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https://www.readbyqxmd.com/read/27936519/a-computational-approach-for-studying-antibody-antigen-interactions-without-prior-structural-information-the-anti-testosterone-binding-antibody-as-a-case-study
#1
Artturi Koivuniemi, Kristiina Takkinen, Tarja Nevanen
Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel the atomistic level properties of antibody-antigen complexes with the help of computational modeling. Thus, here we have studied the feasibility of computational tools to gather atomic scale information regarding the antibody-antigen complexes solely starting from an amino acid sequence. First, we constructed a homology model for the anti-testosterone binding antibody based on the knowledge based classification of complementary determining regions (CDRs) and implicit solvent molecular dynamics simulations...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936513/probing-the-structural-dynamics-of-the-crispr-cas9-rna-guided-dna-cleavage-system-by-coarse-grained-modeling
#2
Wenjun Zheng
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936490/combining-ancestral-sequence-reconstruction-with-protein-design-to-identify-an-interface-hotspot-in-a-key-metabolic-enzyme-complex
#3
Alexandra Holinski, Kristina Heyn, Rainer Merkl, Reinhard Sterner
It is important to identify hotspot residues that determine protein-protein interactions in interfaces of macromolecular complexes. We have applied a combination of ancestral sequence reconstruction and protein design to identify hotspots within imidazole glycerol phosphate synthase (ImGPS). ImGPS is a key metabolic enzyme complex, which links histidine and de novo purine biosynthesis and consists of the cyclase subunit HisF and the glutaminase subunit HisH. Initial fluorescence titration experiments showed that HisH from Zymomonas mobilis (zmHisH) binds with high affinity to the reconstructed HisF from the last universal common ancestor (LUCA-HisF) but not to HisF from Pyrobaculum arsenaticum (paHisF), which differ by 103 residues...
December 9, 2016: Proteins
https://www.readbyqxmd.com/read/27936244/gene-expression-and-silencing-studies-in-phytophthora-infestans-reveal-infection-specific-nutrient-transporters-and-a-role-for-the-nitrate-reductase-pathway-in-plant-pathogenesis
#4
Melania Abrahamian, Audrey M V Ah-Fong, Carol Davis, Kalina Andreeva, Howard S Judelson
To help learn how phytopathogens feed from their hosts, genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated. This identified 453 genes from 19 families. Comparisons with a necrotrophic oomycete, Pythium ultimum, and a hemibiotrophic fungus, Magnaporthe oryzae, revealed diversity in the size of some families although a similar fraction of genes encoded transporters. RNA-seq of infected potato tubers, tomato leaves, and several artificial media revealed that 56 and 207 transporters from P...
December 9, 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27936181/in-vivo-modelling-of-atp1a3-g316s-induced-ataxia-in-c-elegans-using-crispr-cas9-mediated-homologous-recombination-reveals-dominant-loss-of-function-defects
#5
Altar Sorkaç, Ivan C Alcantara, Anne C Hart
The NIH Undiagnosed Diseases Program admitted a male patient with unclassifiable late-onset ataxia-like symptoms. Exome sequencing revealed a heterozygous de novo mutation converting glycine 316 to serine in ATP1A3, which might cause disease. ATP1A3 encodes the Na+/K+ ATPase pump α3-subunit. Using CRISPR/Cas9-mediated homologous recombination for genome editing, we modelled this putative disease-causing allele in Caenorhabditis elegans, recreating the patient amino acid change in eat-6, the orthologue of ATP1A3...
2016: PloS One
https://www.readbyqxmd.com/read/27936173/insights-into-basal-signaling-regulation-oligomerization-and-structural-organization-of-the-human-g-protein-coupled-receptor-83
#6
Anne Müller, Julia Catherine Berkmann, Patrick Scheerer, Heike Biebermann, Gunnar Kleinau
The murine G-protein coupled receptor 83 (mGPR83) is expressed in the hypothalamus and was previously suggested to be involved in the regulation of metabolism. The neuropeptide PEN has been recently identified as a potent GPR83 ligand. Moreover, GPR83 constitutes functionally relevant hetero-oligomers with other G-protein coupled receptors (GPCR) such as the ghrelin receptor (GHSR) or GPR171. Previous deletion studies also revealed that the long N-terminal extracellular receptor domain (eNDo) of mGPR83 may act as an intra-molecular ligand, which participates in the regulation of basal signaling activity, which is a key feature of GPCR function...
2016: PloS One
https://www.readbyqxmd.com/read/27936164/transcriptome-and-metabolome-analyses-in-exogenous-fabp4-and-fabp5-treated-adipose-derived-stem-cells
#7
Tokunori Yamamoto, Masato Furuhashi, Takeshi Sugaya, Tsuyoshi Oikawa, Megumi Matsumoto, Yasuhito Funahashi, Yoshihisa Matsukawa, Momokazu Gotoh, Tetsuji Miura
Adipose-derived stem cells (ADSC), which exist near adipocytes in adipose tissue, have been used as a potential tool of regenerative medicine. Lipid chaperones, fatty acid-binding protein 4 (FABP4) and 5 (FABP5), are abundantly expressed in adipocytes. FABP4 has recently been shown to be secreted from adipocytes during lipolysis in a non-classical pathway and may act as an adipokine. Here, we investigated the role of exogenous FABP4 and FABP5 in transcriptional and metabolic regulation in ADSC. FABP4 and FABP5 were little expressed in ADSC...
2016: PloS One
https://www.readbyqxmd.com/read/27936158/modulation-of-re-initiation-of-measles-virus-transcription-at-intergenic-regions-by-pxd-to-ntail-binding-strength
#8
Louis-Marie Bloyet, Joanna Brunel, Marion Dosnon, Véronique Hamon, Jenny Erales, Antoine Gruet, Carine Lazert, Christophe Bignon, Philippe Roche, Sonia Longhi, Denis Gerlier
Measles virus (MeV) and all Paramyxoviridae members rely on a complex polymerase machinery to ensure viral transcription and replication. Their polymerase associates the phosphoprotein (P) and the L protein that is endowed with all necessary enzymatic activities. To be processive, the polymerase uses as template a nucleocapsid made of genomic RNA entirely wrapped into a continuous oligomer of the nucleoprotein (N). The polymerase enters the nucleocapsid at the 3'end of the genome where are located the promoters for transcription and replication...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27936131/immunolocalization-of-a-histidine-rich-epidermal-differentiation-protein-in-the-chicken-supports-the-hypothesis-of-an-evolutionary-developmental-link-between-the-embryonic-subperiderm-and-feather-barbs-and-barbules
#9
Lorenzo Alibardi, Karin Brigit Holthaus, Supawadee Sukseree, Marcela Hermann, Erwin Tschachler, Leopold Eckhart
The morphogenesis of feathers is a complex process that depends on a tight spatiotemporal regulation of gene expression and assembly of the protein components of mature feathers. Recent comparative genomics and gene transcription studies have indicated that genes within the epidermal differentiation complex (EDC) encode numerous structural proteins of cornifying skin cells in amniotes including birds. Here, we determined the localization of one of these proteins, termed EDMTFH (Epidermal Differentiation Protein starting with a MTF motif and rich in Histidine), which belongs to a group of EDC-encoded proteins rich in aromatic amino acid residues...
2016: PloS One
https://www.readbyqxmd.com/read/27936128/crystal-structure-of-the-streptomyces-coelicolor-sortase-e1-transpeptidase-provides-insight-into-the-binding-mode-of-the-novel-class-e-sorting-signal
#10
Michele D Kattke, Albert H Chan, Andrew Duong, Danielle L Sexton, Michael R Sawaya, Duilio Cascio, Marie A Elliot, Robert T Clubb
Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline...
2016: PloS One
https://www.readbyqxmd.com/read/27936120/sweat-facilitated-amino-acid-losses-in-male-athletes-during-exercise-at-32-34%C3%A2-c
#11
R Hugh Dunstan, Diane L Sparkes, Benjamin J Dascombe, Margaret M Macdonald, Craig A Evans, Christopher J Stevens, Marcus J Crompton, Johan Gottfries, Jesse Franks, Grace Murphy, Ryan Wood, Timothy K Roberts
Sweat contains amino acids and electrolytes derived from plasma and athletes can lose 1-2L of sweat per hour during exercise. Sweat may also contain contributions of amino acids as well as urea, sodium and potassium from the natural moisturizing factors (NMF) produced in the stratum corneum. In preliminary experiments, one participant was tested on three separate occasions to compare sweat composition with surface water washings from the same area of skin to assess contributions from NMF. Two participants performed a 40 minute self-paced cycle session with sweat collected from cleansed skin at regular intervals to assess the contributions to the sweat load from NMF over the period of exercise...
2016: PloS One
https://www.readbyqxmd.com/read/27936116/using-the-amino-acid-network-to-modulate-the-hydrolytic-activity-of-%C3%AE-glycosidases
#12
Fábio K Tamaki, Diorge P Souza, Valquiria P Souza, Cecilia M Ikegami, Chuck S Farah, Sandro R Marana
The active site residues in GH1 β-glycosidases are compartmentalized into 3 functional regions, involved in catalysis or binding of glycone and aglycone motifs from substrate. However, it still remains unclear how residues outside the active site modulate the enzymatic activity. To tackle this question, we solved the crystal structure of the GH1 β-glycosidase from Spodoptera frugiperda (Sfβgly) to systematically map its residue contact network and correlate effects of mutations within and outside the active site...
2016: PloS One
https://www.readbyqxmd.com/read/27936047/cross-neutralizing-antibodies-in-hiv-1-individuals-infected-by-subtypes-b-f1-c-or-the-b-bbr-variant-in-relation-to-the-genetics-and-biochemical-characteristics-of-the-env-gene
#13
Dalziza Victalina de Almeida, Karine Venegas Macieira, Beatriz Gilda Jegerhorn Grinsztejn, Valdiléa Gonçalves Veloso Dos Santos, Monick Lindenmeyer Guimarães
Various HIV-1 env genetic and biochemical features impact the elicitation of cross-reactive neutralizing antibodies in natural infections. Thus, we aimed to investigate cross-neutralizing antibodies in individuals infected with HIV-1 env subtypes B, F1, C or the B/Bbr variant as well as env characteristics. Therefore, plasma samples from Brazilian chronically HIV-1 infected individuals were submitted to the TZM-bl neutralization assay. We also analyzed putative N-glycosylation sites (PNGLs) and the size of gp120 variable domains in the context of HIV-1 subtypes prevalent in Brazil...
2016: PloS One
https://www.readbyqxmd.com/read/27936032/the-rfc1-80g-a-among-common-one-carbon-polymorphisms-relates-to-survival-rate-according-to-dna-global-methylation-in-primary-liver-cancers
#14
Sara Moruzzi, Silvia Udali, Andrea Ruzzenente, Alfredo Guglielmi, Patrizia Guarini, Nicola Martinelli, Simone Conci, Filippo Mazzi, Patrizia Pattini, Stephanie A Tammen, Oliviero Olivieri, Francesca Pizzolo, Sang-Woon Choi, Simonetta Friso
Polymorphisms within one-carbon metabolism genes have been largely studied in relation to cancer risk for the function of this pathway in nucleotide synthesis and DNA methylation. Aims of this study were to explore the possible link among several common functional gene polymorphisms within one-carbon metabolism and survival rate in primary liver cancers, i.e., hepatocellular carcinoma and cholangiocarcinoma, and to assess the additional effect of global DNA methylation on survival rate and mortality risk. Forty-seven primary liver cancer patients were genotyped for ten polymorphisms: DHFR 19bp ins/del, TS 2rpt-3rpt, MTHFD1 1958G>A, MTHFR 677C>T, MTR 2756A>G, MTRR 66A>G, RFC1 80G>A, SHMT1 1420C>T, BHMT 716 A>G, TC II 776C>G...
2016: PloS One
https://www.readbyqxmd.com/read/27936012/sugarcane-transcriptome-analysis-in-response-to-infection-caused-by-acidovorax-avenae-subsp-avenae
#15
Ailton B Santa Brigida, Cristian A Rojas, Clícia Grativol, Elvismary M de Armas, Júlio O P Entenza, Flávia Thiebaut, Marcelo de F Lima, Laurent Farrinelli, Adriana S Hemerly, Sérgio Lifschitz, Paulo C G Ferreira
Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by Acidovorax avenae subsp avenae (Aaa), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a de novo transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with Aaa...
2016: PloS One
https://www.readbyqxmd.com/read/27935978/genome-wide-identification-phylogeny-and-expression-of-aquaporin-genes-in-common-carp-cyprinus-carpio
#16
Chuanju Dong, Lin Chen, Jingyan Feng, Jian Xu, Shahid Mahboob, Khalid Al-Ghanim, Xuejun Li, Peng Xu
BACKGROUND: Aquaporins (Aqps) are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. Among vertebrate species, Aqps are highly conserved in both gene structure and amino acid sequence. These proteins are vital for maintaining water homeostasis in living organisms, especially for aquatic animals such as teleost fish. Studies on teleost Aqps are mainly limited to several model species with diploid genomes. Common carp, which has a tetraploidized genome, is one of the most common aquaculture species being adapted to a wide range of aquatic environments...
2016: PloS One
https://www.readbyqxmd.com/read/27935939/structural-basis-for-inhibitor-induced-aggregation-of-hiv-integrase
#17
Kushol Gupta, Vesa Turkki, Scott Sherrill-Mix, Young Hwang, Grant Eilers, Louis Taylor, Charlene McDanal, Ping Wang, David Temelkoff, Robert T Nolte, Emile Velthuisen, Jerry Jeffrey, Gregory D Van Duyne, Frederic D Bushman
The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication. To investigate the ALLINI inhibitory mechanism, we crystallized full-length HIV-1 IN bound to the ALLINI GSK1264 and determined the structure of the complex at 4.4 Å resolution. The structure shows GSK1264 buried between the IN C-terminal domain (CTD) and the catalytic core domain...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/27935934/beyond-the-hypercube-evolutionary-accessibility-of-fitness-landscapes-with-realistic-mutational-networks
#18
Marcin Zagorski, Zdzislaw Burda, Bartlomiej Waclaw
Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27935841/the-cytoplasmic-tail-domain-of-epstein-barr-virus-gh-regulates-membrane-fusion-activity-through-altering-gh-binding-to-gp42-and-epithelial-cell-attachment
#19
Jia Chen, Theodore S Jardetzky, Richard Longnecker
: Epstein-Barr virus (EBV) is associated with infectious mononucleosis and a variety of cancers as well as lymphoproliferative disorders in immunocompromised patients. EBV mediates viral entry into epithelial and B cells using fusion machinery composed of four glycoproteins: gB, the gH/gL complex, and gp42. gB and gH/gL are required for both epithelial and B cell fusion. The specific role of gH/gL in fusion has been the most elusive among the required herpesvirus entry glycoproteins. Previous mutational studies have focused on the ectodomain of EBV gH and not on the gH cytoplasmic tail domain (CTD)...
November 15, 2016: MBio
https://www.readbyqxmd.com/read/27935840/a-stress-induced-bias-in-the-reading-of-the-genetic-code-in-escherichia-coli
#20
Adi Oron-Gottesman, Martina Sauert, Isabella Moll, Hanna Engelberg-Kulka
: Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant...
November 15, 2016: MBio
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