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Protein structure alignment

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https://www.readbyqxmd.com/read/28098238/expression-of-the-novel-maternal-centrosome-assembly-factor-wdr8-is-required-for-vertebrate-embryonic-mitoses
#1
Daigo Inoue, Manuel Stemmer, Thomas Thumberger, Thomas Ruppert, Felix Bärenz, Joachim Wittbrodt, Oliver J Gruss
The assembly of the first centrosome occurs upon fertilisation when male centrioles recruit pericentriolar material (PCM) from the egg cytoplasm. The mechanisms underlying the proper assembly of centrosomes during early embryogenesis remain obscure. We identify Wdr8 as a novel maternally essential protein that is required for centrosome assembly during embryonic mitoses of medaka (Oryzias latipes). By CRISPR-Cas9-mediated knockout, maternal/zygotic Wdr8-null (m/zWdr8(-/-)) blastomeres exhibit severe defects in centrosome structure that lead to asymmetric division, multipolar mitotic spindles and chromosome alignment errors...
January 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28097887/pseudokinases-update-on-their-functions-and-evaluation-as-new-drug-targets
#2
Dominic P Byrne, Daniel M Foulkes, Patrick A Eyers
The pseudokinase complement of the human kinase superfamily consists of approximately 60 signaling proteins, which lacks one or more of the amino acids typically required to correctly align ATP and metal ions, and phosphorylate protein substrates. Recent studies in the pseudokinase field have begun to expose the biological relevance of pseudokinases, which are now thought to perform a diverse range of physiological roles and are connected to a multitude of human diseases, including cancer. In this review, we discuss how and why members of the 'pseudokinome' represent important new targets for drug discovery, and describe how knowledge of protein structure and function provides informative clues to help guide the rational chemical design or repurposing of inhibitors to target pseudokinases...
January 18, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28095443/morphologic-and-molecular-characterization-of-a-strain-of-zika-virus-imported-into-guangdong-china
#3
Shufen Li, Yongxia Shi, Kui Zheng, Jun Dai, Xiaobo Li, Shuai Yuan, Ling Chen, Jicheng Huang
The recent outbreaks of Zika virus (ZIKV) disease have caused worldwide concerns. Guangdong province is one of the commercial centers in China and communicates frequently with the epidemic areas. To date, 65.2% of the ZIKV infection cases in China were imported via port of entry in Guangdong. The continuous surveillance of imported cases is crucial for the prevention and control of potential ZIKV infection outbreak in China. In this study, a strain of ZIKV was isolated from the serum of a 6-year-old child returning from Venezuela...
2017: PloS One
https://www.readbyqxmd.com/read/28093407/protein-multiple-sequence-alignment-benchmarking-through-secondary-structure-prediction
#4
Quan Le, Fabian Sievers, Desmond G Higgins
MOTIVATION: Multiple sequence alignment (MSA) is commonly used to analyse sets of homologous protein or DNA sequences. This has lead to the development of many methods and packages forMSAover the past 30 years. Being able to compare different methods has been problematic and has relied on gold standard benchmark datasets of 'true' alignments or on MSA simulations. A number of protein benchmark datasets have been produced which rely on a combination of manual alignment and/or automated superposition of protein structures...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28093404/development-and-application-of-an-algorithm-to-compute-weighted-multiple-glycan-alignments
#5
Masae Hosoda, Yukie Akune, Kiyoko F Aoki-Kinoshita
MOTIVATION: A glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan binding proteins (GBPs). However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules...
January 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28093295/in-silico-enhancement-of-the-stability-and-activity-of-keratinocyte-growth-factor
#6
Mansour Poorebrahim, Solmaz Sadeghi, Raziyeh Ghorbani, Matin Asghari, Mohammad Foad Abazari, Hourieh Kalhor, Hamzeh Rahimi
Keratinocyte growth factor (KGF), a member of the fibroblast growth factor (FGF) family, has been implicated in some biological processes such as cell proliferation, development and differentiation. High mitogenic activity of this protein has made it very suitable for repairing radiation-and chemotherapy-induced damages. KGF, which has been developed from human KGF, is clinically applied to reduce the incidence and duration of cancer therapeutic agents. However, the activity of KGF is limited during treatment due to its poor stability...
January 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28093240/the-crystal-structure-of-pseudomonas-aeruginosa-lipoxygenase-ala420gly-mutant-explains-the-improved-oxygen-affinity-and-the-altered-reaction-specificity
#7
Jacqueline Kalms, Swathi Banthiya, Etienne Galemou Yoga, Mats Hamberg, Hermann-Georg Holzhutter, Hartmut Kuhn, Patrick Scheerer
Secreted LOX from Pseudomonas aeruginosa (PA-LOX) has previously been identified as arachidonic acid 15S-lipoxygenating enzyme. Here we report that the substitution of Ala420Gly in PA-LOX leads to an enzyme variant with pronounced dual specificity favoring arachidonic acid 11R-oxygenation. When compared with other LOX-isoforms the oxygen affinity of wild-type PA-LOX is 1-2 orders of magnitude lower (oxygen Km of 0.4mM) but Ala420Gly exchange improved the oxygen affinity (oxygen Km of 0.2mM). Experiments with stereo-specifically deuterated linoleic acid indicated that the formation of both 13S- and 9R-HpODE involves abstraction of the proS-hydrogen from C11 of the fatty acid backbone...
January 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28089379/characterization-of-a-novel-dyp-type-peroxidase-from-streptomyces-avermitilis
#8
Kanako Sugawara, Yuriko Nishihashi, Tomomi Narioka, Toru Yoshida, Mifumi Morita, Yasushi Sugano
DyP-type peroxidases are a heme peroxidase family with unique properties whose members are widely distributed from prokaryotes to eukaryotes. DyP-type peroxidases are subdivided into class P, I and V based on structure-based sequence alignment. Class V enzymes possess degradation activities for anthraquinone dyes, and include extra sequences compared with class P and I. Class V enzymes are mainly found in fungi, with only two such proteins, AnaPX and DyP2, reported in bacteria. Here, we heterologously expressed, purified and biochemically characterized SaDyP2 protein, predicted to belong to class V...
January 11, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28087275/sequence-structure-and-function-relationships-in-flaviviruses-as-assessed-by-evolutive-aspects-of-its-conserved-non-structural-protein-domains
#9
Néli José da Fonseca, Marcelo Querino Lima Afonso, Natan Gonçalves Pedersolli, Lucas Carrijo de Oliveira, Dhiego Souto Andrade, Lucas Bleicher
Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural and seven non-structural proteins. Homologous proteins can be studied by conservation and coevolution analysis as detected in multiple sequence alignments, usually reporting positions which are strictly necessary for the structure and/or function of all members in a protein family or which are involved in a specific sub-class feature requiring the coevolution of residue sets...
January 10, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28080040/insights-into-thiol-aromatic-interactions-a-stereoelectronic-basis-for-s-h-%C3%AF-interactions
#10
Christina R Forbes, Sudipta Kumar Sinha, Himal Kanti Ganguly, Shi Bai, Glenn P A Yap, Sandeep Patel, Neal J Zondlo
Thiols can engage favorably with aromatic rings in S-H/π interactions, within abiological systems and within proteins. However, the underlying bases for S-H/π interactions are not well understood. The crystal structure of Boc-L-4-thiolphenylalanine tert-butyl ester revealed crystal organization centered on the interaction of the thiol S-H with the aromatic ring of an adjacent molecule, with a through-space Hthiol...Caromatic distance of 2.71 Å, below the 2.90 Å sum of the van der Waals radii of H and C...
January 12, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#11
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28077565/mahmi-database-a-comprehensive-metahit-based-resource-for-the-study-of-the-mechanism-of-action-of-the-human-microbiota
#12
Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077065/structure-alignment-based-classification-of-rna-binding-pockets-reveals-regional-rna-recognition-motifs-on-protein-surfaces
#13
Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu
BACKGROUND: Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recognition mechanisms and benefit complementary structural design in bioengineering. RNA-binding events often take place at pockets on protein surfaces. The structural classification of local binding pockets determines the major patterns of RNA recognition. RESULTS: In this work, we provide a novel framework for systematically identifying the structure motifs of protein-RNA binding sites in the form of pockets on regional protein surfaces via a structure alignment-based method...
January 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28074876/scale-up-of-nature-s-tissue-weaving-algorithms-to-engineer-advanced-functional-materials
#14
Joanna L Ng, Lillian E Knothe, Renee M Whan, Ulf Knothe, Melissa L Knothe Tate
We are literally the stuff from which our tissue fabrics and their fibers are woven and spun. The arrangement of collagen, elastin and other structural proteins in space and time embodies our tissues and organs with amazing resilience and multifunctional smart properties. For example, the periosteum, a soft tissue sleeve that envelops all nonarticular bony surfaces of the body, comprises an inherently "smart" material that gives hard bones added strength under high impact loads. Yet a paucity of scalable bottom-up approaches stymies the harnessing of smart tissues' biological, mechanical and organizational detail to create advanced functional materials...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28071988/braided-and-stacked-electrospun-nanofibrous-scaffolds-for-tendon-and-ligament-tissue-engineering
#15
Benjamin B Rothrauff, Brian B Lauro, Guang Yang, Richard E Debski, Volker Musahl, Rocky Tuan
Tendon and ligament injuries are a persistent orthopaedic challenge given their poor innate healing capacity. Non-woven electrospun nanofibrous scaffolds composed of polyesters have been used to mimic the mechanics and topographical cues of native tendons and ligaments. However, non-woven nanofibers have several limitations that prevent broader clinical application, including poor cell infiltration as well as tensile and suture-retention strengths that are inferior to native tissues. In this study, multilayered scaffolds of aligned electrospun nanofibers of two designs - stacked or braided - were fabricated...
January 10, 2017: Tissue Engineering. Part A
https://www.readbyqxmd.com/read/28065899/statistical-inference-of-protein-structural-alignments-using-information-and-compression
#16
James H Collier, Lloyd Allison, Arthur M Lesk, Peter J Stuckey, Maria Garcia de la Banda, Arun S Konagurthu
MOTIVATION: Structural molecular biology depends crucially on computational techniques that compare protein three-dimensional structures and generate structural alignments (the assignment of one-to-one correspondences between subsets of amino acids based on atomic coordinates). Despite its importance, the structural alignment problem has not been formulated, much less solved, in a consistent and reliable way. To overcome these difficulties, we present here a statistical framework for the precise inference of structural alignments, built on the Bayesian and information-theoretic principle of Minimum Message Length (MML)...
January 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28064023/identification-and-characterization-of-a-gamma-interferon-inducible-lysosomal-thiol-reductase-homolog-from-guinea-pig-cavia-porcellus-that-exhibits-thiol-reductase-activity-in-vitro
#17
Lei Ma, Fang Cao, Runze Tang, Jiaxin Zhang, Shuangquan Zhang
Gamma-interferon-inducible lysosomal thiol reductase (GILT) is a key enzyme in the antigen processing and presentation pathway whereby it reduces disulfide bonds at an acidic pH. In this study, a homolog of GILT from guinea pigs (designated gpGILT) was identified and characterized using bioinformatic methods and bioactivity assays. The open reading frame of gpGILT is 705bp in length and encodes 234 amino acids, with a putative molecular weight of about 25.85kDa. The structure of gpGILT is similar to those of humans and zebrafish, containing six introns and seven exons...
December 28, 2016: Research in Veterinary Science
https://www.readbyqxmd.com/read/28063986/evidence-of-structurally-continuous-collagen-fibrils-in-tendons
#18
Rene B Svensson, Andreas Herchenhan, Tobias Starborg, Michael Larsen, Karl E Kadler, Klaus Qvortrup, S Peter Magnusson
: Tendons transmit muscle-generated force through an extracellular matrix of aligned collagen fibrils. The force applied by the muscle at one end of a microscopic fibril has to be transmitted through the macroscopic length of the tendon by mechanisms that are poorly understood. A key element in this structure-function relationship is the collagen fibril length. During embryogenesis short fibrils are produced but they grow rapidly with maturation. There is some controversy regarding fibril length in adult tendon, with mechanical data generally supporting discontinuity while structural investigations favor continuity...
January 5, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28062447/cross-react-a-new-structural-bioinformatics-method-for-predicting-allergen-cross-reactivity
#19
Surendra S Negi, Werner Braun
: The phenomenon of cross-reactivity between allergenic proteins plays an important role to understand how the immune system recognizes different antigen proteins. Allergen proteins are known to cross-react if their sequence comparison shows a high sequence identity which also implies that the proteins have a similar 3D fold. In such cases, linear sequence alignment methods are frequently used to predict cross-reactivity between allergenic proteins. However, the prediction of cross-reactivity between distantly related allergens continues to be a challenging task...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28057858/protasr-an-evolutionary-framework-for-ancestral-protein-reconstruction-with-selection-on-folding-stability
#20
Miguel Arenas, Claudia C Weber, David A Liberles, Ugo Bastolla
The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites...
January 5, 2017: Systematic Biology
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