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1.
Materials (Basel) ; 14(12)2021 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-34199183

RESUMO

Static (DC) and dynamic (AC, at 14 MHz and 8 GHz) magnetic susceptibilities of single crystals of a ferromagnetic superconductor, EuFe2(As1-xPx)2 (x = 0.23), were measured in pristine state and after different doses of 2.5 MeV electron or 3.5 MeV proton irradiation. The superconducting transition temperature, Tc(H), shows an extraordinarily large decrease. It starts at Tc(H=0)≈24K in the pristine sample for both AC and DC measurements, but moves to almost half of that value after moderate irradiation dose. Remarkably, after the irradiation not only Tc moves significantly below the FM transition, its values differ drastically for measurements at different frequencies, ≈16 K in AC measurements and ≈12 K in a DC regime. We attribute such a large difference in Tc to the appearance of the spontaneous internal magnetic field below the FM transition, so that the superconductivity develops directly into the mixed spontaneous vortex-antivortex state where the onset of diamagnetism is known to be frequency-dependent. We also examined the response to the applied DC magnetic fields and studied the annealing of irradiated samples, which almost completely restores the superconducting transition. Overall, our results suggest that in EuFe2(As1-xPx)2 superconductivity is affected by local-moment ferromagnetism mostly via the spontaneous internal magnetic fields induced by the FM subsystem. Another mechanism is revealed upon irradiation where magnetic defects created in ordered Eu2+ lattice act as efficient pairbreakers leading to a significant Tc reduction upon irradiation compared to other 122 compounds. On the other hand, the exchange interactions seem to be weakly screened by the superconducting phase leading to a modest increase of Tm (less than 1 K) after the irradiation drives Tc to below Tm. Our results suggest that FM and SC phases coexist microscopically in the same volume.

2.
Rev Sci Instrum ; 91(7): 073904, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32752837

RESUMO

Uniaxial stress is used to detwin the samples of orthorhombic iron based superconductors to study their intrinsic electronic anisotropy. Here, we describe the development of a new detwinning setup enabling variable-load stress-detwinning with easy sample mounting/dismounting without the need to re-solder the contacts. It enables the systematic study of the anisotropy evolution as a function of an external parameter when the sample is modified between the measurements. In our case, the external parameter is the dose of 2.5 MeV electron irradiation at low temperature. We illustrate the approach by studying resistivity anisotropy in single crystals of Ba1-xKxFe2As2 at x = 0.25, where the much discussed unusual re-entrance of the tetragonal C4 phase, C4 → C2 → C4, is observed on cooling. With the described technique, we found a significant anisotropy increase in the C2 phase after electron irradiation with a dose of 2.35 C/cm2.

3.
Nat Commun ; 9(1): 2796, 2018 07 18.
Artigo em Inglês | MEDLINE | ID: mdl-30022110

RESUMO

The interplay between superconductivity and charge-density wave (CDW) in 2H-NbSe2 is not fully understood despite decades of study. Artificially introduced disorder can tip the delicate balance between two competing long-range orders, and reveal the underlying interactions that give rise to them. Here we introduce disorder by electron irradiation and measure in-plane resistivity, Hall resistivity, X-ray scattering, and London penetration depth. With increasing disorder, the superconducting transition temperature, Tc, varies non-monotonically, whereas the CDW transition temperature, TCDW, monotonically decreases and becomes unresolvable above a critical irradiation dose where Tc drops sharply. Our results imply that the CDW order initially competes with superconductivity, but eventually assists it. We argue that at the transition where the long-range CDW order disappears, the cooperation with superconductivity is dramatically suppressed. X-ray scattering and Hall resistivity measurements reveal that the short-range CDW survives above the transition. Superconductivity persists to much higher dose levels, consistent with fully gapped superconductivity and moderate interband pairing.

4.
Sci Adv ; 2(9): e1600807, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27704046

RESUMO

The mechanism of unconventional superconductivity in iron-based superconductors (IBSs) is one of the most intriguing questions in current materials research. Among non-oxide IBSs, (Ba1-x K x )Fe2As2 has been intensively studied because of its high superconducting transition temperature and fascinating evolution of the superconducting gap structure from being fully isotropic at optimal doping (x ≈ 0.4) to becoming nodal at x > 0.8. Although this marked evolution was identified in several independent experiments, there are no details of the gap evolution to date because of the lack of high-quality single crystals covering the entire K-doping range of the superconducting dome. We conducted a systematic study of the London penetration depth, λ(T), across the full phase diagram for different concentrations of point-like defects introduced by 2.5-MeV electron irradiation. Fitting the low-temperature variation with the power law, Δλ ~ Tn , we find that the exponent n is the highest and the Tc suppression rate with disorder is the smallest at optimal doping, and they evolve with doping being away from optimal, which is consistent with increasing gap anisotropy, including an abrupt change around x ≃ 0.8, indicating the onset of nodal behavior. Our analysis using a self-consistent t-matrix approach suggests the ubiquitous and robust nature of s± pairing in IBSs and argues against a previously suggested transition to a d-wave state near x = 1 in this system.


Assuntos
Compostos de Ferro/química , Fenômenos Físicos , Supercondutividade , Anisotropia , Temperatura Alta , Magnetismo/métodos , Fônons
5.
mBio ; 5(1): e00933-13, 2014 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-24520058

RESUMO

UNLABELLED: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE: At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.


Assuntos
Redes e Vias Metabólicas/genética , Paracoccus denitrificans/genética , Paracoccus denitrificans/metabolismo , Prolina/análogos & derivados , Rhodobacter sphaeroides/genética , Rhodobacter sphaeroides/metabolismo , Isomerases de Aminoácido/química , Temperatura Baixa , Cristalografia por Raios X , Regulação Bacteriana da Expressão Gênica , Metaboloma , Pressão Osmótica , Paracoccus denitrificans/efeitos dos fármacos , Paracoccus denitrificans/efeitos da radiação , Prolina/metabolismo , Conformação Proteica , Rhodobacter sphaeroides/efeitos dos fármacos , Rhodobacter sphaeroides/efeitos da radiação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
6.
Metabolomics ; 2014(August)2014 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-25705145

RESUMO

While recent advances in metabolomic measurement technologies have been dramatic, extracting biological insight from complex metabolite profiles remains a challenge. We present an analytical strategy that uses data obtained from high resolution liquid chromatography-mass spectrometry and a bioinformatics toolset for detecting actively changing metabolic pathways upon external perturbation. We begin with untargeted metabolite profiling to nominate altered metabolites and identify pathway candidates, followed by validation of those pathways with transcriptomics. Using the model organisms Rhodospirillum rubrum and Bacillus subtilis, our results reveal metabolic pathways that are interconnected with methionine salvage. The rubrum-type methionine salvage pathway is interconnected with the active methyl cycle in which re-methylation, a key reaction for recycling methionine from homocysteine, is unexpectedly suppressed; instead, homocysteine is catabolized by the transsulfuration pathway. Notably, the non-mevalonate pathway is repressed, whereas the rubrum-type methionine salvage pathway contributes to isoprenoid biosynthesis upon 5'-methylthioadenosine feeding. In this process, glutathione functions as a coenzyme in vivo when 1-methylthio-d-xylulose 5-phosphate (MTXu 5-P) methylsulfurylase catalyzes dethiomethylation of MTXu 5-P. These results clearly show that our analytical approach enables unexpected metabolic pathways to be uncovered.

7.
Nat Chem Biol ; 8(11): 926-32, 2012 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-23042035

RESUMO

Functional assignment of uncharacterized proteins is a challenge in the era of large-scale genome sequencing. Here, we combine in extracto NMR, proteomics and transcriptomics with a newly developed (knock-out) metabolomics platform to determine a potential physiological role for a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Rhodospirillum rubrum. Our studies unraveled an unexpected link in bacterial central carbon metabolism between S-adenosylmethionine-dependent polyamine metabolism and isoprenoid biosynthesis and also provide an alternative approach to assign enzyme function at the organismic level.


Assuntos
Rhodospirillum rubrum/enzimologia , Ribulose-Bifosfato Carboxilase/metabolismo , S-Adenosilmetionina/metabolismo , Terpenos/metabolismo , Desoxiadenosinas/química , Desoxiadenosinas/metabolismo , Espectroscopia de Ressonância Magnética , Estrutura Molecular , Poliaminas/química , Poliaminas/metabolismo , Proteômica , Ribulose-Bifosfato Carboxilase/química , Ribulose-Bifosfato Carboxilase/genética , S-Adenosilmetionina/química , Terpenos/química , Tionucleosídeos/química , Tionucleosídeos/metabolismo , Transcriptoma/genética
8.
Nucleic Acids Res ; 37(8): 2672-87, 2009 May.
Artigo em Inglês | MEDLINE | ID: mdl-19273533

RESUMO

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.


Assuntos
Mapeamento de Interação de Proteínas/métodos , Inteligência Artificial , Árvores de Decisões , Interações Hidrofóbicas e Hidrofílicas , Complexos Multiproteicos/química
9.
Proteins ; 65(3): 593-606, 2006 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-16948160

RESUMO

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of antibody-antigen complexes, the sign is somewhat ambiguous. From the evolutionary perspective, while protease-inhibitors and sig-naling proteins have optimized their interfaces to suit their biological functions, antibody-antigen interactions are the happenstance, implying that antibody-antigen complexes do not show distinctive interaction types. Persistent interaction types such as pi...pi, amide-carbonyl, and hydroxyl-carbonyl interaction, are also investigated. Analyzing the structural orientations of the pi...pi stacking interactions, we find that herringbone shape is a major configuration in transient protein-protein interfaces. This result is different from that of protein core, where parallel-displaced configurations are the major configuration. We also analyze overall trend of amide-carbonyl and hydroxyl-carbonyl interactions. It is noticeable that nearly 82% of the interfaces have at least one hydroxyl-carbonyl interactions.


Assuntos
Complexos Multiproteicos/química , Mapeamento de Interação de Proteínas , Animais , Complexo Antígeno-Anticorpo/química , Sítios de Ligação , Bases de Dados de Proteínas , Humanos , Ligação de Hidrogênio , Modelos Moleculares , Inibidores de Proteases/química , Ligação Proteica , Conformação Proteica
10.
Proc Natl Acad Sci U S A ; 102(39): 13885-90, 2005 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-16172390

RESUMO

Despite their importance for biological activity, slower molecular motions beyond the nanosecond range remain poorly understood. We have assembled an unprecedented set of experimental NMR data, comprising up to 27 residual dipolar couplings per amino acid, to define the nature and amplitude of backbone motion in protein G using the Gaussian axial fluctuation model in three dimensions. Slower motions occur in the loops, and in the beta-sheet, and are absent in other regions of the molecule, including the alpha-helix. In the beta-sheet an alternating pattern of dynamics along the peptide sequence is found to form a long-range network of slow motion in the form of a standing wave extending across the beta-sheet, resulting in maximal conformational sampling at the interaction site. The alternating nodes along the sequence match the alternation of strongly hydrophobic side chains buried in the protein core. Confirmation of the motion is provided through extensive cross-validation and by independent hydrogen-bond scalar coupling analysis that shows this motion to be correlated. These observations strongly suggest that dynamical information can be transmitted across hydrogen bonds and have important implications for understanding collective motions and long-range information transfer in proteins.


Assuntos
Proteínas/química , Aminoácidos/química , Proteínas de Bactérias/química , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Movimento (Física) , Ressonância Magnética Nuclear Biomolecular , Estrutura Secundária de Proteína
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