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Protein function prediction

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https://www.readbyqxmd.com/read/28092658/mutation-effects-predicted-from-sequence-co-variation
#1
Thomas A Hopf, John B Ingraham, Frank J Poelwijk, Charlotta P I Schärfe, Michael Springer, Chris Sander, Debora S Marks
Many high-throughput experimental technologies have been developed to assess the effects of large numbers of mutations (variation) on phenotypes. However, designing functional assays for these methods is challenging, and systematic testing of all combinations is impossible, so robust methods to predict the effects of genetic variation are needed. Most prediction methods exploit evolutionary sequence conservation but do not consider the interdependencies of residues or bases. We present EVmutation, an unsupervised statistical method for predicting the effects of mutations that explicitly captures residue dependencies between positions...
January 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28092606/molecular-characterization-and-expression-analysis-of-the-nlr-family-card-containing-five-transcripts-in-the-pig
#2
Q Y Yang, T Chen, Y B Chen, D L Lan
The NOD-like receptor (NLR) family caspase recruitment domain-containing 5 (NLRC5) is one of the newly discovered and largest NLR family members. The NLRC5 has recently received extensive attention because of its important role in regulating innate and adaptive immune responses. The NLRC5 in many vertebrates, such as humans, mice, cattle, and horses, has already been proven and studied. However, the NLRC5 gene characteristics of pigs remain unclear. Thus, we completely cloned the NLRC5 cDNA sequence of the pig using the rapid amplification of cDNA ends(RACE) technology...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28092572/pspel-in-silico-prediction-of-self-interacting-proteins-from-amino-acids-sequences-using-ensemble-learning
#3
Jian-Qiang Li, Zhu-Hong You, Xiao Li, Ming Zhong, Xing Chen
Self interacting proteins (SIPs) play an important role in various aspects of the structural and functional organization of the cell. Detecting SIPs is one of the most important issues in current molecular biology. Although a large number of SIPs data has been generated by experimental methods, wet laboratory approaches are both time-consuming and costly. In addition, they yield high false negative and positive rates. Thus, there is a great need for in silico methods to predict SIPs accurately and efficiently...
January 10, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#4
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092028/sh2-ligand-prediction-guidance-for-in-silico-screening
#5
Shawn S C Li, Lei Li
Systematic identification of binding partners for SH2 domains is important for understanding the biological function of the corresponding SH2 domain-containing proteins. Here, we describe two different web-accessible computer programs, SMALI and DomPep, for predicting binding ligands for SH2 domains. The former was developed using a Scoring Matrix method and the latter based on the Support Vector Machine model.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092024/introduction-history-of-sh2-domains-and-their-applications
#6
Bernard A Liu, Kazuya Machida
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091882/identification-of-some-main-streptococcus-iniae-associated-proteins-relationship
#7
Fatima El Aamri, José Ángel Guillén, Daniel Padilla, Félix Acosta, Fernando Real
The surface-associated proteins play a key role in bacterial physiology and pathogenesis, and are the major targets in the development of new vaccines. These proteins contribute to the adaptation of bacteria to different hosts and environments. To study differences at the genomic level, we first sequenced the whole genome of Streptococcus iniae from fish (IUSA-1 strain) and compared it to Streptococcus iniae from human (9117 strain), revealing a high similitude between both strains. To gain further insights into host- and environment-specific differences, we then studied proteins in silico and by High Performance Liquid Chromatography...
January 14, 2017: Veterinary Research Communications
https://www.readbyqxmd.com/read/28090735/high-throughput-protein-targeted-biomolecular-detection-using-frequency-domain-faraday-rotation-spectroscopy
#8
Richard J Murdock, Shawn A Putnam, Soumen Das, Ankur Gupta, Elyse D Z Chase, Sudipta Seal
A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL(-1) and broad detection range of 10 pg mL(-1) ≲ cBSA ≲ 100 µg mL(-1) are observed...
January 16, 2017: Small
https://www.readbyqxmd.com/read/28090303/genotype-phenotype-effects-of-bmpr2-mutations-on-disease-severity-in-mouse-models-of-pulmonary-hypertension
#9
Andrea L Frump, Arunima Datta, Sampa Ghose, James West, Mark P de Caestecker
More than 350 mutations in the type-2 BMP (bone morphogenetic protein) receptor, BMPR2, have been identified in patients with heritable pulmonary arterial hypertension (HPAH). However, only 30% of BMPR2 mutation carriers develop PAH, and we cannot predict which of these carriers will develop clinical disease. One possibility is that the nature of the BMPR2 mutation affects disease severity. This hypothesis has been difficult to test clinically, given the rarity of HPAH and the complexity of the confounding genetic and environmental risk factors...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28090088/the-%C3%AE-trcp-fbxw2-skp2-axis-regulates-lung-cancer-cell-growth-with-fbxw2-acting-as-a-tumour-suppressor
#10
Jie Xu, Weihua Zhou, Fei Yang, Guoan Chen, Haomin Li, Yongchao Zhao, Pengyuan Liu, Hua Li, Mingjia Tan, Xiufang Xiong, Yi Sun
β-TrCP and SKP2 are two well-studied F-box proteins, which often act as oncogenes. Whether and how they communicate with each other is unknown. Here we report that FBXW2, a poorly characterized F-box, is a substrate of β-TrCP1 and an E3 ligase for SKP2. While β-TrCP1 promotes FBXW2 ubiquitylation and shortens its half-life, FBXW2 does the same to SKP2. FBXW2 has tumour suppressor activity against lung cancer cells and blocks oncogenic function of both β-TrCP1 and SKP2. The levels of β-TrCP1-FBXW2-SKP2 are inversely correlated during cell cycle with FBXW2 and β-TrCP/SKP2 being high or low, respectively, in arrested cells, whereas the opposite is true in proliferating cells...
January 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28089896/characterization-and-expression-analysis-of-a-chitinase-gene-pmchi-4-from-black-tiger-shrimp-penaeus-monodon-under-pathogen-infection-and-ambient-ammonia-nitrogen-stress
#11
Kaimin Zhou, Falin Zhou, Jianhua Huang, Qibin Yang, Song Jiang, Lihua Qiu, Lishi Yang, Caiyan Zhu, Shigui Jiang
Chitinase is a multi-gene family, which play important physiological roles in crustaceans, involved in several biological processes, including digestion, molting and defense against viruses. In the present study, a chitinase-4 gene (PmChi-4) was cloned from Penaeus monodon by rapid amplification of cDNA ends (RACE). The full length of PmChi-4 cDNA was 2178 bp, including an 1815 bp open reading frame (ORF) which encoded 604 amino acid residues. The predicted PmChi-4 protein was 67.7 kDa and shared 61%-88% identity with the type of Chi-4s from other crustaceans...
January 9, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28089742/multiple-habp2-variants-in-familial-papillary-thyroid-carcinoma-contribution-of-a-group-of-thyroid-checked-controls
#12
Benjamin Kern, Lucie Coppin, Pauline Romanet, Michel Crépin, Isabelle Szuster, Florence Renaud, Emmanuelle Leteurtre, Frédéric Frénois, Jean-Louis Wemeau, Bruno Carnaille, Catherine Cardot-Bauters, Christine Do Cao, Pascal Pigny
A heterozygous germline variant in the HABP2 gene c.1601G > A (p.Gly534Glu), which negatively impacts its tumor suppressive activity in vitro, has been described in 4-14% of kindreds of European-American ancestry with familial papillary thyroid carcinoma (fPTC). But it is also found in ≈4% of Europeans and European/Americans from public databases that, however, did not provide information on the thyroid function of the controls. To get unbiased results, we decided to compare HABP2 genotypes of patients with fPTC with those of "thyroid-checked" controls...
January 9, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28089609/de-immunized-and-functional-therapeutic-deft-versions-of-a-long-lasting-recombinant-alpha-interferon-for-antiviral-therapy
#13
Eduardo F Mufarrege, Sofía Giorgetti, Marina Etcheverrigaray, Frances Terry, William Martin, Anne S De Groot
Interferon α (IFN-α) exerts potent antiviral, immunomodulatory, and antiproliferative activity and have proven clinical utility in chronic hepatitis B and C virus infections. However, repeated IFN-α administration induces neutralizing antibodies (NAb) against the therapeutic in a significant number of patients. Associations between IFN-α immunogenicity and loss of efficacy have been described. So as to improve the invivo biological efficacy of IFN-α, a long lasting hyperglycosylated protein (4N-IFN) derived from IFN-α2b wild type (WT-IFN) was developed...
January 9, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28089453/serum-uromodulin-is-a-predictive-biomarker-for-cardiovascular-events-and-overall-mortality-in-coronary-patients
#14
Andreas Leiherer, Axel Muendlein, Christoph H Saely, Janine Ebner, Eva M Brandtner, Peter Fraunberger, Heinz Drexel
BACKGROUND: Uromodulin is a protein produced exclusively by the kidneys and present in urine and blood. In contrast to weak and in part contradictory study data on uromodulin in urine samples, the analysis of serum samples recently proved uromodulin's value as superior biomarker for ongoing kidney disease. Whether serum uromodulin is associated with cardiovascular event risk and whether it has predictive power for overall mortality is still unknown and has been evaluated in the present study...
December 29, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/28089252/practical-approaches-for-whole-genome-sequence-analysis-of-heart-and-blood-related-traits
#15
Alanna C Morrison, Zhuoyi Huang, Bing Yu, Ginger Metcalf, Xiaoming Liu, Christie Ballantyne, Josef Coresh, Fuli Yu, Donna Muzny, Elena Feofanova, Navin Rustagi, Richard Gibbs, Eric Boerwinkle
Whole-genome sequencing (WGS) allows for a comprehensive view of the sequence of the human genome. We present and apply integrated methodologic steps for interrogating WGS data to characterize the genetic architecture of 10 heart- and blood-related traits in a sample of 1,860 African Americans. In order to evaluate the contribution of regulatory and non-protein coding regions of the genome, we conducted aggregate tests of rare variation across the entire genomic landscape using a sliding window, complemented by an annotation-based assessment of the genome using predefined regulatory elements and within the first intron of all genes...
January 5, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28088582/ripk1-protects-hepatocytes-from-kupffer-cells-mediated-tnf-induced-apoptosis-in-mouse-models-of-pamp-induced-hepatitis
#16
Aveline Filliol, Claire Piquet-Pellorce, Céline Raguénès-Nicol, Sarah Dion, Muhammad Farooq, Catherine Lucas-Clerc, Peter Vandenabeele, Mathieu J M Bertrand, Jacques Le Seyec, Michel Samson
BACKGROUND & AIMS: The severity of liver diseases is exacerbated by the death of hepatocytes, which can be induced by the sensing of Pathogen Associated Molecular Patterns (PAMPs) derived from the gut microbiota. The molecular mechanisms regulating these cell death pathways are poorly documented. In this study, we investigated the role of the Receptor Interacting Protein Kinase 1 (RIPK1), a protein known to regulate cell fate decisions, in the death of hepatocytes using two in vivo models of PAMP-induced hepatitis...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28088539/the-dna-damage-response-of-c-elegans-affected-by-gravity-sensing-and-radiosensitivity-during-the-shenzhou-8-spaceflight
#17
Ying Gao, Dan Xu, Lei Zhao, Yeqing Sun
Space radiation and microgravity are recognized as primary and inevitable risk factors for humans traveling in space, but the reports regarding their synergistic effects remain inconclusive and vary across studies due to differences in the environmental conditions and intrinsic biological sensitivity. Thus, we studied the synergistic effects on transcriptional changes in the global genome and DNA damage response (DDR) by using dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity when exposure to spaceflight condition (SF) and space radiation (SR)...
January 7, 2017: Mutation Research
https://www.readbyqxmd.com/read/28088356/advancing-the-prediction-accuracy-of-protein-protein-interactions-by-utilizing-evolutionary-information-from-position-specific-scoring-matrix-and-ensemble-classifier
#18
Lei Wang, Zhu-Hong You, Shi-Xiong Xia, Feng Liu, Xing Chen, Xin Yan, Yong Zhou
Protein-Protein Interactions (PPIs) are essential to most biological processes and play a critical role in most cellular functions. With the development of high-throughput biological techniques and in silico methods, a large number of PPI data have been generated for various organisms, but many problems remain unsolved. These factors promoted the development of the in silico methods based on machine learning to predict PPIs. In this study, we propose a novel method by combining ensemble Rotation Forest (RF) classifier and Discrete Cosine Transform (DCT) algorithm to predict the interactions among proteins...
January 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28088302/the-cyp79a1-catalyzed-conversion-of-tyrosine-to-e-p-hydroxyphenylacetaldoxime-unravelled-using-an-improved-method-for-homology-modeling
#19
Dario Vazquez-Albacete, Marco Montefiori, Stefan Kol, Mohammed Saddik Motawia, Birger Lindberg Møller, Lars Olsen, Morten H H Nørholm
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin...
January 11, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#20
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
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