205 results on '"Brenner SE"'
Search Results
102. The COMBREX project: design, methodology, and initial results.
- Author
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Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, and Kasif S
- Subjects
- Humans, Models, Theoretical, Genomics methods
- Abstract
Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2013
- Full Text
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103. PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.
- Author
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Stegle O, Brenner SE, Morris Q, and Listgarten J
- Published
- 2013
104. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris.
- Author
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Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, and Jap BK
- Subjects
- Bacterial Outer Membrane Proteins chemistry, Cell Membrane chemistry, Chromatography, Ion Exchange, Desulfovibrio vulgaris enzymology, Detergents chemistry, Electrophoresis, Polyacrylamide Gel, Escherichia coli chemistry, Mass Spectrometry, Membrane Proteins chemistry, Molecular Weight, Multiprotein Complexes chemistry, Periplasm chemistry, Periplasm enzymology, Protein Interaction Mapping methods, Protein Interaction Maps, Proteome chemistry, Proteomics methods, Sequence Homology, Amino Acid, Solubility, Bacterial Outer Membrane Proteins isolation & purification, Desulfovibrio vulgaris chemistry, High-Throughput Screening Assays methods, Membrane Proteins isolation & purification, Multiprotein Complexes isolation & purification
- Abstract
Cell membranes represent the "front line" of cellular defense and the interface between a cell and its environment. To determine the range of proteins and protein complexes that are present in the cell membranes of a target organism, we have utilized a "tagless" process for the system-wide isolation and identification of native membrane protein complexes. As an initial subject for study, we have chosen the Gram-negative sulfate-reducing bacterium Desulfovibrio vulgaris. With this tagless methodology, we have identified about two-thirds of the outer membrane- associated proteins anticipated. Approximately three-fourths of these appear to form homomeric complexes. Statistical and machine-learning methods used to analyze data compiled over multiple experiments revealed networks of additional protein-protein interactions providing insight into heteromeric contacts made between proteins across this region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be essential for the detection and characterization of environment-driven changes in the outer membrane proteome and in the modeling of stress response pathways. The workflow utilized here should be effective for the global characterization of membrane protein complexes in a wide range of organisms.
- Published
- 2012
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105. Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences.
- Author
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Soergel DA, Dey N, Knight R, and Brenner SE
- Subjects
- High-Throughput Nucleotide Sequencing, Humans, Bacterial Typing Techniques methods, DNA Primers genetics, Gastrointestinal Tract microbiology, Metagenome, RNA, Bacterial genetics, RNA, Ribosomal, 16S genetics
- Abstract
Microbial community profiling using 16S rRNA gene sequences requires accurate taxonomy assignments. 'Universal' primers target conserved sequences and amplify sequences from many taxa, but they provide variable coverage of different environments, and regions of the rRNA gene differ in taxonomic informativeness--especially when high-throughput short-read sequencing technologies (for example, 454 and Illumina) are used. We introduce a new evaluation procedure that provides an improved measure of expected taxonomic precision when classifying environmental sequence reads from a given primer. Applying this measure to thousands of combinations of primers and read lengths, simulating single-ended and paired-end sequencing, reveals that these choices greatly affect taxonomic informativeness. The most informative sequence region may differ by environment, partly due to variable coverage of different environments in reference databases. Using our Rtax method of classifying paired-end reads, we found that paired-end sequencing provides substantial benefit in some environments including human gut, but not in others. Optimal primer choice for short reads totaling 96 nt provides 82-100% of the confident genus classifications available from longer reads.
- Published
- 2012
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106. Genome-scale phylogenetic function annotation of large and diverse protein families.
- Author
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Engelhardt BE, Jordan MI, Srouji JR, and Brenner SE
- Subjects
- Algorithms, Arylsulfotransferase genetics, Computational Biology, Databases, Protein, Genome, Fungal, Models, Statistical, Pyrophosphatases genetics, Schizosaccharomyces pombe Proteins genetics, Nudix Hydrolases, Genome, Molecular Sequence Annotation, Phylogeny, Proteins classification, Proteins genetics
- Abstract
The Statistical Inference of Function Through Evolutionary Relationships (SIFTER) framework uses a statistical graphical model that applies phylogenetic principles to automate precise protein function prediction. Here we present a revised approach (SIFTER version 2.0) that enables annotations on a genomic scale. SIFTER 2.0 produces equivalently precise predictions compared to the earlier version on a carefully studied family and on a collection of 100 protein families. We have added an approximation method to SIFTER 2.0 and show a 500-fold improvement in speed with minimal impact on prediction results in the functionally diverse sulfotransferase protein family. On the Nudix protein family, previously inaccessible to the SIFTER framework because of the 66 possible molecular functions, SIFTER achieved 47.4% accuracy on experimental data (where BLAST achieved 34.0%). Finally, we used SIFTER to annotate all of the Schizosaccharomyces pombe proteins with experimental functional characterizations, based on annotations from proteins in 46 fungal genomes. SIFTER precisely predicted molecular function for 45.5% of the characterized proteins in this genome, as compared with four current function prediction methods that precisely predicted function for 62.6%, 30.6%, 6.0%, and 5.7% of these proteins. We use both precision-recall curves and ROC analyses to compare these genome-scale predictions across the different methods and to assess performance on different types of applications. SIFTER 2.0 is capable of predicting protein molecular function for large and functionally diverse protein families using an approximate statistical model, enabling phylogenetics-based protein function prediction for genome-wide analyses. The code for SIFTER and protein family data are available at http://sifter.berkeley.edu.
- Published
- 2011
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107. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans.
- Author
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Brooks AN, Aspden JL, Podgornaia AI, Rio DC, and Brenner SE
- Subjects
- Animals, Base Sequence, Drosophila melanogaster genetics, Exons, Introns, Drosophila melanogaster metabolism, Evolution, Molecular, RNA Splicing
- Abstract
RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5' and 3' splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes.
- Published
- 2011
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108. Design, synthesis, and evaluation of potent bryostatin analogs that modulate PKC translocation selectivity.
- Author
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Wender PA, Baryza JL, Brenner SE, DeChristopher BA, Loy BA, Schrier AJ, and Verma VA
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- Animals, Bryostatins chemical synthesis, Bryostatins chemistry, Bryostatins pharmacology, CHO Cells, Cricetinae, Cricetulus, Drug Delivery Systems methods, Humans, Isoenzymes antagonists & inhibitors, Isoenzymes genetics, Isoenzymes metabolism, Mice, NIH 3T3 Cells, Protein Kinase C genetics, Protein Transport drug effects, Protein Transport genetics, Drug Design, Protein Kinase C antagonists & inhibitors, Protein Kinase C metabolism, Protein Kinase Inhibitors chemical synthesis, Protein Kinase Inhibitors chemistry, Protein Kinase Inhibitors pharmacology
- Abstract
Modern methods for the identification of therapeutic leads include chemical or virtual screening of compound libraries. Nature's library represents a vast and diverse source of leads, often exhibiting exquisite biological activities. However, the advancement of natural product leads into the clinic is often impeded by their scarcity, complexity, and nonoptimal properties or efficacy as well as the challenges associated with their synthesis or modification. Function-oriented synthesis represents a strategy to address these issues through the design of simpler and therefore synthetically more accessible analogs that incorporate the activity-determining features of the natural product leads. This study illustrates the application of this strategy to the design and synthesis of functional analogs of the bryostatin marine natural products. It is specifically directed at exploring the activity-determining role of bryostatin A-ring functionality on PKC affinity and selectivity. The resultant functional analogs, which were prepared by a flexible, modular synthetic strategy, exhibit excellent affinity to PKC and differential isoform selectivity. These and related studies provide the basic information needed for the design of simplified and thus synthetically more accessible functional analogs that target PKC isoforms, major targets of therapeutic interest.
- Published
- 2011
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109. The developmental transcriptome of Drosophila melanogaster.
- Author
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Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, Lin W, Malone JH, Mattiuzzo NR, Miller D, Sturgill D, Tuch BB, Zaleski C, Zhang D, Blanchette M, Dudoit S, Eads B, Green RE, Hammonds A, Jiang L, Kapranov P, Langton L, Perrimon N, Sandler JE, Wan KH, Willingham A, Zhang Y, Zou Y, Andrews J, Bickel PJ, Brenner SE, Brent MR, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Oliver B, and Celniker SE
- Subjects
- Alternative Splicing genetics, Animals, Base Sequence, Drosophila Proteins genetics, Drosophila melanogaster embryology, Exons genetics, Female, Genes, Insect genetics, Genome, Insect genetics, Male, MicroRNAs genetics, Oligonucleotide Array Sequence Analysis, Protein Isoforms genetics, RNA Editing genetics, RNA, Messenger analysis, RNA, Messenger genetics, RNA, Small Untranslated analysis, RNA, Small Untranslated genetics, Sequence Analysis, Sex Characteristics, Drosophila melanogaster genetics, Drosophila melanogaster growth & development, Gene Expression Profiling, Gene Expression Regulation, Developmental genetics, Transcription, Genetic genetics
- Abstract
Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.
- Published
- 2011
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110. An SF1 affinity model to identify branch point sequences in human introns.
- Author
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Pastuszak AW, Joachimiak MP, Blanchette M, Rio DC, Brenner SE, and Frankel AD
- Subjects
- Base Sequence, Binding Sites, Humans, RNA Splicing Factors, RNA, Messenger chemistry, Sequence Analysis, RNA, DNA-Binding Proteins metabolism, Introns, Models, Genetic, Transcription Factors metabolism
- Abstract
Splicing factor 1 (SF1) binds to the branch point sequence (BPS) of mammalian introns and is believed to be important for the splicing of some, but not all, introns. To help identify BPSs, particularly those that depend on SF1, we generated a BPS profile model in which SF1 binding affinity data, validated by branch point mapping, were iteratively incorporated into computational models. We searched a data set of 117,499 human introns for best matches to the SF1 Affinity Model above a threshold, and counted the number of matches at each intronic position. After subtracting a background value, we found that 87.9% of remaining high-scoring matches identified were located in a region upstream of 3'-splice sites where BPSs are typically found. Since U2AF65 recognizes the polypyrimidine tract (PPT) and forms a cooperative RNA complex with SF1, we combined the SF1 model with a PPT model computed from high affinity binding sequences for U2AF65. The combined model, together with binding site location constraints, accurately identified introns bound by SF1 that are candidates for SF1-dependent splicing.
- Published
- 2011
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111. Conservation of an RNA regulatory map between Drosophila and mammals.
- Author
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Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, and Graveley BR
- Subjects
- Alternative Splicing, Animals, Antigens, Neoplasm genetics, Cells, Cultured, Computational Biology, Conserved Sequence genetics, Drosophila Proteins genetics, Exons, Gene Expression Profiling, Introns, Molecular Sequence Data, Nerve Tissue Proteins genetics, Neuro-Oncological Ventral Antigen, RNA Interference, RNA Precursors genetics, RNA Precursors metabolism, RNA, Messenger genetics, RNA-Binding Proteins genetics, Ribonucleoproteins genetics, Drosophila genetics, Mammals genetics, RNA, Messenger metabolism
- Abstract
Alternative splicing is generally controlled by proteins that bind directly to regulatory sequence elements and either activate or repress splicing of adjacent splice sites in a target pre-mRNA. Here, we have combined RNAi and mRNA-seq to identify exons that are regulated by Pasilla (PS), the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2. We identified 405 splicing events in 323 genes that are significantly affected upon depletion of ps, many of which were annotated as being constitutively spliced. The sequence regions upstream and within PS-repressed exons and downstream from PS-activated exons are enriched for YCAY repeats, and these are consistent with the location of these motifs near NOVA-regulated exons in mammals. Thus, the RNA regulatory map of PS and NOVA1/2 is highly conserved between insects and mammals despite the fact that the target gene orthologs regulated by PS and NOVA1/2 are almost entirely nonoverlapping. This observation suggests that the regulatory codes of individual RNA binding proteins may be nearly immutable, yet the regulatory modules controlled by these proteins are highly evolvable.
- Published
- 2011
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112. Identification of functional elements and regulatory circuits by Drosophila modENCODE.
- Author
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Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, and Kellis M
- Subjects
- Animals, Binding Sites, Computational Biology methods, Drosophila Proteins genetics, Drosophila Proteins metabolism, Drosophila melanogaster growth & development, Drosophila melanogaster metabolism, Epigenesis, Genetic, Gene Expression Regulation, Genes, Insect, Genomics methods, Histones metabolism, Nucleosomes genetics, Nucleosomes metabolism, Promoter Regions, Genetic, RNA, Small Untranslated genetics, RNA, Small Untranslated metabolism, Transcription Factors metabolism, Transcription, Genetic, Chromatin genetics, Chromatin metabolism, Drosophila melanogaster genetics, Gene Regulatory Networks, Genome, Insect, Molecular Sequence Annotation
- Abstract
To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
- Published
- 2010
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113. Biases in Illumina transcriptome sequencing caused by random hexamer priming.
- Author
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Hansen KD, Brenner SE, and Dudoit S
- Subjects
- Nucleotides analysis, DNA Primers, Gene Expression Profiling, Sequence Analysis, DNA
- Abstract
Generation of cDNA using random hexamer priming induces biases in the nucleotide composition at the beginning of transcriptome sequencing reads from the Illumina Genome Analyzer. The bias is independent of organism and laboratory and impacts the uniformity of the reads along the transcriptome. We provide a read count reweighting scheme, based on the nucleotide frequencies of the reads, that mitigates the impact of the bias.
- Published
- 2010
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114. Alignment-free local structural search by writhe decomposition.
- Author
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Zhi D, Shatsky M, and Brenner SE
- Subjects
- Algorithms, Computer Simulation, Databases, Factual, Databases, Protein, Models, Statistical, Molecular Conformation, Probability, Protein Structure, Secondary, Proteins chemistry, Reproducibility of Results, Sequence Alignment methods, Computational Biology methods, Sequence Analysis, Protein methods
- Abstract
Motivation: Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residue-level structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities., Results: We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizing scop domains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test., Availability: The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/.
- Published
- 2010
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115. Automated multi-model reconstruction from single-particle electron microscopy data.
- Author
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Shatsky M, Hall RJ, Nogales E, Malik J, and Brenner SE
- Subjects
- Eukaryotic Initiation Factor-3 chemistry, RNA Polymerase II chemistry, Ribosomes chemistry, Algorithms, Chemistry Techniques, Analytical methods, Image Processing, Computer-Assisted methods, Macromolecular Substances chemistry, Microscopy, Electron methods, Models, Molecular
- Abstract
Biological macromolecules can adopt multiple conformational and compositional states due to structural flexibility and alternative subunit assemblies. This structural heterogeneity poses a major challenge in the study of macromolecular structure using single-particle electron microscopy. We propose a fully automated, unsupervised method for the three-dimensional reconstruction of multiple structural models from heterogeneous data. As a starting reference, our method employs an initial structure that does not account for any heterogeneity. Then, a multi-stage clustering is used to create multiple models representative of the heterogeneity within the sample. The multi-stage clustering combines an existing approach based on Multivariate Statistical Analysis to perform clustering within individual Euler angles, and a newly developed approach to sort out class averages from individual Euler angles into homogeneous groups. Structural models are computed from individual clusters. The whole data classification is further refined using an iterative multi-model projection-matching approach. We tested our method on one synthetic and three distinct experimental datasets. The tests include the cases where a macromolecular complex exhibits structural flexibility and cases where a molecule is found in ligand-bound and unbound states. We propose the use of our approach as an efficient way to reconstruct distinct multiple models from heterogeneous data., ((c) 2010 Elsevier Inc. All rights reserved.)
- Published
- 2010
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116. A new organocatalyzed Michael-Michael cascade reaction generates highly substituted fused carbocycles.
- Author
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McGarraugh PG and Brenner SE
- Subjects
- Catalysis, Cyclization, Cyclobutanes, Molecular Structure, Polycyclic Aromatic Hydrocarbons chemistry, Stereoisomerism, Combinatorial Chemistry Techniques, Ketones chemistry, Polycyclic Aromatic Hydrocarbons chemical synthesis
- Abstract
While beta-ketoesters are useful Michael donors, they were previously ineffective in Michael-Michael cascade reactions using alpha,beta-unsaturated aldehydes in conjunction with diphenylprolinol silyl ether organocatalysts. However, through rational modification of substrates and manipulation of the catalytic cycle, we developed an efficient Michael-Michael cascade reaction using beta-ketoesters of type 9. In this transformation, highly substituted fused carbocycles are generated in a single step in up to 87% yield and 99% ee.
- Published
- 2009
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117. Survey of large protein complexes in D. vulgaris reveals great structural diversity.
- Author
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Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing KH, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, and Glaeser RM
- Subjects
- Bacterial Proteins isolation & purification, Crystallography, X-Ray, Databases, Protein, Desulfovibrio vulgaris chemistry, Models, Molecular, Multiprotein Complexes chemistry, Multiprotein Complexes metabolism, Protein Conformation, Bacterial Proteins chemistry, Desulfovibrio vulgaris metabolism
- Abstract
An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr approximately 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate approximately 10 times greater than that of previous "proteomic" screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.
- Published
- 2009
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118. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.
- Author
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Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, and Brenner SE
- Subjects
- Animals, Codon, Nonsense, Drosophila chemistry, Drosophila metabolism, RNA, Messenger genetics, RNA, Messenger metabolism, Untranslated Regions, Alternative Splicing, Down-Regulation, Drosophila genetics, Genome, Insect, RNA Stability, RNA, Messenger chemistry
- Abstract
Alternative mRNA splicing adds a layer of regulation to the expression of thousands of genes in Drosophila melanogaster. Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are degraded by the nonsense-mediated mRNA decay (NMD) pathway. This coupling of alternative splicing and NMD provides a mechanism for gene regulation that is highly conserved in mammals. NMD is also active in Drosophila, but its effect on the repertoire of alternative splice forms has been unknown, as has the mechanism by which it recognizes targets. Here, we have employed a custom splicing-sensitive microarray to globally measure the effect of alternative mRNA processing and NMD on Drosophila gene expression. We have developed a new algorithm to infer the expression change of each mRNA isoform of a gene based on the microarray measurements. This method is of general utility for interpreting splicing-sensitive microarrays and high-throughput sequence data. Using this approach, we have identified a high-confidence set of 45 genes where NMD has a differential effect on distinct alternative isoforms, including numerous RNA-binding and ribosomal proteins. Coupled alternative splicing and NMD decrease expression of these genes, which may in turn have a downstream effect on expression of other genes. The NMD-affected genes are enriched for roles in translation and mitosis, perhaps underlying the previously observed role of NMD factors in cell cycle progression. Our results have general implications for understanding the NMD mechanism in fly. Most notably, we found that the NMD-target mRNAs had significantly longer 3' untranslated regions (UTRs) than the nontarget isoforms of the same genes, supporting a role for 3' UTR length in the recognition of NMD targets in fly., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2009
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119. Planning the human variome project: the Spain report.
- Author
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Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD, Bapat B, Bernstein IT, Bhak J, Bleoo SL, Blöcker H, Brenner SE, Burn J, Bustamante M, Calzone R, Cambon-Thomsen A, Cargill M, Carrera P, Cavedon L, Cho YS, Chung YJ, Claustres M, Cutting G, Dalgleish R, den Dunnen JT, Díaz C, Dobrowolski S, dos Santos MR, Ekong R, Flanagan SB, Flicek P, Furukawa Y, Genuardi M, Ghang H, Golubenko MV, Greenblatt MS, Hamosh A, Hancock JM, Hardison R, Harrison TM, Hoffmann R, Horaitis R, Howard HJ, Barash CI, Izagirre N, Jung J, Kojima T, Laradi S, Lee YS, Lee JY, Gil-da-Silva-Lopes VL, Macrae FA, Maglott D, Marafie MJ, Marsh SG, Matsubara Y, Messiaen LM, Möslein G, Netea MG, Norton ML, Oefner PJ, Oetting WS, O'Leary JC, de Ramirez AM, Paalman MH, Parboosingh J, Patrinos GP, Perozzi G, Phillips IR, Povey S, Prasad S, Qi M, Quin DJ, Ramesar RS, Richards CS, Savige J, Scheible DG, Scott RJ, Seminara D, Shephard EA, Sijmons RH, Smith TD, Sobrido MJ, Tanaka T, Tavtigian SV, Taylor GR, Teague J, Töpel T, Ullman-Cullere M, Utsunomiya J, van Kranen HJ, Vihinen M, Webb E, Weber TK, Yeager M, Yeom YI, Yim SH, and Yoo HS
- Subjects
- Computational Biology methods, Computational Biology standards, Genetic Predisposition to Disease, Genotype, Humans, Information Dissemination, Mutation, Phenotype, Polymorphism, Genetic, Spain, Databases, Genetic, Genetic Variation, Genome, Human genetics
- Abstract
The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008., ((c) 2009 Wiley-Liss, Inc.)
- Published
- 2009
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120. A method for the alignment of heterogeneous macromolecules from electron microscopy.
- Author
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Shatsky M, Hall RJ, Brenner SE, and Glaeser RM
- Subjects
- Cryoelectron Microscopy methods, DNA Polymerase I ultrastructure, Eukaryotic Initiation Factor-3 ultrastructure, Fourier Analysis, Humans, Imaging, Three-Dimensional methods, RNA, Messenger ultrastructure, RNA-Binding Proteins ultrastructure, Research Design, Ribosome Subunits, Large, Bacterial ultrastructure, Ribosomes ultrastructure, Algorithms, Image Processing, Computer-Assisted methods, Macromolecular Substances, Microscopy, Electron methods
- Abstract
We propose a feature-based image alignment method for single-particle electron microscopy that is able to accommodate various similarity scoring functions while efficiently sampling the two-dimensional transformational space. We use this image alignment method to evaluate the performance of a scoring function that is based on the Mutual Information (MI) of two images rather than one that is based on the cross-correlation function. We show that alignment using MI for the scoring function has far less model-dependent bias than is found with cross-correlation based alignment. We also demonstrate that MI improves the alignment of some types of heterogeneous data, provided that the signal-to-noise ratio is relatively high. These results indicate, therefore, that use of MI as the scoring function is well suited for the alignment of class-averages computed from single-particle images. Our method is tested on data from three model structures and one real dataset.
- Published
- 2009
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121. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members.
- Author
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Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, and Rio DC
- Subjects
- Animals, Base Sequence, Binding Sites, Cells, Cultured, Drosophila metabolism, Molecular Sequence Data, RNA Precursors genetics, Alternative Splicing genetics, Drosophila genetics, Genome, Insect, Heterogeneous-Nuclear Ribonucleoprotein Group A-B genetics, Heterogeneous-Nuclear Ribonucleoprotein Group A-B metabolism, RNA Precursors metabolism, RNA, Messenger metabolism
- Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) have been traditionally seen as proteins packaging RNA nonspecifically into ribonucleoprotein particles (RNPs), but evidence suggests specific cellular functions on discrete target pre-mRNAs. Here we report genome-wide analysis of alternative splicing patterns regulated by four Drosophila homologs of the mammalian hnRNP A/B family (hrp36, hrp38, hrp40, and hrp48). Analysis of the global RNA-binding distributions of each protein revealed both small and extensively bound regions on target transcripts. A significant subset of RNAs were bound and regulated by more than one hnRNP protein, revealing a combinatorial network of interactions. In vitro RNA-binding site selection experiments (SELEX) identified distinct binding motif specificities for each protein, which were overrepresented in their respective regulated and bound transcripts. These results indicate that individual heterogeneous ribonucleoproteins have specific affinities for overlapping, but distinct, populations of target pre-mRNAs controlling their patterns of RNA processing.
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- 2009
- Full Text
- View/download PDF
122. Outcome of a workshop on applications of protein models in biomedical research.
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Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL Jr, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR Jr, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, and Wilson IA
- Subjects
- Animals, Biomedical Research trends, Chemistry, Pharmaceutical methods, Databases, Protein, Drug Discovery methods, Enzymes chemistry, Health Planning Guidelines, Humans, Protein Conformation, Protein Engineering methods, Protein Interaction Mapping methods, Software, Biomedical Research methods, Models, Molecular, Proteins chemistry
- Abstract
We describe the proceedings and conclusions from the "Workshop on Applications of Protein Models in Biomedical Research" (the Workshop) that was held at the University of California, San Francisco on 11 and 12 July, 2008. At the Workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) the requirements and challenges for different applications, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.
- Published
- 2009
- Full Text
- View/download PDF
123. Novel bifunctional sulfonamides catalyze an enantioselective conjugate addition.
- Author
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McGarraugh PG and Brenner SE
- Abstract
A new bifunctional organocatalyst with a novel structural and functional motif has been developed. This bifunctional sulfonamide organocatalyst was used in the conjugate addition of 1,3-dicarbonyl compounds (13) to β-nitrostyrenes (12). Yields up to 91% and enantiomeric excesses up to 79% were obtained in this reaction. This catalyst activates both 13 via its basic moiety and 12 through hydrogen bonding.
- Published
- 2009
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- View/download PDF
124. Phylogenetic molecular function annotation.
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Engelhardt BE, Jordan MI, Repo ST, and Brenner SE
- Abstract
It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called "phylogenomics") is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.
- Published
- 2009
- Full Text
- View/download PDF
125. Data growth and its impact on the SCOP database: new developments.
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Andreeva A, Howorth D, Chandonia JM, Brenner SE, Hubbard TJ, Chothia C, and Murzin AG
- Subjects
- Evolution, Molecular, Genomics, Internet, Proteins genetics, Databases, Protein trends, Protein Structure, Tertiary, Proteins classification
- Abstract
The Structural Classification of Proteins (SCOP) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. The SCOP hierarchy comprises the following levels: Species, Protein, Family, Superfamily, Fold and Class. While keeping the original classification scheme intact, we have changed the production of SCOP in order to cope with a rapid growth of new structural data and to facilitate the discovery of new protein relationships. We describe ongoing developments and new features implemented in SCOP. A new update protocol supports batch classification of new protein structures by their detected relationships at Family and Superfamily levels in contrast to our previous sequential handling of new structural data by release date. We introduce pre-SCOP, a preview of the SCOP developmental version that enables earlier access to the information on new relationships. We also discuss the impact of worldwide Structural Genomics initiatives, which are producing new protein structures at an increasing rate, on the rates of discovery and growth of protein families and superfamilies. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
- Published
- 2008
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126. Common sense for our genomes.
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Brenner SE
- Subjects
- Databases, Genetic, Genetic Predisposition to Disease genetics, Genetic Variation genetics, Genomics economics, Humans, Male, Preventive Medicine trends, Genome, Human genetics, Genomics trends
- Published
- 2007
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127. Developing computational biology.
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Bourne PE and Brenner SE
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- United States, Computational Biology trends, Information Dissemination methods, Periodicals as Topic trends
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- 2007
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- View/download PDF
128. Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements.
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Lareau LF, Inada M, Green RE, Wengrod JC, and Brenner SE
- Subjects
- Animals, Exons genetics, Humans, Introns genetics, Mice, RNA Stability, RNA, Messenger genetics, RNA, Messenger metabolism, RNA-Binding Proteins classification, Alternative Splicing genetics, Conserved Sequence genetics, DNA genetics, RNA-Binding Proteins genetics
- Abstract
The human and mouse genomes share a number of long, perfectly conserved nucleotide sequences, termed ultraconserved elements. Whereas these regions can act as transcriptional enhancers when upstream of genes, those within genes are less well understood. In particular, the function of ultraconserved elements that overlap alternatively spliced exons of genes encoding RNA-binding proteins is unknown. Here we report that in every member of the human SR family of splicing regulators, highly or ultraconserved elements are alternatively spliced, either as alternative 'poison cassette exons' containing early in-frame stop codons, or as alternative introns in the 3' untranslated region. These alternative splicing events target the resulting messenger RNAs for degradation by means of an RNA surveillance pathway called nonsense-mediated mRNA decay. Mouse orthologues of the human SR proteins exhibit the same unproductive splicing patterns. Three SR proteins have been previously shown to direct splicing of their own transcripts, and one of these is known to autoregulate its expression by coupling alternative splicing with decay; our results suggest that unproductive splicing is important for regulation of the entire SR family. We find that unproductive splicing associated with conserved regions has arisen independently in different SR genes, suggesting that splicing factors may readily acquire this form of regulation.
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- 2007
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129. The coupling of alternative splicing and nonsense-mediated mRNA decay.
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Lareau LF, Brooks AN, Soergel DA, Meng Q, and Brenner SE
- Subjects
- Animals, Humans, Alternative Splicing physiology, Codon, Nonsense genetics, RNA Stability
- Abstract
Most human genes exhibit alternative splicing, but not all alternatively spliced transcripts produce functional proteins. Computational and experimental results indicate that a substantial fraction of alternative splicing events in humans result in mRNA isoforms that harbor a premature termination codon (PTC). These transcripts are predicted to be degraded by the nonsense-mediated mRNA decay (NMD) pathway. One explanation for the abundance of PTC-containing isoforms is that they represent splicing errors that are identified and degraded by the NMD pathway. Another potential explanation for this startling observation is that cells may link alternative splicing and NMD to regulate the abundance of mRNA transcripts. This mechanism, which we call "Regulated Unproductive Splicing and Translation" (RUST), has been experimentally shown to regulate expression of a wide variety of genes in many organisms from yeast to human. It is frequently employed for autoregulation of proteins that affect the splicing process itself. Thus, alternative splicing and NMD act together to play an important role in regulating gene expression.
- Published
- 2007
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- View/download PDF
130. An efficient, asymmetric organocatalyst-mediated conjugate addition of nitroalkanes to unsaturated cyclic and acyclic ketones.
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Mitchell CE, Brenner SE, García-Fortanet J, and Ley SV
- Subjects
- Catalysis, Ketones chemistry, Nitro Compounds chemistry
- Abstract
5-Pyrrolidin-2-yltetrazole is a versatile organocatalyst for the asymmetric conjugate addition of nitroalkanes to enones. Using this catalyst, this transformation requires short reaction times, tolerates a broad substrate scope, and possibly proceeds via generation of an iminium species.
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- 2006
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- View/download PDF
131. The RNA Ontology Consortium: an open invitation to the RNA community.
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Leontis NB, Altman RB, Berman HM, Brenner SE, Brown JW, Engelke DR, Harvey SC, Holbrook SR, Jossinet F, Lewis SE, Major F, Mathews DH, Richardson JS, Williamson JR, and Westhof E
- Subjects
- Databases, Genetic, Information Dissemination, Internet, Sequence Alignment, RNA, Societies
- Abstract
The aim of the RNA Ontology Consortium (ROC) is to create an integrated conceptual framework-an RNA Ontology (RO)-with a common, dynamic, controlled, and structured vocabulary to describe and characterize RNA sequences, secondary structures, three-dimensional structures, and dynamics pertaining to RNA function. The RO should produce tools for clear communication about RNA structure and function for multiple uses, including the integration of RNA electronic resources into the Semantic Web. These tools should allow the accurate description in computer-interpretable form of the coupling between RNA architecture, function, and evolution. The purposes for creating the RO are, therefore, (1) to integrate sequence and structural databases; (2) to allow different computational tools to interoperate; (3) to create powerful software tools that bring advanced computational methods to the bench scientist; and (4) to facilitate precise searches for all relevant information pertaining to RNA. For example, one initial objective of the ROC is to define, identify, and classify RNA structural motifs described in the literature or appearing in databases and to agree on a computer-interpretable definition for each of these motifs. To achieve these aims, the ROC will foster communication and promote collaboration among RNA scientists by coordinating frequent face-to-face workshops to discuss, debate, and resolve difficult conceptual issues. These meeting opportunities will create new directions at various levels of RNA research. The ROC will work closely with the PDB/NDB structural databases and the Gene, Sequence, and Open Biomedical Ontology Consortia to integrate the RO with existing biological ontologies to extend existing content while maintaining interoperability.
- Published
- 2006
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132. ANDY: a general, fault-tolerant tool for database searching on computer clusters.
- Author
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Smith A, Chandonia JM, and Brenner SE
- Subjects
- Computing Methodologies, Database Management Systems, Databases, Genetic, Information Storage and Retrieval methods, Internet, Online Systems, Sequence Alignment methods, Sequence Analysis methods
- Abstract
Summary: ANDY (seArch coordination aND analYsis) is a set of Perl programs and modules for distributing large biological database searches, and in general any sequence of commands, across the nodes of a Linux computer cluster. ANDY is compatible with several commonly used distributed resource management (DRM) systems, and it can be easily extended to new DRMs. A distinctive feature of ANDY is the choice of either dedicated or fair-use operation: ANDY is almost as efficient as single-purpose tools that require a dedicated cluster, but it runs on a general-purpose cluster along with any other jobs scheduled by a DRM. Other features include communication through named pipes for performance, flexible customizable routines for error-checking and summarizing results, and multiple fault-tolerance mechanisms., Availability: ANDY is freely available and can be obtained from http://compbio.berkeley.edu/proj/andy., Supplementary Information: Supplemental data, figures, and a more detailed overview of the software are found at http://compbio.berkeley.edu/proj/andy.
- Published
- 2006
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- View/download PDF
133. Target selection and deselection at the Berkeley Structural Genomics Center.
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Chandonia JM, Kim SH, and Brenner SE
- Subjects
- Amino Acids analysis, Bacterial Proteins genetics, California, Codon genetics, Models, Molecular, Protein Conformation, Bacterial Proteins chemistry, Genome, Bacterial, Genomics methods, Mycoplasma genitalium genetics, Mycoplasma pneumoniae genetics
- Abstract
At the Berkeley Structural Genomics Center (BSGC), our goal is to obtain a near-complete structural complement of proteins in the minimal organisms Mycoplasma genitalium and M. pneumoniae, two closely related pathogens. Current targets for structure determination have been selected in six major stages, starting with those predicted to be most tractable to high throughput study and likely to yield new structural information. We report on the process used to select these proteins, as well as our target deselection procedure. Target deselection reduces experimental effort by eliminating targets similar to those recently solved by the structural biology community or other centers. We measure the impact of the 69 structures solved at the BSGC as of July 2004 on structure prediction coverage of the M. pneumoniae and M. genitalium proteomes. The number of Mycoplasma proteins for which the fold could first be reliably assigned based on structures solved at the BSGC (24 M. pneumoniae and 21 M. genitalium) is approximately 25% of the total resulting from work at all structural genomics centers and the worldwide structural biology community (94 M. pneumoniae and 86 M. genitalium) during the same period. As the number of structures contributed by the BSGC during that period is less than 1% of the total worldwide output, the benefits of a focused target selection strategy are apparent. If the structures of all current targets were solved, the percentage of M. pneumoniae proteins for which folds could be reliably assigned would increase from approximately 57% (391 of 687) at present to around 80% (550 of 687), and the percentage of the proteome that could be accurately modeled would increase from around 37% (254 of 687) to about 64% (438 of 687). In M. genitalium, the percentage of the proteome that could be structurally annotated based on structures of our remaining targets would rise from 72% (348 of 486) to around 76% (371 of 486), with the percentage of accurately modeled proteins would rise from 50% (243 of 486) to 58% (283 of 486). Sequences and data on experimental progress on our targets are available in the public databases TargetDB and PEPCdb., (2005 Wiley-Liss, Inc.)
- Published
- 2006
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- View/download PDF
134. The impact of structural genomics: expectations and outcomes.
- Author
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Chandonia JM and Brenner SE
- Subjects
- Amino Acid Sequence, Costs and Cost Analysis, Databases, Protein, Financial Support, Protein Folding, Proteins classification, Publishing, Computational Biology, Genomics economics, Protein Conformation, Proteins chemistry
- Abstract
Structural genomics (SG) projects aim to expand our structural knowledge of biological macromolecules while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and we contrast these results with traditional structural biology. The first structure identified in a protein family enables inference of the fold and of ancient relationships to other proteins; in the year ending 31 January 2005, about half of such structures were solved at a SG center rather than in a traditional laboratory. Furthermore, the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories-even though they work on very challenging structures-is comparable to that of SG centers; moreover, traditional structural biology papers are cited significantly more often, suggesting greater current impact.
- Published
- 2006
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- View/download PDF
135. MeRNA: a database of metal ion binding sites in RNA structures.
- Author
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Stefan LR, Zhang R, Levitan AG, Hendrix DK, Brenner SE, and Holbrook SR
- Subjects
- Binding Sites, Internet, Ions chemistry, Metals metabolism, Nucleic Acid Conformation, RNA metabolism, User-Computer Interface, Databases, Nucleic Acid, Metals chemistry, Models, Molecular, RNA chemistry
- Abstract
Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA 3D structures available from the PDB and Nucleic Acid Database. Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements, in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering. The MeRNA database is accessible at http://merna.lbl.gov.
- Published
- 2006
- Full Text
- View/download PDF
136. A versatile organocatalyst for the asymmetric conjugate addition of nitroalkanes to enones.
- Author
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Mitchell CE, Brenner SE, and Ley SV
- Abstract
5-Pyrrolidin-2-yltetrazole performs as an improved catalyst for the asymmetric addition of a range of nitroalkanes to cyclic and acyclic enones, with good to excellent enantioselectivity.
- Published
- 2005
- Full Text
- View/download PDF
137. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.
- Author
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Price GA, Crooks GE, Green RE, and Brenner SE
- Subjects
- Amino Acid Sequence, Bayes Theorem, Data Interpretation, Statistical, Models, Statistical, Molecular Sequence Data, Proteins analysis, Algorithms, Models, Molecular, Proteins chemistry, Sequence Alignment methods, Sequence Analysis, Protein methods
- Abstract
Motivation: Protein sequence comparison methods are routinely used to infer the intricate network of evolutionary relationships found within the rapidly growing library of protein sequences, and thereby to predict the structure and function of uncharacterized proteins. In the present study, we detail an improved statistical benchmark of pairwise protein sequence comparison algorithms. We use bootstrap resampling techniques to determine standard statistical errors and to estimate the confidence of our conclusions. We show that the underlying structure within benchmark databases causes Efron's standard, non-parametric bootstrap to be biased. Consequently, the standard bootstrap underpredicts average performance when used in the context of evaluating sequence comparison methods. We have developed, as an alternative, an unbiased statistical evaluation based on the Bayesian bootstrap, a resampling method operationally similar to the standard bootstrap., Results: We apply our analysis to the comparative study of amino acid substitution matrix families and find that using modern matrices results in a small, but statistically significant improvement in remote homology detection compared with the classic PAM and BLOSUM matrices., Availability: The sequence sets and code for performing these analyses are available from http://compbio.berkeley.edu/., Contact: brenner@compbio.berkeley.edu.
- Published
- 2005
- Full Text
- View/download PDF
138. Pairwise alignment incorporating dipeptide covariation.
- Author
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Crooks GE, Green RE, and Brenner SE
- Subjects
- Amino Acid Sequence, Dipeptides analysis, Molecular Sequence Data, Proteins analysis, Algorithms, Dipeptides chemistry, Proteins chemistry, Sequence Alignment methods, Sequence Analysis, Protein methods, Software
- Abstract
Motivation: Standard algorithms for pairwise protein sequence alignment make the simplifying assumption that amino acid substitutions at neighboring sites are uncorrelated. This assumption allows implementation of fast algorithms for pairwise sequence alignment, but it ignores information that could conceivably increase the power of remote homolog detection. We examine the validity of this assumption by constructing extended substitution matrices that encapsulate the observed correlations between neighboring sites, by developing an efficient and rigorous algorithm for pairwise protein sequence alignment that incorporates these local substitution correlations and by assessing the ability of this algorithm to detect remote homologies., Results: Our analysis indicates that local correlations between substitutions are not strong on the average. Furthermore, incorporating local substitution correlations into pairwise alignment did not lead to a statistically significant improvement in remote homology detection. Therefore, the standard assumption that individual residues within protein sequences evolve independently of neighboring positions appears to be an efficient and appropriate approximation.
- Published
- 2005
- Full Text
- View/download PDF
139. Protein molecular function prediction by Bayesian phylogenomics.
- Author
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Engelhardt BE, Jordan MI, Muratore KE, and Brenner SE
- Subjects
- Adenosine Deaminase chemistry, Algorithms, Animals, Computer Graphics, Databases, Protein, Phylogeny, Plasmodium falciparum metabolism, Programming Languages, Sequence Alignment, Sequence Analysis, Protein, Software, Computational Biology methods, Genomics methods, Proteins chemistry, Proteomics methods
- Abstract
We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5'-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors.
- Published
- 2005
- Full Text
- View/download PDF
140. The transcriptional landscape of the mammalian genome.
- Author
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Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schönbach C, Sekiguchi K, Semple CA, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, and Hayashizaki Y
- Subjects
- 3' Untranslated Regions, Animals, Base Sequence, Conserved Sequence, DNA, Complementary chemistry, Genome, Human, Genomics, Humans, Promoter Regions, Genetic, Proteins genetics, RNA chemistry, RNA classification, RNA Splicing, RNA, Untranslated chemistry, Regulatory Sequences, Ribonucleic Acid, Genome, Mice genetics, Terminator Regions, Genetic, Transcription Initiation Site, Transcription, Genetic
- Abstract
This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
- Published
- 2005
- Full Text
- View/download PDF
141. RNA structural motifs: building blocks of a modular biomolecule.
- Author
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Hendrix DK, Brenner SE, and Holbrook SR
- Subjects
- Base Sequence, Conserved Sequence, Humans, Models, Genetic, Molecular Sequence Data, Nucleic Acid Conformation, Sequence Homology, Nucleic Acid, Structure-Activity Relationship, Models, Chemical, Models, Molecular, RNA chemistry, RNA genetics, Sequence Analysis, RNA methods
- Abstract
RNAs are modular biomolecules, composed largely of conserved structural subunits, or motifs. These structural motifs comprise the secondary structure of RNA and are knit together via tertiary interactions into a compact, functional, three-dimensional structure and are to be distinguished from motifs defined by sequence or function. A relatively small number of structural motifs are found repeatedly in RNA hairpin and internal loops, and are observed to be composed of a limited number of common 'structural elements'. In addition to secondary and tertiary structure motifs, there are functional motifs specific for certain biological roles and binding motifs that serve to complex metals or other ligands. Research is continuing into the identification and classification of RNA structural motifs and is being initiated to predict motifs from sequence, to trace their phylogenetic relationships and to use them as building blocks in RNA engineering.
- Published
- 2005
- Full Text
- View/download PDF
142. Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila.
- Author
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Blanchette M, Green RE, Brenner SE, and Rio DC
- Subjects
- Animals, Binding Sites, RNA Precursors genetics, RNA, Messenger genetics, Reverse Transcriptase Polymerase Chain Reaction, Drosophila melanogaster genetics, RNA Precursors metabolism, RNA Splicing, RNA, Messenger metabolism
- Abstract
To gain insight into splicing regulation, we developed a microarray to assay all annotated alternative splicing events in Drosophila melanogaster and identified the alternative splice events controlled by four splicing regulators: dASF/SF2, B52/SRp55, hrp48, and PSI. The number of events controlled by each of these factors was found to be highly variable: dASF/SF2 strongly affects >300 splicing events, whereas PSI strongly affects only 43 events. Pairwise analysis also revealed many instances of splice site usage affected by multiple factors and provides the framework to understand the network controlling the alternatively spliced mRNA isoforms that compose the Drosophila transcriptome.
- Published
- 2005
- Full Text
- View/download PDF
143. PLoS Computational Biology: a new community journal.
- Author
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Bourne PE, Brenner SE, and Eisen MB
- Subjects
- Computational Biology, Periodicals as Topic
- Published
- 2005
- Full Text
- View/download PDF
144. An alternative model of amino acid replacement.
- Author
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Crooks GE and Brenner SE
- Subjects
- Amino Acid Sequence, Amino Acid Substitution, Computer Simulation, Markov Chains, Models, Statistical, Molecular Sequence Data, Phylogeny, Sequence Homology, Amino Acid, Algorithms, Evolution, Molecular, Models, Chemical, Models, Genetic, Sequence Alignment methods, Sequence Analysis, Protein methods
- Abstract
Motivation: The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein amino acid profiles and with the success of profile multiple sequence alignment., Results: We propose an alternative model of amino acid replacement during protein evolution based upon the assumption that the variation of the amino acid background distribution from one residue to the next is sufficient to explain the observed sequence correlations of homologs. The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile and profile-profile alignment.
- Published
- 2005
- Full Text
- View/download PDF
145. A generalized affine gap model significantly improves protein sequence alignment accuracy.
- Author
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Zachariah MA, Crooks GE, Holbrook SR, and Brenner SE
- Subjects
- Algorithms, Amino Acid Sequence, Databases, Protein, GTPase-Activating Proteins chemistry, Models, Biological, Models, Molecular, Models, Statistical, Molecular Sequence Data, Phylogeny, Protein Conformation, Reproducibility of Results, Sequence Homology, Amino Acid, Software, Computational Biology methods, Proteins chemistry, Proteomics methods, Sequence Alignment methods, Sequence Analysis, Protein methods
- Abstract
Sequence alignment underpins common tasks in molecular biology, including genome annotation, molecular phylogenetics, and homology modeling. Fundamental to sequence alignment is the placement of gaps, which represent character insertions or deletions. We assessed the ability of a generalized affine gap cost model to reliably detect remote protein homology and to produce high-quality alignments. Generalized affine gap alignment with optimal gap parameters performed as well as the traditional affine gap model in remote homology detection. Evaluation of alignment quality showed that the generalized affine model aligns fewer residue pairs than the traditional affine model but achieves significantly higher per-residue accuracy. We conclude that generalized affine gap costs should be used when alignment accuracy carries more importance than aligned sequence length., ((c) 2004 Wiley-Liss, Inc.)
- Published
- 2005
- Full Text
- View/download PDF
146. Structural genomics of minimal organisms and protein fold space.
- Author
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Kim SH, Shin DH, Liu J, Oganesyan V, Chen S, Xu QS, Kim JS, Das D, Schulze-Gahmen U, Holbrook SR, Holbrook EL, Martinez BA, Oganesyan N, DeGiovanni A, Lou Y, Henriquez M, Huang C, Jancarik J, Pufan R, Choi IG, Chandonia JM, Hou J, Gold B, Yokota H, Brenner SE, Adams PD, and Kim R
- Subjects
- Cloning, Molecular, Crystallization, Bacterial Proteins genetics, Genome, Bacterial genetics, Models, Molecular, Mycoplasma genitalium genetics, Mycoplasma pneumoniae genetics, Protein Folding, Proteomics methods
- Abstract
The initial aim of the Berkeley Structural Genomics Center is to obtain a near-complete structural complement of two minimal organisms, closely related pathogens Mycoplasma genitalium and M. pneumoniae. The former has fewer than 500 genes and the latter fewer than 700 genes. To achieve this goal, the current protein targets have been selected starting with those predicted to be most tractable and likely to yield new structural and functional information. During the past 3 years, the semi-automated structural genomics pipeline has been set up from cloning, expression, purification, and ultimately to structural determination. The results from the pipeline substantially increased the coverage of the protein fold space of M. pneumoniae and M. genitalium. Furthermore, about 1/2 of the structures of 'unique' protein sequences revealed new and novel folds, and over 2/3 of the structures of previously annotated 'hypothetical proteins' inferred their molecular functions.
- Published
- 2005
- Full Text
- View/download PDF
147. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches.
- Author
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Chandonia JM and Brenner SE
- Subjects
- Animals, Databases, Protein, Humans, Proteins genetics, Gene Targeting methods, Genome, Multigene Family, Proteins chemistry, Proteomics methods
- Abstract
Structural genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy that is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the "Pfam5000" strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These strategies include complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at the European Bioinformatics Institute (EBI). Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68% of all prokaryotic proteins (covering 59% of residues) and 61% of eukaryotic proteins (40% of residues). More fine-grained coverage that would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example, to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: A significant fraction (about 30-40% of the proteins and 40-60% of the residues) of each proteome is classified in small families, which may have little overlap with other species of interest. Random selection of targets from one or more genomes is similar to the Pfam5000 strategy in that proteins from larger families are more likely to be chosen, but substantial effort would be spent on small families.
- Published
- 2005
- Full Text
- View/download PDF
148. Synthetic bryostatin analogues activate the RasGRP1 signaling pathway.
- Author
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Stone JC, Stang SL, Zheng Y, Dower NA, Brenner SE, Baryza JL, and Wender PA
- Subjects
- Animals, Antigens, CD biosynthesis, Antigens, Differentiation, T-Lymphocyte biosynthesis, Bryostatins, Cell Aggregation drug effects, Cell Membrane metabolism, Cells, Cultured, DNA-Binding Proteins genetics, Extracellular Signal-Regulated MAP Kinases metabolism, Guanine Nucleotide Exchange Factors genetics, Humans, Immunologic Factors chemistry, Immunologic Factors pharmacology, Lactones chemistry, Lactones pharmacology, Lectins, C-Type, Macrolides, Mice, Mutation, Phosphorylation, Protein Kinase C physiology, Protein Transport drug effects, Signal Transduction drug effects, T-Lymphocytes drug effects, T-Lymphocytes metabolism, T-Lymphocytes physiology, Tetradecanoylphorbol Acetate pharmacology, Thymus Gland cytology, Transfection, DNA-Binding Proteins physiology, Guanine Nucleotide Exchange Factors physiology, Immunologic Factors chemical synthesis, Lactones chemical synthesis
- Abstract
The functional properties of four diacylglycerol (DAG) analogues were compared using cell-signaling assays based on the protein RasGRP1, a DAG-regulated Ras activator. Compounds 1 and 2, synthetic analogues of bryostatin 1, were compared to authentic bryostatin 1 and phorbol 12-myristate-13-acetate (PMA). The two "bryologues" were able to activate RasGRP1 signaling rapidly in cultured cells and isolated mouse thymocytes. They elicited expression of the T cell activation marker CD69 in human T cells. DAG analogues promptly recruited RasGRP1 to cell membranes, but they did not induce RasGRP1 proteolysis. Bryostatin 1 and compounds 1 and 2 appeared to be less potent than PMA at inducing aggregation of mouse thymocytes, a PKC-dependent, RasGRP1-independent response. In addition to sharing potential anticancer properties with bryostatin 1, compounds 1 and 2 might be clinically useful as modulators of the immune system.
- Published
- 2004
- Full Text
- View/download PDF
149. Measurements of protein sequence-structure correlations.
- Author
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Crooks GE, Wolfe J, and Brenner SE
- Subjects
- Amino Acid Sequence, Amino Acids chemistry, Likelihood Functions, Protein Conformation, Proteins chemistry, Proteins metabolism
- Abstract
Correlations between protein structures and amino acid sequences are widely used for protein structure prediction. For example, secondary structure predictors generally use correlations between a secondary structure sequence and corresponding primary structure sequence, whereas threading algorithms and similar tertiary structure predictors typically incorporate interresidue contact potentials. To investigate the relative importance of these sequence-structure interactions, we measured the mutual information among the primary structure, secondary structure and side-chain surface exposure, both for adjacent residues along the amino acid sequence and for tertiary structure contacts between residues distantly separated along the backbone. We found that local interactions along the amino acid chain are far more important than non-local contacts and that correlations between proximate amino acids are essentially uninformative. This suggests that knowledge-based contact potentials may be less important for structure predication than is generally believed., (Copyright 2004 Wiley-Liss, Inc.)
- Published
- 2004
- Full Text
- View/download PDF
150. Simplified analogs of bryostatin with anticancer activity display greater potency for translocation of PKCdelta-GFP.
- Author
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Baryza JL, Brenner SE, Craske ML, Meyer T, and Wender PA
- Subjects
- Animals, Antineoplastic Agents chemistry, Bryostatins, Cell Line, Tumor, Dose-Response Relationship, Drug, Endocytosis drug effects, Kinetics, Lactones chemistry, Macrolides, Microscopy, Confocal, Microscopy, Fluorescence, Molecular Structure, Rats, Structure-Activity Relationship, Antineoplastic Agents pharmacology, Green Fluorescent Proteins metabolism, Lactones pharmacology, Protein Kinase C metabolism, Recombinant Fusion Proteins metabolism
- Abstract
Structurally simplified analogs of bryostatin 1, a marine natural product in clinical trials for the treatment of cancer, have been shown to be up to 50 times more potent than bryostatin 1 at inducing the translocation of PKCdelta-GFP from the cytosol of rat basophilic leukemia (RBL) cells. The end distribution of the protein is similar for all three compounds, despite a significant difference in translocation kinetics. The potency of the compounds for inducing the translocation response appears to be only qualitatively related to their binding affinity for PKC, highlighting the importance of using binding affinity in conjunction with real-time measurements of protein localization for the pharmacological profiling of biologically active agents.
- Published
- 2004
- Full Text
- View/download PDF
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