keyword
MENU ▼
Read by QxMD icon Read
search

Homology modelling

keyword
https://www.readbyqxmd.com/read/28812259/evolutionary-dynamics-in-the-fungal-polarization-network-a-mechanistic-perspective
#1
REVIEW
Eveline T Diepeveen, Leila Iñigo de la Cruz, Liedewij Laan
Polarity establishment underlies proper cell cycle completion across virtually all organisms. Much progress has been made in generating an understanding of the structural and functional components of this process, especially in model species. Here we focus on the evolutionary dynamics of the fungal polarization protein network in order to determine general components and mechanistic principles, species- or lineage-specific adaptations and the evolvability of the network. The currently available genomic and proteomic screens in a variety of fungal species have shown three main characteristics: (1) certain proteins, processes and functions are conserved throughout the fungal clade; (2) orthologous functions can never be assumed, as various cases have been observed of homologous loci with dissimilar functions; (3) species have, typically, various species- or lineage-specific proteins incorporated in their polarization network...
August 15, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28812061/behavioral-comorbidities-and-drug-treatments-in-a-zebrafish-scn1lab-model-of-dravet-syndrome
#2
Brian P Grone, Tiange Qu, Scott C Baraban
Loss-of-function mutations in SCN1A cause Dravet syndrome (DS), a catastrophic childhood epilepsy in which patients experience comorbid behavioral conditions, including movement disorders, sleep abnormalities, anxiety, and intellectual disability. To study the functional consequences of voltage-gated sodium channel mutations, we use zebrafish with a loss-of-function mutation in scn1lab, a zebrafish homolog of human SCN1A. Homozygous scn1lab(s552/s552) mutants exhibit early-life seizures, metabolic deficits, and early death...
July 2017: ENeuro
https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#3
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811634/molecular-cloning-and-expression-of-osmotin-in-a-baculovirus-insect-system-purified-osmotin-mitigates-amyloid-beta-deposition-in-neuronal-cells
#4
Noman Bin Abid, Gwangho Yoon, Myeong Ok Kim
Osmotin is a pathogenesis-related plant protein, have gained focus of research because of its homology with mammalian adiponectin. The therapeutic properties of osmotin have been explored in recent years as it exhibits neuroprotective effects against amyloid beta-, glutamate- and ethanol-induced synaptic dysfunction and neurodegeneration. In the present study, the full-length gene of the tobacco plant osmotin was cloned and expressed in the Sf9 insect cell line using the baculovirus expression system. In vitro analysis of purified Osmotin protein showed excellent cell viability, p-AMPK activation and a reduction in amyloid-beta deposition...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811600/exploring-leishmania-secretory-proteins-to-design-b-and-t-cell-multi-epitope-subunit-vaccine-using-immunoinformatics-approach
#5
Nazia Khatoon, Rajan Kumar Pandey, Vijay Kumar Prajapati
Visceral leishmaniasis (VL) is a fatal form of leishmaniasis which affects 70 countries, worldwide. Increasing drug resistance, HIV co-infection, and poor health system require operative vaccination strategy to control the VL transmission dynamics. Therefore, a holistic approach is needed to generate T and B memory cells to mediate long-term immunity against VL infection. Consequently, immunoinformatics approach was applied to design Leishmania secretory protein based multi-epitope subunit vaccine construct consisting of B and T cell epitopes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811564/computational-identification-of-y-linked-markers-and-genes-in-the-grass-carp-genome-by-using-a-pool-and-sequence-method
#6
Aidi Zhang, Rong Huang, Liangming Chen, Lv Xiong, Libo He, Yongming Li, Lanjie Liao, Zuoyan Zhu, Yaping Wang
The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811335/the-conserved-and-unique-genetic-architecture-of-kernel-size-and-weight-in-maize-and-rice
#7
Jie Liu, Juan Huang, Huan Guo, Liu Lan, Hongze Wang, Yuancheng Xu, Xiaohong Yang, Wenqiang Li, Hao Tong, Yingjie Xiao, Qingchun Pan, Feng Qiao, Mohammad Sharif Raihan, Haijun Liu, Xuehai Zhang, Ning Yang, Xiaqing Wang, Min Deng, Minliang Jin, Lijun Zhao, Xin Luo, Yang Zhou, Xiang Li, Wei Zhan, Nannan Liu, Hong Wang, Gengshen Chen, Qing Li, Jianbing Yan
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28811154/theoretical-study-on-electron-structure-and-charge-transport-properties-of-tetraazapentacene-derivatives
#8
Xiao-Dan Tang
By Means of Marcus electron transfer theory, the charge transport properties of tetraazapentacene (4N-PEN) derivatives were systematically explored. The reorganization energies were studied by both adiabatic potential-energy surfaces and normal mode analysis. The charge diffusion constants were evaluated from the random walk simulation. From the perspective of homology modeling, a selected 4N-PEN derivative without experimental crystal structure was built into three kinds of possible packing modes with reference to its relative analogues and then fully optimized...
June 23, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28811134/a-new-chemotype-inhibitor-for-the-human-organic-cation-transporter-3-hoct3
#9
Xiaolei Pan, Kavita A Iyer, Hebing Liu, Douglas H Sweet, Małgorzata Dukat
Human organic cation transporters (OCTs) represent an understudied neurotransmitter uptake mechanism for which no selective agents have yet been identified. Several neurotransmitters (e.g. serotonin, norepinephrine) are low-affinity substrates for these transporters, but possess higher affinity for other transporters (e.g. the serotonin or norepinephrine transporters; SERT and NET, respectively). We have identified a new class of OCT inhibitors with a phenylguanidine structural scaffold. Here, we examine the actions of a series of such compounds and report preliminary structure-activity relationships (SARs) - the first dedicated SAR study of OCT3 action...
August 5, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28808438/atsas-2-8-a-comprehensive-data-analysis-suite-for-small-angle-scattering-from-macromolecular-solutions
#10
D Franke, M V Petoukhov, P V Konarev, A Panjkovich, A Tuukkanen, H D T Mertens, A G Kikhney, N R Hajizadeh, J M Franklin, C M Jeffries, D I Svergun
ATSAS is a comprehensive software suite for the analysis of small-angle scattering data from dilute solutions of biological macromolecules or nanoparticles. It contains applications for primary data processing and assessment, ab initio bead modelling, and model validation, as well as methods for the analysis of flexibility and mixtures. In addition, approaches are supported that utilize information from X-ray crystallography, nuclear magnetic resonance spectroscopy or atomistic homology modelling to construct hybrid models based on the scattering data...
August 1, 2017: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28808380/identification-and-analysis-of-jasmonate-pathway-genes-in-coffea-canephora-robusta-coffee-by-in-silico-approach
#11
Kosaraju Bharathi, H L Sreenath
BACKGROUND: Coffea canephora is the commonly cultivated coffee species in the world along with Coffea arabica. Different pests and pathogens affect the production and quality of the coffee. Jasmonic acid (JA) is a plant hormone which plays an important role in plants growth, development, and defense mechanisms, particularly against insect pests. The key enzymes involved in the production of JA are lipoxygenase, allene oxide synthase, allene oxide cyclase, and 12-oxo-phytodienoic reductase...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28808284/molecular-rationale-behind-the-differential-substrate-specificity-of-bacterial-rnd-multi-drug-transporters
#12
Venkata Krishnan Ramaswamy, Attilio V Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
Resistance-Nodulation-cell Division (RND) transporters AcrB and AcrD of Escherichia coli expel a wide range of substrates out of the cell in conjunction with AcrA and TolC, contributing to the onset of bacterial multidrug resistance. Despite sharing an overall sequence identity of ~66% (similarity ~80%), these RND transporters feature distinct substrate specificity patterns whose underlying basis remains elusive. We performed exhaustive comparative analyses of the putative substrate binding pockets considering crystal structures, homology models and conformations extracted from multi-copy μs-long molecular dynamics simulations of both AcrB and AcrD...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807849/danshen-improves-survival-of-patients-with-colon-cancer-and-dihydroisotanshinone-i-inhibit-the-proliferation-of-colon-cancer-cells-via-apoptosis-and-skp2-signaling-pathway
#13
Yin-Yin Lin, I-Yun Lee, Wen-Shih Huang, Yu-Shin Lin, Feng-Che Kuan, Li-Hsin Shu, Yu-Ching Cheng, Yao-Hsu Yang, Ching-Yuan Wu
ETHNOPHARMACOLOGICAL RELEVANCE: Danshen (Salvia miltiorrhiza Bunge) is widely used in traditional Chinese medicine. However, it's definite clinical effect and mechanism on colon carcinoma is unclear. AIM OF THE STUDY: To test the hypothesis that the protective effect of danshen on colon cancer and discover the bioactive compounds through in vitro study. MATERIALS AND METHODS: We conducted a nationwide cohort study by using population-based data from the Taiwan National Health Insurance Research Database (NHIRD)...
August 11, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28807751/a-novel-pmca3-mutation-in-an-ataxic-patient-with-hypomorphic-phosphomannomutase-2-pmm2-heterozygote-mutations-biochemical-characterization-of-the-pump-defect
#14
Mattia Vicario, Tito Calì, Domenico Cieri, Francesca Vallese, Raissa Bortolotto, Raffaele Lopreiato, Francesco Zonta, Marta Nardella, Alessia Micalizzi, Dirk J Lefeber, Enza Maria Valente, Enrico Bertini, Giuseppe Zanotti, Ginevra Zanni, Marisa Brini, Ernesto Carafoli
The neuron-restricted isoform 3 of the plasma membrane Ca(2+) ATPase plays a major role in the regulation of Ca(2+) homeostasis in the brain, where the precise control of Ca(2+) signaling is a necessity. Several function-affecting genetic mutations in the PMCA3 pump associated to X-linked congenital cerebellar ataxias have indeed been described. Interestingly, the presence of co-occurring mutations in additional genes suggest their synergistic action in generating the neurological phenotype as digenic modulators of the role of PMCA3 in the pathologies...
August 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28805297/mesenchymal-stem-cells-deliver-exogenous-mir-21-via-exosomes-to-inhibit-nucleus-pulposus-cell-apoptosis-and-reduce-intervertebral-disc-degeneration
#15
Xiaofei Cheng, Guoying Zhang, Liang Zhang, Ying Hu, Kai Zhang, Xiaojiang Sun, Changqing Zhao, Hua Li, Yan Michael Li, Jie Zhao
Although mesenchymal stem cells (MSCs) transplantation into the IVD (intervertebral disc) may be beneficial in inhibiting apoptosis of nucleus pulposus cells (NPCs) and alleviating IVD degeneration, the underlying mechanism of this therapeutic process has not been fully explained. The purpose of this study was to explore the protective effect of MSC-derived exosomes (MSC-exosomes) on NPC apoptosis and IVD degeneration and investigate the regulatory effect of miRNAs in MSC-exosomes and associated mechanisms for NPC apoptosis...
August 14, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28804564/incrna-h19-promotes-tongue-squamous-cell-carcinoma-progression-through-%C3%AE-catenin-gsk3%C3%AE-emt-signaling-via-association-with-ezh2
#16
Da-Ming Zhang, Zhao-Yu Lin, Zhao-Hui Yang, You-Yuan Wang, Di Wan, Jiang-Long Zhong, Pei-Lin Zhuang, Zhi-Quan Huang, Bin Zhou, Wei-Liang Chen
H19 is involved in tumor metastasis and associated with tumor progression. Enhancer of zest homolog 2 (EZH2) is overexpressed in multiple cancer types and correlates with tumor proliferation, epithelial-mesenchymal transition, and poor prognosis. However, the interaction between H19 and EZH2 to promote tongue squamous cell carcinoma (TSCC) progression remains largely uncharacterized. Insitu hybridization and quantitative reverse-transcription PCR (qRT-PCR) were performed to measure H19 expression in primary TSCC and adjacent normal tissues and cell lines...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28803907/cu-sensing-transcription-factor-mac1-coordinates-with-the-ctr-transporter-family-to-regulate-cu-acquisition-and-virulence-in-aspergillus-fumigatus
#17
Zhendong Cai, Wenlong Du, Qiuqiong Zeng, Nanbiao Long, Chuanchao Dai, Ling Lu
Copper (Cu) is an essential trace element and is regarded as an important virulence factor in fungal pathogens. Previous studies suggest that a putative Cu-sensing transcription factor Mac1 and the Cu transporter Ctr family play important roles during fungal development and virulence. However, how Cu importers of the Ctr family are involved in the Cu acquisition and what is the functional relationship between them have not been fully investigated yet. Here, we demonstrate that the yeast Mac1 homolog in the opportunistic human pathogen Aspergillus fumigatus is required during colony development under low Cu conditions...
August 10, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28803330/bime2-a-novel-gene-required-for-interhomolog-meiotic-recombination-in-the-protist-model-organism-tetrahymena
#18
Anura Shodhan, Maria Novatchkova, Josef Loidl
Meiotic recombination is initiated by DNA double-strand breaks (DSBs). Most DSBs are converted into nonreciprocal exchanges (gene conversions) or crossovers (COs) between sister chromatids. Only a minority of DSBs are processed toward interhomolog COs, the precursors of the chiasmata that connect homologous chromosomes. Dmc1, the meiosis-specific paralog of the universal recombination protein Rad51, is required for interhomolog COs; in its absence, univalents are primarily formed. Here, we report a ciliate-specific novel meiotic gene, BIME2, which also promotes interhomolog crossing over...
August 12, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28802835/residues-in-the-eighth-transmembrane-domain-of-the-proton-coupled-folate-transporter-slc46a1-play-an-important-role-in-defining-the-aqueous-translocation-pathway-and-in-folate-substrate-binding
#19
Srinivas Aluri, Rongbao Zhao, Andras Fiser, I David Goldman
The proton-coupled folate transporter (PCFT-SLC46A1) is required for intestinal folate absorption and folate transport across the choroid plexus. This report addresses the structure/function of the 8th transmembrane helix. Based upon biotinylation of cysteine-substituted residues by MTSEA-biotin, 14 contiguous exofacial residues to Leu316 were accessible to the extracellular compartment of the 23 residues in this helix (Leu303-Leu325). Pemetrexed blocked biotinylation of six Cys-substituted residues deep within the helix implicating an important role for this region in folate binding...
August 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28802806/comparing-parietal-quantity-processing-mechanisms-between-humans-and-macaques
#20
REVIEW
Ben M Harvey, Stefania Ferri, Guy A Orban
Quantity processing studies typically assume functional homology between regions within macaque and human intraparietal sulcus (IPS), where apparently similar locations respond to broadly similar tasks. However, macaque single cell neurophysiology is difficult to compare to human functional magnetic resonance imaging (fMRI); particularly in multivoxel pattern analysis and adaptation paradigms, or where different tasks are used. fMRI approaches incorporating neural tuning models allow closer comparison, revealing human numerosity-selective responses only outside the IPS...
August 9, 2017: Trends in Cognitive Sciences
keyword
keyword
109484
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"