keyword
MENU ▼
Read by QxMD icon Read
search

protein folding

keyword
https://www.readbyqxmd.com/read/28651352/circular-rna-profiling-reveals-that-circular-rnas-from-anxa2-can-be-used-as-new-biomarkers-for-multiple-sclerosis
#1
Iparraguirre Leire, Muñoz-Culla Maider, Prada Iñigo, Castillo-Triviño Tamara, Olascoaga Javier, Otaegui David
Multiple Sclerosis is an autoimmune disease, with higher prevalence in women, in whom the immune system is dysregulated. This dysregulation has been shown to correlate with changes in transcriptome expression as well as in gene-expression regulators, such as non-coding RNAs (e.g. microRNAs). Indeed, some of these have been suggested as biomarkers for multiple sclerosis even though few biomarkers have reached the clinical practice.Recently, a novel family of non-coding RNAs, circular RNAs, has emerged as a new player in the complex network of gene-expression regulation...
June 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28651197/ascorbic-acid-protects-coccomyxa-subellipsoidea-against-metal-toxicity-through-modulation-of-ros-no-balance-and-metal-uptake
#2
Jozef Kováčik, Gabriela Rotková, Marek Bujdoš, Petr Babula, Viera Peterková, Peter Matúš
Impact of exogenous ascorbic acid (AsA, 100μM) on acute metal toxicity (Pb and Hg, 24h of exposure to 100μM) in unicellular green alga Coccomyxa subellipsoidea was studied. Hg (often extensively) depleted amount of pigments, potassium, soluble proteins, endogenous AsA, non-protein thiols and nitric oxide signal but elevated ROS signal and activities of catalase and superoxide dismutase. Responses to Pb application (if any) were less visible with ROS signal being slightly elevated and amount of non-protein thiols being slightly reduced...
June 16, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28651101/competitive-ligands-facilitate-dissociation-of-the-complex-of-bifunctional-inhibitor-and-protein-kinase
#3
Taavi Ivan, Erki Enkvist, Hedi Sinijarv, Asko Uri
Dissociation of the complex of a ligand and a protein usually follows the kinetic profile of the first order process and the rate of dissociation is not affected by the presence of competitive ligands. We discovered that dissociation of the complex between a bifunctional ligand and a protein kinase (the catalytic subunit of cAMP-dependent protein kinase), an enzyme possessing 2 different substrate binding sites, was accelerated (facilitated) over 50-fold in the presence of competitive ligands at higher concentrations...
June 20, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28651056/significantly-improved-protein-folding-thermodynamics-using-a-dispersion-corrected-water-model-and-a-new-residue-specific-force-field
#4
Hao-Nan Wu, Fan Jiang, Yun-Dong Wu
An accurate potential energy model is crucial for biomolecular simulations. Despite many recent improvements of classical protein force fields, there are remaining key issues: much weaker temperature-dependence of folding/unfolding equilibrium, and overly collapsed unfolded or disordered states. For the later problem, a new water model (TIP4P-D) has been proposed to correct the significantly underestimated water dispersion interactions. Here, using TIP4P-D, we reveal problems in current force fields through failures in folding model systems (a polyalanine peptide, Trp-cage and the GB1 hairpin)...
June 26, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28651051/molecular-precision-at-micrometer-length-scales-hierarchical-assembly-of-dna-protein-nanostructures
#5
Daniel Schiffels, Veronika A Szalai, J Alexander Liddle
Robust self-assembly across length scales is a ubiquitous feature of biological systems, but remains challenging for synthetic structures. Taking a cue from biology - where disparate molecules work together to produce large, functional assemblies - we demonstrate how to engineer microscale structures with nanoscale features: Our self-assembly approach begins by using DNA polymerase to controllably create double-stranded DNA (dsDNA) sections on a single-stranded template. The single-stranded DNA (ssDNA) sections are then folded into a mechanically flexible skeleton by the origami method...
June 26, 2017: ACS Nano
https://www.readbyqxmd.com/read/28651013/loss-of-prion-protein-induces-a-primed-state-of-type-i-interferon-responsive-genes
#6
Giulia Malachin, Malin R Reiten, Øyvind Salvesen, Håvard Aanes, Jorke H Kamstra, Kerstin Skovgaard, Peter M H Heegaard, Cecilie Ersdal, Arild Espenes, Michael A Tranulis, Maren K Bakkebø
The cellular prion protein (PrPC) has been extensively studied because of its pivotal role in prion diseases; however, its functions remain incompletely understood. A unique line of goats has been identified that carries a nonsense mutation that abolishes synthesis of PrPC. In these animals, the PrP-encoding mRNA is rapidly degraded. Goats without PrPC are valuable in re-addressing loss-of-function phenotypes observed in Prnp knockout mice. As PrPC has been ascribed various roles in immune cells, we analyzed transcriptomic responses to loss of PrPC in peripheral blood mononuclear cells (PBMCs) from normal goat kids (n = 8, PRNP+/+) and goat kids without PrPC (n = 8, PRNPTer/Ter) by mRNA sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28651008/production-and-purification-of-human-hsp90%C3%AE-in-escherichia-coli
#7
Martina Radli, Dmitry B Veprintsev, Stefan G D Rüdiger
The molecular chaperone Hsp90 is an essential member of the cellular proteostasis system. It plays an important role in the stabilisation and activation of a large number of client proteins and is involved in fatal disease processes, e.g. Alzheimer disease, cancer and cystic fibrosis. This makes Hsp90 a crucial protein to study. Mechanistic studies require large amounts of protein but the production and purification of recombinant human Hsp90 in Escherichia coli is challenging and laborious. Here we identified conditions that influence Hsp90 production, and optimised a fast and efficient purification protocol...
2017: PloS One
https://www.readbyqxmd.com/read/28650973/interferon-signaling-in-peromyscus-leucopus-confers-a-potent-and-specific-restriction-to-vector-borne-flaviviruses
#8
Adaeze O Izuogu, Kristin L McNally, Stephen E Harris, Brian H Youseff, John B Presloid, Christopher Burlak, Jason Munshi-South, Sonja M Best, R Travis Taylor
Tick-borne flaviviruses (TBFVs), including Powassan virus and tick-borne encephalitis virus cause encephalitis or hemorrhagic fevers in humans with case-fatality rates ranging from 1-30%. Despite severe disease in humans, TBFV infection of natural rodent hosts has little noticeable effect. Currently, the basis for resistance to disease is not known. We hypothesize that the coevolution of flaviviruses with their respective hosts has shaped the evolution of potent antiviral factors that suppress virus replication and protect the host from lethal infection...
2017: PloS One
https://www.readbyqxmd.com/read/28650961/mfpred-rapid-and-accurate-prediction-of-protein-peptide-recognition-multispecificity-using-self-consistent-mean-field-theory
#9
Aliza B Rubenstein, Manasi A Pethe, Sagar D Khare
Multispecificity-the ability of a single receptor protein molecule to interact with multiple substrates-is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces, including enzyme-substrate complexes. The ability to perform structure-based prediction of multispecificity would aid in the identification of novel enzyme substrates, protein interaction partners, and enable design of novel enzymes targeted towards alternative substrates. The relatively slow speed of current biophysical, structure-based methods limits their use for prediction and, especially, design of multispecificity...
June 26, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28650775/urine-interleukin-18-il-18-as-a-biomarker-of-total-body-irradiation-a-preliminary-study-in-nonhuman-primates
#10
Mang Xiao, David L Bolduc, XiangHong Li, Wanchang Cui, Kevin P Hieber, Rolf Bünger, Natalia I Ossetrova
We have reported that circulating IL-18 can be used as a radiation biomarker in mice, minipigs and nonhuman primates (NHPs, Macaca mulatta). Here, we report the levels of IL-18 in individual NHP's urine before and at 6 h-7 days after 5.0, 6.5 and 8.5 Gy (60)Co total-body irradiation (TBI) using enzyme linked immunosorbent assay (ELISA). Six animals (3.5-5.5 kg, 3-4 years old) per radiation dose were investigated. Correlation values between urine IL-18 and blood cell counts and serum chemistry parameters including lactate dehydrogenase (LDH), lipase, and serum total protein (TP), as well as between urine IL-18 and 60-day survival, were analyzed...
June 26, 2017: Radiation Research
https://www.readbyqxmd.com/read/28650476/cry2h-seq-a-massively-multiplexed-assay-for-deep-coverage-interactome-mapping
#11
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett, Rosa Castanon, Adeline Goubil, Joseph Feeney, Ronan O'Malley, Shao-Shan C Huang, Zhuzhu Z Zhang, Mary Galli, Joseph R Ecker
Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions...
June 26, 2017: Nature Methods
https://www.readbyqxmd.com/read/28650443/sulfated-glycopeptide-nanostructures-for-multipotent-protein-activation
#12
Sungsoo S Lee, Timmy Fyrner, Feng Chen, Zaida Álvarez, Eduard Sleep, Danielle S Chun, Joseph A Weiner, Ralph W Cook, Ryan D Freshman, Michael S Schallmo, Karina M Katchko, Andrew D Schneider, Justin T Smith, Chawon Yun, Gurmit Singh, Sohaib Z Hashmi, Mark T McClendon, Zhilin Yu, Stuart R Stock, Wellington K Hsu, Erin L Hsu, Samuel I Stupp
Biological systems have evolved to utilize numerous proteins with capacity to bind polysaccharides for the purpose of optimizing their function. A well-known subset of these proteins with binding domains for the highly diverse sulfated polysaccharides are important growth factors involved in biological development and tissue repair. We report here on supramolecular sulfated glycopeptide nanostructures, which display a trisulfated monosaccharide on their surfaces and bind five critical proteins with different polysaccharide-binding domains...
June 19, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28650260/group-4-late-embryogenesis-abundant-proteins-as-a-model-to-study-intrinsically-disordered-proteins-in-plants
#13
Cesar L Cuevas-Velazquez, Jose Luis Reyes, Alejandra A Covarrubias
Late Embryogenesis Abundant (LEA) proteins comprise a heterogeneous group of proteins that accumulate to high levels in the dry seed and in vegetative plant tissues under water deficit. We recently reported that group 4 LEA proteins from Arabidopsis thaliana, regardless of their structural disorder prevalent in aqueous solution, are able to fold into α-helix when subjected to water deficit and/or macromolecular crowding environments. Interestingly, the ability to gain structure under water limiting conditions is circumscribed to the N-terminal conserved region...
June 26, 2017: Plant Signaling & Behavior
https://www.readbyqxmd.com/read/28650169/increasing-protein-production-rates-can-decrease-the-rate-at-which-functional-protein-is-produced-and-their-steady-state-levels
#14
Ajeet K Sharma, Edward P O'Brien
The rate at which soluble, functional protein is produced by the ribosome has recently been found to vary in complex and unexplained ways as various translation-associated rates are altered through synonymous codon substitutions. To understand this phenomenon, here, we combine a well-established ribosome-traffic model with a master-equation model of co-translational domain folding to explore the scenarios that are possible for the protein production rate, J , and the functional-nascent protein production rate, F , as the rates of various translation processes are altered for five different E...
June 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28650111/photochromic-dopamine-receptor-ligands-based-on-dithienylethenes-and-fulgides
#15
Daniel Lachmann, Carolin Studte, Barbara Männel, Harald Huebner, Peter Gmeiner, Burkhard König
We describe the incorporation of the well-investigated class of photochromic dithienylethenes (DTEs) and fulgides into known dopamine receptor ligands like 1,4-disubstituted aromatic and hydroxybenzoxazinone piperazines as well as aminoindanes. Subtype and functional selective photochromic ligands were obtained and characterized by NMR and UV-VIS spectroscopic measurements. The photophysical properties of the DTE based dopamine ligands revealed a high fatigue resistance for the diarylmaleimides, but the ringclosure could not be accomplished in polar solvents due to a known twisted intramolecular charge transfer (TICT)...
June 26, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28650069/transcriptional-engineering-of-the-glyceraldehyde-3-phosphate-dehydrogenase-promoter-for-improved-heterologous-protein-production-in-pichia-pastoris
#16
Özge Ata, Roland Prielhofer, Brigitte Gasser, Diethard Mattanovich, Pınar Çalık
The constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (PGAP ), which is one of the benchmark promoters of Pichia pastoris, was analyzed in terms of putative transcription factor binding sites. We constructed a synthetic library with distinct regulatory properties through deletion and duplication of these putative transcription factor binding sites and selected transcription factor (TF) genes were overexpressed or deleted to understand their roles on heterologous protein production. Using enhanced green fluorescent protein, an expression strength in a range between 0...
June 26, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28650060/an-adaptive-bias-hybrid-md-kmc-algorithm-for-protein-folding-and-aggregation
#17
Emanuel K Peter, Joan-Emma Shea
In this paper, we present a novel hybrid Molecular Dynamics/kinetic Monte Carlo (MD/kMC) algorithm and apply it to protein folding and aggregation in explicit solvent. The new algorithm uses a dynamical definition of biases throughout the MD component of the simulation, normalized in relation to the unbiased forces. The algorithm guarantees sampling of the underlying ensemble in dependency of one average linear coupling factor 〈α〉τ. We test the validity of the kinetics in simulations of dialanine and compare dihedral transition kinetics with long-time MD-simulations...
June 26, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28650026/the-effect-of-pegylated-hollow-gold-nanoparticles-on-stem-cell-migration-potential-application-in-tissue-regeneration
#18
Maria Del Mar Encabo-Berzosa, Maria Sancho-Albero, Alejandra Crespo, Vanesa Andreu, Victor Sebastian, Silvia Irusta, Manuel Arruebo, Pilar Martín-Duque, Jesus Santamaria
Mesenchymal stem cells (MSCs) not only can be differentiated into different cell types but also have tropism towards injured or inflamed tissues serving as repair cells. Here we have demonstrated that MSCs containing gold nanoparticles (GNPs) whose surface has been functionalized with PEG show accelerated cell migration, successful scaffold colonization and regeneration. We report the impact of GNPs on the migration (by the wound healing assay), and proliferation (by flow cytometry analysis and by the detection of metabolic mitochondrial activity) on the behaviour of different cell lines including MSCs, HeLa cells, and human dermal fibroblasts...
June 26, 2017: Nanoscale
https://www.readbyqxmd.com/read/28649967/structural-perturbations-on-huntingtin-n17-domain-during-its-folding-on-2d-nanomaterials
#19
Leili Zhang, Mei Feng, Ruhong Zhou, Binquan Luan
A globular protein's folded structure in its physiological environment is largely determined by its amino acid sequence. Recently, newly discovered transformer proteins as well as intrinsically disordered proteins may adopt the folding-upon-binding mechanism where their secondary structures are highly dependent on their binding partners. Due to the various applications of nanomaterials in biological sensors and potential wearable devices, it is important to discover possible conformational changes of proteins on nanomaterials...
June 26, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28649918/molecular-analysis-of-hsp70-mechanisms-in-plants-and-their-function-in-response-to-stress
#20
Magaji G Usman, Mohd Y Rafii, Mohammad Y Martini, Oladosu A Yusuff, Mohd R Ismail, Gous Miah
Studying the strategies of improving abiotic stress tolerance is quite imperative and research under this field will increase our understanding of response mechanisms to abiotic stress such as heat. The Hsp70 is an essential regulator of protein having the tendency to maintain internal cell stability like proper folding protein and breakdown of unfolded proteins. Hsp70 holds together protein substrates to help in movement, regulation, and prevent aggregation under physical and or chemical pressure. However, this review reports the molecular mechanism of heat shock protein 70 kDa (Hsp70) action and its structural and functional analysis, research progress on the interaction of Hsp70 with other proteins and their interaction mechanisms as well as the involvement of Hsp70 in abiotic stress responses as an adaptive defense mechanism...
June 25, 2017: Biotechnology & Genetic Engineering Reviews
keyword
keyword
50928
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"