journal
MENU ▼
Read by QxMD icon Read
search

Biophysical Journal

journal
https://www.readbyqxmd.com/read/28088300/cytoplasmic-rna-protein-particles-exhibit-non-gaussian-subdiffusive-behavior
#1
Thomas J Lampo, Stella Stylianidou, Mikael P Backlund, Paul A Wiggins, Andrew J Spakowitz
The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia coli and Saccharomyces cerevisiae cells. As shown previously, these RNA-protein particles exhibit subdiffusive behavior that is viscoelastic in its origin. Examining the ensemble of particle displacements reveals a Laplace distribution at all observed timescales rather than the Gaussian distribution predicted by the central limit theorem...
January 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28065389/gaussianity-fair-the-riddle-of-anomalous-yet-non-gaussian-diffusion
#2
Ralf Metzler
No abstract text is available yet for this article.
January 5, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28040197/heterogeneous-spatial-distribution-of-transcriptional-activity-in-budding-yeast-nuclei
#3
Naoko Tokuda, Masaki Sasai
Recent microscopic and simulation studies have shown that the genome structure fluctuates dynamically in the nuclei of budding yeast Saccharomyces cerevisiae. This genome-wide movement should lead to the fluctuations of individual genes in their territorial regions. This raises an intriguing question of whether the resulting distribution of genes is correlated to their transcriptional activity. An effective method for examining this correlation is to analyze how the spatial distribution of genes and their transcriptional activity are modified by mutation...
December 28, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/28038734/partially-assembled-nucleosome-structures-at%C3%A2-atomic-detail
#4
Georgy N Rychkov, Andrey V Ilatovskiy, Igor B Nazarov, Alexey V Shvetsov, Dmitry V Lebedev, Alexander Y Konev, Vladimir V Isaev-Ivanov, Alexey V Onufriev
The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation...
December 27, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/28012548/facilitated-dissociation-kinetics-of-dimeric-nucleoid-associated-proteins-follow-a-universal-curve
#5
Katelyn Dahlke, Charles E Sing
Recent experimental work has demonstrated facilitated dissociation of certain nucleoid-associated proteins that exhibit an unbinding rate that depends on the concentration of freely diffusing proteins or DNA in solution. This concentration dependence arises due to binding competition with these other proteins or DNA. The identity of the binding competitor leads to different qualitative trends, motivating an investigation to understand observed differences in facilitated dissociation. We use a coarse-grained simulation that takes into account the dimeric nature of many nucleoid-associated proteins by allowing an intermediate binding state...
December 21, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27989542/chromatin-is-stretched-but-intact-when-the-nucleus-is-squeezed-through-constrictions
#6
D Thirumalai, Guang Shi
No abstract text is available yet for this article.
December 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27955889/contributions-of-sequence-to-the-higher-order-structures-of-dna
#7
REVIEW
Stefjord Todolli, Pamela J Perez, Nicolas Clauvelin, Wilma K Olson
One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers...
December 9, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27931745/histone-acetylation-regulates-chromatin-accessibility-role-of-h4k16-in-inter-nucleosome-interaction
#8
Ruihan Zhang, Jochen Erler, Jörg Langowski
The N-terminal tail of histone H4 is an indispensable mediator for inter-nucleosome interaction, which is required for chromatin fiber condensation. H4K16 acetylation (H4K16Ac) activates gene transcription by influencing both chromatin structure and interplay with nonhistone proteins. To understand the influence of H4K16Ac on inter-nucleosome interaction, we performed a simulation study for the H4 tail in the context of two nucleosomes in neighboring unit cells in the crystal structure. The binding conformation of H4 tail with/without K16Ac was sampled by replica exchange with solute tempering, and the free energy landscape was explored by metadynamics...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/28076821/2017%C3%A2-ushers-in-new-editorial-board-members-and%C3%A2-more
#9
EDITORIAL
Leslie M Loew, Beth Staehle
No abstract text is available yet for this article.
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076820/probing-conformational-changes-during-the-gating-cycle-of-a-potassium-channel-in-lipid-bilayers
#10
Elwin A W van der Cruijsen, Alexander V Prokofyev, Olaf Pongs, Marc Baldus
Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K(+) channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K(+) gating. Yet, the direct observation of the full gating cycle of KcsA has remained structurally elusive, and crystal structures mimicking these gating events require mutations in or stabilization of functionally relevant channel segments...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076819/full-spectral-multiplexing-of-bioluminescence-resonance-energy-transfer-in-three-trpv-channels
#11
Hermanus Johannes Ruigrok, Guillaume Shahid, Bertrand Goudeau, Florence Poulletier de Gannes, Emmanuelle Poque-Haro, Annabelle Hurtier, Isabelle Lagroye, Pierre Vacher, Stéphane Arbault, Neso Sojic, Bernard Veyret, Yann Percherancier
Multiplexed bioluminescence resonance energy transfer (BRET) assays were developed to monitor the activation of several functional transient receptor potential (TRP) channels in live cells and in real time. We probed both TRPV1 intramolecular rearrangements and its interaction with Calmodulin (CaM) under activation by chemical agonists and temperature. Our BRET study also confirmed that: (1) capsaicin and heat promoted distinct transitions, independently coupled to channel gating, and that (2) TRPV1 and Ca(2+)-bound CaM but not Ca(2+)-free CaM were preassociated in resting live cells, while capsaicin activation induced both the formation of more TRPV1/CaM complexes and conformational changes...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076818/one-way-allosteric-communication-between-the-two-disulfide-bonds-in-tissue-factor
#12
Beifei Zhou, Philip J Hogg, Frauke Gräter
Tissue factor (TF) is a transmembrane glycoprotein that plays distinct roles in the initiation of extrinsic coagulation cascade and thrombosis. TF contains two disulfide bonds, one each in the N-terminal and C-terminal extracellular domains. The C-domain disulfide, Cys186-Cys209, has a -RHStaple configuration in crystal structures, suggesting that this disulfide carries high pre-stress. The redox state of this disulfide has been proposed to regulate TF encryption/decryption. Ablating the N-domain Cys49-Cys57 disulfide bond was found to increase the redox potential of the Cys186-Cys209 bond, implying an allosteric communication between the domains...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076817/elucidation-of-single-hydrogen-bonds-in-gtpases-via-experimental-and-theoretical-infrared-spectroscopy
#13
Daniel Mann, Udo Höweler, Carsten Kötting, Klaus Gerwert
Time-resolved Fourier transform infrared (FTIR) spectroscopy is a powerful tool to elucidate label-free the reaction mechanisms of proteins. After assignment of the absorption bands to individual groups of the protein, the order of events during the reaction mechanism can be monitored and rate constants can be obtained. Additionally, structural information is encoded into infrared spectra and can be decoded by combining the experimental data with biomolecular simulations. We have determined recently the infrared vibrations of GTP and guanosine diphosphate (GDP) bound to Gαi1, a ubiquitous GTPase...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076816/mutation-g1629e-increases-von-willebrand-factor-cleavage-via-a-cooperative-destabilization-mechanism
#14
Camilo Aponte-Santamaría, Svenja Lippok, Judith J Mittag, Tobias Obser, Reinhard Schneppenheim, Carsten Baldauf, Frauke Gräter, Ulrich Budde, Joachim O Rädler
The large multimeric glycoprotein von Willebrand Factor (VWF) plays a pivotal adhesive role during primary hemostasis. VWF is cleaved by the protease ADAMTS13 as a down-regulatory mechanism to prevent excessive VWF-mediated platelet aggregation. For each VWF monomer, the ADAMTS13 cleavage site is located deeply buried inside the VWF A2 domain. External forces in vivo or denaturants in vitro trigger the unfolding of this domain, thereby leaving the cleavage site solvent-exposed and ready for cleavage. Mutations in the VWF A2 domain, facilitating the cleavage process, cause a distinct form of von Willebrand disease (VWD), VWD type 2A...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076815/fluorescent-labeling-preserving-ocp-photoactivity-reveals-its-reorganization-during-the-photocycle
#15
Eugene G Maksimov, Nikolai N Sluchanko, Kirill S Mironov, Evgeny A Shirshin, Konstantin E Klementiev, Georgy V Tsoraev, Marcus Moldenhauer, Thomas Friedrich, Dmitry A Los, Suleyman I Allakhverdiev, Vladimir Z Paschenko, Andrei B Rubin
Orange carotenoid protein (OCP), responsible for the photoprotection of the cyanobacterial photosynthetic apparatus under excessive light conditions, undergoes significant rearrangements upon photoconversion and transits from the stable orange to the signaling red state. This is thought to involve a 12-Å translocation of the carotenoid cofactor and separation of the N- and C-terminal protein domains. Despite clear recent progress, the detailed mechanism of the OCP photoconversion and associated photoprotection remains elusive...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076814/gsmtx4-mechanism-of-inhibiting-mechanosensitive-ion-channels
#16
Radhakrishnan Gnanasambandam, Chiranjib Ghatak, Anthony Yasmann, Kazuhisa Nishizawa, Frederick Sachs, Alexey S Ladokhin, Sergei I Sukharev, Thomas M Suchyna
GsMTx4 is a spider venom peptide that inhibits cationic mechanosensitive channels (MSCs). It has six lysine residues that have been proposed to affect membrane binding. We synthesized six analogs with single lysine-to-glutamate substitutions and tested them against Piezo1 channels in outside-out patches and independently measured lipid binding. Four analogs had ∼20% lower efficacy than the wild-type (WT) peptide. The equilibrium constants calculated from the rates of inhibition and washout did not correlate with the changes in inhibition...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076813/signatures-of-mechanosensitive-gating
#17
REVIEW
Richard G Morris
The question of how mechanically gated membrane channels open and close is notoriously difficult to address, especially if the protein structure is not available. This perspective highlights the relevance of micropipette-aspirated single-particle tracking-used to obtain a channel's diffusion coefficient, D, as a function of applied membrane tension, σ-as an indirect assay for determining functional behavior in mechanosensitive channels. While ensuring that the protein remains integral to the membrane, such methods can be used to identify not only the gating mechanism of a protein, but also associated physical moduli, such as torsional and dilational rigidity, which correspond to the protein's effective shape change...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076812/spermine-condenses-dna-but-not-rna-duplexes
#18
Andrea M Katz, Igor S Tolokh, Suzette A Pabit, Nathan Baker, Alexey V Onufriev, Lois Pollack
Interactions between the polyamine spermine and nucleic acids drive important cellular processes. Spermine condenses DNA and some RNAs, such as poly(rA):poly(rU). A large fraction of the spermine present in cells is bound to RNA but apparently does not condense it. Here, we study the effect of spermine binding to short duplex RNA and DNA, and compare our findings with predictions of molecular-dynamics simulations. When small numbers of spermine are introduced, RNA with a designed sequence containing a mixture of 14 GC pairs and 11 AU pairs resists condensation relative to DNA of an equivalent sequence or to 25 bp poly(rA):poly(rU) RNA...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076811/modeling-the-effect-of-curvature-on-the-collective-behavior-of-cells-growing-new-tissue
#19
Mohd Almie Alias, Pascal R Buenzli
The growth of several biological tissues is known to be controlled in part by local geometrical features, such as the curvature of the tissue interface. This control leads to changes in tissue shape that in turn can affect the tissue's evolution. Understanding the cellular basis of this control is highly significant for bioscaffold tissue engineering, the evolution of bone microarchitecture, wound healing, and tumor growth. Although previous models have proposed geometrical relationships between tissue growth and curvature, the role of cell density and cell vigor remains poorly understood...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076810/dna-occupancy-of-polymerizing-transcription-factors-a-chemical-model-of-the-ets-family-factor-yan
#20
C Matthew Hope, Ilaria Rebay, John Reinitz
Transcription factors use both protein-DNA and protein-protein interactions to assemble appropriate complexes to regulate gene expression. Although most transcription factors operate as monomers or dimers, a few, including the E26 transformation-specific family repressors Drosophila melanogaster Yan and its human homolog TEL/ETV6, can polymerize. Although polymerization is required for both the normal and oncogenic function of Yan and TEL/ETV6, the mechanisms by which it influences the recruitment, organization, and stability of transcriptional complexes remain poorly understood...
January 10, 2017: Biophysical Journal
journal
journal
23362
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"