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https://www.readbyqxmd.com/read/28633822/effects-of-pulsed-ultrasound-on-rheological-and-structural-properties-of-chicken-myofibrillar-protein
#1
Jing-Yu Wang, Yu-Ling Yang, Xiao-Zhi Tang, Wen-Xi Ni, Lei Zhou
The effects of pulsed ultrasound (PUS) (power: 240w) with varying time (0, 3, 6, 9, 12 and 15min) on rheological and structural properties of chicken myofibrillar protein (CMP) were examined. PUS treatment significantly caused a decrease in the viscosity coefficients (k) but an increase in the flow index (n) value of CMP solutions within short time (0-6min), while had no significant effect for longer time (9-15min). Besides, at 6min, the solubility and microstructure of CMP samples were optimum. The primary structure of CMP was not altered by PUS treatment...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28633819/effects-of-ultrasound-pretreatment-with-different-frequencies-and-working-modes-on-the-enzymolysis-and-the-structure-characterization-of-rice-protein
#2
Xue Yang, Yunliang Li, Suyun Li, Ayobami Olayemi Oladejo, Siyu Ruan, Yucheng Wang, Shanfen Huang, Haile Ma
The effects of ultrasound pretreatment with different frequencies and working modes, including mono-frequency ultrasound (MFU), dual-frequency ultrasound (DFU) and tri-frequency ultrasound (TFU), on the degree of hydrolysis (DH) of rice protein (RP) and angiotensin-I-converting enzyme (ACE) inhibitory activity of RP hydrolysate were investigated. Ultraviolet-visible (UV) spectroscopy, fourier transform infrared (FTIR) spectroscopy, surface hydrophobicity and scanning electron microscopy (SEM) of RP pretreated with ultrasound were measured...
September 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28632275/architectures-of-soft-robotic-locomotion-enabled-by-simple-mechanical-principles
#3
Liangliang Zhu, Yunteng Cao, Yilun Liu, Zhe Yang, Xi Chen
In nature, a variety of limbless locomotion patterns flourish, from the small or basic life forms (Escherichia coli, amoebae, etc.) to the large or intelligent creatures (e.g., slugs, starfishes, earthworms, octopuses, jellyfishes, and snakes). Many bioinspired soft robots based on locomotion have been developed in the past few decades. In this work, based on the kinematics and dynamics of two representative locomotion modes (i.e., worm-like crawling and snake-like slithering), we propose a broad set of innovative designs for soft mobile robots through simple mechanical principles...
June 20, 2017: Soft Matter
https://www.readbyqxmd.com/read/28632082/the-%C3%AE-helix-alignment-of-proteins-in-water-solution-toward-a-high-frequency-electromagnetic-field-a-ftir-spectroscopy-study
#4
Emanuele Calabrò, Salvatore Magazù
The aim of this article was to study the effects of mobile phone electromagnetic waves at 1750 MHz on the Amide I and Amide II vibration bands of some proteins in bidistilled water solution by means of Fourier transform infrared (FTIR) spectroscopy and Fourier self-deconvolution (FSD) analysis. The proteins that were used for the experiment were hemoglobin, myoglobin, bovine serum albumin and lysozyme. The exposure system consisted of microwaves emitted by an operational mobile phone at the frequency at 1750 MHz at the average power density of 1 W/m(2)...
June 20, 2017: Electromagnetic Biology and Medicine
https://www.readbyqxmd.com/read/28631437/control-of-virulence-gene-transcription-by-indirect-readout-in-vibrio-cholerae-and-salmonella-enterica-serovar-typhimurium
#5
Charles J Dorman, Matthew J Dorman
Indirect readout mechanisms of transcription control rely on the recognition of DNA shape by transcription factors (TFs). TFs may also employ a direct readout mechanism that involves the reading of the base sequence in the DNA major groove at the binding site. TFs with winged helix-turn-helix (wHTH) motifs use an alpha helix to read the base sequence in the major groove while inserting a beta sheet 'wing' into the adjacent minor groove. Such wHTH proteins are important regulators of virulence gene transcription in many pathogens; they also control housekeeping genes...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28631168/the-function-of-osbhlh068-is-partially-redundant-with-its-homolog-atbhlh112-in-the-regulation-of-the-salt-stress-response-but-has-opposite-functions-to-control-flowering-in-arabidopsis
#6
Hung-Chi Chen, Vicki Hsieh-Feng, Pei-Chun Liao, Wan-Hsing Cheng, Li-Yu Liu, Yun-Wei Yang, Ming-Hsin Lai, Men-Chi Chang
The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown...
June 19, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28630813/mutations-in-the-sh1-helix-alter-the-thermal-properties-of-myosin-ii
#7
Kotomi Shibata, Tsubasa Koyama, Shohei Inde, Sosuke Iwai, Shigeru Chaen
The myosin II SH1 helix is a joint that links the converter subdomain to the rest of the myosin motor domain and possibly plays a key role in the arrangement of the converter/lever arm. Several point mutations within the SH1 helix in human myosin IIs have been shown to cause diseases. To reveal whether these SH1 helix mutations affect not only motile activities but also thermal properties of myosin II, here we introduced the E683K or R686C point mutation into the SH1 helix in Dictyostelium myosin II. Thermal inactivation as well as thermal aggregation rates of these mutant proteins demonstrated that these mutations decreased the thermal stability of myosin II...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28630402/exploration-of-binding-and-inhibition-mechanism-of-a-small-molecule-inhibitor-of-influenza-virus-h1n1-hemagglutinin-by-molecular-dynamics-simulation
#8
Shanshan Guan, Tianao Wang, Ziyu Kuai, Mengdan Qian, Xiaopian Tian, Xiuqi Zhang, Yongjiao Yu, Song Wang, Hao Zhang, Hao Li, Wei Kong, Yaming Shan
Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28630153/membrane-spanning-%C3%AE-helical-barrels-as-tractable-protein-design-targets
#9
REVIEW
Ai Niitsu, Jack W Heal, Kerstin Fauland, Andrew R Thomson, Derek N Woolfson
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28629777/mechanistic-insights-into-transcription-coupled-dna-repair
#10
REVIEW
Bibhusita Pani, Evgeny Nudler
Transcription-coupled DNA repair (TCR) acts on lesions in the transcribed strand of active genes. Helix distorting adducts and other forms of DNA damage often interfere with the progression of the transcription apparatus. Prolonged stalling of RNA polymerase can promote genome instability and also induce cell cycle arrest and apoptosis. These generally unfavorable events are counteracted by RNA polymerase-mediated recruitment of specific proteins to the sites of DNA damage to perform TCR and eventually restore transcription...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28629774/genome-instabilities-arising-from-ribonucleotides-in-dna
#11
REVIEW
Hannah L Klein
Genomic DNA is transiently contaminated with ribonucleotide residues during the process of DNA replication through misincorporation by the replicative DNA polymerases α, δ and ε, and by the normal replication process on the lagging strand, which uses RNA primers. These ribonucleotides are efficiently removed during replication by RNase H enzymes and the lagging strand synthesis machinery. However, when ribonucleotides remain in DNA they can distort the DNA helix, affect machineries for DNA replication, transcription and repair, and can stimulate genomic instabilities which are manifest as increased mutation, recombination and chromosome alterations...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28629512/erythropoietin-receptor-structural-domains
#12
Qingxin Li, CongBao Kang
Erythropoietin (EPO) is a hormone that is important for regulating red blood cell production. It is functional through binding to its receptor-EpoR. EpoR is a single-span membrane protein. It contains an extracellular region, a transmembrane domain, and a C-terminus. The extracellular region is important for binding to EPO, and its conformation is critical for signal transduction. The transmembrane domain contains 21 residues forming a helix which plays an important role in transferring ligand-induced conformational changes of the extracellular domain across the cell membrane...
2017: Vitamins and Hormones
https://www.readbyqxmd.com/read/28628649/insights-into-the-binding-mode-of-mek-type-iii-inhibitors-a-step-towards-discovering-and-designing-allosteric-kinase-inhibitors-across-the-human-kinome
#13
Zheng Zhao, Lei Xie, Philip E Bourne
Protein kinases are critical drug targets for treating a large variety of human diseases. Type-III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors...
2017: PloS One
https://www.readbyqxmd.com/read/28628237/wing-phosphorylation-is-a-major-functional-determinant-of-the-lrs14-type-biofilm-and-motility-regulator-abfr1-in-sulfolobus-acidocaldarius
#14
Lingling Li, Ankan Banerjee, Lisa Franziska Bischof, Hassan Ramadan Maklad, Lena Hoffmann, Anna-Lena Henche, Fabian Veliz, Wolfgang Bildl, Uwe Schulte, Alvaro Orell, Lars-Oliver Essen, Eveline Peeters, Sonja-Verena Albers
In response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm-forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix-turn-helix DNA-binding proteins of the archaea-specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small-angle X-ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling...
June 19, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28628166/nucleopolypeptides-with-dna-triggered-%C3%AE-helix-to-%C3%AE-sheet-transition
#15
Michel Nguyen, Jean-Luc Stigliani, Genevieve Pratviel, Colin Bonduelle
Synthetic polypeptides are versatile polymers outstandingly relevant to prepare bioinspired materials. In this work, we present a new class of smart polypeptide polymers, called nucleopolypeptides, having lateral chains functionalized with thymidine nucleobases. Structural studies performed by circular dichroism have revealed that the secondary structure of the polymers was influenced by nucleotide interaction and DNA sequence variation affording a selective helix-to-beta sheet transition with oligo(AAAAA)6...
June 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28628118/oncoppi-informed-discovery-of-mitogen-activated-protein-kinase-kinase-3-as-a-novel-binding-partner-of-c-myc
#16
A A Ivanov, V Gonzalez-Pecchi, L F Khuri, Q Niu, Y Wang, Y Xu, Y Bai, X Mo, E V Prochownik, M A Johns, Y Du, F R Khuri, H Fu
Mitogen-activated protein kinase kinase 3 (MKK3) is a dual threonine/tyrosine protein kinase that regulates inflammation, proliferation and apoptosis through specific phosphorylation and activation of the p38 mitogen-activated protein kinase. However, the role of MKK3 beyond p38-signaling remains elusive. Recently, we reported a protein-protein interaction (PPI) network of cancer-associated genes, termed OncoPPi, as a resource for the scientific community to generate new biological models. Analysis of the OncoPPi connectivity identified MKK3 as one of the major hub proteins in the network...
June 19, 2017: Oncogene
https://www.readbyqxmd.com/read/28625058/structural-basis-for-substrate-helix-remodeling-and-cleavage-loop-activation-in-the-varkud-satellite-ribozyme
#17
Saurja DasGupta, Nikolai B Suslov, Joseph A Piccirilli
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme resulting in a rearrangement of the substrate helix register into a so-called 'shifted' conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme...
June 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28624493/expression-of-the-c-terminal-domain-of-human-apolipoprotein-a-i-using-a-chimeric-apolipoprotein
#18
Daniel E Sallee, James V C Horn, Lukas A Fuentes, Paul M M Weers
Human apolipoprotein A-I (apoA-I) is the most abundant protein in high-density lipoprotein, an anti-atherogenic lipid-protein complex responsible for reverse cholesterol transport. The protein is composed of an N-terminal helix bundle domain, and a small C-terminal (CT) domain. To facilitate study of CT-apoA-I, a novel strategy was employed to produce this small domain in a bacterial expression system. A protein construct was designed of insect apolipophorin III (apoLp-III) and residues 179-243 of apoA-I, with a unique a methionine residue positioned between the two proteins and an N-terminal His-tag to facilitate purification...
June 14, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28623663/structural-mechanism-of-atp-independent-transcription-initiation-by-rna-polymerase-i
#19
Yan Han, Chunli Yan, Thi Hoang Duong Nguyen, Ashleigh J Jackobel, Ivaylo Ivanov, Bruce A Knutson, Yuan He
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location...
June 17, 2017: ELife
https://www.readbyqxmd.com/read/28623264/structural-characterization-of-the-smrt-corepressor-interacting-with-histone-deacetylase-7
#20
Danielle C Desravines, Itziar Serna Martin, Robert Schneider, Philippe J Mas, Nataliia Aleksandrova, Malene Ringkjøbing Jensen, Martin Blackledge, Darren J Hart
The 2525 amino acid SMRT corepressor is an intrinsically disordered hub protein responsible for binding and coordinating the activities of multiple transcription factors and chromatin modifying enzymes. Here we have studied its interaction with HDAC7, a class IIa deacetylase that interacts with the corepressor complex together with the highly active class I deacetylase HDAC3. The binding site of class IIa deacetylases was previously mapped to an approximate 500 amino acid region of SMRT, with recent implication of short glycine-serine-isoleucine (GSI) containing motifs...
June 16, 2017: Scientific Reports
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