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https://www.readbyqxmd.com/read/29350952/fast-data-sorting-with-modified-principal-component-analysis-to-distinguish-unique-single-molecular-break-junction-trajectories
#1
J M Hamill, X T Zhao, G Mészáros, M R Bryce, M Arenz
A simple and fast analysis method to sort large data sets into groups with shared distinguishing characteristics is described and applied to single molecular break junction conductance versus electrode displacement data. The method, based on principal component analysis, successfully sorts data sets based on the projection of the data onto the first or second principal component of the correlation matrix without the need to assert any specific hypothesis about the expected features within the data. This is an improvement on the current correlation matrix analysis approach because it sorts data automatically, making it more objective and less time consuming, and our method is applicable to a wide range of multivariate data sets...
January 5, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29349585/molecularly-imprinted-core-shell-cdse-sio2-cds-as-a-ratiometric-fluorescent-probe-for-4-nitrophenol-sensing
#2
Mingyue Liu, Zhao Gao, Yanjun Yu, Rongxin Su, Renliang Huang, Wei Qi, Zhimin He
4-Nitrophenol (4-NP) is a priority pollutant in water and is both carcinogenic and genotoxic to humans and wildlife even at very low concentrations. Thus, we herein fabricated a novel molecularly imprinted core-shell nanohybrid as a ratiometric fluorescent sensor for the highly sensitive and selective detection of 4-NP. This sensor was functioned by the transfer of fluorescence resonance energy between photoluminescent carbon dots (CDs) and 4-NP. This sensor was synthesized by linking organosilane-functionalized CDs to silica-coated CdSe quantum dots (CdSe@SiO2) via Si-O bonds...
January 18, 2018: Nanoscale Research Letters
https://www.readbyqxmd.com/read/29349024/the-crossing-internal-suture-augmentation-technique-to-protect-the-all-inside-anterior-cruciate-ligament-reconstruction-graft
#3
Mohamed Aboalata, Ashraf Elazab, Abdelsamie Halawa, Moheib S Ahmed, Andreas B Imhoff, Yehia Bassiouny
The crossing internal suture augmentation technique is an all-inside technique of anterior cruciate ligament reconstruction with augmentation of the hamstring tendon autograft with a braided ultrahigh-molecular-weight polyester-polyethylene suture tape resting on the adjustable cortical buttons on both the femoral and tibial sides. The internal suture augmentation acts as a backbone supporting and protecting the graft until the process of healing and ligamentization of the graft is completed. The ends of the suture tape are tied on the tibial button and additionally fixed to the tibia with a knotless anchor as a backup fixation with the knee in full extension...
December 2017: Arthroscopy Techniques
https://www.readbyqxmd.com/read/29347811/orientation-shape-coupling-between-liquid-crystal-and-membrane-through-the-anchoring-effect
#4
Shun Okushima, Toshihiro Kawakatsu
We perform a series of Monte Carlo simulations on an interface between a liquid crystal (LC) material in isotropic phase in its bulk and a surfactant membrane. These two objects are simulated using coarse-grained molecular models. We estimate physical properties of the membrane such as the interfacial tension and the bending rigidity, focusing on the anchoring effects of the membrane on the LC. According to our simulation results, when the strength of the homeotropic anchoring denoted by the anchoring parameter ξ is increased, the interfacial tension decreases and the bending rigidity first increases in ξ<ξ_{m}, and it then decreases in ξ_{m}<ξ...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29344147/systematic-analysis-of-the-molecular-mechanism-of-microrna-124-in-hepatoblastoma-cells
#5
Guiming Wang, Hong Liu, Zhigang Wei, Hongyan Jia, Yu Liu, Jiansheng Liu
The present study aimed to identify the molecular mechanisms of microRNA-124 (miRNA-124/miR-124) in hepatoblastoma. The GSE6207 microarray dataset, obtained from the Gene Expression Omnibus database, included samples extracted from HepG2 cells transfected with miR-124 duplex (the experimental group) or negative control (the control group) at 4, 8, 16, 24, 32, 72 and 120 h after transfection. Differentially expressed genes (DEGs) were screened between the two groups. miR-124 activity was inferred based on the expression of its target genes...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#6
Xinghong Dai, Danyang Gong, Hanyoung Lim, Jonathan Jih, Ting-Ting Wu, Ren Sun, Z Hong Zhou
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29341608/molecular-dynamics-pinpoint-the-global-fluorine-effect-in-balanoids-binding-to-pkc%C3%AE%C2%B5-and-pka
#7
Ari Hardianto, Fei Liu, Shoba Ranganathan
(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with little selectivity. While PKA is known as a tumour promoter, PKC isozymes can be tumour promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood...
January 17, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29341226/molecular-details-of-spontaneous-insertion-and-interaction-of-hcv-non-structure-3-protease-protein-domain-with-pip2-containing-membrane
#8
Huynh Minh Hung, Tran Dieu Hang, Minh Tho Nguyen
Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level...
January 17, 2018: Proteins
https://www.readbyqxmd.com/read/29340240/refining-amino-acid-hydrophobicity-for-dynamics-simulation-of-membrane-proteins
#9
Ronald D Hills
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues...
2018: PeerJ
https://www.readbyqxmd.com/read/29337209/the-role-of-d-allo-isoleucine-in-the-deposition-of-the-anti-leishmania-peptide-bombinin-h4-as-revealed-by-31p-solid-state-nmr-vcd-spectroscopy-and-md-simulation
#10
Batsaikhan Mijiddorj, Shiho Kaneda, Hisako Sato, Yuki Kitahashi, Namsrai Javkhlantugs, Akira Naito, Kazuyoshi Ueda, Izuru Kawamura
Bombinin H4 is an antimicrobial peptide that was isolated from the toad Bombina variegata. Bombinin H family peptides are active against gram-positive, gram-negative bacteria, and fungi as well as the parasite Leishmania. Among them, bombinin H4 (H4), which contains d-allo-isoleucine (d-allo-Ile) as the second residue in its sequence, is the most active, and its l-isomer is bombinin H2 (H2). H4 has a significantly lower LC50 than H2 against Leishmania. However, the atomic-level mechanism of the membrane interaction and higher activity of H4 has not been clarified...
January 11, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29331981/variant-in-c-terminal-region-of-intestinal-alkaline-phosphatase-associated-with-benign-familial-hyperphosphatasaemia
#11
Takayuki Ishige, Sakae Itoga, Emi Utsuno, Motoi Nishimura, Masaharu Yoshikawa, Naoya Kato, Kazuyuki Matsushita, Osamu Yokosuka, Fumio Nomura
BACKGROUND: A genetic diagnosis has been rarely performed in benign familial hyperphosphatasaemia, and molecular mechanism largely remains unclear. OBJECTIVES: We encountered a case with benign familial hyperphosphatasaemia of intestinal alkaline phosphatase (IAP). To elucidate the molecular mechanism, we performed ALPI gene sequencing and in vitro protein expression analysis. METHODS: ALPI gene was sequenced by long-range PCR and massively parallel sequencing...
January 13, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29329339/accessibility-and-contribution-to-glucan-masking-of-natural-and-genetically-tagged-versions-of-yeast-wall-protein-1-of-candida-albicans
#12
Bruce L Granger
Yeast wall protein 1 (Ywp1) is an abundant glycoprotein of the cell wall of the yeast form of Candida albicans, the most prevalent fungal pathogen of humans. Antibodies that bind to the polypeptide backbone of isolated Ywp1 show little binding to intact yeast cells, presumably because the Ywp1 epitopes are masked by the polysaccharides of the mannoproteins that form the outer layer of the cell wall. Rare cells do exhibit much greater anti-Ywp1 binding, however, and one of these was isolated and characterized...
2018: PloS One
https://www.readbyqxmd.com/read/29328918/transmembrane-pickets-connect-cyto-and-pericellular-skeletons-forming-barriers-to-receptor-engagement
#13
Spencer A Freeman, Anthony Vega, Magdalena Riedl, Richard F Collins, Phillip P Ostrowski, Elliot C Woods, Carolyn R Bertozzi, Markku I Tammi, Diane S Lidke, Pauline Johnson, Satyajit Mayor, Khuloud Jaqaman, Sergio Grinstein
Phagocytic receptors must diffuse laterally to become activated upon clustering by multivalent targets. Receptor diffusion, however, can be obstructed by transmembrane proteins ("pickets") that are immobilized by interacting with the cortical cytoskeleton. The molecular identity of these pickets and their role in phagocytosis have not been defined. We used single-molecule tracking to study the interaction between Fcγ receptors and CD44, an abundant transmembrane protein capable of indirect association with F-actin, hence likely to serve as a picket...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29324326/studying-the-recognition-mechanism-of-tcar-and-ssdna-using-molecular-dynamic-simulations
#14
Jing-Rong Fan, Hong-Xing Zhang, Yu-Guang Mu, Qing-Chuan Zheng
The transcription regulator teicoplanin-associate locus regulator (TcaR) plays a vital role in interfering with ssDNA replication and resisting ssDNA phage invasion. Although recent studies demonstrated that TcaR had strong interaction with ssDNA, the dynamics and interaction mechanism of dimeric TcaR bound to ssDNA have not been rationalized at the atomic level. In our study, MD simulations combined with MM-GB/SA calculations were employed to study recognition mechanism between TcaR and ssDNA. The results illuminate that electrostatic interaction is the main driving force for the binding process...
December 5, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29323878/electrical-matching-at-metal-molecule-contacts-for-efficient-heterogeneous-charge-transfer
#15
Shino Sato, Shigeru Iwase, Kotaro Namba, Tomoya Ono, Kenji Hara, Atsushi Fukuoka, Kohei Uosaki, Katsuyoshi Ikeda
In a metal/molecule hybrid system, unavoidable electrical mismatch exists between metal continuum states and frontier molecular orbitals. This causes energy loss in the electron conduction across the metal/molecule interface. For efficient use of energy in a metal/molecule hybrid system, it is necessary to control interfacial electronic structures. Here we demonstrate that electrical matching between a gold substrate and π-conjugated molecular wires can be obtained by using monoatomic foreign metal interlayers, which can change the degree of d-π* back donation at metal/anchor contacts...
January 11, 2018: ACS Nano
https://www.readbyqxmd.com/read/29323391/growth-of-regular-nanometric-molecular-arrays-on-a-functional-2d-template-based-on-a-chemical-guest-host-approach
#16
Zhijing Feng, Gregor Kladnik, Giovanni Comelli, Carlo Dri, Albano Cossaro
A regular 2D array of crown molecules, which would spontaneously self-assemble into disordered molecular clusters, is obtained by exploiting a guest-host process, based on the chemical affinity between amino and carboxylic groups on a gold surface. First a carboxylic organic template is formed, which then serves as a host for amino-functionalized crown molecules. The amino-carboxylic interaction thereby drives the formation of a monolayer of guest molecules, regularly distributed at the nanometer scale, preventing their aggregation in unordered clusters observed on a bare gold surface...
January 11, 2018: Nanoscale
https://www.readbyqxmd.com/read/29319703/tailoring-2d-and-3d-molecular-sieves-structures-for-polyolefin-composites-do-all-roads-lead-to-remarkable-performances
#17
H M Moura, N L Gibbons, S A Miller, H O Pastore
Multiple synthetic strategies were performed in order to tether a zirconium-based catalyst to the 2D and 3D molecular sieves for olefin polymerizations. The anchoring of fluorene silane to the mesoporous MCM-41 was performed in order to obtain a stable catalyst for olefin polymerization (1@MCM-41). Using spectroscopic methods, this system was shown to have the metal center locked on a face down conformation with the surface. Also, immobilized zirconium complexes have been prepared on three different types of aminopropyl-modified supports (2@magadiite, 2@MCM-41 and 3@MCM-48)...
January 10, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29317735/syntaxins-on-granules-promote-docking-of-granules-via-interactions-with-munc18
#18
Maria Borisovska
SNAREs and SNARE-binding accessory proteins are believed to be central molecular components of neurotransmitter release, although the precise sequence of molecular events corresponding to distinct physiological states is unclear. The mechanism of docking of vesicles to the plasma membrane remains elusive, as the anchoring protein residing on vesicles is unknown. Here I show that targeting small amounts of syntaxin to granules by transmembrane domain alteration leads to a substantial enhancement of syntaxin clustering beneath granules, as well as of morphological granule docking...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317505/g%C3%AE-identity-dictates-efficacy-of-g%C3%AE-%C3%AE-signaling-and-macrophage-migration
#19
Kanishka Senarath, John L Payton, Dinesh Kankanamge, Praneeth Siripurapu, Mithila Tennakoon, Ajith Karunarathne
G protein βγ subunit (Gβγ) is a major signal transducer and controls processes ranging from cell migration to gene transcription. Despite having significant subtype heterogeneity and exhibiting diverse cell and tissue-specific expression levels, Gβγ is often considered a unified signaling entity with a defined functionality. However, the molecular and mechanistic basis of Gβγ's signaling specificity is unknown. Here, we demonstrate that Gγ subunits, bearing the sole plasma membrane (PM)-anchoring motif, control the PM affinity of Gβγ and thereby differentially modulate Gβγ effector signaling in a Gγ-specific manner...
January 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29311144/differentiation-and-characterization-of-excitatory-and-inhibitory-synapses-by-cryo-electron-tomography-and-correlative-microscopy
#20
Chang-Lu Tao, Yun-Tao Liu, Rong Sun, Bin Zhang, Lei Qi, Sakar Shivakoti, Chong-Li Tian, Peijun Zhang, Pak-Ming Lau, Z Hong Zhou, Guo-Qiang Bi
As key functional units in neural circuits, different types of neuronal synapses play distinct roles in brain information processing, learning and memory. Synaptic abnormalities are believed to underlie various neurological and psychiatric disorders. Here, by combining cryo-electron tomography and cryo-correlative light and electron microscopy, we distinguished intact excitatory and inhibitory synapses of cultured hippocampal neurons, and visualized the in situ three-dimensional organization of synaptic organelles and macromolecules in their native state...
January 8, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
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