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Protein structure alignment

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https://www.readbyqxmd.com/read/28815397/detecting-and-accounting-for-multiple-sources-of-positional-variance-in-peak-list-registration-analysis-and-spin-system-grouping
#1
Andrey Smelter, Eric C Rouchka, Hunter N B Moseley
Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values...
August 16, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28813599/tetraterpene-synthase-substrate-and-product-specificity-in-the-green-microalga-botryococcus-braunii-race-l
#2
Hem Raj Thapa, Su Tang, James C Sacchettini, Timothy P Devarenne
Recently, the biosynthetic pathway for lycopadiene, a C40 tetraterpenoid hydrocarbon, was deciphered from the L race of Botryococcus braunii, an alga that produces hydrocarbon oils capable of being converted into combustible fuels. The lycopadiene pathway is initiated by the squalene synthase (SS)-like enzyme lycopaoctaene synthase (LOS), which catalyzes the head-to-head condensation of two C20 geranylgeranyl diphosphate (GGPP) molecules to produce C40 lycopaoctaene. LOS shows unusual substrate promiscuity for SS or SS-like enzymes by utilizing C15 farnesyl diphosphate (FPP) and C20 phytyl diphosphate in addition to GGPP as substrates...
August 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28808384/molecular-authentication-of-the-traditional-medicinal-plant-lakshman-booti-smithia-conferta-sm-and-its-adulterants-through-dna-barcoding
#3
Suraj D Umdale, Parthraj R Kshirsagar, Manoj M Lekhak, Nikhil B Gaikwad
BACKGROUND: Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton. leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine. AIM: This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808132/defining-electron-bifurcation-in-the-electron-transferring-flavoprotein-family
#4
Amaya M Garcia Costas, Saroj Poudel, Anne-Frances Miller, Gerrit J Schut, Rhesa N Ledbetter, Kathryn R Fixen, Lance C Seefeldt, Michael W W Adams, Caroline S Harwood, Eric S Boyd, John W Peters
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low and high potential electrons. It is the third recognized form of energy conservation in biology and has recently been described in select electron transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via ETF quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer as well as a non-redox active adenosine monophosphate (AMP)...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28803692/a-janus-faced-im30-ring-involved-in-thylakoid-membrane-fusion-is-assembled-from-im30-tetramers
#5
Michael Saur, Raoul Hennig, Phoebe Young, Kristiane Rusitzka, Nadja Hellmann, Jennifer Heidrich, Nina Morgner, Jürgen Markl, Dirk Schneider
Biogenesis and dynamics of thylakoid membranes likely involves membrane fusion events. Membrane attachment of the inner membrane-associated protein of 30 kDa (IM30) affects the structure of the lipid bilayer, finally resulting in membrane fusion. Yet, how IM30 triggers membrane fusion is largely unclear. IM30 monomers pre-assemble into stable tetrameric building blocks, which further align to form oligomeric ring structures, and differently sized IM30 rings bind to membranes. Based on a 3D reconstruction of IM30 rings, we locate the IM30 loop 2 region at the bottom of the ring and show intact membrane binding but missing fusogenic activity of loop 2 mutants...
August 2, 2017: Structure
https://www.readbyqxmd.com/read/28801228/identification-of-the-first-cathelicidin-gene-from-skin-of-chinese-giant-salamanders-andrias-davidianus-with-its-potent-antimicrobial-activity
#6
Hui Yang, Baoyue Lu, Dandan Zhou, Lin Zhao, Weijia Song, Lixin Wang
Cathelicidins, as effector molecules, play important roles against infections and represent a crucial component of the innate immune system in vertebrates. They are widely studied in mammals, but little is known in amphibians. In the present study, we report the identification and characterization of a novel cathelicidin from Chinese giant salamander Andrias davidianus, which is the first study in Caudata amphibian. The cDNA sequence encodes a predicted 148-amino-acid polypeptide, which composed of a 20-residue signal peptide, a 94-residue conserved cathelin domain and a 34-residue mature peptide...
August 9, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28800110/response-of-dermal-fibroblasts-to-biochemical-and-physical-cues-in-aligned-polycaprolactone-silk-fibroin-nanofiber-scaffolds-for-application-in-tendon-tissue-engineering
#7
Chih-Hao Chen, Shih-Hsien Chen, Chang-Yi Kuo, Meng-Lun Li, Jyh-Ping Chen
Silk fibroin (SF) and fiber alignment were introduced into polycaprolactone (PCL)-based electrospun nanofibers as chemical and physical cues for tendon tissue engineering applications. The physicochemical properties of random PCL (RP) nanofibers, random PCL/SF (RPSF) nanofibers and aligned PCL/SF (APSF) nanofibers were characterized for fiber orientation and SF blending effects. An in vitro cell culture with rabbit dermal fibroblasts (RDFBs) on nanofibers indicated that SF promotes cell proliferation to a higher extent than fiber alignment...
August 11, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28798063/alignment-of-the-protein-substrate-hairpin-along-the-seca-two-helix-finger-primes-protein-transport-in-escherichia-coli
#8
Qi Zhang, Sudipta Lahiri, Tithi Banerjee, Zhongmou Sun, Donald Oliver, Ishita Mukerji
A conserved hairpin-like structure comprised of a signal peptide and early mature region initiates protein transport across the SecY or Sec61α channel in Bacteria or Archaea and Eukarya, respectively. When and how this initiator substrate hairpin forms remains a mystery. Here, we have used the bacterial SecA ATPase motor protein and SecYEG channel complex to address this question. Engineering of a functional miniprotein substrate onto the end of SecA allowed us to efficiently form ternary complexes with SecYEG for spectroscopic studies...
August 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28797638/a-novel-tnfaip8-gene-mediates-l-arginine-metabolism-in-apostichopus-japonicus
#9
Yina Shao, Huahui Chen, Miao Lv, Chenghua Li, Weiwei Zhang, Ye Li, Xuelin Zhao, Yongbo Bao
Tumor necrosis factor (TNF)-α-induced protein 8 (TNFAIP8) family is a newly identified protein with vital roles in maintaining immune homeostasis. In the current study, we first cloned and characterized a TNFAIP8 gene from the invertebrate sea cucumber Apostichopus japonicus. The gene was designated as AjTNFAIP8. The full-length cDNA of AjTNFAIP8 was 1455 bp long and encoded a matured protein of 201 amino acid residues. Structural analysis indicated that AjTNFAIP8 had a death effector domain (DED)-like domain and composed of six α-helices...
August 7, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28795237/the-adaptive-evolution-database-taed-a-new-release-of-a-database-of-phylogenetically-indexed-gene-families-from-chordates
#10
Russell A Hermansen, Benjamin P Oswald, Stormy Knight, Stephen D Shank, David Northover, Katharine L Korunes, Stephen N Michel, David A Liberles
With the large collections of gene and genome sequences, there is a need to generate curated comparative genomic databases that enable interpretation of results in an evolutionary context. Such resources can facilitate an understanding of the co-evolution of genes in the context of a genome mapped onto a phylogeny, of a protein structure, and of interactions within a pathway. A phylogenetically indexed gene family database, the adaptive evolution database (TAED), is presented that organizes gene families and their evolutionary histories in a species tree context...
August 9, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28792792/the-effect-of-rgd-ngr-peptide-modification-of-melanoma-differentiation-associated-gene-7-interleukin-24-on-its-receptor-attachment-an-in-silico-analysis
#11
Samaneh Bina, Seyed Younes Hosseini, Fatemeh Shenavar, Ebrahim Hosseini, Mojtaba Mortazavi
Melanoma differentiation-associated gene-7 (mda-7/interleukin [IL]-24), a unique tumor suppressor gene, induces selective apoptosis in tumor cells. Secreted IL-24 binds to heterodimeric receptor complexes of IL-20R1/IL-20R2, IL-22R1/IL-20R2, or sigma-1 receptor (Sig1R) that consequently enhances apoptosis. However, this mechanism is not well understood and most likely involves different pathways. Targeting of cytokine by tumor homing peptides (THPs) to the tumor cell surface molecule-like integrin shows to be beneficial in gene immunotherapy approaches...
August 2017: Cancer Biotherapy & Radiopharmaceuticals
https://www.readbyqxmd.com/read/28776025/three-dimensional-positioning-and-structure-of-chromosomes-in-a-human-prophase-nucleus
#12
Bo Chen, Mohammed Yusuf, Teruo Hashimoto, Ana Katrina Estandarte, George Thompson, Ian Robinson
The human genetic material is packaged into 46 chromosomes. The structure of chromosomes is known at the lowest level, where the DNA chain is wrapped around a core of eight histone proteins to form nucleosomes. Around a million of these nucleosomes, each about 11 nm in diameter and 6 nm in thickness, are wrapped up into the complex organelle of the chromosome, whose structure is mostly known at the level of visible light microscopy to form a characteristic cross shape in metaphase. However, the higher-order structure of human chromosomes, between a few tens and hundreds of nanometers, has not been well understood...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28774490/hmgb3-modulates-ros-production-via-activating-tlr-cascade-in-apostichopus-japonicus
#13
Zhimeng Lv, Zhen Zhang, Zhixin Wei, Chenghua Li, Yina Shao, Weiwei Zhang, Xuelin Zhao, Jinbo Xiong
High mobility group box protein 3 (HMGB3) regulates proliferation and inflammatory response in vertebrates. However, its functional roles in invertebrates are largely unknown. In this study, a HMGB3 homologue molecule was identified from Apostichopus japonicus (designated as AjHMGB3) by RACE approach. The full-length cDNA of AjHMGB3 was of 2298 bp with an open reading frame of 1320 bp encoding a 439-amino-acid (aa) residue protein. Structural analysis then conducted and the results revealed that AjHMGB3 processed two conserved HMGBs (133-204 and 210-279 aa) and an acidic tail...
August 1, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28766097/ranking-docking-poses-by-graph-matching-of-protein-ligand-interactions-lessons-learned-from-the-d3r-grand-challenge-2
#14
Priscila da Silva Figueiredo Celestino Gomes, Franck Da Silva, Guillaume Bret, Didier Rognan
A novel docking challenge has been set by the Drug Design Data Resource (D3R) in order to predict the pose and affinity ranking of a set of Farnesoid X receptor (FXR) agonists, prior to the public release of their bound X-ray structures and potencies. In a first phase, 36 agonists were docked to 26 Protein Data Bank (PDB) structures of the FXR receptor, and next rescored using the in-house developed GRIM method. GRIM aligns protein-ligand interaction patterns of docked poses to those of available PDB templates for the target protein, and rescore poses by a graph matching method...
August 1, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28763035/a-motif-in-the-f-homomorph-of-rabbit-haemorrhagic-disease-virus-polymerase-is-important-for-the-subcellular-localisation-of-the-protein-and-its-ability-to-induce-redistribution-of-golgi-membranes
#15
Nadya Urakova, Andrew C Warden, Peter A White, Tanja Strive, Michael Frese
Rabbit haemorrhagic disease virus (RHDV) is a calicivirus that infects and frequently kills rabbits. Previously, we showed that the RHDV RNA-dependent RNA polymerase (RdRp) is associated with distinct, but yet uncharacterised subcellular structures and is capable of inducing a redistribution of Golgi membranes. In this study, we identified a partially hidden hydrophobic motif that determines the subcellular localisation of recombinant RHDV RdRp in transfected cells. This novel motif, 189LLWGCDVGVAVCAAAVFHNICY210, is located within the F homomorph, between the conserved F3 and A motifs of the core RdRp domain...
August 1, 2017: Viruses
https://www.readbyqxmd.com/read/28762605/ensemblator-v3-robust-atom-level-comparative-analyses-and-classification-of-protein-structure-ensembles
#16
Andrew E Brereton, P Andrew Karplus
Ensembles of protein structures are increasingly used to represent the conformational variation of a protein as determined by experiment and/or by molecular simulations, as well as uncertainties that may be associated with structure determinations or predictions. Making the best use of such information requires the ability to quantitatively compare entire ensembles. For this reason, we recently introduced the Ensemblator (Clark et al. [2015] Protein Sci 24, 1528), a novel approach to compare user-defined groups of models, in residue level detail...
August 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28762578/identification-and-functionality-prediction-of-pathogenesis-related-protein-1-from-legume-family
#17
Meenakshi Tellis, Monika Mathur, Gayatri Gurjar, Narendra Kadoo, Vidya Gupta
The production and accumulation of pathogenesis related (PR) proteins in plants is one of the important responses to biotic and abiotic stress. Large number of identified PR proteins has been categorized into 17 functional families based on their structure, phylogenetics and biological activities. However, they are not widely studied in legume crops. Using 29 PR1 proteins from Arabidopsis thaliana, as query, here we have predicted 92 candidate PR1 proteins through the PSI-BLAST and HMMER programs. These candidate proteins were comprehensively analysed with, multiple sequence alignment, domain architecture studies, signal peptide and motif extraction followed by phylogenetic analysis...
August 1, 2017: Proteins
https://www.readbyqxmd.com/read/28760694/effects-of-tissue-fixation-and-dehydration-on-tendon-collagen-nanostructure
#18
Mikael J Turunen, Hanifeh Khayyeri, Manuel Guizar-Sicairos, Hanna Isaksson
Collagen is the most prominent protein in biological tissues. Tissue fixation is often required for preservation or sectioning of the tissue. This may affect collagen nanostructure and potentially provide incorrect information when analyzed after fixation. We aimed to unravel the effect of 1) ethanol and formalin fixation and 2) 24h air-dehydration on the organization and structure of collagen fibers at the nano-scale using small and wide angle X-ray scattering. Samples were divided into 4 groups: ethanol fixed, formalin fixed, and two untreated sample groups...
July 28, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28756483/identification-of-structure-stabilizing-interactions-in-enzymes-a-novel-mechanism-to-impact-enzyme-activity
#19
Marisol Serrano, Veronica Gonzalez, Supriyo Ray, Maria D Chavez, Mahesh Narayan
Cruzain, a cysteine protease in the cathepsin family, is pivotal to the life-cycle of Trypanosoma cruzi, the etiological agent in Chagas disease. Current inhibitors of cruzain suffer from drawbacks involving gastrointestinal and neurological side effects and as a result have spurred the search for alternative anti-trypanocidals. Through sequence alignment studies and intra-residue interaction analysis of the pro-protein of cruzain (pro-cruzain), we have identified a host of non-active site residues that are conserved among the cathepsins...
July 29, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28754701/genome-sequence-and-composition-of-a-tolyporphin-producing-cyanobacterium-microbial-community
#20
Rebecca-Ayme Hughes, Yunlong Zhang, Ran Zhang, Philip G Williams, Jonathan S Lindsey, Eric S Miller
The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a non-extant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Herein, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates...
July 28, 2017: Applied and Environmental Microbiology
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