Structure-Function Analysis of the HrpB2-HrcU Interaction in the Xanthomonas citri Type III Secretion System

Bacterial type III secretion systems deliver protein virulence factors to host cells. Here we characterize the interaction between HrpB2, a small protein secreted by the Xanthomonas citri subsp. citri type III secretion system, and the cytosolic domain of the inner membrane protein HrcU, a paralog of the flagellar protein FlhB. We show that a recombinant fragment corresponding to the C-terminal cytosolic domain of HrcU produced in E. coli suffers cleavage within a conserved Asn264-Pro265-Thr266-His267 (NPTH) sequence. A recombinant HrcU cytosolic domain with N264A, P265A, T266A mutations at the cleavage site (HrcU(AAAH)) was not cleaved and interacted with HrpB2. Furthermore, a polypeptide corresponding to the sequence following the NPTH cleavage site also interacted with HrpB2 indicating that the site for interaction is located after the NPTH site. Non-polar deletion mutants of the hrcU and hrpB2 genes resulted in a total loss of pathogenicity in susceptible citrus plants and disease symptoms could be recovered by expression of HrpB2 and HrcU from extrachromossomal plasmids. Complementation of the Delta hrcU mutant with HrcU(AAAH) produced canker lesions similar to those observed when complemented with wild-type HrcU. HrpB2 secretion however, was significantly reduced in the Delta hrcU mutant complemented with HrcU(AAAH), suggesting that an intact and cleavable NPTH site in HrcU is necessary for total functionally of T3SS in X. citri subsp. citri. Complementation of the Delta hrpB2 X. citri subsp. citri strain with a series of hrpB2 gene mutants revealed that the highly conserved HrpB2 C-terminus is essential for T3SS-dependent development of citrus canker symptoms in planta.

Structure, Dynamics, and RNA Interaction Analysis of the Human SBDS Protein

Shwachman-Bodian-Diamond syndrome is an autosomal recessive genetic syndrome with pleiotropic phenotypes, including pancreatic deficiencies, bone marrow dysfunctions with increased risk of myelodysplasia or leukemia, and skeletal abnormalities. This syndrome has been associated with mutations in the SBDS gene, which encodes a conserved protein showing orthologs in Archaea and eukaryotes. The Shwachman-Bodian-Diamond syndrome pleiotropic phenotypes may be an indication of different cell type requirements for a fully functional SBDS protein. RNA-binding activity has been predicted for archaeal and yeast SBDS orthologs, with the latter also being implicated in ribosome biogenesis. However, full-length SBDS orthologs function in a species-specific manner, indicating that the knowledge obtained from model systems may be of limited use in understanding major unresolved issues regarding SBDS function, namely, the effect of mutations in human SBDS on its biochemical function and the specificity of RNA interaction. We determined the solution structure and backbone dynamics of the human SBDS protein and describe its RNA binding site using NMR spectroscopy. Similarly to the crystal structures of Archaea, the overall structure of human SBDS comprises three well-folded domains. However, significant conformational exchange was observed in NMR dynamics experiments for the flexible linker between the N-terminal domain and the central domain, and these experiments also reflect the relative motions of the domains. RNA titrations monitored by heteronuclear correlation experiments and chemical shift mapping analysis identified a classic RNA binding site at the N-terminal FYSH (fungal, Yhr087wp, Shwachman) domain that concentrates most of the mutations described for the human SBDS. (C) 2010 Elsevier Ltd. All rights reserved.

Intersubband-induced spin-orbit interaction in quantum wells

Recently, we have found an additional spin-orbit (SO) interaction in quantum wells with two subbands [Bernardes , Phys. Rev. Lett. 99, 076603 (2007)]. This new SO term is nonzero even in symmetric geometries, as it arises from the intersubband coupling between confined states of distinct parities, and its strength is comparable to that of the ordinary Rashba. Starting from the 8x8 Kane model, here we present a detailed derivation of this new SO Hamiltonian and the corresponding SO coupling. In addition, within the self-consistent Hartree approximation, we calculate the strength of this new SO coupling for realistic symmetric modulation-doped wells with two subbands. We consider gated structures with either a constant areal electron density or a constant chemical potential. In the parameter range studied, both models give similar results. By considering the effects of an external applied bias, which breaks the structural inversion symmetry of the wells, we also calculate the strength of the resulting induced Rashba couplings within each subband. Interestingly, we find that for double wells the Rashba couplings for the first and second subbands interchange signs abruptly across the zero bias, while the intersubband SO coupling exhibits a resonant behavior near this symmetric configuration. For completeness we also determine the strength of the Dresselhaus couplings and find them essentially constant as function of the applied bias.

Anomalous Rashba spin-orbit interaction in InAs/GaSb quantum wells

We theoretically investigate the Rashba spin-orbit interaction in InAs/GaSb quantum wells (QWs). We find that the Rashba spin-splitting (RSS) sensitively depends on the thickness of the InAs layer. The RSS exhibits nonlinear behavior for narrow InAs/GaSb QWs and the oscillating feature for wide InAs/GaSb QWs. The nonlinear and oscillating behaviors arise from the weakened and enhanced interband coupling. The RSS also show asymmetric features respect to the direction of the external electric field. (C) 2008 American Institute of Physics.

Ultra-high-energy cosmic rays from centaurus A: jet interaction with gaseous shells

Ultra-high-energy cosmic rays (UHECRs), with energies above similar to 6 x 10(19) eV, seem to show a weak correlation with the distribution of matter relatively near to us in the universe. It has earlier been proposed that UHECRs could be accelerated in either the nucleus or the outer lobes of the nearby radio galaxy Cen A. We show that UHECR production at a spatially intermediate location about 15 kpc northeast from the nucleus, where the jet emerging from the nucleus is observed to strike a large star-forming shell of gas, is a plausible alternative. A relativistic jet is capable of accelerating lower energy heavy seed cosmic rays (CRs) to UHECRs on timescales comparable to the time it takes the jet to pierce the large gaseous cloud. In this model, many CRs arising from a starburst, with a composition enhanced in heavy elements near the knee region around PeV, are boosted to ultra-high energies by the relativistic shock of a newly oriented jet. This model matches the overall spectrum shown by the Auger data and also makes a prediction for the chemical composition as a function of particle energy. We thus predict an observable anisotropy in the composition at high energy in the sense that lighter nuclei should preferentially be seen toward the general direction of Cen A. Taking into consideration the magnetic field models for the Galactic disk and a Galactic magnetic wind, this scenario may resolve the discrepancy between HiRes and Auger results concerning the chemical composition of UHECRs.

The role of electron localization in the atomic structure of transition-metal 13-atom clusters: the example of Co(13), Rh(13), and Hf(13)

The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation-LDA) and semilocal (generalized gradient approximation-GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA + U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA + U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.

An oracle approach for interaction neighborhood estimation in random fields

We consider the problem of interaction neighborhood estimation from the partial observation of a finite number of realizations of a random field. We introduce a model selection rule to choose estimators of conditional probabilities among natural candidates. Our main result is an oracle inequality satisfied by the resulting estimator. We use then this selection rule in a two-step procedure to evaluate the interacting neighborhoods. The selection rule selects a small prior set of possible interacting points and a cutting step remove from this prior set the irrelevant points. We also prove that the Ising models satisfy the assumptions of the main theorems, without restrictions on the temperature, on the structure of the interacting graph or on the range of the interactions. It provides therefore a large class of applications for our results. We give a computationally efficient procedure in these models. We finally show the practical efficiency of our approach in a simulation study.

Solution structure of the human signaling protein RACK1

Background: The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results: In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS) experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413) follows a stoichiometry of 1:1. The binding constant (KB) observed for RACK1-Ki-1/57(122-413) interaction was of around (1.5 +/- 0.2) x 10(6) M(-1) and resulted in a dissociation constant (KD) of (0.7 +/- 0.1) x 10(-6) M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion: Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions.

On the wake-induced vibration of tandem circular cylinders: the vortex interaction excitation mechanism

The mechanism of wake-induced vibrations (WIV) of a pair of cylinders in a tandem arrangement is investigated by experiments. A typical WIV response is characterized by a build-up of amplitude persisting to high reduced velocities; this is different from a typical vortex-induced vibration (VIV) response, which occurs in a limited resonance range. We suggest that WIV of the downstream cylinder is excited by the unsteady vortex-structure interactions between the body and the upstream wake. Coherent vortices interfering with the downstream cylinder induce fluctuations in the fluid force that are not synchronized with the motion. A favourable phase lag between the displacement and the fluid force guarantees that a positive energy transfer from the flow to the structure sustains the oscillations. If the unsteady vortices are removed from the wake of the upstream body then WIV will not be excited. An experiment performed in a steady shear flow turned out to be central to the understanding of the origin of the fluid forces acting on the downstream cylinder.

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Use of virtual screening, flexible docking, and molecular interaction fields to design novel HMG-CoA reductase inhibitors for the treatment of hypercholesterolemia

Dietary changes associated with drug therapy can reduce high serum cholesterol levels and dramatically decrease the risk of coronary artery disease, stroke, and overall mortality. Statins are hypolipemic drugs that are effective in the reduction of cholesterol serum levels, attenuating cholesterol synthesis in liver by competitive inhibition regarding the substrate or molecular target HMG-CoA reductase. We have herewith used computer-aided molecular design tools, i.e., flexible docking, virtual screening in large data bases, molecular interaction fields to propose novel potential HMG-CoA reductase inhibitors that are promising for the treatment of hypercholesterolemia.

Molecular dynamics, flexible docking, virtual screening, ADMET predictions, and molecular interaction field studies to design novel potential MAO-B inhibitors

Monoamine oxidase is a flavoenzyme bound to the mitochondrial outer membranes of the cells, which is responsible for the oxidative deamination of neurotransmitter and dietary amines. It has two distinct isozymic forms, designated MAO-A and MAO-B, each displaying different substrate and inhibitor specificities. They are the well-known targets for antidepressant, Parkinson`s disease, and neuroprotective drugs. Elucidation of the x-ray crystallographic structure of MAO-B has opened the way for the molecular modeling studies. In this work we have used molecular modeling, density functional theory with correlation, virtual screening, flexible docking, molecular dynamics, ADMET predictions, and molecular interaction field studies in order to design new molecules with potential higher selectivity and enzymatic inhibitory activity over MAO-B.

Dermaseptin 01 as antimicrobial peptide with rich biotechnological potential: study of peptide interaction with membranes containing Leishmania amazonensis lipid-rich extract and membrane models

This article addresses the interactions of the synthetic antimicrobial peptide dermaseptin 01 (GLWSTIKQKGKEAAIAAA-KAAGQAALGAL-NH(2), DS 01) with phospholipid (PL) monolayers comprising (i) a lipid-rich extract of Leishmania amazonensis (LRE-La), (ii) zwitterionic PL (dipalmitoylphosphatidylcholine, DPPC), and (iii) negatively charged PL (dipalmitoylphosphatidylglycerol, DPPG). The degree of interaction of DS 01 with the different biomembrane models was quantified from equilibrium and dynamic liquid-air interface parameters. At low peptide concentrations, interactions between DS 01 and zwitterionic PL, as well as with the LRE-La monolayers were very weak, whereas with negatively charged PLs the interactions were stronger. For peptide concentrations above 1 mu g/ml, a considerable expansion of negatively charged monolayers occurred. In the case of DPPC, it was possible to return to the original lipid area in the condensed phase, suggesting that the peptide was expelled from the monolayer. However, in the case of DPPG, the average area per lipid molecule in the presence of DS 01 was higher than pure PLs even at high surface pressures, suggesting that at least part of DS 01 remained incorporated in the monolayer. For the LRE-La monolayers, DS 01 also remained in the monolayer. This is the first report on the antiparasitic activity of AMPs using Langmuir monolayers of a natural lipid extract from L. amazonensis. Copyright (C) 2011 European Peptide Society and John Wiley & Sons, Ltd.

Interaction of equatorial waves through resonance with the diurnal cycle of tropical heating

In this work, a new theoretical mechanism is presented in which equatorial Rossby and inertio-gravity wave modes may interact with each other through resonance with the diurnal cycle of tropical deep convection. We have adopted the two-layer incompressible equatorial primitive equations forced by a parametric heating that roughly represents deep convection activity in the tropical atmosphere. The heat source was parametrized in the simplest way according to the hypothesis that it is proportional to the lower-troposphere moisture convergence, with the background moisture state function mimicking the structure of the ITCZ. In this context, we have investigated the possibility of resonant interaction between equatorially trapped Rossby and inertio-gravity modes through the diurnal cycle of the background moisture state function. The reduced dynamics of a single resonant duo shows that when this diurnal variation is considered, a Rossby wave mode can undergo significant amplitude modulations when interacting with an inertio-gravity wave mode, which is not possible in the context of the resonant triad non-linear interaction. Therefore, the results suggest that the diurnal variation of the ITCZ can be a possible dynamical mechanism that leads the Rossby waves to be significantly affected by high frequency modes.

Deep crustal structure of the Parana Basin from receiver functions and Rayleigh-wave dispersion: Evidence for a fragmented cratonic root

The deep crustal structure of the Parana Basin of southern Brazil is investigated by analyzing P- and PP-wave receiver functions at 17 Brazilian Lithosphere Seismic Project stations within the basin. The study area can be described as a typical Paleozoic intracratonic basin that hosts one of the largest Large Igneous Province of the world and makes a unique setting for investigating models of basin subsidence and their interaction with mantle plumes. Our study consists of (1) an analysis of the Moho interaction phases in the receiver functions to obtain the thickness and bulk Vp/Vs ratio of the basin`s underlying crust and (2) a joint inversion with Rayleigh-wave dispersion velocities from an independent tomographic study to delineate the detailed S-wave velocity variation with depth. The results of our analysis reveal that Moho depths and bulk Vp/Vs ratios (including sediments) vary between 41 and 48 km and between 1.70 and 1.76, respectively, with the largest values roughly coinciding with the basin`s axis, and that S-wave velocities in the lower crust are generally below 3.8 km/s. Select sites within the basin, however, show lower crustal S-wave velocities slightly above 3.9 km/s suggestive of underplated mafic material. We show that these observations are consistent with a fragmented cratonic root under the Parana basin that defined a zone of weakness for the initial Paleozoic subsidence of the basin and which allowed localized mafic underplating of the crust along the suture zones by Cenozoic magmatism.