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Protein structure prediction

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https://www.readbyqxmd.com/read/28444931/study-of-structure-dependent-chromatographic-behavior-of-glycopeptides-using-reversed-phase-nanolc
#1
Petr Kozlik, Radoslav Goldman, Miloslav Sanda
Analysis of glycosylation is challenging due to micro- and macro-heterogeneity of the protein attachment. A combination of liquid chromatography with tandem mass spectrometry is one of the most powerful tools for glycopeptide analysis. In this work, we show the effect of various monosaccharide units on the retention time of glycopeptides. Retention behavior of several glycoforms of six peptides obtained from tryptic digest of haptoglobin, hemopexin and sex hormone binding globulin was studied on a reversed phase chromatographic column...
April 26, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28444810/large-differences-in-proportions-of-harmful-and-benign-amino-acid-substitutions-between-proteins-and-diseases
#2
Gerard C P Schaafsma, Mauno Vihinen
Genes and proteins are known to have differences in their sensitivity to alterations. Despite numerous sequencing studies, proportions of harmful and harmless substitutions are not known for proteins and groups of proteins. To address this question, we predicted the outcome for all possible single amino acid substitutions in nine representative protein groups by using the PON-P2 method. The effects on 996 proteins were studied and vast differences were noticed. Proteins in the cancer group harbour the largest proportion of harmful variants (42...
April 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28443104/genome-wide-identification-and-characterization-of-apple-bhlh-transcription-factors-and-expression-analysis-in-response-to-drought-and-salt-stress
#3
Ke Mao, Qinglong Dong, Chao Li, Changhai Liu, Fengwang Ma
The bHLH (basic helix-loop-helix) transcription factor family is the second largest in plants. It occurs in all three eukaryotic kingdoms, and plays important roles in regulating growth and development. However, family members have not previously been studied in apple. Here, we identified 188 MdbHLH proteins in apple "Golden Delicious" (Malus × domestica Borkh.), which could be classified into 18 groups. We also investigated the gene structures and 12 conserved motifs in these MdbHLHs. Coupled with expression analysis and protein interaction network prediction, we identified several genes that might be responsible for abiotic stress responses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28443071/deletion-of-lipoteichoic-acid-synthase-impacts-expression-of-genes-encoding-cell-surface-proteins-in-lactobacillus-acidophilus
#4
Kurt Selle, Yong J Goh, Brant R Johnson, Sarah O'Flaherty, Joakim M Andersen, Rodolphe Barrangou, Todd R Klaenhammer
Lactobacillus acidophilus NCFM is a well-characterized probiotic microorganism, supported by a decade of genomic and functional phenotypic investigations. L. acidophilus deficient in lipoteichoic acid (LTA), a major immunostimulant in Gram-positive bacteria, has been shown to shift immune system responses in animal disease models. However, the pleiotropic effects of removing LTA from the cell surface in lactobacilli are unknown. In this study, we surveyed the global transcriptional and extracellular protein profiles of two strains of L...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28443063/on-the-molecular-evolution-of-leptin-leptin-receptor-and-endospanin
#5
Richard Lyle Londraville, Jeremy W Prokop, Robert Joel Duff, Qin Liu, Matthew Tuttle
Over a decade passed between Friedman's discovery of the mammalian leptin gene (1) and its cloning in fish (2) and amphibians (3). Since 2005, the concept of gene synteny conservation (vs. gene sequence homology) was instrumental in identifying leptin genes in dozens of species, and we now have leptin genes from all major classes of vertebrates. This database of LEP (leptin), LEPR (leptin receptor), and LEPROT (endospanin) genes has allowed protein structure modeling, stoichiometry predictions, and even functional predictions of leptin function for most vertebrate classes...
2017: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/28442765/the-gpr139-reference-agonists-1a-and-7c-and-tryptophan-and-phenylalanine-share-a-common-binding-site
#6
Anne Cathrine Nøhr, Willem Jespers, Mohamed A Shehata, Leonard Floryan, Vignir Isberg, Kirsten Bayer Andersen, Johan Åqvist, Hugo Gutiérrez-de-Terán, Hans Bräuner-Osborne, David E Gloriam
GPR139 is an orphan G protein-coupled receptor expressed in the brain, in particular in the habenula, hypothalamus and striatum. It has therefore been suggested that GPR139 is a possible target for metabolic disorders and Parkinson's disease. Several surrogate agonist series have been published for GPR139. Two series published by Shi et al. and Dvorak et al. included agonists 1a and 7c respectively, with potencies in the ten-nanomolar range. Furthermore, Isberg et al. and Liu et al. have previously shown that tryptophan (Trp) and phenylalanine (Phe) can activate GPR139 in the hundred-micromolar range...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442542/missense-mutations-in-the-wd40-domain-of-ahi1-cause-non-syndromic-retinitis-pigmentosa
#7
Thanh-Minh T Nguyen, Sarah Hull, Ronald Roepman, L Ingeborgh van den Born, Machteld M Oud, Erik de Vrieze, Lisette Hetterschijt, Stef J F Letteboer, Sylvia E C van Beersum, Ellen A Blokland, Helger G Yntema, Frans P M Cremers, Paul A van der Zwaag, Gavin Arno, Erwin van Wijk, Andrew R Webster, Lonneke Haer-Wigman
BACKGROUND: Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). METHODS: Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling...
April 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28441108/novel-clades-of-the-hu-ihf-superfamily-point-to-unexpected-roles-in-the-eukaryotic-centrosome-chromosome-partitioning-and-biological-conflicts
#8
A Maxwell Burroughs, Gurmeet Kaur, Dapeng Zhang, L Aravind
The HU superfamily of proteins, with a unique DNA-binding mode, has been extensively studied as the primary chromosome-packaging protein of the bacterial superkingdom. Representatives also play a role in DNA-structuring during recombination events and in eukaryotic organellar genome maintenance. However, beyond these well-studied roles, little is understood of the functional diversification of this large superfamily. Using sensitive sequence and structure analysis methods we identify multiple novel clades of the HU superfamily...
April 25, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28440912/performance-of-in-silico-tools-for-the-evaluation-of-p16ink4a-cdkn2a-variants-in-cagi
#9
Marco Carraro, Giovanni Minervini, Manuel Giollo, Yana Bromberg, Emidio Capriotti, Rita Casadio, Roland Dunbrack, Lisa Elefanti, Pietro Fariselli, Carlo Ferrari, Julian Gough, Panagiotis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Chiara Menin, Pier Luigi Martelli, Abhishek Niroula, Lipika R Pal, Susanna Repo, Maria Chiara Scaini, Mauno Vihinen, Qiong Wei, Qifang Xu, Yuedong Yang, Yizhou Yin, Jan Zaucha, Huiying Zhao, Yaoqi Zhou, Steven E Brenner, John Moult, Silvio C E Tosatto
Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of ten variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene...
April 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28440410/a-novel-notch3-mutation-identified-in-patients-with-oral-cancer-by-whole-exome-sequencing
#10
Yanjun Yi, Zhuowei Tian, Houyu Ju, Guoxin Ren, Jingzhou Hu
Oral cancer is a serious disease caused by environmental factors and/or susceptible genes. In the present study, in order to identify useful genetic biomarkers for cancer prediction and prevention, and for personalized treatment, we detected somatic mutations in 5 pairs of oral cancer tissues and blood samples using whole exome sequencing (WES). Finally, we confirmed a novel nonsense single-nucleotide polymorphism (SNP; chr19:15288426A>C) in the NOTCH3 gene with sanger sequencing, which resulted in a N1438T mutation in the protein sequence...
April 25, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28440302/performance-of-machine-learning-scoring-functions-in-structure-based-virtual-screening
#11
Maciej Wójcikowski, Pedro J Ballester, Pawel Siedlecki
Classical scoring functions have reached a plateau in their performance in virtual screening and binding affinity prediction. Recently, machine-learning scoring functions trained on protein-ligand complexes have shown great promise in small tailored studies. They have also raised controversy, specifically concerning model overfitting and applicability to novel targets. Here we provide a new ready-to-use scoring function (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439920/understanding-human-thiol-dioxygenase-enzymes-structure-to-function-and-biology-to-pathology
#12
REVIEW
Bibekananda Sarkar, Mahesh Kulharia, Anil K Mantha
Amino acid metabolism is a significant metabolic activity in humans, especially of sulphur-containing amino acids, methionine and cysteine (Cys). Cys is cytotoxic and neurotoxic in nature; hence, mammalian cells maintain a constant intracellular level of Cys. Metabolism of Cys is mainly regulated by two thiol dioxygenases: cysteine dioxygenase (CDO) and 2-aminoethanethiol dioxygenase (ADO). CDO and ADO are the only human thiol dioxygenases reported with a role in Cys metabolism and localized to mitochondria...
April 24, 2017: International Journal of Experimental Pathology
https://www.readbyqxmd.com/read/28439455/the-evolution-of-logic-circuits-for-the-purpose-of-protein-contact-map-prediction
#13
Samuel D Chapman, Christoph Adami, Claus O Wilke, Dukka B Kc
Predicting protein structure from sequence remains a major open problem in protein biochemistry. One component of predicting complete structures is the prediction of inter-residue contact patterns (contact maps). Here, we discuss protein contact map prediction by machine learning. We describe a novel method for contact map prediction that uses the evolution of logic circuits. These logic circuits operate on feature data and output whether or not two amino acids in a protein are in contact or not. We show that such a method is feasible, and in addition that evolution allows the logic circuits to be trained on the dataset in an unbiased manner so that it can be used in both contact map prediction and the selection of relevant features in a dataset...
2017: PeerJ
https://www.readbyqxmd.com/read/28439280/insights-on-structure-and-function-of-a-late-embryogenesis-abundant-protein-from-amaranthus-cruentus-an-intrinsically-disordered-protein-involved-in-protection-against-desiccation-oxidant-conditions-and-osmotic-stress
#14
Alma L Saucedo, Eric E Hernández-Domínguez, Luis A de Luna-Valdez, Angel A Guevara-García, Abraham Escobedo-Moratilla, Esaú Bojorquéz-Velázquez, Federico Del Río-Portilla, Daniel A Fernández-Velasco, Ana P Barba de la Rosa
Late embryogenesis abundant (LEA) proteins are part of a large protein family that protect other proteins from aggregation due to desiccation or osmotic stresses. Recently, the Amaranthus cruentus seed proteome was characterized by 2D-PAGE and one highly accumulated protein spot was identified as a LEA protein and was named AcLEA. In this work, AcLEA cDNA was cloned into an expression vector and the recombinant protein was purified and characterized. AcLEA encodes a 172 amino acid polypeptide with a predicted molecular mass of 18...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28438996/morphotype-of-bacteroids-in-different-legumes-correlates-with-the-number-and-type-of-symbiotic-ncr-peptides
#15
Jesús Montiel, J Allan Downie, Attila Farkas, Péter Bihari, Róbert Herczeg, Balázs Bálint, Peter Mergaert, Attila Kereszt, Éva Kondorosi
In legume nodules, rhizobia differentiate into nitrogen-fixing forms called bacteroids, which are enclosed by a plant membrane in an organelle-like structure called the symbiosome. In the Inverted Repeat-Lacking Clade (IRLC) of legumes, this differentiation is terminal due to irreversible loss of cell division ability and is associated with genome amplification and different morphologies of the bacteroids that can be swollen, elongated, spherical, and elongated-branched, depending on the host plant. In Medicago truncatula, this process is orchestrated by nodule-specific cysteine-rich peptides (NCRs) delivered into developing bacteroids...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28438806/emerging-affinity-based-proteomic-technologies-for-large-scale-plasma-profiling-in-cardiovascular-disease
#16
REVIEW
J Gustav Smith, Robert E Gerszten
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets...
April 25, 2017: Circulation
https://www.readbyqxmd.com/read/28438488/whole-genome-sequencing-predicts-novel-human-disease-models-in-rhesus-macaques
#17
Benjamin N Bimber, Ranjani Ramakrishnan, Rita Cervera-Juanes, Ravi Madhira, Samuel M Peterson, Robert B Norgren, Betsy Ferguson
Rhesus macaques are an important pre-clinical model of human disease. To advance our understanding of genomic variation that may influence disease, we surveyed genome-wide variation in 21 rhesus macaques. We employed best-practice variant calling, validated with Mendelian inheritance. Next, we used alignment data from our cohort to detect genomic regions likely to produce inaccurate genotypes, potentially due to either gene duplication or structural variation between individuals. We generated a final dataset of >16 million high confidence variants, including 13 million in Chinese-origin rhesus macaques, an increasingly important disease model...
April 21, 2017: Genomics
https://www.readbyqxmd.com/read/28437460/an-aggregation-removal-model-for-the-formation-and-size-determination-of-post-synaptic-scaffold-domains
#18
Jonas Ranft, Leandro G Almeida, Pamela C Rodriguez, Antoine Triller, Vincent Hakim
The formation and stability of synapses are key questions in neuroscience. Post-synaptic domains have been classically conceived as resulting from local insertion and turnover of proteins at the synapse. However, insertion is likely to occur outside the post-synaptic domains and advances in single-molecule imaging have shown that proteins diffuse in the plane of the membrane prior to their accumulation at synapses. We quantitatively investigated this scenario using computer simulations and mathematical analysis, taking for definiteness the specific case of inhibitory synapse components, i...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437379/associations-of-lifetime-trauma-and-chronic-stress-with-c-reactive-protein-in-adults-ages-50-and-older-examining-the-moderating-role-of-perceived-control
#19
Ari J Elliot, Christopher J Mooney, Frank J Infurna, Benjamin P Chapman
OBJECTIVE: To investigate whether high perceived control mitigates systemic inflammatory risk associated with traumatic and chronic stress exposures in older adults. METHODS: A sample of community-dwelling adults ages 50 and older (N=4,779) was drawn from the Health and Retirement Study (HRS). Structural equation models tested interactions of lifetime trauma and chronic stress with mastery and perceived constraints predicting baseline levels and four-year change in C-reactive protein (CRP)...
April 21, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28436435/structure-and-function-of-the-divalent-anion-na-symporter-from-vibrio-cholerae-and-a-humanized-variant
#20
Rongxin Nie, Steven Stark, Jindrich Symersky, Ronald S Kaplan, Min Lu
Integral membrane proteins of the divalent anion/Na(+) symporter (DASS) family translocate dicarboxylate, tricarboxylate or sulphate across cell membranes, typically by utilizing the preexisting Na(+) gradient. The molecular determinants for substrate recognition by DASS remain obscure, largely owing to the absence of any substrate-bound DASS structure. Here we present 2.8-Å resolution X-ray structures of VcINDY, a DASS from Vibrio cholerae that catalyses the co-transport of Na(+) and succinate. These structures portray the Na(+)-bound VcINDY in complexes with succinate and citrate, elucidating the binding sites for substrate and two Na(+) ions...
April 24, 2017: Nature Communications
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