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Biophysical Journal

Aurélien Bour, Sergei G Kruglik, Morgan Chabanon, Padmini Rangamani, Nicolas Puff, Stephanie Bonneau
Unsaturated lipid oxidation is a fundamental process involved in different aspects of cellular bioenergetics; dysregulation of lipid oxidation is often associated with cell aging and death. To study how lipid oxidation affects membrane biophysics, we used a chlorin photosensitizer to oxidize vesicles of various lipid compositions and degrees of unsaturation in a controlled manner. We observed different shape transitions that can be interpreted as an increase in the area of the targeted membrane followed by a decrease...
February 2, 2019: Biophysical Journal
Chetana Baliga, Benjamin Selmke, Irina Worobiew, Peter Borbat, Siddhartha P Sarma, Wolfgang E Trommer, Raghavan Varadarajan, Nilesh Aghera
pH is an important factor that affects the protein structure, stability, and activity. Here, we probe the nature of the low-pH structural form of the homodimeric CcdB (controller of cell death B) protein. Characterization of CcdB protein at pH 4 and 300 K using circular dichroism spectroscopy, 8-anilino-1-naphthalene-sulphonate binding, and Trp solvation studies suggests that it forms a partially unfolded state with a dry core at equilibrium under these conditions. CcdB remains dimeric at pH 4 as shown by multiple techniques, such as size-exclusion chromatography coupled to multiangle light scattering, analytical ultracentrifugation, and electron paramagnetic resonance...
February 1, 2019: Biophysical Journal
Fraser G Ferens, Trushar R Patel, George Oriss, Deborah A Court, Jörg Stetefeld
The oligomeric organization of the voltage-dependent anion-selective channel (VDAC) and its interactions with hexokinase play integral roles in mitochondrially mediated apoptotic signaling. Various small to large assemblies of VDAC are observed in mitochondrial outer membranes, but they do not predominate in detergent-solubilized VDAC samples. In this study, a cholesterol analog, cholesteryl-hemisuccinate (CHS), was shown to induce the formation of detergent-soluble VDAC multimers. The various oligomeric states of VDAC induced by the addition of CHS were deciphered through an integrated biophysics approach using microscale thermophoresis, analytical ultracentrifugation, and size-exclusion chromatography small angle x-ray scattering...
February 1, 2019: Biophysical Journal
Elza Kuzmenkina, Elena Novikova, Wanchana Jangsangthong, Jan Matthes, Stefan Herzig
Voltage-dependent calcium (CaV ) 1.3 channels are involved in the control of cellular excitability and pacemaking in neuronal, cardiac, and sensory cells. Various proteins interact with the alternatively spliced channel C-terminus regulating gating of CaV 1.3 channels. Binding of a regulatory calcium-binding protein calmodulin (CaM) to the proximal C-terminus leads to the boosting of channel activity and promotes calcium-dependent inactivation (CDI). The C-terminal modulator domain (CTM) of CaV 1.3 channels can interfere with the CaM binding, thereby inhibiting channel activity and CDI...
February 1, 2019: Biophysical Journal
Madhuresh Sumit, Andreja Jovic, Richard R Neubig, Shuichi Takayama, Jennifer J Linderman
Mammalian cells respond in a variable manner when provided with physiological pulses of ligand, such as low concentrations of acetylcholine present for just tens of seconds or TNFα for just tens of minutes. For a two-pulse stimulation, some cells respond to both pulses, some do not respond, and yet others respond to only one or the other pulse. Are these different response patterns the result of the small number of ligands being able to only stochastically activate the pathway at random times or an output pattern from a deterministic algorithm responding differently to different stimulation intervals? If the response is deterministic in nature, what parameters determine whether a response is generated or skipped? To answer these questions, we developed a two-pulse test that utilizes different rest periods between stimulation pulses...
January 30, 2019: Biophysical Journal
Michael D N Stolle, Cécile Fradin
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study...
January 30, 2019: Biophysical Journal
Csaba Daday, Laura Marlene Mateyka, Frauke Gräter
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial heart disease linked to mutations in several desmosomal proteins, but the specific effects of these mutations on the molecular level are poorly understood. Among the many documented ARVC-related genetic variants, a striking hotspot of nine mutations has been identified in the plakin domain of desmoplakin. This hotspot can be found at the meeting point of three different subdomains of desmoplakin: two spectrin repeats and a Src homology 3 domain...
January 30, 2019: Biophysical Journal
Michael H L Nguyen, Mitchell DiPasquale, Brett W Rickeard, Christopher B Stanley, Elizabeth G Kelley, Drew Marquardt
Methanol is a common solubilizing agent used to study transmembrane proteins/peptides in biological and synthetic membranes. Using small angle neutron scattering and a strategic contrast-matching scheme, we show that methanol has a major impact on lipid dynamics. Under increasing methanol concentrations, isotopically distinct 1,2-dimyristoyl-sn-glycero-3-phosphocholine large unilamellar vesicle populations exhibit increased mixing. Specifically, 1,2-dimyristoyl-sn-glycero-3-phosphocholine transfer and flip-flop kinetics display linear and exponential rate enhancements, respectively...
January 29, 2019: Biophysical Journal
Tai-Ming Hsu, Yi-Ren Chang
Bacterial high-copy-number (hcn) plasmids provide an excellent model to study the underlying physical mechanisms of DNA segment segregation in an intracellular context. Using two-color fluorescent repressor-operator systems and a synthetic repressible replication origin, we tracked the motion and segregation of single hcn plasmid molecules in individual cells. The plasmid diffusion dynamics revealed between-plasmid temporal associations (clustering) as well as entropic and elastic recoiling forces in the confined intracellular spaces outside of nucleoids...
January 29, 2019: Biophysical Journal
Robert Zöllner, Tom Cronenberg, Nadzeya Kouzel, Anton Welker, Michael Koomey, Berenike Maier
Bacterial type 4 pili (T4P) are extracellular polymers that initiate the formation of microcolonies and biofilms. T4P continuously elongate and retract. These pilus dynamics crucially affect the local order, shape, and fluidity of microcolonies. The major pilin subunit of the T4P bears multiple post-translational modifications. By interfering with different steps of the pilin glycosylation and phosphoform modification pathways, we investigated the effect of pilin post-translational modification on the shape and dynamics of microcolonies formed by Neisseria gonorrhoeae...
January 29, 2019: Biophysical Journal
Rommie E Amaro
No abstract text is available yet for this article.
January 26, 2019: Biophysical Journal
Nikki M Curthoys, Michael J Mlodzianoski, Matthew Parent, Michael B Butler, Prakash Raut, Jaqulin Wallace, Jennifer Lilieholm, Kashif Mehmood, Melissa S Maginnis, Hang Waters, Brad Busse, Joshua Zimmerberg, Samuel T Hess
The lipid phosphatidylinositol 4,5-bisphosphate (PIP2) forms nanoscopic clusters in cell plasma membranes; however, the processes determining PIP2 mobility and thus its spatial patterns are not fully understood. Using super-resolution imaging of living cells, we find that PIP2 is tightly colocalized with and modulated by overexpression of the influenza viral protein hemagglutinin (HA). Within and near clusters, HA and PIP2 follow a similar spatial dependence, which can be described by an HA-dependent potential gradient; PIP2 molecules move as if they are attracted to the center of clusters by a radial force of 0...
January 25, 2019: Biophysical Journal
Milka Doktorova, Frederick A Heberle, Drew Marquardt, Radda Rusinova, R Lea Sanford, Thasin A Peyear, John Katsaras, Gerald W Feigenson, Harel Weinstein, Olaf S Andersen
Unlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Nonenzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms...
January 25, 2019: Biophysical Journal
Justin R Porter, Katelyn E Moeder, Carrie A Sibbald, Maxwell I Zimmerman, Kathryn M Hart, Michael J Greenberg, Gregory R Bowman
Proteins are dynamic molecules that undergo conformational changes to a broad spectrum of different excited states. Unfortunately, the small populations of these states make it difficult to determine their structures or functional implications. Computer simulations are an increasingly powerful means to identify and characterize functionally relevant excited states. However, this advance has uncovered a further challenge: it can be extremely difficult to identify the most salient features of large simulation data sets...
January 25, 2019: Biophysical Journal
Bart Smeets, Maxim Cuvelier, Jiri Pešek, Herman Ramon
We consider a cell as an elastic, contractile shell surrounding a liquid incompressible cytoplasm and with nonspecific adhesion. We perform numerical simulations of this model to study the mechanics of cell-cell separation. By variation of parameters, we are able to recover well-known limits of the Johnson-Kendall-Roberts theory, the Derjaguin-Muller-Toporov model, adhesive vesicles with surface tension (Brochard-Wyart and de Gennes derivation), and thin elastic shells. We further locate biological cells on this parameter space by comparison to existing experiments on S180 cells...
January 24, 2019: Biophysical Journal
Naohiro Nishikawa, Yoshitake Sakae, Takuya Gouda, Yuichiro Tsujimura, Yuko Okamoto
A peptide β2 -m21-31 , which is a fragment from residue 21 to residue 31 of β2 -microgloblin, is experimentally known to self-assemble and form amyloid fibrils. In order to understand the mechanism of amyloid fibril formations, we applied the replica-exchange molecular dynamics method to the system consisting of three fragments of β2 -m21-31 . From the analyses on the temperature dependence, we found that there is a clear phase transition temperature in which the peptides aggregate with each other. Moreover, we found by the free energy analyses that there are two major stable states: One of them is like amyloid fibrils and the other is amorphous aggregates...
January 23, 2019: Biophysical Journal
Miao Yu, Tiago Castanheira Silva, Andries van Opstal, Stefan Romeijn, Hayley A Every, Wim Jiskoot, Geert-Jan Witkamp, Marcel Ottens
In this study, we developed a microfluidics method, using a so-called H-cell microfluidics device, for the determination of protein diffusion coefficients at different concentrations, pHs, ionic strengths, and solvent viscosities. Protein transfer takes place in the H-cell channels between two laminarly flowing streams with each containing a different initial protein concentration. The protein diffusion coefficients are calculated based on the measured protein mass transfer, the channel dimensions, and the contact time between the two streams...
January 22, 2019: Biophysical Journal
John Paul Glaves, Joseph O Primeau, L Michel Espinoza-Fonseca, M Joanne Lemieux, Howard S Young
The interaction of phospholamban (PLN) with the sarco-endoplasmic reticulum Ca2+ -ATPase (SERCA) pump is a major regulatory axis in cardiac muscle contractility. The prevailing model involves reversible inhibition of SERCA by monomeric PLN and storage of PLN as an inactive pentamer. However, this paradigm has been challenged by studies demonstrating that PLN remains associated with SERCA and that the PLN pentamer is required for the regulation of cardiac contractility. We have previously used two-dimensional (2D) crystallization and electron microscopy to study the interaction between SERCA and PLN...
January 22, 2019: Biophysical Journal
Jay G Gandhi, Donald L Koch, Matthew J Paszek
The glycocalyx is a thick coat of proteins and carbohydrates on the outer surface of all eukaryotic cells. Overproduction of large, flexible or rod-like biopolymers, including hyaluronic acid and mucins, in the glycocalyx strongly correlates with the aggression of many cancer types. However, theoretical frameworks to predict the effects of these changes on cancer cell adhesion and other biophysical processes remain limited. Here, we propose a detailed modeling framework for the glycocalyx incorporating important physical effects of biopolymer flexibility, excluded volume, counterion mobility, and coupled membrane deformations...
January 15, 2019: Biophysical Journal
Shingo Gibo, Gen Kurosawa
Time series of biological rhythms are of various shapes. Here, we investigated the waveforms of circadian rhythms in gene-protein dynamics using a newly developed, to our knowledge, index to quantify the degree of distortion from a sinusoidal waveform. In general, most biochemical reactions accelerate with increasing temperature, but the period of circadian rhythms remains relatively stable with temperature change, a phenomenon known as "temperature compensation." Despite extensive research, the mechanism underlying this remains unclear...
January 15, 2019: Biophysical Journal
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