Abstract:
:A recipe is given for designing theoretical models for donor-acceptor systems in which fluorescence energy transfer and motion takes place simultaneously. This recipe is based on the idea that a system exhibiting both motion and fluorescence energy transfer can be modeled by specifying a number of "states" and the rates of transitions between them. A state in this context is a set of specific coordinates and conditions that describe the system at a certain moment in time. As time goes on, the coordinates and conditions for the system change, and this evolution can be described as a series of transitions from one state to the next. The recipe is applied to a number of example systems in which the donors and/or acceptors undergo either rotational or translational motion. In each example, fluorescence intensities and anisotropies for the donor and acceptor are calculated from solutions of eigensystems. The proposed method allows for analyzing time-resolved fluorescence energy transfer data without restrictive assumptions for motional averaging regimes and the orientation factor. It is shown that the fluorescence quantities depend on the size of the motional step (i.e., on the number of states), only if fluorescence energy transfer occurs. This finding indicates that fluorescence energy transfer studies may reveal whether the dynamics of a system (e.g., a protein) is better described in terms of transitions between a relatively small number of discrete states (jumping) or a large number of dense states (diffusion).
journal_name
Biophys Jjournal_title
Biophysical journalauthors
van der Meer BW,Raymer MA,Wagoner SL,Hackney RL,Beechem JM,Gratton Edoi
10.1016/S0006-3495(93)81490-5subject
Has Abstractpub_date
1993-04-01 00:00:00pages
1243-63issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(93)81490-5journal_volume
64pub_type
杂志文章abstract::The Ca(2+) permeability of N-methyl-D-aspartate receptor (NMDA-R) channels was studied in human embryonic kidney cells transfected with the NR1-NR2A subunit combination. To determine the fractional Ca(2+) current (P(f)), measurements of fura-2-based Ca(2+) influx and whole-cell currents were made in symmetrical monova...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79782-5
更新日期:1996-05-01 00:00:00
abstract::Orientational order parameters of two diphenylhexatriene (DPH)-based fluorescent probes, 2-(3-(diphenylhexatrienyl)propanoyl)-1-hexadecanoyl-sn-glycero-3-p hosphocholine (DPHpPC) and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH), in dipalmitoylphosphatidylcholine (DPPC) Langmuir-Blodgett monolayers...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78908-2
更新日期:1997-06-01 00:00:00
abstract::Measurements were made of exchange rates of oxygen, carbon dioxide, and krypton-85 with blood at 37.5 degrees C. Gas transfer took place across a 1 mil silicone rubber membrane. The blood was in a rotating disk boundary layer flow, and the controlling resistance to transfer was the concentration boundary layer. Measur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(67)86624-4
更新日期:1967-11-01 00:00:00
abstract::Proteolysis of the multimeric blood coagulation protein von Willebrand Factor (VWF) by ADAMTS13 is crucial for prevention of microvascular thrombosis. ADAMTS13 cleaves VWF within the mechanosensitive A2 domain, which is believed to open under shear flow. In this study, we combine fluorescence correlation spectroscopy ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.12.023
更新日期:2016-02-02 00:00:00
abstract::We have analyzed repellent signal processing in Escherichia coli by flash photorelease of leucine from photolabile precursors. We found that 1). response amplitudes of free-swimming cell populations increased with leucine jump concentration, with an apparent Hill coefficient of 1.3 and a half-maximal dose of 14.4 micr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.103.033043
更新日期:2004-06-01 00:00:00
abstract::We investigate the validity of continuum electrostatics in the gramicidin A channel using a recently determined high-resolution structure. The potential and electric field acting on ions in and around the channel are computed by solving Poisson's equation. These are then used in Brownian dynamics simulations to obtain...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)73905-2
更新日期:2002-09-01 00:00:00
abstract::Forces applied by cells to substrates can be measured using soft substrates with embedded displacement markers. Traction forces are retrieved from microscopic images by determining the displacements of these markers and fitting the generating forces. Here we show that using elastic films of 5-10-microm thickness one c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.111328
更新日期:2007-11-01 00:00:00
abstract::In a recent publication, the structural details of an interaction between the Rhodobacter sphaeroides reaction center and the anionic phospholipid diphosphatidyl glycerol (cardiolipin) were described (K. E. McAuley, P. K. Fyfe, J. P. Ridge, N. W. Isaacs, R. J. Cogdell, and M. R. Jones, 1999, Proc. Natl. Acad. Sci. U.S...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76112-7
更新日期:2001-03-01 00:00:00
abstract::The single photon response in vertebrate phototransduction is highly reproducible despite a number of random components of the activation cascade, including the random activation site, the random walk of an activated receptor, and its quenching in a random number of steps. Here we use a previously generated and tested...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.114058
更新日期:2008-05-01 00:00:00
abstract::Ubiquinol cytochrome c oxidoreductase (bc1 complex) serves as an important electron junction in many respiratory systems. It funnels electrons coming from NADH and ubiquinol to cytochrome c, but it is also capable of producing significant amounts of the free radical superoxide. In situ and in other experimental system...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.08.018
更新日期:2017-10-03 00:00:00
abstract::A number of models proposed to account for the sodium conductance changes are shown to fall into two classes. The Hodgkin-Huxley (HH) model falls into a class (I) in which the conductance depends on two or more independent variables controlled by independent processes. The Mullins, Hoyt, and Goldman models fall into c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(68)86540-3
更新日期:1968-10-01 00:00:00
abstract::The photochemical reaction process of bacteriorhodopsin in the nanosecond time range (-120-860 ns) was measured in the 1400-900 cm-1 region with an improved time resolved dispersive-type infrared spectrometer. The system is equipped with a newly developed detection unit whose instrumental response to a 5-ns laser puls...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80386-3
更新日期:1995-05-01 00:00:00
abstract::The formation and function of the mitotic spindle depends upon force generation by multiple molecular motors and by the dynamics of microtubules, but how these force-generating mechanisms relate to one another is unclear. To address this issue we have modeled the separation of spindle poles as a function of time durin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74895-4
更新日期:2003-02-01 00:00:00
abstract::The glycocalyx is a thick coat of proteins and carbohydrates on the outer surface of all eukaryotic cells. Overproduction of large, flexible or rod-like biopolymers, including hyaluronic acid and mucins, in the glycocalyx strongly correlates with the aggression of many cancer types. However, theoretical frameworks to ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.12.023
更新日期:2019-02-19 00:00:00
abstract::We report detection and quantification of ultraviolet (UV) damage in DNA at a single molecule level by atomic force microscopy (AFM). By combining the supercoiled plasmid relaxation assay with AFM imaging, we find that high doses of medium wave ultraviolet (UVB) and short wave ultraviolet (UVC) light not only produce ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.108209
更新日期:2007-09-01 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::Membrane fusion proceeds via formation of intermediate nonbilayer structures. The stalk model of fusion intermediate is commonly recognized to account for the major phenomenology of the fusion process. However, in its current form, the stalk model poses a challenge. On one hand, it is able to describe qualitatively th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75450-7
更新日期:2002-02-01 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::Molecular dynamics simulations were performed to describe the function of the ion-channel-forming toxin α-hemolysin (αHL) in lipid membranes that were composed of either 1,2-diphytanoyl-sn-glycero-3-phospho-choline or 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-choline. The simulations highlight the importance of lipid ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.09.009
更新日期:2018-11-06 00:00:00
abstract::The light-harvesting complex I (LH-I) of Rhodobacter sphaeroides has been modeled computationally as a hexadecamer of alphabeta-heterodimers, based on a close homology of the heterodimer to that of light-harvesting complex II (LH-II) of Rhodospirillum molischianum. The resulting LH-I structure yields an electron densi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77558-7
更新日期:1998-08-01 00:00:00
abstract::Transcription factor (TF) proteins rapidly locate unique target sites on long genomic DNA molecules--and bind to them--during gene regulation. The search mechanism is known to involve a combination of three-dimensional diffusion through the bulk of the cell and one-dimensional sliding diffusion along the DNA. It is be...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.129825
更新日期:2008-08-01 00:00:00
abstract::Recent studies have indicated that the tip links and kinocilial links of sensory hair bundles in the inner ear have similar properties and share a common epitope, and that cadherin 23 may also be a component of each link type. Transmission electron microscopy was therefore used to study and compare the fine structure ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.049031
更新日期:2004-12-01 00:00:00
abstract::The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.02.020
更新日期:2020-05-05 00:00:00
abstract::The analysis of single-molecule fluorescence resonance energy transfer (FRET) trajectories has become one of significant biophysical interest. In deducing the transition rates between various states of a system for time-binned data, researchers have relied on simple, but often arbitrary methods of extracting rates fro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.082487
更新日期:2006-09-01 00:00:00
abstract::The electrostatic free energies of native and acetylated lysozymes were computed by the fixed charge model (Tanford, C., and J. G. Kirkwood, 1957, J. Am. Chem. Soc., 79:5333-5339). For each computation, the charges were transformed into a sphere of fixed radius without changing their depths or the distance between cha...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84302-1
更新日期:1983-12-01 00:00:00
abstract::Concentrated solutions of bovine beta-lactoglobulin were studied using osmotic stress and rheological techniques. At pH 6.0 and 8.0, the osmotic pressure was largely independent of NaCl concentration and could be described by a hard sphere equation of state. At pH 5.1, close to the isoelectric point, the osmotic press...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.064246
更新日期:2005-08-01 00:00:00
abstract::A pulsed source neutron spectrometer has been used to measure vibrational spectra (20-4000 cm-1) of dry and hydrated type I collagen fibers, and of two model polypeptides, polyproline II and (prolyl-prolyl-glycine)10, at temperatures of 30 and 120 K. the collagen spectra provide the first high resolution neutron views...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79942-8
更新日期:1995-08-01 00:00:00
abstract::How do Ca channels conduct Ca ions during the cardiac action potential? We attempt to answer this question by applying a two-microelectrode technique, previously used for Na and K currents, in which we record the patch current and the action potential at the same time (Mazzanti, M., and L. J. DeFelice. 1987. Biophys. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82448-6
更新日期:1990-10-01 00:00:00
abstract::The effect of agarose on nucleation of hen egg white lysozyme crystal was examined quantitatively using a temperature-jumping technique. For the first time, to our knowledge, the inhibition of agarose during the nucleation of lysozyme was quantified in two respects: a), the effect of increasing interfacial nucleation ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.135574
更新日期:2008-12-15 00:00:00
abstract::The impedance measured in a strip of heart tissue from the moth Hyalophora cecropia is fitted by circuit models of several configurations. The circuits include: (a) a single R-C circuit (b) a double R-C circuit (c) terminated transmission lines, and (d) a pattern of cells with cell-to-cell transmission paths. The last...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(74)70001-7
更新日期:1974-02-01 00:00:00