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Homology modelling

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https://www.readbyqxmd.com/read/27913751/new-fungal-defensin-like-peptides-provide-evidence-for-fold-change-of-proteins-in-evolution
#1
Yucheng Wu, Bin Gao, Shunyi Zhu
Defensins containing a consensus cystine framework, Cys[1]..Cys[2]X3Cys[3]..Cys[4]..Cys[5]X1Cys[6] ("X", any amino acids normally except Cys; "...", variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming a cystine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation...
December 2, 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27913310/targeted-disruption-of-the-orphan-receptor-gpr151-does-not-alter-pain-related-behaviour-despite-a-strong-induction-in-dorsal-root-ganglion-expression-in-a-model-of-neuropathic-pain
#2
Fiona E Holmes, Niall Kerr, Ying-Ju Chen, Penny Vanderplank, Craig A McArdle, David Wynick
BACKGROUND: Gpr151 is an orphan GPCR whose function is unknown. The restricted pattern of neuronal expression in the habenula, dorsal horn of the spinal cord and dorsal root ganglion plus homology with the galanin family of receptors imply a role in nociception. RESULTS: Real-time quantitative RT-PCR demonstrated a 49.9±2.9 fold highly significant (P<0.001) increase in Gpr151 mRNA expression in the dorsal root ganglion 7days after the spared nerve injury model of neuropathic pain...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27911897/heterologous-protection-against-asian-zika-virus-challenge-in-rhesus-macaques
#3
Matthew T Aliota, Dawn M Dudley, Christina M Newman, Emma L Mohr, Dane D Gellerup, Meghan E Breitbach, Connor R Buechler, Mustafa N Rasheed, Mariel S Mohns, Andrea M Weiler, Gabrielle L Barry, Kim L Weisgrau, Josh A Eudailey, Eva G Rakasz, Logan J Vosler, Jennifer Post, Saverio Capuano, Thaddeus G Golos, Sallie R Permar, Jorge E Osorio, Thomas C Friedrich, Shelby L O'Connor, David H O'Connor
BACKGROUND: Zika virus (ZIKV; Flaviviridae, Flavivirus) was declared a public health emergency of international concern by the World Health Organization (WHO) in February 2016, because of the evidence linking infection with ZIKV to neurological complications, such as Guillain-Barre Syndrome in adults and congenital birth defects including microcephaly in the developing fetus. Because development of a ZIKV vaccine is a top research priority and because the genetic and antigenic variability of many RNA viruses limits the effectiveness of vaccines, assessing whether immunity elicited against one ZIKV strain is sufficient to confer broad protection against all ZIKV strains is critical...
December 2016: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/27911737/the-conservation-of-phosphate-binding-residues-among-pht1-transporters-suggests-that-distinct-transport-affinities-are-unlikely-to-result-from-differences-in-the-phosphate-binding-site
#4
REVIEW
S Antony Ceasar, Alison Baker, Stephen P Muench, S Ignacimuthu, Stephen A Baldwin
The plant PHosphate Transporter 1 (PHT1) family of membrane proteins belongs to the major facilitator super family and plays a major role in the acquisition of inorganic phosphate (Pi) from the soil and its transport within the plant. These transporters have been well characterized for expression patterns, localization, and in some cases affinity. Furthermore, the crystal structure of a high-affinity eukaryotic phosphate transporter from the fungus Piriformospora indica (PiPT) has revealed important information on the residues involved in Pi transport...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911022/membrane-defects-and-genetic-redundancy-are-we-at-a-turning-point-for-dyt1-dystonia
#5
REVIEW
Ana Cascalho, Julie Jacquemyn, Rose E Goodchild
Heterozygosity for a 3-base pair deletion (ΔGAG) in TOR1A/torsinA is one of the most common causes of hereditary dystonia. In this review, we highlight current understanding of how this mutation causes disease from research spanning structural biochemistry, cell science, neurobiology, and several model organisms. We now know that homozygosity for ΔGAG has the same effects as Tor1a(KO) , implicating a partial loss of function mechanism in the ΔGAG/+ disease state. In addition, torsinA loss specifically affects neurons in mice, even though the gene is broadly expressed, apparently because of differential expression of homologous torsinB...
December 2, 2016: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/27910803/the-prognostic-and-predictive-value-of-tmprss2-erg-gene-fusion-and-erg-protein-expression-in-prostate-cancer-biopsies
#6
Kasper Drimer Berg
BACKGROUND: The clinical course of prostate carcinoma (PCa) is very heterogeneous. Consequently, a personalised approach for risk stratification and treatment planning is important. Recently, it has become evident that PCa, also at the genomic level, is heterogeneous. An early and common alteration is the gene fusion between the transmembrane protease serine 2 (TMPRSS2) gene and the v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) gene resulting in expression of the oncoprotein ERG...
December 2016: Danish Medical Journal
https://www.readbyqxmd.com/read/27910195/mulberrofuran-g-protects-ischemic-injury-induced-cell-death-via-inhibition-of-nox4-mediated-ros-generation-and-er-stress
#7
Sungeun Hong, Jaeyoung Kwon, Dong-Woo Kim, Hak Ju Lee, Dongho Lee, Woongchon Mar
The aim of this study was to investigate the neuroprotective effect of mulberrofuran G (MG) in in vitro and in vivo models of cerebral ischemia. MG was isolated from the root bark of Morus bombycis. MG inhibited nicotinamide adenine dinucleotide phosphate oxidase (NOX) enzyme activity and oxygen-glucose deprivation/reoxygenation (OGD/R)-induced NOX4 protein expression in SH-SY5Y cells. MG inhibited the expression of activated caspase-3 and caspase-9 and cleaved poly adenine dinucleotide phosphate-ribose polymerase in OGD/R-induced SH-SY5Y cells...
December 2, 2016: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/27910041/efficient-genome-editing-in-induced-pluripotent-stem-cells-with-engineered-nucleases-in-vitro
#8
Vittavat Termglinchan, Timon Seeger, Caressa Chen, Joseph C Wu, Ioannis Karakikes
Precision genome engineering is rapidly advancing the application of the induced pluripotent stem cells (iPSCs) technology for in vitro disease modeling of cardiovascular diseases. Targeted genome editing using engineered nucleases is a powerful tool that allows for reverse genetics, genome engineering, and targeted transgene integration experiments to be performed in a precise and predictable manner. However, nuclease-mediated homologous recombination is an inefficient process. Herein, we describe the development of an optimized method combining site-specific nucleases and the piggyBac transposon system for "seamless" genome editing in pluripotent stem cells with high efficiency and fidelity in vitro...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27909446/functional-toxicogenomic-profiling-expands-insight-into-modulators-of-formaldehyde-toxicity-in-yeast
#9
Matthew North, Brandon D Gaytán, Carlos Romero, Vanessa Y De La Rosa, Alex Loguinov, Martyn T Smith, Luoping Zhang, Chris D Vulpe
Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. Accordingly, occupational and environmental exposure to FA is prevalent worldwide. Various adverse effects, including nasopharyngeal, sinonasal, and lymphohematopoietic cancers, have been linked to FA exposure, prompting designation of FA as a human carcinogen by U.S. and international scientific entities. Although the mechanism(s) of FA toxicity have been well studied, additional insight is needed in regard to the genetic requirements for FA tolerance...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27909020/the-design-and-transformation-of-biofundamentals-a-nonsurvey-introductory-evolutionary-and-molecular-biology-course
#10
Michael W Klymkowsky, Jeremy D Rentsch, Emina Begovic, Melanie M Cooper
Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master...
2016: CBE Life Sciences Education
https://www.readbyqxmd.com/read/27908830/protective-efficacy-of-fc-targeting-conserved-influenza-virus-m2e-antigen-expressed-by-lactobacillus-plantarum
#11
Wen-Tao Yang, Gui-Lian Yang, Qian Wang, Hai-Bin Huang, Yan-Long Jiang, Chun-Wei Shi, Jian-Zhong Wang, Ke-Yan Huang, Yu-Bei Jin, Chun-Feng Wang
The influenza A (H1N1) virus is a highly contagious acute respiratory disease affecting pigs and humans. This disease causes severe economic loss in many countries, and developing mucosal vaccines is an efficient strategy to control the influenza virus. The neonatal Fc receptor (FcRn) plays an important role in transferring IgG across polarized epithelial cells. In the present study, an oral vaccine was developed using Lactobacillus plantarum to deliver the internal influenza viral protein M2e fused to an IgG Fc fragment...
November 28, 2016: Antiviral Research
https://www.readbyqxmd.com/read/27908641/free-energy-perturbation-calculation-of-relative-binding-free-energy-between-broadly-neutralizing-antibodies-and-the-gp120-glycoprotein-of-hiv-1
#12
Anthony J Clark, Tatyana Gindin, Baoshan Zhang, Lingle Wang, Robert Abel, Colleen S Murret, Fang Xu, Amy Bao, Nina J Lu, Tongqing Zhou, Peter D Kwong, Lawrence Shapiro, Barry Honig, Richard A Friesner
Direct calculation of relative binding affinities between antibodies and antigens is a long-sought goal. However, despite substantial efforts, no generally applicable computational method has been described. Here we describe a systematic free energy perturbation (FEP) protocol and calculate the binding affinities between the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class. The protocol has been adapted from successful studies of small molecules to address the challenges associated with modeling protein-protein interactions...
November 28, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27907832/modeling-of-the-catalytic-core-of-arabidopsis-thaliana-dicer-like-4-protein-and-its-complex-with-double-stranded-rna
#13
Agnieszka Mickiewicz, Joanna Sarzyńska, Maciej Miłostan, Anna Kurzyńska-Kokorniak, Agnieszka Rybarczyk, Piotr Łukasiak, Tadeusz Kuliński, Marek Figlerowicz, Jacek Błażewicz
Plant Dicer-like proteins (DCLs) belong to the Ribonuclease III (RNase III) enzyme family. They are involved in the regulation of gene expression and antiviral defense through RNA interference pathways. A model plant, Arabidopsis thaliana encodes four DCL proteins (AtDCL1-4) that produce different classes of small regulatory RNAs. Our studies focus on AtDCL4 that processes double-stranded RNAs (dsRNAs) into 21 nucleotide trans-acting small interfering RNAs. So far, little is known about the structures of plant DCLs and the complexes they form with dsRNA...
November 17, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27906638/gene-duplications-and-losses-among-vertebrate-deoxyribonucleoside-kinases-of-the-non-tk1-family
#14
Zeeshan Mutahir, Louise Slot Christiansen, Anders R Clausen, Martin W Berchtold, Zoran Gojkovic, Birgitte Munch-Petersen, Wolfgang Knecht, Jure Piškur
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK)...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#15
Caitlyn L McCafferty, Yuri V Sergeev
The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905512/plant-phenolic-volatiles-inhibit-quorum-sensing-in-pectobacteria-and-reduce-their-virulence-by-potential-binding-to-expi-and-expr-proteins
#16
Janak Raj Joshi, Netaly Khazanov, Hanoch Senderowitz, Saul Burdman, Alexander Lipsky, Iris Yedidia
Quorum sensing (QS) is a population density-dependent regulatory system in bacteria that couples gene expression to cell density through accumulation of diffusible signaling molecules. Pectobacteria are causal agents of soft rot disease in a range of economically important crops. They rely on QS to coordinate their main virulence factor, production of plant cell wall degrading enzymes (PCWDEs). Plants have evolved an array of antimicrobial compounds to anticipate and cope with pathogens, of which essential oils (EOs) are widely recognized...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27905217/to-crispr-and-beyond-the-evolution-of-genome-editing-in-stem-cells
#17
Kuang-Yui Chen, Paul S Knoepfler
The goal of editing the genomes of stem cells to generate model organisms and cell lines for genetic and biological studies has been pursued for decades. There is also exciting potential for future clinical impact in humans. While recent, rapid advances in targeted nuclease technologies have led to unprecedented accessibility and ease of gene editing, biology has benefited from past directed gene modification via homologous recombination, gene traps and other transgenic methodologies. Here we review the history of genome editing in stem cells (including via zinc finger nucleases, transcription activator-like effector nucleases and CRISPR-Cas9), discuss recent developments leading to the implementation of stem cell gene therapies in clinical trials and consider the prospects for future advances in this rapidly evolving field...
December 1, 2016: Regenerative Medicine
https://www.readbyqxmd.com/read/27905063/efficient-gene-targeting-in-mouse-zygotes-mediated-by-crispr-cas9-protein
#18
Chris J Jung, Junli Zhang, Elizabeth Trenchard, Kent C Lloyd, David B West, Barry Rosen, Pieter J de Jong
The CRISPR/Cas9 system has rapidly advanced targeted genome editing technologies. However, its efficiency in targeting with constructs in mouse zygotes via homology directed repair (HDR) remains low. Here, we systematically explored optimal parameters for targeting constructs in mouse zygotes via HDR using mouse embryonic stem cells as a model system. We characterized several parameters, including single guide RNA cleavage activity and the length and symmetry of homology arms in the construct, and we compared the targeting efficiency between Cas9, Cas9nickase, and dCas9-FokI...
November 30, 2016: Transgenic Research
https://www.readbyqxmd.com/read/27904902/a-novel-hirudin-derivative-inhibiting-thrombin-without-bleeding-for-subcutaneous-injection
#19
Bing Zhao, Yanling Zhang, Yinong Huang, Jinchao Yu, Yaran Li, Qi Wang, Yixin Ma, Hou-Yan Song, Min Yu, Wei Mo
Currently, anticoagulants would be used to prevent thrombosis. Thrombin is an effector enzyme for haemostasis and thrombosis. We designed a direct thrombin inhibitor peptide (DTIP) using molecular simulation and homology modelling and demonstrated that the C-terminus of DTIP interacts with exosite I, and N-terminus with the activity site of thrombin, respectively. DTIP interfered with thrombin-mediated coagulation in human, rat and mouse plasma (n=10 per group) and blocked clotting in human whole blood in vitro...
December 1, 2016: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/27903800/genetic-variability-of-myxoma-virus-genomes
#20
Christoph Braun, Andrea Thürmer, Rolf Daniel, Anne-Kathrin Schultz, Ingo Bulla, Horst Schirrmeier, Dietmar Mayer, Andreas Neubert, Claus-Peter Czerny
: Myxomatosis is a recurrent problem on rabbit farms throughout Europe despite the success of vaccines. To identify gene variations of field and vaccine strains that may be responsible for changes in virulence, immunomodulation, and immunoprotection, the genomes of 6 Myxoma virus strains (MYXV) were sequenced: German field isolates Munich-1, FLI-H, 2604, 3207, vaccine strain MAV, and challenge strain ZA. The analyzed genomes ranged from 147.6 kb (strain MAV) to 161.8 kb (strain 3207) in size...
November 30, 2016: Journal of Virology
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