A three-component protocol for the enantiodifferentiation of amines using triphenyl borate and BINOL: is it an ion pair or an amine-coordinated complex?

The structure of the borate complex responsible for the enantiodifferentiation of amines using a previously reported three-component protocol has been established. The choice between an ion pair and an amine-coordinated complex with the N atom of the amine coordinated to the B atom is favored for the former structure based on the DFT-calculated B-11 NMR chemical shifts. In contrast to expectations, the anisotropies of the quadrupolar B-11 nucleus for the two structures were calculated to be indistinguishable with regard to their effect on the linewidth of the NMR signal. (C) 2014 Elsevier Ltd. All rights reserved.

Immunogen design for HIV-1 and influenza

Vaccines provide the most cost effective defense against pathogens. Although vaccines have been designed for a number of viral diseases, a vaccine against HIV-1 still remains elusive. In contrast while there are excellent influenza vaccines, these need to be changed every few years because of antigenic drift and shift The recent discovery of a large number of broadly neutralizing antibodies (bNAbs) and structural characterization of the conserved epitopes targeted by them presents an opportunity for structure based HIV-1 and influenza A vaccine design. We discuss strategies to design immunogens either targeting a particular antigenic region or focusing on native structure stabilization. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. (C) 2014 Elsevier B.V. All rights reserved.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

An overview of recent advances in structural bioinformatics of protein-protein interactions and a guide to their principles

Rich data bearing on the structural and evolutionary principles of protein protein interactions are paving the way to a better understanding of the regulation of function in the cell. This is particularly the case when these interactions are considered in the framework of key pathways. Knowledge of the interactions may provide insights into the mechanisms of crucial `driver' mutations in oncogenesis. They also provide the foundation toward the design of protein protein interfaces and inhibitors that can abrogate their formation or enhance them. The main features to learn from known 3-D structures of protein protein complexes and the extensive literature which analyzes them computationally and experimentally include the interaction details which permit undertaking structure-based drug discovery, the evolution of complexes and their interactions, the consequences of alterations such as post-translational modifications, ligand binding, disease causing mutations, host pathogen interactions, oligomerization, aggregation and the roles of disorder, dynamics, allostery and more to the protein and the cell. This review highlights some of the recent advances in these areas, including design, inhibition and prediction of protein protein complexes. The field is broad, and much work has been carried out in these areas, making it challenging to cover it in its entirety. Much of this is due to the fast increase in the number of molecules whose structures have been determined experimentally and the vast increase in computational power. Here we provide a concise overview. (C) 2014 Elsevier Ltd. All rights reserved.

Spontaneous Lorentz violation: the case of infrared QED

It is by now clear that the infrared sector of quantum electrodynamics (QED) has an intriguingly complex structure. Based on earlier pioneering work on this subject, two of us recently proposed a simple modification of QED by constructing a generalization of the U(1) charge group of QED to the ``Sky'' group incorporating the well-known spontaneous Lorentz violation due to infrared photons, but still compatible in particular with locality (Balachandran and Vaidya, Eur Phys J Plus 128:118, 2013). It was shown that the ``Sky'' group is generated by the algebra of angle-dependent charges and a study of its superselection sectors has revealed a manifest description of spontaneous breaking of the Lorentz symmetry. We further elaborate this approach here and investigate in some detail the properties of charged particles dressed by the infrared photons. We find that Lorentz violation due to soft photons may be manifestly codified in an angle-dependent fermion mass, modifying therefore the fermion dispersion relations. The fact that the masses of the charged particles are not Lorentz invariant affects their spin content, and time dilation formulas for decays should also get corrections.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

SInCRe-structural interactome computational resource for Mycobacterium tuberculosis

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein-protein and protein-small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein-protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host-pathogen protein-protein interactions. Together they provide prerequisites for identification of off-target binding.

An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Estrutura das assembleias de peixes de igarapés de terra firme da bacia do rio Machado/RO

No presente estudo foi avaliada (i) a estrutura das assembleias de peixes de igarapés de terra-firme ao longo do contínuo fluvial do rio Machado, na bacia do rio Amazonas, (ii) os efeitos de alterações ambientais sobre as assembleias de peixes de igarapés através de comparações entre áreas íntegras (em uma Unidade de conservação) e alteradas por ação antrópica na bacia hidrográfica do rio Machado, e (iii) a organização espacial das assembleias de peixes de tributários de baixa ordem na bacia do rio Machado através da avaliação dos padrões de co-ocorrência das espécies, identificando os possíveis fatores estruturadores dessas assembleias e através de uma Análise de Parcimônia de Endemismo (PAE). As amostragens foram realizadas entre os meses de agosto e setembro de 2011, junho e agosto de 2012 e julho de 2013, totalizando 81 igarapés. Os peixes foram coletados durante uma hora em um trecho de 80 metros, com o auxilio de uma rede de mão (picaré) e um puçá. Para o capítulo 1, um maior número de indivíduos e espécies foram encontradas no trecho baixo quando comparado o trecho alto da bacia. Todavia, somente foram encontradas diferenças significativas entre o trecho alto e os trechos médio e baixo. Assim, rejeitamos nossa hipótese de diferenças entre os trechos analisados, onde esperávamos que a riqueza e abundância de espécies de igarapés aumentaria no gradiente longitudinal cabeceira-foz do rio Machado. Contudo, apesar da não confirmação da hipótese, um padrão de adição e substituição de espécies foi observado do trecho alto para o médio, e um padrão de substituição de espécies foi observado do trecho médio para o baixo. Referente ao capítulo 2, apontamos que apesar da área desflorestada não apresentar diferenças marcantes na riqueza de espécies e abundância, quando comparada com a área com igarapés conservados, esta (área desflorestada) apresentou elevada similaridade a nível composicional entre os igarapés amostrados (menor diversidade beta), diferentemente dos igarapés localizados na Rebio, que apresentaram maior número de espécies com hábitos mais especializados. Igarapés desflorestados apresentaram homogeneização da sua ictiofauna em comparação com igarapés providos de mata ripária, refletindo a maior homogeneização estrutural encontrada em igarapés com baixo percentual de cobertura vegetal. Dessa forma, a retirada da cobertura vegetal em igarapés com comunidades mais diversificads e especializadas, como os da Rebio Jaru, promoveria a homogeneização das espécies acarretando a perda destas, assim como a substituição destas por espécies tolerantes a condições ambientais comuns a ambientes alterados. Para o capítulo 3, embora não tenhamos encontrado áreas de endemismo na bacia analisada, apontamos que a influência da estrutura física dos igarapés sobre a composição de espécies é o principal fator modulador da estruturação da assembleia de peixes. Todavia, tal fator não se aplica a estruturação da assembleia baseada na coocorrência de espécies, haja vista que, a análise de toda a bacia com diferentes níveis de uso de solo, apresentou um padrão organizacional não aleatório

Para que serve uma enfermaria de clínica médica?: reflexões a partir de um hospital universitário.

Esse trabalho propõe uma reflexão sobre a relação entre a organização da estrutura hospitalar baseada em sua divisão por enfermarias de especialidades e a perpetuação da lógica fragmentadora própria da Biomedicina, racionalidade médica hegemônica ocidental. O campo estudado foi o Hospital Universitário Pedro Ernesto. Através de entrevistas semiestruturadas com médicos clínicos, especialistas e profissionais responsáveis pela regulação de vagas desse hospital é discutida a existência de dois discursos diferentes: o discurso clínico e o discurso especialista. A partir da análise dessas entrevistas, foi apontada e debatida a profunda relação entre esses discursos, a estrutura hospitalar e a assistência médica oferecida aos pacientes. A análise realizada evidencia que embora os dois discursos estejam absolutamente inseridos no paradigma biomédico, a clínica médica se identifica e é identificada como responsável pelo paciente como um todo, enquanto as especialidades são reconhecidas como responsáveis apenas por uma determinada parte. Essa diferença apresentou influência tanto na forma de cuidar do paciente, como na função de cada serviço dentro do hospital. As enfermarias de clínica se caracterizaram por serem setores consensualmente capazes de conduzir satisfatoriamente a maioria dos pacientes.Se por um lado a abrangência da clínica é motivo de orgulho para os clínicos, por outro, a falta de autonomia decorrente dessa característica determina um sentimento de depreciação por parte desses profissionais. Esse trabalho foi realizado sob perspectiva hermenêutica filosófica proposta por Hans-Georg Gadamer e com o auxílio dos conceitos de paradigma proposto por Thomas Kuhn e estilo de pensamento elaborado por Ludwik Fleck.

The unsteady development of a turbulent wake through a downstream low-pressure turbine blade passage

This paper presents two-dimensional LDA measurements of the convection of a wake through a low-pressure (LP) turbine cascade. Previous studies have shown the wake convection to be kinematic but have not provided details of the turbulent field. The spatial resolution of these measurements has facilitated the calculation of the production of turbulent kinetic energy and this has revealed a mechanism for turbulence production as the wake converts through the bladerow. The measured ensemble-averaged velocity field confirmed the previously reported kinematics of wake convection while the measurements of the turbulence quantities showed the wake fluid to be characterised by elevated levels of turbulent kinetic energy (TKE) and to have an anisotropic structure. Based on the measured mean and turbulence quantities, the production of turbulent kinetic energy was calculated. This highlighted a TKE production mechanism that resulted in increased levels of turbulence over the rear suction surface where boundary layer transition occurs. The turbulence production mechanism within the bladerow was also observed to produce more nearly isotropic turbulence. Production occurs when the principal stresses within the wake are aligned with the mean strains. This coincides with the maximum distortion of the wake within the blade passage and provides a mechanism for the production of turbulence outside of the boundary layer.

RDM lifetime measurements in 107Cd

Lifetimes for decays linking near-yrast states in 107Cd have been measured using the recoil distance method (RDM). The nucleus of interest was populated via the 98Mo(12C,3n)107Cd fusion-evaporation reaction at an incident beam energy of 60 MeV. From the measured lifetimes, transition probabilities have been deduced and compared with the theoretical B(E2) values for limiting cases of harmonic vibrational and axially deformed rotational systems. Our initial results suggest a rotor-like behaviour for the structure based on the unnatural-parity, h11/2 orbital in 107Cd, providing further evidence for the role of this 'shape-polarizing' orbital in stabilizing the nuclear deformation in the A ∼ 100 transitional region. © 2005 IOP Publishing Ltd.

Design of surface emitting distributed feedback quantum cascade laser with single-lobe far-field pattern and high outcoupling efficiency

A 7.8-mu m surface emitting second-order distributed feedback quantum cascade laser (DFB QCL) structure with metallized surface grating is studied. The modal property of this structure is described by utilizing coupled-mode theory where the coupling coefficients are derived from exact Floquet-Bloch solutions of infinite periodic structure. Based on this theory, the influence of waveguide structure and grating topography as well as device length on the laser performance is numerically investigated. The optimized surface emitting second-order DFB QCL structure design exhibits a high surface outcoupling efficiency of 22% and a low threshold gain of 10 cm(-1). Using a pi phase-shift in the centre of the grating, a high-quality single-lobe far-field radiation pattern is obtained.