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Biophysical Journal

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https://www.readbyqxmd.com/read/29685391/interactions-of-hp1-bound-to-h3k9me3-dinucleosome-by-molecular-simulations-and-biochemical-assays
#1
Shuhei Watanabe, Yuichi Mishima, Masahiro Shimizu, Isao Suetake, Shoji Takada
Heterochromatin protein 1 (HP1), associated with heterochromatin formation, recognizes an epigenetically repressive marker, trimethylated lysine 9 in histone H3 (H3K9me3), and generally contributes to long-term silencing. How HP1 induces heterochromatin is not fully understood. Recent experiments suggested that not one, but two nucleosomes provide a platform for this recognition. Integrating previous and new biochemical assays with computational modeling, we provide near-atomic structural models for HP1 binding to the dinucleosomes...
April 20, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29680157/rediscovering-bacteria-through-single-molecule-imaging-in-living-cells
#2
REVIEW
Achillefs N Kapanidis, Alessia Lepore, Meriem El Karoui
Bacteria are microorganisms central to health and disease, serving as important model systems for our understanding of molecular mechanisms and for developing new methodologies and vehicles for biotechnology. In the past few years, our understanding of bacterial cell functions has been enhanced substantially by powerful single-molecule imaging techniques. Using single fluorescent molecules as a means of breaking the optical microscopy limit, we can now reach resolutions of ∼20 nm inside single living cells, a spatial domain previously accessible only by electron microscopy...
April 18, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29655483/chromatin-fiber-folding-directed-by-cooperative-histone-tail-acetylation-and-linker-histone-binding
#3
Gavin D Bascom, Tamar Schlick
In eukaryotic chromatin, islands of histone tail acetylation are found near transcription start sites and enhancers, whereas linker histones (LHs) are localized in intergenic regions with wild-type (WT) histone tails. However, the structural mechanisms by which acetylation, in combination with LH binding, modulates chromatin compaction and hence transcription regulation are unknown. To explore the folding propensity by which these features may govern gene expression, we analyze 20 kb fibers that contain regularly spaced acetylation islands of two sizes (2 or 5 kb) with various LH levels by mesoscale modeling...
April 11, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29653838/a-multicolor-split-fluorescent-protein-approach-to-visualize-listeria-protein-secretion-in-infection
#4
Dilara Batan, Esther Braselmann, Michael Minson, Dieu My Thanh Nguyen, Pascale Cossart, Amy E Palmer
Listeria monocytogenes is an intracellular food-borne pathogen that has evolved to enter mammalian host cells, survive within them, spread from cell to cell, and disseminate throughout the body. A series of secreted virulence proteins from Listeria are responsible for manipulation of host-cell defense mechanisms and adaptation to the intracellular lifestyle. Identifying when and where these virulence proteins are located in live cells over the course of Listeria infection can provide valuable information on the roles these proteins play in defining the host-pathogen interface...
April 10, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29653837/the-relation-between-%C3%AE-helical-conformation-and-amyloidogenicity
#5
Boris Haimov, Simcha Srebnik
Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer's, Parkinson's, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions...
April 10, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29650370/open-boundary-molecular-dynamics-of-a-dna-molecule-in-a-hybrid-explicit-implicit-salt-solution
#6
Julija Zavadlav, Jurij Sablić, Rudolf Podgornik, Matej Praprotnik
The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only at specific ionic conditions: either at nominally zero salt concentration, i.e., including only counterions enforcing the system's electroneutrality, or at excessive salt concentrations. Here, we introduce an efficient molecular dynamics simulation approach for an atomistic DNA molecule at realistic physiological ionic conditions...
April 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29650369/spt-and-imaging-fcs-provide-complementary-information-on-the-dynamics-of-plasma-membrane-molecules
#7
Marie-Lena I E Harwardt, Marina S Dietz, Mike Heilemann, Thorsten Wohland
The dynamics of biomolecules in the plasma membrane is of fundamental importance to understanding cellular processes. Cellular signaling often starts with extracellular ligand binding to a membrane receptor, which then transduces an intracellular signal. Ligand binding and receptor-complex activation often involve a complex rearrangement of proteins in the membrane, which results in changes in diffusion properties. Two widely used methods to characterize biomolecular diffusion are single-particle tracking (SPT) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS)...
April 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29650368/protein-corona-in-response-to-flow-effect-on-protein-concentration-and-structure
#8
Dhanya T Jayaram, Samantha M Pustulka, Robert G Mannino, Wilbur A Lam, Christine K Payne
Nanoparticles used in cellular applications encounter free serum proteins that adsorb onto the surface of the nanoparticle, forming a protein corona. This protein layer controls the interaction of nanoparticles with cells. For nanomedicine applications, it is important to consider how intravenous injection and the subsequent shear flow will affect the protein corona. Our goal was to determine if shear flow changed the composition of the protein corona and if these changes affected cellular binding. Colorimetric assays of protein concentration and gel electrophoresis demonstrate that polystyrene nanoparticles subjected to flow have a greater concentration of serum proteins adsorbed on the surface, especially plasminogen...
April 9, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29628212/chromatin-higher-order-folding-a-perspective-with-linker-dna-angles
#9
REVIEW
Sergei A Grigoryev
The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29628211/major-determinants-of-nucleosome-positioning
#10
REVIEW
Răzvan V Chereji, David J Clark
The compact structure of the nucleosome limits DNA accessibility and inhibits the binding of most sequence-specific proteins. Nucleosomes are not randomly located on the DNA but positioned with respect to the DNA sequence, suggesting models in which critical binding sites are either exposed in the linker, resulting in activation, or buried inside a nucleosome, resulting in repression. The mechanisms determining nucleosome positioning are therefore of paramount importance for understanding gene regulation and other events that occur in chromatin, such as transcription, replication, and repair...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29628210/formation-of-chromatin-subcompartments-by-phase-separation
#11
REVIEW
Fabian Erdel, Karsten Rippe
Chromatin is partitioned on multiple length scales into subcompartments that differ from each other with respect to their molecular composition and biological function. It is a key question how these compartments can form even though diffusion constantly mixes the nuclear interior and rapidly balances concentration gradients of soluble nuclear components. Different biophysical concepts are currently used to explain the formation of "chromatin bodies" in a self-organizing manner and without consuming energy...
April 5, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29606412/ensemble-docking-in-drug-discovery
#12
REVIEW
Rommie E Amaro, Jerome Baudry, John Chodera, Özlem Demir, J Andrew McCammon, Yinglong Miao, Jeremy C Smith
Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.
March 29, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29605081/fcs-analysis-of-protein-mobility-on-lipid-monolayers
#13
Alena Khmelinskaia, Jonas Mücksch, Franco Conci, Grzegorz Chwastek, Petra Schwille
In vitro membrane model systems are used to dissect complex biological phenomena under controlled unadulterated conditions. In this context, lipid monolayers are a powerful tool to particularly study the influence of lipid packing on the behavior of membrane proteins. Here, monolayers deposited in miniaturized fixed area-chambers, which require only minute amounts of protein, were used and shown to faithfully reproduce the characteristics of Langmuir monolayers. This assay is ideally suited to be combined with single-molecule sensitive fluorescence correlation spectroscopy (FCS) to characterize diffusion dynamics...
March 29, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29580552/evidence-for-dna-sequence-encoding-of-an-accessible-nucleosomal-array-across-vertebrates
#14
Frédéric G Brunet, Benjamin Audit, Guénola Drillon, Françoise Argoul, Jean-Nicolas Volff, Alain Arneodo
Nucleosome-depleted regions around which nucleosomes order following the "statistical" positioning scenario were recently shown to be encoded in the DNA sequence in human. This intrinsic nucleosomal ordering strongly correlates with oscillations in the local GC content as well as with the interspecies and intraspecies mutation profiles, revealing the existence of both positive and negative selection. In this letter, we show that these predicted nucleosome inhibitory energy barriers (NIEBs) with compacted neighboring nucleosomes are indeed ubiquitous to all vertebrates tested...
March 23, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29580551/determination-of-dynamical-heterogeneity-from-dynamic-neutron-scattering-of-proteins
#15
Derya Vural, Jeremy C Smith, Henry R Glyde
Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain...
March 23, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29576193/role-of-salt-valency-in-the-switch-of-h-ns-proteins-between-dna-bridging-and-dna-stiffening-modes
#16
Marc Joyeux
This work investigates the interactions of H-NS proteins and bacterial genomic DNA through computer simulations performed with a coarse-grained model. The model was developed specifically to study the switch of H-NS proteins from the DNA-stiffening to the DNA-bridging mode, which has been observed repeatedly upon addition of multivalent cations to the buffer but is still not understood. Unraveling the corresponding mechanism is all the more crucial, as the regulation properties of H-NS proteins, as well as other nucleoid proteins, are linked to their DNA-binding properties...
March 22, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29477335/out-of-the-randomness-correlating-noise-in-biological-systems
#17
REVIEW
Maddalena Collini, Margaux Bouzin, Giuseppe Chirico
The study of the dynamics of biological systems requires one to follow relaxation processes in time with micron-size spatial resolution. This need has led to the development of different fluorescence correlation techniques with high spatial resolution and a tremendous (from nanoseconds to seconds) temporal dynamic range. Spatiotemporal information can be obtained even on complex dynamic processes whose time evolution is not forecast by simple Brownian diffusion. Our discussion of the most recent applications of image correlation spectroscopy to the study of anomalous sub- or superdiffusion suggests that this field still requires the development of multidimensional image analyses based on analytical models or numerical simulations...
February 21, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/29459089/the-role-of-quantum-decoherence-in-fret
#18
REVIEW
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
https://www.readbyqxmd.com/read/29448982/stochastic-gating-as-a-novel-mechanism-for-channel-selectivity
#19
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
https://www.readbyqxmd.com/read/29397876/how-to-follow-a-traveler-with-a-brownian-swagger
#20
Karl E Duderstadt
No abstract text is available yet for this article.
February 1, 2018: Biophysical Journal
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