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protein folding

Claudia Doi Antunes, Malson Neilson Lucena, Daniela Pereira Garçon, Francisco Assis Leone, John Campbell McNamara
Fresh caught Clibanarius vittatus [SW, 31‰ salinity (S)] were acclimated to a dilute medium (15‰ S) for 10 days, employing silver staining to locate gill ion transporting tissue, immunofluorescence to localize the Na+/K+-ATPase α-subunit in the lamellae, and electron microscopy to portray ultrastructural changes in the gill epithelia. Na+/K+-ATPase activity was characterized kinetically in a gill microsomal fraction, including synergistic stimulation by NH4+ plus K+. Silver staining revealed that all 26 phyllobranchiate arthro- and pleurobranchiae participate in ion transport...
July 2017: Journal of Experimental Zoology. Part A, Ecological and Integrative Physiology
Lijun Li, Hui Liao, Yan Yang, Jianye Gong, Jianan Liu, Zedong Jiang, Yanbing Zhu, Anfeng Xiao, Hui Ni
To improve the thermostability of α-L-rhamnosidase (r-Rha1), an enzyme previously identified from Aspergillus niger JMU-TS528, multiple arginine (Arg) residues were introduced into the r-Rha1 sequence to replace several lysine (Lys) residues that located on the surface of the folded r-Rha1. Hinted by in silico analysis, five surface Lys residues (K134, K228, K406, K440, K573) were targeted to produce a list of 5 single-residue mutants and 4 multiple-residue mutants using site-directed mutagenesis. Among these mutants, a double Lys to Arg mutant, i...
January 17, 2018: International Journal of Biological Macromolecules
Gabriela Mercado, Valentina Castillo, Paulina Soto, Nélida López, Jeffrey M Axten, Pablo Sardi, Jeroen J M Hoozemans, Claudio Hetz
Parkinson's disease (PD) is the second most common neurodegenerative disorder, leading to the progressive decline of motor control due to the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Accumulating evidence suggest that altered proteostasis is a salient feature of PD, highlighting perturbations to the endoplasmic reticulum (ER), the main compartment involved in protein folding and secretion. PERK is a central ER stress sensor that enforces adaptive programs to recover homeostasis through a block of protein translation and the induction of the transcription factor ATF4...
January 17, 2018: Neurobiology of Disease
Akira R Kinjo
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since a given polypeptide can be either foldable or unfoldable, a kind of "folding transition" is expected at the boundary of a protein family in the sequence space. By Monte Carlo simulations of a statistical mechanical model of protein sequence alignment that coherently incorporates both short-range and long-range interactions as well as variable-length insertions to reproduce the statistics of the multiple sequence alignment of a given protein family, we demonstrate the existence of such transition between natural-like sequences and random sequences in the sequence subspaces for 15 domain families of various folds...
January 17, 2018: Journal of Theoretical Biology
Jiang Zhu, Shuangli Li, Theresa A Ramelot, Michael A Kennedy, Maili Liu, Yunhuang Yang
Human protein TGIF1 is an essential regulator of cell fate with broad roles in different tissues, and has been implicated in holoprosencephaly (HPE) and many cancers. The function of TGIF1 in transcriptional regulation depends on its three-amino acid loop extension (TALE) type of homeodomain (HD). Two missense mutations that led to P192A and R219C substitutions in TGIF1-HD were previously found in HPE patients and suggested to be the causes for these cases. However, how these mutations affected TGIF1 function has not been investigated from a structural view...
January 16, 2018: Biochemical and Biophysical Research Communications
Marie-Theres Vielberg, Verena C Bauer, Michael Groll
The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral β-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallised Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases...
January 17, 2018: Journal of Molecular Biology
Dipak Dilip Chaudhari, Rajbir Singh, Rashmi Hogarehalli Mallappa, Namita Rokana, Jai Kumar Kaushik, Rajesh Bajaj, Virender Kumar Batish, Sunita Grover
BACKGROUND & OBJECTIVES: Milk proteins play a beneficial role in the regulation of food intake, postprandial glycaemia and enteroendocrine hormone secretions and thus are receiving considerable attention for the management of metabolic inflammatory disorders such as type 2 diabetes mellitus (T2DM). The objective of this study was to evaluate the efficacy of peptide/s obtained from milk proteins (casein and whey) as well as from the milk fermented with Lactobacillus helveticus as secretagogues for gut hormones and to purify and characterize the active peptides...
September 2017: Indian Journal of Medical Research
Zeyland Joanna, Hryhorowicz Magdalena, Nowak-Terpiłowska Agnieszka, Jura Jacek, Słomski Ryszard, Smorąg Zdzisław, Gajda Barbara, Lipiński Daniel
Two sgRNAs were designed to target the region of exon 2 of the pULBP1 gene by microinjection. The co-injection of modified Cas9-D10A nickase with a pair of sgRNAs into the zygote's cytoplasm easily and efficiently generated biallelic modification of the pULBP1 gene in one step. Five out of nine F0 generation piglets showed insertions or deletions in the targeting site of the pULBP1 gene, indicating that pULBP1 mutation efficiency reached about 56% (5/9). Quantitative determination of pULBP1 showed approximately a 1...
January 2018: 3 Biotech
Aparna Singh, Anil Kumar Singh
Thirteen halophilic archaea were isolated from Kandla and Bhayander salt pans. These isolates were grouped into three different genera Halobacterium, Haloferax and Haloarcula based on morphological and biochemical characterization, polar lipid analysis, Amplified 16S rDNA restriction analysis (ARDRA) and 16S rDNA sequence analysis. Biochemical characterization suggested the ability of isolates to produce protease, amylase and poly-hydroxybutyrate (PHB) indicating their biotechnological potential. The isolates were further screened for the amount of extracellular protease produced...
January 2018: 3 Biotech
Akshaykumar A Nayak, Kamalesh Dattaram Mumbrekar, Satish Rao
In a scenario of accidental mass radiation exposure, transportation and analyzing samples may take its time resulting in loss of biomarker information over this period. The present study aims to use phosphatases inhibitors for longer retention of foci signals to adopt γ-H2AX as a biodosimetric biomarker for the management of early triage. Peripheral blood lymphocytes isolated from healthy individuals irradiated in vitro with X-rays, and γ-H2AX analysed using fluorescent microscopy and flow cytometric methods...
January 22, 2018: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
Sandrine Pereira, Larry Bodgi, Mirlande Duclos, Aurélien Canet, Mélanie L Ferlazzo, Clément Devic, Adeline Granzotto, Sophie Deneuve, Guillaume Vogin, Nicolas Foray
PURPOSE: To examine the possibility of predicting clinical radiosensitivity by quantifying the nuclear forms of autophosphorylated ATM protein (pATM) via a specific enzyme-linked immunosorbent assay (ELISA). METHODS AND MATERIALS: This study was performed on 30 skin fibroblasts from 9 radioresistant patients and 21 patients with adverse tissue reaction events. Patients were divided into 2 groups: radioresistant (toxicity grade <2) and radiosensitive (toxicity grade ≥2)...
February 1, 2018: International Journal of Radiation Oncology, Biology, Physics
Izabela Kaminska, Johann Bohlen, Sebastian Mackowski, Philip Tinnefeld, Guillermo P Acuna
In this contribution, we fabricate hybrid constructs based on a natural light-harvesting complex, peridinin-chlorophyll a-protein, coupled to dimer optical antennas self-assembled with the help of the DNA origami technique. This approach enables controlled positioning of individual complexes at the hotspot of the optical antennas based on large, colloidal gold and silver nanoparticles. Our approach allows us to selectively excite the different pigments present in the harvesting complex, reaching a fluorescence enhancement of 500-fold...
January 22, 2018: ACS Nano
Kazunari Yoneda, Haruhiko Sakuraba, Tomohiro Araki, Toshihisa Ohshima
A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C...
January 20, 2018: Extremophiles: Life Under Extreme Conditions
Sanjay K S Patel, Sachin V Otari, Jinglin Li, Dong Rip Kim, Sun Chang Kim, Byung-Kwan Cho, Vipin C Kalia, Yun Chan Kang, Jung-Kul Lee
Herein, we report the preparation of a cross-linked protein-metal hybrid nanoflower (NF) system for laccase immobilization. The immobilized laccase showed effective encapsulation yield and activity recovery of 78.1% and 204%, respectively. The catalytic efficiency (kcatVmax-1) of cross-linked NF (CL-NF) was 2.2-fold more than that of free laccase. The CL-NF also exhibited significantly higher stability towards pH and temperature changes. It exhibited excellent storage stability and tolerance towards solvents and inhibitors as compared with the free enzyme...
January 4, 2018: Journal of Hazardous Materials
Mengrui Liu, Hongliang Du, Abdur Rauf Khan, Jianbo Ji, Aihua Yu, Guangxi Zhai
In this report, redox/enzyme responsive chondroitin sulfate-ss-deoxycholic acid (CSCD) conjugates were synthesized using cystamine as the linkage which could self-assemble to form self-assembled nanoparticles (175.6 + 5.2 nm) in the aqueous environment. Docetaxel (DTX) was loaded in nanoparticles with desired loading efficiency for the inhibition of tumor growth and metastasis of melanoma. Interestingly, nanoparticles were demonstrated to respond to hyaluronidase-1 (Hyal-1) which could degrade chondroitin sulfate (CS) backbones...
March 15, 2018: Carbohydrate Polymers
Flavien Labre, Sophie Mathieu, Patricia Chaud, Pierre-Yves Morvan, Romuald Vallée, William Helbert, Sébastien Fort
Alginate oligosaccharides (AOS) with a weight average molecular weight of 5 kDa were efficiently amidated with amino acids and carbohydrates in aqueous media in the presence of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM). Here, alanine, leucine, serine, as well as mannose and rhamnose, were amidated at high yields with a good control of the degree of substitution (DS). Amino acid- and carbohydrate-grafted AOS showed improved stability against degradation by alginate lyases having different specificities...
March 15, 2018: Carbohydrate Polymers
Ibtisam Al-Harrasi, Rashid Al-Yahyai, Mahmoud W Yaish
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation...
2018: PloS One
Rei Shibue, Takahiro Sasamoto, Masami Shimada, Bowen Zhang, Akihiko Yamagishi, Satoshi Akanuma
Modern organisms commonly use the same set of 20 genetically coded amino acids for protein synthesis with very few exceptions. However, earlier protein synthesis was plausibly much simpler than modern one and utilized only a limited set of amino acids. Nevertheless, few experimental tests of this issue with arbitrarily chosen amino acid sets had been reported prior to this report. Herein we comprehensively and systematically reduced the size of the amino acid set constituting an ancestral nucleoside kinase that was reconstructed in our previous study...
January 19, 2018: Scientific Reports
Sanjeev Noel, Sul A Lee, Mohanraj Sadasivam, Abdel R A Hamad, Hamid Rabb
Oxidant stress modifies T lymphocyte activation and function. Previous work demonstrated that murine T cell-specific kelch like-ECH-associated protein 1 (Keap1) deletion enhances antioxidant capacity and protects from experimental acute kidney injury. In this study, we used CRISPR technology to develop clinically translatable human T cell-specific KEAP1 deletion. Delivery of KEAP1 exon 2 specific Cas9:guide RNA in Jurkat T cells led to significant (∼70%) editing and upregulation of NRF2-regulated antioxidant genes NADPH dehydrogenase quinone 1 (NQO1) (up to 11-fold), heme oxygenase 1 (HO1) (up to 11-fold), and GCLM (up to 2-fold)...
January 19, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Myron K Evans, Michael C Brown, Joseph Geradts, Xuhui Bao, Timothy J Robinson, Mohit Kumar Jolly, Peter Vermeulen, Gregory M Palmer, Matthias Gromeier, Herbert Levine, Michael A Morse, Steven Van Laere, Gayathri R Devi
Hyperactivation of the NFκB pathway is a distinct feature of inflammatory breast cancer (IBC), a highly proliferative and lethal disease. Gene expression studies in IBC patient tissue have linked epidermal growth factor receptor (EGFR/HER2)-mediated MAPK signaling to NFκB hyperactivity, but the mechanism(s) by which this occurs remain unclear. Here, we report that the X-linked inhibitor of apoptosis protein (XIAP) plays a central role in linking these two pathways. XIAP overexpression correlated with poor prognoses in breast cancer patients and was frequently observed in untreated IBC patient primary tumors...
January 19, 2018: Cancer Research
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