Abstract：
:The results of variable dielectric coefficient Poisson-Boltzmann calculations of the counter-ion concentration in the vicinity of an all-atom model of the B-form of DNA are presented with an emphasis on the importance of spatial variations in the dielectric properties of the solvent, particularly at the macro-ion-solvent interface. Calculations of the distribution of hard-sphere electrolyte ions of various dimensions are reported. The presence of a dielectric boundary significantly increases the magnitude of the electrostatic potential with a concomitant increase in the accumulation of small counter-ions in the groove regions of DNA. Because ions with radii greater than 2 A have restricted access to the minor groove, the effect there is less significant than it is within the major groove. Changes in the dielectric coefficient for the electrolyte solution, allowing variation from 10 to 25, 40, 60, and 78.5 within the first 7.4 A of the surface of DNA, substantially increases the calculated surface concentration of counter-ions of all sizes. A lower dielectric coefficient near the macro-ion surface also tends to increase the counter-ion density in regions where the electrostatic potential is more negative than -kT. Regardless of the choice of dielectric coefficient, the number of ions in regions where the electrostatic potential is less than -kT remains the same for 0.153 M added 1-1 monovalent electrolyte as for the case without added salt. The strong dependence of the calculated distribution of counter-ion density on the choice of dielectric coefficients representing the solvent continuum suggests that care must be taken to properly characterize the physical system when studying electrostatic properties using these methods.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Pack GR,Garrett GA,Wong L,Lamm Gdoi
10.1016/S0006-3495(93)81187-1subject
Has Abstractpub_date
1993-10-01 00:00:00pages
1363-70issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(93)81187-1journal_volume
65pub_type
杂志文章abstract：:The current rapid expansion of biological knowledge offers a great opportunity to rationally engineer biological systems that respond to signals such as light and chemical inducers by producing specific proteins. Turning on and off the production of proteins on demand holds great promise for creating significant biote...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.105.064204
更新日期：2005-12-01 00:00:00
abstract：:Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, alpha and beta. Hydrogen bonds between betaArg-56 and alphaCys-114 sulfenic acid (alp...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.107.116665
更新日期：2008-05-15 00:00:00
abstract：:Myosin subfragment 1 (S1) can be specifically modified at Lys-553 with the fluorescent probe FHS (6-[fluorescein-5(and 6)-carboxamido]hexanoic acid succinimidyl ester) (Bertrand, R., J. Derancourt, and R. Kassab. 1995. Biochemistry. 34:9500-9507), and solvent quenching of FHS-S1 with iodide has been shown to be sensit...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(00)76698-7
更新日期：2000-03-01 00:00:00
abstract：:A model is presented for the steric interaction between a plasma membrane protein and the membrane cytoskeleton in the human erythrocyte. The cytoskeleton is treated as a network of polymer chains attached to a flat bilayer, and the membrane protein is a hemisphere of effective radius R(e) with center on the bilayer e...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(95)79909-X
更新日期：1995-08-01 00:00:00
abstract：:FKBP12 was removed from ryanodine receptors (RyRs) by incubation of rabbit skeletal muscle terminal cisternae membranes with rapamycin. The extent of FKBP12 removal was estimated by immunostaining Western blots of terminal cisternae proteins. Single FKBP12-depleted RyR channels, incorporated into planar lipid bilayers...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(97)78654-5
更新日期：1997-01-01 00:00:00
abstract：:Air dried films of purple membranes (PM) from Halobacterium halobium containing the photochromic protein bacteriorhodopsin (BR) were prepared and the BR-photocycle of this material analyzed. The absorption maxima of the initial state B (lambda(max) = 570 nm) and the photochemical intermediate M (lambda(max) = 412 nm),...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(90)82355-9
更新日期：1990-07-01 00:00:00
abstract：:We have previously observed that the hydrophobic polyelectrolyte poly(2-ethylacrylic acid) solubilizes lipid membranes in a pH-dependent manner, and we have exploited this phenomenon to prepare lipid vesicles that release their contents in response to pH, light, or glucose (Thomas, J. L., and D. A. Tirrell. Acc. Chem....
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(94)80575-2
更新日期：1994-09-01 00:00:00
abstract：:The molecular motor protein myosin VI moves toward the minus-end of actin filaments with a step size of 30-36 nm. Such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographic...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2011.05.010
更新日期：2011-06-22 00:00:00
abstract：:To characterize elastic properties and geometrical parameters of individual, whole myosin molecules during their interaction with actin we sparsely adsorbed myosin molecules to nanometer-sized microspheres. Thermally driven position fluctuations of these microspheres were recorded with the three-dimensional detection ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.104.047795
更新日期：2005-01-01 00:00:00
abstract：:This paper describes the relation between the quantum yield of photosynthesis in the red alga Porphyridium cruentum, and the spectral composition of light, changed by filtering white light through aqueous phycobilin solutions of increasing optical density. At sufficiently high densities of the filter solution, no meas...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/s0006-3495(60)86876-2
更新日期：1960-09-01 00:00:00
abstract：:A computational analysis of d(GGGGTTTTGGGG)(2) guanine quadruplexes containing either lateral or diagonal four-thymidine loops was carried out using molecular dynamics (MD) simulations in explicit solvent, locally enhanced sampling (LES) simulations, systematic conformational search, and free energy molecular-mechanic...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.103.034751
更新日期：2004-07-01 00:00:00
abstract：:Microbial capsules are important for virulence, but their architecture and physical properties are poorly understood. The human pathogenic fungus Cryptococcus neoformans has a large polysaccharide capsule that is necessary for virulence and is the target of protective antibody responses. To study the C. neoformans cap...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2009.04.043
更新日期：2009-08-19 00:00:00
abstract：:Gaining information about receptor profiles on cells, and subsequently finding the most efficient ligands for these signaling receptors, remain challenging tasks in stem cell and cancer research as well as drug development. We introduce a live-cell method with great potential in both screening for surface receptors an...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2013.10.013
更新日期：2013-12-17 00:00:00
abstract：:The conformational deformability of nucleic acids can influence their function and recognition by proteins. A class of DNA binding proteins including the TATA box binding protein binds to the DNA minor groove, resulting in an opening of the minor groove and DNA bending toward the major groove. Explicit solvent molecul...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.106.083816
更新日期：2006-08-01 00:00:00
abstract：:We have used fluorescence-quenching measurements to characterize the partitioning of a variety of indolyl-labeled phospho- and sphingolipids between gel or liquid-ordered and liquid-disordered lipid domains in several types of lipid bilayers where such domains coexist. In both cholesterol-free and cholesterol-containi...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(03)74857-7
更新日期：2003-01-01 00:00:00
abstract：:The two-microelectrode, voltage-clamp technique was applied to rabbit cardiac Purkinje fibers to study the interaction of tetrodotoxin (TTX) with the slowly inactivating Na current. Binding of TTX to rested, inactivated, and activated channels was estimated by measuring the relative decrease of current at the beginnin...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(87)83315-5
更新日期：1987-01-01 00:00:00
abstract：:The interplay between epigenetic modification and chromatin compaction is implicated in the regulation of gene expression, and it comprises one of the most fascinating frontiers in cell biology. Although a complete picture is still lacking, it is generally accepted that the differentiation of embryonic stem (ES) cells...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2012.10.015
更新日期：2012-11-21 00:00:00
abstract：:Ca2+ release from the endoplasmic reticulum (ER) contributes to Ca2+ transients in frog sympathetic ganglion neurons. Here we use video-rate confocal fluo-4 fluorescence imaging to show that single action potentials reproducibly trigger rapidly rising Ca2+ transients at 1-3 local hot spots within the peripheral ER-ric...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(04)74094-1
更新日期：2004-01-01 00:00:00
abstract：:Thermal inactivation of T(4) and lambda bacteriophage shows two components of differing sensitivity are present. These cannot be interpreted as owing to nucleic acid and protein. One protein function-the inhibition of radiation-induced DNA degradation-is lost with quite different thermal kinetics. lambda heated in the...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(71)86195-7
更新日期：1971-01-01 00:00:00
abstract：:We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotatin...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(98)77908-1
更新日期：1998-04-01 00:00:00
abstract：:Bioluminescence rhythms from cellular reporters have become the most common method used to quantify oscillations in circadian gene expression. These experimental systems can reveal phase and amplitude change resulting from circadian disturbances, and can be used in conjunction with mathematical models to lend further ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2014.10.026
更新日期：2014-12-02 00:00:00
abstract：:The interactions between vitamin-A and beta-lactoglobulin have been investigated. We have found that two different complexes can be formed: one involving vitamin-A, and one involving a derivative of vitamin-A that most probably has a retro-beta-ionylidene structure. Room temperature absorption spectra for these comple...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(79)85192-9
更新日期：1979-12-01 00:00:00
abstract：:VP16, a protein encoded by herpes simplex virus, has a well-characterized 78 amino acid acidic activation domain. When tethered to DNA, tandem repeats of an eight amino acid motif taken from this region stimulate the transcription of a nearby gene. This work addresses how these minimal activation motifs interact with ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(98)77640-4
更新日期：1998-10-01 00:00:00
abstract：:Fluorescent labels are often used in bioassays as a means to detect and characterize ligand-receptor binding. This is due in part to the inherently high sensitivity of fluorescence-based technology and the relative accessibility of the technique. There is often little concern raised as to whether or not the fluorescen...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.107.127688
更新日期：2008-07-01 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 presence of tryptophan residues as intrinsic fluorophores in most proteins makes them an obvious choice for fluorescence spectroscopic analyses of such proteins. Membrane proteins have been reported to have a significantly higher tryptophan content than soluble proteins. The role of tryptophan residues in the stru...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(97)78116-5
更新日期：1997-08-01 00:00:00
abstract：:Skeletal muscle contraction is a canonical example of motor-driven force generation. Despite the long history of research in this topic, a mechanistic explanation of the collective myosin force generation is lacking. We present a theoretical model of muscle contraction based on the conformational movements of individu...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.104.056846
更新日期：2005-06-01 00:00:00
abstract：:A kinetic model is proposed to reproduce the time courses of the concentration change in paused leader RNA, terminated leader RNA, and readthrough RNA in the single-round transcription experiments on trp leader region of Escherichia coli and its mutants, L132, L75, and L75L135 (Winkler, M. E., and C. Yanofsky, 1981, B...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(87)83362-3
更新日期：1987-03-01 00:00:00
abstract：:We have used identified neurons from the abdominal ganglion of the mollusc Aplysia to construct and analyze two circuits in vitro. Each of these circuits was capable of producing two patterns of persistent activity; that is, they had bistable output states. The output could be switched between the stable states by a b...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(90)82591-1
更新日期：1990-04-01 00:00:00
abstract：:Nonbleachable rhodopsins containing retinal moieties with fixed 11-ene structures have been prepared. When the nonbleachable rhodopsin analogue corresponding to the natural pigment was flash-photolysed at 20.8 degrees C, no absorption changes occurred at the monitoring wavelengths of 380, 480, and 580 nm for the time ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(81)84809-6
更新日期：1981-08-01 00:00:00
