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1.
Cell ; 156(3): 482-94, 2014 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-24485456

RESUMO

SYG-1 and SYG-2 are multipurpose cell adhesion molecules (CAMs) that have evolved across all major animal taxa to participate in diverse physiological functions, ranging from synapse formation to formation of the kidney filtration barrier. In the crystal structures of several SYG-1 and SYG-2 orthologs and their complexes, we find that SYG-1 orthologs homodimerize through a common, bispecific interface that similarly mediates an unusual orthogonal docking geometry in the heterophilic SYG-1/SYG-2 complex. C. elegans SYG-1's specification of proper synapse formation in vivo closely correlates with the heterophilic complex affinity, which appears to be tuned for optimal function. Furthermore, replacement of the interacting domains of SYG-1 and SYG-2 with those from CAM complexes that assume alternative docking geometries or the introduction of segmental flexibility compromised synaptic function. These results suggest that SYG extracellular complexes do not simply act as "molecular velcro" and that their distinct structural features are important in instructing synaptogenesis. PAPERFLICK:


Assuntos
Proteínas de Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/citologia , Imunoglobulinas/metabolismo , Proteínas do Tecido Nervoso/metabolismo , Sinapses/metabolismo , Sequência de Aminoácidos , Animais , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/química , Adesão Celular , Dimerização , Imunoglobulinas/química , Modelos Moleculares , Dados de Sequência Molecular , Proteínas do Tecido Nervoso/química , Neurônios/citologia , Neurônios/metabolismo , Estrutura Terciária de Proteína , Alinhamento de Sequência , Sinapses/química
2.
Proc Natl Acad Sci U S A ; 118(10)2021 03 09.
Artigo em Inglês | MEDLINE | ID: mdl-33649232

RESUMO

Human respiratory syncytial virus (RSV) nonstructural protein 2 (NS2) inhibits host interferon (IFN) responses stimulated by RSV infection by targeting early steps in the IFN-signaling pathway. But the molecular mechanisms related to how NS2 regulates these processes remain incompletely understood. To address this gap, here we solved the X-ray crystal structure of NS2. This structure revealed a unique fold that is distinct from other known viral IFN antagonists, including RSV NS1. We also show that NS2 directly interacts with an inactive conformation of the RIG-I-like receptors (RLRs) RIG-I and MDA5. NS2 binding prevents RLR ubiquitination, a process critical for prolonged activation of downstream signaling. Structural analysis, including by hydrogen-deuterium exchange coupled to mass spectrometry, revealed that the N terminus of NS2 is essential for binding to the RIG-I caspase activation and recruitment domains. N-terminal mutations significantly diminish RIG-I interactions and result in increased IFNß messenger RNA levels. Collectively, our studies uncover a previously unappreciated regulatory mechanism by which NS2 further modulates host responses and define an approach for targeting host responses.


Assuntos
Proteína DEAD-box 58 , Helicase IFIH1 Induzida por Interferon , Interferon beta , Receptores Imunológicos , Proteínas não Estruturais Virais , Cristalografia por Raios X , Proteína DEAD-box 58/química , Proteína DEAD-box 58/metabolismo , Medição da Troca de Deutério , Células HEK293 , Humanos , Helicase IFIH1 Induzida por Interferon/química , Helicase IFIH1 Induzida por Interferon/metabolismo , Interferon beta/química , Interferon beta/metabolismo , Ligação Proteica , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Receptores Imunológicos/química , Receptores Imunológicos/metabolismo , Proteínas não Estruturais Virais/química , Proteínas não Estruturais Virais/metabolismo
3.
J Struct Biol ; 215(2): 107945, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-36889560

RESUMO

Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these conditions result in a broader PSF that requires larger padding and slower calculations to integrate information for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined to optimize data processing. Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an image that has complex values. This is a complex value image considered in real space, opposed to standard SPR data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept provides multiple advantages because the particle box size can be small and calculations crucial for high resolution reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus refinement can be performed on the small box data.


Assuntos
Algoritmos , Processamento de Imagem Assistida por Computador , Microscopia Crioeletrônica/métodos , Processamento de Imagem Assistida por Computador/métodos , Tamanho da Partícula
4.
Nature ; 533(7604): 561-4, 2016 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-27144356

RESUMO

ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral sterols in liver and intestines. Mutations disrupting G5G8 cause sitosterolaemia, a disorder characterized by sterol accumulation and premature atherosclerosis. Here we use crystallization in lipid bilayers to determine the X-ray structure of human G5G8 in a nucleotide-free state at 3.9 Å resolution, generating the first atomic model of an ABC sterol transporter. The structure reveals a new transmembrane fold that is present in a large and functionally diverse superfamily of ABC transporters. The transmembrane domains are coupled to the nucleotide-binding sites by networks of interactions that differ between the active and inactive ATPases, reflecting the catalytic asymmetry of the transporter. The G5G8 structure provides a mechanistic framework for understanding sterol transport and the disruptive effects of mutations causing sitosterolaemia.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Lipoproteínas/química , Esteróis/metabolismo , Membro 5 da Subfamília G de Transportadores de Cassetes de Ligação de ATP , Membro 8 da Subfamília G de Transportadores de Cassetes de Ligação de ATP , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Adenosina Trifosfatases/metabolismo , Sequência de Aminoácidos , Sítios de Ligação , Biocatálise , Cristalografia por Raios X , Humanos , Hipercolesterolemia/genética , Enteropatias/genética , Bicamadas Lipídicas/química , Bicamadas Lipídicas/metabolismo , Erros Inatos do Metabolismo Lipídico/genética , Lipoproteínas/genética , Lipoproteínas/metabolismo , Modelos Moleculares , Dados de Sequência Molecular , Nucleotídeos , Fitosteróis/efeitos adversos , Fitosteróis/genética , Dobramento de Proteína , Multimerização Proteica , Estrutura Terciária de Proteína
5.
PLoS Comput Biol ; 16(5): e1007775, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32413045

RESUMO

The human genome harbors a variety of genetic variations. Single-nucleotide changes that alter amino acids in protein-coding regions are one of the major causes of human phenotypic variation and diseases. These single-amino acid variations (SAVs) are routinely found in whole genome and exome sequencing. Evaluating the functional impact of such genomic alterations is crucial for diagnosis of genetic disorders. We developed DeepSAV, a deep-learning convolutional neural network to differentiate disease-causing and benign SAVs based on a variety of protein sequence, structural and functional properties. Our method outperforms most stand-alone programs, and the version incorporating population and gene-level information (DeepSAV+PG) has similar predictive power as some of the best available. We transformed DeepSAV scores of rare SAVs in the human population into a quantity termed "mutation severity measure" for each human protein-coding gene. It reflects a gene's tolerance to deleterious missense mutations and serves as a useful tool to study gene-disease associations. Genes implicated in cancer, autism, and viral interaction are found by this measure as intolerant to mutations, while genes associated with a number of other diseases are scored as tolerant. Among known disease-associated genes, those that are mutation-intolerant are likely to function in development and signal transduction pathways, while those that are mutation-tolerant tend to encode metabolic and mitochondrial proteins.


Assuntos
Doença/genética , Previsões/métodos , Genoma Humano/genética , Alelos , Sequência de Aminoácidos/genética , Biologia Computacional/métodos , Aprendizado Profundo , Redes Reguladoras de Genes/genética , Humanos , Mutação/genética , Mutação de Sentido Incorreto/genética , Rede Nervosa , Fases de Leitura Aberta/genética , Análise de Sequência/métodos , Sequenciamento do Exoma/métodos
6.
Nucl Instrum Methods Phys Res B ; 489: 30-40, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33603257

RESUMO

Intense X-rays available at powerful synchrotron beamlines provide macromolecular crystallographers with an incomparable tool for investigating biological phenomena on an atomic scale. The resulting insights into the mechanism's underlying biological processes have played an essential role and shaped biomedical sciences during the last 30 years, considered the "golden age" of structural biology. In this review, we analyze selected aspects of the impact of synchrotron radiation on structural biology. Synchrotron beamlines have been used to determine over 70% of all macromolecular structures deposited into the Protein Data Bank (PDB). These structures were deposited by over 13,000 different research groups. Interestingly, despite the impressive advances in synchrotron technologies, the median resolution of macromolecular structures determined using synchrotrons has remained constant throughout the last 30 years, at about 2 Å. Similarly, the median times from the data collection to the deposition and release have not changed significantly. We describe challenges to reproducibility related to recording all relevant data and metadata during the synchrotron experiments, including diffraction images. Finally, we discuss some of the recent opinions suggesting a diminishing importance of X-ray crystallography due to impressive advances in Cryo-EM and theoretical modeling. We believe that synchrotrons of the future will increasingly evolve towards a life science center model, where X-ray crystallography, Cryo-EM, and other experimental and computational resources and knowledge are encompassed within a versatile research facility. The recent response of crystallographers to the COVID-19 pandemic suggests that X-ray crystallography conducted at synchrotron beamlines will continue to play an essential role in structural biology and drug discovery for years to come.

7.
Mol Genet Genomics ; 294(1): 211-226, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30293092

RESUMO

Giant-Skippers (Megathymini) are unusual thick-bodied, moth-like butterflies whose caterpillars feed inside Yucca roots and Agave leaves. Giant-Skippers are attributed to the subfamily Hesperiinae and they are endemic to southern and mostly desert regions of the North American continent. To shed light on the genotypic determinants of their unusual phenotypic traits, we sequenced and annotated a draft genome of the largest Giant-Skipper species, the Bear (Megathymus ursus violae). The Bear skipper genome is the least heterozygous among sequenced Lepidoptera genomes, possibly due to much smaller population size and extensive inbreeding. Their lower heterozygosity helped us to obtain a high-quality genome with an N50 of 4.2 Mbp. The ~ 430 Mb genome encodes about 14000 proteins. Phylogenetic analysis supports placement of Giant-Skippers with Grass-Skippers (Hesperiinae). We find that proteins involved in odorant and taste sensing as well as in oxidative reactions have diverged significantly in Megathymus as compared to Lerema, another Grass-Skipper. In addition, the Giant-Skipper has lost several odorant and gustatory receptors and possesses many fewer (1/3-1/2 of other skippers) anti-oxidative enzymes. Such differences may be related to the unusual life style of Giant-Skippers: they do not feed as adults, and their caterpillars feed inside Yuccas and Agaves, which provide a source of antioxidants such as polyphenols.


Assuntos
Genoma de Inseto , Mariposas/genética , Análise de Sequência de DNA/métodos , Yucca/parasitologia , Animais , Tamanho do Genoma , Mariposas/fisiologia , Fenótipo , Filogenia , Raízes de Plantas/parasitologia
8.
Proc Natl Acad Sci U S A ; 113(44): 12444-12449, 2016 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-27791135

RESUMO

The ring-shaped cohesin complex topologically entraps chromosomes and regulates chromosome segregation, transcription, and DNA repair. The cohesin core consists of the structural maintenance of chromosomes 1 and 3 (Smc1-Smc3) heterodimeric ATPase, the kleisin subunit sister chromatid cohesion 1 (Scc1) that links the two ATPase heads, and the Scc1-bound adaptor protein Scc3. The sister chromatid cohesion 2 and 4 (Scc2-Scc4) complex loads cohesin onto chromosomes. Mutations of cohesin and its regulators, including Scc2, cause human developmental diseases termed cohesinopathy. Here, we report the crystal structure of Chaetomium thermophilum (Ct) Scc2 and examine its interaction with cohesin. Similar to Scc3 and another Scc1-interacting cohesin regulator, precocious dissociation of sisters 5 (Pds5), Scc2 consists mostly of helical repeats that fold into a hook-shaped structure. Scc2 binds to Scc1 through an N-terminal region of Scc1 that overlaps with its Pds5-binding region. Many cohesinopathy mutations target conserved residues in Scc2 and diminish Ct Scc2 binding to Ct Scc1. Pds5 binding to Scc1 weakens the Scc2-Scc1 interaction. Our study defines a functionally important interaction between the kleisin subunit of cohesin and the hook of Scc2. Through competing with Scc2 for Scc1 binding, Pds5 might contribute to the release of Scc2 from loaded cohesin, freeing Scc2 for additional rounds of loading.


Assuntos
Proteínas de Ciclo Celular/metabolismo , Chaetomium/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Proteínas Fúngicas/metabolismo , Sequência de Aminoácidos , Proteínas de Ciclo Celular/química , Proteínas de Ciclo Celular/genética , Chaetomium/genética , Cromátides , Proteínas Cromossômicas não Histona/química , Proteínas Cromossômicas não Histona/genética , Segregação de Cromossomos , Cristalografia por Raios X , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Modelos Moleculares , Ligação Proteica , Domínios Proteicos , Estrutura Secundária de Proteína , Homologia de Sequência de Aminoácidos , Coesinas
9.
J Synchrotron Radiat ; 25(Pt 2): 451-467, 2018 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-29488925

RESUMO

A method of analysis is presented that allows for the separation of specific radiation-induced changes into distinct components in real space. The method relies on independent component analysis (ICA) and can be effectively applied to electron density maps and other types of maps, provided that they can be represented as sets of numbers on a grid. Here, for glucose isomerase crystals, ICA was used in a proof-of-concept analysis to separate temperature-dependent and temperature-independent components of specific radiation-induced changes for data sets acquired from multiple crystals across multiple temperatures. ICA identified two components, with the temperature-independent component being responsible for the majority of specific radiation-induced changes at temperatures below 130 K. The patterns of specific temperature-independent radiation-induced changes suggest a contribution from the tunnelling of electron holes as a possible explanation. In the second case, where a group of 22 data sets was collected on a single thaumatin crystal, ICA was used in another type of analysis to separate specific radiation-induced effects happening on different exposure-level scales. Here, ICA identified two components of specific radiation-induced changes that likely result from radiation-induced chemical reactions progressing with different rates at different locations in the structure. In addition, ICA unexpectedly identified the radiation-damage state corresponding to reduced disulfide bridges rather than the zero-dose extrapolated state as the highest contrast structure. The application of ICA to the analysis of specific radiation-induced changes in real space and the data pre-processing for ICA that relies on singular value decomposition, which was used previously in data space to validate a two-component physical model of X-ray radiation-induced changes, are discussed in detail. This work lays a foundation for a better understanding of protein-specific radiation chemistries and provides a framework for analysing effects of specific radiation damage in crystallographic and cryo-EM experiments.

10.
Genomics ; 109(5-6): 485-493, 2017 10.
Artigo em Inglês | MEDLINE | ID: mdl-28757157

RESUMO

Sequencing complete genomes of all major phylogenetic groups of organisms opens unprecedented opportunities to study evolution and genetics. We report draft genomes of Calephelis nemesis and Calephelis virginiensis, representatives of the family Riodinidae. They complete the genomic coverage of butterflies at the family level. At 809 and 855 Mbp, respectively, they become the largest available Lepidoptera genomes. Comparison of butterfly genomes shows that the divergence between Riodinidae and Lycaenidae dates to the time when other families started to diverge into subfamilies. Thus, Riodinidae may be considered a subfamily of Lycaenidae. Calephelis species exhibit unique gene expansions in actin-disassembling factor, cofilin, and chitinase. The functional implications of these gene expansions are not clear, but they may aid molting of caterpillars covered in extensive setae. The two Calephelis species diverged about 5 million years ago and they differ in proteins involved in metabolism, circadian clock, regulation of development, and immune responses.


Assuntos
Borboletas/classificação , Genoma de Inseto , Análise de Sequência de DNA/métodos , Animais , Borboletas/genética , Evolução Molecular , Tamanho do Genoma , Filogenia
11.
Proc Biol Sci ; 284(1848)2017 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-28179510

RESUMO

Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.


Assuntos
Borboletas/crescimento & desenvolvimento , Código de Barras de DNA Taxonômico , Genoma de Inseto , Genoma Mitocondrial , Animais , América Central , DNA Mitocondrial/genética , Filogenia , Estados Unidos
12.
PLoS Comput Biol ; 12(6): e1004985, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-27336403

RESUMO

Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz.


Assuntos
Archaea/genética , Bactérias/genética , Biologia Computacional/métodos , Transferência Genética Horizontal/genética , Genoma Arqueal/genética , Genoma Bacteriano/genética , Algoritmos , Evolução Molecular , Filogenia
13.
Curr Genomics ; 18(4): 366-374, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29081692

RESUMO

BACKGROUND: The Hoary Edge Skipper (Achalarus lyciades) is an eastern North America endemic butterfly from the Eudaminae subfamily of skippers named for an underside whitish patch near the hindwing edge. Its caterpillars feed on legumes, in contrast to Grass skippers (subfamily Hesperiinae) which feed exclusively on monocots. RESULTS: To better understand the evolution and phenotypic diversification of Skippers (family Hesperiidae), we sequenced, assembled and annotated a complete genome draft and transcriptome of a wild-caught specimen of A. lyciades and compared it with the available genome of the Clouded Skipper (Lerema accius) from the Grass skipper subfamily. The genome of A. lyciades is nearly twice the size of L. accius (567 Mbp vs. 298 Mbp), however it encodes a smaller number of proteins (15881 vs. 17411). Gene expansions we identified previously in L. accius apparently did not occur in the genome of A. lyciades. For instance, a family of hypothetical cellulases that diverged from an endochitinase (possibly associated with feeding of L. accius caterpillars on nutrient-poor grasses) is absent in A. lyciades. While L. accius underwent gene expansion in pheromone binding proteins, A. lyciades has more opsins. This difference may be related to the mate recognition mechanisms of the two species: visual cues might be more important for the Eudaminae skippers (which have more variable wing patterns), whereas odor might be more important for Grass skippers (that are hardly distinguishable by their wings). Phylogenetically, A. lyciades is a sister species of L. accius, the only other Hesperiidae with a complete genome. CONCLUSIONS: A new reference genome of a dicot-feeding skippers, the first from the Eudaminae subfamily, reveals its larger size and suggests hypotheses about phenotypic traits and differences from monocot-feeding skippers.

14.
Nature ; 468(7323): 533-8, 2010 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-21107423

RESUMO

Members of the Wiskott-Aldrich syndrome protein (WASP) family control cytoskeletal dynamics by promoting actin filament nucleation with the Arp2/3 complex. The WASP relative WAVE regulates lamellipodia formation within a 400-kilodalton, hetero-pentameric WAVE regulatory complex (WRC). The WRC is inactive towards the Arp2/3 complex, but can be stimulated by the Rac GTPase, kinases and phosphatidylinositols. Here we report the 2.3-ångstrom crystal structure of the WRC and complementary mechanistic analyses. The structure shows that the activity-bearing VCA motif of WAVE is sequestered by a combination of intramolecular and intermolecular contacts within the WRC. Rac and kinases appear to destabilize a WRC element that is necessary for VCA sequestration, suggesting the way in which these signals stimulate WRC activity towards the Arp2/3 complex. The spatial proximity of the Rac binding site and the large basic surface of the WRC suggests how the GTPase and phospholipids could cooperatively recruit the complex to membranes.


Assuntos
Actinas/metabolismo , Modelos Moleculares , Família de Proteínas da Síndrome de Wiskott-Aldrich/química , Animais , Células HeLa , Humanos , Insetos/citologia , Fosforilação , Estrutura Quaternária de Proteína , Proteínas rac1 de Ligação ao GTP/metabolismo
15.
Proc Natl Acad Sci U S A ; 110(28): 11355-60, 2013 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-23776203

RESUMO

Cohesin, along with positive regulators, establishes sister-chromatid cohesion by forming a ring to circle chromatin. The wings apart-like protein (Wapl) is a key negative regulator of cohesin and forms a complex with precocious dissociation of sisters protein 5 (Pds5) to promote cohesin release from chromatin. Here we report the crystal structure and functional characterization of human Wapl. Wapl contains a flexible, variable N-terminal region (Wapl-N) and a conserved C-terminal domain (Wapl-C) consisting of eight HEAT (Huntingtin, Elongation factor 3, A subunit, and target of rapamycin) repeats. Wapl-C folds into an elongated structure with two lobes. Structure-based mutagenesis maps the functional surface of Wapl-C to two distinct patches (I and II) on the N lobe and a localized patch (III) on the C lobe. Mutating critical patch I residues weaken Wapl binding to cohesin and diminish sister-chromatid resolution and cohesin release from mitotic chromosomes in human cells and Xenopus egg extracts. Surprisingly, patch III on the C lobe does not contribute to Wapl binding to cohesin or its known regulators. Although patch I mutations reduce Wapl binding to intact cohesin, they do not affect Wapl-Pds5 binding to the cohesin subcomplex of sister chromatid cohesion protein 1 (Scc1) and stromal antigen 2 (SA2) in vitro, which is instead mediated by Wapl-N. Thus, Wapl-N forms extensive interactions with Pds5 and Scc1-SA2. Wapl-C interacts with other cohesin subunits and possibly unknown effectors to trigger cohesin release from chromatin.


Assuntos
Proteínas de Transporte/química , Proteínas de Ciclo Celular/antagonistas & inibidores , Proteínas Cromossômicas não Histona/antagonistas & inibidores , Proteínas Nucleares/química , Proteínas Proto-Oncogênicas/química , Proteínas de Transporte/genética , Proteínas de Ciclo Celular/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Humanos , Modelos Moleculares , Mutação , Proteínas Nucleares/genética , Conformação Proteica , Proteínas Proto-Oncogênicas/genética , Coesinas
16.
Proteins ; 83(3): 411-27, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-25546158

RESUMO

Constructing a model of a query protein based on its alignment to a homolog with experimentally determined spatial structure (the template) is still the most reliable approach to structure prediction. Alignment errors are the main bottleneck for homology modeling when the query is distantly related to the template. Alignment methods often misalign secondary structural elements by a few residues. Therefore, better alignment solutions can be found within a limited set of local shifts of secondary structures. We present a refinement method to improve pairwise sequence alignments by evaluating alignment variants generated by local shifts of template-defined secondary structures. Our method SFESA is based on a novel scoring function that combines the profile-based sequence score and the structure score derived from residue contacts in a template. Such a combined score frequently selects a better alignment variant among a set of candidate alignments generated by local shifts and leads to overall increase in alignment accuracy. Evaluation of several benchmarks shows that our refinement method significantly improves alignments made by automatic methods such as PROMALS, HHpred and CNFpred. The web server is available at http://prodata.swmed.edu/sfesa.


Assuntos
Proteínas/química , Proteínas/metabolismo , Proteômica/métodos , Alinhamento de Sequência/métodos , Sequência de Aminoácidos , Bases de Dados de Proteínas , Dados de Sequência Molecular , Estrutura Secundária de Proteína , Termodinâmica
17.
BMC Genomics ; 16: 639, 2015 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-26311350

RESUMO

BACKGROUND: Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics. RESULTS: We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model. CONCLUSION: Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and provides a rich dataset for comparative genomics and phylogenetic studies of Lepidoptera.


Assuntos
Borboletas/classificação , Borboletas/genética , Genoma de Inseto , Mariposas/classificação , Mariposas/genética , Fenótipo , Filogenia , Característica Quantitativa Herdável , Animais , Biologia Computacional/métodos , Estudos de Associação Genética , Genômica/métodos , Anotação de Sequência Molecular , Família Multigênica , Polimorfismo de Nucleotídeo Único
18.
Proc Natl Acad Sci U S A ; 109(10): 3802-7, 2012 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-22355143

RESUMO

Mint adaptor proteins bind to the amyloid precursor protein (APP) and regulate APP processing associated with Alzheimer's disease; however, the molecular mechanisms underlying Mint regulation in APP binding and processing remain unclear. Biochemical, biophysical, and cellular experiments now show that the Mint1 phosphotyrosine binding (PTB) domain that binds to APP is intramolecularly inhibited by the adjacent C-terminal linker region. The crystal structure of a C-terminally extended Mint1 PTB fragment reveals that the linker region forms a short α-helix that folds back onto the PTB domain and sterically hinders APP binding. This intramolecular interaction is disrupted by mutation of Tyr633 within the Mint1 autoinhibitory helix leading to enhanced APP binding and ß-amyloid production. Our findings suggest that an autoinhibitory mechanism in Mint1 is important for regulating APP processing and may provide novel therapies for Alzheimer's disease.


Assuntos
Proteínas Adaptadoras de Transdução de Sinal/química , Precursor de Proteína beta-Amiloide/química , Proteínas do Tecido Nervoso/química , Doença de Alzheimer/metabolismo , Bioquímica/métodos , Biofísica/métodos , Cristalografia por Raios X/métodos , Análise Mutacional de DNA , Células HEK293 , Humanos , Cinética , Espectroscopia de Ressonância Magnética/métodos , Conformação Molecular , Neurônios/metabolismo , Ligação Proteica , Estrutura Terciária de Proteína , Tirosina/química
19.
Proc Natl Acad Sci U S A ; 109(50): 20661-6, 2012 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-23185024

RESUMO

Filoviruses, marburgvirus (MARV) and ebolavirus (EBOV), are causative agents of highly lethal hemorrhagic fever in humans. MARV and EBOV share a common genome organization but show important differences in replication complex formation, cell entry, host tropism, transcriptional regulation, and immune evasion. Multifunctional filoviral viral protein (VP) 35 proteins inhibit innate immune responses. Recent studies suggest double-stranded (ds)RNA sequestration is a potential mechanism that allows EBOV VP35 to antagonize retinoic-acid inducible gene-I (RIG-I) like receptors (RLRs) that are activated by viral pathogen-associated molecular patterns (PAMPs), such as double-strandedness and dsRNA blunt ends. Here, we show that MARV VP35 can inhibit IFN production at multiple steps in the signaling pathways downstream of RLRs. The crystal structure of MARV VP35 IID in complex with 18-bp dsRNA reveals that despite the similar protein fold as EBOV VP35 IID, MARV VP35 IID interacts with the dsRNA backbone and not with blunt ends. Functional studies show that MARV VP35 can inhibit dsRNA-dependent RLR activation and interferon (IFN) regulatory factor 3 (IRF3) phosphorylation by IFN kinases TRAF family member-associated NFkb activator (TANK) binding kinase-1 (TBK-1) and IFN kB kinase e (IKKe) in cell-based studies. We also show that MARV VP35 can only inhibit RIG-I and melanoma differentiation associated gene 5 (MDA5) activation by double strandedness of RNA PAMPs (coating backbone) but is unable to inhibit activation of RLRs by dsRNA blunt ends (end capping). In contrast, EBOV VP35 can inhibit activation by both PAMPs. Insights on differential PAMP recognition and inhibition of IFN induction by a similar filoviral VP35 fold, as shown here, reveal the structural and functional plasticity of a highly conserved virulence factor.


Assuntos
Marburgvirus/imunologia , Marburgvirus/patogenicidade , Proteínas Virais Reguladoras e Acessórias/química , Proteínas Virais Reguladoras e Acessórias/imunologia , Sequência de Aminoácidos , Animais , Sequência de Bases , Cristalografia por Raios X , Células HEK293 , Interações Hospedeiro-Patógeno , Humanos , Quinase I-kappa B/antagonistas & inibidores , Imunidade Inata , Interferon Tipo I/antagonistas & inibidores , Doença do Vírus de Marburg/etiologia , Doença do Vírus de Marburg/imunologia , Doença do Vírus de Marburg/virologia , Marburgvirus/química , Modelos Biológicos , Modelos Moleculares , Dados de Sequência Molecular , Proteínas Serina-Treonina Quinases/antagonistas & inibidores , Estrutura Terciária de Proteína , RNA/química , RNA/genética , RNA/metabolismo , Homologia de Sequência de Aminoácidos , Virulência/imunologia
20.
BMC Genomics ; 15: 590, 2014 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-25015739

RESUMO

BACKGROUND: The fungal genus Stachybotrys produces several diverse toxins that affect human health. Its strains comprise two mutually-exclusive toxin chemotypes, one producing satratoxins, which are a subclass of trichothecenes, and the other producing the less-toxic atranones. To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. Two of these strains produce atranones and two produce satratoxins. RESULTS: Comparative analysis of these four 35-Mbp genomes revealed several chemotype-specific gene clusters that are predicted to make secondary metabolites. The largest, which was named the core atranone cluster, encodes 14 proteins that may suffice to produce all observed atranone compounds via reactions that include an unusual Baeyer-Villiger oxidation. Satratoxins are suggested to be made by products of multiple gene clusters that encode 21 proteins in all, including polyketide synthases, acetyltransferases, and other enzymes expected to modify the trichothecene skeleton. One such satratoxin chemotype-specific cluster is adjacent to the core trichothecene cluster, which has diverged from those of other trichothecene producers to contain a unique polyketide synthase. CONCLUSIONS: The results suggest that chemotype-specific gene clusters are likely the genetic basis for the mutually-exclusive toxin chemotypes of Stachybotrys. A unified biochemical model for Stachybotrys toxin production is presented. Overall, the four genomes described here will be useful for ongoing studies of this mold's diverse toxicity mechanisms.


Assuntos
Genes Fúngicos , Família Multigênica , Stachybotrys/genética , Motivos de Aminoácidos , Vias Biossintéticas/genética , Proteínas Fúngicas/genética , Anotação de Sequência Molecular , Fenótipo , Filogenia , Proteoma/genética , Análise de Sequência de DNA , Tricotecenos/genética
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