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Protein function prediction

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https://www.readbyqxmd.com/read/28545124/cornet-assigning-function-to-networks-of-co-evolving-residues-by-automated-literature-mining
#1
Tom van den Bergh, Giorgio Tamo, Alberto Nobili, Yifeng Tao, Tianwei Tan, Uwe T Bornscheuer, Remko K P Kuipers, Bas Vroling, René M de Jong, Kalyanasundaram Subramanian, Peter J Schaap, Tom Desmet, Bernd Nidetzky, Gert Vriend, Henk-Jan Joosten
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data extracted from literature on interactively displayed groups of co-evolving residue positions to shed light on the functions associated with these groups and the residues in them. We used CorNet to analyse six enzyme super-families and found that groups of strongly co-evolving residues tend to consist of residues involved in a same function such as activity, specificity, co-factor binding, or enantioselectivity...
2017: PloS One
https://www.readbyqxmd.com/read/28544117/increased-expression-of-stim1-orai1-in-platelets-of-stroke-patients-predictive-of-poor-outcomes
#2
M Dong, N Zheng, L J Ren, H Zhou, J Liu
BACKGROUND AND PURPOSE: The platelet activation that is mediated by store-operated Ca(2+) entry via stromal interaction molecule (STIM1) and Orai1 Ca(2+) influx channels has been shown to play a key role in ischaemic stroke (IS). This study aimed to evaluate the impact of platelet STIM1/Orai1 protein expression on outcomes of IS. METHODS: A total of 160 patients with acute non-cardioembolic IS, among whom 45 patients had small-vessel diseases and 115 patients had large-vessel diseases, were evaluated...
May 23, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/28544077/identification-and-analysis-of-5-enolpyruvylshikimate-3-phosphate-synthase-epsps-gene-from-glyphosate-resistant-ochrobactrum-intermedium-sq20
#3
Sadiqa Firdous, Samina Iqbal, Samina Anwar, Hina Jabeen
BACKGROUND: Glyphosate is a herbicide that acts by inhibition of the enzyme, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), entailed in catalysis of an essential step in the biosynthesis of aromatic amino acids. The objective of the current study was to isolate glyphosate resistant bacterial strains and subsequent characterization of the gene(s) encoding glyphosate resistance in these isolates. By enrichment culture technique, a glyphosate resistant bacterium, Ochrobactrum intermedium Sq20 was isolated from glyphosate contaminated indigenous soil and characterized...
May 25, 2017: Pest Management Science
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#4
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28543713/potential-protective-role-of-grainyhead-like-genes-in-the-development-of-clear-cell-renal-cell-carcinoma
#5
Magdalena Pawlak, Agnieszka Kikulska, Tomasz Wrzesinski, Tobias Rausch, Zbigniew Kwias, Bartek Wilczynski, Vladimir Benes, Joanna Wesoly, Tomasz Wilanowski
The involvement of Grainyhead-like (GRHL) transcription factors in various cancers is well documented. However, little is known about their role in clear cell renal cell carcinoma (ccRCC). We discovered that the expression of two of these factors - GRHL1 and GRHL2-is downregulated in ccRCC samples, and their expression is correlated with the expression of VHL gene. This suggests a functional link between the GRHL transcription factors and one of the best known tumor suppressors. Although the GRHL genes are not mutated in ccRCC, some of the single nucleotide polymorphisms in these genes may indicate an increased risk of ccRCC development and/or may allow to assess patients' prognoses and predict their responses to various forms of therapy...
May 23, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28542952/compensatory-and-decompensatory-alterations-in-cardiomyocyte-ca-2-dynamics-in-hearts-with-diastolic-dysfunction-following-aortic-banding
#6
Sara Gattoni, Åsmund Treu Røe, Jan Magnus Aronsen, Ivar Sjaastad, William E Louch, Nicolas P Smith, Steven A Niederer
KEY POINTS: At the cellular level cardiac hypertrophy causes remodelling, leading to changes in ionic channel, pump and exchanger densities and kinetics. Previous studies have focused on quantifying changes in channels, pumps and exchangers without quantitatively linking these changes with emergent cellular scale functionality. Two biophysical cardiac cell models were created, parameterized and validated and are able to simulate electrophysiology and calcium dynamics in myocytes from control sham operated rats and aortic-banded rats exhibiting diastolic dysfunction...
May 21, 2017: Journal of Physiology
https://www.readbyqxmd.com/read/28542837/phenotype-and-natural-history-of-variant-late-infantile-ceroid-lipofuscinosis-5
#7
Alessandro Simonati, Ruth E Williams, Nardo Nardocci, Minna Laine, Roberta Battini, Angela Schulz, Barbara Garavaglia, Francesca Moro, Francesco Pezzini, Filippo M Santorelli
AIM: To characterize the phenotypic profile of a cohort of children affected with CLN5, a rare form of neuronal ceroid-lipofuscinosis (NCL), and to trace the features of the natural history of the disease. METHOD: Records of 15 children (nine males, six females) were obtained from the data sets of the DEM-CHILD International NCL Registry. Disease progression was measured by rating six functional domains at different time points along the disease course. All patients underwent mutation analysis of the CLN5 gene and ultrastructural investigations of peripheral tissues...
May 25, 2017: Developmental Medicine and Child Neurology
https://www.readbyqxmd.com/read/28542634/crystallographic-characterization-of-the-high-potential-iron-sulfur-protein-in-the-oxidized-state-at-0-8-%C3%A3-resolution
#8
Hiraku Ohno, Kazuki Takeda, Satomi Niwa, Tomotaka Tsujinaka, Yuya Hanazono, Yu Hirano, Kunio Miki
High-potential iron-sulfur protein (HiPIP) is a soluble electron carrier protein of photosynthetic bacteria with an Fe4S4 cluster. Although structural changes accompanying the electron transfer are important for understanding of the functional mechanism, the changes have not been clarified in sufficient detail. We previously reported the high-resolution crystal structures of HiPIP from a thermophilic purple bacterium Thermochromatium tepidum in the reduced state. In order to perform a detailed comparison between the structures in different redox states, the oxidized structure should also be revealed at high resolution...
2017: PloS One
https://www.readbyqxmd.com/read/28542596/progressive-mitochondrial-protein-lysine-acetylation-and-heart-failure-in-a-model-of-friedreich-s-ataxia-cardiomyopathy
#9
Amanda R Stram, Gregory R Wagner, Brian D Fogler, P Melanie Pride, Matthew D Hirschey, R Mark Payne
INTRODUCTION: The childhood heart disease of Friedreich's Ataxia (FRDA) is characterized by hypertrophy and failure. It is caused by loss of frataxin (FXN), a mitochondrial protein involved in energy homeostasis. FRDA model hearts have increased mitochondrial protein acetylation and impaired sirtuin 3 (SIRT3) deacetylase activity. Protein acetylation is an important regulator of cardiac metabolism and loss of SIRT3 increases susceptibility of the heart to stress-induced cardiac hypertrophy and ischemic injury...
2017: PloS One
https://www.readbyqxmd.com/read/28542500/uterine-and-systemic-inflammation-influences-ovarian-follicular-function-in-postpartum-dairy-cows
#10
Soon Hon Cheong, Ocilon G Sá Filho, Victor A Absalon-Medina, Augusto Schneider, W R Butler, Robert O Gilbert
The objective of this study was to determine the effects of uterine and systemic inflammatory responses to uterine bacterial contamination at calving in dairy cows on the growth and ovulatory outcomes of the first dominant follicle postpartum. Ovulatory capability of the first dominant follicle postpartum was predicted in 53 multiparous cows by using a combination of follicle growth characteristics and circulating estradiol concentrations. Endotoxin levels were assayed in follicular fluid samples that were aspirated the day after ovulatory outcome prediction...
2017: PloS One
https://www.readbyqxmd.com/read/28541675/prediction-of-bond-vector-autocorrelation-functions-from-larmor-frequency-selective-order-parameter-analysis-of-nmr-relaxation-data
#11
Janet S Anderson, Griselda Hernandez, David M LeMaster
Protein molecular dynamics interpretation of the standard R1, R2 and heteronuclear NOE relaxation measurements has typically been limited to a single S(2) order parameter which is often insufficient to characterize the rich content of these NMR experiments. In the absence of exchange linebroadening, an optimized reduced spectral density analysis of these measurements can yield spectral density values at three distinct frequencies. Surprisingly, these three discrete spectral density values have proven to be sufficient for a Larmor frequency-selective order parameter analysis of the 223 methine and methylene H-C bonds of the B3 domain of Protein G (GB3) to accurately back-calculate the entire curve of the corresponding bond vector autocorrelation functions upon which the NMR relaxation behavior depends...
May 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28541472/homozygous-deletion-of-sun5-in-three-men-with-decapitated-spermatozoa
#12
Razan A Elkhatib, Marine Paci, Guy Longepied, Jacqueline Saias-Magnan, Blandine Courbiere, Marie-Roberte Guichaoua, Nicolas Levy, Catherine Metzler-Guillemain, Michael J Mitchell
A recent study of 17 men with decapitated spermatozoa found that 8 carried two rare SUN5 alleles, and concluded that loss of SUN5 function causes acephalic spermatozoa syndrome. Consistent with this, the SUN5 protein localises to the head-tail junction in normal spermatozoa, and SUN proteins are known to form links between the cytoskeleton and the nucleus. However, six of the ten SUN5 variants reported were missense with an unknown effect on function, and only one man carried two certain loss-of-function (LOF) alleles: p...
May 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28541224/protein-protein-interaction-interface-residue-pair-prediction-based-on-deep-learning-architecture
#13
Zhenni Zhao, Xinqi Gong
MOTIVATION: Proteins usually fulfill their biological functions by interacting with other proteins. Although some methods have been developed to predict the binding sites of a monomer protein, these are not sufficient for prediction of the interaction between two monomer proteins. The correct prediction of interface residue pairs from two monomer proteins is still an open question and has great significance for practical experimental applications in the life sciences. We hope to build a method for the prediction of interface residue pairs that is suitable for those applications...
May 19, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28540883/the-relationship-between-serum-homocysteine-and-highly-sensitive-c-reactive-protein-levels-in-children-on-regular-hemodialysis
#14
Manal Abdel-Salam, Soheir Ibrahim, Shaimaa Abdelmalik Pessar, Eman Al-Morsy
Hyperhomocysteinemia has attracted a lot of attention in renal patients, not only because of its close relationship with renal function but also because it has been implicated as an independent cardiovascular risk factor in these patients. An increased level of C-reactive protein (CRP) has been reported to be a strong predictor of cardiovascular mortality in hemodialysis (HD) patients. The aim of this study was to assess the association between homocysteine (Hcy) and highly sensitive CRP (hsCRP) in cardiovascular risk prediction in children with chronic kidney disease (CKD) on HD...
May 2017: Saudi Journal of Kidney Diseases and Transplantation
https://www.readbyqxmd.com/read/28540183/the-draft-genome-of-corchorus-olitorius-cv-jro-524-navin
#15
Debabrata Sarkar, Ajay Kumar Mahato, Pratik Satya, Avijit Kundu, Sangeeta Singh, Pawan Kumar Jayaswal, Akshay Singh, Kaushlendra Bahadur, Sasmita Pattnaik, Nisha Singh, Avrajit Chakraborty, Nur Alam Mandal, Debajeet Das, Tista Basu, Amitha Mithra Sevanthi, Dipnarayan Saha, Subhojit Datta, Chandan Sourav Kar, Jiban Mitra, Karabi Datta, Pran Gobinda Karmakar, Tilak Raj Sharma, Trilochan Mohapatra, Nagendra Kumar Singh
Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28539731/improved-annotations-of-23-differentially-expressed-hypothetical-proteins-in-methicillin-resistant-s-aureus
#16
Jessica Marklevitz, Laura K Harris
Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. These strains are appearing in the community with increasing frequency. New diagnostic and therapeutic options are needed to combat this deadly infection. Interestingly, around 50% of the proteins in S. aureus are annotated as hypothetical. Methods to select hypothetical proteins related to antibiotic resistance have been inadequate...
2017: Bioinformation
https://www.readbyqxmd.com/read/28539440/uncovering-the-repertoire-of-endogenous-flaviviral-elements-in-aedes-mosquito-genomes
#17
Yasutsugu Suzuki, Lionel Frangeul, Laura B Dickson, Hervé Blanc, Yann Verdier, Joelle Vinh, Louis Lambrechts, Maria-Carla Saleh
Endogenous viral elements derived from non-retroviral RNA viruses were described in various animal genomes. Whether they have a biological function such as host immune protection against related viruses is a field of intense study. Here, we investigated the repertoire of endogenous flaviviral elements (EFVEs) in Aedes mosquitoes, the vectors of arboviruses such as dengue and chikungunya viruses. Previous studies identified three EFVEs from Ae. albopictus and one from Ae. aegypti cell lines. However, in-depth characterization of EFVEs in wild-type mosquito populations and individuals in vivo has not been performed...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28539390/mfn2-deletion-in-brown-adipose-tissue-protects-from-insulin-resistance-and-impairs-thermogenesis
#18
Kiana Mahdaviani, Ilan Y Benador, Shi Su, Raffi A Gharakhanian, Linsey Stiles, Kyle M Trudeau, Maria Cardamone, Violeta Enríquez-Zarralanga, Eleni Ritou, Tamar Aprahamian, Marcus F Oliveira, Barbara E Corkey, Valentina Perissi, Marc Liesa, Orian S Shirihai
BAT-controlled thermogenic activity is thought to be required for its capacity to prevent the development of insulin resistance. This hypothesis predicts that mediators of thermogenesis may help prevent diet-induced insulin resistance. We report that the mitochondrial fusion protein Mitofusin 2 (Mfn2) in BAT is essential for cold-stimulated thermogenesis, but promotes insulin resistance in obese mice. Mfn2 deletion in mice through Ucp1-cre (BAT-Mfn2-KO) causes BAT lipohypertrophy and cold intolerance. Surprisingly however, deletion of Mfn2 in mice fed a high fat diet (HFD) results in improved insulin sensitivity and resistance to obesity, while impaired cold-stimulated thermogenesis is maintained...
May 24, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28539261/g-protein-coupled-receptor-91-signaling-in-diabetic-retinopathy-and-hypoxic-retinal-diseases
#19
Jianyan Hu, Tingting Li, Xinhua Du, Qiang Wu, Yun-Zheng Le
G protein-coupled receptor 91 (GPR91) is a succinate-specific receptor and activation of GPR91 could initiate a complex signal transduction cascade and upregulate inflammatory and pro-angiogenic cytokines. In the retina, GPR91 is predominately expressed in ganglion cells, a major cellular entity involved in the pathogenesis of diabetic retinopathy (DR) and other hypoxic retinal diseases. During the development of DR and retinopathy of prematurity (ROP), chronic hypoxia causes an increase in the levels of local succinate...
May 21, 2017: Vision Research
https://www.readbyqxmd.com/read/28539189/the-individual-and-population-genetics-of-antibody-immunity
#20
REVIEW
Corey T Watson, Jacob Glanville, Wayne A Marasco
Antibodies (Abs) produced by immunoglobulin (IG) genes are the most diverse proteins expressed in humans. While part of this diversity is generated by recombination during B-cell development and mutations during affinity maturation, the germ-line IG loci are also diverse across human populations and ethnicities. Recently, proof-of-concept studies have demonstrated genotype-phenotype correlations between specific IG germ-line variants and the quality of Ab responses during vaccination and disease. However, the functional consequences of IG genetic variation in Ab function and immunological outcomes remain underexplored...
May 20, 2017: Trends in Immunology
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