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1.
Int J Infect Dis ; 99: 441-448, 2020 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-32800860

RESUMO

INTRODUCTION: The World Health Organization has identified the need for a non-sputum-based test capable of detecting active tuberculosis (TB) as a priority. The plasma kynurenine-to-tryptophan (K/T) ratio, largely mediated by activity of the enzyme indoleamine 2,3-dioxygenase, may have potential as a suitable biomarker for active TB. METHOD: We evaluated a commercial enzyme-linked immunosorbent assay (ELISA) in comparison to mass spectrometry for measuring the K/T ratio. We also used ELISA to determine the K/T ratio in plasma from patients with active TB compared to latently infected controls, with and without HIV. RESULTS: The two methods showed good agreement, with a mean bias of 0.01 (limit of agreement from -0.06 to 0.10). Using ELISA, it was found that HIV-infected patients with active TB disease had higher K/T ratios than those without TB (median, 0.101 [interquartile range (IQR), 0.091-0.140] versus 0.061 [IQR, 0.034-0.077], P<0.0001). At a cutoff of 0.080, the K/T ratio produced a sensitivity of 90%, a specificity of 80%, a positive predictive value (PPV) of 82%, and a negative predictive value (NPV) of 90%. In a receiver operating characteristics analysis, the K/T ratio had an area under the curve of 0.93. HIV-uninfected patients with active TB also had higher K/T ratios than those with latent TB infections (median, 0.064 [IQR, 0.040-0.088] versus 0.022 [IQR, 0.016-0.027], P<0.0001). A cutoff of 0.040 gave a sensitivity of 85%, a specificity of 92%, a PPV of 91%, and an NPV of 84%. CONCLUSION: The plasma K/T ratio is a sensitive biomarker for active TB. The K/T ratio can be measured from blood using ELISA. The K/T ratio should be evaluated as an initial test for TB.

2.
Acta Crystallogr D Struct Biol ; 76(Pt 3): 272-284, 2020 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-32133991

RESUMO

The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode.

3.
Acta Crystallogr D Struct Biol ; 76(Pt 1): 1-8, 2020 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-31909738

RESUMO

The conventional approach to search-model identification in molecular replacement (MR) is to screen a database of known structures using the target sequence. However, this strategy is not always effective, for example when the relationship between sequence and structural similarity fails or when the crystal contents are not those expected. An alternative approach is to identify suitable search models directly from the experimental data. SIMBAD is a sequence-independent MR pipeline that uses either a crystal lattice search or MR functions to directly locate suitable search models from databases. The previous version of SIMBAD used the fast AMoRe rotation-function search. Here, a new version of SIMBAD which makes use of Phaser and its likelihood scoring to improve the sensitivity of the pipeline is presented. It is shown that the additional compute time potentially required by the more sophisticated scoring is counterbalanced by the greater sensitivity, allowing more cases to trigger early-termination criteria, rather than running to completion. Using Phaser solved 17 out of 25 test cases in comparison to the ten solved with AMoRe, and it is shown that use of ensemble search models produces additional performance benefits.


Assuntos
Modelos Moleculares , Proteínas/química , Software , Cristalografia/métodos , Bases de Dados de Proteínas , Conformação Proteica
4.
Acta Crystallogr D Struct Biol ; 75(Pt 12): 1051-1062, 2019 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31793899

RESUMO

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Where the lack of a suitable homologue precludes conventional MR, one option is to predict the target structure using bioinformatics. Such modelling, in the absence of homologous templates, is called ab initio or de novo modelling. Recently, the accuracy of such models has improved significantly as a result of the availability, in many cases, of residue-contact predictions derived from evolutionary covariance analysis. Covariance-assisted ab initio models representing structurally uncharacterized Pfam families are now available on a large scale in databases, potentially representing a valuable and easily accessible supplement to the PDB as a source of search models. Here, the unconventional MR pipeline AMPLE is employed to explore the value of structure predictions in the GREMLIN and PconsFam databases. It was tested whether these deposited predictions, processed in various ways, could solve the structures of PDB entries that were subsequently deposited. The results were encouraging: nine of 27 GREMLIN cases were solved, covering target lengths of 109-355 residues and a resolution range of 1.4-2.9 Å, and with target-model shared sequence identity as low as 20%. The cluster-and-truncate approach in AMPLE proved to be essential for most successes. For the overall lower quality structure predictions in the PconsFam database, remodelling with Rosetta within the AMPLE pipeline proved to be the best approach, generating ensemble search models from single-structure deposits. Finally, it is shown that the AMPLE-obtained search models deriving from GREMLIN deposits are of sufficiently high quality to be selected by the sequence-independent MR pipeline SIMBAD. Overall, the results help to point the way towards the optimal use of the expanding databases of ab initio structure predictions.


Assuntos
Cristalografia por Raios X/métodos , Modelos Moleculares , Proteínas/química , Algoritmos , Bases de Dados de Proteínas , Conformação Proteica , Software
5.
Acta Crystallogr D Struct Biol ; 74(Pt 7): 595-605, 2018 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-29968670

RESUMO

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here, SIMBAD, a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD, this approach has solved novel cases that have otherwise proved difficult to solve.


Assuntos
Cristalografia por Raios X/métodos , Bases de Dados de Proteínas , Software , Algoritmos , Sequência de Aminoácidos , Cristalização/normas , Modelos Moleculares
6.
Acta Crystallogr D Struct Biol ; 74(Pt 3): 167-182, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29533225

RESUMO

Increasing sophistication in molecular-replacement (MR) software and the rapid expansion of the PDB in recent years have allowed the technique to become the dominant method for determining the phases of a target structure in macromolecular X-ray crystallography. In addition, improvements in bioinformatic techniques for finding suitable homologous structures for use as MR search models, combined with developments in refinement and model-building techniques, have pushed the applicability of MR to lower sequence identities and made weak MR solutions more amenable to refinement and improvement. MrBUMP is a CCP4 pipeline which automates all stages of the MR procedure. Its scope covers everything from the sourcing and preparation of suitable search models right through to rebuilding of the positioned search model. Recent improvements to the pipeline include the adoption of more sensitive bioinformatic tools for sourcing search models, enhanced model-preparation techniques including better ensembling of homologues, and the use of phase improvement and model building on the resulting solution. The pipeline has also been deployed as an online service through CCP4 online, which allows its users to exploit large bioinformatic databases and coarse-grained parallelism to speed up the determination of a possible solution. Finally, the molecular-graphics application CCP4mg has been combined with MrBUMP to provide an interactive visual aid to the user during the process of selecting and manipulating search models for use in MR. Here, these developments in MrBUMP are described with a case study to explore how some of the enhancements to the pipeline and to CCP4mg can help to solve a difficult case.


Assuntos
Gráficos por Computador , Conformação Proteica , Proteínas/análise , Proteínas/química , Design de Software , Simulação por Computador , Cristalografia por Raios X , Humanos , Modelos Moleculares
7.
Acta Crystallogr D Struct Biol ; 74(Pt 3): 183-193, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29533226

RESUMO

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.


Assuntos
Conformação Proteica , Proteínas/análise , Proteínas/química , Software , Simulação por Computador , Cristalografia por Raios X , Humanos , Modelos Moleculares
8.
Proteins ; 86(5): 548-565, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29388242

RESUMO

Antimicrobial resistance within a wide range of infectious agents is a severe and growing public health threat. Antimicrobial peptides (AMPs) are among the leading alternatives to current antibiotics, exhibiting broad spectrum activity. Their activity is determined by numerous properties such as cationic charge, amphipathicity, size, and amino acid composition. Currently, only around 10% of known AMP sequences have experimentally solved structures. To improve our understanding of the AMP structural universe we have carried out large scale ab initio 3D modeling of structurally uncharacterized AMPs that revealed similarities between predicted folds of the modeled sequences and structures of characterized AMPs. Two of the peptides whose models matched known folds are Lebocin Peptide 1A (LP1A) and Odorranain M, predicted to form ß-hairpins but, interestingly, to lack the intramolecular disulfide bonds, cation-π or aromatic interactions that generally stabilize such AMP structures. Other examples include Ponericin Q42, Latarcin 4a, Kassinatuerin 1, Ceratotoxin D, and CPF-B1 peptide, which have α-helical folds, as well as mixed αß folds of human Histatin 2 peptide and Garvicin A which are, to the best of our knowledge, the first linear αßß fold AMPs lacking intramolecular disulfide bonds. In addition to fold matches to experimentally derived structures, unique folds were also obtained, namely for Microcin M and Ipomicin. These results help in understanding the range of protein scaffolds that naturally bear antimicrobial activity and may facilitate protein design efforts towards better AMPs.


Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Modelos Moleculares , Dobramento de Proteína , Sequência de Aminoácidos , Proteínas de Anfíbios/química , Venenos de Formiga/química , Bacteriocinas/química , Dissulfetos/química , Histatinas/química , Humanos , Peptídeos/química , Estabilidade Proteica , Estrutura Secundária de Proteína , Relação Estrutura-Atividade
9.
Acta Crystallogr D Struct Biol ; 73(Pt 12): 985-996, 2017 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-29199978

RESUMO

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.


Assuntos
Membrana Celular/química , Proteínas de Membrana/química , Conformação Proteica em alfa-Hélice , Algoritmos , Simulação por Computador , Cristalografia por Raios X , Humanos , Modelos Moleculares , Software
10.
Opt Lett ; 42(20): 4215-4218, 2017 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-29028051

RESUMO

The period of fiber Bragg gratings is adapted by shaping the wavefronts of ultrashort laser pulses applied in a phase mask inscription technique. A specially designed deformable mirror, based on a dielectric substrate to withstand high peak powers, is utilized to deform the wavefront. A shift of about 11 nm is demonstrated for a Bragg wavelength around 1550 nm.

11.
Bioinformatics ; 33(14): 2209-2211, 2017 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-28369168

RESUMO

Summary: Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. Availability and Implementation: ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. Contact: hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Algoritmos , Software , Sequência de Aminoácidos , Proteínas/química , Alinhamento de Sequência , Interface Usuário-Computador
12.
IUCrJ ; 3(Pt 4): 259-70, 2016 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-27437113

RESUMO

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing ß-structure, decoy quality and MR performance were further improved by the use of a ß-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with ß-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

13.
Nature ; 532(7599): 340-2, 2016 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-27049949

RESUMO

Quasars are associated with and powered by the accretion of material onto massive black holes; the detection of highly luminous quasars with redshifts greater than z = 6 suggests that black holes of up to ten billion solar masses already existed 13 billion years ago. Two possible present-day 'dormant' descendants of this population of 'active' black holes have been found in the galaxies NGC 3842 and NGC 4889 at the centres of the Leo and Coma galaxy clusters, which together form the central region of the Great Wall--the largest local structure of galaxies. The most luminous quasars, however, are not confined to such high-density regions of the early Universe; yet dormant black holes of this high mass have not yet been found outside of modern-day rich clusters. Here we report observations of the stellar velocity distribution in the galaxy NGC 1600--a relatively isolated elliptical galaxy near the centre of a galaxy group at a distance of 64 megaparsecs from Earth. We use orbit superposition models to determine that the black hole at the centre of NGC 1600 has a mass of 17 billion solar masses. The spatial distribution of stars near the centre of NGC 1600 is rather diffuse. We find that the region of depleted stellar density in the cores of massive elliptical galaxies extends over the same radius as the gravitational sphere of influence of the central black holes, and interpret this as the dynamical imprint of the black holes.

14.
Opt Lett ; 40(12): 2766-9, 2015 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-26076257

RESUMO

In this Letter, we present a direct writing technique for two-dimensional periodic volume Bragg gratings (VBGs) in fused silica based on the phase mask technology, ultrashort laser pulses, and three-beam interference. An algorithm to predict the grating pattern and its diffraction behavior under collimated, spectral broad illumination is developed. The predicted data are in good agreement with the measurements.

15.
J Immunol ; 194(12): 6164-6176, 2015 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-25948811

RESUMO

Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.


Assuntos
Epitopos de Linfócito T/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Modelos Imunológicos , Receptores de Antígenos de Linfócitos T/metabolismo , Software , Subpopulações de Linfócitos T/imunologia , Algoritmos , Alelos , Biologia Computacional/métodos , Conjuntos de Dados como Assunto , Epitopos de Linfócito T/genética , Epitopos de Linfócito T/metabolismo , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Antígenos de Histocompatibilidade Classe II/genética , Antígenos de Histocompatibilidade Classe II/metabolismo , Teste de Histocompatibilidade , Humanos , Internet , Peptídeos/química , Peptídeos/genética , Peptídeos/imunologia , Ligação Proteica , Receptores de Antígenos de Linfócitos T/genética , Reprodutibilidade dos Testes , Especificidade do Receptor de Antígeno de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo
16.
IUCrJ ; 2(Pt 2): 198-206, 2015 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-25866657

RESUMO

Coiled-coil protein folds are among the most abundant in nature. These folds consist of long wound α-helices and are architecturally simple, but paradoxically their crystallographic structures are notoriously difficult to solve with molecular-replacement techniques. The program AMPLE can solve crystal structures by molecular replacement using ab initio search models in the absence of an existent homologous protein structure. AMPLE has been benchmarked on a large and diverse test set of coiled-coil crystal structures and has been found to solve 80% of all cases. Successes included structures with chain lengths of up to 253 residues and resolutions down to 2.9 Å, considerably extending the limits on size and resolution that are typically tractable by ab initio methodologies. The structures of two macromolecular complexes, one including DNA, were also successfully solved using their coiled-coil components. It is demonstrated that both the ab initio modelling and the use of ensemble search models contribute to the success of AMPLE by comparison with phasing attempts using single structures or ideal polyalanine helices. These successes suggest that molecular replacement with AMPLE should be the method of choice for the crystallo-graphic elucidation of a coiled-coil structure. Furthermore, AMPLE may be able to exploit the presence of a coiled coil in a complex to provide a convenient route for phasing.

17.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 2): 338-43, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25664744

RESUMO

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.


Assuntos
Proteínas/química , Software , Conformação Proteica , Fatores de Tempo
18.
Opt Lett ; 39(24): 6915-8, 2014 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-25503029

RESUMO

A Ti:Al(3)O(2) multipass chirped pulse amplification system is outfitted with a single-grating, simultaneous spatial and temporal focusing (SSTF) compressor platform. For the first time, this novel design has the ability to easily vary the beam aspect ratio of an SSTF beam, and thus the degree of pulse-front tilt at focus, while maintaining a net zero-dispersion system. Accessible variation of pulse front tilt gives full spatiotemporal control over the intensity distribution at the focus and could lead to better understanding of effects such as nonreciprocal writing and SSTF-material interactions.

19.
J Virol ; 88(1): 758-62, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24155387

RESUMO

The Nipah virus phosphoprotein (P) is multimeric and tethers the viral polymerase to the nucleocapsid. We present the crystal structure of the multimerization domain of Nipah virus P: a long, parallel, tetrameric, coiled coil with a small, α-helical cap structure. Across the paramyxoviruses, these domains share little sequence identity yet are similar in length and structural organization, suggesting a common requirement for scaffolding or spatial organization of the functions of P in the virus life cycle.


Assuntos
Biopolímeros/química , Vírus Nipah/química , Fosfoproteínas/química , Cristalografia por Raios X , Conformação Proteica
20.
Opt Lett ; 38(13): 2354-6, 2013 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-23811926

RESUMO

We report on the inscription of apodized Bragg grating waveguides (BGWs) in fused silica using a modulated high repetition rate fs laser system. Tailoring of the grating's coupling strength is facilitated by appropriately substructuring the modulation of the inscribing laser radiation. The proposed alteration delivers an unchanged constant mean refractive index entailing homogeneous guiding properties along the entire waveguide. The BGWs fabricated using a Gaussian apodized modulation profile exhibit a 10 dB improvement in sideband suppression compared to waveguide gratings written with a uniform modulation profile.

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