Abstract:
:The conformation of mononucleosome complexes reconstituted with recombinant core histones on a 614-basepair-long DNA fragment containing the Xenopus borealis 5S rRNA nucleosome positioning sequence was studied by scanning/atomic force microscopy in the absence or presence of linker histone H1. Imaging without prior fixation was conducted with air-dried samples and with mononucleosomes that were injected directly into the scanning force microscopy fluid cell and visualized in buffer. From a quantitative analysis of approximately 1,700 complexes, the following results were obtained: i), In the absence of H1, a preferred location of the nucleosome at the X. borealis 5S rRNA sequence in the center of the DNA was detected. From the distribution of nucleosome positions, an energy difference of binding to the 5S rRNA sequence of DeltaDeltaG approximately 3 kcal mol(-1) as compared to a random sequence was estimated. Upon addition of H1, a significantly reduced preference of nucleosome binding to this sequence was observed. ii), The measured entry-exit angles of the DNA at the nucleosome in the absence of H1 showed two maxima at 81 +/- 29 degrees and 136 +/- 18 degrees (air-dried samples), and 78 +/- 25 degrees and 137 +/- 25 degrees (samples imaged in buffer solution). In the presence of H1, the species with the smaller entry-exit angle was stabilized, yielding average values of 88 +/- 34 degrees for complexes in air and 85 +/- 10 degrees in buffer solution. iii), The apparent contour length of the nucleosome complexes was shortened by 34 +/- 13 nm as compared to the free DNA due to wrapping of the DNA around the histone octamer complex. Considering an 11 nm diameter of the nucleosome core complex, this corresponds to a total of 145 +/- 34 basepairs that are wound around the nucleosome.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Kepert JF,Tóth KF,Caudron M,Mücke N,Langowski J,Rippe Kdoi
10.1016/S0006-3495(03)74815-2subject
Has Abstractpub_date
2003-12-01 00:00:00pages
4012-22issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(03)74815-2journal_volume
85pub_type
杂志文章abstract::A significant amount of work has been devoted to obtaining a detailed atomistic knowledge of the human hemoglobin mechanism. Despite this impressive research, to date, the ligand diffusion processes remain unclear and controversial. Using recently developed computational techniques, PELE, we are capable of addressing ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.01.011
更新日期:2012-02-22 00:00:00
abstract::The effect of weak, nonspecific interaction between molecules confined within restricted elements of volume ("pores") and the boundary surfaces of the pore, upon the reactivity and physical state of the confined molecules, is explored by means of simple models. A confined molecule is represented by a rectangular paral...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80304-8
更新日期:1995-04-01 00:00:00
abstract::Spontaneous conversion of beta-amyloid peptide (Abeta) from soluble monomer to insoluble fibril may underlie the neurodegeneration associated with Alzheimer's disease. A complete description of Abeta self-association kinetics requires identification of the oligomeric species present and the pathway of association, as ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75831-6
更新日期:2001-09-01 00:00:00
abstract::We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.11.4012
更新日期:2012-01-04 00:00:00
abstract::The possibility that the chlorophyll (chl) ring distortions observed in the crystal structures of chl-protein complexes are involved in the transition energy modulation, giving rise to the spectral forms, is investigated. The out-of-plane chl-macrocycle distortions are described using an orthonormal set of deformation...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.104554
更新日期:2007-09-15 00:00:00
abstract::Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.04.019
更新日期:2020-06-02 00:00:00
abstract::To determine the effect of hydration on the dynamics of a protein complex, we used deuterium nuclear magnetic resonance (NMR) techniques to examine a trimethoprim (TMP)/E. coli dihydrofolate reductase (DHFR) complex in its lyophilized, partially hydrated, polycrystalline, and ammonium sulfate-precipitated states. The ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81486-3
更新日期:1993-04-01 00:00:00
abstract::Dipole moment, enthalpy, and entropy changes were calculated for hypothetical structural units which control the opening and closing of ionic channels in axon membranes. The changes of these thermodynamic functions were calculated both for activation (transition to intermediate complex) and for the structural transfor...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(75)85815-2
更新日期:1975-03-01 00:00:00
abstract::The skeletal muscles of chickens, frogs, and fish have been reported to express two isoforms (alpha and beta) of the sarcoplasmic reticulum calcium release channel (ryanodine receptor or RYR), while mammals express only one. We have studied patterns of RYR isoform expression in skeletal muscles from a variety of fish,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81303-1
更新日期:1993-12-01 00:00:00
abstract::Cellular differentiation proceeds along complicated pathways, even when it is induced by extracellular signaling molecules. One of the major reasons for this complexity is the highly multidimensional internal dynamics of cells, which sometimes causes apparently stochastic responses in individual cells to extracellular...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.10.002
更新日期:2014-11-18 00:00:00
abstract::The effect of a transmembrane peptide on the domain structure of a two-component, two-phase lipid bilayer composed of dimyristoyl phosphatidylcholine (DMPC) and distearoyl phosphatidylcholine (DSPC) was examined by spin label electron spin resonance (ESR) spectroscopy. The peptide, pOmpA, is the hydrophobic, 25-residu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80989-0
更新日期:1994-06-01 00:00:00
abstract::The structure of a membrane-embedded alpha-helical reference protein, the M13 major coat protein, is characterized under different conditions of hydrophobic mismatch using fluorescence resonance energy transfer in combination with high-throughput mutagenesis. We show that the structure is similar in both thin (14:1) a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.112698
更新日期:2007-11-15 00:00:00
abstract::Magic-angle spinning nuclear magnetic resonance is well suited for the study of membrane proteins in the nativelike lipid environment. However, the natural cellular membrane is invariably more complex than the proteoliposomes most often used for solid-state NMR (SSNMR) studies, and differences may affect the structure...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.02.018
更新日期:2015-04-07 00:00:00
abstract::Studies in Shaker, a voltage-dependent potassium channel, suggest a coupling between activation and inactivation. This coupling is controversial in hERG, a fast-inactivating voltage-dependent potassium channel. To address this question, we transferred to hERG the S3-S4 linker of the voltage-independent channel, rolf, ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.05.060
更新日期:2009-09-02 00:00:00
abstract::Zebrafish (Danio rerio) swim within days of fertilization, powered by muscles of the axial myotomes. Forces generated by these muscles can be measured rapidly in whole, intact larval tails by adapting protocols developed for ex vivo muscle mechanics. But it is not known how well these measurements reflect the function...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.06.036
更新日期:2020-08-18 00:00:00
abstract::The B1 domain of protein G has been a classic model system of folding for decades, the subject of numerous experimental and computational studies. Most of the experimental work has focused on whether the protein folds via an intermediate, but the evidence is mostly limited to relatively slow kinetic observations with ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.06.037
更新日期:2014-08-19 00:00:00
abstract::A detailed analysis is made of the model system of two parallel cylindrical polyelectrolytes which contain ionizable groups on their surfaces and are immersed in an ionic bathing medium. The interaction between the cylinders is examined by considering the interplay between repulsive electrostatic forces and attractive...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(73)85987-9
更新日期:1973-04-01 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::We perform single-molecule flow experiments using confocal microscopy and a microfluidic device for shear rates up to 20,000 s-1 and present results for the shear-induced unraveling and elongation of tethered von Willebrand factor (VWF) multimers. Further, we employ companion Brownian dynamics simulations to help expl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.04.025
更新日期:2019-06-04 00:00:00
abstract::Fibrin polymerizes to produce branching fibers forming a three-dimensional network, which has been difficult to visualize by conventional microscopy. Three-dimensional images of whole clots at high resolution were obtained from stereo-pair intermediate-voltage electron micrographs. Computer software was developed to p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80327-9
更新日期:1995-04-01 00:00:00
abstract::The glucose transporters (GLUT/SLC2A) are members of the major facilitator superfamily. Here, we generated a three-dimensional model for Glut1 using a two-step strategy: 1), GlpT structure as an initial homology template and 2), evolutionary homology using glucose-6-phosphate translocase as a template. The resulting s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.047886
更新日期:2004-11-01 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::The solutions to a general class of axon partial differential equations proposed by FitzHugh which includes the Hodgkin-Huxley equations are studied. It is shown that solutions to the partial differential equations are exactly the solutions to a related set of integral equations. An iterative procedure for constructin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(70)86355-X
更新日期:1970-11-01 00:00:00
abstract::Inactivation is a fundamental property of voltage-gated ion channels. Fast inactivation of Na(+) channels involves channel block by the III-IV cytoplasmic interdomain linker. The mechanisms of nonfast types of inactivation (intermediate, slow, and ultraslow) are unclear, although the ionic environment and P-loops rear...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.100248
更新日期:2007-09-01 00:00:00
abstract::Previous studies on aurein 2.2 and 2.3 in DMPC/DMPG and POPC/POPG membranes have shown that bilayer thickness and phosphatidylglycerol content have a significant impact on the interaction of these peptides with membrane bilayers. Further examination with the DiSC(3)5 assay has indicated that aurein 2.2 induces greater...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.08.077
更新日期:2010-11-03 00:00:00
abstract::We have studied the photoinduced volume changes, energetics, and kinetics in the early steps of the bacteriorhodopsin (BR) photocycle with pulsed, time-resolved photoacoustics. Our data show that there are two volume changes. The fast volume change ( < or = 200 ns) is an expansion (2.5 +/- 0.3 A3/molecule) and is obse...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79235-4
更新日期:1996-07-01 00:00:00
abstract::Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a prot...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.07.003
更新日期:2011-09-07 00:00:00
abstract::Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.06.046
更新日期:2011-08-17 00:00:00
abstract::A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.05.005
更新日期:2017-06-20 00:00:00
abstract::Dual-color fluorescence cross-correlation analysis is a powerful tool for probing interactions of different fluorescently labeled molecules in aqueous solution. The concept is the selective observation of coordinated spontaneous fluctuations in two separate detection channels that unambiguously reflect the existence o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)73935-0
更新日期:2002-09-01 00:00:00