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K R Williams

Publications and source records attributed to K R Williams.

At least 55 records · Page 3Linked to original sources
PubMed1995

Mutagenesis of the COOH-terminal region of bacteriophage T4 regA protein.

The bacteriophage T4 regA protein is a translational repressor that regulates the synthesis of > 12 T4 proteins. Earlier studies demonstrated that photocross-linking of the 122-residue regA protein to (dT)16 occurs at two sites, with the major site occurring at Phe-106. Amino acid substitutions were introduced at Phe-106 to evaluate its role in nucleic acid binding. Binding affinities of mutants F106C, F106V, and F106Y for nonspecific and specific RNA ligands indicated little difference between the Kapp of the mutants and wild type regA protein, for either poly(U) or for a specific gene 44 oligoribonucleotide. Thus, Phe-106 does not contribute measurably to the overall free energy of binding. Partial proteolysis of regA protein was carried out to further probe its domain structure. Chymotryptic cleavage produced a fragment of 11,095 Da that has reduced affinity for poly(U) and that contains the first 93 residues of regA protein. Interestingly, proteolysis of regA protein is reduced in the presence of the specific target, gene 44 RNA. Two deletion mutants, 1-->94 and 1-->109, have also been cloned and purified. The binding affinities of these deletion mutants indicated a 100-1000-fold reduction in their affinities for poly(U). These studies indicate the last 13 amino acids in regA protein make a significant contribution to RNA binding.

Amino Acid Sequence↗
PubMed1995

Wettability of denture soft-lining materials.

Data on the wettability of long-term resilient denture base lining materials have previously been obtained by static methods. This study determined the dynamic contact angle of a range of long-term resilient lining materials and the surface free energy properties of these materials. This method was a rapid and convenient method for determining wettability parameters. The equilibrium contact angle revealed the Flexor and Novus materials to be the least wetted with the Molloplast-B material, and CoeSuper-Soft material was wetted similarly to Trevalon material. The contact angle hysteresis indicated that all the soft-lining materials tested would improve denture stability under dislodgment forces. The surface-free energies appeared to be similar for all the soft-lining materials but were significantly lower than that of Trevalon.

Acrylic Resins↗
PubMed1995

A 3-D finite element analysis of the natural frequencies of vibration of a stapes prosthesis replacement reconstruction of the middle ear.

In this work, the natural frequencies of vibration of two different stapes prosthesis replacement reconstructions have been analysed using the finite element method. Prosthesis 1 was constructed of fine stainless steel wire and a Teflon base, while prosthesis 2 was made entirely of Teflon. The results have indicated that generally, the first natural frequency of vibration falls as the prostheses become larger and more bulky. However, the fall in the first natural for prosthesis 1 was modest when compared with that of the isolated tympanic membrane. An important variable influencing frequencies and mode of vibration of the reconstruction was the tightness of fit of the prostheses within the remaining ossicular chain. The tightness of fit in this work was modelled as a range of spring constants applied at the stapes pseudo footplate, together with a series of joint elements at the incus tip/prosthesis head for the Teflon implant. When these spring constraints were below approximately 10 N/mm, the reconstruction exhibited normal mode 1 vibration behaviour, but at larger spring values, an abnormal mode 1 became established resembling the normal mode 2 vibration characteristics. The formation of new geometries and surfaces following reconstruction, introduces new constraints between umbo and stapes footplate particularly at the natural/artificial interfaces. These unnatural constraints may inhibit and modify the natural movements normally occurring at the stapes footplate leading to abnormal modes of vibration.

Ear Ossicles↗
PubMed1995

Stress in bone adjacent to dental implants.

Finite element analysis (FEA) was employed to assess patterns of stress in bone adjacent to an implant after application of loads through an attached distal extension cantilever. Under all loading conditions, the highest stresses occurred at the distal cervical bone margin adjacent to the cantilever. In clinical studies, this is not consistently the site of the greatest bone changes seen radiographically. This suggests that extrapolation of FEA studies to clinical implantology should be approached with caution until further data become available on both mechanical properties of bone and patterns of bone remodelling induced by defined functional stresses in mandible and maxillae.

Bone Remodeling↗
PubMed1994

Both RNA-binding domains in heterogenous nuclear ribonucleoprotein A1 contribute toward single-stranded-RNA binding.

Heterogenous nuclear ribonucleoproteins (hnRNPs) such as hnRNP A1 are tightly associated with heterogenous nuclear RNAs (hnRNAs) within eukaryotic nuclei and are thought to be involved in hnRNA processing and splice site selection. The NH2-terminal two-thirds of hnRNP A1 contains two 92-amino acid RNA binding domains (RBDs) that are arranged in tandem and are more than 30% homologous with each other. Following this region is a flexible glycine-rich COOH-terminal domain. We have studied the nucleic acid binding properties of the two isolated RBDs (residues 1-92 and 93-184, respectively) and of A1 fragments corresponding to residues 1-184 and 1-196 (i.e., the latter fragment is called UP1) in order to evaluate their relative contributions to A1 binding. We have determined that the individual RBDs of A1 bind poly[r(epsilon A)], a fluorescent single-stranded RNA (ssRNA), with a surprisingly low apparent association constant of only 1.5 x 10(4) M-1 (1-92) and 4.5 x 10(4) M-1 (93-184), respectively. We hypothesize that this low affinity represents a basal level of binding that is common to most RBD-containing proteins. Oligonucleotide binding studies suggest the interaction site size for the 93-184 fragment is approximately 4 nucleotides or less and salt sensitivity studies indicate that only about 27% of the free energy of binding of this RBD derives from ionic interactions. Since the affinity of the 1-184 fragment is at least 10-fold above that of either of its component RBDs, both must contribute to binding. This conclusion is further supported by the increased occluded site size of 1-184 (n = 14 +/- 2), as compared to its 93-184 RBD (n = 6 +/- 1), and by the biphasic binding that was observed for the UP1:poly(U) interaction at pH 6.0. Our finding that the affinity of the 1-184 fragment is 1000-fold less than the product of the affinities of its 1-92 and 93-184 RBDs is consistent with these domains being joined by a flexible linker. By comparing the affinities of the 1-184 fragment with that for A1, we conclude that together the two RBDs in A1 account for only 53% of the free energy of A1 binding. Comparative binding studies with UP1 demonstrate that the short region spanning residues 185-->195 represents an important determinant of the binding affinity of A1 and, since this region contains a site of dimethylation, it may provide a mechanism for regulating the affinity of A1 for specific nucleic acid targets.

Amino Acid Sequence↗
PubMed1994

Purification and nucleic acid binding properties of a fragment of type C1/C2 heterogeneous nuclear ribonucleoprotein from thymic nuclear extracts.

A single-strand nucleic acid binding protein (C/F) that has an apparent molecular weight of 12,000 on SDS-polyacrylamide gel electrophoresis and that was originally thought to be the 12-kDa alpha-subunit of the AB form of terminal deoxynucleotidyl transferase (TdT) from calf thymus has been purified and identified as a fragment of the type C1/C2 hnRNP proteins. On the basis of NH2-terminal sequencing and mass spectrometric analysis, C/F contains approximately 94 residues and spans from residue 9 to approximately residue 102 in the type C1/C2 hnRNP proteins. C/F is presumably produced in vitro via limited proteolysis of the type C1/C2 hnRNP proteins following cell disruption. Since C/F corresponds almost exactly to the approximately 90-residue conserved ribonucleoprotein binding domain (RBD) that is shared by many eukaryotic RNA binding proteins, it provided an opportunity to better characterize the domain structure of the type C1/C2 hnRNP proteins and to compare the nucleic acid binding properties of the type C1/C2 and A1 [see Shamoo et al. (1994) Biochemistry, preceding paper in this issue] RNA binding domains. Like the type A1 RBD, the type C1/C2 RBD has an apparent occluded site size of 6-7 nucleotides. The type C1/C2 RBD binds non-cooperatively to homopolynucleotides and has preferential affinity for RNA and for single as opposed to double-stranded nucleic acids. The type C1/C2 RBD has about a 100-fold higher affinity than the type A1 RBD does for RNA and some of this increased affinity results from additional ionic interactions. The latter account for approximately 50% of the free energy of binding of the type C1/C2 RBD. While the type C1/C2 hnRNP proteins exist in vivo as a very tight tetramer with the structure (C1)3C2 [Barnett et al. (1989) Mol. Cell. Biol. 9, 492-498], the isolated type C1/C2 RBD is a monomer. Hence, the determinants for tetramerization appear to lie outside the type C1/C2 RBD. Phenylalanine 19 was identified as the only point of photochemical cross-linking of the type C1/C2 RBD to [d(T)]8. This residue corresponds to the major site of cross-linking of the A1 RBD to [d(T)]8 [Merrill, B. M., Stone, K. L., Cobianchi, F., Wilson, S. H., & Williams, K. R. (1988) J. Biol. Chem. 263, 3307-3313].(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1994

Determination of the secondary structure and folding topology of an RNA binding domain of mammalian hnRNP A1 protein using three-dimensional heteronuclear magnetic resonance spectroscopy.

The secondary structure and folding topology of the first RNA binding domain of the human hnRNP A1 protein was determined by multidimensional heteronuclear NMR spectroscopy. The 92 amino acid long domain exhibits a beta alpha beta beta alpha beta folding pattern, arranged in a four-stranded antiparallel beta-sheet flanked by two alpha-helices, which is very similar to that found for other members of this family. Regions of marked variation between the structurally characterized RNA binding proteins of this class to date are mainly localized in the loops connecting the secondary structure elements.

Amino Acid Sequence↗
PubMed1994

The relationship between mass and acceleration for impacts on padded surfaces.

It is shown analytically that when an object impacts a deformable surface, the acceleration it experiences is inversely proportional to its mass. This is because acceleration is reduced by deformation of the surface, and more massive objects deform the surface more. Since head injury is thought to depend more on acceleration than applied force, this result implies that children may be at greater risk than adults when striking a padded surface. To test the theoretical prediction, 2.69 and 7.40 kg missiles were dropped 31.8 cm onto three deformable surfaces: dry sod, moist sod, and an artificial playing surface. Impact force was measured with a force plate, and divided by missile mass to obtain acceleration. For each test surface, the smaller mass produced a larger acceleration than the larger mass, confirming the theoretical result. Additionally, load-deformation characteristics of the three surfaces were measured, and the results used to predict the effects of mass on acceleration during impact. The predicted results agreed well with the experimental data for the artificial surface (2.3% difference) and moist sod (5.7% difference), but less well for dry sod (21% difference).

Acceleration↗
PubMed1994

Survey findings on dental fees. A comparison from 1982-93.

The cost of health care services, including dental services, continues to rise at a rate higher than the prices of all goods and services included in the CPI for urban consumers. Increases for physician services, medical care and hospital room rates exceed those for dental care. Dentists generally do not raise their fees across-the-board, but vary increases from procedure to procedure. Increases for certain common dental procedures and services were close to the CPI for consumer goods and services. Fees for such basic preventive and diagnostic procedures--including oral exams, prophylaxes and X-rays--increased at rates well below the overall CPI for dental services.

Data Collection↗
PubMed1994

High heeled shoes: their effect on center of mass position, posture, three-dimensional kinematics, rearfoot motion, and ground reaction forces.

This study investigated changes in center of mass position, forefoot loading, lumbar curvature, and pelvic tilt during standing and ground reaction forces, rearfoot motion, sagittal lower extremity kinematics, and shoulder and pelvic rotations of women walking at 1.4 m.s-1 in different heights of high heeled shoes. Three different heel heights (1.91, 3.81, 7.62cm) were worn by each of 11 women. Vertical forces applied to the forefoot during standing increased with increased heel height. No significant differences in average lumbar curvature or pelvic tilt among shoe heights were found. Significant increases in vertical and anteroposterior forces during walking were found with increased heel height, and foot abduction angle during support showed significant less abduction with higher heels. With an increase in heel height the minimum vertical force (at midstance) and the maximum vertical force during the second half of support both occurred later in the support phase, whereas the maximum and minimum anteroposterior forces occurred earlier in support. Rearfoot angle measures obtained from high-speed video analysis showed a significantly greater angle of supination at footstrike and a smaller angle of maximum pronation in the high compared with the low heeled shoes. Ankle angles throughout the gait cycle showed a significant increase in plantarflexion with increased heel height. Maximum knee angle during swing and knee extension velocity decreased with increased heel height. Other sagittal plane kinematic measures and measures to hip and shoulder rotation derived from three-dimensional (3-D) cine data showed few consistent effects of heel height.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1993

Translational repression by the bacteriophage T4 gene 32 protein involves specific recognition of an RNA pseudoknot structure.

An RNA pseudoknot has been shown to form the 5'-end of bacteriophage T4 gene 32 mRNA that is essential to autoregulation of gene 32 (g32) mRNA by gene product 32 (gp32), a single-stranded nucleic acid binding protein. Structure-mapping of RNA oligonucleotides with structure-specific RNases indicate that two stem regions consisting of nucleotides -67 to -64 base-paired to -52 to -55 (stem-1) and nucleotides -62 to -56 base-paired to -40 to -46 (stem-2) can fold into a "pseudoknotted" structure that may be analogous to the semi-continuous a-helical pseudoknot. Our results suggest that the g32 mRNA pseudoknot can form under conditions where specific autoregulation by gp32 is observed. Although the g32 mRNA pseudoknot is stabilized by Mg2+, it exists in equilibrium with a 3'-hairpin structure. Gel mobility studies carried out with defined length oligonucleotides indicate the gp32 does, in fact, bind tightly to the pseudoknot. These studies agree with the proposal of McPheeters et al., that the pseudoknot represents a nucleation site essential for autogenous gp32 translation regulation. Although disruption of tertiary structure interactions in this pseudoknot (with EDTA) significantly reduces the ability of gp32 to specifically recognize its own mRNA, in vitro mutagenesis studies suggest the sequence of stem-2 and of the loop region (nucleotides -47 to -50) also represent important determinants for specific gp32 autoregulation. Based on a competition assay relying on gel mobility shifts, the order of importance of the major elements of the pseudoknot are stem-1 > sequence of stem-2 or loop-2 > stem-2. In this assay, disruption of stem-1 decreased the ability of the resulting structure to compete for gp32 binding by approximately fourfold. Both stem-1 and stem-2 appear to be essential to maintain high-level expression from gp32 mRNA in an in vitro transcription/translation system. Taken together, these results support the translation control model in which the pseudoknot region is a nucleation point for cooperative gp32 binding, which then proceeds in a 3' direction through a long stretch of single-stranded RNA that includes the initiation codon for gene 32.

Bacteriophage T4↗
PubMed1993

Synthesis and use of an internal amino acid sequencing standard peptide.

A sequenceable internal standard has been made that can be added to samples destined for automated amino acid sequencing and that provides a means for continuously monitoring instrument performance. The 41-residue standard peptide is composed of two unnatural amino acids, norleucine and succinyl-lysine, and has the structure [norleucine-(succinyl-lysine)4]8-norleucine. The phenylthiohydantoin derivatives of the latter two amino acids are well separated via reversed-phase HPLC from the phenylthiohydantoin derivatives of the 20 naturally occurring amino acids. In addition, the standard peptide can be readily synthesized and it has excellent solubility, stability, and sequencing characteristics. The placement of norleucine at every fifth residue in this peptide permits accurate repetitive yield and carryover calculations following runs that are as short as six cycles. Use of this internal standard permits the early detection of suboptimal instrument performance and is especially helpful in differentiating between two common reasons (blocked NH2-terminus versus an instrument problem) for the failure of an automated protein sequencer to provide an NH2-terminal sequence.

Amino Acid Sequence↗
PubMed1993

Surface analysis of titanium implants.

Medical grade titanium samples were examined using X-ray photoelectron spectroscopy before and after immersion in various proteins. Additionally, an implant removed from a patient following clinical failure was examined using scanning ion and electron microscopy. The surface of the as-received samples was found to be mainly TiO2, with contaminants of H2O/OH-, calcium and nitrogen which remained after autoclaving. The immersed proteins adhered to the titanium surface, possibly via a Ca-O link. The failed clinical sample was found to be partially fibrously encapsulated with evidence of calcification. Small amounts of TiOOH were detected at the fibrous periphery, supporting the theory of Tengvall and co-workers that in vivo titanium implants are covered in a gel of this material.

Bone and Bones↗
PubMed1993

Use of monoclonal antibodies MSN-1 and B72.3 in the prediction of the natural history of endometrial hyperplasia.

Forty patients, originally diagnosed as endometrial hyperplasia, were reviewed histopathologically and evaluated for immunohistochemical staining with antibodies directed against TAG-72 and MSN-1 antigens. All patients had follow-up endometrial biospies or hysterectomies from 1 to 13 years later. The extent of regression to normal of nonhyperplastic endometrium, persistence as any type of endometrial hyperplasia, or progression to endometrial adenocarcinoma was correlated with the histologic hyperplastic subtype and immunohistochemical staining. As expected, cases of complex or atypical hyperplasia more often progressed to carcinoma than cases of simple or no hyperplasia. Interestingly, MSN-1 positivity was more prevalent in cases of higher grades than lower grades of hyperplasia and was associated with the tendency to show persistent hyperplasia or progression to carcinoma. B72.3 positivity was uncommon in the hyperplastic endometrium and was not correlated with clinical regression or progression. Although the tendency for progression of endometrial hyperplasia to endometrial carcinoma is best judged histologically, MSN-1 may add prognostic information in subgroups of hyperplasia.

Adenocarcinoma↗
PubMed1993

The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis.

The 45-kD autoantigen associated with juvenile rheumatoid arthritis (JRA) has been isolated from HeLa cell nuclei and purified about 2500-fold to near homogeneity in a five-step chromatographic procedure. Purification of the antigen was monitored by immunoblot assays using a nearly monospecific anti-45-kD serum from a child with JRA. Tryptic peptide mapping and partial amino acid sequencing of the purified 45-kD antigen demonstrated its identity with the DEK protein. DEK is a 43-kD protein of unknown function expressed by the putative oncogene dek located on chromosome 6. As a result of a (6;9) translocation offociated with a rare subtype of acute myeloid leukaemia a chimeric protein containing most of DEK amino acids at the N-terminus is found in leukaemic cells (von Linden et al., Mol Cell Biol. 1992; 12: 1687-97). The 43-kD DEK was detected by immunoblotting with serum from a patient with JRA in a variety of rat tissues, and was most abundant in the spleen and in bone marrow.

Amino Acid Sequence↗
PubMed1993

Natural frequencies of vibration of a fibre supported human tympanic membrane analysed by the finite element method.

A finite element programme developed previously to calculate the natural frequencies of vibration of the human tympanic membrane, has been modified to take into account both natural and geometric rigidities. The natural rigidities take the form of internal membrane stress/strain parameters, while the geometric rigidities are the flexural and membrane stress resultants. The first six natural frequencies calculated are similar to those measured by Laser holography on cadaver membranes and analysed recently by interference techniques. Using a generalized stress/strain constitutional relationship, the natural frequencies were found to be linearly related to the square root of the forces within the membrane. It was proposed in our earlier work, that these internal stresses as well as maintaining the complex shape of the tympanic membrane, serve to enhance its frequency range and response. The role of the radial and circular fibres embedded within the ground substance of the membrane on the frequencies and mode shapes have also been examined by super-imposing beam elements on the semi-loof membrane elements. It was found that the modes of vibration of the membrane are restricted to a fairly simple pattern up to beam moduli values of approximately 50 MPa. Above this beam modulus, the normal mode shape was observed with a gradually increasing complex vibration pattern as the frequency increases. This new treatment of membrane re-enforcement suggests a non-Hookean behaviour of the drum displacements. In order to account for the earlier measured frequencies of Tonndorf & Khanna, the previously proposed internal stress/strain parameters are believed to be less important and have been calculated to be small compared with the membrane modulus.

Humans↗
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↗