Biomedical subjects

James R Thompson

Publications and source records attributed to James R Thompson.

14 recordsLinked to original sources

PubMed2006

Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.

Histone lysine methylation has been linked to the recruitment of mammalian DNA repair factor 53BP1 and putative fission yeast homolog Crb2 to DNA double-strand breaks (DSBs), but how histone recognition is achieved has not been established. Here we demonstrate that this link occurs through direct binding of 53BP1 and Crb2 to histone H4. Using X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, we show that, despite low amino acid sequence conservation, both 53BP1 and Crb2 contain tandem tudor domains that interact with histone H4 specifically dimethylated at Lys20 (H4-K20me2). The structure of 53BP1/H4-K20me2 complex uncovers a unique five-residue 53BP1 binding cage, remarkably conserved in the structure of Crb2, that best accommodates a dimethyllysine but excludes a trimethyllysine, thus explaining the methylation state-specific recognition of H4-K20. This study reveals an evolutionarily conserved molecular mechanism of targeting DNA repair proteins to DSBs by direct recognition of H4-K20me2.

Amino Acid Sequence↗

PubMed2006

Biophysical properties of the extra-cellular domain of the calcium-sensing receptor.

The Calcium-Sensing Receptor (CaSR) is a G-protein-coupled receptor that regulates calcium homeostasis by altering parathyroid hormone release, and which binds divalent and trivalent cations, amino acids, polyamines, and polycationic ligands. To obtain information about the structural properties of the CaSR, we expressed milligram quantities of a pure, homogeneous, and functional fragment of the human CaSR extracellular domain (residues 20-535). The expressed and purified protein is folded and binds both neomycin and calcium. It forms dimers in the absence of reducing agents such as beta-mercaptoethanol. Thermal denaturation studies show it has enthalpy and entropy values of unfolding equal to DeltaH=-178+/-4 kJ/mol and DeltaS=-535+/-13 J/mol/K. The protein has significant secondary structure with alpha-helical, beta-sheet, beta-turns, and disordered content of 36.6+/-6.7%, 13.3+/-5.3%, 20.2+/-3.3%, and 29.4+/-4.0%, respectively. The described method for the expression and purification of CaSR should prove useful for further structural studies of this physiologically important protein.

Animals↗

PubMed2006

Metal-binding properties of human centrin-2 determined by micro-electrospray ionization mass spectrometry and UV spectroscopy.

We analyzed the metal-binding properties of human centrin-2 (HsCen-2) and followed the changes in HsCen-2 structure upon metal-binding using micro-electrospray ionization mass spectrometry (muESI-MS). Apo-HsCen-2 is mostly monomeric. The ESI spectra of HsCen-2 show two charge-state distributions, representing two conformations of the protein. HsCen-2 binds four moles calcium/mol protein: one mol of calcium with high affinity, one additional mol of calcium with lower affinity, and two moles of calcium at low affinity sites. HsCen-2 binds four moles of magnesium/mol protein. The conformation giving the lower charge-state HsCen-2 by ESI, binds calcium and magnesium more readily than does the higher charge-state HsCen-2. Both conformations of HsCen-2 bind calcium more readily than magnesium. Calcium was more effective in displacing magnesium bound to HsCen-2 than vice versa. Binding of a peptide from a known binding partner, the xeroderma pigmentosum complementation group protein C (XPC), to apo-HsCen-2, occurs in the presence or the absence of calcium. Near and far-UV CD spectra of HsCen-2 show little difference with addition of calcium or magnesium. Minor changes in secondary structure are noted. Melting curves derived from temperature dependence of molar ellipticity at 222 nm for HsCen-2 show that calcium increases protein stability whereas magnesium does not. Delta 25 HsCen-2 behaves similarly to HsCen-2. We conclude that HsCen-2 binds calcium and magnesium and that calcium modulates HsCen-2 structure and function by increasing its stability without undergoing significant changes in secondary or tertiary structure.

Binding Sites↗

PubMed2006

The structure of the human centrin 2-xeroderma pigmentosum group C protein complex.

Human centrin-2 plays a key role in centrosome function and stimulates nucleotide excision repair by binding to the xeroderma pigmentosum group C protein. To determine the structure of human centrin-2 and to develop an understanding of molecular interactions between centrin and xeroderma pigmentosum group C protein, we characterized the crystal structure of calcium-loaded full-length centrin-2 complexed with a xeroderma pigmentosum group C peptide. Our structure shows that the carboxyl-terminal domain of centrin-2 binds this peptide and two calcium atoms, whereas the amino-terminal lobe is in a closed conformation positioned distantly by an ordered alpha-helical linker. A stretch of the amino-terminal domain unique to centrins appears disordered. Two xeroderma pigmentosum group C peptides both bound to centrin-2 also interact to form an alpha-helical coiled-coil. The interface between centrin-2 and each peptide is predominantly nonpolar, and key hydrophobic residues of XPC have been identified that lead us to propose a novel binding motif for centrin.

Amino Acid Motifs↗

PubMed2005

Is awesome really awesome? How the inclusion of informal terms on an AAC device influences children's attitudes toward peers who use AAC.

Two videotapes were created of a child communicating with a voice output augmentative and alternative communication (AAC) device. In one the child communicated using formal English only and in the other the child communicated using formal English and age appropriate informal terms. Children in grades 4 and 5 viewed either the formal English only or the formal and informal English videotape. After viewing the videotape, children completed a measure of self-reported attitudes toward children who use AAC. Results indicated effects for gender and for the gender by grade interaction. These results are discussed along with clinical implications.

Attitude↗

PubMed2005

Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase.

An active conformation of phosphoglycerate dehydrogenase (PGDH) from Escherichia coli has been obtained using X-ray crystallography. The X-ray crystal structure is used to examine the potential intermediates for V(max) regulation, for the redox reaction, and for cooperative effects of serine binding. The crystal structure at 2.2 A resolution contains bound NAD(+) cofactor, either sulfate or phosphate anions, and alpha-ketoglutarate, a nonphysiological substrate. A PGDH subunit is formed from three distinct domains: regulatory (RBD), substrate (SBD), and nucleotide binding (NBD). The crystal conformation of the homotetramer points to the fact that, in the absence of serine, coordinated movement of the RBD-SBD domains occurs relative to the NBD. The result is a conformational change involving the steric relationships of both the domains and the subunits. Within the active site of each subunit is a bound molecule of alpha-ketoglutarate and the coenzyme, NAD. The catalytic or active site cleft is changed slightly although it is still solvent exposed; therefore, the catalytic reaction probably involves additional conformational changes. By comparing the inhibited with the uninhibited complex, it is possible to describe changes in conformation that are involved in the inhibitory signal transduction of serine.

Carbohydrate Dehydrogenases↗

PubMed2004

Simulation-based estimation of stochastic process parameters in tumor growth.

Models are generally developed at the micro level. Data are generally gathered at the macro level. Obtaining the macromodel which is the natural consequence of the underlying micro model is generally not feasible. SIMEST gives a means whereby the micromodel is used to generate, for a given assumed set of parameters, simulated sets of macro data. These data are compared with the actual clinical macro data. The parameters are then adjusted to obtain concordance with the clinical data. In this manner, simulation gives us a means of parameter estimation without the necessity of generating the macro model.

Algorithms↗

PubMed2004

Certified mail fails to reach an Emergency Department population.

The objective of this study was to determine if correspondence sent by regular mail would be delivered more often than correspondence sent by certified mail. Correspondence was prospectively randomized and mailed by United States Postal Service using either regular mail service or certified mail service. Mailings were analyzed based on patient demographic information, whether or not mail was returned, and the reason for the return. Certified mail was sent to 145 patients; 58 (40%) of the mailings were returned. Wrong addresses accounted for only 23 (16%) of these, whereas the addressee never claimed 35 (24%). Regular mail was sent to 126 patients, and 19 (15%) of the letters were returned. Wrong addresses accounted for 18 (14%) of these letters, and only 1 (1%) was refused for delivery. In conclusion, when compared with certified mail, regular mail is a more effective means of reaching patients with follow-up information after an Emergency Department visit.

Correspondence as Topic↗

PubMed2003

Exercise training-induced adaptations of immune response are mediated by beta-adrenergic receptors in aged but not young mice.

Beta-adrenergic blockade was used to determine whether the exercise training-induced adaptations of immune response to viral infection were mediated by catecholamines in young and old mice. Young (2 mo) and older (16 mo) male BALB/c mice were randomly assigned to an exercise or control group, and half of the mice in each group received the beta-adrenergic receptor antagonist nadolol. After 8 wk of moderate exercise training, mice were challenged with herpes simplex virus (HSV) 24 h postexercise. The results showed that exercise treatment increased anti-HSV IgM antibody, enhanced IL-10, and altered the kinetics of IFN-gamma and IL-2 production in young and old mice. Unique to older mice, exercise decreased mitogen-induced proliferation, increased splenocytes, and tended to decrease memory cells (CD44(hi+)). In contrast, exercise increased mitogen-induced proliferation but decreased the number of splenic lymphocyte and CD4+ cells in young mice. beta-Adrenergic blockade blunted the exercise-induced changes in anti-HSV IgM, IL-2, IFNgamma, and mitogen-induced proliferation in old but not young mice. The findings suggest that some of the immunomodulatory effects of chronic exercise are mediated via beta-adrenergic receptors and that the role of beta-adrenergic receptors is age dependent.

Adaptation, Physiological↗

PubMed2003

High-yield solvothermal formation of magnetic CoPt alloy nanowires.

One-dimensional (1D) magnetic nanomaterials have attracted much attention recently because of their applications in magnetic recording and spintronics. Nevertheless, it remains a challenge to prepare free-standing magnetic nanowires in high yield. This Communication reports the successful high-yield synthesis of an interesting 1D ferromagnetic CoPt alloy by direct decomposition of platinum acetylacetonate and cobalt carbonyl compound in ethylenediamine solvent through a solvothermal reaction. The CoPt alloy nanowires obtained have a tunable diameter of 10-50 nm and a length along the longitudinal axis of up to several microns, depending on crystallization temperature and reaction time. A unique formation mechanism involving coarsening and ripening under solvothermal conditions was discovered. This research opens new opportunities in synthesizing nanomaterials through low-temperature solvothermal processes.

Journal Article↗

PubMed2003

Ingestion of a dietary supplement containing dehydroepiandrosterone (DHEA) and androstenedione has minimal effect on immune function in middle-aged men.

OBJECTIVE: This study investigated the effects of four weeks of intake of a supplement containing dehydroepiandrosterone (DHEA), androstenedione and herbal extracts on immune function in middle-aged men. DESIGN: Subjects consumed either an oral placebo or an oral supplement for four weeks. The supplement contained a total daily dose of 150 mg DHEA, 300 mg androstenedione, 750 mg Tribulus terrestris, 625 mg chrysin, 300 mg indole-3-carbinol and 540 mg saw palmetto. MEASUREMENTS: Peripheral blood mononuclear cells were used to assess phytohemagglutinin(PHA)-induced lymphocyte proliferation and cytokine production. The cytokines measured were interleukin (IL)-2, IL-4, IL-10, IL-1beta, and interferon (IFN)-gamma. Serum free testosterone, androstenedione, estradiol, dihydrotestosterone (DHT) were also measured. RESULTS: The supplement significantly increased serum levels of androstenedione, free testosterone, estradiol and DHT during week 1 to week 4. Supplement intake did not affect LPS or ConA proliferation and had minimal effect on PHA-induced proliferation. LPS-induced production of IL-1beta, and PHA-induced IL-2, IL-4, IL-10, or IFN-gamma production was not altered by the supplement. The addition of the same supplement, DHEA or androstenedione alone to lymphocyte cultures in vitro did not alter lymphocyte proliferation, IL-2, IL-10, or IFN-gamma, but did increase IL-4. In addition, serum HDL-C concentration significantly declined. CONCLUSION: These findings suggest that, although chronic intake of a complex dietary supplement containing DHEA, androstenedione and herbal extracts increases serum androgen levels, it has minimal effect on immune function in middle-aged men.

Adjuvants, Immunologic↗

PubMed2002

Retinoic acid induces parietal endoderm but not primitive endoderm and visceral endoderm differentiation in F9 teratocarcinoma stem cells with a targeted deletion of the Rex-1 (Zfp-42) gene.

Cultured murine F9 teratocarcinoma stem cells resemble pluripotent stem cells of the inner cell mass of the mouse blastocyst and, depending upon their treatment, can be induced to differentiate along the primitive endoderm, the parietal endoderm (PE), or the visceral endoderm (VE) pathway. The Rex-1 gene encodes a zinc finger family transcription factor which is expressed at high levels in undifferentiated F9 stem cells, embryonic stem cells, and in other types of stem cells. To examine whether the Rex-1 protein plays a role in F9 cell differentiation, homologous recombination was employed to generate F9 cell lines which lack both alleles of Rex-1. F9 wild type cells in monolayer culture require both retinoic acid and cyclic AMP analogs to differentiate into PE, whereas the F9 Rex-1(-/-) cells differentiate into PE, as assessed by several molecular markers, including thrombomodulin and laminin B1, in the presence of RA alone. The F9 Rex-1(-/-) cells do not completely differentiate into VE after RA treatment in aggregate culture; they do not express alpha-fetoprotein, a definitive marker of VE differentiation. These results indicate that the Rex-1 transcription factor regulates the differentiation of F9 stem cells along several distinct cell lineages found in the early embryo.

Animals↗

PubMed2002

Lipid-protein interactions in lipovitellin.

The refined molecular structure of lipovitellin is described using synchrotron cryocrystallographic data to 1.9 A resolution. Lipovitellin is the predominant lipoprotein found in the yolk of egg-laying animals and is involved in lipid and metal storage. It is thought to be related in amino acid sequence to segments of apolipoprotein B and the microsomal transfer protein responsible for the assembly of low-density lipoproteins. Lipovitellin contains a heterogeneous mixture of about 16% (w/w) noncovalently bound lipid, mostly phospholipid. Previous X-ray structural studies at ambient temperature described several different protein domains including a large cavity in each subunit of the dimeric protein. The cavity was free of any visible electron density for lipid molecules at room temperature, suggesting that only dynamic interactions exist with the protein. An important result from this crystallographic study at 100 K is the appearance of some bound ordered lipid along the walls of the binding cavity. The precise identification of the lipid type is difficult because of discontinuities in the electron density. Nonetheless, the conformations of 7 phospholipids and 43 segments of hydrocarbon chains greater than 5 atoms in length have been discovered. The conformations of the bound lipid and the interactions between protein and lipid provide insights into the factors governing lipoprotein formation.

Crystallography, X-Ray↗

PubMed2002

Integrating supports in assessment and planning.

A systematic approach for addressing the support needs of persons with mental retardation and related developmental disabilities is presented and a new scale to measure individual differences in support needs described. The process employed in developing the scale is explained, including the establishment of a typology of support areas that was drawn from a review of the professional literature, a validation process using Q-sort methodology, and a pilot field test. Critical issues and practical challenges associated with efforts to measure and address the support needs of individuals are discussed.

Adult↗