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Protein design

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https://www.readbyqxmd.com/read/29166558/understanding-the-cellular-uptake-of-ph-responsive-zwitterionic-gold-nanoparticles-a-computer-simulation-study
#1
Xuebo Quan, Daohui Zhao, Libo Li, Jian Zhou
Surface functionalization of nanoparticles (NPs) with stealth polymers (e.g., hydrophilic and zwitterionic polymers) has become a common strategy to resist non-specific protein adsorption recently. Understanding the role of surface decoration on NP-biomembrane interactions is of great significance to promote the application of NPs in biomedical fields. Herein, using coarse-grained molecular dynamics (CGMD) simulations, we investigate the interactions between stealth polymer-coated gold nanoparticles (AuNPs) and lipid membranes...
November 22, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29166010/conformational-dynamics-of-asparagine-at-coiled-coil-interfaces
#2
Franziska Thomas, Ai Niitsu, Alain Oregioni, Gail J Bartlett, Derek N Woolfson
Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds or not...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29165690/the-regulatory-g4-motif-of-the-kirsten-ras-kras-gene-is-sensitive-to-guanine-oxidation-implications-on-transcription
#3
Susanna Cogoi, Annalisa Ferino, Giulia Miglietta, Erik B Pedersen, Luigi E Xodo
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165614/long-term-health-in-recipients-of-transplanted-in-vitro-propagated-spermatogonial-stem-cells
#4
Callista L Mulder, Lisa A E Catsburg, Yi Zheng, Cindy M de Winter-Korver, Saskia K M van Daalen, Madelon van Wely, Steven Pals, Sjoerd Repping, Ans M M van Pelt
STUDY QUESTION: Is testicular transplantation of in vitro propagated spermatogonial stem cells associated with increased cancer incidence and decreased survival rates in recipient mice? SUMMARY ANSWER: Cancer incidence was not increased and long-term survival rate was not altered after transplantation of in vitro propagated murine spermatogonial stem cells (SSCs) in busulfan-treated recipients as compared to non-transplanted busulfan-treated controls. WHAT IS KNOWN ALREADY: Spermatogonial stem cell autotransplantation (SSCT) is a promising experimental reproductive technique currently under development to restore fertility in male childhood cancer survivors...
November 18, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29165591/translation-can-affect-the-antisense-activity-of-rnase-h1-dependent-oligonucleotides-targeting-mrnas
#5
Xue-Hai Liang, Joshua G Nichols, Hong Sun, Stanley T Crooke
RNase H1-dependent antisense oligonucleotides (ASOs) can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. Here we show that mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165486/optical-control-of-mitochondrial-reductive-reactions-in-living-cells-using-an-electron-donor-acceptor-linked-molecule
#6
Yuta Takano, Reina Munechika, Vasudevanpillai Biju, Hideyoshi Harashima, Hiroshi Imahori, Yuma Yamada
It has been known for decades that intracellular redox reactions control various vital functions in living systems, which include the synthesis of biomolecules, the modulation of protein functions, and cell signaling. Although there have been several reports on the control of such functions using DNA and RNA, the non-invasive optical control of biological functions is an important ongoing challenge. In this study, a hybrid of an electron donor-acceptor linked molecule based on a ferrocene(Fc)-porphyrin(ZnP)-fullerene(C60) analogue and an elaborately designed nano-carrier, referred to herein as a MITO-Porter, resulted in a successful photoinduced intermolecular electron transfer reaction via the long-lived intramolecular charge separation, leading to site-specific reductive reactions in the mitochondria of living HeLa cells...
November 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/29165475/effect-of-the-water-fraction-isolated-from-fructus-ligustri-lucidi-extract-on-bone-metabolism-via-antagonizing-a-calcium-sensing-receptor-in-experimental-type-1-diabetic-rats
#7
Nan-Nan Sha, Yong-Jian Zhao, Dong-Feng Zhao, Daniel Kam-Wah Mok, Qi Shi, Yong-Jun Wang, Yan Zhang
Our previous studies have demonstrated that the extract of Fructus Ligustri Lucidi (FLL) can maintain in vivo calcium homeostasis in aged and ovariectomized rats. This study was designed to elucidate the action of water fraction isolated from the FLL extract on bone metabolism and a calcium-sensing receptor (CaSR) in parathyroid glands and kidneys of diabetic rats. The streptozotocin-induced diabetic rats were treated with vehicle, FLL extract, and the water fraction (WF) isolated from the FLL extract for 4 weeks...
November 22, 2017: Food & Function
https://www.readbyqxmd.com/read/29165449/short-two-armed-lanthanide-binding-tags-for-paramagnetic-nmr-spectroscopy-based-on-chiral-1-4-7-10-tetrakis-2-hydroxypropyl-1-4-7-10-tetraazacyclododecane-scaffolds
#8
Michael D Lee, Matthew L Dennis, Bim Graham, James D Swarbrick
A new pair of enantiomeric two-armed lanthanide-binding tags have been developed for paramagnetic NMR studies of proteins. The tags produce large and significantly different paramagnetic effects to one another when bound to the same tagging site. Additionally, they are less sensitive to sample pH than our previous two-armed tag designs.
November 22, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29165076/pasylation-as-a-powerful-technology-for-improving-the-pharmacokinetic-properties-of-biopharmaceuticals
#9
Sajjad Ahmadpour, Seyed Jalal Hosseinimehr
One of the major challenges of short plasma half-life biopharmaceuticals is to daily high dose administration that leads to economic problems, patient inconvenience and undesirable side effects. Increasing the hydrodynamic volume beyond the pore size of the glomerular basal membrane is a general approach to increase the size of the small biopharmaceuticals with low half-life in blood circulation. PASylation technology is one of these approaches that are designed based on the genetic fusion of biopharmaceutical with a hydrophilic random coil sequence of tri proline (Pro), alanine (Ala), and serine (Ser) amino acids...
November 20, 2017: Current Drug Delivery
https://www.readbyqxmd.com/read/29165068/identifying-candidates-for-breast-cancer-using-interactions-of-chemicals-and-proteins
#10
Jing Lu, Kangle Shang, Yi Bi
Breast cancer is one of the major cause of cancer death in women worldwide. Therefore, it is urgent to discovery novel drugs or design effective treatments for this disease. However, the research and development of drugs by using only experimental methods is always time-consuming and expensive. With the development of computer science, some advanced computational methods can make full use of known knowledge to design candidate drugs, thereby reducing the cost and time of experimental testing. In this study, a computational method was proposed to identify novel candidates for breast cancer...
November 20, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/29165067/optimized-virtual-screening-workflow-towards-target-based-polynomial-scoring-functions-for-hiv-1-protease
#11
Val Oliveira Pintro, Walter F Azevedo
BACKGROUND: One key step in the development of inhibitors for an enzyme is the application of computational methodologies to predict protein-ligand interactions. The abundance of structural and ligand-binding information for HIV-1 protease opens up the possibility to apply computational methods to develop scoring functions targeted to this enzyme. OBJECTIVE: Our goal here is to develop an integrated molecular docking approach to investigate protein-ligand interactions with focus on the HIV-1 protease...
November 20, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/29165065/electrochemical-nucleic-acid-based-biosensing-of-drugs-of-abuse-and-pharmaceuticals
#12
Susana Campuzano, Maia Pedrero, Jose M Pingarron
Nowadays, studies of the interactions of DNA with small molecular drugs, especially anti-tumor agents, antibiotics and drugs of abuse are currently performed to explore their mechanism of action and develop new drugs with lower side effects and high curative properties. Currently, electrochemical biosensors are considered a very promising alternative analytical tool to conventional more complex techniques for drug determination due to rapidness, low cost, high sensitivity, compatibility with microfabrication technology, intuitively understandable design and simple operation mode...
November 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/29164876/live-cell-imaging-of-endogenous-rnas-using-pumilio-homology-domain-mutants-principles-and-applications
#13
Hideaki Yoshimura
Recently, dynamic changes in RNA location in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescence labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction to cells and transgenic organisms in cell type and tissue specific manner by genetic engineering techniques...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29164851/an-integrated-redox-cycling-for-electrochemical-enzymatic-signal-enhancement
#14
Md Rajibul Akanda, Huangxian Ju
Highly sensitive analytical methods for the detection of proteins are still an urgent demand in early medical diagnosis and discovery of biomarkers with ultralow abundance. Here an integrated electrochemical-chemical-enzymatic redox cycling is designed for significant enhancement of electrochemical enzymatic signal in biorecognition. This strategy efficiently utilizes the high specificity of outer-sphere to inner-sphere redox reaction to mediate the enzymatic redox cycling with the nonenzymatic redox cycling...
November 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29164837/serum-surfactant-protein-d-and-exhaled-nitric-oxide-as-biomarkers-of-early-lung-damage-in-systemic-sclerosis
#15
Alida Benfante, Riccardo Messina, Alessandra Patern├▓, Nicola Scichilone
BACKGROUND: Interstitial lung disease (ILD) complicates the course of systemic sclerosis (SSc), representing the main cause of death in these patients. The identification of parameters that can predict the early onset and progression of ILD in SSc represents an unmet need in clinical practice. The study was designed to explore whether the surfactant proteins (SP) A and D may be used as noninvasive tools for the early identification of ILD in SSc. Alveolar exhaled nitric oxide (NO) was investigated as a surrogate marker of distal inflammation...
November 21, 2017: Minerva Medica
https://www.readbyqxmd.com/read/29164777/formulation-and-characterization-of-poly-propylacrylic-acid-poly-lactic-co-glycolic-acid-blend-microparticles-for-ph-dependent-membrane-disruption-and-cytosolic-delivery
#16
Lawrence P Fernando, Jamal S Lewis, Brian C Evans, Craig L Duvall, Benjamin G Keselowsky
Poly(lactic-co-glycolic acid) (PLGA) is widely used as a vehicle for delivery of pharmaceutically relevant payloads. PLGA is readily fabricated as a nano- or microparticle (MP) matrix to load both hydrophobic and hydrophilic small molecular drugs as well as biomacromolecules such as nucleic acids and proteins. However, targeting such payloads to the cell cytosol is often limited by MP entrapment and degradation within acidic endolysosomes. Poly(propylacrylic acid) (PPAA) is a polyelectrolyte polymer with membrane disruptive capability triggered at low pH...
November 22, 2017: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/29164729/identification-and-characterization-of-a-histamine-binding-lipocalin-like-molecule-from-the-relapsing-fever-tick-ornithodoros-turicata
#17
G Neelakanta, H Sultana, D E Sonenshine, J F Andersen
Lipocalins are low molecular weight membrane transporters that are abundantly expressed in the salivary glands and other tissues of ticks. In this study, we identified a lipocalin-like molecule, designated as otlip, from the soft ticks Ornithodoros turicata, the vector for the relapsing fever causing spirochete Borrelia turicatae. We noted that the expression of otlip was developmentally regulated, with adult ticks expressing significantly higher levels in comparison to the larvae or nymphal ticks. Expression of otlip was evident in both fed and unfed O...
November 22, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/29164557/adiponectin-attenuates-endoplasmic-reticulum-stress-and-alveolar-epithelial-apoptosis-in-copd-rats
#18
Y-L Zhao, F Li, Y-W Liu, Y-J Shi, Z-H Li, G-K Cao, W Zhu
OBJECTIVE: The present study was designed to evaluate the effect of Adiponectin (APN) against alveolar epithelial apoptosis in chronic obstructive pulmonary disease (COPD) rat models. MATERIALS AND METHODS: Thirty-six male Sprague-Dawley (SD) rats were randomly assigned to three groups: Sham group, COPD group, and COPD + APN group (2.5 ug/kg/day). To assess the effect of APN, histopathological evaluations, lung function, and the apoptotic index (AI) of alveolar septal cells, were performed...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29164392/maturation-and-cytokine-pattern-of-human-dendritic-cells-in-response-to-different-yeasts
#19
Silvia Boschi Bazan, Barbara Walch-R├╝ckheim, Manfred J Schmitt, Frank Breinig
Activated dendritic cells (DC) induce and polarize T-cell responses by expression of distinct maturation markers and cytokines. This study systematically investigated the capacity of different biotechnically relevant yeast species and strains including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Pichia pastoris, Hansenula polymorpha, Yarrowia lipolytica, and Candida glabrata to initiate maturation of human DC. As important prerequisite for T-cell activation, all yeasts were shown to effectively induce, though to a different extent, the expression of the activation marker CD83, the co-stimulatory molecules CD80, CD86, CD54, CD58, and CD40, as well as the antigen-presenting molecules MHCs I and II...
November 21, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/29164150/potential-anticancer-mechanisms-of-a-novel-egfr-dna-targeting-combi-molecule-jdf12-against-du145-prostate-cancer-cells-an-itraq-based-proteomic-analysis
#20
Haofeng Zheng, Guancan Liang, Yanxiong Chen, Sijie Lin, Wei Liu, Youqiang Fang
The development of multitargeting drugs is an emerging trend in cancer research. To promote further development and clinical application of multitargeting drugs, this research was performed. MTT assay and flow cytometry of Annexin V/propidium iodide staining were used to confirm the proapoptotic efficacy of a novel combi-targeting molecule, JDF12, against DU145 prostate cancer (PCa) cells. Differentially expressed proteins between control and JDF12-treated cultures were revealed by isobaric tags for relative and absolute quantitation (iTRAQ), and part of them was confirmed by quantitative PCR...
2017: BioMed Research International
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