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Protein structure alignment

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https://www.readbyqxmd.com/read/29148771/an-qm-mm-study-of-the-reaction-catalyzed-by-alkyladenine-dna-glycosylase-examination-of-the-substrate-specificity-of-a-dna-repair-enzyme
#1
Stefan A P Lenz, Stacey D Wetmore
Human alkyladenine DNA glycosylase (AAG) functions as part of the base excision repair pathway to excise structurally diverse oxidized and alkylated DNA purines. Specifically, AAG uses a water molecule activated by a general base and a non-specific active site lined with aromatic residues to cleave the N-glycosidic bond. Despite broad substrate specificity, AAG does not target the natural purines (adenine (A) and guanine (G)). Using the ONIOM(QM:MM) methodology, we provide fundamental atomic level details of AAG bound to DNA-containing a neutral substrate (hypoxanthine (Hx)), a non-substrate (G), or a cationic substrate (7-methylguanine (7MeG)), and probe changes in the reaction pathway that occur when AAG targets different nucleotides...
November 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29147019/identification-and-characterization-of-serine-protease-inhibitors-in-a-parasitic-wasp-pteromalus-puparum
#2
Lei Yang, Yaotian Mei, Qi Fang, Jiale Wang, Zhichao Yan, Qisheng Song, Zhe Lin, Gongyin Ye
Serine protease inhibitors (SPIs) regulate protease-mediated activities by inactivating their cognate proteinases, and are involved in multiple physiological processes. SPIs have been extensively studied in vertebrates and invertebrates; however, little SPI information is available in parasitoids. Herein, we identified 57 SPI genes in total through the genome of a parasitoid wasp, Pteromalus puparum. Gene structure analyses revealed that these SPIs contain 7 SPI domains. Depending on their mode of action, these SPIs can be categorized into serpins, canonical inhibitors and alpha-2-macroglobulins (A2Ms)...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29143380/polo-like-kinase-1-inhibition-results-in-misaligned-chromosomes-and-aberrant-spindles-in-porcine-oocytes-during-the-first-meiotic-division
#3
Y Liao, D Lin, P Cui, B Abbasi, C Chen, Z Zhang, Y Zhang, Y Dong, R Rui, S Ju
Polo-like kinase 1 (Plk1), a type of serine/threonine protein kinase, has been implicated in various functions in the regulation of mitotic processes. However, these kinase's roles in meiotic division are not fully understood, particularly in the meiotic maturation of porcine oocytes. In this study, the expression and spatiotemporal localization of Plk1 were initially assessed in the meiotic process of pig oocytes by utilizing Western blotting with immunofluorescent staining combined with confocal microscopy imaging technique...
November 16, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/29143142/prevalence-of-ns5b-resistance-associated-variants-in-treatment-na%C3%A3-ve-asian-patients-with-chronic-hepatitis-c
#4
Song Yang, Huichun Xing, Shenghu Feng, Wei Ju, Shunai Liu, Xiaomei Wang, Weini Ou, Jun Cheng, Calvin Q Pan
There is little information on the association between baseline non-structural protein (NS) 5b resistance-associated variants (RAVs) and treatment failure in hepatitis C patients. This study examined the frequencies of natural hepatitis C virus (HCV) NS5B resistance-associated variants (RAVs) in an Asian cohort. Samples from Asian HCV patients enrolled between October 2009 and September 2014 were analyzed for NS5B RAVs within the region from amino acid 230 to 371. Serum samples were tested by PCR genotyping, with sequence alignment performed using the neighbor-joining method...
November 15, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29142246/a-comprehensive-structural-biochemical-and-biological-profiling-of-the-human-nudix-hydrolase-family
#5
Jordi Carreras-Puigvert, Marinka Zitnik, Ann-Sofie Jemth, Megan Carter, Judith E Unterlass, Björn Hallström, Olga Loseva, Zhir Karem, José Manuel Calderón-Montaño, Cecilia Lindskog, Per-Henrik Edqvist, Damian J Matuszewski, Hammou Ait Blal, Ronnie P A Berntsson, Maria Häggblad, Ulf Martens, Matthew Studham, Bo Lundgren, Carolina Wählby, Erik L L Sonnhammer, Emma Lundberg, Pål Stenmark, Blaz Zupan, Thomas Helleday
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142123/initiation-elongation-and-realignment-during-influenza-virus-mrna-synthesis
#6
Aartjan J W Te Velthuis, Judith Oymans
The RNA-dependent RNA polymerase (RdRp) of the influenza A virus replicates and transcribes the viral genome segments in the nucleus of the host cell. To transcribe these viral genome segments, the RdRp 'snatches' capped RNA oligonucleotides from nascent host cell mRNAs and aligns these primers to the ultimate or penultimate nucleotide of the segments for the initiation of viral mRNA synthesis. It has been proposed that this initiation process is not processive and that the RdRp uses a prime-realign mechanism during transcription...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29141686/anisotropic-m%C3%A3-ller-glial-scaffolding-supports-a-multiplex-lattice-mosaic-of-photoreceptors-in-zebrafish-retina
#7
Mikiko Nagashima, Jeremy Hadidjojo, Linda K Barthel, David K Lubensky, Pamela A Raymond
BACKGROUND: The multiplex, lattice mosaic of cone photoreceptors in the adult fish retina is a compelling example of a highly ordered epithelial cell pattern, with single cell width rows and columns of cones and precisely defined neighbor relationships among different cone types. Cellular mechanisms patterning this multiplex mosaic are not understood. Physical models can provide new insights into fundamental mechanisms of biological patterning. In earlier work, we developed a mathematical model of photoreceptor cell packing in the zebrafish retina, which predicted that anisotropic mechanical tension in the retinal epithelium orients planar polarized adhesive interfaces to align the columns as cone photoreceptors are generated at the retinal margin during post-embryonic growth...
November 15, 2017: Neural Development
https://www.readbyqxmd.com/read/29134579/investigation-on-secondary-structure-perturbations-of-proteins-embedded-in-solid-lipid-matrices-as-a-novel-indicator-of-their-biological-activity-upon-in-vitro-release
#8
Farrukh Zeeshan, Misbah Tabbassum, Lene Jorgensen, Natalie J Medlicott
Protein biologics are prone to conformational changes during formulation development. Limited methods are available for conformational analysis of proteins in solid state and in the presences of formulation excipients. The aim of this study was to investigate the secondary structures of proteins encased in solid lipid matrices as a novel indicator of their stability upon in vitro release. Model proteins namely catalase and lysozyme were incorporated into lipid namely Precirol® AT05 (glycerol palmitostearate, melting point 58°C) at 30% w/w loading using melting and mixing and wet granulation methods...
October 6, 2017: AAPS PharmSciTech
https://www.readbyqxmd.com/read/29134248/the-ancient-claudin-dni2-facilitates-yeast-cell-fusion-by-compartmentalizing-dni1-into-a-membrane-subdomain
#9
M-Ángeles Curto, Sandra Moro, Francisco Yanguas, Carmen Gutiérrez-González, M-Henar Valdivieso
Dni1 and Dni2 facilitate cell fusion during mating. Here, we show that these proteins are interdependent for their localization in a plasma membrane subdomain, which we have termed the mating fusion domain. Dni1 compartmentation in the domain is required for cell fusion. The contribution of actin, sterol-dependent membrane organization, and Dni2 to this compartmentation was analysed, and the results showed that Dni2 plays the most relevant role in the process. In turn, the Dni2 exit from the endoplasmic reticulum depends on Dni1...
November 13, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/29131864/comparison-of-histone-like-hu-protein-dna-binding-properties-and-hu-ihf-protein-sequence-alignment
#10
Dmitri Kamashev, Yulia Agapova, Sergey Rastorguev, Anna A Talyzina, Konstantin M Boyko, Dmitry A Korzhenevskiy, Anna Vlaskina, Raif Vasilov, Vladimir I Timofeev, Tatiana V Rakitina
BACKGROUND: The structure and function of bacterial nucleoid are controlled by histone-like proteins of HU/IHF family, omnipresent in bacteria and also founding archaea and some eukaryotes.HU protein binds dsDNA without sequence specificity and avidly binds DNA structures with propensity to be inclined such as forks, three/four-way junctions, nicks, overhangs and DNA bulges. Sequence comparison of thousands of known histone-like proteins from diverse bacteria phyla reveals relation between HU/IHF sequence, DNA-binding properties and other protein features...
2017: PloS One
https://www.readbyqxmd.com/read/29131478/gene-isolation-using-degenerate-primers-targeting-protein-motif-a-laboratory-exercise
#11
Brandon Pei Hui Yeo, Lian Chee Foong, Sheh May Tam, Vivian Lee, Siaw San Hwang
Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the isolation and characterization of many plant resistance gene analogues (RGAs), is featured in the development of a series of laboratory experiments using important molecular biology techniques...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29129633/sequence-and-structure-insights-of-kazal-type-thrombin-inhibitor-protein-studied-with-phylogeny-homology-modeling-and-dynamic-mm-gbsa-studies
#12
Aparna Jadhav, RadhaCharan Dash, Raj Hirwani, Malik Abdin
Despite the wide medical importance of serine protease inhibitors, many of kazal type proteins are still to be explored. These thrombin inhibiting proteins are found in the digestive system of hematophagous organisms mainly Arthropods. We studied one of such protein i.e. Kazal type-1 protein from sand-fly Phlebotomus papatasi as its structure and interaction with thrombin is unclear. Initially, Dipetalin a kazal-follistasin domain protein was run through PSI-BLAST to retrieve related sequences. Using this set of sequence a phylogenetic tree was constructed, which identified a distantly related kazal type-1 protein...
November 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29128216/strain-hardening-and-anisotropy-in-tensile-fracture-properties-of-sheared-model-mozzarella-cheeses
#13
Prateek Sharma, Peter A Munro, Tzvetelin T Dessev, Peter G Wiles, E Allen Foegeding
We studied the tensile fracture properties of model Mozzarella cheeses with varying amounts of shear work input (3.3-73.7 kJ/kg). After manufacture, cheeses were elongated by manual rolling at 65°C followed by tensile testing at 21°C on dumbbell-shaped samples cut both parallel and perpendicular to the rolling direction. Strain hardening parameters were estimated from stress-strain curves using 3 different methods. Fracture stress and strain for longitudinal samples did not vary significantly with shear work input up to 26...
November 8, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29125993/substrate-and-mechanotransduction-influence-serca2a-localization-in-human-pluripotent-stem-cell-derived-cardiomyocytes-affecting-functional-performance
#14
Sebastian Martewicz, Elena Serena, Susi Zatti, Gordon Keller, Nicola Elvassore
Physical cues are major determinants of cellular phenotype and evoke physiological and pathological responses on cell structure and function. Cellular models aim to recapitulate basic functional features of their in vivo counterparts or tissues in order to be of use in in vitro disease modeling or drug screening and testing. Understanding how culture systems affect in vitro development of human pluripotent stem cell (hPSC)-derivatives allows optimization of cellular human models and gives insight in the processes involved in their structural organization and function...
October 16, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29121344/rational-design-of-pleurotus-eryngii-versatile-ligninolytic-peroxidase-for-enhanced-ph-and-thermal-stability-through-structure-based-protein-engineering
#15
Yu Gao, Jian-Jun Li, Lanyan Zheng, Yuguang Du
Versatile peroxidase (VP) from Pleurotus eryngii is a high redox potential peroxidase. It has aroused great biotechnological interest due to its ability to oxidize a wide range of substrates, but its application is still limited due to low pH and thermal stability. Since CiP (Coprinopsis cinerea peroxidase) and PNP (peanut peroxidase) exhibited higher pH and thermal stability than VP, several motifs, which might contribute to their pH and thermal stability, were identified through structure and sequence alignment...
November 7, 2017: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29117247/a-mobile-loop-near-the-active-site-acts-as-a-switch-between-the-dual-activities-of-a-viral-protease-deubiquitinase
#16
Isabelle Jupin, Maya Ayach, Lucile Jomat, Sonia Fieulaine, Stéphane Bressanelli
The positive-strand RNA virus Turnip yellow mosaic virus (TYMV) encodes an ovarian tumor (OTU)-like protease/deubiquitinase (PRO/DUB) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity, and in removal of ubiquitin chains from ubiquitylated substrates through its DUB activity. Here, the crystal structures of TYMV PRO/DUB mutants and molecular dynamics simulations reveal that an idiosyncratic mobile loop participates in reversibly constricting its unusual catalytic site by adopting "open", "intermediate" or "closed" conformations...
November 8, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29115198/the-consequences-of-unemployment-on-diet-composition-and-purchase-behaviour-a-longitudinal-study-from-denmark
#17
Sinne Smed, Inge Tetens, Thomas Bøker Lund, Lotte Holm, Annemette Ljungdalh Nielsen
OBJECTIVE: To explore and describe quantitatively the effect over time of unemployment on food purchase behaviour and diet composition. DESIGN: Longitudinal data from 2008-2012, with monthly food purchase data aligned with register data on unemployment measured as a dichotomous indicator as well as a trend accounting for the duration. SETTING: A household panel which registers daily food purchases combined with detailed nutritional information and registration of the duration of unemployment at individual level...
November 8, 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/29109430/the-first-draft-reference-genome-of-the-american-mink-neovison-vison
#18
Zexi Cai, Bent Petersen, Goutam Sahana, Lone B Madsen, Knud Larsen, Bo Thomsen, Christian Bendixen, Mogens Sandø Lund, Bernt Guldbrandtsen, Frank Panitz
The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It's an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29106973/reconstitution-of-snare-proteins-into-solid-supported-lipid-bilayer-stacks-and-x-ray-structure-analysis
#19
Yihui Xu, Jan Kuhlmann, Martha Brennich, Karlo Komorowski, Reinhard Jahn, Claudia Steinem, Tim Salditt
SNAREs are known as an important family of proteins mediating vesicle fusion. For various biophysical studies, they have been reconstituted into supported single bilayers via proteoliposome adsorption and rupture. In this study we extended this method to the reconstitution of SNAREs into supported multilamellar lipid membranes, i.e. oriented multibilayer stacks, as an ideal model system for x-ray structure analysis (x-ray reflectivity and diffraction). The reconstitution was implemented through a pathway of proteomicelle, proteoliposome and multibilayer...
October 26, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29097729/akap350-recruits-eb1-to-the-spindle-poles-ensuring-proper-spindle-orientation-and-lumen-formation-in-3d-epithelial-cell-cultures
#20
Evangelina Almada, Facundo M Tonucci, Florencia Hidalgo, Anabela Ferretti, Solange Ibarra, Alejandro Pariani, Rodrigo Vena, Cristián Favre, Javier Girardini, Arlinet Kierbel, M Cecilia Larocca
The organization of epithelial cells to form hollow organs with a single lumen requires the accurate three-dimensional arrangement of cell divisions. Mitotic spindle orientation is defined by signaling pathways that provide molecular links between specific spots at the cell cortex and astral microtubules, which have not been fully elucidated. AKAP350 is a centrosomal/Golgi scaffold protein, implicated in the regulation of microtubule dynamics. Using 3D epithelial cell cultures, we found that cells with decreased AKAP350 expression (AKAP350KD) formed polarized cysts with abnormal lumen morphology...
November 2, 2017: Scientific Reports
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