Abstract:
:In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber structure can have consequences for the initiation and repression of the transcription process, and when the remodeling process spreads along the fiber, it also results in long-range effects essential for fiber condensation. There are three regulatory levels of relevance that can be distinguished for this process: the intrinsic sequence preference of the histone octamer, which rules the positioning of the nucleosome along the DNA, notably in relation to the genetic information coded in DNA; the recognition or selection of nucleosomal substrates by remodeling complexes; and, finally, the motor action on the nucleosome exerted by the chromatin remodeler. Recent work has been able to provide crucial insights at each of these three levels that add new twists to this exciting and unfinished story, which we highlight in this perspective.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Blossey R,Schiessel Hdoi
10.1016/j.bpj.2017.12.008subject
Has Abstractpub_date
2018-05-22 00:00:00pages
2255-2261issue
10eissn
0006-3495issn
1542-0086pii
S0006-3495(17)35088-9journal_volume
114pub_type
杂志文章,评审abstract::Cellular membranes are laterally organized into domains of distinct structures and compositions by the differential interaction affinities between various membrane lipids and proteins. A prominent example of such structures are lipid rafts, which are ordered, tightly packed domains that have been widely implicated in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.03.020
更新日期:2018-04-24 00:00:00
abstract::Neutron diffraction from oriented multibilayers has been used to study the bilayer interaction of the amphipathic peptide salmon calcitonin. Penetration of calcitonin into bilayers composed of dioleoylphosphatidylcholine increases with the addition of 15% (mol) of the anionic phospholipid dioleoylphosphatidylglycerol....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78861-1
更新日期:1997-05-01 00:00:00
abstract::Photosystem II catalyzes photosynthetic water oxidation in plants, green algae, and cyanobacteria. The manganese-containing active site cycles through a series of five oxidation states, S(n), where n refers to the number of oxidizing equivalents stored. In this report, reaction-induced Fourier transform infrared and e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74680-3
更新日期:2003-10-01 00:00:00
abstract::Oriented purple membranes were equilibrated under controlled (2)H(2)O relative humidity ranging from 15% to 93% and introduced into the magnetic field of an NMR spectrometer with the membrane normal parallel to the magnetic field direction. Deuterium solid-state NMR spectra of these samples resolved four deuteron popu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74480-4
更新日期:2003-07-01 00:00:00
abstract::Diphtheria toxin (DT) contains separate domains for receptor-specific binding, translocation, and enzymatic activity. After binding to cells, DT is taken up into endosome-like acidic compartments where the translocation domain inserts into the endosomal membrane and releases the catalytic domain into the cytosol. The ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.113498
更新日期:2008-03-15 00:00:00
abstract::Experimental approaches such as fiber diffraction and cryo-electron microscopy reconstruction have defined regulatory positions of tropomyosin on actin but have not, as yet, succeeded at determining key atomic-level contacts between these proteins or fully substantiated the dynamics of their interactions at a structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.017
更新日期:2020-07-07 00:00:00
abstract::Moesin, a protein of the ezrin, radixin, and moesin family, which links the plasma membrane to the cytoskeleton, is involved in multiple physiological and pathological processes, including viral budding and infection. Its interaction with the plasma membrane occurs via a key phosphoinositide, the phosphatidyl(4,5)inos...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.10.041
更新日期:2018-01-09 00:00:00
abstract::Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove g...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.047126
更新日期:2004-11-01 00:00:00
abstract::Both the solution and the oriented film absorption and circular dichroic spectra of the bacteriorhodopsin (bR(568)) and M(412) intermediate of the purple membrane photocycle were compared over the wavelength region 800-183 nm to assess structural changes during this photocycle. The main findings are (a) loss of the ex...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83943-6
更新日期:1985-04-01 00:00:00
abstract::Conductance noise measurement of the open states of alamethicin transmembrane channels reveals excess noise attributable to cooperative low-frequency molecular dynamics that can generate fluctuations approximately 1 A rms in the effective channel pore radius. Single-channel currents through both persistent and nonpers...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80103-7
更新日期:1995-12-01 00:00:00
abstract::O-acetylserine sulfhydrylase, a homo-dimeric enzyme from Salmonella typhimurium, covalently binds one pyridoxal 5'-phosphate molecule per subunit as a fluorescent coenzyme. Different tautomers of the Schiff base between the coenzyme and lysine 41 generate structured absorption and fluorescence spectra upon one-photon ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76167-X
更新日期:2001-04-01 00:00:00
abstract::Rates of diffusion through the extracellular space of thin sheets of myocardium from the right ventricular outflow tract of kittens were estimated at 23 degrees C for 45Ca2+ and an inert reference tracer, [14C]sucrose. The myocardial sheets were mounted in an Ussing chamber and equilibrated with Tyrode solution with v...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(77)85539-2
更新日期:1977-10-01 00:00:00
abstract::Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for translation which accounts for all the elementary steps of transl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.126128
更新日期:2008-08-01 00:00:00
abstract::A model alpha-helical peptide encapsulated in a reverse micelle is used to study the structure and dynamics of proteins under constrained environments that mimic the membrane-water environment in cells. Molecular dynamics simulations of the self assembly of systems composed of a peptide, sodium bis(2-ethylhexyl) sulfo...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2009.03.014
更新日期:2009-05-20 00:00:00
abstract::The current-voltage (I-V) relation of the background current, IK1, was studied in isolated canine cardiac Purkinje myocytes using the whole-cell, patch-clamp technique. Since Ba2+ and Cs+ block IK1, these cations were used to separate the I-V relation of IK1 from that of the whole cell. The I-V relation of IK1 was mea...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83241-1
更新日期:1987-10-01 00:00:00
abstract::A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving force for helix insertion. However, an opposing effect...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79744-8
更新日期:1996-04-01 00:00:00
abstract::Cardiomyocytes have intracellular diffusion restrictions, which spatially compartmentalize ADP and ATP. However, the models that predict diffusion restrictions have used data sets generated in rat heart permeabilized fibers, where diffusion distances may be heterogeneous. This is avoided by using isolated, permeabiliz...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.03.025
更新日期:2010-06-16 00:00:00
abstract::Structures of truncated versions of the influenza A virus M2 proton channel have been determined recently by x-ray crystallography in the open conformation of the channel, and by NMR in the closed state. The structures differ in the position of the bound inhibitors. The x-ray structure shows a single amantadine molecu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.09.004
更新日期:2009-11-18 00:00:00
abstract::Odorant-induced currents in mammalian olfactory receptor neurons have proved difficult to obtain reliably using conventional whole-cell recording. By using a mathematical model of the electrical circuit of the patch and rest-of-cell, we demonstrate how cell-attached patch measurements can be used to quantitatively ana...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78791-5
更新日期:1997-03-01 00:00:00
abstract::Annexins, found in most eukaryotic species, are cytosolic proteins that are able to bind negatively-charged phospholipids in a calcium-dependent manner. Annexin A4 (AnxA4) has been implicated in diverse cellular processes, including the regulation of exocytosis and ion-transport; however, its precise mechanistic role ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.02.057
更新日期:2013-05-07 00:00:00
abstract::In response to external stimuli, cells modulate their adhesive state by regulating the number and intrinsic affinity of receptor/ligand bonds. A number of studies have shown that cell adhesion is dramatically reduced at room or lower temperatures as compared with physiological temperature. However, the underlying mech...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.06.037
更新日期:2010-09-08 00:00:00
abstract::Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a functio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.08.038
更新日期:2013-10-01 00:00:00
abstract::The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.09.026
更新日期:2010-11-17 00:00:00
abstract::Fluorescence contributions from immobile sources present a challenge for fluorescence fluctuation spectroscopy (FFS) because the absence of signal fluctuations from stationary fluorophores leads to a biased analysis. This is especially of concern for cellular FFS studies on proteins that interact with immobile structu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.115642
更新日期:2008-03-15 00:00:00
abstract::A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of protein-association reactions and other events whose frequencies of outcomes are constricted by free energy barriers. The method features a weighted ensemble of trajectories in configuration space with energy levels dictating the prop...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79552-8
更新日期:1996-01-01 00:00:00
abstract::Photoreverse reactions of octopus rhodopsin (Rh) from acid-metarhodopsin (Acid-Meta), which is the final product of the photoreaction of Rh, to Rh were studied by the time-resolved transient absorption and transient grating methods. The time course of the absorption signal showed a rapid change within 500 ns followed ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.101741
更新日期:2007-05-15 00:00:00
abstract::A fundamental question concerning the ClC Cl-/H+ antiporters is the nature of their proton transport (PT) pathway. We addressed this issue by using a novel computational methodology capable of describing the explicit PT dynamics in the ClC-ec1 protein. The main result is that the Glu203 residue delivers a proton from ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.04.038
更新日期:2009-07-08 00:00:00
abstract::Crystals have been grown of "sperm whale" myoglobin produced in Escherichia coli from a synthetic gene and the structure has been solved to 1.9 A resolution. Because of a remaining initiator methionine, this protein crystallizes in a different space group from native sperm whale myoglobin. The three-dimensional struct...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82540-6
更新日期:1990-02-01 00:00:00
abstract::We present the measurement of the force required to rupture a single protein-sugar bond using a methodology that provides selective discrimination between specific and nonspecific binding events and helps verify the presence of a single functional molecule on the atomic force microscopy tip. In particular, the interac...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74299-X
更新日期:2004-04-01 00:00:00
abstract::To determine if hydrophobic surfactant proteins affect the stability of pulmonary surfactant monolayers at an air/water interface, the studies reported here compared the kinetics of collapse for the complete set of lipids in calf surfactant with and without the proteins. Monomolecular films spread at the surface of ca...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.111823
更新日期:2007-12-15 00:00:00