Abstract:
:A recent analysis of the normal modes of vibration of a ring formed by bringing together and sealing, with or without the addition of twist, the ends of rods that are straight when stress free is taken as the basis for a theory of the statistical thermodynamics of a canonical ensemble of DNA minicircles with specified linking number difference deltaLk and number N of base pairs. It is assumed that N corresponds to a circumference in the range of one or two persistence lengths. For such an ensemble, the theory yields an expression for the average writhe (Wr), which can be employed to calculate the free energy, entropy, and enthalpy of supercoiling, deltaGsc, deltaSsc, and deltaHsc. The results obtained for the dependence of deltaGsc on deltaLk and N are in accord with experimental observations of equilibrium distributions of topoisomers of plasmids with N approximately 200 bp.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Tobias Idoi
10.1016/S0006-3495(98)77962-7subject
Has Abstractpub_date
1998-05-01 00:00:00pages
2545-53issue
5eissn
0006-3495issn
1542-0086pii
S0006-3495(98)77962-7journal_volume
74pub_type
杂志文章abstract::The three-dimensional structure of chromatin affects DNA accessibility and is therefore a key regulator of gene expression. However, the path of the DNA between consecutive nucleosomes, and the resulting chromatin fiber organization remain controversial. The conformational space available for the folding of the nucleo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.11.040
更新日期:2010-03-17 00:00:00
abstract::Transmembrane osmotic gradients applied on large unilamellar 1-palmitoyl-2-oleoyl-phosphatidylcholine vesicles were used to modulate the potency of melittin to induce leakage. Melittin, an amphipathic peptide, changes the permeability of vesicles, as studied using the release of entrapped calcein, a fluorescent marker...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79622-4
更新日期:1996-02-01 00:00:00
abstract::Advances in biotechnology and computer science are providing the possibility to construct mathematical models for complex biological networks and systematically understand their properties. Traditional network identification approaches, however, cannot accurately recover the model parameters from the noisy laboratory ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74201-0
更新日期:2004-03-01 00:00:00
abstract::Imaging in any plane other than horizontal in a microscope typically requires a reconstruction from multiple optical slices that significantly decreases the spatial and temporal resolution that can be achieved. This can limit the precision with which molecular events can be detected, for example, at intercellular cont...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.143198
更新日期:2008-11-15 00:00:00
abstract::The prion protein (PrP), widely recognized to misfold into the causative agent of the transmissible spongiform encephalopathies, has previously been shown to bind to lipid membranes with binding influenced by both membrane composition and pH. Aside from the misfolding events associated with prion pathogenesis, PrP can...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.09.027
更新日期:2014-11-18 00:00:00
abstract::Surface and subsurface dynamics of Rat Basophilic Leukemia cells, a model system of stimulated secretion, were imaged using Scanning Force Microscopy (SFM) at a rate of 50-60 s/image. Cytoskeletal elements and organelles were tracked within quiescent cells and those activated after IgE receptor crosslinking. In additi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80964-6
更新日期:1994-05-01 00:00:00
abstract::Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.12.017
更新日期:2013-01-22 00:00:00
abstract::The four-way DNA (Holliday) junction is an important postulated intermediate in the process of genetic recombination. Earlier studies have suggested that the junction exists in two alternative conformations, depending upon the salt concentration present. At high salt concentrations the junction folds into a stacked X ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80765-9
更新日期:1994-01-01 00:00:00
abstract::Prions are pathological isoforms of the cellular prion protein that is responsible for transmissible spongiform encephalopathies (TSE). Cellular prion protein interacts with copper, Cu(II), through octarepeat and nonoctarepeat (non-OR) binding sites. The molecular details of Cu(II) coordination within the non-OR regio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.025
更新日期:2020-02-04 00:00:00
abstract::The cellular cytoplasm is a complex, heterogeneous environment (both spatially and temporally) that exhibits viscoelastic behavior. To further develop our quantitative insight into cellular transport, we analyze data sets of mRNA molecules fluorescently labeled with MS2-GFP tracked in real time in live Escherichia col...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.11.3208
更新日期:2017-02-07 00:00:00
abstract::Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R(∗)) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The class...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.05.050
更新日期:2014-09-02 00:00:00
abstract::Biological spread cells exist in a perpetually fluctuating state and therefore cannot be described in terms of a unique deterministic system. For modeling approaches to provide novel insight and uncover new mechanisms that drive cell behavior, a framework is required that progresses from traditional deterministic meth...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.11.007
更新日期:2018-12-18 00:00:00
abstract::We examined the state-, voltage-, and time dependences of interaction between 4-AP and a mammalian A-type K channel clone (rKv1.4) expressed in Xenopus oocytes using whole-cell and single-channel recordings. 4-AP blocked rKv1.4 from the cytoplasmic side of the membrane. The development of block required channel openin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80462-X
更新日期:1994-07-01 00:00:00
abstract::The effects of rigor and cycling cross-bridges on distributions of calcium (Ca) bound within sarcomeres of rabbit psoas muscle fibers were compared using electron probe x-ray microanalysis. Calcium in the overlap region of rigor fibers, after correction for that bound to thick filaments, was significantly higher than ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.093757
更新日期:2007-01-15 00:00:00
abstract::A growth cone is a motile structure at the tips of axons that is driven by the actin network and guides axon extension. Low actin adhesion to the substrate creates a stationary actin treadmill that allows leading-edge protrusion when adhesion increases in response to guidance cues. We use experimental measurements in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.03.003
更新日期:2012-04-04 00:00:00
abstract::Interactions of membrane anchored molecules such as glycolipids with a membrane surface are important in determining headgroup conformation. It is therefore essential to represent these membrane surface interactions in molecular modeling studies of glycolipids and other membrane bound molecules. We introduce here an e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81729-0
更新日期:1992-12-01 00:00:00
abstract::Proliferation of mammalian cells, even under conditions of unlimited growth, presents a complex problem because of the interaction of deterministic and stochastic processes. Division of the cell cycle into a finite number of parts establishes a multidimensional vector space. In this space an arbitrary culture can be r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86656-0
更新日期:1966-05-01 00:00:00
abstract::The muscle nicotinic receptor (AChR) is a pentamer of four different subunits, each of which contains four transmembrane domains (M1-M4). We recently showed that channel opening and closing rates of the AChR depend on a hydrogen bond involving a threonine at position 14' of the M4 domain in the alpha-subunit. To deter...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75541-0
更新日期:2002-04-01 00:00:00
abstract::Interactions between proteins are often sufficiently weak that their study through the use of conventional structural techniques becomes problematic. Of the few techniques capable of providing experimental measures of weak protein-protein interactions, perhaps the most useful is the second virial coefficient, B(22), w...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76042-0
更新日期:2001-02-01 00:00:00
abstract::Equations describing the movement of sugars during induced uphill transport were derived on the assumption of a simple carrier transport mechanism and subjected to experimental verification. Since there was good agreement between the experimental points and the theoretical curves, no changes in the original postulates...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(65)86726-1
更新日期:1965-07-01 00:00:00
abstract::Hybrid global optimization methods attempt to combine the beneficial features of two or more algorithms, and can be powerful methods for solving challenging nonconvex optimization problems. In this paper, novel classes of hybrid global optimization methods, termed alternating hybrids, are introduced for application as...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74905-4
更新日期:2003-02-01 00:00:00
abstract::We investigated the origins of greater clot rigidity associated with FXIIIa-dependent cross-linking. Fibrin clots were examined in which cross-linking was controlled through the use of two inhibitors: a highly specific active-center-directed synthetic inhibitor of FXIIIa, 1,3-dimethyl-4,5-diphenyl-2[2(oxopropyl)thio]i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77114-6
更新日期:1999-11-01 00:00:00
abstract::Microtubules are cytoskeletal filaments whose self-assembly occurs by abrupt switching between states of roughly constant growth and shrinkage, a process known as dynamic instability. Understanding the mechanism of dynamic instability offers potential for controlling microtubule-dependent cellular processes such as ne...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79953-2
更新日期:1995-09-01 00:00:00
abstract::We have identified two kinetically distinct modes of block, by lidocaine, of cardiac sodium channels, activated by batrachotoxin and incorporated into planar lipid bilayers. Here, we analyze the slow blocking mode which appears as a series of nonconducting events that increase in frequency and duration with increasing...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81043-9
更新日期:1993-07-01 00:00:00
abstract::Protein solubility in aqueous solutions depends in a complicated and not well understood way on pH, salt type, and salt concentration. Why for instance does the use of two different monovalent salts, potassium thiocyanate and potassium chloride, produce such different results? One important and previously neglected so...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74512-3
更新日期:2003-08-01 00:00:00
abstract::The conformation of single laminin molecules adsorbed on synthetic substrates is directly observed making use of the phase magnitude in tapping mode atomic force microscopy (AFM). With AFM, it is not possible to differentiate the proteins on the substrate if use is made of the height signal, since the roughness of the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.102491
更新日期:2007-07-01 00:00:00
abstract::To detect changes in capsid structure that occur when a preassembled bacteriophage T7 capsid both packages and cleaves to mature-size longer (concatameric) DNA, the kinetics and thermodynamics are determined here for the binding of the protein-specific probe, 1,1'-bi(4-anilino)naphthalene-5,5'-di-sulfonic acid (bis-AN...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81724-1
更新日期:1992-11-01 00:00:00
abstract::In the rabbit corneal stroma, the swelling pressure, P, has been reported to have an anomalous (negative) temperature coefficient, alpha P, contradicting traditional Donnan swelling theory. A parallel-plate, diffuse double layer Gouy-Chapman model was used to resolve this discrepancy. The present model incorporates th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82584-4
更新日期:1990-03-01 00:00:00
abstract::Bin/Amphiphysin/Rvs-homology (BAR) domains generate and sense membrane curvature by binding the negatively charged membrane to their positively charged concave surfaces. N-BAR domains contain an N-terminal extension (helix-0) predicted to form an amphipathic helix upon membrane binding. We determined the NMR structure...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.134155
更新日期:2008-11-01 00:00:00
abstract::Förster resonance energy transfer (FRET)-based biosensors for the quantitative analysis of intracellular signaling, including sensors for monitoring cyclic adenosine monophosphate (cAMP), are of increasing interest. The measurement of the donor/acceptor emission ratio in tandem biosensors excited at the donor excitati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.125666
更新日期:2008-12-01 00:00:00