration from 25 to 250 mM. This variation in site size is best explained by assuming that A1 can interact with nucleic acids via at least two different binding modes. Both A1 and UP1 have higher affinity for single-stranded as opposed to double-stranded nucleic acids and bind preferentially to single-stranded RNA as compared to DNA. Comparative studies on the binding of A1 versus UP1 to poly[r(epsilon A)] demonstrate that in addition to cooperative protein/protein interactions, the glycine-rich COOH-terminal domain of A1 is also directly involved in protein/nucleic acid interactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1991

Single-stranded DNA binding proteins (SSBs) from prokaryotic transmissible plasmids.

The DNA and protein sequences of single-stranded DNA binding proteins (SSBs) encoded by the plP71a, plP231a, and R64 conjugative plasmids have been determined and compared to Escherichia coli SSB and the SSB encoded by F-plasmid. Although the amino acid sequences of all of these proteins are highly conserved within the NH2-terminal two-thirds of the protein, they diverge in the COOH-terminal third region. A number of amino acid residues which have previously been implicated as being either directly or indirectly involved in DNA binding are conserved in all of these SSBs. These residues include Trp-40, Trp-54, Trp-88, His-55, and Phe-60. On the basis of these sequence comparisons and DNA binding studies, a role for Tyr-70 in DNA binding is suggested for the first time. Although the COOH-terminal third of these proteins diverges more than their NH2-terminal regions, the COOH-terminal five amino acid residues of all five of these proteins are identical. In addition, all of these proteins share the characteristic property of having a protease resistant, NH2-terminal core and an acidic COOH-terminal region. Despite the high degree of sequence homology among the plasmid SSB proteins, the F-plasmid SSB appears unique in that it was the only SSB tested that neither bound well to poly(dA) nor was able to stimulate DNA polymerase III holoenzyme elongation rates. Poly [d(A-T)] melting studies suggest that at least three of the plasmid encoded SSBs are better helix-destabilizing proteins than is the E. coli SSB protein.

Amino Acid Sequence↗
PubMed1991

State-of-the-art biomolecular core facilities: a comprehensive survey.

A survey of 124 protein and/or nucleic acid chemistry facilities has provided a basis for estimating the resources needed to establish a facility, the financial support needed to keep it operating, and the technical capabilities it might reasonably be expected to achieve. Based on these data, an average core facility occupied 870 ft2, was staffed by three full-time personnel, and was equipped with 4-5 major instrument systems. Because user fees generated an average of about $101,000/year in income compared with an average operating budget of about $197,000/year, even a facility that charged user fees would, on average, still require an annual subsidy of about $96,000. Although most government and industrial core facilities did not assess user fees, at least 83 of the 124 respondents did have a preestablished schedule of service charges that enabled a compilation to be made of the average cost of providing a number of typical facility analyses and syntheses. The greater than 100-fold range in charges assessed in core facilities for seemingly identical services was shown to result from the equally large range in the degree of subsidization of these laboratories. Although an average facility might be expected to offer four or five of the following six major services--amino acid sequencing, amino acid analysis, HPLC peptide isolation, peptide synthesis, fragmentation of proteins and DNA synthesis--less than 10% of the responding laboratories provided mass spectrometry, capillary zone electrophoresis, or RNA synthesis. With the exception of peptide synthesis, which had an average turn-around time of about 24 days, all other major services had turn-around times that averaged in the range of 4-9 days. Additional data are summarized regarding average sample throughput in core laboratories and the amount of protein that is needed for hydrolysis/amino acid analysis and sequencing.

Amino Acid Sequence↗
PubMed1991

Mechanics and materials in middle ear reconstruction.

The normal anatomy and physiology of the middle ear is not reproduced in ossiculoplasty and an artificial mechanism for the transmission of sound results. This is true for all types of graft, be they of natural or man-made material. There are, therefore, 2 areas for consideration when looking at the problems encountered in such reconstructions: first, the materials' biocompatability and, secondly, the mechanical effects of the positioning of the graft in the reconstructed ossicular chain. The present work examines these mechanical effects using the finite element method to determine stress and displacement levels in the reconstructed ossicular chain. It is found that the stress levels at the implant-stapedial joint increases as the implant is gradually moved down the malleus. In contrast there is thought to be an increase in sound transmission as the implant is moved down the malleus. Changes in rigidity and hardness of the implant appear to make only modest stress attenuations at the implant-stapes interface.

Biomechanical Phenomena↗
PubMed1990

Mammalian heterogeneous nuclear ribonucleoprotein A1. Nucleic acid binding properties of the COOH-terminal domain.

A1 is a core protein of the eukaryotic heterogeneous nuclear ribonucleoprotein complex and is under study here as a prototype single-stranded nucleic acid-binding protein. A1 is a two-domain protein, NH2-terminal and COOH-terminal, with highly conserved primary structure among vertebrate homologues sequenced to date. It is well documented that the NH2-terminal domain has single-stranded DNA and RNA binding activity. We prepared a proteolytic fragment of rat A1 representing the COOH-terminal one-third of the intact protein, the region previously termed COOH-terminal domain. This purified fragment of 133 amino acids binds to DNA and also binds tightly to the fluorescent reporter poly(ethenoadenylate), which is used to access binding parameters. In solution with 0.41 M NaCl, the equilibrium constant is similar to that observed with A1 itself, and binding is cooperative. The purified COOH-terminal fragment can be photochemically cross-linked to bound nucleic acid, confirming that COOH-terminal fragment residues are in close contact with the polynucleotide lattice. These binding results with isolated COOH-terminal fragment indicate that the COOH-terminal domain in intact A1 can contribute directly to binding properties. Contact between both COOH-terminal domain and NH2-terminal domain residues in an intact A1:poly(8-azidoadenylate) complex was confirmed by photochemical cross-linking.

Amino Acid Sequence↗
PubMed1990

A novel function for zinc(II) in a nucleic acid-binding protein. Contribution of zinc(II) toward the cooperativity of bacteriophage T4 gene 32 protein binding.

The contribution of Zn(II) toward the binding of bacteriophage T4 gene 32 single-stranded nucleic acid-binding protein (gp32) has been examined by the use of two independent approaches. Studies carried out with successively longer oligonucleotides which have the general structure p(dT)n, where n is equal to 8, 16, 24, or 32 nucleotides, suggest that removal of Zn(II) decreases the cooperativity of binding by as much as 30-fold. Hence, whereas apo-gp32 and native gp32 have similar apparent affinities for the single-site lattice p(dT)8, native gp32 has an approximately 10-fold higher affinity compared to apo-gp32 for a two-site lattice, such as p(dT)16. In contrast to native gp32, where full cooperativity (in terms of the strength of a single gp32-gp32 interaction) is reached with only a two-site lattice, the cooperativity of apo-gp32 binding appears to increase approximately 4-fold upon going from a two- to a four-site lattice such as p(dT)32. The conclusion reached from these oligonucleotide studies agrees well with a series of titrations with polyribo(ethenoadenylic) acid, in 0.275-0.40 M NaCl. These latter studies indicate that the 6-38-fold higher affinity of native gp32 as compared to apo-gp32 for polyribo(ethenoadenylic) acid results primarily from the higher cooperativity of binding of native gp32. By stabilizing a specific subdomain within gp32 that is essential along with the NH2-terminal domain (residues 1-9), Zn(II) contributes from 20 to 50% of the free energy of cooperative gp32-gp32 interactions that occur along a polynucleotide lattice.

Amino Acid Sequence↗
PubMed1990

IgA-induced avidity maturation of IgA Fc receptors on murine T lymphocytes.

The analysis of 30 well characterized murine T lymphocyte populations using a cytofluorometric IgA binding assay has identified many populations that are constitutive and/or inducible for IgA receptor expression, and has identified two distinct mechanisms by which IgA up-regulates the IgA-binding properties of murine T cells. Studies with lymphomas, hybridomas, Ag-specific clones and activated normal splenic T cells identified many examples of CD4 and CD8 lineage cells that constitutively expressed IgA receptors. T cell populations that constitutively expressed IgA receptors exhibited enhanced IgA binding after incubation with oligomeric IgA for 18 h. The IgA-induced up-regulation of IgA binding resulted from two distinct processes: 1) an increase in the number of surface membrane IgA binding sites and 2) an increase in the avidity of IgA binding without a change in the number of binding sites. The IgA-induced avidity increase was reflected by a 5- to 10-fold decrease in the apparent Kd. Depending on the T cell population examined the enhanced binding of IgA involved one or both of these mechanisms. T cell populations that did not constitutively express IgA receptors failed to bind IgA after prolonged incubation with oligomeric IgA suggesting that if such cells can express IgA receptors they require other signals to induce their expression. Consistent with this possibility is the finding that resting splenic T cells did not bind IgA but their activation with Con A or mAb anti-T3 resulted in high level expression of IgA receptors. These studies have identified multiple distinct mechanisms that alter the IgA-binding properties of murine T cells and are discussed in terms of their possible physiologic significance.

Animals↗
PubMed1990

Purification and cDNA cloning of ARPP-16, a cAMP-regulated phosphoprotein enriched in basal ganglia, and of a related phosphoprotein, ARPP-19.

ARPP-16 (cAMP-regulated phosphoprotein of Mr = 16,000) is a substrate for cAMP-dependent protein kinase and is enriched in the basal ganglia. ARPP-16 has been purified to homogeneity from the soluble fraction of bovine caudate nuclei. An additional substrate for cAMP-dependent protein kinase of Mr = 19,000 (ARPP-19) was found to cross-react with rabbit anti-serum prepared against purified ARPP-16. Immunological analysis indicated that ARPP-16 was enriched in the basal ganglia while ARPP-19 was present in similar levels in all brain regions studied and was also present in non-neuronal tissues. ARPP-19 was also purified to homogeneity from bovine caudate nucleus cytosol. Using oligonucleotide probes based on the partial amino acid sequence of purified ARPP-16, cDNA clones for ARPP-16 and ARPP-19 were isolated from a bovine caudate nucleus cDNA library and sequenced. The predicted amino acid sequences of the two proteins were identical except that ARPP-19 had an additional 16 amino acids at the NH2-terminal. The two cDNA clones share an identical 3'-untranslated region of 756 nucleotides. The cDNA clone for ARPP-16 contained 806 additional nucleotides located 3' to this common sequence. The 5'-untranslated regions of the two clones were entirely different. The results suggest the possibility that ARPP-16 and ARPP-19 are produced by alternative transcription and splicing.

Amino Acid Sequence↗
PubMed1990

Primary amino acid sequence of alpha-trichosanthin and molecular models for abrin A-chain and alpha-trichosanthin.

Ricin A-chain, abrin A-chain, and alpha-trichosanthin are members of a larger group of proteins called ribosome-inactivating proteins. These proteins all function to catalytically inactivate eukaryotic 60 S ribosomal subunits leading to rapid shutdown of protein synthesis. They are homologous in sequence and are probably evolutionarily related. We have determined the complete primary amino acid sequence of alpha-trichosanthin and have found it to be homologous, as expected, to that of abrin A-chain and ricin A-chain. A crystal structure for ricin, which includes ricin A-chain and ricin B-chain, has been determined from x-ray diffraction data. Based on the sequence homologies of these proteins, we fit the primary sequences of abrin A-chain and alpha-trichosanthin to the backbone structure for ricin A-chain and have generated energy-minimized molecular models for them. These models should prove useful in studying the structural-functional relationships of these proteins in particular and of the class in general.

Abrin↗