Abstract:
:We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and circular DNA. At a high concentration of Abf2p DNA collapses into a tight nucleoprotein complex. We quantified the compaction of linear DNA by measuring the end-to-end distance of the DNA molecule at increasing concentrations of Abf2p. We also derived a polymer statistical mechanics model that provides a quantitative description of compaction observed in our experiments. This model shows that sharp bends in the DNA backbone are often sufficient to cause DNA compaction. Comparison of our model with the experimental data showed excellent quantitative correlation and allowed us to determine binding characteristics for Abf2p. These studies indicate that Abf2p compacts DNA through a simple mechanism that involves bending of the DNA backbone. We discuss the implications of such a mechanism for mitochondrial DNA maintenance and organization.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Friddle RW,Klare JE,Martin SS,Corzett M,Balhorn R,Baldwin EP,Baskin RJ,Noy Adoi
10.1016/S0006-3495(04)74231-9subject
Has Abstractpub_date
2004-03-01 00:00:00pages
1632-9issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(04)74231-9journal_volume
86pub_type
杂志文章abstract::The sequence of events involved in the transition from attached liposomes to bilayer patches on hydrophilic and hydrophobic solid supports were visualized in situ by Tapping Mode atomic force microscopy in liquid. In a smooth manner, the attached liposomes spread and flattened from the outer edges toward the center un...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76549-0
更新日期:2000-12-01 00:00:00
abstract::We have interrogated the isothermal folding behavior of the DNA i-motif of the human telomere, dC19, and a high-stability i-motif-forming sequence in the promoter of the human DNA repair gene RAD17 using human physiological solution and temperature conditions. We developed a circular-dichroism-spectroscopy-based pH ti...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.03.012
更新日期:2018-04-24 00:00:00
abstract::The reaction of c-cytochromes with iron hexacyanides is similar in mechanism to the interaction of cytochromes with their physiological oxidants and reductants in that the formation of complexes precedes electron transfer. Analysis of the kinetics of oxidation and reduction of a number of c-cytochromes by solving the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84754-6
更新日期:1981-12-01 00:00:00
abstract::A beat-to-beat variation in the cardiac action potential duration is a phenomenon known as alternans. Alternans has been linked to ventricular fibrillation, and thus the ability to predict the onset of alternans could be clinically beneficial. Theoretically, it has been proposed that the slope of a restitution curve, ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.009
更新日期:2011-02-16 00:00:00
abstract::We apply fluorescence lifetime imaging to the membrane phase-sensing dye di-4-ANEPPDHQ in model membranes and live cells. We show that the 1700 ps lifetime shift between liquid-disordered and liquid-ordered phases offers greater contrast than the 60 nm spectral shift previously reported. Detection of cholesterol-rich ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.084673
更新日期:2006-06-01 00:00:00
abstract::A detailed picture of water and ion properties in small pores is important for understanding the behavior of biological ion channels. Several recent modeling studies have shown that small, hydrophobic pores exclude water and ions even if they are physically large enough to accommodate them, a mechanism called hydropho...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.080432
更新日期:2006-05-15 00:00:00
abstract::In cardiac muscle, troponin (Tn) and tropomyosin inhibit actin and myosin interactions through the steric blocking of myosin binding to F-actin. Ca2+ binding to Tn C modulates this inhibition. Thin filaments become activated upon Ca2+ binding, which enables strong binding of myosin with a concomitant release of ATP hy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.08.033
更新日期:2018-11-06 00:00:00
abstract::Interactions between amyloid-β peptide (Aβ) and the cell membrane include interaction with membrane lipids and binding to membrane receptors, both of which are considered to be the toxicity mechanisms of Aβ. However, it is unclear whether both mechanisms lead to cytotoxicity. Thus, we aimed to analyze these two mechan...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.07.035
更新日期:2020-09-15 00:00:00
abstract::Two piezoelectric constants (polarization per unit stress, d=d'-id'', and polarization per unit strain, e=e'-ie''), the elastic constant, and dielectric constant are determined for oriented collagen at different hydration levels at 10 Hz from -150 to 50 degrees C. With no hydration (approximately 0% H2O), d' increases...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(76)85741-4
更新日期:1976-08-01 00:00:00
abstract::Regulation of the F-actin severing activity of gelsolin by Ca2+ has been investigated under physiologic ionic conditions. Tryptophan fluorescence intensity measurements indicate that gelsolin contains at least two Ca2+ binding sites with affinities of 2.5 x 10(7) M-1 and 1.5 x 10(5) M-1. At F-actin and gelsolin concen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77751-3
更新日期:1998-12-01 00:00:00
abstract::Cofilin/ADF, beryllium fluoride complex (BeFx), and phalloidin have opposing effects on actin filament structure and dynamics. Cofilin/ADF decreases the stability of F-actin by enhancing disorder in subdomain 2, and by severing and accelerating the depolymerization of the filament. BeFx and phalloidin stabilize the su...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087767
更新日期:2006-12-15 00:00:00
abstract::The oligomeric structure was determined for four recombinant kinesin derivatives containing N-terminal fragments of the kinesin alpha-subunit. Some of the proteins were dimeric (two-headed) molecules with mechanochemical properties similar to those of intact kinesin. Comparison of the primary and quaternary structures...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:
更新日期:1995-04-01 00:00:00
abstract::Phytochromes sense red/far-red light and control many biological processes in plants, fungi, and bacteria. Although the crystal structures of dark- and light-adapted states have been determined, the molecular mechanisms underlying photoactivation remain elusive. Here, we demonstrate that the conserved tongue region of...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.11.025
更新日期:2020-01-21 00:00:00
abstract::The organization of the normal collagen molecule and fibrils is reviewed and the detection, assay, and isolation of a collagenolytic enzyme from amphibian tadpole tissue are described and its possible significance in metamorphosis is discussed ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(64)86928-9
更新日期:1964-01-01 00:00:00
abstract::We describe Franck-Condon simulations of vibrational cooling effects on absorption difference spectra in chlorophyll a (Chl a). The relative contributions of vibrational equilibration in the electronic ground and excited states depend on the pump and probe wavelengths. For Franck-Condon-active vibrational modes exhibi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80145-1
更新日期:1995-12-01 00:00:00
abstract::Kv1 potassium channels are widely distributed in mammalian tissues and are involved in a variety of functions from controlling the firing rate of neurons to maturation of T-lymphocytes. Here we show that the newly described KCNE4 beta-subunit has a drastic inhibitory effect on currents generated by Kv1.1 and Kv1.3 pot...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74585-8
更新日期:2003-09-01 00:00:00
abstract::Electron-electron double resonance (ELDOR) and saturation-recovery spectroscopy employing 14N:15N stearic acid spin-label pairs have been used to study the effects of cholesterol on lateral diffusion and vertical fluctuations in lipid bilayers. The 14N:15N continuous wave electron-electron double resonance (CW ELDOR) ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83296-4
更新日期:1987-12-01 00:00:00
abstract::The processes of cell growth and budding of the yeast cells Saccharomyces cerevisiae, which were gently immobilized on 3% agar and submerged in culture medium, were successfully imaged with an atomic force microscope for 6-7 h. Similar experiments on chemically fixed cells did not detect any appreciable change in thei...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80147-5
更新日期:1995-12-01 00:00:00
abstract::A newly developed microscope using acousto-optic tunable filters (AOTFs) was used to generate in vivo hemoglobin saturation (SO2) and oxygen tension (PO2) maps in the cerebral cortex of mice. SO2 maps were generated from the spectral analysis of reflected absorbance images collected at different wavelengths, and PO2 m...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78155-4
更新日期:1997-09-01 00:00:00
abstract::Cellular processes are noisy due to the stochastic nature of biochemical reactions. As such, it is impossible to predict the exact quantity of a molecule or other attributes at the single-cell level. However, the distribution of a molecule over a population is often deterministic and is governed by the underlying regu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.07.025
更新日期:2014-09-02 00:00:00
abstract::An analytical electromechanical model of a spherical cell exposed to an alternating electric field was used to calculate shear stress generated in the cellular membrane. Shape deformation of Neurospora crassa (slime) spheroplasts was measured. Statistical analysis permitted empirical evaluation of creep of the cellula...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81866-0
更新日期:1992-03-01 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::Some new approaches to the kinetic study of the reduction of cytochrome aa3 by cytochrome c are presented. The primary innovations are the use of a spectrometer which can acquire multiwavelength data as fast as every 10 microseconds, and the application of a variety of analytical methods which can utilize simultaneous...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81170-6
更新日期:1993-09-01 00:00:00
abstract::We developed a multicellular model characterized by a high degree of heterogeneity to investigate possible mechanisms that underlie circadian network synchronization and rhythmicity in the suprachiasmatic nucleus (SCN). We populated a two-dimensional grid with 400 model neurons coupled via γ-aminobutyric acid (GABA) a...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.04.051
更新日期:2011-07-06 00:00:00
abstract::Fluorescence correlation spectroscopy (FCS) has been used to measure the diffusion of fluorescently labeled beads in solutions of polymerized actin or buffer. The results, obtained at actin concentrations of 1 mg/ml, show that small beads (0.09 micron in diameter) diffuse nearly as rapidly in the actin gel as in buffe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81686-7
更新日期:1992-10-01 00:00:00
abstract::The opening of basepairs plays a key role in DNA replication and transcription, and in the action of DNA repair and modification enzymes. In this article, we have used proton exchange to define the energetics of the pathways for basepair opening in two DNA 17-mer duplexes. The rates of exchange of imino protons with s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.065763
更新日期:2005-11-01 00:00:00
abstract::Wiener kernels have been measured for the light growth response of a number of mutants of Phycomyces which show abnormal phototropism (mad mutants). Representative mutants were chosen from the six complementation groups (madA to madF) associated with the light response pathway. One group, madA, associated with the inp...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(75)85881-4
更新日期:1975-10-01 00:00:00
abstract::Crystals of ion-free gramicidin A (P212121: a = 24.61, b = 32.28, c = 32.52) have been investigated using neutron diffraction. A difference analysis of crystals soaked in ethanol/H2O as opposed to ethanol-d6/D2O has led to single isomorphous replacement Fourier projections of the structure at 5-A resolution. The grami...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84186-7
更新日期:1984-03-01 00:00:00
abstract::We study the effect of ergosterol on the physical properties of 1-[(2)H(31)]palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) multibilayers using deuterium nuclear magnetic resonance. NMR spectra were taken as a function of temperature and ergosterol concentration up to 70 mol %. The spectral first moments sh...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.12.4279
更新日期:2010-04-07 00:00:00
abstract::The ability to discriminate between different cations efficiently is essential for the proper physiological functioning of many membrane transport proteins. One obvious mechanism of ion selectivity is when a binding site is structurally constrained by the protein architecture and its geometry is precisely adapted to f...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.03.038
更新日期:2010-06-16 00:00:00