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https://www.readbyqxmd.com/read/28107634/electrolyte-gradient-based-modulation-of-molecular-transport-through-nanoporous-gold-membranes
#1
Daniel A McCurry, Ryan C Bailey
Nanopores, and nanoporous materials in general, are interesting for applications in chemical and biomolecular transport as pore sizes are on the same scale as the dimension of many (bio)chemical species. Many studies have focused on either single pores or small arrays of cylindrical pores, which are convenient in terms of their amenability towards computational modeling of transport phenomenon. However, the limited overall porosity may inhibit transport flux as well as the eventual implementation of these materials as active separation elements...
January 20, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28103588/quantifying-kinetics-from-time-series-of-single-molecule-fret-efficiency-histograms
#2
Stephan Benke, Daniel Nettels, Hagen Hofmann, Benjamin Schuler
Single-molecule fluorescence spectroscopy is a powerful approach for probing biomolecular structure and dynamics, including protein folding. For the investigation of nonequilibrium kinetics, F��rster resonance energy transfer (FRET) in combination with confocal multiparameter detection has proven particularly versatile, owing to the large number of observables and the broad range of accessible timescales, especially in combination with rapid microfluidic mixing. However, a comprehensive kinetic analysis of the resulting time series of transfer efficiency histograms and complementary observables can be challenging owing to the complexity of the data...
January 19, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28094510/nanoporous-gold-based-electrode-morphology-libraries-for-investigating-structure-property-relationships-in-nucleic-acid-based-electrochemical-biosensors
#3
Zimple Matharu, Pallavi Daggumati, Ling Wang, Tatiana S Dorofeeva, Zidong Li, Erkin Seker
Nanoporous gold (np-Au) electrode coatings significantly enhance performance of electrochemical nucleic acid biosensors due to their three-dimensional nanoscale network, high electrical conductivity, facile surface functionalization, and biocompatibility. Contrary to planar electrodes, the np-Au electrodes also exhibit sensitive detection in the presence of common biofouling media due to their porous structure. However, the pore size of the nano-matrix plays a critical role in dictating the extent of biomolecular capture and transport...
January 17, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28093096/structural-biology-of-supramolecular-assemblies-by-magic-angle-spinning-nmr-spectroscopy
#4
Caitlin M Quinn, Tatyana Polenova
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/28092459/toward-high-throughput-and-multiplexed-imaging-of-genome-organization
#5
Eric F Joyce
Dr. Eric Joyce from the Department of Genetics at the University of Pennsylvania was awarded The President's Innovation award at the annual Society of Biomolecular Imaging and Informatics meeting held in Boston, September 2016. Chromosome interactions are a fundamental aspect of nuclear organization that can activate and silence genes or even direct chromosome rearrangements. However, the molecular mechanisms underlying how chromosomal segments find each other and form stable interactions within cells remain unknown...
January 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28090735/high-throughput-protein-targeted-biomolecular-detection-using-frequency-domain-faraday-rotation-spectroscopy
#6
Richard J Murdock, Shawn A Putnam, Soumen Das, Ankur Gupta, Elyse D Z Chase, Sudipta Seal
A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL(-1) and broad detection range of 10 pg mL(-1) ≲ cBSA ≲ 100 µg mL(-1) are observed...
January 16, 2017: Small
https://www.readbyqxmd.com/read/28088751/chip-based-digital-surface-plasmon-resonance-sensing-platform-for-ultrasensitive-biomolecular-detection
#7
Ming-Yang Pan, Kuang-Li Lee, Likarn Wang, Pei-Kuen Wei
A chip-based ultrasensitive surface plasmon resonance (SPR) sensor in a checkerboard nanostructure on plastic substrates is presented for digital detection. The sensing elements on the checkerboard are composed of silver-capped nanoslit arrays, which were fabricated using the thermal-embossing nanoimprint method, to meet the demand for low-cost and rapid fabrication. Sharp Fano resonances in the optimized nanoslit arrays provide high-intensity sensitivities (20,000% per refractive index unit), with an element size of 12...
January 7, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28088101/sequenced-defined-biomolecules-for-nanomaterial-synthesis-functionalization-and-assembly
#8
REVIEW
Joseph M Slocik, Rajesh R Naik
Biomolecules represent an invaluable resource to nanotechnology by providing a large diversity of highly functional biomolecular templates. As a result, these have been extensively used for controlling the synthesis, functionalization, and assembly of nanomaterials, while also creating materials with new properties and structures. In the following, we focus on the use of peptides to achieve these goals and describe their general utility, sequence programmability, and use as templates. Also, we highlight several recent advances in the identification and selection of high affinity nanomaterial-binding peptides, provide a few examples of peptide functionalized surfaces and peptide templated materials, and describe how simple modifications to well characterized nanomaterial-binding peptides can be used to manipulate interactions and physiochemical properties...
January 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28076817/elucidation-of-single-hydrogen-bonds-in-gtpases-via-experimental-and-theoretical-infrared-spectroscopy
#9
Daniel Mann, Udo Höweler, Carsten Kötting, Klaus Gerwert
Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076801/msmbuilder-statistical-models-for-biomolecular-dynamics
#10
Matthew P Harrigan, Mohammad M Sultan, Carlos X Hernández, Brooke E Husic, Peter Eastman, Christian R Schwantes, Kyle A Beauchamp, Robert T McGibbon, Vijay S Pande
MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov state models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models and time-structure based independent component analysis...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28075594/high-curvature-nanostructuring-enhances-probe-display-for-biomolecular-detection
#11
Phil De Luna, Sahar Mahshid, Jagotamoy Das, Binquan Luan, Edward H Sargent, Shana O Kelley, Ruhong Zhou
High-curvature electrodes facilitate rapid and sensitive detection of a broad class of molecular analytes. These sensors have reached detection limits not attained using bulk macroscale materials. It has been proposed that immobilized DNA probes are displayed at a high deflection angle on the sensor surface, allowing greater accessibility and more efficient hybridization. Here we report the first use of all-atom molecular dynamics simulations coupled with electrochemical experiments to explore the dynamics of ssDNA immobilized on high-curvature vs...
January 11, 2017: Nano Letters
https://www.readbyqxmd.com/read/28074503/bioorthogonal-diversification-of-peptides-through-selective-ruthenium-ii-catalyzed-c-h-activation
#12
Alexandra Schischko, Hongjun Ren, Nikolaos Kaplaneris, Lutz Ackermann
Methods for the chemoselective modification of amino acids and peptides are powerful techniques in biomolecular chemistry. Among other applications, they enable the total synthesis of artificial peptides. In recent years, significant momentum has been gained by exploiting palladium-catalyzed cross-coupling for peptide modification. Despite major advances, the prefunctionalization elements on the coupling partners translate into undesired byproduct formation and lengthy synthetic operations. In sharp contrast, we herein illustrate the unprecedented use of versatile ruthenium(II)carboxylate catalysis for the step-economical late-stage diversification of α- and β-amino acids, as well as peptides, through chemo-selective C-H arylation under racemization-free reaction conditions...
January 11, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28074088/accurate-optimization-of-amino-acid-form-factors-for-computing-small-angle-x-ray-scattering-intensity-of-atomistic-protein-structures
#13
Dudu Tong, Sichun Yang, Lanyuan Lu
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures...
August 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28070925/bioorthogonal-fluorescent-labelling-of-biopolymers-via-inverse-electron-demand-diels-alder-reactions
#14
Eszter Kozma, Orsolya Demeter, Péter Kele
Inverse electron demand Diels-Alder (IEDDA) based biorthogonal labelling schemes have attracted much attention lately in chemical biology. The appealing features of this reaction such as the fast reaction kinetics, fully biorthogonal nature, and high selectivity helped chemical biologists to get deeper understanding of biochemical processes at the molecular level. By listing the components and debating the possibilities and limitations that lay behind these reagents we provide a recent snapshot of IEDDA-based biomolecular manipulation field with special focus on fluorescent modulation schemes through bioorthogonalized building blocks...
January 10, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28068769/high-resolution-coarse-grained-model-of-hydrated-anion-exchange-membranes-that-accounts-for-hydrophobic-and-ionic-interactions-through-short-ranged-potentials
#15
Jibao Lu, Liam C Jacobson, Yamila A Perez Sirkin, Valeria Molinero
Molecular simulations provide a versatile tool to study the structure, anion conductivity, and stability of anion-exchange membrane (AEM) materials and can provide a fundamental understanding of the relation between structure and property of membranes that is key for their use in fuel cells and other applications. The quest for large spatial and temporal scales required to model the multiscale structure and transport processes in the polymer electrolyte membranes, however, cannot be met with fully atomistic models, and the available coarse-grained (CG) models suffer from several challenges associated with their low-resolution...
January 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28068076/bioavailability-and-kidney-responses-to-diclofenac-in-the-fathead-minnow-pimephales-promelas
#16
Lisa K Bickley, Ronny van Aerle, Andrew Ross Brown, Adam Hargreaves, Russell Huby, Victoria Cammack, Richard Jackson, Eduarda M Santos, Charles R Tyler
Diclofenac is one of the most widely prescribed non-steroidal anti-inflammatory drugs worldwide. It is frequently detected in surface waters; however, whether this pharmaceutical poses a risk to aquatic organisms is debated. Here we quantified the uptake of diclofenac by the fathead minnow (Pimephales promelas) following aqueous exposure (0.2 to 25.0 µg L(-1)) for 21 days, and evaluated the tissue and biomolecular responses in the kidney. Diclofenac accumulated in a concentration- and time- dependent manner in the plasma of exposed fish...
January 9, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28068057/topological-control-of-extracellular-matrix-growth-a-native-like-model-for-cell-morphodynamics-studies
#17
David Caballero, Josep Samitier
The interaction of cells with their natural environment influences a large variety of cellular phenomena, including cell adhesion, proliferation, and migration. The complex extracellular matrix network has challenged the attempts to replicate in vitro the heterogeneity of the cell environment and has threatened, in general, the relevance of in vitro studies. In this work, we describe a new and extremely versatile approach to generate native-like extracellular matrices with controlled morphologies for the in vitro study of cellular processes...
January 18, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28067766/wavelength-scanning-spr-imaging-sensors-based-on-an-acousto-optic-tunable-filter-and-a-white-light-laser
#18
Youjun Zeng, Lei Wang, Shu-Yuen Wu, Jianan He, Junle Qu, Xuejin Li, Ho-Pui Ho, Dayong Gu, Bruce Zhi Gao, Yonghong Shao
A fast surface plasmon resonance (SPR) imaging biosensor system based on wavelength interrogation using an acousto-optic tunable filter (AOTF) and a white light laser is presented. The system combines the merits of a wide-dynamic detection range and high sensitivity offered by the spectral approach with multiplexed high-throughput data collection and a two-dimensional (2D) biosensor array. The key feature is the use of AOTF to realize wavelength scan from a white laser source and thus to achieve fast tracking of the SPR dip movement caused by target molecules binding to the sensor surface...
January 5, 2017: Sensors
https://www.readbyqxmd.com/read/28067047/solvatochromic-and-fluorogenic-dyes-as-environment-sensitive-probes-design-and-biological-applications
#19
Andrey S Klymchenko
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes...
January 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28064429/structural-insight-into-the-gene-expression-profiling-of-the-hcn-operon-in-pseudomonas-aeruginosa
#20
Nilkanta Chowdhury, Angshuman Bagchi
Pseudomonas aeruginosa is a common opportunistic human pathogen. It generally attacks immunosuppressed patients like AIDS, cancer, cystic fibrosis, etc. The virulence of P. aeruginosa is mediated by various virulence factors. One of such potential virulence factors is HCN synthesized by HCN synthase enzyme, which is encoded by the hcnABC operon. The expressions of the genes of this operon are regulated by three transcriptional regulators, viz., LasR, ANR, and RhlR. In our previous work, we analyzed the molecular details of the functionalities of LasR...
January 7, 2017: Applied Biochemistry and Biotechnology
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