The leucine zipper may induce electrophoretic mobility anomalies without DNA bending

Numerous proteins bend DNA upon binding, a phenomenon of potential significance for regulation of gene expression and chromatin. DNA bending is commonly predicted from the presence of electrophoretic mobility anomalies in protein–DNA complexes. However, as compared with electrophoretic methods, several DNA binding oncoprotein families do not display comparable evidence of DNA bends in x-ray structural studies. Herein, circularization kinetics and affinity measurements with prebent DNA templates were employed to assess bending and DNA structural preferences for Max and other basic helix–loop–helix/leucine zipper proteins. In this way, proteins in the Myc/Max basic helix–loop–helix/leucine zipper family were found not to bend DNA in solution but to actually stabilize DNA in an unbent configuration that resists circularization. The mobility anomaly was found to be induced by the leucine zipper protein motif, rather than structural distortions of DNA. Thus rigid protein domain structures may induce anomalous electrophoretic mobility. Moreover, the energetic preference of non-DNA bending proteins for unbent templates suggests mechanisms whereby chromatin structure may regulate transcription.

p53-induced DNA bending and twisting: p53 tetramer binds on the outer side of a DNA loop and increases DNA twisting

DNA binding activity of p53 is crucial for its tumor suppressor function. Our recent studies have shown that four molecules of the DNA binding domain of human p53 (p53DBD) bind the response elements with high cooperativity and bend the DNA. By using A-tract phasing experiments, we find significant differences between the bending and twisting of DNA by p53DBD and by full-length human wild-type (wt) p53. Our data show that four subunits of p53DBD bend the DNA by 32–36°, whereas wt p53 bends it by 51–57°. The directionality of bending is consistent with major groove bends at the two pentamer junctions in the consensus DNA response element. More sophisticated phasing analyses also demonstrate that p53DBD and wt p53 overtwist the DNA response element by ≈35° and ≈70°, respectively. These results are in accord with molecular modeling studies of the tetrameric complex. Within the constraints imposed by the protein subunits, the DNA can assume a range of conformations resulting from correlated changes in bend and twist angles such that the p53–DNA tetrameric complex is stabilized by DNA overtwisting and bending toward the major groove at the CATG tetramers. This bending is consistent with the inherent sequence-dependent anisotropy of the duplex. Overall, the four p53 moieties are placed laterally in a staggered array on the external side of the DNA loop and have numerous interprotein interactions that increase the stability and cooperativity of binding. The novel architecture of the p53 tetrameric complex has important functional implications including possible p53 interactions with chromatin.

DNA bending by an adenine–thymine tract and its role in gene regulation

To gain insight into the structural basis of DNA bending by adenine–thymine tracts (A-tracts) and their role in DNA recognition by gene-regulatory proteins, we have determined the crystal structure of the high-affinity DNA target of the cancer-associated human papillomavirus E2 protein. The three independent B-DNA molecules of the crystal structure determined at 2.2-Å resolution are examples of A-tract-containing helices where the global direction and magnitude of curvature are in accord with solution data, thereby providing insights, at the base pair level, into the mechanism of DNA bending by such sequence motifs. A comparative analysis of E2–DNA conformations with respect to other structural and biochemical studies demonstrates that (i) the A-tract structure of the core region, which is not contacted by the protein, is critical for the formation of the high-affinity sequence-specific protein–DNA complex, and (ii) differential binding affinity is regulated by the intrinsic structure and deformability encoded in the base sequence of the DNA target.

Fos and Jun bend the AP-1 site: effects of probe geometry on the detection of protein-induced DNA bending.

The effect of Fos and Jun binding on the structure of the AP-1 recognition site is controversial. Results from phasing analysis and phase-sensitive detection studies of DNA bending by Fos and Jun have led to opposite conclusions. The differences between these assays, the length of the spacer between two bends and the length of the sequences flanking the bends, are investigated here using intrinsic DNA bend standards. Both an increase in the spacer length as well as a decrease in the length of flanking sequences resulted in a reduction in the phase-dependent variation in electrophoretic mobilities. Probes with a wide separation between the bends and short flanking sequences, such as those used in the phase-sensitive detection studies, displayed no phase-dependent mobility variation. This shape-dependent variation in electrophoretic mobilities was reproduced by complexes formed by truncated Fos and Jun. Results from ligase-catalyzed cyclization experiments have been interpreted to indicate the absence of DNA bending in the Fos-Jun-AP-1 complex. However, truncated Fos and Jun can alter the relative rates of inter- and intramolecular ligation through mechanisms unrelated to DNA bending, confounding the interpretation of cyclization data. The analogous phase- and shape-dependence of the electrophoretic mobilities of the Fos-Jun-AP-1 complex and an intrinsic DNA bend confirm that Fos and Jun bend DNA, which may contribute to their functions in transcription regulation.

Design of artificial sequence-specific DNA bending ligands.

Proteins that bend DNA are important regulators of biological processes. Sequence-specific DNA bending ligands have been designed that bind two noncontiguous sites in the major groove and induce a bend in the DNA. An oligonucleotide containing pyrimidine segments separated by a central variable linker domain simultaneously binds by triple helix formation two 15-bp purine tracts separated by 10 bp. Bend angles of 61 degrees, 50 degrees, and 38 degrees directed towards the minor groove were quantitated by phasing analysis for linkers of four, five, and six T residues, respectively. The design and synthesis of nonnatural architectural factors may provide a new class of reagents for use in biology and human medicine.

DNA bending by hexamethylene-tethered ammonium ions.

DNA is bent when complexed with certain proteins. We are exploring the hypothesis that asymmetric neutralization of phosphate charges will cause the DNA double helix to collapse toward the neutralized face. We have previously shown that DNA spontaneously bends toward one face of the double helix when it is partially substituted with neutral methylphosphonate linkages. We have now synthesized DNA duplexes in which cations are tethered by hexamethylene chains near specific phosphates. Electrophoretic phasing experiments demonstrate that tethering six ammonium ions on one helical face causes DNA to bend by approximately 5 degrees toward that face, in qualitative agreement with predictions. Ion pairing between tethered cations and DNA phosphates provides a new model for simulating the electrostatic consequences of phosphate neutralization by proteins.

Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model.

Integration host factor (IHF) is a DNA-bending protein that binds to an upstream activating sequence (UAS1) and, on a negatively supercoiled DNA template, activates transcription from the ilvPG promoter of the ilvG-MEDA operon of Escherichia coli. The transcriptional initiation site of the ilvGMEDA operon is located 92 bp downstream of UAS1. Activation is still observed when the orientation of the upstream IHF binding site is reversed. This manipulation places the IHF binding site on the opposite face of the DNA helix, directs the IHF-induced DNA bend in the opposite direction, and presents the opposite face of the nonsymmetrical, heterodimeric, IHF molecule to the downstream RNA polymerase. Lymphoid enhancer-binding factor, LEF-1, is a DNA-bending, lymphoid-specific, mammalian transcription factor that shares no amino acid sequence similarity with IHF. When the IHF site in UAS1 is replaced with a LEF-1 site, LEF-1 activates transcription from the downstream ilvPG promoter in E. coli as well as it is activated by its natural activator, IHF. These results suggest that specific interactions between IHF and RNA polymerase are not required for activation. The results of DNA structural studies show that IHF forms a protein-DNA complex in the UAS1 region that, in the absence of RNA polymerase, alters the structure of the DNA helix in the -10 hexanucleotide region of the downstream ilvPG promoter. The results of in vitro abortive transcription assays show that IIIF also increases the apparent rate of RNA polymerase isomerization from a closed to an open complex. We suggest, therefore, that IHF activates transcription by forming a higher-order protein-DNA complex in the UAS1 region that structurally alters the DNA helix in a way that facilitates open complex formation at the downstream ilvPG promoter site.

Analytical method to measure bending deformations in prismatic optical films

The aim of this work is to provide an analytical method based on experimental measurements in order to obtain the prismatic film deformation for different curvatures of Hollow Cylindrical Prismatic Light Guides (CPLG). To conform cylindrical guides is necessary bend the film to guide the light, changes induced by curving the film give rise to deformation shifts. Light losses affected by deformation has been experimentally evaluated and numerically analyzed. The effect of deformation in prism angle is specially increased for CPLG of curvatures higher than 20 m-1. An experimental method for accurate transmittance measurements related to bending is presented.

Static versus dynamic heterogeneities in the D=3 Edwards-Anderson-ising spin glass

We numerically study the aging properties of the dynamical heterogeneities in the Ising spin glass. We find that a phase transition takes place during the aging process. Statics-dynamics correspondence implies that systems of finite size in equilibrium have static heterogeneities that obey finite-size scaling, thus signaling an analogous phase transition in the thermodynamical limit. We compute the critical exponents and the transition point in the equilibrium setting, and use them to show that aging in dynamic heterogeneities can be described by a finite-time scaling ansatz, with potential implications for experimental work.

Influência da rigidez vertical no comportamento mecânico e dimensionamento da via permanente ferroviária.

A via permanente representa um elemento imprescindível na composição do transporte ferroviário e seu desempenho deve ser adequado, de forma a garantir tanto segurança quanto conforto. Assim, diversos aspectos devem ser analisados ainda na fase de projeto, através de dimensionamentos que confrontem diferentes parâmetros da resposta da via e os limites estabelecidos. Dessa forma, o conhecimento do comportamento mecânico da via, devido aos esforços impostos pela passagem do material rodante, passa a ser essencial no projeto de uma estrutura que garanta os requisitos necessários, sem ser inviável economicamente. Visto que esse comportamento mecânico é muito sensível à rigidez vertical da estrutura, o presente trabalho apresenta análises da influência desse parâmetro na resposta da via e, consequentemente, no seu dimensionamento. Nesse contexto, o trabalho abrange tanto o caso de vias em lastro solicitadas por trens de carga, quanto o caso de vias em laje solicitadas por trens de passageiros em meios urbanos. No primeiro caso são realizados estudos paramétricos, por meio de modelos clássicos e um modelo mecanicista, para a análise de momentos fletores e deflexões nos trilhos, bem como tensões verticais nas camadas de lastro, sub-lastro e subleito. Já no segundo caso, são realizados estudos paramétricos relativos à transmissibilidade e à atenuação de vibrações causadoras de ruído secundário. Também é feita uma análise da influência da rigidez vertical na amplificação dinâmica das cargas estáticas, que pode ser aplicada a ambos os casos citados e até extrapolada para casos de vias de alta velocidade. Os resultados mostraram que aumentos de rigidez vertical resultam em ganhos do ponto de vista de momentos fletores e deflexões nos trilhos, além de maior resistência e capacidade de dissipação de tensões verticais nas camadas de lastro, sub-lastro e subleito. Por outro lado, esses aumentos também levaram a maiores tensões nas camadas subjacentes à grade citadas, além de atenuações de vibrações em menores intervalos de frequência e maiores amplificações dinâmicas das cargas estáticas em vias de alta velocidade. Assim, é mostrado que a influência da rigidez vertical, tanto da via como um todo quanto de alguns elementos específicos, não deve ser analisada de forma genérica, pois, dependendo do parâmetro da resposta da via considerado no dimensionamento, seu aumento pode representar uma influência positiva ou negativa.

Effects of static stretching following a dynamic warm-up on speed, agility and power

Static stretching prior to sport has been shown to decrease force production in comparison to the increasing popularity of dynamic warm-up methods. However some athletes continue to use a bout of static stretching following dynamic methods. The purpose of this study was to investigate the effects on speed, agility and power following a period of additional static stretching following a dynamic warm-up routine. Twenty-five male University students who participated in team sports performed two warm-up protocols concentrating on the lower body one week apart through a randomised cross over design. The dynamic warm-up (DW) protocol used a series of specific progressive exercises lasting 10 minutes over a distance of 20m. The dynamic warm-up plus static stretching (DWS) protocol used the same DW protocol followed by a 5 minute period during which 7 muscle groups were stretched. Following each warm-up the subjects performed a countermovement vertical jump, 20m sprint and Illinois agility test, 1 minute apart. The results demonstrated no significant differences in speed, agility and jump performance following the two protocols DW and DWS. The study concludes that performing static stretching following a dynamic warm-up prior to performance does not significantly affect speed, agility and vertical jump performance.

A Comparative Study of Registration Methods for RGB-D Video of Static Scenes

The use of RGB-D sensors for mapping and recognition tasks in robotics or, in general, for virtual reconstruction has increased in recent years. The key aspect of these kinds of sensors is that they provide both depth and color information using the same device. In this paper, we present a comparative analysis of the most important methods used in the literature for the registration of subsequent RGB-D video frames in static scenarios. The analysis begins by explaining the characteristics of the registration problem, dividing it into two representative applications: scene modeling and object reconstruction. Then, a detailed experimentation is carried out to determine the behavior of the different methods depending on the application. For both applications, we used standard datasets and a new one built for object reconstruction.

Relationship between static and dynamic elastic modulus of calcarenite heated at different temperatures: the San Julián's stone

The San Julián’s stone is the main material used to build the most important historical buildings in Alicante city (Spain). This paper describes the analysis developed to obtain the relationship between the static and the dynamic modulus of this sedimentary rock heated at different temperatures. The rock specimens have been subjected to heating processes at different temperatures to produce different levels of weathering on 24 specimens. The static and dynamic modulus has been measured for every specimen by means of the ISRM standard and ultrasonic tests, respectively. Finally, two analytic formulas are proposed for the relationship between the static and the dynamic modulus for this stone. The results have been compared with some relationships proposed by different researchers for other types of rock. The expressions presented in this paper can be useful for the analysis, using non-destructive techniques, of the integrity level of historical constructions built with San Julián’s stone affected by fires.

Seismic behavior of a masonry chimney with severe cracking condition: preliminary study

This paper presents a structural analysis of a masonry chimney built in the 1940s, which is currently being cataloged as local interest heritage. This structure has not served any industrial purpose for the last thirty years. The chimney is located in the town of Agost (Alicante - Spain) and directly exposed to the prevailing winds from the sea, as it is approximately 12 km away from the waterfront and there are not any significant barriers, which could protect the structure against the wind. There are longitudinal cracks and fissures all along the shaft because of the chimney’s geometrical characteristics, the effect of the masonry creep and especially the lack of maintenance. Moreover, there is also a permanent bending deformation in the upper 1/3 of the height due to the wind pressure. A numerical analysis for the static behavior against gravity and wind loads was performed using the structure’s current conditions after a detailed report of its geometry, its construction system and the cracking pattern. Afterwards, the dynamic behavior was studied, i.e. a seismic analysis using both response spectra and accelerograms in order to examine the structural stability. This work shows the pre-monitoring analysis before any experimental testing. Using the current results the future test conditions will be determined (e.g. number of sensors and monitoring point location, excitation systems, etc) prior to a possible structural reinforcement by applying composite material (fiber reinforced polymers).