SEARCH · PubMed Health

Results for “Boxing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,387 records · Page 77Linked to original sources

PubMed2002

The SOCS box: a tale of destruction and degradation.

Although initially identified in the suppressor of cytokine signaling (SOCS) family of proteins, the C-terminal SOCS box has now been identified in more than 40 proteins in nine different families. Growing evidence suggests that the SOCS box, similar to the F-box, acts as a bridge between specific substrate-binding domains and the more generic proteins that comprise a large family of E3 ubiquitin protein ligases. In this way, SOCS proteins regulate protein turnover by targeting proteins for polyubiquitination and, therefore, for proteasome-mediated degradation.

Amino Acid Sequence↗

PubMed2003

Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells.

In mammalian cells, all small nucleolar RNAs (snoRNAs) that guide rRNA modification are encoded within the introns of host genes. An optimal position about 70 nts upstream of the 3' splice site of the host intron is critical for efficient expression of box C/D snoRNAs in vivo, suggesting synergy with splicing. Here, we have used a coupled in vitro splicing-snoRNA processing system to demonstrate that assembly of box C/D snoRNP proteins is the step affected by snoRNA location, and that active splicing is essential for snoRNP assembly. Splicing blockage experiments further reveal that snoRNP proteins bind specifically at the spliceosomal C1 complex stage. In contrast, splicing-independent snoRNP assembly can occur in vitro on snoRNAs that possess stable external stems. In vivo analyses confirm that a stable stem can compensate for the unusual position of those few box C/D snoRNAs located far from the 3' splice site of their host intron.

Animals↗

PubMed2002

Basal and parathyroid hormone induced expression of the human 25-hydroxyvitamin D 1alpha-hydroxylase gene promoter in kidney AOK-B50 cells: role of Sp1, Ets and CCAAT box protein binding sites.

The regulation of the gene for renal 25-hydroxyvitamin D 1alpha- hydroxylase (1alpha(OH)ase; CYP27B1) by parathyroid hormone (PTH) under hypocalcemic conditions is fundamentally important for the maintenance of calcium and phosphate homeostasis. The molecular mechanism that underlies this hormonal response is of current interest and has been investigated in the present study by transfection analysis of the human 1alpha(OH)ase promoter in kidney AOK-B50 cells. We have shown that the first 305 bp of promoter can be induced by hormone in transient transfection assays and also within a chromatin environment when stably integrated. Mutagenesis of possible transcription factor binding sites within this promoter length has shown that three sites clustered within the region from -66 to -135 contribute to basal expression. A likely Sp1 and a CCAAT box site are particularly important for basal expression although these sites are not likely to functionally cooperate in a major way. Mutagenesis of the CCAAT box site consistently reduced PTH induction although mutagenesis of the Sp1, Ets and other possible binding sites in the 305 bp of promoter has no significant effect on the level of PTH induction. Other experiments showed that PTH induction but not basal expression was sensitive to the protein kinase inhibitor H89. We have therefore identified for the first time the sites in the 1alpha(OH)ase promoter responsible for basal expression and provide evidence for the role of a CCAAT box binding protein in a PTH mechanism of induction that involves an H89 sensitive step.

25-Hydroxyvitamin D3 1-alpha-Hydroxylase↗

PubMed2000

Yeast Rrp9p is an evolutionarily conserved U3 snoRNP protein essential for early pre-rRNA processing cleavages and requires box C for its association.

Pre-rRNA processing in eukaryotic cells requires participation of several snoRNPs. These include the highly conserved and abundant U3 snoRNP, which is essential for synthesis of 18S rRNA. Here we report the characterization of Rrp9p, a novel yeast U3 protein, identified via its homology to the human U3-55k protein. Epitope-tagged Rrp9p specifically precipitates U3 snoRNA, but Rrp9p is not required for the stable accumulation of this snoRNA. Genetic depletion of Rrp9p inhibits the early cleavages of the primary pre-rRNA transcript at A0, A1, and A2 and, consequently, production of 18S, but not 25S and 5.8S, rRNA. The hU3-55k protein can partially complement a yeast rrp9 null mutant, indicating that the function of this protein has been conserved. Immunoprecipitation of extracts from cells that coexpress epitope-tagged Rrp9p and various mutant forms of U3 snoRNA limits the region required for association of Rrp9p to the U3-specific box B/C motif. Box C is essential, whereas box B plays a supportive role.

Amino Acid Sequence↗

PubMed1993

The specific interactions of HMG 1 and 2 with negatively supercoiled DNA are modulated by their acidic C-terminal domains and involve cysteine residues in their HMG 1/2 boxes.

Sedimentation and gel retardation studies show a stronger interaction of HMG 1 and 2 with negatively supercoiled DNA than with linear, nicked-circular, or positively supercoiled ds-DNA. An apparent unwinding angle of 58 degrees was obtained for HMG 1 and 2 when assayed by protection of negatively supercoiled DNA from topoisomerase I relaxation or when assayed by the supercoiling of nicked-circular DNA with T4 DNA ligase. The protection of negatively supercoiled DNA was linear up to molar ratios of about 250:1. There was little change in binding reactions or in the protection of supercoiled DNA at ratios above 250:1, indicating that both activities saturate and that HMG 1 and 2 have binding site sizes of about 20 bp. P1, the major tryptic fragment of HMG 1 or 2 which retains the two DNA binding HMG 1/2 boxes, displays a 2-fold increase in binding to all types of ds-DNA compared to intact HMG 1 or 2. However P1 protects negatively supercoiled DNA from topoisomerase I relaxation about 5-fold less than intact HMG 1 or 2. Complete protection with P1 occurs at a molar ratio 1040:1, indicating a DNA binding site size of about 4 bp and an apparent unwinding angle of 10 degrees. P1 binding to closed-circular ss-DNA also involves a binding site of about 4 bp. Adding the acidic C-terminal fragment to P1 reversed its binding and allowed topoisomerase I to relax supercoiled DNA. These findings highlight the importance of the acidic C-terminal domains of HMG 1 and 2 in limiting electrostatic interactions of the HMG 1/2 boxes with ds- or ss-DNA. N-Ethylmaleimide inhibited the binding of intact HMG 1 or 2 to negatively supercoiled DNA, but did not inhibit the electrostatic binding of HMG 1 or 2 to ss-DNA, or of P1 to any form of DNA (ds or ss). These results suggest that cysteine residues are involved in the specific interaction of HMG 1 or 2 with negatively supercoiled DNA and that the acidic C-terminal domains modulate an intramolecular conformational change involving sulfhydryls within the HMG 1/2 boxes.

Animals↗

PubMed1993

Helix stop signals in proteins and peptides: the capping box.

The alpha-helix [Pauling, L., Corey, R. B., & Branson, H. R. (1951) Proc. Natl. Acad. Sci. U.S.A. 37, 205-211] is a common motif in both proteins and peptides. Despite intense investigation, predictive understanding of helices is still lacking. A recent hypothesis [Presta, L. G., & Rose, G. D. (1988) Science 240, 1632-1641] proposed that the structural specificity of helices resides, in part, in those residues that flank helix termini. If so, then signals that arrest helix propagation--i.e., helix stop signals--should be found among these flanking residues. Evidence is presented for the existence of one such signal, a reciprocal backbone-side-chain hydrogen-bonding interaction, dubbed the capping box. In proteins, the capping box is found uniquely at helix N-termini. In peptides, the capping box can function as a helix stop signal, as shown in the work of Kallenbach and co-workers.

Amino Acid Sequence↗

PubMed2003

Novel phosphorylation target in the serum response factor MADS box regulates alpha-actin transcription.

Serum response factor (SRF) is a phosphoprotein that regulates skeletal and cardiac alpha-actin gene transcription. Myotonic dystrophy protein kinase (DMPK), a muscle- and neuron-restricted kinase, enhanced SRF-mediated promoter activity of the skeletal and cardiac alpha-actin genes in C2C12 myoblasts as well as in nonmyogenic cells. DMPK phosphorylated SRF in vitro in the alphaI coil of the DNA-binding domain in the MADS box, a highly conserved region required for DNA binding, dimerization, and co-activator interaction in COS and CV1 cells. Threonine 159 in the MADS box alphaI coil was a specific phosphorylation target in vitro as well as in vivo of both DMPK and protein kinase C-alpha. Substitution of threonine 159 with the nonphosphorylatable residue alanine markedly diminished activation of the cardiac alpha-actin promoter in the presence of kinase, while its substitution with aspartic acid, to introduce a negative charge and mimic phosphorylation, restored activation completely. Phosphorylation of the MADS box may constitute a novel mechanism for regulation of SRF-dependent actin gene transcription.

Actins↗

PubMed1996

Factors that affect the stabilization of alpha-helices in short peptides by a capping box.

It was reported recently that the capping box sequences of four N-terminal residues are very important for the stabilization of alpha-helices in proteins and peptides. To elucidate factors that affect the stabilization of alpha-helices in short peptides by this motif, we analyzed conformational properties of side chains of five N-terminal residues in several analogs of neuropeptide Y (NPY). The analysis revealed three previously unreported factors that appear to be important for stabilization of an alpha-helix: (a) a second capping box hydrogen bond for the side chains of Ser, Thr, and Cys; (b) long-range electrostatic interactions between the first (N-cap) and fifth (N4) residues; and (c) capping interactions of alpha-amino groups with the N4 residue. These factors were incorporated into the parameter set of a recently published, statistical mechanics approach that showed excellent accuracy in the prediction of the helical propensities of short peptides in water [Muñoz, V., & Serrano, L. (1995) J. Mol. Biol. 245, 275-296, 297-308]. A significant improvement in the agreement between theoretical predictions and experimental data was achieved. The present results also clarify the nature of capping box stabilization of alpha-helices in peptides and proteins, indicating that the total influence of hydrogen bonding, local interactions between side chains, helix macrodipole--charge/dipole interactions, and solvation possibilities must all be taken into account. All these factors are associated with approximately the same energy, but with different residues at the N-cap position, they may have opposite effects on the helix stability of peptides. Thus, a delicate balance of interactions of different types controls the stabilization properties of N-cap residues in alpha-helices.

Amino Acid Sequence↗

PubMed2000

Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal.

Protein-directed reorganization of DNA underlies mechanisms of transcription, replication, and recombination. A molecular model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the major groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-determining region of the Y chromosome. We observe in the human SRY-HMG:DNA complex extraordinarily large perturbations to Raman bands associated with vibrational modes of the DNA backbone and accompanying large increases in intensities of Raman bands attributable to base unstacking. In contrast, DNA major-groove binding, as occurs for the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemistry 39, 548-556], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are due primarily to perturbation of specific vibrational modes of deoxyribose moieties and presumably reflect desolvation at the nonpolar interface of protein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and are proposed as a baseline for comparative analysis of mutations in SRY that cause human sex reversal.

Amino Acid Sequence↗

PubMed2001

Construction of a square-planar molecular box: self-assembly of palladium(II) complexes of 3,6,9,16,19,22-hexaazatricyclo[22.2.2.2(11,14)]triacon-11,13,24,26(1),27,29-hexaene through hydrogen-bonding interactions.

Binuclear palladium(II) complexes of the macrocyclic polyamine 3,6,9,16,19,22-hexaazatricyclo[22.2.2.2(11,14)]triacon-11,13,24,26(1),2 7,29-hexaene (L) are used to construct molecules having special shapes. In this study two binuclear palladium(II) complexes [Pd(2)LI(2)]I(2)and [Pd(2)LCl(2)](NO(3))(2).H(2)O are synthesized and structurally characterized. X-ray crystallography shows that both complexes exist as one-dimensional chains formed via intermolecular hydrogen-bonding N(3)-H(3C)---X in which X is I and Cl. Moreover, the ligands in both complexes adopt a boatlike conformation that may facilitate the formation of the tetranuclear complex. The cationic aqua complex [Pd(2)L(H(2)O)(m)(NO(3))(n)]((4-n)+, obtained by the treatment of [Pd(2)LI(2)]I(2)and [Pd(2)LCl(2)]Cl(2) with AgNO(3), is used as a building block for the construction of a tetranuclear palladium(II) complex [Pd(4)L(2)(C(2)O(4))(2)](NO(3))(4).6H(2)O. X-ray crystallography shows that the tetranuclear complex forms an open, hydrophobic box. These molecular boxes are connected via the hydrogen bond N(3)-H(3C)---O(4B) (symmetry code B: x, 1 + y, z) into a one-dimensional chain. A two-dimensional structure is formed via pi-pi stacking of the plane defined by C6 to C11 in the one chain and its symmetry-related plane (symmetry code C: -x, -1 - y, 2 - z) in another chain. This study exemplifies a new method for the assembly of molecular boxes using a macrocyclic ligand.

Journal Article↗

PubMed2004

Porphyrin boxes constructed by homochiral self-sorting assembly: optical separation, exciton coupling, and efficient excitation energy migration.

meso-Pyridine-appended zinc(II) porphyrins Mn and their meso-meso-linked dimers Dn assemble spontaneously, in noncoordinating solvents such as CHCl3, into tetrameric porphyrin squares Sn and porphyrin boxes Bn, respectively. Interestingly, formation of Bn from Dn proceeds via homochiral self-sorting assembly, which has been verified by optical separations of B1 and B2. Optically pure enantiomers of B1 and B2 display strong Cotton effects in the CD spectra, which reflect the length of the pyridyl arm, thus providing evidence for the exciton coupling between the noncovalent neighboring porphyrin rings. Excitation energy migration processes within Bn have been investigated by steady-state and time-resolved spectroscopic methods in conjunction with polarization anisotropy measurements. Both the pump-power dependence on the femtosecond transient absorption and the transient absorption anisotropy decay profiles are directly associated with the excitation energy migration process within the Bn boxes, where the exciton-exciton annihilation time and the polarization anisotropy rise time are well described in terms of the Förster-type incoherent energy hopping model by assuming a number of hopping sites of N = 4 and an exciton coherence length of L = 2. Consequently, the excitation energy hopping rates between the zinc(II) diporphyrin units have been estimated for B1 (48 ps)(-1), B2 (98 +/- 3 ps)(-1), and B3 (361 +/- 6 ps)(-1). Overall, the self-assembled porphyrin boxes Bn serve as a well-defined three-dimensional model for the light-harvesting complex.

Biomimetic Materials↗

PubMed1999

Predicting a future lifetime through Box-Cox transformation.

In predicting a future lifetime based on a sample of past lifetimes, the Box-Cox transformation method provides a simple and unified procedure that is shown in this article to meet or often outperform the corresponding frequentist solution in terms of coverage probability and average length of prediction intervals. Kullback-Leibler information and second-order asymptotic expansion are used to justify the Box-Cox procedure. Extensive Monte Carlo simulations are also performed to evaluate the small sample behavior of the procedure. Certain popular lifetime distributions, such as Weibull, inverse Gaussian and Birnbaum-Saunders are served as illustrative examples. One important advantage of the Box-Cox procedure lies in its easy extension to linear model predictions where the exact frequentist solutions are often not available.

Equipment Failure↗

PubMed2001

Methylation of the Opaque2 box in zein genes is parent-dependent and affects O2 DNA binding activity in vitro.

In the maize endosperm, the expression of the subfamily 4 (SF4) of the zein genes is under the transcriptional control of the Opaque2 (O2) basic leucine zipper transcriptional activator, which binds to the O2-box 5'-TCCACGTAGA-3'. Southern experiments showed that the O2-box core sequence ACGT is heavily methylated in sporophytic tissues but becomes hypomethylated in the endosperm. DNA analyses of two inbred lines and their reciprocal crosses indicate that the hypomethylation state is established on the maternal complements of the endosperm. Electrophoretic mobility shift assay (EMSA) and southwestern experiments with endosperm protein extracts and recombinant O2 using oligonucleotides with methylated and unmethylated cytosines in the O2-box indicate an inhibitory effect of modified sequences on O2-binding activity. These results suggest that DNA methylation modulates O2 activity in vivo and shed light on molecular mechanisms involved in the parent-dependent zein gene expression in maize endosperm.

Base Sequence↗

PubMed2002

KAP-2, a protein that binds to the H-box in a bean chalcone synthase promoter, is a novel plant transcription factor with sequence identity to the large subunit of human Ku autoantigen.

The KAP-2 protein that binds to the H-box (CCTACC) element in the bean CHS15 chalcone synthase promoter was purified, and internal peptide sequence used to design primers leading to the cloning of KAP-2 from bean (Phaseolus vulgaris) and barrel medic (Medicago truncatula). KAP-2 shares sequence similarity to the large subunit of mammalian Ku autoantigen, a protein proposed to be involved in control of DNA recombination and transcription. KAP-2 sequences were present in genomic DNA from a range of legumes, and a related protein is found in Arabidopsis thaliana. Recombinant KAP-2 expressed in insect cells showed the same binding specificity for the CHS15 H-box as the protein purified from bean cell extracts. In vitro transcription assays confirmed that KAP-2 stimulates transcription from a promoter harboring the H-box cis element.

Acyltransferases↗

PubMed1976

Facilitation and nonfacilitation of active avoidance behavior of rats with septal lesions in the shuttle box and running wheel.

It was hypothesized that facilitation of avoidance performance of rats with septal lesions occurs only in tasks that punish responses having the same topography as the avoidance response, such as intertrial responses, or tasks that have aversive consequences for making the avoidance response, such as a brightly illuminated safe compartment. Twenty-eight male rats were trained in two shuttle box tasks, and 24 were trained in two running-wheel avoidance tasks under conditions of punishment or nonpunishment of intertrial responses. Rats with septal lesions performed better than control rats in both the shuttle box and the wheel tasks when intertrial responses were punished. When intertrial responding was not punished, experimental and control groups did not differ in avoidance performance. Avoidance performance of punished and unpunished rats with septal lesions did not differ from each other or from unpunished control rats in either wheel or shuttle box tasks. These results were discussed in the context of the species-specific defense reaction (SSDR) avoidance theory of Bolles. It was suggested that septal lesions interfere with the suppression of ineffective SSDRs.

Animals↗

PubMedDate not supplied

Structural analysis of murine genes containing homoeo box sequences and their expression in embryonal carcinoma cells.

The presence of homoeo box sequences in the genomes of vertebrates has suggested that these metazoans possess the equivalent of the homoeotic genes that have a key role in regulating the development of the fruitfly Drosophila melanogaster. We report here that a novel murine homoeo box-containing gene is expressed in embryonal carcinoma stem cells. Transcripts of the sequences that flank the homoeo box of this gene are found in these cells before and after induced differentiation, whereas a specific transcript that seems to contain the homoeo sequence is only present after differentiation.

Animals↗

PubMedDate not supplied

A TATA box implicated in E1A transcriptional activation of a simple adenovirus 2 promoter.

Adenovirus E1A proteins stimulate transcription by RNA polymerases II and III from many promoters. The detailed mechanism of transcriptional activation (transactivation) by E1A proteins remains unclear, but genetic and biochemical results suggest that E1A products might act to stimulate the activity of cellular transcription factors. In this study, a detailed mutational analysis of the adenovirus E1B promoter was undertaken to define the DNA sequences required for proper basal transcription and E1A transactivation. Two key findings emerged: first the E1B promoter is an unusually simple RNA polymerase II promoter requiring only two sequence elements for proper regulation, the TATA box and a binding site for transcription factor Sp1; and second only mutations in the TATA box interfere with E1A-transactivation, suggesting that E1A mediates its effect on this promoter through the TATA-box transcription factor.

Adenovirus Early Proteins↗

PubMed1988

Divergent homeo box proteins recognize similar DNA sequences in Drosophila.

A member of a small group of genes in Drosophila that define the segmentation pattern of the early embryo even-skipped (eve), which plays a key role in a network of interactions among segmentation genes. It appears to control morphogenesis by regulating the expression of the segmentation gene engrailed (en), and by autoregulating its own expression (M. Frasch and M.L., in preparation). Here we show that these regulatory interactions could occur at the level of transcription as a full-length eve protein binds with high affinity to specific sequences located near the 5' ends of the eve and en genes. The en binding sites contain at least one copy of a 10-base pair consensus sequence: T-C-A-A-T-T-A-A-A-T. In contrast, the 5' eve binding sites are relatively G-C rich and do not share obvious similarities with the 10-base pair consensus sequence associated with en. Other homeo box proteins can recognize both classes of eve binding sites, lending support to the proposal that regulatory interactions among homeo box genes involve a competition of different homeo box proteins for similar cis regulatory sequences.

Animals↗