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Biophysical Journal

Philip C Nelson
Resonance energy transfer has become an indispensable experimental tool for single-molecule and single-cell biophysics. Its physical underpinnings, however, are subtle: it involves a discrete jump of excitation from one molecule to another, and so we regard it as a strongly quantum-mechanical process. And yet its kinetics differ from what many of us were taught about two-state quantum systems, quantum superpositions of the states do not seem to arise, and so on. Although J. R. Oppenheimer and T. Förster navigated these subtleties successfully, it remains hard to find an elementary derivation in modern language...
February 16, 2018: Biophysical Journal
Alexander M Berezhkovskii, Sergey M Bezrukov
An ideal channel, responsible for metabolite fluxes in and out of the cells and cellular compartments, is supposed to be selective for a particular set of molecules only. However, such a channel has to be wide enough to accommodate relatively large metabolites, and, therefore, it allows passage of smaller solutes, for example, sodium, potassium, and chloride ions, thus compromising membrane's barrier function. Here we show that stochastic gating is able to provide a mechanism for the selectivity of wide channels in favor of large metabolites...
February 12, 2018: Biophysical Journal
Karl E Duderstadt
No abstract text is available yet for this article.
February 1, 2018: Biophysical Journal
Dino Osmanovic, Yitzhak Rabin
A significant part of the proteome is composed of intrinsically disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work, we consider IDPs that have the tendency to aggregate, model them as heteropolymers that contain a small number of associating monomers, and use computer simulations to compare the aggregation of such IDPs that are grafted to a surface or free in solution. We then discuss how such grafting may affect the analysis of in vitro experiments and could also be used to suppress harmful aggregation...
January 30, 2018: Biophysical Journal
Soohyung Park, Logesvaran Krshnan, Melissa J Call, Matthew E Call, Wonpil Im
T cell receptors (TCRs) are octameric assemblies of type-I membrane proteins in which a receptor heterodimer (αβ, δγ, or pre-Tαβ) is associated with three dimeric signaling modules (CD3δε, CD3γε, and ζζ) at the T cell or pre-T cell surface. In the human αβTCR, the α and β transmembrane (TM) domains form a specific structure that acts as a hub for assembly with the signaling modules inside the lipid bilayer. Conservation of key polar contacts across the C-terminal half of this TM interface suggests that the structure is a common feature of all TCR types...
January 29, 2018: Biophysical Journal
Assaf Amitai
No abstract text is available yet for this article.
January 26, 2018: Biophysical Journal
David P Hoogerheide, Philip A Gurnev, Tatiana K Rostovtseva, Sergey M Bezrukov
A growing number of new technologies are supported by a single- or multi-nanopore architecture for capture, sensing, and delivery of polymeric biomolecules. Nanopore-based single-molecule DNA sequencing is the premier example. This method relies on the uniform linear charge density of DNA, so that each DNA strand is overwhelmingly likely to pass through the nanopore and across the separating membrane. For disordered peptides, folded proteins, or block copolymers with heterogeneous charge densities, by contrast, translocation is not assured, and additional strategies to monitor the progress of the polymer molecule through a nanopore are required...
January 12, 2018: Biophysical Journal
Hannah H Tuson, Matthew H Foley, Nicole M Koropatkin, Julie S Biteen
Bacteroides thetaiotaomicron (Bt) is a prominent member of the human gut microbiota with an extensive capacity for glycan harvest. This bacterium expresses a five-protein complex in the outer membrane, called the starch utilization system (Sus), which binds, degrades, and imports starch into the cell. Sus is a model system for the many glycan-targeting polysaccharide utilization loci found in Bt and other members of the Bacteroidetes phylum. Our previous work has shown that SusG, a lipidated amylase in the outer membrane, explores the entire cell surface but diffuses more slowly as it interacts with starch...
January 12, 2018: Biophysical Journal
Ralf Blossey, Helmut Schiessel
In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation...
January 5, 2018: Biophysical Journal
João L Carvalho-de-Souza, Bernardo I Pinto, David R Pepperberg, Francisco Bezanilla
Millisecond pulses of laser light delivered to gold nanoparticles residing in close proximity to the surface membrane of neurons can induce membrane depolarization and initiate an action potential. An optocapacitance mechanism proposed as the basis of this effect posits that the membrane-interfaced particle photothermally induces a cell-depolarizing capacitive current, and predicts that delivering a given laser pulse energy within a shorter period should increase the pulse's action-potential-generating effectiveness by increasing the magnitude of this capacitive current...
December 19, 2017: Biophysical Journal
Anna Rubio-Cosials, Federica Battistini, Alexander Gansen, Anna Cuppari, Pau Bernadó, Modesto Orozco, Jörg Langowski, Katalin Tóth, Maria Solà
Human mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been yet discerned whether a tight U-turn or an alternative conformation, such as a V-shape, is formed in solution. Here, single-molecule FRET experiments on freely diffusing TFAM/LSP complexes containing different DNA lengths show that a DNA U-turn is induced by progressive and cooperative binding of the two TFAM HMG-box domains and the linker between them...
December 13, 2017: Biophysical Journal
Ivan E Ivanov, Paul Lebel, Florian C Oberstrass, Charles H Starr, Angelica C Parente, Athena Ierokomos, Zev Bryant
Single-molecule methods provide direct measurements of macromolecular dynamics, but are limited by the number of degrees of freedom that can be followed at one time. High-resolution rotor bead tracking (RBT) measures DNA torque, twist, and extension, and can be used to characterize the structural dynamics of DNA and diverse nucleoprotein complexes. Here, we extend RBT to enable simultaneous monitoring of additional degrees of freedom. Fluorescence-RBT (FluoRBT) combines magnetic tweezers, infrared evanescent scattering, and single-molecule FRET imaging, providing real-time multiparameter measurements of complex molecular processes...
December 13, 2017: Biophysical Journal
Shuhui Yin, Nancy Song, Haw Yang
The position-time trajectory of a biological subject moving in a complex environment contains rich information about how it interacts with the local setting. Whether the subject be an animal or an intracellular endosomal vesicle, the two primary modes of biological locomotion are directional movement and random walk, respectively characterized by velocity and diffusion coefficient. This contribution introduces a method to quantitatively divide a single-particle trajectory into segments that exhibit changes in the diffusion coefficient, velocity, or both...
December 11, 2017: Biophysical Journal
György Vámosi, David Rueda
No abstract text is available yet for this article.
December 8, 2017: Biophysical Journal
Thomas Bowling, Julien Meaud
Distortion product otoacoustic emissions are sounds that are emitted by the cochlea due to the nonlinearity of the outer hair cells. These emissions play an important role both in clinical settings and research laboratories. However, how distortion products propagate from their generation location to the middle ear remains unclear; whether distortion products propagate as a slow reverse traveling wave, or as a fast compression wave, through the cochlear fluid has been debated. In this article, we evaluate the contributions of the slow reverse wave and fast compression wave to the propagation of intracochlear distortion products using a physiologically based nonlinear model of the gerbil cochlea...
February 6, 2018: Biophysical Journal
Andrew E Blanchard, Chen Liao, Ting Lu
Quantitative modeling of gene circuits is fundamentally important to synthetic biology, as it offers the potential to transform circuit engineering from trial-and-error construction to rational design and, hence, facilitates the advance of the field. Currently, typical models regard gene circuits as isolated entities and focus only on the biochemical processes within the circuits. However, such a standard paradigm is getting challenged by increasing experimental evidence suggesting that circuits and their host are intimately connected, and their interactions can potentially impact circuit behaviors...
February 6, 2018: Biophysical Journal
Pencho Yordanov, Jörg Stelling
In pharmacology and systems biology, it is a fundamental problem to determine how biological systems change their dose-response behavior upon perturbations. In particular, it is unclear how topologies, reactions, and parameters (differentially) affect the dose response. Because parameters are often unknown, systematic approaches should directly relate network structure and function. Here, we outline a procedure to compare general non-monotone dose-response curves and subsequently develop a comprehensive theory for differential dose responses of biochemical networks captured by non-equilibrium steady-state linear framework models...
February 6, 2018: Biophysical Journal
Bin Xu, Alexandra Jilkine
Regulation of polarized cell growth is essential for many cellular processes, including spatial coordination of cell morphology changes during growth and division. We present a mathematical model of the core mechanism responsible for the regulation of polarized growth dynamics by the small GTPase Cdc42. The model is based on the competition of growth zones of Cdc42 localized at the cell tips for a common substrate (inactive Cdc42) that diffuses in the cytosol. We consider several potential ways of implementing negative feedback between Cd42 and its GEF in this model that would be consistent with the observed oscillations of Cdc42 in fission yeast...
February 6, 2018: Biophysical Journal
Guang-Kui Xu, Xi-Qiao Feng, Huajian Gao
Mechanical cues from the microenvironments play a regulating role in many physiological and pathological processes, such as stem cell differentiation and cancer cell metastasis. Experiments showed that cells adhered on a compliant substrate may change orientation with an externally applied strain in the substrate. By accounting for actin polymerization, actin retrograde flow, and integrin binding dynamics, here we develop a mechanism-based tensegrity model to study the orientations of polarized cells on a compliant substrate under biaxial stretches...
February 6, 2018: Biophysical Journal
Ágnes Szabó, Tímea Szendi-Szatmári, László Ujlaky-Nagy, Ildikó Rádi, György Vereb, János Szöllősi, Peter Nagy
Because the degree of labeling (DOL) of cell-bound antibodies, often required in quantitative fluorescence measurements, is largely unknown, we investigated the effect of labeling with two different fluorophores (AlexaFluor546, AlexaFluor647) in a systematic way using antibody stock solutions with different DOLs. Here, we show that the mean DOL of the cell-bound antibody fraction is lower than that of the stock using single molecule fluorescence measurements. The effect is so pronounced that the mean DOL levels off at approximately two fluorophores/IgG for some antibodies...
February 6, 2018: Biophysical Journal
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