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Biophysical Journal

Heath E Johnson, Jason M Haugh
Filopodia are thin, fingerlike structures that contain bundled actin filaments and project from the cell periphery. These structures are dogmatically endowed with the ability to sense cues in the microenvironment, implying that filopodia foster local signal transduction, yet their small diameter hampers the imaging of dynamic processes therein. To overcome this challenge, we analyzed total internal reflection fluorescence images of migrating fibroblasts coexpressing either a plasma membrane marker or tagged AktPH domain, a translocation biosensor for signaling through the phosphoinositide 3-kinase pathway, along with a cytosolic volume marker...
October 3, 2016: Biophysical Journal
Bin Zhang, Peter G Wolynes
Energy landscape theory, developed in the context of protein folding, provides, to our knowledge, a new perspective on chromosome architecture. We review what has been learned concerning the topology and structure of both the interphase and mitotic chromosomes from effective energy landscapes constructed using Hi-C data. Energy landscape thinking raises new questions about the nonequilibrium dynamics of the chromosome and gene regulation.
September 30, 2016: Biophysical Journal
Yifei Qi, Jeffery B Klauda, Wonpil Im
Site-directed spin-labeling electron paramagnetic resonance spectroscopy is a useful tool to obtain information about the environment of specific residues. One of its applications is to investigate membrane protein topology based on the accessibility of the spin label, with the assumption that the position of the spin label in the membrane is close to that of the native residue. This assumption is valid in proteins with well-ordered structures, but could be problematic in small peptides because the labeling may cause a perturbation that is large enough to change local interactions between the peptide and the membrane...
September 27, 2016: Biophysical Journal
Robert Blackwell, Oliver Sweezy-Schindler, Christopher Edelmaier, Zachary R Gergely, Patrick J Flynn, Salvador Montes, Ammon Crapo, Alireza Doostan, J Richard McIntosh, Matthew A Glaser, Meredith D Betterton
Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood. We have developed a biophysical model of kinetochore capture in small fission-yeast nuclei using hybrid Brownian dynamics/kinetic Monte Carlo simulation techniques...
September 27, 2016: Biophysical Journal
Weili Hong, Anjneya Takshak, Olaolu Osunbayo, Ambarish Kunwar, Michael Vershinin
No abstract text is available yet for this article.
October 18, 2016: Biophysical Journal
Wei Dong, Elizabeth S Olson
Cochlear frequency tuning is based on a mildly tuned traveling-wave response that is enhanced in amplitude and sharpness by outer hair cell (OHC)-based forces. The nonlinear and active character of this enhancement is the fundamental manifestation of cochlear amplification. Recently, mechanical (pressure) and electrical (extracellular OHC-generated voltage) responses were simultaneously measured close to the sensory tissue's basilar membrane. Both pressure and voltage were tuned and showed traveling-wave phase accumulation, evidence that they were locally generated responses...
October 18, 2016: Biophysical Journal
Shawn P Reese, Niloofar Farhang, Randy Poulson, Gennie Parkman, Jeffrey A Weiss
In vitro polymerized type I collagen hydrogels have been used extensively as a model system for three-dimensional (3D) cell and tissue culture, studies of fibrillogenesis, and investigation of multiscale force transmission within connective tissues. The nanoscale organization of collagen fibrils plays an essential role in the mechanics of these gels and emergent cellular behavior in culture, yet quantifying 3D structure with nanoscale resolution to fully characterize fibril organization remains a significant technical challenge...
October 18, 2016: Biophysical Journal
Jelle Hendrix, Tomas Dekens, Waldemar Schrimpf, Don C Lamb
Combining imaging with correlation spectroscopy, as in raster image correlation spectroscopy (RICS), makes it possible to extract molecular translational diffusion constants and absolute concentrations, and determine intermolecular interactions from single-channel or multicolor confocal laser-scanning microscopy (CLSM) images. Region-specific RICS analysis remains very challenging because correlations are always calculated in a square region-of-interest (ROI). In this study, we describe a generalized image correlation spectroscopy algorithm that accepts arbitrarily shaped ROIs...
October 18, 2016: Biophysical Journal
Jacques Pécréaux, Stefanie Redemann, Zahraa Alayan, Benjamin Mercat, Sylvain Pastezeur, Carlos Garzon-Coral, Anthony A Hyman, Jonathon Howard
Precise positioning of the mitotic spindle is important for specifying the plane of cell division, which in turn determines how the cytoplasmic contents of the mother cell are partitioned into the daughter cells, and how the daughters are positioned within the tissue. During metaphase in the early Caenorhabditis elegans embryo, the spindle is aligned and centered on the anterior-posterior axis by a microtubule-dependent machinery that exerts restoring forces when the spindle is displaced from the center. To investigate the accuracy and stability of centering, we tracked the position and orientation of the mitotic spindle during the first cell division with high temporal and spatial resolution...
October 18, 2016: Biophysical Journal
Tom Bongiorno, Jena L Chojnowski, James D Lauderdale, Todd Sulchek
Healthy eyes contain a population of limbal stem cells (LSCs) that continuously renew the corneal epithelium. However, each year, 1 million Americans are afflicted with severely reduced visual acuity caused by corneal damage or disease, including LSC deficiency (LSCD). Recent advances in corneal transplant technology promise to repair the cornea by implanting healthy LSCs to encourage regeneration; however, success is limited to transplanted tissues that contain a sufficiently high percentage of LSCs. Attempts to screen limbal tissues for suitable implants using molecular stemness markers are confounded by the poorly understood signature of the LSC phenotype...
October 18, 2016: Biophysical Journal
Seonghoon Kim, Dhilon S Patel, Soohyung Park, Joanna Slusky, Jeffery B Klauda, Göran Widmalm, Wonpil Im
Lipid A is the lipid anchor of a lipopolysaccharide in the outer leaflet of the outer membrane of Gram-negative bacteria. In general, lipid A consists of two phosphorylated N-acetyl glucosamine and several acyl chains that are directly linked to the two sugars. Depending on the bacterial species and environments, the acyl chain number and length vary, and lipid A can be chemically modified with phosphoethanolamine, aminoarabinose, or glycine residues, which are key to bacterial pathogenesis. In this work, homogeneous lipid bilayers of 21 distinct lipid A types from 12 bacterial species are modeled and simulated to investigate the differences and similarities of their membrane properties...
October 18, 2016: Biophysical Journal
Francis D O Ablan, B Logan Spaller, Kaitlyn I Abdo, Paulo F Almeida
Hundreds of cationic antimicrobial and cell-penetrating peptides (CPPs) form amphipathic α-helices when bound to lipid membranes. Here, we test two hypotheses for the differences in the ability of these peptides to translocate across membranes. The first, which we now call the hydrophobicity hypothesis, is that peptide translocation is determined by the Gibbs energy of insertion into the bilayer from the membrane interface. The second, which we call the charge-distribution hypothesis, is that translocation is determined by whether the distribution of cationic residues in the peptide can transiently stabilize a high-energy inserted intermediate by forming salt bridges to the phosphates of lipid headgroups...
October 18, 2016: Biophysical Journal
Aritreyee Datta, Vikas Yadav, Anirban Ghosh, Jaesun Choi, Dipita Bhattacharyya, Rajiv K Kar, Humaira Ilyas, Arkajyoti Dutta, Eunseol An, Jayanta Mukhopadhyay, Dongkuk Lee, Kaustuv Sanyal, Ayyalusamy Ramamoorthy, Anirban Bhunia
There is a significant need for developing compounds that kill Cryptococcus neoformans, the fungal pathogen that causes meningoencephalitis in immunocompromised individuals. Here, we report the mode of action of a designed antifungal peptide, VG16KRKP (VARGWKRKCPLFGKGG) against C. neoformans. It is shown that VG16KRKP kills fungal cells mainly through membrane compromise leading to efflux of ions and cell metabolites. Intracellular localization, inhibition of in vitro transcription, and DNA binding suggest a secondary mode of action for the peptide, hinting at possible intracellular targets...
October 18, 2016: Biophysical Journal
Alice Strohmeier, Gesche Först, Philipp Tauber, Rolf Schubert
The interaction of liposomal membranes composed of soybean phosphatidylcholine with the bile salts (BSs) cholate (Ch), glycocholate (GC), chenodeoxycholate (CDC), and glycochenodeoxycholate (GCDC) was studied. The BSs differed with regard to their lipophilicity, pKa values, and the size of their hydrophilic moiety. Their membrane interactions were investigated using Laurdan as a membrane-anchored fluorescent dye. The apparent membrane/water partition coefficient, D, at pH 7.4 was calculated from binding plots and compared with direct binding measurements using ultracentrifugation as a reference...
October 18, 2016: Biophysical Journal
Nuria Roldan, Thomas K M Nyholm, J Peter Slotte, Jesús Pérez-Gil, Begoña García-Álvarez
To allow breathing and prevent alveolar collapse, lung surfactant (LS) develops a complex membranous system at the respiratory surface. LS is defined by a specific protein and lipid composition, including saturated and unsaturated phospholipid species and cholesterol. Surfactant protein C (SP-C) has been suggested to be an essential element for sustaining the presence of cholesterol in surfactant without functional impairment. In this work, we used a fluorescent sterol-partitioning assay to assess the effect of the surfactant proteins SP-B and SP-C on cholesterol distribution in membranes...
October 18, 2016: Biophysical Journal
Maite L Ortiz-Suarez, Firdaus Samsudin, Thomas J Piggot, Peter J Bond, Syma Khalid
OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers...
October 18, 2016: Biophysical Journal
Fredrik Elinder, Michael Madeja, Hugo Zeberg, Peter Århem
The transmembrane voltage needed to open different voltage-gated K (Kv) channels differs by up to 50 mV from each other. In this study we test the hypothesis that the channels' voltage dependences to a large extent are set by charged amino-acid residues of the extracellular linkers of the Kv channels, which electrostatically affect the charged amino-acid residues of the voltage sensor S4. Extracellular cations shift the conductance-versus-voltage curve, G(V), by interfering with these extracellular charges...
October 18, 2016: Biophysical Journal
Béla Voß, Reinhard Seifert, U Benjamin Kaupp, Helmut Grubmüller
Ligand-protein binding processes are essential in biological systems. A well-studied system is the binding of cyclic adenosine monophosphate to the cyclic nucleotide binding domain of the bacterial potassium channel MloK1. Strikingly, the measured on-rate for cyclic adenosine monophosphate binding is two orders of magnitude slower than a simple Smoluchowski diffusion model would suggest. To resolve this discrepancy and to characterize the ligand-binding path in structural and energetic terms, we calculated 1100 ligand-binding molecular dynamics trajectories and tested two scenarios: In the first scenario, the ligand transiently binds to the protein surface and then diffuses along the surface into the binding site...
October 18, 2016: Biophysical Journal
Krystal A Morales, Yuan Yang, Taylor R Cole, Tatyana I Igumenova
Ca(2+)-dependent conserved-region 2 (C2) domains target their host signaling proteins to anionic membranes. The Ca(2+)-binding event is a prerequisite for membrane association. Here, we investigate multiscale metal-ion-dependent dynamics of the C2 domain of protein kinase Cα (C2α) using NMR spectroscopy. Interactions with metal ions attenuate microsecond-timescale motions of the loop regions, indicating that preorganization of the metal-binding loops occurs before membrane insertion. Binding of a full complement of Ca(2+) ions has a profound effect on the millisecond-timescale dynamics of the N- and C-terminal regions of C2α...
October 18, 2016: Biophysical Journal
Daniel R Ripoll, Ilja Khavrutskii, Anders Wallqvist, Sidhartha Chaudhury
Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone...
October 18, 2016: Biophysical Journal
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