Phase transition from a d(x(2)-y(2)) to d(x(2)-y(2))+id(xy) superconductor

The temperature dependencies of specific heat and spin susceptibility of a coupled dx2-y2 + idxy superconductor in the presence of a weak dxy component are investigated in the tight-binding model (1) on square lattice and (2) on a lattice with orthorhombic distortion. As the temperature is lowered past the critical temperature Tc, first a less ordered dx2-y2 superconductor is created, which changes to a more ordered dx2-y2 + idxy superconductor at Tcl(< Tc). This manifests in two second order phase transitions identified by two jumps in specific heat at Tc and Tc1. The temperature dependencies of the superconducting observables exhibit a change from power-law to exponential behavior as temperature is lowered below Tc1 and confirm the new phase transition. © 1998 Published by Elsevier Science B.V. All rights reserved.

Simulação atomística de sistema em nanoescala

Pós-graduação em Física - IGCE

QUANTUM FIELD THEORY IN GRAPHENE

This is a short nontechnical introduction to applications of the Quantum Field Theory methods to graphene. We derive the Dirac model from the tight binding model and describe calculations of the polarization operator (conductivity). Later on, we use this quantity to describe the Quantum Hall Effect, light absorption by graphene, the Faraday effect, and the Casimir interaction.

Progress in the mathematical theory of quantum disordered systems

We review recent progress in the mathematical theory of quantum disordered systems: the Anderson transition, including some joint work with Marchetti, the (quantum and classical) Edwards-Anderson (EA) spin-glass model and return to equilibrium for a class of spin-glass models, which includes the EA model initially in a very large transverse magnetic field. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4770066]

Structure of the haptoglobin-haemoglobin complex

Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies(1), haemoglobin is released into the plasma, where it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin-haemoglobin complex, which represents a virtually irreversible non-covalent protein-protein interaction(2). Here we present the crystal structure of the dimeric porcine haptoglobin-haemoglobin complex determined at 2.9 angstrom resolution. This structure reveals that haptoglobin molecules dimerize through an unexpected beta-strand swap between two complement control protein (CCP) domains, defining a new fusion CCP domain structure. The haptoglobin serine protease domain forms extensive interactions with both the alpha- and beta-subunits of haemoglobin, explaining the tight binding between haptoglobin and haemoglobin. The haemoglobin-interacting region in the alpha beta dimer is highly overlapping with the interface between the two alpha beta dimers that constitute the native haemoglobin tetramer. Several haemoglobin residues prone to oxidative modification after exposure to haem-induced reactive oxygen species are buried in the haptoglobin-haemoglobin interface, thus showing a direct protective role of haptoglobin. The haptoglobin loop previously shown to be essential for binding of haptoglobin-haemoglobin to the macrophage scavenger receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin alpha-subunit. Small-angle X-ray scattering measurements of human haptoglobin-haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show that the rigid dimeric complex can bind two receptors. Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of multimeric haptoglobin-haemoglobin for CD163 (ref. 4).

Numerical study of graphene as a channel material for field-effect transistors

Graphene excellent properties make it a promising candidate for building future nanoelectronic devices. Nevertheless, the absence of an energy gap is an open problem for the transistor application. In this thesis, graphene nanoribbons and pattern-hydrogenated graphene, two alternatives for inducing an energy gap in graphene, are investigated by means of numerical simulations. A tight-binding NEGF code is developed for the simulation of GNR-FETs. To speed up the simulations, the non-parabolic effective mass model and the mode-space tight-binding method are developed. The code is used for simulation studies of both conventional and tunneling FETs. The simulations show the great potential of conventional narrow GNR-FETs, but highlight at the same time the leakage problems in the off-state due to various tunneling mechanisms. The leakage problems become more severe as the width of the devices is made larger, and thus the band gap smaller, resulting in a poor on/off current ratio. The tunneling FET architecture can partially solve these problems thanks to the improved subthreshold slope; however, it is also shown that edge roughness, unless well controlled, can have a detrimental effect in the off-state performance. In the second part of this thesis, pattern-hydrogenated graphene is simulated by means of a tight-binding model. A realistic model for patterned hydrogenation, including disorder, is developed. The model is validated by direct comparison of the momentum-energy resolved density of states with the experimental angle-resolved photoemission spectroscopy. The scaling of the energy gap and the localization length on the parameters defining the pattern geometry is also presented. The results suggest that a substantial transport gap can be attainable with experimentally achievable hydrogen concentration.

Untersuchungen zur Regulation der Trehalaseaktivität bei der Wanderheuschrecke Locusta migratoria

Flugfähige Insekten sind äußerst leistungsfähige Tiere. Ihre Flugmuskulatur ist das Gewebe mit der höchsten ATP-Umsatzrate im Tierreich. Der hohe Energieumsatz ist möglich durch einen vollständig aeroben Stoffwechsel der Flugmuskulatur, der durch die effiziente Sauerstoffversorgung über das Tracheensystem gewährleistet wird. Andererseits haben Insekten einen offenen Blutkreislauf, d.h. ihre Gewebe werden nicht über Kapillaren mit Substraten versorgt, sondern von der Hämolymphe umspült, die daher eine hohe Konzentration an energieliefernden Substraten haben muss. Als schnell verfügbares Substrat nutzen Wanderheuschrecken bei Beginn eines Fluges als Hauptsubstrat Trehalose, die in hoher Konzentration als Hämolymphzucker vorliegt (20 bis 40mal höhere Konzentration als Glucose). Trehalose ist, anders als Glucose, ein nicht-reduzierender Zucker und daher nicht toxisch. Allerdings muss das Disaccharid Trehalose zu Glucose hydrolysiert werden, bevor sie im Zellstoffwechsel verwertet werden kann. Diese Funktion erfüllt die Trehalase (EC 3.2.1.28), ein Enzym, das membrangebunden ist und nach Zellfraktionierung in der Mikrosomenfraktion erscheint. Es ist schon lange offensichtlich, dass die Aktivität der Trehalase regulierbar sein muss und zwar reversibel (eine Eigenschaft, die für Hydrolasen ungewöhnlich ist), der Mechanismus ist allerdings bislang nicht klar, da alle üblichen Typen von Aktivitätsregulation nicht verwirklicht zu sein scheinen. Die meisten Autoren vermuten, dass die Regulation über den Transport des Substrats erfolgt. Ein Trehalosetransporter konnte allerdings bisher in der Flugmuskulatur von Locusta nicht nachgewiesen werden. In dieser Arbeit stelle ich Experimente vor, die dafür sprechen, dass Trehalase als Ektoenzym aktiv ist (overte Form), während eine inaktive Form (latente Form) in Vesikeln im Cytoplasma vorliegt und per Exocytose reversibel in die Plasmamembran transloziert werden kann. Für die Testung dieser Arbeitshypothese nutzte ich Trehazolin, einen sehr spezifischen Inhibitor der Trehalase, der äußerst fest und dauerhaft im aktiven Zentrum des Enzyms bindet. Dazu war es nötig, die Flugmuskulatur zu fraktionieren, um die Effekte von Trehazolin auf die verschiedenen Formen der Trehalase (gebunden, löslich, overt, latent) zu analysieren. Mit der Arbeitshypothese vereinbar sind die folgenden Befunde: (1) In die Hämolymphe injiziertes Trehazolin hemmt bevorzugt die overte Trehalase und erst bei höheren Dosen und nach längerer Zeit die latente Form. (2) Trehazolin wirkt in hoher Dosis (50µg pro Tier) auch nach Verfütterung, allerdings stark abgeschwächt, da nach 24 Stunden ein signifikanter Effekt nur auf die overte, aber nicht auf die latente Form sichtbar war. (3) In einem Langzeitversuch über 30 Tage führte die einmalige Injektion von 20µg Trehazolin zu einer schnellen Hemmung der overten Trehalase, der eine verzögerte Hemmung der latenten Aktivität folgte. Der Zeitverlauf von Hemmung und Erholung spricht für eine Vorläufer-Produkt-Beziehung zwischen latenter und overter Form. (4) Flugaktivität der Tiere führt zu einer starken Verminderung der latenten Aktivität, falls Trehazolin in der Hämolymphe der Tiere vorhanden war. (5) Neuropeptide könnten die Translokation fördern. Insulin hat einen entsprechenden Effekt, der aber unabhängig ist von der Flugaktivität. (6) Der PI3-Kinasehemmstoff Wortmannin stabilisiert die latente Form der Trehalase. Auch andere Organe als die Flugmuskulatur besitzen Trehalase, aber mit deutlich geringerer Aktivität. In der Sprungmuskulatur könnte auch eine latente Form vorhanden sein, für Darm und Gehirn ist das nicht wahrscheinlich.

Resolving Atomic Connectivity in Graphene Nanostructure Junctions

We report on the structural characterization of junctions between atomically well-defined graphene nanoribbons (GNRs) by means of low-temperature, noncontact scanning probe microscopy. We show that the combination of simultaneously acquired frequency shift and tunneling current maps with tight binding (TB) simulations allows a comprehensive characterization of the atomic connectivity in the GNR junctions. The proposed approach can be generally applied to the investigation of graphene nanomaterials and their interconnections and is thus expected to become an important tool in the development of graphene-based circuitry.

α1-Antitrypsin Portland, a bioengineered serpin highly selective for furin: Application as an antipathogenic agent

The important role of furin in the proteolytic activation of many pathogenic molecules has made this endoprotease a target for the development of potent and selective antiproteolytic agents. Here, we demonstrate the utility of the protein-based inhibitor α1-antitrypsin Portland (α1-PDX) as an antipathogenic agent that can be used prophylactically to block furin-dependent cell killing by Pseudomonas exotoxin A. Biochemical analysis of the specificity of a bacterially expressed His- and FLAG-tagged α1-PDX (α1-PDX/hf) revealed the selectivity of the α1-PDX/hf reactive site loop for furin (Ki, 600 pM) but not for other proprotein convertase family members or other unrelated endoproteases. Kinetic studies show that α1-PDX/hf inhibits furin by a slow tight-binding mechanism characteristic of serpin molecules and functions as a suicide substrate inhibitor. Once bound to furin’s active site, α1-PDX/hf partitions with equal probability to undergo proteolysis by furin at the C-terminal side of the reactive center -Arg355-Ile-Pro-Arg358-↓ or to form a kinetically trapped SDS-stable complex with the enzyme. This partitioning between the complex-forming and proteolytic pathways contributes to the ability of α1-PDX/hf to differentially inhibit members of the proprotein convertase family. Finally, we propose a structural model of the α1-PDX-reactive site loop that explains the high degree of enzyme selectivity of this serpin and which can be used to generate small molecule furin inhibitors.

Mechanism-based inhibition of the melatonin rhythm enzyme: Pharmacologic exploitation of active site functional plasticity

Serotonin N-acetyltransferase is the enzyme responsible for the diurnal rhythm of melatonin production in the pineal gland of animals and humans. Inhibitors of this enzyme active in cell culture have not been reported previously. The compound N-bromoacetyltryptamine was shown to be a potent inhibitor of this enzyme in vitro and in a pineal cell culture assay (IC50 ≈ 500 nM). The mechanism of inhibition is suggested to involve a serotonin N-acetyltransferase-catalyzed alkylation reaction between N-bromoacetyltryptamine and reduced CoA, resulting in the production of a tight-binding bisubstrate analog inhibitor. This alkyltransferase activity is apparently catalyzed at a functionally distinct site compared with the acetyltransferase activity active site on serotonin N-acetyltransferase. Such active site plasticity is suggested to result from a subtle conformational alteration in the protein. This plasticity allows for an unusual form of mechanism-based inhibition with multiple turnovers, resulting in “molecular fratricide.” N-bromoacetyltryptamine should serve as a useful tool for dissecting the role of melatonin in circadian rhythm as well as a potential lead compound for therapeutic use in mood and sleep disorders.

Design of potent and selective human cathepsin K inhibitors that span the active site

Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallographic, MS, NMR spectroscopic, and kinetic studies of the mechanisms of inhibition indicate that different intermediates or transition states are being represented that are dependent on the conditions of measurement and the specific groups flanking the carbonyl in the inhibitor. The species observed crystallographically are most consistent with tetrahedral intermediates that may be close approximations of those that occur during substrate hydrolysis. Initial kinetic studies suggest the possibility of irreversible and reversible active-site modification. Representative inhibitors have demonstrated antiresorptive activity both in vitro and in vivo and therefore are promising leads for therapeutic agents for the treatment of osteoporosis. Expansion of these inhibitor concepts can be envisioned for the many other cysteine proteases implicated for therapeutic intervention.

The anticoagulant activation of antithrombin by heparin

Antithrombin, a plasma serpin, is relatively inactive as an inhibitor of the coagulation proteases until it binds to the heparan side chains that line the microvasculature. The binding specifically occurs to a core pentasaccharide present both in the heparans and in their therapeutic derivative heparin. The accompanying conformational change of antithrombin is revealed in a 2.9-Å structure of a dimer of latent and active antithrombins, each in complex with the high-affinity pentasaccharide. Inhibitory activation results from a shift in the main sheet of the molecule from a partially six-stranded to a five-stranded form, with extrusion of the reactive center loop to give a more exposed orientation. There is a tilting and elongation of helix D with the formation of a 2-turn helix P between the C and D helices. Concomitant conformational changes at the heparin binding site explain both the initial tight binding of antithrombin to the heparans and the subsequent release of the antithrombin–protease complex into the circulation. The pentasaccharide binds by hydrogen bonding of its sulfates and carboxylates to Arg-129 and Lys-125 in the D-helix, to Arg-46 and Arg-47 in the A-helix, to Lys-114 and Glu-113 in the P-helix, and to Lys-11 and Arg-13 in a cleft formed by the amino terminus. This clear definition of the binding site will provide a structural basis for developing heparin analogues that are more specific toward their intended target antithrombin and therefore less likely to exhibit side effects.

Dissociation of the Tubulin-sequestering and Microtubule Catastrophe-promoting Activities of Oncoprotein 18/Stathmin

Oncoprotein 18/stathmin (Op18) has been identified recently as a protein that destabilizes microtubules, but the mechanism of destabilization is currently controversial. Based on in vitro microtubule assembly assays, evidence has been presented supporting conflicting destabilization models of either tubulin sequestration or promotion of microtubule catastrophes. We found that Op18 can destabilize microtubules by both of these mechanisms and that these activities can be dissociated by changing pH. At pH 6.8, Op18 slowed microtubule elongation and increased catastrophes at both plus and minus ends, consistent with a tubulin-sequestering activity. In contrast, at pH 7.5, Op18 promoted microtubule catastrophes, particularly at plus ends, with little effect on elongation rates at either microtubule end. Dissociation of tubulin-sequestering and catastrophe-promoting activities of Op18 was further demonstrated by analysis of truncated Op18 derivatives. Lack of a C-terminal region of Op18 (aa 100–147) resulted in a truncated protein that lost sequestering activity at pH 6.8 but retained catastrophe-promoting activity. In contrast, lack of an N-terminal region of Op18 (aa 5–25) resulted in a truncated protein that still sequestered tubulin at pH 6.8 but was unable to promote catastrophes at pH 7.5. At pH 6.8, both the full length and the N-terminal–truncated Op18 bound tubulin, whereas truncation at the C-terminus resulted in a pronounced decrease in tubulin binding. Based on these results, and a previous study documenting a pH-dependent change in binding affinity between Op18 and tubulin, it is likely that tubulin sequestering observed at lower pH resulted from the relatively tight interaction between Op18 and tubulin and that this tight binding requires the C-terminus of Op18; however, under conditions in which Op18 binds weakly to tubulin (pH 7.5), Op18 stimulated catastrophes without altering tubulin subunit association or dissociation rates, and Op18 did not depolymerize microtubules capped with guanylyl (α, β)-methylene diphosphonate–tubulin subunits. We hypothesize that weak binding between Op18 and tubulin results in free Op18, which is available to interact with microtubule ends and thereby promote catastrophes by a mechanism that likely involves GTP hydrolysis.

The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae

The modified nucleoside 1-methyladenosine (m1A) is found at position 58 in the TΨC loop of many eukaryotic tRNAs. The absence of m1A from all tRNAs in Saccharomyces cerevisiae mutants lacking Gcd10p elicits severe defects in processing and stability of initiator methionine tRNA (tRNAiMet). Gcd10p is found in a complex with Gcd14p, which contains conserved motifs for binding S-adenosylmethionine (AdoMet). These facts, plus our demonstration that gcd14Δ cells lacked m1A, strongly suggested that Gcd10p/Gcd14p complex is the yeast tRNA(m1A)methyltransferase [(m1A)MTase]. Supporting this prediction, affinity-purified Gcd10p/Gcd14p complexes used AdoMet as a methyl donor to synthesize m1A in either total tRNA or purified tRNAiMet lacking only this modification. Kinetic analysis of the purified complex revealed KM values for AdoMet or tRNAiMet of 5.0 μM and 2.5 nM, respectively. Mutations in the predicted AdoMet-binding domain destroyed GCD14 function in vivo and (m1A)MTase activity in vitro. Purified Flag-tagged Gcd14p alone had no enzymatic activity and was severely impaired for tRNA-binding compared with the wild-type complex, suggesting that Gcd10p is required for tight binding of the tRNA substrate. Our results provide a demonstration of a two-component tRNA MTase and suggest that binding of AdoMet and tRNA substrates depends on different subunits of the complex.

Stimulation of bacteriophage T4 middle transcription by the T4 proteins MotA and AsiA occurs at two distinct steps in the transcription cycle

The bacteriophage T4 encodes proteins that are responsible for tightly regulating mRNA synthesis throughout phage development in Escherichia coli. The three classes of T4 promoters (early, middle, and late) are utilized sequentially by the host RNA polymerase as a result of phage-induced modifications. One such modification is the tight binding of the T4 AsiA protein to the σ70 subunit of the RNA polymerase. This interaction is pivotal for the transition between T4 early and middle transcription, since it both inhibits recognition of host and T4 early promoters and stimulates T4 middle mode synthesis. The activation of T4 middle transcription also requires the T4 MotA protein, bound specifically to its recognition sequence, the “Mot box,” which is centered at position −30 of these promoters. Accordingly, the two T4 proteins working in concert are sufficient to effectively switch the transcription specificity of the RNA polymerase holoenzyme. Herein, we investigate the mechanism of transcription activation and report that, while the presence of MotA and AsiA increases the initial recruitment of RNA polymerase to a T4 middle promoter, it does not alter the intrinsic stability of the discrete complexes formed. In addition, we have characterized the RNA polymerase-promoter species by UV laser footprinting and followed their evolution from open into initiating complexes. These data, combined with in vitro transcription assays, indicate that AsiA and MotA facilitate promoter escape, thereby stimulating the production of full-length transcripts.