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Single molecule biophysics

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https://www.readbyqxmd.com/read/28716648/applications-of-high-speed-atomic-force-microscopy-to-real-time-visualization-of-dynamic-biomolecular-processes
#1
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
#2
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...
July 17, 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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28626560/selective-single-molecule-nanopore-sensing-of-proteins-using-dna-aptamer-functionalised-gold-nanoparticles
#14
Xiaoyan Lin, Aleksandar P Ivanov, Joshua B Edel
Single molecule detection methods, such as nanopore sensors have found increasing importance in applications ranging from gaining a better understanding of biophysical processes to technology driven solutions such as DNA sequencing. However, challenges remain especially in relation to improving selectivity to probe specific targets or to alternatively enable detection of smaller molecules such as small-sized proteins with a sufficiently high signal-to-noise ratio. In this article, we propose a solution to these technological challenges by using DNA aptamer-modified gold nanoparticles (AuNPs) that act as a molecular carrier through the nanopore sensor...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28625737/insights-into-the-conformations-and-dynamics-of-intrinsically-disordered-proteins-using-single-molecule-fluorescence
#15
REVIEW
Gregory-Neal Gomes, Claudiu C Gradinaru
Most proteins are not static structures, but many of them are found in a dynamic state, exchanging conformations on various time scales as a key aspect of their biological function. An entire spectrum of structural disorder exists in proteins and obtaining a satisfactory quantitative description of these states remains a challenge. Single-molecule fluorescence spectroscopy techniques are uniquely suited for this task, by measuring conformations without ensemble averaging and kinetics without interference from asynchronous processes...
June 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28615444/the-human-mitochondrial-single-strand-dna-binding-protein-displays-distinct-kinetics-and-thermodynamics-of-dna-binding-and-exchange
#16
Yufeng Qian, Kenneth A Johnson
The human mitochondrial SSB (mtSSB) is a homo-tetrameric protein, involved in mtDNA replication and maintenance. Although mtSSB is structurally similar to SSB from Escherichia coli (EcoSSB), it lacks the C-terminal disordered domain but little is known about the biophysics of mtSSB-ssDNA interactions. Here, we characterized the kinetics and thermodynamics of mtSSB binding to ssDNA by equilibrium titrations and stopped-flow kinetic measurements. We show that the mtSSB tetramer can bind to ssDNA in two distinct binding modes: (SSB)30 and (SSB)60, defined by DNA binding site sizes of 30 and 60 nt, respectively...
June 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28591514/elastin-like-polypeptide-linkers-for-single-molecule-force-spectroscopy
#17
Wolfgang Ott, Markus A Jobst, Magnus S Bauer, Ellis Durner, Lukas F Milles, Michael A Nash, Hermann E Gaub
Single-molecule force spectroscopy (SMFS) is by now well established as a standard technique in biophysics and mechanobiology. In recent years, the technique has benefitted greatly from new approaches to bioconjugation of proteins to surfaces. Indeed, optimized immobilization strategies for biomolecules and refined purification schemes are being steadily adapted and improved, which in turn has enhanced data quality. In many previously reported SMFS studies, poly(ethylene glycol) (PEG) was used to anchor molecules of interest to surfaces and/or cantilever tips...
June 27, 2017: ACS Nano
https://www.readbyqxmd.com/read/28538142/an-introduction-to-infinite-hmms-for-single-molecule-data-analysis
#18
REVIEW
Ioannis Sgouralis, Steve Pressé
The hidden Markov model (HMM) has been a workhorse of single-molecule data analysis and is now commonly used as a stand-alone tool in time series analysis or in conjunction with other analysis methods such as tracking. Here, we provide a conceptual introduction to an important generalization of the HMM, which is poised to have a deep impact across the field of biophysics: the infinite HMM (iHMM). As a modeling tool, iHMMs can analyze sequential data without a priori setting a specific number of states as required for the traditional (finite) HMM...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28529337/dynamic-chromatin-technologies-from-individual-molecules-to-epigenomic-regulation-in-cells
#19
REVIEW
Olivier Cuvier, Beat Fierz
The establishment and maintenance of chromatin states involves multiscale dynamic processes integrating transcription factor and multiprotein effector dynamics, cycles of chemical chromatin modifications, and chromatin structural organization. Recent developments in genomic technologies are emerging that are enabling a view beyond ensemble- and time-averaged properties and are revealing the importance of dynamic chromatin states for cell fate decisions, differentiation and reprogramming at the single-cell level...
August 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28505809/dissociation-rates-from-single-molecule-pulling-experiments-under-large-thermal-fluctuations-or-large-applied-force
#20
Masoud Abkenar, Thomas H Gray, Alessio Zaccone
Theories that are used to extract energy-landscape information from single-molecule pulling experiments in biophysics are all invariably based on Kramers' theory of the thermally activated escape rate from a potential well. As is well known, this theory recovers the Arrhenius dependence of the rate on the barrier energy and crucially relies on the assumption that the barrier energy is much larger than k_{B}T (limit of comparatively low thermal fluctuations). As was shown already in Dudko et al. [Phys. Rev...
April 2017: Physical Review. E
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