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K R Williams

Publications and source records attributed to K R Williams.

At least 91 records · Page 5Linked to original sources
PubMed1990

Studies of the domain structure of mammalian DNA polymerase beta. Identification of a discrete template binding domain.

Characterization of the domain structure of DNA polymerase beta is reported. Large scale overproduction of the rat protein in Escherichia coli was achieved, and the purified recombinant protein was verified by sequencing tryptic peptides. This protein is both a single-stranded DNA binding protein and a DNA polymerase consisting of one polypeptide chain of 334 amino acids. As revealed by controlled proteolysis experiments, the protein is organized in two relatively protease-resistant segments linked by a short protease-sensitive region. One of these protease-resistant segments represents the NH2-terminal 20% of the protein. This NH2-terminal domain (of about 75 residues) has strong affinity for single-stranded nucleic acids. The other protease-resistant segment, representing the COOH-terminal domain of approximately 250 residues, does not bind to nucleic acids. Neither domain, tested as purified proteins, has substantial DNA polymerase activity. The results suggest that the NH2-terminal domain is principally responsible for the template binding activity of the intact protein.

Amino Acid Sequence↗
PubMed1990

A finite element analysis of the natural frequencies of vibration of the human tympanic membrane. Part I.

The present work examines the natural frequencies of vibration of the decoupled human tympanic membrane using the finite element method. A model comprising 49 isoparametric semi-loof thin shell elements was built, based on shape measurements of Kirikae (1960) and our own measurements on several local cadaver ears. A range of material data input was used similar to that assessed earlier by Funnell and Laszlo (1978). The present results indicate the natural vibration mode shapes are simple at low frequencies, but become more complex at higher values as found earlier (Tonndorf and Khanna, 1972; Funnell and Laszlo, 1978), but at reduced frequencies. Data input of the real drum thickenesses and dimensions considerably increases the natural frequencies by about 50% above those for a uniformly thick membrane. It is suggested that realistic eardrum natural frequencies may result from the use of a membrane internal stress parameter in the data file in order to simulate the interplay between radial and circular fibres resulting in the observed drum curvature.

Ear, Middle↗
PubMed1990

Finite element analysis of fixed prostheses attached to osseointegrated implants.

The effect of defined stresses on cantilevered prostheses attached to osseointegrated implants was assessed by finite element analysis. The effect of stress on a cantilever, consisting of a ductile alloy in contact with a brittle polymer, was demonstrated to be complex. The distribution of applied stresses also influenced the results. Possible fracture and distortion of both materials were demonstrated. Finite element analysis is a particularly useful system for predicting stress behavior and can be employed to produce an optimal prosthetic design that reduces the potential for clinical failure.

Acrylic Resins↗
PubMed1989

p10 single-stranded nucleic acid binding protein from murine leukemia virus binds metal ions via the peptide sequence Cys26-X2-Cys29-X4-His34-X4-Cys39.

The RNA binding protein of 56 residues encoded by the extreme 3' region of the gag gene of Rauscher murine leukemia virus (MuLV) has been chemically synthesized by a solid-phase synthesis approach. Since the peptide contains a Cys26-X2-Cys29-X4-His34-X2-Cys39 sequence that is shared by all retroviral gag polyproteins which has been proposed to be a metal binding region, it was of considerable interest to examine the metal binding properties of the complete p10 protein. As postulated, p10 binds the metal ions Cd(II), Co(II), and Zn(II). The Co(II) protein shows a set of d-d absorption bands typical of a tetrahedral Co(II) complex at 695 (epsilon = 565 M-1 cm-1), 642 (epsilon = 655 M-1 cm-1), and 615 nm (epsilon = 510 M-1 cm-1) and two intense bands at 349 (epsilon = 2460 M-1 cm-1) and 314 nm (epsilon = 4240 M-1 cm-1) typical of Co(II)----(-)S- charge transfer. The ultraviolet absorption spectrum also indicates Cd(II) binding by the appearance of a Cd(II)----(-)S- charge-transfer band at 255 nm. The 113Cd NMR spectrum of 113Cd(II)-p10 reveals one signal at delta = 648 ppm. This chemical shift correlates well with that predicted for ligation of 113Cd(II) to three -S- from the three Cys residues of p10. The chemical shift of 113Cd(II)-p10 changes by only 4 ppm upon binding of d(pA)6, indicating that the chelate complex is little changed by oligonucleotide binding.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Phosphorylation of DARPP-32, a dopamine- and cAMP-regulated phosphoprotein, by casein kinase II.

DARPP-32 (dopamine- and cAMP-regulated phosphorprotein, Mr = 32,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is an inhibitor of protein phosphatase-1 and is enriched in dopaminoceptive neurons possessing the D1 dopamine receptor. Purified bovine DARPP-32 was phosphorylated in vitro by casein kinase II to a stoichiometry greater than 2 mol of phosphate/mol of protein whereas two structurally and functionally related proteins, protein phosphatase inhibitor-1 and G-substrate, were poor substrates for this enzyme. Sequencing of chymotryptic and thermolytic phosphopeptides from bovine DARPP-32 phosphorylated by casein kinase II suggested that the main phosphorylated residues were Ser45 and Ser102. In the case of rat DARPP-32, the identification of these phosphorylation sites was confirmed by manual Edman degradation. The phosphorylated residues are located NH2-terminal to acidic amino acid residues, a characteristic of casein kinase II phosphorylation sites. Casein kinase II phosphorylated DARPP-32 with an apparent Km value of 3.4 microM and a kcat value of 0.32 s-1. The kcat value for phosphorylation of Ser102 was 5-6 times greater than that for Ser45. Studies employing synthetic peptides encompassing each phosphorylation site confirmed this difference between the kcat values for phosphorylation of the two sites. In slices of rat caudate-putamen prelabeled with [32P]phosphate, DARPP-32 was phosphorylated on seryl residues under basal conditions. Comparison of thermolytic phosphopeptide maps and determination of the phosphorylated residue by manual Edman degradation identified the main phosphorylation site in intact cells as Ser102. In vitro, DARPP-32 phosphorylated by casein kinase II was dephosphorylated by protein phosphatases-1 and -2A. Phosphorylation by casein kinase II did not affect the potency of DARPP-32 as an inhibitor of protein phosphatase-1, which depended only on phosphorylation of Thr34 by cAMP-dependent protein kinase. However, phosphorylation of DARPP-32 by casein kinase II facilitated phosphorylation of Thr34 by cAMP-dependent protein kinase with a 2.2-fold increase in the Vmax and a 1.4-fold increase in the apparent Km. Phosphorylation of DARPP-32 by casein kinase II in intact cells may therefore modulate its phosphorylation in response to increased levels of cAMP.

Amino Acid Sequence↗
PubMed1989

Primary structure differences between proteins C1 and C2 of HeLa 40S nuclear ribonucleoprotein particles.

Partial acid cleavage, comparative HPLC tryptic peptide mapping and amino acid sequencing of the C1 and C2 proteins of HeLa heterogeneous nuclear ribonucleoprotein (hnRNP) particles demonstrate that proteins C1 and C2 differ in primary structure by the presence of a 13 amino acid insert sequence in C2. This C2 insert sequence occurs after either glycine 106 or serine 107 in C1. The additional 13 amino acids that are present in C2 account for the observed molecular weight difference between the C1 and C2 hnRNP proteins on SDS polyacrylamide gel electrophoresis. Because C1 and C2 appear identical except for the 13 residue insert and because the 3' and 5' untranslated regions of the corresponding mRNAs also appear to be the same (Swanson et al., Mol. Cell. Biol. 7: 1731-1739), it is possible that both polypeptides are produced from a single transcription unit through an alternative splicing mechanism.

Amino Acid Sequence↗
PubMed1989

Site-specific mutagenesis of T4 gene 32: the role of tyrosine residues in protein-nucleic acid interactions.

Bacteriophage T4 gene 32 encodes a single-stranded DNA (ssDNA) binding protein (gp32) required for T4 DNA replication, recombination, and repair. Previous physicochemical studies on gp32 and other ssDNA binding proteins have suggested that binding may involve hydrophobic interactions that result from the close approach of several aromatic amino acid side chains with the nucleic acid bases. In the case of gp32, five tyrosines and two phenylalanines have previously been implicated in gp32.ssDNA complex formation. Site-directed mutagenesis of T4 gene 32 was employed to produce a set of eight gp32 mutant proteins, each of which encoded a single substitution at one of the eight tyrosine residues within gp32. The mutant gp32 proteins were then subjected to physicochemical analysis to evaluate the role of each tyrosine residue in gp32 structure and function. Oligonucleotide binding studies suggest that tyrosine residues 84, 99, 106, 115, and 186 each contribute from 0.3 to 0.7 kcal/mol to ssDNA binding, which corresponds to 3-7% of the overall binding energy for gp32.ssDNA complex formation. Replacement of tyrosine residues 73 and 92 appears to lead to large structural changes that may be the result of disrupting the zinc binding subdomain within gp32.

Calorimetry, Differential Scanning↗
PubMed1989

The 44P subunit of the T4 DNA polymerase accessory protein complex catalyzes ATP hydrolysis.

The genes encoding all three T4 DNA polymerase accessory proteins have been cloned into overexpression plasmids. Induction of cells harboring these plasmids results in the synthesis of each accessory protein at levels that approach 10% of the total cellular protein. The solubility of the accessory proteins after induction at 42 degrees C ranges from about 60% to greater than 95%. A plasmid that allows overexpression of the 44P/62P complex has been manipulated further to overexpress selectively the 44P subunit without 62P, permitting us to assess how each subunit contributes to the properties of the 44P/62P complex. A comparison of 44P and 44P/62P by conventional hydrodynamic techniques shows that 44P forms a subcomplex nearly as large as the 44P/62P complex. In addition, 44P catalyzes DNA-dependent ATP hydrolysis with a specific activity similar to that of the 44P/62P ATPase. However, unlike the 44P/62P complex, the ATPase activity of 44P alone is only slightly stimulated by 45P. This suggests that one role of the 62P subunit is to facilitate a productive interaction of 44P and 45P.

Adenosine Triphosphate↗
PubMed1989

ARPP-21, a cyclic AMP-regulated phosphoprotein (Mr = 21,000) enriched in dopamine-innervated brain regions. Amino acid sequence of the site phosphorylated by cyclic AMP in intact cells and kinetic studies of its phosphorylation in vitro.

ARPP-21 (cyclic AMP-regulated phosphoprotein, Mr = 21,000) is a cytosolic neuronal phosphoprotein that is highly enriched in regions of mammalian brain that receive dopaminergic innervation, in particular the striatum. The state of phosphorylation of ARPP-21 in brain slices prepared from rat striatum was shown to be regulated by 8-bromo-cyclic AMP. Phosphorylation occurred exclusively on seryl residues contained within a single tryptic phosphopeptide as analyzed by two-dimensional thin layer electrophoresis/chromatography. The tryptic phosphopeptide derived from ARPP-21 phosphorylated in intact cells comigrated with the tryptic phosphopeptide derived from purified ARPP-21 phosphorylated by the catalytic subunit of cyclic AMP-dependent protein kinase in vitro. Purified cyclic AMP-dependent protein kinase catalyzed the incorporation of 1.1 mol of [32P]phosphate/mol of ARPP-21 exclusively on seryl residues. The amino acid sequence surrounding the site in purified ARPP-21 phosphorylated by cyclic AMP-dependent protein kinase in vitro was determined by analyzing two overlapping chymotryptic peptides isolated from [32P]phospho-ARPP-21 by reverse phase high performance liquid chromatography. A combination of gas phase and solid phase amino acid sequencing yielded a phosphorylation site sequence of -Glu-Arg-Arg-Lys-Ser(P)-Lys-Ser-Gly-Ala-Gly-. Initial rate studies of the phosphorylation of purified ARPP-21 by the catalytic subunit of cyclic AMP-dependent protein kinase yielded an apparent Km of 0.78 microM and a kcat of 2.2 s-1. A synthetic peptide based on the phosphorylation site of ARPP-21 was phosphorylated on the corresponding seryl residue with an apparent Km of 40 microM and a kcat of 4.0 s-1. These results are compatible with a physiological role for the phosphorylation of ARPP-21 by cyclic AMP-dependent protein kinase in vivo, regulated by first messengers acting via cyclic AMP, e.g. dopamine and vasoactive intestinal peptide.

Amino Acid Sequence↗
PubMed1989

ARPP-21, a cyclic AMP-regulated phosphoprotein enriched in dopamine-innervated brain regions. I. Amino acid sequence of ARPP-21B from bovine caudate nucleus.

ARPP-21 (cAMP-regulated phosphoprotein, Mr = 21,000 as determined by SDS-PAGE) is a major cytosolic substrate for cAMP-stimulated protein phosphorylation in dopamine-innervated regions of the rat CNS. It has recently been purified to homogeneity from bovine caudate nucleus and characterized (Hemmings and Greengard, 1989). ARPP-21 is isolated as 2 isoforms, ARPP-21A and ARPP-21B. The amino acid sequence of purified bovine ARPP-21B has now been determined by gas-phase sequencing. The S-14C-carboxymethylated protein was subjected to enzymatic cleavage with trypsin, chymotrypsin, subtilisin, and endoproteinase Lys-C. The resulting peptides were purified by high-performance liquid chromatography, and selected peptides were subjected to amino acid analysis and/or amino acid sequencing by automated Edman degradation. ARPP-21B consists of a single NH2-terminal blocked polypeptide chain of 88 residues, with a calculated molecular mass of 9561 Da, including an NH2-terminal acetyl group inferred by deblocking with an acylaminopeptidase. This molecular mass is significantly lower than earlier estimates based on SDS-PAGE or hydrodynamic measurements. The seryl residue phosphorylated by cAMP-dependent protein kinase (Hemmings et al., 1989) is located at position 55. The molecule contains 1 cysteinyl residue, at position 71, and contains no methionyl, tyrosyl, phenylalanyl, tryptophanyl, or histidinyl residues. Determination of the primary structure of ARPP-21, one of several phosphoproteins localized to dopaminoceptive neurons in the basal ganglia, provides a framework for further investigations into the molecular mechanisms involved in dopaminergic neurotransmission.

Amino Acid Sequence↗
PubMed1988

Thermal denaturation of T4 gene 32 protein: effects of zinc removal and substitution.

Gene 32 protein (g32P), the single-stranded (ss) DNA binding protein from bacteriophage T4, is a zinc metalloprotein. The intrinsic zinc is one of the factors required for the protein to bind cooperatively to a ssDNA lattice. We have used differential scanning calorimetry to determine how the thermodynamic parameters characterizing the denaturation of g32P are affected by removal or substitution of the intrinsic zinc. Over a wide concentration range (1-10 mg/mL), the native Zn(II) protein unfolds at a tm of 55 degrees C with an associated mean enthalpy change of 139 kcal mol-1. Under the same conditions, the metal-free apoprotein denatures over a relatively broader temperature range centered at 49 degrees C, with a mean enthalpy change of 84 kcal mol-1. Substitution of Zn(II) in g32P by either Cd(II) or Co(II) does not significantly change the enthalpy of denaturation but does affect the thermal stability of the protein. All metallo forms of g32P when bound to poly(dT) undergo highly cooperative denaturational transitions characterized by asymmetric differential scanning calorimetry peaks with increases in tm of 4-5 degrees C compared to the unliganded metalloprotein. Removal of the metal ion from g32P significantly reduces the cooperativity of binding to poly(dT) [Giedroc, D. P., Keating, K. M., Williams, K. R., & Coleman, J. E. (1987) Biochemistry 26, 5251-5259], and presumably as a consequence of this, apo-g32P shows no change in either the shape or the midpoint of the thermal transition on binding to poly(dT).(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗
PubMed1988

Phenylalanines that are conserved among several RNA-binding proteins form part of a nucleic acid-binding pocket in the A1 heterogeneous nuclear ribonucleoprotein.

We have studied the domain structure of the A1 heterogeneous nuclear ribonucleoprotein using both partial proteolysis and photochemical cross-linking to oligodeoxynucleotides. Both the intact A1 protein and its proteolytic fragment, the UP1 protein, can be cleaved by Staphylococcus aureus V-8 protease to produce two polypeptides of 92 amino acids. These two polypeptides correspond to the internal repeat sequence previously noted by us to occur in UP1. The two polypeptides can be purified via single-stranded DNA cellulose chromatography and independently cross-linked to [32P]p(dT)8, indicating that each domain can bind to single-stranded nucleic acids. Purification and sequencing of A1 tryptic peptides that had been cross-linked to oligothymidylic acid revealed that 4 phenylalanine residues, phenylalanines 16, 58, 107, and 149 are the sites of covalent adduct formation, with phenylalanine 16 being the major site of cross-linking. These phenylalanine residues are internally homologous when the repeat sequences in A1 are aligned, that is, phenylalanines 16 and 107 occupy analogous positions in the 91-residue repeat, as do phenylalanines 58 and 149. An examination of the primary structures of a variety of eucaryotic RNA-binding proteins with sequence homology to A1 reveals that the cross-linked phenylalanines in A1 are highly conserved among all of these proteins. Our results provide the first experimental evidence that conserved residues in the 90-amino acid repeating domains shared by A1 and other single-stranded nucleic acid binding-proteins form part of an RNA-binding pocket.

Amino Acid Sequence↗
PubMed1988

Mammalian heterogeneous nuclear ribonucleoprotein complex protein A1. Large-scale overproduction in Escherichia coli and cooperative binding to single-stranded nucleic acids.

Characterization of mammalian heterogeneous nuclear ribonucleoprotein complex protein A1 is reported after large-scale overproduction of the protein in Escherichia coli and purification to homogeneity. A1 is a single-stranded nucleic acid binding protein of 320 amino acids and 34,214 Da. The protein has two domains. The NH2-terminal domain is globular, whereas the COOH-terminal domain of about 120 amino acids has low probability of alpha-helix structure and is glycinerich. Nucleic acid binding properties of recombinant A1 were compared with those of recombinant and natural proteins corresponding to the NH2-terminal domain. A1 bound to single-stranded DNA-cellulose with higher affinity than the NH2-terminal domain peptides. Protein-induced fluorescence enhancement was used to measure equilibrium binding properties of the proteins. A1 binding to poly (ethenoadenylate) was cooperative with the intrinsic association constant of 1.5 X 10(5) M-1 at 0.4 M NaCl and a cooperativity parameter of 30. The NH2-terminal domain peptides bound noncooperatively and with a much lower association constant. With these peptides and with intact A1, binding was fully reversed by increasing [NaCl]; yet. A1 binding was much less salt-sensitive than binding by the NH2-terminal domain peptides. A synthetic polypeptide analog of the COOH-terminal domain was prepared and was found to bind tightly to poly-(ethenoadenylate). The results are consistent with the idea that the COOH-terminal domain contributes to A1 binding through both cooperative protein-protein interaction and direct interaction with the nucleic acid.

Amino Acids↗
PubMed1988

Photochemical crosslinking of bacteriophage T4 single-stranded DNA-binding protein (gp32) to oligo-p(dT)8: identification of phenylalanine-183 as the site of crosslinking.

Using ultraviolet light, both the 33,000-dalton single-stranded DNA-binding protein from T4 bacteriophage (gp32) as well as a 25,000-dalton limited trypsin cleavage product of gp32 (core gp32*) that retains high affinity for single-stranded DNA can be crosslinked to an oligodeoxynucleotide, p(dT)8. After photolysis, a single tryptic peptide crosslinked to p(dT)8 was isolated by anion-exchange high-performance liquid chromatography. Gas-phase sequencing of this modified peptide gave the following sequence: Gln-Val-Ser-Gly-(X)-Ser-Asn-Tyr-Asp-Glu-Ser-Lys, which corresponds to residues 179-190 in gp32. Based on the absence of the expected phenylthiohydantoin derivative of phenylalanine 183 at cycle 5 (X) we infer that crosslinking has occurred at this position and that phenylalanine 183 is at the interface of the gp32:p(dT)8 complex in an orientation that allows covalent bond formation with the thymine radical produced by ultraviolet irradiation.

Cross-Linking Reagents↗
PubMed1988

The tympanic membrane in cross section: a finite element analysis.

This paper applies the technique of finite element analysis to the tympanic membrane. A two-dimensional cross-sectional model of the tympanic membrane and malleus is described. A variety of experiments have been performed on this model, and the displacements under a uniform load are analysed. The shape of the displaced membrane and the movement of the umbo were found to be sensitive to a number of factors. These include the elastic modulus of the membrane, the presence and position of the axis or rotation of the malleus, and the size of the pars flaccida. Some implications of these results are discussed.

Humans↗
PubMed1988

Comb wax mediates the acquisition of nest-mate recognition cues in honey bees.

Honey bees, Apis mellifera, acquire nest-mate recognition cues from wax, the predominant material used in nest construction. Exposure of a newly emerged worker bee to wax-comb substrate significantly reduced the acceptability of that worker to sister bees. Cues acquired from the comb provided colony-specific information about the identity of worker bees; moreover, the effect of comb exposure has been previously shown to override individually produced cues. Food odors (anise oil), when dissolved in paraffin wax, affected worker-recognition characteristics but food odors did not affect these characteristics when fed to bees in sugar candy. Paraffin wax alone did not affect the recognition cues of bees, showing that the wax can be a neutral medium for the transmission of cues. The wax comb in the colony and the hydrocarbon outer layer of the bee cuticle may be a continuous medium for any hydrocarbon-soluble substances used by honey bees in nest-mate recognition; if so, a mechanism by which environmental cues are acquired by honey bees is provided.

Journal Article↗
PubMed1988

The size, operation, and technical capabilities of protein and nucleic acid core facilities.

A survey of 40 protein and nucleic acid chemistry facilities has provided data about the capabilities of core facilities and the cost of the services they provide. Approximately 43% of the +158,000 average annual operating budget for a typical university facility is derived from service charges. After correcting for the various degrees of subsidization of the different facilities, it was found that it costs a typical university facility +65 to carry out an acid hydrolysis and amino acid analysis on a protein. A 25-residue peptide can be synthesized and cleaved for +2078, whereas sequencing the same peptide costs +874. A 25-residue oligonucleotide can be synthesized for +258. The total work output per month of an average facility corresponds to 65 amino acid analyses, 15 amino acid sequencing runs, three peptide syntheses, and 16 oligonucleotide syntheses. Depending on the approach used, from 85 to nearly 200 pmol of protein are required to obtain an accurate amino acid composition. To sequence the first 15 amino acids in a protein typically requires 150 pmol compared with 1.2 nmol of protein required to first carry out a tryptic digest and then isolate and sequence the first 15 residues in one of the resulting tryptic peptides.

Amino Acid Sequence↗