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https://www.readbyqxmd.com/read/28453938/simulated-force-quench-dynamics-shows-gb1-protein-is-not-a-two-state-folder
#1
Ronen Berkovich, Jagannath Mondal, Inga Paster, Bruce J Berne
Single molecule force spectroscopy is a useful technique for investigating mechanically induced protein unfolding and refolding under reduced forces by monitoring the end-to-end distance of the protein, Ree. The data is often interpreted via a "two-state" model based on the assumption that Ree alone is a good reaction coordinate and the thermodynamic behavior is then ascribed to the free energy as a function of this one reaction coordinate. In this paper, we determined the free energy surface (PMF) of GB1 protein from atomistic simulations in explicit solvent under different applied forces as a function of two collective variables (Ree, and the fraction of native contacts ρ)...
April 28, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28453854/the-dynamics-of-the-monomeric-restriction-endonuclease-bcni-during-its-interaction-with-dna
#2
Georgij Kostiuk, Jasmina Dikic, Friedrich W Schwarz, Giedrius Sasnauskas, Ralf Seidel, Virginijus Siksnys
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, '/' designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA...
April 27, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28453853/single-molecule-sequencing-revealing-the-presence-of-distinct-jc-polyomavirus-populations-in-patients-with-progressive-multifocal-leukoencephalopathy
#3
Hanna Seppälä, Elina Virtanen, Mika Saarela, Pia Laine, Lars Paulín, Laura Mannonen, Petri Auvinen, Eeva Auvinen
Background.: Progressive multifocal leukoencephalopathy (PML) is a fatal disease caused by reactivation of JC polyomavirus (JCPyV) in immunosuppressed individuals and lytic infection by neurotropic JCPyV in glial cells. The exact content of neurotropic mutations within individual JCPyV strains has not been studied to our knowledge. Methods.: We exploited the capacity of single-molecule real-time sequencing technology to determine the sequence of complete JCPyV genomes in single reads...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28453281/designing-ligands-to-isolate-znln-and-zn2ln-complexes-field-induced-single-ion-magnet-behavior-of-the-zndy-zn2dy-and-zn2er-analogues
#4
Matilde Fondo, Julio Corredoira-Vázquez, Ana M García-Deibe, Jesús Sanmartín-Matalobos, Juan Manuel Herrera, Enrique Colacio
A new H3L Schiff base ligand with three defined compartments, namely, two internal NNO and one external O6, was designed to allocate metal ions of different size. This ligand allows isolating heterodinuclear [ZnLn(HL)(NO3)(OAc)(D)](NO3) (Ln = Tb, D = H2O, ZnTb; Ln = Dy, D = CH3OH, ZnDy; and Ln = Er, D = CH3OH, ZnEr) complexes, where one of the NNO pockets allocates a zinc(II) ion, while the other one is empty, or heterotrinuclear [Zn2Ln(L)(NO3)2(OAc)2(H2O)] (Ln = Dy, Zn2Dy and Ln = Er, Zn2Er) compounds, where each NNO compartment accommodates Zn(II)...
April 28, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28448050/single-molecule-analysis-of-laser-localized-psoralen-adducts
#5
Jing Huang, Himabindu Gali, Julia Gichimu, Marina A Bellani, Durga Pokharel, Manikandan Paramasivam, Michael M Seidman
The DNA Damage Response (DDR) has been extensively characterized in studies of double strand breaks (DSBs) induced by laser micro beam irradiation in live cells. The DDR to helix distorting covalent DNA modifications, including interstrand DNA crosslinks (ICLs), is not as well defined. We have studied the DDR stimulated by ICLs, localized by laser photoactivation of immunotagged psoralens, in the nuclei of live cells. In order to address fundamental questions about adduct distribution and replication fork encounters, we combined laser localization with two other technologies...
April 20, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447789/exploring-the-role-of-n-6-substituents-in-potent-dual-acting-5-c-ethyl-tetrazolyl-adenosine-derivatives-synthesis-binding-functional-assays-and-antinociceptive-effects-in-mice
#6
Riccardo Petrelli, Mirko Scortichini, Sonja Kachler, Serena Boccella, Carmen Cerchia, Ilaria Torquati, Fabio Del Bello, Daniela Salvemini, Ettore Novellino, Livio Luongo, Sabatino Maione, Kenneth A Jacobson, Antonio Lavecchia, Karl-Norbert Klotz, Loredana Cappellacci
Structural determinants of affinity of N(6)-substituted-5'-C-(ethyl-tetrazol-2-yl)-adenosine and 2-chloro-adenosine derivatives at adenosine receptor (AR) subtypes were studied with binding and molecular modeling. Small N(6)-cycloalkyl and 3-halo-benzyl groups furnished potent dual acting A1AR agonists and A3AR antagonists. 4 was the most potent dual acting human (h) A1AR agonist (Ki = 0.45 nM) and A3AR antagonist (Ki = 0.31 nM) and highly selective versus A2A; 11 and 26 were most potent at both h and rat (r) A3AR...
April 27, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28446335/quantitative-nano-characterization-of-polymers-using-atomic-force-microscopy
#7
Milad Radiom, Svilen Kozhuharov, Phally Kong, Michela di Giannantonio, Mathieu A Ayer, Plinio Maroni, Andreas F M Kilbinger, Katharina M Fromm, Christoph Weder, Michal Borkovec
The present article offers an overview on the use of atomic force microscopy (AFM) to characterize the nanomechanical properties of polymers. AFM imaging reveals the conformations of polymer molecules at solid- liquid interfaces. In particular, for polyelectrolytes, the effect of ionic strength on the conformations of molecules can be studied. Examination of force versus extension profiles obtained using AFM-based single molecule force spectroscopy gives information on the entropic and enthalpic elasticities in pN to nN force range...
April 26, 2017: Chimia
https://www.readbyqxmd.com/read/28445749/equilibrium-ensembles-for-insulin-folding-from-bias-exchange-metadynamics
#8
Richa Singh, Rohit Bansal, Anurag Singh Rathore, Gaurav Goel
Earliest events in the aggregation process, such as single molecule reconfiguration, are extremely important and the most difficult to characterize in experiments. To this end, we have used well-tempered bias exchange metadynamics simulations to determine the equilibrium ensembles of an insulin molecule under amyloidogenic conditions of low pH and high temperature. A bin-based clustering method that uses statistics accumulated in bias exchange metadynamics trajectories was employed to construct a detailed thermodynamic and kinetic model of insulin folding...
April 25, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28445644/broadband-fluorescence-enhancement-with-self-assembled-silver-nanoparticle-optical-antennas
#9
Carolin Vietz, Izabela Kaminska, Maria Sanz Paz, Philip Tinnefeld, Guillermo P Acuna
Plasmonic structures are known to affect the fluorescence properties of dyes placed in close proximity. This effect has been exploited in combination with single-molecule techniques for several applications in the field of biosensing. Among these plasmonic structures, top-down zero-mode waveguides stand out due to their broadband capabilities. In contrast, optical antennas based on gold nanostructures exhibit fluorescence enhancement on a narrow fraction of the visible spectrum typically restricted to the red to near-infrared region...
April 28, 2017: ACS Nano
https://www.readbyqxmd.com/read/28445393/molecular-diode-studies-based-on-a-highly-sensitive-molecular-measurement-technique
#10
REVIEW
Madoka Iwane, Shintaro Fujii, Manabu Kiguchi
In 1974, molecular electronics pioneers Mark Ratner and Arieh Aviram predicted that a single molecule could act as a diode, in which electronic current can be rectified. The electronic rectification property of the diode is one of basic functions of electronic components and since then, the molecular diode has been investigated as a first single-molecule device that would have a practical application. In this review, we first describe the experimental fabrication and electronic characterization techniques of molecular diodes consisting of a small number of molecules or a single molecule...
April 26, 2017: Sensors
https://www.readbyqxmd.com/read/28443849/specific-single-molecule-detection-of-glucose-in-a-supramolecularly-designed-tunnel-junction
#11
Tomoaki Nishino, Hiroshi Shiigi, Manabu Kiguchi, Tsutomu Nagaoka
Scanning tunneling microscopy tips were functionalized with a boronic acid derivative. In combination with a similarly modified substrate, the molecular tip forms a supramolecular complex selectively with a glucose molecule. The conductance of the resulting single complex allows one to achieve the specific single-molecule detection of glucose.
April 26, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28443848/semiempirical-modeling-of-electrochemical-charge-transfer
#12
Rebecca L Gieseking, Mark A Ratner, George C Schatz
Nanoelectrochemical experiments using detection based on tip enhanced Raman spectroscopy (TERS) show a broad distribution of single-molecule formal potentials E°' for large π-conjugated molecules; theoretical studies are needed to understand the origins of this distribution. In this paper, we present a theoretical approach to determine E°' for electrochemical reactions involving a single molecule interacting with an electrode represented as a metal nanocluster and apply this method to the Ag20-pyridine system...
April 26, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28443838/charge-detection-mass-spectrometry-weighing-heavier-things
#13
REVIEW
David Z Keifer, Elizabeth E Pierson, Martin F Jarrold
Charge detection mass spectrometry (CDMS) is a single molecule method where the mass of each ion is directly determined from individual measurements of its mass-to-charge ratio and charge. CDMS is particularly valuable for the analysis of high mass and heterogeneous analytes, where conventional MS methods are often confounded. In the last few years, CDMS has received a renaissance. Technical developments have improved the resolution and dramatically increased the breadth of problems that can be addressed. These improvements have moved CDMS more into the mainstream as interest in the application of mass spectrometry to high molecular weight species has grown...
April 26, 2017: Analyst
https://www.readbyqxmd.com/read/28441775/progress-in-the-correlative-atomic-force-microscopy-and-optical-microscopy
#14
REVIEW
Lulu Zhou, Mingjun Cai, Ti Tong, Hongda Wang
Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed...
April 24, 2017: Sensors
https://www.readbyqxmd.com/read/28439036/reclassification-of-the-specialized-metabolite-producer-pseudomonas-mesoacidophila-atcc-31433-as-a-member-of-the-burkholderia-cepacia-complex
#15
E Joel Loveridge, Cerith Jones, Matthew J Bull, Suzy C Moody, Małgorzata W Kahl, Zainab Khan, Louis Neilson, Marina Tomeva, Sarah E Adams, Andrew C Wood, Daniel Rodriguez-Martin, Ingrid Pinel, Julian Parkhill, Eshwar Mahenthiralingam, John Crosby
Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, which produces the monobactam isosulfazecin and the β-lactam potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433 its complete genome was determined using single molecule real time DNA sequence analysis. The 7.8 Mb genome comprised four replicons: three chromosomal, each encoding ribosomal RNA, and one plasmid. Phylogenetic analysis demonstrated that P...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28438136/normalized-long-read-rna-sequencing-in-chicken-reveals-transcriptome-complexity-similar-to-human
#16
Richard I Kuo, Elizabeth Tseng, Lel Eory, Ian R Paton, Alan L Archibald, David W Burt
BACKGROUND: Despite the significance of chicken as a model organism, our understanding of the chicken transcriptome is limited compared to human. This issue is common to all non-human vertebrate annotations due to the difficulty in transcript identification from short read RNAseq data. While previous studies have used single molecule long read sequencing for transcript discovery, they did not perform RNA normalization and 5'-cap selection which may have resulted in lower transcriptome coverage and truncated transcript sequences...
April 24, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28437460/an-aggregation-removal-model-for-the-formation-and-size-determination-of-post-synaptic-scaffold-domains
#17
Jonas Ranft, Leandro G Almeida, Pamela C Rodriguez, Antoine Triller, Vincent Hakim
The formation and stability of synapses are key questions in neuroscience. Post-synaptic domains have been classically conceived as resulting from local insertion and turnover of proteins at the synapse. However, insertion is likely to occur outside the post-synaptic domains and advances in single-molecule imaging have shown that proteins diffuse in the plane of the membrane prior to their accumulation at synapses. We quantitatively investigated this scenario using computer simulations and mathematical analysis, taking for definiteness the specific case of inhibitory synapse components, i...
April 24, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28437075/fluorescent-photoswitchable-diarylethenes-for-biolabeling-and-single-molecule-localization-microscopies-with-optical-superresolution
#18
Benoit Roubinet, Michael Weber, Heydar Shojaei, Mark Bates, Mariano L Bossi, Vladimir N Belov, Masahiro Irie, Stefan W Hell
A modular assembly of water soluble diarylethenes (DAEs), applicable as bio-markers for optical nanoscopy, is reported. Reversibly photoswitchable 1,2-bis(2-alkyl-6-phenyl-1-benzothiophene-1,1-dioxide-3-yl)perfluorocyclopentenes possessing a fluorescent "closed" form were decorated with one or two methoxy group(s) attached to the para-position(s) of phenyl ring(s) and two, four or eight carboxylic acid groups. Antibody conjugates of these DAEs feature low aggregation, efficient photoswitching in aqueous buffers, specific staining of cellular structures and photophysical properties (high emission efficiencies and low cycloreversion quantum yields) enabling their application in superresolution microscopy...
April 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28436659/fluorescence-and-scattering-light-cross-correlation-spectroscopy-and-its-applications-in-homogeneous-immunoassay
#19
Jinjie Wang, Xiangyi Huang, Heng Liu, Chaoqing Dong, Jicun Ren
In this work we propose fluorescence and scattering light cross-correlation spectroscopy (FSCCS) based on laser confocal configuration using silver nanoparticle (SNPs) and Alexa Fluor 488 (Alexa) as probe pairs. FSCCS is a single molecule (particle) method, and its principle is similar to that of fluorescence cross-correlation spectroscopy (FCCS). We established the setup of FSCCS using single wavelength laser and developed an immunoassay model of FSCCS. The reliability and adaptability of FSCCS method were evaluated by homogeneous sandwich immunoassay mode...
April 24, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28436526/structural-implications-on-the-excitation-dynamics-of-fluorescent-3h-indolium-cations
#20
Ek Raj Thapaliya, Jaume Garcia-Amorós, Santi Nonell, Burjor Captain, Françisco M Raymo
Fluorescent 3H-indolium cations are valuable components for the realization of activatable fluorophores for bioimaging applications. Their relatively poor fluorescent quantum yields in organic solvents, however, appear to be in contradiction to their good performance in analytical methods based on single-molecule detection. The elucidation of the structural factors governing the excitation dynamics of these compounds is, therefore, essential to rationalize these effects and possibly guide the future design of activatable probes with improved performance...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
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