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Protein denaturation

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https://www.readbyqxmd.com/read/29034192/evaluation-of-analgesic-and-anti-inflammatory-activity-of-bridelia-retusa-spreng-bark
#1
Anil U Tatiya, Ajay K Saluja, Mohan G Kalaskar, Sanjay J Surana, Prakash H Patil
Several species of Bridelia have been used in the condition of pain & arthritis in Indian folk medicine. Present study revealed the preliminary phytochemical investigation and evaluation of analgesic, anti-inflammatory and anti-arthritic activity as well as underlying mechanism of bark of Bridelia retusa Spreng. (Euphorbiaceae). The bark was subjected to extraction using pet.ether, ethyl acetate and acetone. All the extracts were significantly inhibit abdominal writhings response and licking time in late phase of formalin test...
October 2017: Journal of Traditional and Complementary Medicine
https://www.readbyqxmd.com/read/29034084/protein-unfolding-mechanisms-and-their-effects-on-folding-experiments
#2
REVIEW
Lisa J Lapidus
In this review, I discuss the various methods researchers use to unfold proteins in the lab in order to understand protein folding both in vitro and in vivo. The four main techniques, chemical-, heat-, pressure- and force-denaturation, produce distinctly different unfolded conformational ensembles. Recent measurements have revealed different folding kinetics from different unfolding mechanisms. Thus, comparing these distinct unfolded ensembles sheds light on the underlying free energy landscape of folding.
2017: F1000Research
https://www.readbyqxmd.com/read/29033289/foldability-of-a-natural-de-novo-evolved-protein
#3
Dixie Bungard, Jacob S Copple, Jing Yan, Jimmy J Chhun, Vlad K Kumirov, Scott G Foy, Joanna Masel, Vicki H Wysocki, Matthew H J Cordes
The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation...
October 7, 2017: Structure
https://www.readbyqxmd.com/read/29032782/pelleting-and-extrusion-can-ameliorate-negative-effects-of-toasting-of-rapeseed-meal-on-protein-digestibility-in-growing-pigs
#4
S Salazar-Villanea, E M A M Bruininx, H Gruppen, W H Hendriks, P Carré, A Quinsac, A F B van der Poel
Toasting time (TT) of rapeseed meal (RSM), the diet processing (DP) method and the interaction between both on the apparent CP digestion along the gastrointestinal tract and the apparent ileal digestibility (AID) of amino acids of growing pigs were investigated. The experiment consisted of a 3×3 factorial design of TT of RSM (0, 60 and 120 min) and DP method (mash, pelleting and extrusion). In total, 81 boars with a starting BW of 20 kg were euthanized 4 h after their last feeding. The gastrointestinal tract was dissected and the small intestine divided in three sections of similar length...
October 16, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29032211/discrete-senps-macromolecule-binding-manipulated-by-hydrophilic-interaction
#5
Amol V Pansare, Amol A Shedge, Vishwnath R Patil
Nanoparticle-protein conjugates are promising probes for biological diagnostics and versatile building blocks for nanotechnology. Here we demonstrate the interaction of SeNPs with BSA macromolecule simply by physical adsorption method. The interaction between SeNPs and BSA has been investigated by UV-Vis, fluorescence, circular dichroism (CD) spectroscopic and thermal methods. The esterase-like activity of BSA towards PNPA was investigated in the presence of SeNPs. The effects of SeNPs on the stability and conformational changes of BSA were studied, which indicated that the binding of SeNPs with BSA induced relative changes in secondary structure of protein...
October 12, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29031180/design-of-silk-proteins-with-increased-heme-binding-capacity-and-fabrication-of-silk-heme-materials
#6
Trevor D Rapson, Jian-Wei Liu, Alagacone Sriskantha, Mustafa Musameh, Christopher J Dunn, Jeffrey S Church, Andrea Woodhead, Andrew C Warden, Mark J Riley, Jeffrey R Harmer, Christopher J Noble, Tara D Sutherland
In our previous studies, heme was bound into honeybee silk to generate materials that could function as nitric oxide sensors or as recoverable heterogeneous biocatalysts. In this study, we sought to increase the heme-binding capacity of the silk protein by firstly redesigning the heme binding site to contain histidine as the coordinating residue and secondly, by adding multiple histidine residues within the core of the coiled coil core region of the modified silk protein. We used detergent and a protein denaturant to confirm the importance of the helical structure of the silk for heme coordination...
September 4, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/29030997/rna-interference-and-functional-characterization-of-a-tergal-gland-alpha-amylase-in-the-german-cockroach-blattella-germanica-l
#7
A J Myers, A D Gondhalekar, M Fardisi, K D Pluchar, K D Saltzmann, G W Bennett, M E Scharf
German cockroach males possess tergal glands that secrete a combination of oligosaccharides, lipids and proteins. Four major proteins occur in the secretion, with one being the 63 kDa alpha-amylase Blattella germanica Tergal Gland protein-1 (BGTG-1). Denaturing and starch gel electrophoresis coupled with peptide sequencing verified amylase activity for the BGTG-1 protein. BGTG-1 gene expression profiles were determined by using quantitative real-time PCR to compare messenger RNA abundance among isolated tissues of males, females and gravid females...
October 14, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/29030191/effect-of-ph-and-surfactant-on-the-protein-a-perspective-from-theory-and-experiments
#8
Rachana Srivastava, Md Sayem Alam
In the present study, we are aimed to explore the bovine serum albumin (BSA) and sodium dodecyl sulfate (SDS) interaction that can readily show the consequence of the change in concentration of protein with surfactants' various concentration and the different pH's, 4.0, 4.7, 7.0 of the medium through the many spectroscopic techniques. The BSA and SDS denaturation fully influenced by the pH. The results interpreted in terms of electrostatic and hydrophobic contributions to the stability of different phases formed in the system...
October 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29030186/counteraction-of-the-deleterious-effects-of-urea-on-structure-and-stability-of-mammalian-kidney-proteins-by-osmolytes
#9
Mohammad Aasif Dar, Wahiduzzaman, Asimul Islam, Md Imtaiyaz Hassan, Faizan Ahmad
Owing to the urine concentrating mechanism of kidney cells, urea concentration is very high (3.0-5.0M) in mammalian kidneys which may denature many kidney proteins. Methylamines are known to counteract the deleterious effects of urea on structure, stability and function of proteins at 2:1 molar ratio of urea to methylamines. It is known that mammalian kidney cells also contain stabilizing osmolytes, non-methylamines (myo-inositol and sorbitol). A question arises: Do these non-methylmine osmolytes have ability to counteract the deleterious effects of urea on kidney proteins? To answer this question, we took two kidney proteins, namely, sheep serum albumin and Human carbonic anhydrase II...
October 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29024433/cation-induced-stabilization-and-denaturation-of-dna-origami-nanostructures-in-urea-and-guanidinium-chloride
#10
Saminathan Ramakrishnan, Georg Krainer, Guido Grundmeier, Michael Schlierf, Adrian Keller
The stability of DNA origami nanostructures under various environmental conditions constitutes an important issue in numerous applications, including drug delivery, molecular sensing, and single-molecule biophysics. Here, the effect of Na(+) and Mg(2+) concentrations on DNA origami stability is investigated in the presence of urea and guanidinium chloride (GdmCl), two strong denaturants commonly employed in protein folding studies. While increasing concentrations of both cations stabilize the DNA origami nanostructures against urea denaturation, they are found to promote DNA origami denaturation by GdmCl...
October 12, 2017: Small
https://www.readbyqxmd.com/read/29023459/chlorophyte-aspartyl-aminopeptidases-ancient-origins-expanded-families-new-locations-and-secondary-functions
#11
Sang-Youl Park, Melissa A Scranton, Jason E Stajich, Ashley Yee, Linda L Walling
M18 aspartyl aminopeptidases (DAPs) are well characterized in microbes and animals with likely functions in peptide processing and vesicle trafficking. In contrast, there is a dearth of knowledge on plant aminopeptidases with a preference for proteins and peptides with N-terminal acidic residues. During evolution of the Plantae, there was an expansion and diversification of the M18 DAPs. After divergence of the ancestral green algae from red and glaucophyte algae, a duplication yielded the DAP1 and DAP2 lineages...
2017: PloS One
https://www.readbyqxmd.com/read/29023395/validation-of-molecular-dynamics-simulations-for-prediction-of-three-dimensional-structures-of-small-proteins
#12
Koichi Kato, Tomoki Nakayoshi, Shuichi Fukuyoshi, Eiji Kurimoto, Akifumi Oda
Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures...
October 12, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29016117/formation-of-polyphenol-denatured-protein-flocs-in-alcohol-beverages-sweetened-with-refined-cane-sugars
#13
Gillian Eggleston, Alexa Triplett
The sporadic appearance of floc from refined, white cane sugars in alcohol beverages remains a technical problem for both beverage manufacturers and sugar refiners. Cane invert sugars mixed with 60% pure alcohol and water, increased light scattering by up to ~1000-fold. Insoluble and soluble starch, fat, inorganic ash, oligosaccharides, Brix, and pH were not involved in the prevailing floc formation mechanism. Strong polynomial correlations existed between the haze floc and indicator values I.V. (color at 420 nm pH 9...
October 10, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28994167/optimization-and-physicochemical-properties-of-nutritional-protein-isolate-from-pork-liver-with-ultrasound-assisted-alkaline-extraction
#14
Ye Zou, Huan Bian, Pengpeng Li, Zhilan Sun, Chong Sun, Muhan Zhang, Zhiming Geng, Weimin Xu, Daoying Wang
The aim of this study was to investigate the optimal conditions of ultrasound-assisted alkaline extraction (UAAE) on pork liver protein isolate (UPLPI) and its physico-chemical properties. Response surface methodology was used to determine the optimal conditions for UAAE, which were at ultrasonic power 265 W, ultrasonic time 42 min, NaOH concentration 0.80%, temperature 50°C, and solvent/raw material ratio 70. The extraction yield and efficiency of UPLPI were significantly improved over the conventional alkaline extraction (PLPI)...
October 10, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28987934/isothermal-chemical-denaturation-of-large-proteins-path-dependence-and-irreversibility
#15
Lucas Wafer, Marek Kloczewiak, Sharon M Polleck, Yin Luo
State functions (e.g., ΔG) are path independent and quantitatively describe the equilibrium states of a thermodynamic system. Isothermal chemical denaturation (ICD) is often used to extrapolate state function parameters for protein unfolding in native buffer conditions. The approach is prudent when the unfolding/refolding processes are path independent and reversible, but may lead to erroneous results if the processes are not reversible. The reversibility was demonstrated in several early studies for smaller proteins, but was assumed in some reports for large proteins with complex structures...
October 4, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28986262/a-simple-elution-strategy-for-biotinylated-proteins-bound-to-streptavidin-conjugated-beads-using-excess-biotin-and-heat
#16
Joleen S Cheah, Soichiro Yamada
Protein-protein interactions are the molecular basis of cell signaling. Recently, proximity based biotin identification (BioID) has emerged as an alternative approach to traditional co-immunoprecipitation. In this protocol, a mutant biotin ligase promiscuously labels proximal binding partners with biotin, and resulting biotinylated proteins are purified using streptavidin conjugated beads. This approach does not require preservation of protein complexes in vitro, making it an ideal approach to identify transient or weak protein complexes...
October 3, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28984389/binding-of-trace-elements-ag-cd-co-cu-ni-and-tl-to-cytosolic-biomolecules-in-livers-of-juvenile-yellow-perch-perca-flavescens-collected-from-lakes-representing-metal-contamination-gradients
#17
Antoine Caron, Maikel Rosabal, Ophélie Drevet, Patrice Couture, Peter G C Campbell
Biomolecules involved in handling cytosolic metals in the liver of the yellow perch (Perca flavescens) were characterized in juvenile fish collected from four lakes constituting metal contamination gradients. Using size-exclusion liquid chromatography coupled to an inductively-coupled mass spectrometer (SEC-ICP-MS), we determined metal distributions among ligands of different molecular weights in the cytosol, before and after a heat denaturation step designed to isolate metallothionein-like peptides and proteins (MTLPs)...
October 6, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28982013/characterization-of-a-thermostable-endoglucanase-from-i-cellulomonas-fim-i-i-atcc484
#18
Hirak Saxena, Bryan Hsu, Marc de Asis, Mirko Zierke, Lyann Sim, Stephen G Withers, Warren Wakarchuk
Bacteria in the genus Cellulomonas are well known as secretors of a variety of mesophilic carbohydrate degrading enzymes (e.g. cellulases and hemicellulases), active against plant cell wall polysaccharides. Recent proteomic analysis of the mesophilic bacterium <i>Cellulomonas fimi</i> ATCC484 revealed uncharacterized enzymes for the hydrolysis of plant cell wall biomass. Celf_1230 (CfCel6C), a secreted protein of Cellulomonas fimi ATCC484, is a novel member of the GH6 family of cellulases which could be successfully expressed in Escherichia coli...
October 5, 2017: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/28975780/role-of-urea-aromatic-stacking-interactions-in-stabilizing-the-aromatic-residues-of-the-protein-in-urea-induced-denatured-state
#19
Siddharth Goyal, Aditya Chattopadhyay, Koushik Kasavajhala, U Deva Priyakumar
A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states. Experiments use thermal, chemical or mechanical stress to perturb the folding equilibrium for examining protein stability and protein folding process. Elucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explores the nature of urea-aromatic interactions relevant in urea assisted protein denaturation. Free energy profiles corresponding to the unfolding of Trp-cage mini-protein in the presence and absence of urea at three different temperatures demonstrate the distortion of the hydrophobic core to be a crucial step...
October 4, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28973014/microsecond-time-scale-kinetics-of-transient-biochemical-reactions
#20
Sandra Mitić, Marc J F Strampraad, Wilfred R Hagen, Simon de Vries
To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs integrated with a 30 mm long flow-cell of 109 μm optical path length constructed from two parallel sheets of silver foil; it produces ultraviolet-visible spectra that are linear in absorbance up to 3.5 with a spectral resolution of 0...
2017: PloS One
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