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Biophysical Journal

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https://www.readbyqxmd.com/read/28242011/multivalent-molecules-as-modulators-of-rna-granule-size-and-composition
#1
Cibele Vieira Falkenberg, John H Carson, Michael L Blinov
RNA granules are ensembles of specific RNA and protein molecules that mediate localized translation in eukaryotic cells. The mechanisms for formation and selectivity of RNA granules are unknown. Here we present a model for assembly of one type of RNA granule based on experimentally measured binding interactions among three core multivalent molecular components necessary for such assembly: specific RNA molecules that contain a cis-acting sequence called the A2 response element (A2RE), hnRNP A2 proteins that bind specifically (with high affinity) to A2RE sequences or nonspecifically (with lower affinity) to other RNA sequences, and heptavalent protein cytoskeleton-associated protein 5 (CKAP5, an alternative name for TOG protein) that binds both hnRNP A2 molecules and RNA...
February 24, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28237025/geometric-requirements-for-tectorial-membrane-traveling-waves-in-the-presence-of-cochlear-loads
#2
Jonathan B Sellon, Roozbeh Ghaffari, Dennis M Freeman
Recent studies suggest that wave motions of the tectorial membrane (TM) play a critical role in determining the frequency selectivity of hearing. However, frequency tuning is also thought to be limited by viscous loss in subtectorial fluid. Here, we analyze effects of this loss and other cochlear loads on TM traveling waves. Using a viscoelastic model, we demonstrate that hair bundle stiffness has little effect on TM traveling waves calculated with physiological parameters, that the limbal attachment can cause small (<20%) increases in TM wavelength, and that viscous loss in the subtectorial fluid can cause small (<20%) decreases in TM wave decay constants...
February 22, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28214480/nonlinear-actin-deformations-lead-to-network-stiffening-yielding-and-nonuniform-stress-propagation
#3
Bekele Gurmessa, Shea Ricketts, Rae M Robertson-Anderson
We use optical tweezers microrheology and fluorescence microscopy to apply nonlinear microscale strains to entangled and cross-linked actin networks, and measure the resulting stress and actin filament deformations. We couple nonlinear stress response and relaxation to the velocities and displacements of individual fluorescent-labeled actin segments, at varying times throughout the strain and varying distances from the strain path, to determine the underlying molecular dynamics that give rise to the debated nonlinear response and stress propagation of cross-linked and entangled actin networks at the microscale...
February 15, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28162235/opportunities-and-challenges-in-rna-structural-modeling-and-design
#4
REVIEW
Tamar Schlick, Anna Marie Pyle
We describe opportunities and challenges in RNA structural modeling and design, as recently discussed during the second Telluride Science Research Center workshop organized in June 2016. Topics include fundamental processes of RNA, such as structural assemblies (hierarchical folding, multiple conformational states and their clustering), RNA motifs, and chemical reactivity of RNA, as used for structural prediction and functional inference. We also highlight the software and database issues associated with RNA structures, such as the multiple approaches for motif annotation, the need for frequent database updating, and the importance of quality control of RNA structures...
February 2, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297658/multiscale-modeling-of-complex-formation-and-cd80-depletion-during-immune-synapse-development
#5
István P Sugár, Jayajit Das, Ciriyam Jayaprakash, Stuart C Sealfon
The mechanisms that discriminate self- and foreign antigen before T cell activation are unresolved. As part of the immune system's adaptive response to specific infections or neoplasms, antigen-presenting cells (APC) and effector T cells form transcellular molecular complexes. CTLA4 expression on regulatory or effector T cells reduces T cell activation. The CTLA4 transendocytosis hypothesis proposes that CTLA4 depletes CD80 and CD86 proteins from the APC membrane, rendering the APC incapable of activating T cells...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297657/modeling-the-actin-myosin-atpase-cross-bridge-cycle-for-skeletal-and-cardiac-muscle-myosin%C3%A2-isoforms
#6
Srbolujub M Mijailovich, Djordje Nedic, Marina Svicevic, Boban Stojanovic, Jonathan Walklate, Zoltan Ujfalusi, Michael A Geeves
Modeling the complete actin.myosin ATPase cycle has always been limited by the lack of experimental data concerning key steps of the cycle, because these steps can only be defined at very low ionic strength. Here, using human β-cardiac myosin-S1, we combine published data from transient and steady-state kinetics to model a minimal eight-state ATPase cycle. The model illustrates the occupancy of each intermediate around the cycle and how the occupancy is altered by changes in actin concentration for [actin] = 1-20Km...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297656/the-long-chain-sphingoid-base-of-ceramides-determines-their-propensity-for-lateral-segregation
#7
Md Abdullah Al Sazzad, Tomokazu Yasuda, Michio Murata, J Peter Slotte
We examined how the length of the long-chain base or the N-linked acyl chain of ceramides affected their lateral segregation in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Lateral segregation and ceramide-rich phase formation was ascertained by a lifetime analysis of trans-parinaric acid (tPA) fluorescence. The longer the length of the long-chain base (d16:1, d17:1, d18:1, d19:1, and d20:1 in N-palmitoyl ceramide), the less ceramide was needed for the onset of lateral segregation and ceramide-rich phase formation...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297655/formation-of-large-hypericin-aggregates-in-giant-unilamellar-vesicles-experiments-and-modeling
#8
Jaroslava Joniova, Matúš Rebič, Alena Strejčková, Veronika Huntosova, Jana Staničová, Daniel Jancura, Pavol Miskovsky, Gregor Bánó
The incorporation of hypericin (Hyp) from aqueous solutions into giant unilamellar vesicle (GUV) membranes has been studied experimentally and by means of kinetic Monte Carlo modeling. The time evolution of Hyp fluorescence originating from Hyp monomers dissolved in the GUV membrane has been recorded by confocal microscopy and while trapping individual GUVs in optical tweezers. It was shown that after reaching a maximum, the fluorescence intensity gradually decreased toward longer times. Formation of oversized Hyp clusters has been observed on the GUV surface at prolonged time...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297654/role-of-pore-lining-residues-in-defining-the-rate-of-water-conduction-by-aquaporin-0
#9
Patrick O Saboe, Chiara Rapisarda, Shreyas Kaptan, Yu-Shan Hsiao, Samantha R Summers, Rita De Zorzi, Danijela Dukovski, Jiaheng Yu, Bert L de Groot, Manish Kumar, Thomas Walz
Compared to other aquaporins (AQPs), lens-specific AQP0 is a poor water channel, and its permeability was reported to be pH-dependent. To date, most water conduction studies on AQP0 were performed on protein expressed in Xenopus oocytes, and the results may therefore also reflect effects introduced by the oocytes themselves. Experiments with purified AQP0 reconstituted into liposomes are challenging because the water permeability of AQP0 is only slightly higher than that of pure lipid bilayers. By reconstituting high amounts of AQP0 and using high concentrations of cholesterol to reduce the permeability of the lipid bilayer, we improved the signal-to-noise ratio of water permeability measurements on AQP0 proteoliposomes...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297653/atomistic-study-of-intramolecular-interactions-in-the-closed-state-channelrhodopsin-chimera-c1c2
#10
Monika R VanGordon, Gaurav Gyawali, Steven W Rick, Susan B Rempe
Channelrhodopsins (ChR1 and ChR2) are light-activated ion channels that enable photomobility of microalgae from the genus Chlamydomonas. Despite common use of ChR2 in optogenetics for selective control and monitoring of individual neurons in living tissue, the protein structures remain unresolved. Instead, a crystal structure of the ChR chimera (C1C2), an engineered combination of helices I-V from ChR1, without its C-terminus, and helices VI-VII from ChR2, is used as a template for ChR2 structure prediction...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297652/moving-in-the-right-direction-protein-vibrational-steering-function
#11
Katherine A Niessen, Mengyang Xu, Alessandro Paciaroni, Andrea Orecchini, Edward H Snell, Andrea G Markelz
Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297651/glycan-determinants-of-heparin-tau-interaction
#12
Jing Zhao, Isabelle Huvent, Guy Lippens, David Eliezer, Anqiang Zhang, Quanhong Li, Peter Tessier, Robert J Linhardt, Fuming Zhang, Chunyu Wang
Tau aggregates into paired helical filaments within neurons, a pathological hallmark of Alzheimer's disease. Heparin promotes tau aggregation and recently has been shown to be involved in the cellular uptake of tau aggregates. Although the tau-heparin interaction has been extensively studied, little is known about the glycan determinants of this interaction. Here, we used surface plasmon resonance (SPR) and NMR spectroscopy to characterize the interaction between two tau fragments, K18 and K19, and several polysaccharides, including heparin, heparin oligosaccharides, chemically modified heparin, and related glycans...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297650/rotation-mechanism-of-molecular-motor-v1-atpase-studied-by-multiscale-molecular-dynamics-simulation
#13
Yuta Isaka, Toru Ekimoto, Yuichi Kokabu, Ichiro Yamato, Takeshi Murata, Mitsunori Ikeguchi
Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of three catalytic pairs induce the 120° rotation of the central stalk, we performed multiscale molecular dynamics (MD) simulations in which coarse-grained and all-atom MD simulations were combined using a fluctuation matching methodology...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297649/influence-of-flexible-%C3%AF-on-the-activity-of-e-%C3%A2-coli-rna-polymerase-a-thermodynamic-analysis
#14
Debipreeta Bhowmik, Neerupma Bhardwaj, Dipankar Chatterji
The Escherichia coli RNA polymerase (RNAP) is a multisubunit protein complex containing the smallest subunit, ω. Despite the evolutionary conservation of ω and its role in assembly of RNAP, E. coli mutants lacking rpoZ (codes for ω) are viable due to the association of RNAP with the global chaperone protein GroEL. With an aim to get better insight into the structure and functional role of ω, we isolated a dominant negative mutant of ω (ω6), which is predominantly α-helical, in contrast to largely unstructured native ω, and then studied its assembly with reconstituted core1 (α2ββ') by a biophysical approach...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297648/phosphorylation-induced-mechanical-regulation-of%C3%A2-intrinsically-disordered-neurofilament-proteins
#15
Eti Malka-Gibor, Micha Kornreich, Adi Laser-Azogui, Ofer Doron, Irena Zingerman-Koladko, Jan Harapin, Ohad Medalia, Roy Beck
The biological function of protein assemblies has been conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it has been found that some assemblies contain long flexible regions that adopt multiple structural conformations. These include neurofilament proteins that constitute the stress-responsive supportive network of neurons. Herein, we show that the macroscopic properties of neurofilament networks are tuned by enzymatic regulation of the charge found on the flexible protein regions...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297647/solvent-slaved-dynamic-processes-observed-by-tryptophan-phosphorescence-of-human-serum-albumin
#16
Andrew R Draganski, Joel M Friedman, Richard D Ludescher
Despite extensive experimental and computational efforts to understand the nature of the hierarchy of protein fluctuations and the modulating role of the protein hydration shell, a detailed microscopic description of the dynamics of the protein-solvent system has yet to be achieved. By using single tryptophan protein phosphorescence, we follow site-specific internal protein dynamics over a broad temperature range and demonstrate three independent dynamic processes. Process I is seen at temperatures below the bulk solvent Tg, has low activation energy, and is likely due to fast vibrations that may be enabled by water mobility on the protein surface...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297646/inferring-mechanistic-parameters-from-amyloid-formation-kinetics-by-approximate-bayesian-computation
#17
Eri Nakatani-Webster, Abhinav Nath
Amyloid formation is implicated in a number of human diseases, and is thought to proceed via a nucleation-dependent polymerization mechanism. Experimenters often wish to relate changes in amyloid formation kinetics, for example, in response to small molecules to specific mechanistic steps along this pathway. However, fitting kinetic fibril formation data to a complex model including explicit rate constants results in an ill-posed problem with a vast number of potential solutions. The levels of uncertainty remaining in parameters calculated from these models, arising both from experimental noise and high levels of degeneracy or codependency in parameters, is often unclear...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297645/on-the-mechanism-of-homology-search-by-reca-protein-filaments
#18
Maria P Kochugaeva, Alexey A Shvets, Anatoly B Kolomeisky
Genetic stability is a key factor in maintaining, survival, and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria, this task is accomplished by RecA proteins that are active as nucleoprotein filaments formed on single-stranded segments of DNA. A critical step in the homologous recombination is a search for a corresponding homologous region on DNA, which is called a homology search...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297644/dna-endonuclease-complex-dynamics-by-simultaneous-fret-and-fluorophore-intensity-in-evanescent-field
#19
Marijonas Tutkus, Tomas Marciulionis, Giedrius Sasnauskas, Danielis Rutkauskas
The single-molecule Förster resonance energy transfer (FRET) is a powerful tool to study interactions and conformational changes of biological molecules in the distance range from a few to 10 nm. In this study, we demonstrate a method to augment this range with longer distances. The method is based on the intensity changes of a tethered fluorophore, diffusing in the exponentially decaying evanescent excitation field. In combination with FRET it allowed us to reveal and characterize the dynamics of what had been inaccessible conformations of the DNA-protein complex...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28297643/effects-of-polymer-length-and-salt-concentration-on-the-transport-of-ssdna-in-nanofluidic-channels
#20
Weixin Qian, Kentaro Doi, Satoyuki Kawano
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer...
March 14, 2017: Biophysical Journal
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