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https://www.readbyqxmd.com/read/28532099/interaction-of-insulin-with-colloidal-zns-quantum-dots-functionalized-by-various-surface-capping-agents
#1
Ghader Hosseinzadeh, Ali Maghari, Seyed Morteza Famil Farniya, Amir Homayoun Keihan, Ali A Moosavi-Movahedi
Interaction of quantum dots (QDs) and proteins strongly influenced by the surface characteristics of the QDs at the protein-QD interface. For a precise control of these surface-related interactions, it is necessary to improve our understanding in this field. In this regard, in the present work, the interaction between the insulin and differently functionalized ZnS quantum dots (QDs) were studied. The ZnS QDs were functionalized with various functional groups of hydroxyl (OH), carboxyl (COOH), amine (NH2), and amino acid (COOH and NH2)...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28532097/influence-of-telopeptides-on-the-structural-and-physical-properties-of-polymeric-and-monomeric-acid-soluble-type-i-collagen
#2
Róisín Holmes, Steve Kirk, Giuseppe Tronci, Xuebin Yang, David Wood
Currently two factors hinder the use of collagen as building block of regenerative devices: the limited mechanical strength in aqueous environment, and potential antigenicity. Polymeric collagen is naturally found in the cross-linked state and is mechanically tougher than the monomeric, acid-soluble collagen ex vivo. The antigenicity of collagen, on the other hand, is mainly ascribed to inter-species variations in amino acid sequences of the non-helical terminal telopeptides. These telopeptides can be removed through enzymatic treatment to produce atelocollagen, although the effect of this cleavage on triple helix organization, amino acidic composition and thermal properties is often disregarded...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#3
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531354/monomeric-polyglutamine-structures-that-evolve-into-fibrils
#4
David Punihaole, Ryan S Jakubek, Riley James Workman, Lauren E Marbella, Patricia Campbell, Jeffry D Madura, Sanford A Asher
We investigate the solution and fibril conformations and structural transitions of the polyglutamine (polyQ) peptide, D2Q10K2 (Q10), by synergistically using UV Resonance Raman (UVRR) spectroscopy and Molecular Dynamics (MD) simulations. We show that Q10 adopts two distinct, monomeric solution conformational states, a collapsed β-strand and a PPII-like structure that do not readily interconvert. This clearly indicates a high activation barrier in solution that prevents equilibration between these structures...
May 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28530801/hydrogen-bonding-environment-of-the-n3-h-group-of-fmn-in-the-lov-domains-of-phototropins
#5
Tatsuya Iwata, Dai Nozaki, Atsushi Yamamoto, Takayuki Koyama, Yasuzo Nishina, Kiyoshi Shiga, Satoru Tokutomi, Masashi Unno, Hideki Kandori
LOV (light-oxygen-voltage) domain is a flavin-binding blue-light receptor domain originally found in plant phototropin, a photoreceptor for phototropism, chloroplast movement and stomata opening. LOV domains are available as optogenetics tools for photosensory domain of fusion proteins. Therefore, it is important to investigate how LOV domains show light-induced structural changes not only for the elucidation of regulation mechanism of kinase domain but also for the appropriate activation of other functional domains by LOV domain...
May 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28530710/engineering-protein-stability-with-atomic-precision-in-a-monomeric-miniprotein
#6
Emily G Baker, Christopher Williams, Kieran L Hudson, Gail J Bartlett, Jack W Heal, Kathryn L Porter Goff, Richard B Sessions, Matthew P Crump, Derek N Woolfson
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i...
May 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28530653/structure-of-a-pre-catalytic-spliceosome
#7
Clemens Plaschka, Pei-Chun Lin, Kiyoshi Nagai
Intron removal requires assembly of the spliceosome on pre-mRNA and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 snRNP associates with U4/U6.U5 tri-snRNP through U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The U2 snRNP 3' region is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5'-splice site...
May 22, 2017: Nature
https://www.readbyqxmd.com/read/28530585/the-structure-and-amphipathy-characteristics-of-modified-%C3%AE-zeins-by-sds-or-alkali-in-conjunction-with-heating-treatment
#8
Shi-Rong Dong, Hong-Hua Xu, Jun-Yan Tan, Ming-Ming Xie, Guo-Ping Yu
γ-Zein was modified by SDS or alkali combined with heating treatments in water and in 70% ethanol to change its amphipathic properties and explore the relationship between amphipathic characteristic and structure. γ-Zein water-dispersibility was dramatically increased via alkali or SDS combined with heating treatments, but their ethanol-dispersibilities were significantly different during ethanol evaporation. High both water-dispersibility and ethanol-dispersibility were found from alkali modified γ-zein while high water-dispersibility but low ethanol-dispersibility were obtained from SDS modified γ-zein, indicating that alkali modified γ-zein had better amphipathic characteristic compared with SDS modified γ-zein...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28530565/analysis-of-binding-properties-and-interaction-of-thiabendazole-and-its-metabolite-with-human-serum-albumin-via-multiple-spectroscopic-methods
#9
Qiaomei Sun, Jiawei He, Hongqin Yang, Shanshan Li, Ludan Zhao, Hui Li
Thiabendazole (TBZ), which is oxidized into 5-hydroxythiabendazole (5-OH-TBZ) in vivo, is a commonly used food preservative. Interactions of TBZ and 5-OH-TBZ with human serum albumin (HSA) were comprehensively studied via multiple spectroscopic methods and molecular docking. This study focussed on the mechanistic and structural information on binding of TBZ and 5-OH-TBZ to HSA to evaluate the impact of the food additive on HSA. (1)H NMR spectra of the two ligands showed the binding exists. ITC and fluorescence spectroscopy results revealed that TBZ was a stronger ligand, with a binding constant of 10(5)l/mol and formed a more stable complex with HSA than did 5-OH-TBZ via electrostatic interaction...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28528776/structural-basis-of-tpr-mediated-oligomerization-and-activation-of-oncogenic-fusion-kinases
#10
Kuntal Pal, Abhishek Bandyopadhyay, X Edward Zhou, Qingping Xu, David P Marciano, Joseph S Brunzelle, Smitha Yerrum, Patrick R Griffin, George Vande Woude, Karsten Melcher, H Eric Xu
The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature...
May 18, 2017: Structure
https://www.readbyqxmd.com/read/28527394/elucidation-of-penetration-enhancement-mechanism-of-emu-oil-using-ftir-microspectroscopy-at-emira-laboratory-of-sesame-synchrotron
#11
Randa S H Mansour, Alsayed A Sallam, Imad I Hamdan, Enam A Khalil, Ibraheem Yousef
It has been proposed that Emu oil possesses skin permeation-enhancing effect. This study aimed to address its possible penetration enhancement mechanism(s) using IR microscopy, in accordance with LPP theory. The penetration of Emu oil through the layers of human skin was accomplished by monitoring oil-IR characteristic feature at 3006cm(-1). The unsaturated components of Emu oil accumulated at about 270μm depth of skin surface. The interaction of Emu oil with lipid and protein constituents of SC was investigated in comparison with a commonly used enhancer, IPM...
May 12, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28527333/transcriptome-wide-analysis-of-jasmonate-treated-by-2-cells-reveals-new-transcriptional-regulators-associated-with-alkaloid-formation-in-tobacco
#12
Yuping Yang, Pengcheng Yan, Che Yi, Wenzheng Li, Yuhui Chai, Lingling Fei, Ping Gao, Heping Zhao, Yingdian Wang, Michael P Timko, Bingwu Wang, Shengcheng Han
Jasmonates (JAs) are well-known regulators of stress, defence, and secondary metabolism in plants, with JA perception triggering extensive transcriptional reprogramming, including both activation and/or repression of entire metabolic pathways. We performed RNA sequencing based transcriptomic profiling of tobacco BY-2 cells before and after treatment with methyl jasmonate (MeJA) to identify novel transcriptional regulators associated with alkaloid formation. A total of 107,140 unigenes were obtained through de novo assembly, and at least 33,213 transcripts (31%) encode proteins, in which 3419 transcription factors (TFs) were identified, representing 72 gene families, as well as 840 transcriptional regulators (TRs) distributed among 19 gene families...
May 4, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28527037/frequency-voltage-controlled-light-transmittance-in-ferroelectric-liquid-crystal-cells
#13
Aleksey A Kudreyko, Nail G Migranov, Olga V Bachurina, Song Wanqing
Light transmittance of a short-pitch deformed-helix ferroelectric liquid crystal cell was numerically studied when low and high voltage frequencies ([Formula: see text] kHz and [Formula: see text] kHz, respectively) are applied to the cell. The reported finding in the decay of light transmittance at increasing frequency is obtained due to reasonable simplifications of the temporal dependence of director's azimuthal angle. By taking experimentally known data, we numerically demonstrate that the increase in temperature of ferroelectric liquid crystals yields an insignificant change of light transmittance within all visible spectra...
May 2017: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/28525579/modulation-of-cyclobutane-thymine-photodimer-formation-in-t11-tracts-in-rotationally-phased-nucleosome-core-particles-and-dna-minicircles
#14
Kesai Wang, John-Stephen A Taylor
Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggests that DNA bending causes the modulation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we have developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been rotationally phased with respect to the histone octamer by TG motifs...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28524849/structural-basis-for-conductance-through-tric-cation-channels
#15
Min Su, Feng Gao, Qi Yuan, Yang Mao, De-Lin Li, Youzhong Guo, Cheng Yang, Xiao-Hui Wang, Renato Bruni, Brian Kloss, Hong Zhao, Yang Zeng, Fa-Ben Zhang, Andrew R Marks, Wayne A Hendrickson, Yu-Hang Chen
Mammalian TRICs function as K(+)-permeable cation channels that provide counter ions for Ca(2+) handling in intracellular stores. Here we describe the structures of two prokaryotic homologues, archaeal SaTRIC and bacterial CpTRIC, showing that TRIC channels are symmetrical trimers with transmembrane pores through each protomer. Each pore holds a string of water molecules centred at kinked helices in two inverted-repeat triple-helix bundles (THBs). The pores are locked in a closed state by a hydrogen bond network at the C terminus of the THBs, which is lost when the pores assume an open conformation...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28522854/genetic-tools-to-study-juvenile-hormone-action-in-drosophila
#16
A A Baumann, M J Texada, H M Chen, J N Etheredge, D L Miller, S Picard, R Warner, J W Truman, L M Riddiford
The insect juvenile hormone receptor is a basic helix-loop-helix (bHLH), Per-Arnt-Sim (PAS) domain protein, a novel type of hormone receptor. In higher flies like Drosophila, the ancestral receptor germ cell-expressed (gce) gene has duplicated to yield the paralog Methoprene-tolerant (Met). These paralogous receptors share redundant function during development but play unique roles in adults. Some aspects of JH function apparently require one receptor or the other. To provide a foundation for studying JH receptor function, we have recapitulated endogenous JH receptor expression with single cell resolution...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522372/effective-antimicrobial-activity-of-a-peptide-mutant-cbf-14-2-against-penicillin-resistant-bacteria-based-on-its-unnatural-amino-acids
#17
Wei Kang, Hanhan Liu, Lingman Ma, Mengxiao Wang, Shanshan Wei, Pengbo Sun, Meiling Jiang, Min Guo, Changlin Zhou, Jie Dou
Broad spectrum activities, a unique mode of actions and rare resistant variants make antimicrobial peptide (AMP) a potential alternative to antibiotics. However, AMPs still have limitations in clinical development due to their physiological stability, toxicity and manufacturing costs. Cbf-14, derived from cathelicidin-BF has been proven to be effective against drug-resistant bacteria. Herein, a series of Cbf-14 mutants were designed to overcome these limitations. Design strategies included substitutions of lysine (Lys) or leucine (Leu) with similar residues such as ornithine (Orn) and norleucine (Ile), which are unnatural amino acids, to generate AMPs with enhanced therapeutic potential...
May 15, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28522193/ph-triggered-re-assembly-of-nanosphere-to-nanofiber-the-role-of-peptide-conformational-change-for-enhanced-cancer-therapy
#18
Peiqing Liang, Junjiong Zheng, Shulin Dai, Jiayu Wang, Zhaoqing Zhang, Ting Kang, Changyun Quan
pH-triggered conformational change and subsequent re-assembly of nanostructures provide a new strategy in nanomedicine for controlled drug release and enhanced therapy. Here, we reported the development of a novel pH-responsive nano-assembly as a drug carrier from peptide amphiphile (PA) consisting of mimicking peptide and stearic acid moieties. The mimicking peptide is a basic 17-amino acid peptide derived from antennapedia homeodomain, and undergoes a conformational transition of the secondary structure from β-sheet at pH7...
May 15, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28521820/destabilization-of-the-twist1-e12-complex-dimerization-following-the-r154p-point-mutation-of-twist1-an-in-silico-approach
#19
Charlotte Bouard, Raphael Terreux, Agnès Tissier, Laurent Jacqueroud, Arnaud Vigneron, Stéphane Ansieau, Alain Puisieux, Léa Payen
BACKGROUND: The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues...
May 18, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28521505/orientation-and-conformation-of-osteocalcin-adsorbed-onto-calcium-phosphate-and-silica-surfaces
#20
Luisa A Scudeller, Selvi Srinivasan, Alexandre M Rossi, Patrick S Stayton, Gary P Drobny, David G Castner
Adsorption isotherms, circular dichroism (CD) spectroscopy, x-ray photoelectron spectroscopy (XPS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to investigate the adsorption of human osteocalcin (hOC) and decarboxylated (i.e., Gla converted back to Glu) hOC (dhOC) onto various calcium phosphate surfaces as well as silica surfaces. The adsorption isotherms and XPS nitrogen signals were used to track the amount of adsorbed hOC and dhOC. The intensities of key ToF-SIMS amino acid fragments were used to assess changes in the structure of adsorbed hOC and dhOC...
May 18, 2017: Biointerphases
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