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Results for “Transition Elements”

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At least 919 records · Page 51Linked to original sources

PubMed2005

Protein conformational transitions coupled to binding in molecular recognition of unstructured proteins: deciphering the effect of intermolecular interactions on computational structure prediction of the p27Kip1 protein bound to the cyclin A-cyclin-dependent kinase 2 complex.

The relationship between folding mechanism coupled to binding and structure prediction of the tertiary complexes is studied for the p27(Kip) (1) protein which has an intrinsically disordered unbound form and undergoes a functional folding transition during complex formation with the phosphorylated cyclin A-cyclin-dependent kinase 2 (Cdk2) binary complex. Hierarchy of p27(Kip1) structural loss determined in our earlier studies from temperature-induced Monte Carlo simulations and subsequent characterization of the transition state ensemble (TSE) for the folding reaction have shown that simultaneous ordering of the p27(Kip1) native intermolecular interface for the beta-hairpin and beta-strand secondary structure elements is critical for nucleating a rapid kinetic transition to the native tertiary complex. In the present study, we investigate the effect of forming specific intermolecular interactions on structure prediction of the p27(Kip1) tertiary complex. By constraining different secondary structure elements of p27(Kip1) in their native bound conformations and conducting multiple simulated annealing simulations, we analyze differences in the success rate of predicting the native structure of p27(Kip1) in the tertiary complex. In accordance with the nucleation-condensation mechanism, we have found that further stabilization of the native intermolecular interface for the beta-hairpin and beta-strand elements of p27(Kip1), that become ordered in the TSE, but are hardly populated in the unbound state, results in a consistent acquisition of the native bound structure. Conversely, the excessive stablization of the local secondary structure elements, which are rarely detected in the TSE, has a detrimental effect on convergence to the native bound structure.

Cell Cycle↗

PubMed2004

Synthesis, characterization and thermal analysis of some new transition metal complexes of a polydentate Schiff base.

A new polydentate Schiff base (H3L) was synthesized from the condensation of 2,6-diformyl-4-methylphenol and S-methylhydrazine-carbodithionate. The 1:1 metal complexes were obtained from the interaction of H3L and the metal ions Cr(III), Co(II), Ni(II), Cu(II), Cd(II) and Hg(II). The complexes were characterized by elemental analysis and IR spectroscopy. Detailed studies of the thermal properties of the complexes were investigated by thermogravimetry techniques.

Hot Temperature↗

PubMed1986

Transit peptides of nuclear-encoded chloroplast proteins share a common amino acid framework.

We have identified three major blocks of amino acid homology shared by the transit peptides of two nuclear-encoded chloroplast proteins, the light-harvesting chlorophyll a/b-protein (LHCP) II of the thylakoid membrane and the small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) of the stroma. These previously unrecognized homology blocks lie at the beginning, middle and end of both transit sequences, and are separated by differing lengths of unshared (interblock) sequence in the two proteins. These interblocks may be dispensible or they might confer a specific property on the individual proteins, such as facilitating proper compartmentalization within the chloroplast. We propose that these three shared sequence elements form a common framework in transit-bearing chloroplast precursors which mediates the common functions performed by each transit peptide. Ferredoxin, the only other such nuclear-encoded protein for which a published transit sequence exists, conforms to the predictions of this hypothesis. These findings stand in contrast to mitochondrial leader sequences and the well-studied signal peptides of secretory and certain integral membrane proteins in which no such framework has been observed.

Amino Acid Sequence↗

PubMed2005

High-power efficient tunable Nd:GdVO4 laser at 1083 nm.

An efficient tunable diode-pumped Nd:GdVO4 laser at 1083 nm has been constructed by suppressing the higher gain transition near 1063 nm. With 12.5 W diode pump power, the free-running output power centered about 1083 nm was up to 3.4 W, corresponding to an optical-to-optical conversion efficiency of 30.1%. When a simple uncoated etalon was used as a wavelength-selective element, the output power at each helium transition was higher than 2.5 W.

Journal Article↗

PubMed2005

Mass, EPR, IR and electronic spectroscopic studies on newly synthesized macrocyclic ligand and its transition metal complexes.

Manganese(II), cobalt(II), nickel(II) and copper(II) complexes have been synthesized with a new tetradentate ligand viz. 1,3,7,9-tetraaza-2,4,8,10-tetraketo-6,12-diphenyl-cyclododecane (L) and characterized by the elemental analysis, molar conductance measurements, magnetic susceptibility measurements, mass, 1H NMR, IR, electronic and EPR spectral studies. The molar conductance measurements of the complexes in DMF correspond to be nonelectrolytic nature for Mn(II), Co(II) and Cu(II) while 1:2 electrolytes for Ni(II) complexes. Thus, these complexes may be formulated as [M(L)X2] and [Ni(L)]X2 (where M=Mn(II), Co(II) and Cu(II) and X=Cl- and NO3-). On the basis of IR, electronic and EPR spectral studies an octahedral geometry has been assigned for Mn(II) and Co(II) complexes, square-planar for Ni(II) whereas tetragonal for Cu(II) complexes. The ligand and its complexes were also evaluated against the growth of bacteria and pathogenic fungi in vitro.

Anti-Infective Agents↗

PubMed2005

Modern spectroscopic techniques in the characterization of Schiff base macrocyclic ligand and its complexes with transition metals.

Mn(II), Co(II), Ni(II), and Cu(II) complexes with a new azamacrocyclic tetradentate [N(4)] ligand i.e. 2,3,9,10-tetraphenyl;l,4,8,11-tetraazacyclotetradeca;1,3,8,10-tetraene (L) have been synthesized and characterized by elemental analysis, molar conductance measurements, magnetic susceptibility measurements, mass, (1)HNMR, IR, electronic and EPR spectral studies. On the basis of their non-electrolytic nature, the probable formula of the complexes is proposed to be [M(L)X(2)], where M=Mn(II), Co(II), Ni(II), and Cu(II), X=Cl(-) and NO(3)(-), in dimethylformamide (DMF). All the complexes are of high-spin type and found to have six coordinated, octahedral geometry for Mn(II), Co(II), and Ni(II) complexes, and tetragonal for Cu(II) complexes. Macrocyclic ligand and its complexes have also been screened against pathogenic bacteria and fungi in vitro as growth inhibiting agent.

Cobalt↗

PubMed2005

Unfolding dynamics of the protein ubiquitin: insight from simulation.

The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known " state" of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process.

Computer Simulation↗

PubMed1993

The influence of basal cartilage calcification on dynamic juxtaarticular stress transmission.

Dynamic finite element analysis is used to elucidate the manner in which juxtaarticular stress distributions depend on the transitional mechanical properties of the calcified cartilage layer. A finite element model is used to study how these stresses change in response to the thinning of the articular cartilage layer associated with tidemark advancement. The finite element results indicate that shear stress levels within the deepest layer of articular cartilage are increased when tidemark advancement with concomitant cartilage-thinning and calcified cartilage/subchondral plate thickening is modeled. The cartilage-thinning associated with tidemark advancement, observed both clinically and experimentally, may be an explanation for what has previously been considered wear-related thinning.

Animals↗

PubMed1993

Trace elemental analysis at nanometer spatial resolution by parallel-detection electron energy loss spectroscopy.

Parallel-detection electron energy loss spectroscopy (EELS) combined with scanning transmission electron microscopy (STEM) and a field emission source provides an unprecedented sensitivity for elemental microanalysis. By deflecting the energy loss spectrum across a parallel detector and computing the difference spectrum from sequentially collected energy-shifted spectra, the effects due to detector pattern noise are nearly eliminated so that signals less than 0.1% of the background can be readily detected. Measurements on a series of glass standard reference materials show that EELS provides both high spatial resolution and trace sensitivity at the 10 atomic ppm level for a wide range of elements including the alkaline earths, 3-d transition metals, and the lanthanides. For analytical volumes with dimensions of the order of 10 nm, this translates into near-single atom detectability.

Electrons↗

PubMed1991

Changes in element concentration and distribution in breast-milk fractions of a healthy lactating mother.

Daily changes in components of breast milk with number of days of lactation after delivery were demonstrated by determining concentrations and distributions of several elements simultaneously. Concentrations of calcium, copper, magnesium, phosphorus, sulfur, and zinc were determined simultaneously by inductively coupled argon plasma-atomic-emission spectrometry (ICP) for whole milk and milk fractions (skimmed milk and whey) collected from 2 to 196 d postpartum from a healthy lactating mother. Calcium and phosphorus concentrations increased in transitional milk. With days postpartum, the other elements decreased from the highest concentrations in colostrum milk, the modes of decrease being characteristic for each element. Distributions of copper, iron, phosphorus, sulfur, and zinc in whey were determined on a gel-filtration column by HPLC with ICP detection (HPLC-ICP method). Distributions of the five elements and absorbance peaks at 254 and 280 nm changed dramatically day by day at the beginning (colostrum milk), resulting in constant distributions after 30 d (mature milk). These results suggest the important roles of daily changing constituents in breast milk, especially in colostrum milk, in the nutrition of the newborn. Several element peaks on a gel-filtration column were identified by comparison with standard samples.

Adult↗

PubMed2002

Self-induced structural switches in RNA.

Many biologically active RNAs show a switch in their secondary structure, which is accompanied by changes in their function. Such changes in secondary structure often require trans-acting factors, e.g. RNA chaperones. However, several biologically active RNAs do not require trans-acting factors for this structural switch, which is therefore indicated here as a "self-induced switch". These self-induced structural switches have several characteristics in common. They all start from a metastable structure, which is maintained for some time allowing or blocking a particular function of the RNA. Hereafter, a structural element becomes available, e.g. during transcription, triggering a rapid transition into a stable conformation, which again is accompanied by either a gain or loss of function. A further common element of this type of switches is the involvement of a branch migration or strand displacement reaction, which lowers the energy barrier of the reaction sufficiently to allow rapid refolding. Here, we review a number of these self-induced switches in RNA secondary structure as proposed for several systems. A general model for this type of switches is presented, showing its importance in the biology of functionally active RNAs.

Animals↗

PubMed2002

Dysfunction of rat liver mitochondria by selenite: induction of mitochondrial permeability transition through thiol-oxidation.

Selenium is an essential trace element in mammals and is thought to play a chemopreventive role in human cancer, possibly by inducing tumor cell apoptosis. Mitochondria play a pivotal role in the induction of apoptosis in many cell types. The effects of selenite on mitochondrial function were therefore investigated. Selenite induced the oxidation and cross-linking of protein thiol groups, mitochondrial permeability transition (MPT), a decrease in the mitochondrial membrane potential, and the release of cytochrome c in mitochondria isolated from rat liver. Induction of the MPT by selenite was prevented by cyclosporin A, EGTA, or N-ethylmaleimide. These results thus indicate that selenite induces the MPT as a result of direct modification of protein thiol groups, resulting in the release of cytochrome c and a loss of mitochondrial membrane potential.

Animals↗

PubMed2024

Exploring Regulatory Roles of Transposable Elements in EMT and MET through Data-Driven Analysis: Insights from regulaTER.

Gene expression is regulated at the transcriptional and translational levels and a plethora of epigenetic mechanisms. Regulation of gene expression by transposable elements is well documented. However, a comprehensive analysis of their regulatory roles is challenging due to the lack of dedicated approaches to define their contribution. Here, we present regulaTER, a new R library dedicated to deciphering the regulatory potential of transposable elements in a given phenotype. regulaTER utilizes a variety of genomics data of any origin and combines gene expression level information to predict the regulatory roles of transposable elements. We further validated its capabilities using data generated from an epithelial-mesenchymal and mesenchymal-epithelial transition cellular model. regulaTER stands out as an essential asset for uncovering the impact of transposable elements on the regulation of gene expression, with high flexibility to perform a range of transposable element-focused analyses. Our results also provided insights on the contribution of the MIR and B element subfamilies in regulating EMT and MET through the FoxA transcription factor family. regulaTER is publicly available and can be downloaded from https://github.com/karakulahg/regulaTER.

DNA Transposable Elements↗

PubMed2001

Effects of abrupt surface-profile transitions in nonparaxial diffractive optics.

It is shown that the failure of the thin-element approximation of diffractive optics may, in the first approximation, be attributed to local diffraction effects caused by the abrupt vertical transitions in binary surface-relief profiles. We determine the field disturbance caused by a single-step transition (of given height) by rigorous diffraction theory. Associating such a disturbance with each individual transition point in the profile, we obtain a computationally efficient refinement of the thin-element approximation for the analysis and design of diffractive elements in the nonparaxial domain. The results agree well with those obtained by global application of rigorous diffraction theory, provided that the smallest features in the binary profile are larger than approximately one optical wavelength.

Journal Article↗

PubMed2004

Dendritic to globular morphology transition in ternary alloy solidification.

The evolution of solidification microstructures in ternary metallic alloys is investigated by adaptive finite element simulations of a general multicomponent phase-field model. A morphological transition from dendritic to globular growth is found by varying the alloy composition at a fixed undercooling. The dependence of the growth velocity and of the impurity segregation in the solid phase on the composition is analyzed and indicates a smooth type of transition between the dendritic and globular growth structures.

Journal Article↗

PubMed2001

Sucrase-isomaltase gene transcription requires the hepatocyte nuclear factor-1 (HNF-1) regulatory element and is regulated by the ratio of HNF-1 alpha to HNF-1 beta.

The mouse sucrase-isomaltase (SI) gene is an enterocyte-specific gene expressed in a complex developmental pattern. We previously reported that a short, evolutionarily conserved gene promoter regulates developmental expression of SI in mouse small intestine. Herein, we investigated the role of a hepatocyte nuclear factor-1 (HNF-1) cis-acting element to regulate SI gene expression in vivo. Transgenic SI gene constructs with a mutated HNF-1 element (SIF3) revealed a strong reduction in promoter activity in comparison with a wild-type construct in mice and during Caco-2 cell differentiation. Nuclear proteins isolated from enterocytes showed increased binding of the HNF-1 alpha complex with a concomitant decrease in the HNF-1 beta-containing complex to the SIF3 element both during the suckling-weaning developmental transition and Caco-2 cell differentiation. These changes coincided with a strong induction of SI gene transcription. In transfection experiments, HNF-1 alpha activated the SI promoter via the SIF3 element, and co-expression of HNF-1 beta impaired this transcriptional activation. These findings demonstrate the essential role of the HNF-1 regulatory element to support SI gene transcription in vivo and suggest that the ratio of HNF-1 alpha to HNF-1 beta plays a role in the transcriptional activity of this gene during intestinal development.

Animals↗

PubMed2005

Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing.

Developing a detailed understanding of the structure and energetics of protein folding transition states is a key step in describing the folding process. The phi-value analysis approach allows the energetic contribution of side-chains to be mapped out by comparing wild-type with individual mutants where conservative changes are introduced. Studies where multiple substitutions are made at individual sites are much rarer but are potentially very useful for understanding the contribution of each element of a side-chain to transition state formation, and for distinguishing the relative importance of specific packing versus hydrophobic interactions. We have made a series of conservative mutations at multiple buried sites in the N-terminal domain of L9 in order to assess the relative importance of specific side-chain packing versus less specific hydrophobic stabilization of the transition state. A total of 28 variants were prepared using both naturally occurring and non-naturally occurring amino acids at six sites. Analysis of the mutants by NMR and CD showed no perturbation of the structure. There is no correlation between changes in hydrophobicity and changes in stability. In contrast, there is excellent linear correlation between the hydrophobicity of a side-chain and the log of the folding rate, ln(k(f)). The correlation between ln(k(f)) and the change in hydrophobicity holds even for substitutions that change the shape and/or size of a side-chain significantly. For most sites, the correlation with the logarithm of the unfolding rate, ln(k(u)), is much worse. Mutants with more hydrophobic amino acid substitutions fold faster, and those with less hydrophobic amino acid substitutions fold slower. The results show that hydrophobic interactions amongst core residues are an important driving force for forming the transition state, and are more important than specific tight packing interactions. Finally, a number of substitutions lead to negative phi-values and the origin of these effects are described.

Amino Acids↗

PubMed2005

Examination of the bonding in binary transition-metal monophosphides MP (M = Cr, Mn, Fe, Co) by X-ray photoelectron spectroscopy.

The binary transition-metal monophosphides CrP, MnP, FeP, and CoP have been studied with X-ray photoelectron spectroscopy. The shifts in phosphorus 2p(3/2) core line binding energies relative to that of elemental phosphorus indicated that the degree of ionicity of the metal-phosphorus bond decreases on progressing from CrP to CoP. The metal 2p(3/2) core line binding energies differ only slightly and show similar line shapes to those of the elemental metals, reaffirming the notion that these transition-metal phosphides have considerable metallic character. The satellite structure observed in the Co 2p(3/2) X-ray photoelectron spectra of Co metal and CoP was examined by reflection electron energy loss spectroscopy and has been attributed to plasmon loss, not final state effects as has been previously suggested. Valence-band spectra of the transition-metal phosphides agree well with the density of states profiles determined from band structure calculations. The electron populations of the different electronic states were extracted from the fitted valence-band spectra, and these confirm the presence of strong M-P and weak P-P bonding interactions. Atomic charges determined from the P 2p core line spectra and the fitted valence-band spectra support the approximate formulation M(1+)P(1-) for these phosphides.

Journal Article↗