scholarly journals Signal processing for molecular and cellular biological physics: an emerging field

2013 ◽  
Vol 371 (1984) ◽  
pp. 20110546 ◽  
Author(s):  
Max A. Little ◽  
Nick S. Jones
Keyword(s):  
Signal Processing ◽  
Optical Tweezers ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Digital Signal ◽  
Force Microscopy ◽  
Cellular Processes ◽  
Atomic Force ◽  
Non Gaussian ◽  
Autocorrelated Noise

Recent advances in our ability to watch the molecular and cellular processes of life in action—such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer—raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

scholarly journals Protein O-Fucosyltransferase 1 Undergoes Interdomain Flexibility in Solution

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2105
Author(s):  
Erandi Lira-Navarrete ◽  
María Carmen Pallarés ◽  
Fabio Castello ◽  
Maria J. Ruedas-Rama ◽  
Angel Orte ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Catalytic Cycle ◽  
Conformational Behavior ◽  
Single Molecule Fluorescence ◽  
Force Microscopy ◽  
Atomic Force ◽  
Dynamic Population

Protein O-fucosyltransferase 1 (PoFUT1) is a GT-B fold enzyme that fucosylates proteins containing EGF-like repeats. GT-B glycosyltransferases have shown a remarkable grade of plasticity adopting closed and open conformations as a way of tuning their catalytic cycle, a feature that has not been observed for PoFUT1. Here, we analyzed Caenorhabditis elegans PoFUT1 (CePoFUT1) conformational behavior in solution by atomic force microscopy (AFM) and single-molecule fluorescence resonance energy transfer (SMF-FRET). Our results show that this enzyme is very flexible and adopts mainly compact conformations and to a lesser extend a highly dynamic population that oscillates between compact and highly extended conformations. Overall, our experiments illustrate the inherent complexity of CePoFUT1 dynamics, which might play a role during its catalytic cycle.

scholarly journals Nanomechanics and co-transcriptional folding of Spinach and Mango

2019 ◽  
Author(s):  
Jaba Mitra ◽  
Taekjip Ha
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Mechanical Stability ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Rna Aptamers ◽  
Cellular Processes ◽  
Force Relaxation ◽  
And Function

AbstractRecent advances in fluorogen-binding RNA aptamers known as “light-up” aptamers provide an avenue for protein-free detection of RNA in cells. Crystallographic studies have revealed a G-Quadruplex (GQ) structure at the core of light-up aptamers such as Spinach, Mango and Corn. Detailed biophysical characterization of folding of such aptamers is still lacking despite the potential implications on their in vivo folding and function. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to examine mechanical responses of Spinach2, iMangoIII and MangoIV. Spinach2 unfolded in four discrete steps as force is increased to 7 pN and refolded in reciprocal steps upon force relaxation. Binding of DFHBI-1T fluorogen preserved the step-wise unfolding behavior although at slightly higher forces. In contrast, GQ core unfolding in iMangoIII and MangoIV occurred in one discrete step at forces > 10 pN and refolding occurred at lower forces showing hysteresis. Binding of the cognate fluorogen, TO1, did not significantly alter the mechanical stability of Mangos. In addition to K+, which is needed to stabilize the GQ cores, Mg2+ was needed to obtain full mechanical stability of the aptamers. Co-transcriptional folding analysis using superhelicases showed that co-transcriptional folding reduces misfolding and allows a folding pathway different from refolding. As the fundamental cellular processes like replication, transcription etc. exert pico-Newton levels of force, these aptamers may unfold in vivo and subsequently misfold.

scholarly journals Membrane fusion studied by colloidal probes

2021 ◽  
Vol 50 (2) ◽  
pp. 223-237 ◽  
Author(s):  
Hannes Witt ◽  
Filip Savić ◽  
Sarah Verbeek ◽  
Jörn Dietz ◽  
Gesa Tarantola ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Optical Tweezers ◽  
Three Dimensional ◽  
Biological Processes ◽  
Supported Membranes ◽  
Supported Bilayers ◽  
Force Microscopy ◽  
Advantages And Disadvantages ◽  
Atomic Force ◽  
Colloidal Probes

AbstractMembrane-coated colloidal probes combine the benefits of solid-supported membranes with a more complex three-dimensional geometry. This combination makes them a powerful model system that enables the visualization of dynamic biological processes with high throughput and minimal reliance on fluorescent labels. Here, we want to review recent applications of colloidal probes for the study of membrane fusion. After discussing the advantages and disadvantages of some classical vesicle-based fusion assays, we introduce an assay using optical detection of fusion between membrane-coated glass microspheres in a quasi two-dimensional assembly. Then, we discuss free energy considerations of membrane fusion between supported bilayers, and show how colloidal probes can be combined with atomic force microscopy or optical tweezers to access the fusion process with even greater detail.

scholarly journals Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose

2020 ◽  
Vol 21 (14) ◽  
pp. 5004
Author(s):  
Ekaterina O. Serebrovskaya ◽  
Nadezda M. Podvalnaya ◽  
Varvara V. Dudenkova ◽  
Anna S. Efremova ◽  
Nadya G. Gurskaya ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Mammalian Cells ◽  
Fluorescent Proteins ◽  
Fluorescent Sensor ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Hydrogen Peroxide Treatment ◽  
Damage Response

Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with the WWE domain of RNF146 E3 ubiquitin ligase protein. This bipartite sensor named sPARroW (sensor for PAR relying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.

scholarly journals Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy

2019 ◽  
Vol 116 (17) ◽  
pp. 8350-8359 ◽  
Author(s):  
Jaba Mitra ◽  
Monika A. Makurath ◽  
Thuy T. M. Ngo ◽  
Alice Troitskaia ◽  
Yann R. Chemla ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Conformational Changes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Force Spectroscopy ◽  
Telomeric Dna ◽  
Telomeric Sequences ◽  
Substitution Mutant

G-quadruplexes (GQs) can adopt diverse structures and are functionally implicated in transcription, replication, translation, and maintenance of telomere. Their conformational diversity under physiological levels of mechanical stress, however, is poorly understood. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to measure human telomeric sequences under tension. Abrupt GQ unfolding with K+in solution occurred at as many as four discrete levels of force. Added to an ultrastable state and a gradually unfolding state, there were six mechanically distinct structures. Extreme mechanical diversity was also observed with Na+, although GQs were mechanically weaker. Our ability to detect small conformational changes at low forces enabled the determination of refolding forces of about 2 pN. Refolding was rapid and stochastically redistributed molecules to mechanically distinct states. A single guanine-to-thymine substitution mutant required much higher ion concentrations to display GQ-like unfolding and refolded via intermediates, contrary to the wild type. Contradicting an earlier proposal, truncation to three hexanucleotide repeats resulted in a single-stranded DNA-like mechanical behavior under all conditions, indicating that at least four repeats are required to form mechanically stable structures.

Growth Front Roughening of Room Temperature Deposited Oligomer Thin Films

2000 ◽  
Vol 648 ◽  
Author(s):  
D. Tsamouras ◽  
G. Palasantzas ◽  
J. Th. M. De Hosson ◽  
G. Hadziioannou
Keyword(s):  
Thin Films ◽  
Film Thickness ◽  
Room Temperature ◽  
Growth Front ◽  
Silicon Substrates ◽  
Height Distribution ◽  
Force Microscopy ◽  
Atomic Force ◽  
Roughness Amplitude ◽  
Non Gaussian

AbstractGrowth front scaling aspects are investigated for PPV-type oligomer thin films vapor- deposited onto silicon substrates at room temperature. For film thickness d~15-300 nm, commonly used in optoelectronic devices, correlation function measurement by atomic force microscopy yields roughness exponents in the range H=0.45±0.04, and an rms roughness amplitude which evolves with film thickness as a power law σ∝ dβ with β=0.28±0.05. The non-Gaussian height distribution and the measured scaling exponents (H and β) suggest a roughening mechanism close to that described by the Kardar-Parisi-Zhang scenario.

Simultaneous Determination of E, G and ν of Soft Hydrogels Using Theory of Elasticity

2009 ◽  
Author(s):  
Uday Chippada ◽  
Xue Jiang ◽  
Lulu Li ◽  
Rene Schloss ◽  
Bernard Yurke ◽  
...  
Keyword(s):  
Poisson’S Ratio ◽  
Theory Of Elasticity ◽  
Complete Characterization ◽  
Poisson's Ratio ◽  
Force Microscopy ◽  
Cellular Processes ◽  
Atomic Force ◽  
Significant Research

Hydrogels have been used as substrates by many researchers in the study of cellular processes. The mechanical properties of these gels play a significant role in the growth of the cells. Significant research using several methods like compression, indentation, atomic force microscopy and manipulation of beads has been performed in the past to characterize the stiffness of these substrates. However, most of the methods employed assume the gel to be incompressible, with a Poisson’s ratio of 0.5. However, Poisson’s ratio can differ from 0.5. Hence, a more complete characterization of the elastic properties of hydrogels requires that one experimentally obtain the value of at least two of the three quantities: Poisson’s ratio, shear modulus, and elastic modulus.

scholarly journals Profound Nanoscale Structural and Biomechanical Changes in DNA Helix upon Treatment with Anthracycline Drugs

2020 ◽  
Vol 21 (11) ◽  
pp. 4142
Author(s):  
Aleksandra Kaczorowska ◽  
Weronika Lamperska ◽  
Kaja Frączkowska ◽  
Jan Masajada ◽  
Sławomir Drobczyński ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Regulatory Elements ◽  
Dna Molecules ◽  
Anthracycline Antibiotics ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Analysis ◽  
Dna Regulatory Elements

In our study, we describe the outcomes of the intercalation of different anthracycline antibiotics in double-stranded DNA at the nanoscale and single molecule level. Atomic force microscopy analysis revealed that intercalation results in significant elongation and thinning of dsDNA molecules. Additionally, using optical tweezers, we have shown that intercalation decreases the stiffness of DNA molecules, that results in greater susceptibility of dsDNA to break. Using DNA molecules with different GC/AT ratios, we checked whether anthracycline antibiotics show preference for GC-rich or AT-rich DNA fragments. We found that elongation, decrease in height and decrease in stiffness of dsDNA molecules was highest in GC-rich dsDNA, suggesting the preference of anthracycline antibiotics for GC pairs and GC-rich regions of DNA. This is important because such regions of genomes are enriched in DNA regulatory elements. By using three different anthracycline antibiotics, namely doxorubicin (DOX), epirubicin (EPI) and daunorubicin (DAU), we could compare their detrimental effects on DNA. Despite their analogical structure, anthracyclines differ in their effects on DNA molecules and GC-rich region preference. DOX had the strongest overall effect on the DNA topology, causing the largest elongation and decrease in height. On the other hand, EPI has the lowest preference for GC-rich dsDNA. Moreover, we demonstrated that the nanoscale perturbations in dsDNA topology are reflected by changes in the microscale properties of the cell, as even short exposition to doxorubicin resulted in an increase in nuclei stiffness, which can be due to aberration of the chromatin organization, upon intercalation of doxorubicin molecules.

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