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https://www.readbyqxmd.com/read/28088083/specificity-and-stability-of-transient-protein-protein-interactions
#1
REVIEW
Sneha Vishwanath, Anshul Sukhwal, Ramanathan Sowdhamini, Narayanaswamy Srinivasan
Remarkable features that are achieved in a protein-protein complex to precise levels are stability and specificity. Deviation from the normal levels of specificity and stability, which is often caused by mutations, could result in disease conditions. Chemical nature, 3-D arrangement and dynamics of interface residues code for both specificity and stability. This article reviews roles of interfacial residues in transient protein-protein complexes. It is proposed that aside from hotspot residues conferring stability to the complex, a small set of 'rigid' residues at the interface that maintain conformation between complexed and uncomplexed forms, play a major role in conferring specificity...
January 11, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28087982/the-impact-of-ces1-genotypes-on-the-pharmacokinetics-of-methylphenidate-in-healthy-danish-subjects
#2
Claus Stage, Gesche Jürgens, Louise Schow Guski, Ragnar Thomsen, Ditte Bjerre, Laura Ferrero-Miliani, Yassine Kamal Lyauk, Henrik Berg Rasmussen, Kim Dalhoff
AIM: This study investigated the influence of CES1 variations, including the SNP rs71647871 (G143E) and variation in copy number, on the pharmacokinetics of a single oral dose of 10 mg methylphenidate. METHODS: CES1 genotype was obtained from 200 healthy Danish Caucasian volunteers. Based on the genotype, 44 (19 males and 25 females) were invited to participate in an open, prospective trial involving six predefined genotypes: three groups with two, three, and four CES1 copies, respectively; a group of carriers of the CES1 143E allele; a group of individuals homozygous for CES1A1c (CES1VAR); and a group having three CES1 copies, in which the duplication, CES1A2, had increased transcriptional activity...
January 14, 2017: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28087897/fgfr1-analyses-in-four-patients-with-hypogonadotropic-hypogonadism-with-split-hand-foot-malformation-implications-for-the-promoter-region
#3
Kohnosuke Ohtaka, Yasuko Fujisawa, Fumio Takada, Yukihiro Hasegawa, Tatsuya Miyoshi, Tomonobu Hasegawa, Hideaki Miyoshi, Hiraku Kameda, Misuzu Kurokawa Seo, Maki Fukami, Tsutomu Ogata
Heterozygous loss-of-function mutations of FGFR1 cause various disorders including hypogonadotropic hypogonadism with split-hand/foot malformation (HH-SHFM). We examined FGFR1 in four Japanese patients with HH-SHFM (cases 1-4) and the mother of case 4 with HH only. Cases 1 and 2 had heterozygous loss-of-function mutations with no dominant negative effect [c.289G>A, p.(G97S); and c.2231G>C, p.(R744T)], and case 3 had a splice donor site mutation [c.1663+1G>T]. Notably, case 4 had a maternally inherited 8,312 bp microdeletion that involved non-coding exon 1U and impaired FGFR1 expression...
January 13, 2017: Human Mutation
https://www.readbyqxmd.com/read/28087842/novel-determinants-of-mammalian-primary-microrna-processing-revealed-by-systematic-evaluation-of-hairpin-containing-transcripts-and-human-genetic-variation
#4
Christine Anne Roden, Jonathan Gaillard, Shaveta Kanoria, William Rennie, Syndi Barish, Jijun Cheng, Wen Pan, Jun Liu, Chris Cotsapas, Ye Ding, Jun Lu
Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36+/-3nt is optimal for pri-miRNA processing...
January 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28087835/study-of-tio2-p25-nanoparticles-genotoxicity-on-lung-blood-and-liver-cells-in-lung-overload-and-non-overload-conditions-after-repeated-respiratory-exposure-in-rats
#5
Charlène Relier, Marielle Dubreuil, Omar Lozano Garcia, Eugenia Cordelli, Jorge Mejia, Patrizia Eleuteri, Franck Robidel, Thomas Loret, Francesca Pacchierotti, Stéphane Lucas, Ghislaine Lacroix, Bénédicte Trouiller
Inhaled titanium dioxide (TiO2) nanoparticles (NPs) can have negative health effects, and have been shown to cause respiratory tract cancer in rats. Inflammation has been linked to oxidative stress, and both have been described as possible mechanisms for genotoxicity of NPs, but rarely examined side-by-side in animal studies. In the present study, a wide range of complementary endpoints have been performed to study TiO2 P25 NP-induced genotoxicity in lung overload and non-overload conditions. Additionally, lung burden, inflammation, cytotoxicity and oxidative stress have also been evaluated in order to link genotoxicity with these responses...
January 13, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28087830/recognition-of-the-magnaporthe-oryzae-effector-avr-pia-by-the-decoy-domain-of-the-rice-nlr-immune-receptor-rga5
#6
Diana Ortiz, Karine De Guillen, Stella Cesari, Véronique Chalvon, Jérome Gracy, André Padilla, Thomas Kroj
Nucleotide-binding domain and leucine-rich repeat proteins (NLRs) are important receptors in plant immunity that allow recognition of pathogen effectors. The rice NLR RGA5 recognizes the Magnaporthe oryzae effector AVR-Pia through direct interaction. Here, we gained detailed insights into the molecular and structural bases of AVR-Pia-RGA5 interaction and the role of the RATX1 decoy domain of RGA5. NMR titration combined with in vitro and in vivo protein-protein interaction analyses identified the AVR-Pia interaction surface that binds to the RATX1 domain...
January 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28087784/interactions-between-zinc-and-allosteric-modulators-of-the-glycine-receptor
#7
Garrett L Cornelison, Anna W Daszkowski, Natasha C Pflanz, S John Mihic
The glycine receptor is a pentameric ligand-gated ion channel involved in fast inhibitory neurotransmission in the central nervous system. Zinc is an allosteric modulator of glycine receptor function, enhancing the effects of glycine at nM to low μM concentrations, and inhibiting its effects at higher concentrations. Low nM concentrations of contaminating zinc in electrophysiological buffers are capable of synergistically enhancing receptor modulation by other compounds such as ethanol. This suggests that, unless accounted for, previous studies of glycine receptor modulation were measuring the effects of modulator plus co-modulation by zinc on receptor function...
January 13, 2017: Journal of Pharmacology and Experimental Therapeutics
https://www.readbyqxmd.com/read/28087782/mutation-supply-and-relative-fitness-shape-the-genotypes-of-ciprofloxacin-resistant-escherichia-coli
#8
Douglas L Huseby, Franziska Pietsch, Gerrit Brandis, Linnéa Garoff, Angelica Tegehall, Diarmaid Hughes
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087781/deleterious-variants-in-asian-rice-and-the-potential-cost-of-domestication
#9
Qingpo Liu, Yongfeng Zhou, Peter L Morrell, Brandon S Gaut
Many SNPs are predicted to encode deleterious amino acid variants. These slightly deleterious mutations can provide unique insights into population history, the dynamics of selection, and the genetic bases of phenotypes. This is especially true for domesticated species, where a history of bottlenecks and selection may affect the frequency of deleterious variants and signal a 'cost of domestication'. Here we investigated the numbers and frequencies of deleterious variants in Asian rice (O. sativa), focusing on two varieties (japonica and indica) and their wild relative (O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#10
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087770/article-discoveries
#11
Anke Konrad, Owen Thompson, Robert H Waterston, Donald G Moerman, Peter D Keightley, Ulfar Bergthorsson, Vaishali Katju
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10 and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087769/enzyme-efficiency-but-not-thermostability-drives-cefotaxime-resistance-evolution-in-tem-1-%C3%AE-lactamase
#12
Jennifer Knies, Fei Cai, Daniel M Weinreich
A leading intellectual challenge in evolutionary genetics is to identify the specific phenotypes that drive adaptation. Enzymes offer a particularly promising opportunity to pursue this question, because many enzymes' contributions to organismal fitness depend on a comparatively small number of experimentally accessible properties. Moreover, on first principles the demands of enzyme thermostability stand in opposition to the demands of catalytic activity. This observation, coupled with the fact that enzymes are only marginally thermostable, motivates the widely held hypothesis that mutations conferring functional improvement require compensatory mutations to restore thermostability...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087737/a-homozygous-mutation-in-trim36-causes-autosomal-recessive-anencephaly-in-an-indian-family
#13
Nivedita Singh, Vishwanath Kumble Bhat, Ankana Tiwari, Srinivas G Kodaganur, Sagar J Tontanahal, Astha Sarda, K V Malini, Arun Kumar
Anencephaly is characterized by the absence of brain tissues and cranium. During primary neurulation stage of the embryo, the rostral part of the neural pore fails to close, leading to anencephaly. Anencephaly shows a heterogeneous etiology, ranging from environmental to genetic causes. The autosomal recessive inheritance of anencephaly has been reported in several populations. In this study, we employed whole-exome sequencing and identified a homozygous missense mutation c.1522C>A (p.Pro508Thr) in the TRIM36 gene as the cause of autosomal recessive anencephaly (APH) in an Indian family...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087732/novel-gnb1-mutations-disrupt-assembly-and-function-of-g-protein-heterotrimers-and-cause-global-developmental-delay-in-humans
#14
Katja Lohmann, Ikuo Masuho, Dipak N Patil, Hauke Baumann, Eva Hebert, Sofia Steinrücke, Daniel Trujillano, Nickolas K Skamangas, Valerija Dobricic, Irina Hüning, Gabriele Gillessen-Kaesbach, Ana Westenberger, Dusanka Savic-Pavicevic, Alexander Münchau, Gabriela Oprea, Christine Klein, Arndt Rolfs, Kirill A Martemyanov
Global developmental delay (GDD), often accompanied by intellectual disability, seizures and other features is a severe, clinically and genetically highly heterogeneous childhood-onset disorder. In cases where genetic causes have been identified, de-novo mutations in neuronally expressed genes are a common scenario. These mutations can be best identified by exome sequencing of parent-offspring trios. De novo mutations in the guanine nucleotide-binding protein, beta 1 (GNB1) gene, encoding the Gβ1 subunit of heterotrimeric G proteins, have recently been identified as a novel genetic cause of GDD...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087720/a-liminal-stage-after-predictive-testing-for-huntington-disease
#15
Marcela Gargiulo, Sophie Tezenas du Montcel, Marie France Jutras, Ariane Herson, Cecile Cazeneuve, Alexandra Durr
BACKGROUND: Following predictive testing for Huntington disease (HD), knowledge of one's carrier status may have consequences on disease onset. Our study aimed to address two questions. First, does knowledge of being a carrier of the pathological HD mutation trigger onset of the disease? Second, does this knowledge influence self-awareness and allow carriers to identify signs and symptoms of disease onset? METHODS: Between 2012 and 2015, 75 HD mutation carriers were examined using the Unified Huntington's Disease Rating Scale (UHDRS) motor score...
January 13, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28087719/genetics-insight-into-the-amyotrophic-lateral-sclerosis-frontotemporal-dementia-spectrum
#16
REVIEW
Ai-Ling Ji, Xia Zhang, Wei-Wei Chen, Wen-Juan Huang
Recent genetic discoveries have dramatically changed our understanding of two major neurodegenerative conditions. Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are common, devastating diseases of the brain. For decades, ALS and FTD were classified as movement and cognitive disorders, respectively, due to their distinct clinical phenotypes. The recent identification of chromosome 9 open reading frame 72 (C9orf72) as the major gene causative of familial forms of ALS and FTD uncovered a new reality of a continuous FTD/ALS spectrum...
January 13, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28087715/sf3b1-hsh155-heat-motif-mutations-affect-interaction-with-the-spliceosomal-atpase-prp5-resulting-in-altered-branch-site-selectivity-in-pre-mrna-splicing
#17
Qing Tang, Susana Rodriguez-Santiago, Jing Wang, Jia Pu, Andrea Yuste, Varun Gupta, Alberto Moldón, Yong-Zhen Xu, Charles C Query
Mutations in the U2 snRNP component SF3B1 are prominent in myelodysplastic syndromes (MDSs) and other cancers and have been shown recently to alter branch site (BS) or 3' splice site selection in splicing. However, the molecular mechanism of altered splicing is not known. We show here that hsh155 mutant alleles in Saccharomyces cerevisiae, counterparts of SF3B1 mutations frequently found in cancers, specifically change splicing of suboptimal BS pre-mRNA substrates. We found that Hsh155p interacts directly with Prp5p, the first ATPase that acts during spliceosome assembly, and localized the interacting regions to HEAT (Huntingtin, EF3, PP2A, and TOR1) motifs in SF3B1 associated with disease mutations...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087713/functional-genomics-reveals-that-tumors-with-activating-phosphoinositide-3-kinase-mutations-are-dependent-on-accelerated-protein-turnover
#18
Teresa Davoli, Kristen E Mengwasser, Jingjing Duan, Ting Chen, Camilla Christensen, Eric C Wooten, Anthony N Anselmo, Mamie Z Li, Kwok-Kin Wong, Kristopher T Kahle, Stephen J Elledge
Activating mutations in the phosphoinositide 3-kinase (PI3K) signaling pathway are frequently identified in cancer. To identify pathways that support PI3K oncogenesis, we performed a genome-wide RNAi screen in isogenic cell lines harboring wild-type or mutant PIK3CA to search for PI3K synthetic-lethal (SL) genes. A combined analysis of these results with a meta-analysis of two other large-scale RNAi screening data sets in PI3K mutant cancer cell lines converged on ribosomal protein translation and proteasomal protein degradation as critical nononcogene dependencies for PI3K-driven tumors...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087700/two-small-molecules-restore-stability-to-a-sub-population-of-the-cystic-fibrosis-transmembrane-conductance-regulator-with-the-predominant-disease-causing-mutation
#19
Xin Meng, Yiting Wang, Xiaomeng Wang, Joe A Wrennall, Tracy L Rimington, Hongyu Li, Zhiwei Cai, Robert C Ford, David N Sheppard
Cystic fibrosis (CF) is caused by mutations that disrupt the plasma membrane expression, stability, and function of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel. Two small molecules, the CFTR corrector lumacaftor and the potentiator ivacaftor, are now used clinically to treat CF, although some studies suggest that they have counteracting effects on CFTR stability. Here, we investigated the impact of these compounds on the instability of F508del-CFTR, the most common CF mutation...
January 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28087698/inhibition-of-trpml1-by-lysosomal-adenosine-involved-in-severe-combined-immunodeficiency-diseases
#20
Xi Zoë Zhong, Yuanjie Zou, Xue Sun, Gaofeng Dong, Qi Cao, Aditya Pandey, Jan K Rainey, Xiaojuan Zhu, Xian-Ping Dong
Impaired adenosine homeostasis has been associated with numerous human diseases. Lysosomes are referred to as the cellular recycling centers which generate adenosine by breaking down nucleic acids or ATP. Recent studies have suggested that lysosomal adenosine overload causes lysosome defects which phenocopy patients with mutations in TRPML1, a lysosomal Ca2+ channel, suggesting that lysosomal adenosine overload may impair TRPML1 and then lead to subsequent lysosomal dysfunction. In this study, we demonstrate that lysosomal adenosine is elevated by deleting adenosine deaminase (ADA), an enzyme responsible for adenosine degradation...
January 13, 2017: Journal of Biological Chemistry
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