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Single molecule biophysics

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https://www.readbyqxmd.com/read/28799205/effects-of-fluorophore-attachment-on-protein-conformation-and-dynamics-studied-by-spfret-and-nmr
#1
Carolina Sanchez, Lena Voith-von-Voithenberg, Lisa Warner, Don C Lamb, Michael Sattler
Fluorescence-based techniques are widely used to study biomolecular conformations, intra- and intermolecular interactions, and conformational dynamics of macromolecules. Especially for fluorescent-based single-molecule experiments, the choice of the fluorophore and labeling position are highly important. Here, we have studied the biophysical and structural effects that are associated with the conjugation of fluorophores to cysteines in the splicing factor U2AF65 by using single pair Förster resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) spectroscopy...
August 10, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28789884/single-molecule-imaging-and-manipulation-of-biomolecular-machines-and-systems
#2
REVIEW
Ryota Iino, Tatsuya Iida, Akihiko Nakamura, Ei-Ichiro Saita, Huijuan You, Yasushi Sako
Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. Scope of Review We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems...
August 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28777580/a-first-step-towards-a-universal-fluorescent-probe-unravelling-the-photodynamics-of-an-amino-maleimide-fluorophore
#3
Michael Staniforth, Wen-Dong Quan, Tolga N V Karsili, Lewis A Baker, Rachel K O'Reilly, Vasilios G Stavros
Continuous advancements in biophysics and medicine at the molecular level make the requirements to image structure-function processes in living cells ever more acute. While fluorophores such as the green fluorescent protein have proven instrumental towards such efforts, the advent of non-diffraction limited microscopy limits the utility of such fluorescent tags. Monoaminomaleimides are small, single molecule fluorophores that have been shown to possess stark variations in their emission spectra in different solvent environments, making them a potentially powerful tool for myriad applications...
August 4, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28766344/cell-shaping-micropatterns-for-quantitative-super-resolution-microscopy-imaging-of-membrane-mechanosensing-proteins
#4
Anthony Fernandez, Markville Bautista, Ramunas Stanciauskas, Taerin Chung, Fabien Pinaud
Patterning cells on microcontact-printed substrates is a powerful approach to control cell morphology and introduce specific mechanical cues on a cell's molecular organization. Although global changes in cellular architectures caused by micropatterns can easily be probed with diffraction-limited optical microscopy, studying molecular reorganizations at the nanoscale demands micropatterned substrates that accommodate the optical requirements of single molecule microscopy techniques. Here, we developed a simple micropatterning strategy that provides control of cellular architectures and is optimized for nanometer accuracy single molecule tracking and three-dimensional super-resolution imaging of plasma and nuclear membrane proteins in cells...
August 9, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28746830/biophysical-characterization-of-e-coli-tolc-interaction-with-the-known-blocker-hexaamminecobalt
#5
A Gilardi, S P Bhamidimarri, M Brönstrup, U Bilitewski, R K R Marreddy, K M Pos, L Benier, P Gribbon, M Winterhalter, B Windshügel
BACKGROUND: The tripartite efflux pump AcrAB-TolC in E. coli is involved in drug resistance by transporting antibiotics out of the cell. The outer membrane protein TolC can be blocked by various cations, including hexaamminecobalt, thereby TolC represents a potential target for reducing antimicrobial resistance as its blockage may improve efficacy of antibiotics. METHODS: We utilized single channel electrophysiology measurements for studying TolC conductance in the absence and presence of the known TolC blocker hexaamminecobalt...
July 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28745869/high-resolution-imaging-and-multiparametric-characterization-of-native-membranes-by-combining-confocal-microscopy-an-atomic-force-microscopy-based-toolbox
#6
Pawel R Laskowski, Moritz Pfreundschuh, Mirko Stauffer, Zöhre Ucurum, Dimitrios Fotiadis, Daniel J Müller
To understand how membrane proteins function requires characterizing their structure, assembly, and inter- and intramolecular interactions in physiologically relevant conditions. Conventionally, such multiparametric insight is revealed by applying different biophysical methods. Here we introduce the combination of confocal microscopy, force-distance curve-based (FD-based) atomic force microscopy (AFM), and single-molecule force spectroscopy (SMFS) for the identification of native membranes and the subsequent multiparametric analysis of their membrane proteins...
August 1, 2017: ACS Nano
https://www.readbyqxmd.com/read/28741941/efficient-delivery-of-quantum-dots-into-the-cytosol-of-cells-using-cell-penetrating-poly-disulfide-s
#7
Emmanuel Derivery, Eline Bartolami, Stefan Matile, Marcos Gonzalez-Gaitan
Quantum dots (QDs) are extremely bright, photostable, nanometer particles broadly used to investigate single molecule dynamics in vitro. However, the use of QDs in vivo to investigate single molecule dynamics is impaired by the absence of an efficient way to chemically deliver them into the cytosol of cells. Indeed, current methods (using cell-penetrating peptides for instance) provide very low yields: QDs stay at the plasma membrane or are trapped in endosomes. Here, we introduce a technology based on cell-penetrating poly(disulfide)s that solves this problem: we deliver about 70 QDs per cell, and 90% appear to freely diffuse in the cytosol...
August 2, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28716648/applications-of-high-speed-atomic-force-microscopy-to-real-time-visualization-of-dynamic-biomolecular-processes
#8
REVIEW
Takayuki Uchihashi, Simon Scheuring
BACKGROUND: Many biological processes in a living cell are consequences of sequential and hierarchical dynamic events of biological macromolecules such as molecular interactions and conformational changes. Hence, knowledge of structures, assembly and dynamics of proteins is the foundation for understanding how biological molecules work. Among several techniques to analyze dynamics of proteins, high-speed atomic force microscopy (HS-AFM) is unique to provide direct information about both structure and dynamics of single proteins at work...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28714698/microrna-intercellular-transfer-and-bioelectrical-regulation-of-model-multicellular-ensembles-by-the-gap-junction-connectivity
#9
Javier Cervera, Salvador Meseguer, Salvador Mafe
We have studied theoretically the microRNA (miRNA) intercellular transfer through voltage-gated gap junctions in terms of a biophysically grounded system of coupled differential equations. Instead of modeling a specific system, we use a general approach describing the interplay between the genetic mechanisms and the single-cell electric potentials. The dynamics of the multicellular ensemble are simulated under different conditions including spatially inhomogeneous transcription rates and local intercellular transfer of miRNAs...
August 2, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28714316/through-a-window-brightly-a-review-of-selected-nanofabricated-thin-film-platforms-for-spectroscopy-imaging-and-detection
#10
Jason R Dwyer, Maher Harb
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing...
January 1, 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28710349/lipid-driven-nanodomains-in-giant-lipid-vesicles-are-fluid-and-disordered
#11
Alena Koukalová, Mariana Amaro, Gokcan Aydogan, Gerhard Gröbner, Philip T F Williamson, Ilya Mikhalyov, Martin Hof, Radek Šachl
It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for 'rafts'. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28694303/single-molecule-fluorescence-microscopy-review-shedding-new-light-on-old-problems
#12
Sviatlana Shashkova, Mark C Leake
Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared to many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilise light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples...
July 10, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28694112/atomic-force-microscopy-as-a-tool-for-assessing-the-cellular-elasticity-and-adhesiveness-to-identify-cancer-cells-and-tissues
#13
REVIEW
Joanna Zemła, Joanna Danilkiewicz, Barbara Orzechowska, Joanna Pabijan, Sara Seweryn, Małgorzata Lekka
From the first experiments of the atomic force microscopy (AFM) with biological samples, the range of its potential applications grows extensively. One of them is the use of AFM to characterize biophysical fingerprints of cancer progression in search of non-labelled biomarkers of the disease. The technique offers various functionalities, starting from surface imaging to detection of interaction forces, delivering quantitative parameters that can describe changes characteristic for various diseases, including cancer...
July 8, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28668122/single-molecule-methods-for-nucleotide-excision-repair-building-a-system-to-watch-repair-in-real-time
#14
Muwen Kong, Emily C Beckwitt, Luke Springall, Neil M Kad, Bennett Van Houten
Single-molecule approaches to solving biophysical problems are powerful tools that allow static and dynamic real-time observations of specific molecular interactions of interest in the absence of ensemble-averaging effects. Here, we provide detailed protocols for building an experimental system that employs atomic force microscopy and a single-molecule DNA tightrope assay based on oblique angle illumination fluorescence microscopy. Together with approaches for engineering site-specific lesions into DNA substrates, these complementary biophysical techniques are well suited for investigating protein-DNA interactions that involve target-specific DNA-binding proteins, such as those engaged in a variety of DNA repair pathways...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28656582/an-historical-perspective-of-the-discovery-of-titin-filaments
#15
REVIEW
Cris Dos Remedios, Darcy Gilmour
This review takes readers back to 1949, when two Australian scientists, Draper and Hodge, reported the first high-resolution electron microscopy images of striated muscle. In 1953, Jean Hanson and Hugh Huxley published phase-contrast microscopy and electron microscopy images that established the filamentous nature of the sarcomere, namely the myosin-containing thick filaments and actin-containing thin filaments. They discussed a putative third filament system, possibly a thinner actin-containing S filament, that appeared to connect one Z disc to the next...
June 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28655766/a-new-approach-for-generating-bispecific-antibodies-based-on-a-common-light-chain-format-and-the-stable-architecture-of-human-immunoglobulin-g1
#16
Camilla De Nardis, Linda J A Hendriks, Emilie Poirier, Tudor Arvinte, Piet Gros, Alexander B H Bakker, John de Kruif
Bispecific antibodies combine two different antigen binding sites in a single molecule, enabling more specific targeting, novel mechanisms of action and higher clinical efficacies. Although they have the potential to outperform conventional monoclonal antibodies, many bispecific antibodies have issues regarding production, stability and pharmacokinetic properties. Here we describe a new approach for generating bispecific antibodies using a common light chain format and exploiting the stable architecture of human immunoglobulin G1...
June 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28650961/mfpred-rapid-and-accurate-prediction-of-protein-peptide-recognition-multispecificity-using-self-consistent-mean-field-theory
#17
Aliza B Rubenstein, Manasi A Pethe, Sagar D Khare
Multispecificity-the ability of a single receptor protein molecule to interact with multiple substrates-is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces, including enzyme-substrate complexes. The ability to perform structure-based prediction of multispecificity would aid in the identification of novel enzyme substrates, protein interaction partners, and enable design of novel enzymes targeted towards alternative substrates. The relatively slow speed of current biophysical, structure-based methods limits their use for prediction and, especially, design of multispecificity...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28646215/single-molecule-and-multiple-bond-characterization-of-catch-bond-associated-cytoadhesion-in-malaria
#18
Ying Bena Lim, Juzar Thingna, Jianshu Cao, Chwee Teck Lim
The adhesion of malaria infected red blood cells (iRBCs) to host endothelial receptors in the microvasculature, or cytoadhesion, is associated with severe disease pathology such as multiple organ failure and cerebral malaria. Malaria iRBCs have been shown to bind to several receptors, of which intercellular adhesion molecule 1 (ICAM-1) upregulation in brain microvasculature is the only one correlated to cerebral malaria. We utilize a biophysical approach to study the interactions between iRBCs and ICAM-1. At the single molecule level, force spectroscopy experiments reveal that ICAM-1 forms catch bond interactions with Plasmodium falciparum parasite iRBCs...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28636917/kinesin-processivity-is-determined-by-a-kinetic-race-from-a-vulnerable-one-head-bound-state
#19
Keith J Mickolajczyk, William O Hancock
Kinesin processivity, defined as the average number of steps that occur per interaction with a microtubule, is an important biophysical determinant of the motor's intracellular capabilities. Despite its fundamental importance to the diversity of tasks that kinesins carry out in cells, no existing quantitative model fully explains how structural differences between kinesins alter kinetic rates in the ATPase cycle to produce functional changes in processivity. Here we use high-resolution single-molecule microscopy to directly observe the stepping behavior of kinesin-1 and -2 family motors with different length neck-linker domains...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28630155/haemolytic-actinoporins-interact-with-carbohydrates-using-their-lipid-binding-module
#20
Koji Tanaka, Jose M M Caaveiro, Koldo Morante, Kouhei Tsumoto
Pore-forming toxins (PFTs) are proteins endowed with metamorphic properties that enable them to stably fold in water solutions as well as in cellular membranes. PFTs produce lytic pores on the plasma membranes of target cells conducive to lesions, playing key roles in the defensive and offensive molecular systems of living organisms. Actinoporins are a family of potent haemolytic toxins produced by sea anemones vigorously studied as a paradigm of α-helical PFTs, in the context of lipid-protein interactions, and in connection with nanopore technologies...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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