Abstract:
:Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically encoded FRET-based biosensors. A variety of procedures have been described for measuring FRET efficiency or the relative abundance of donor-acceptor complexes, based on analysis of the donor fluorescence lifetime or the spectrally resolved fluorescence intensity. The latter methods are preferable if one wants to not only quantify the apparent FRET efficiencies but also calculate donor-acceptor stoichiometry and observe fast dynamic changes in the interactions among donor and acceptor molecules in live cells. This review focuses on a comparison of the available intensity-based approaches used to measure FRET. We discuss their strengths and weaknesses in terms of FRET quantification, and provide several examples of biological applications.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Zeug A,Woehler A,Neher E,Ponimaskin EGdoi
10.1016/j.bpj.2012.09.031subject
Has Abstractpub_date
2012-11-07 00:00:00pages
1821-7issue
9eissn
0006-3495issn
1542-0086pii
S0006-3495(12)01072-7journal_volume
103pub_type
杂志文章,评审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::The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes. Because Vm also plays a role in signal transduction, measuring it is of great interest. Over the years, a variety...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.030
更新日期:2020-01-07 00:00:00
abstract::ATP-sensitive K(+)-channels link metabolism and excitability in neurons, myocytes, and pancreatic islets. Mutations in the pore-forming subunit (Kir6.2; KCNJ11) cause neonatal diabetes, developmental delay, and epilepsy by decreasing sensitivity to ATP inhibition and suppressing electrical activity. Mutations of resid...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.138685
更新日期:2008-11-15 00:00:00
abstract::Fluorescence correlation spectroscopy (FCS) is a sensitive and widely used technique for measuring diffusion. FCS data are conventionally modeled with a finite number of diffusing components and fit with a least-square fitting algorithm. This approach is inadequate for analyzing data obtained from highly heterogeneous...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75006-1
更新日期:2003-03-01 00:00:00
abstract::A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-con...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78205-5
更新日期:1997-10-01 00:00:00
abstract::Microsecond rotational motions of nitroxide spin labels are measured primarily with saturation transfer electron paramagnetic resonance (ST-EPR). In the present study we have used model system experiments to quantitatively evaluate different ST-EPR spectral parameters, both in-phase and out-of-phase, with an emphasis ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83720-1
更新日期:1986-04-01 00:00:00
abstract::The molecular code of specific DNA recognition by proteins as a paradigm in molecular biology remains an unsolved puzzle primarily because of the subtle interplay between direct protein-DNA interaction and the indirect contribution from water and ions. Transformation of the nonspecific, low affinity complex to a speci...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.063263
更新日期:2005-08-01 00:00:00
abstract::The effect of cross-bridge clustering and head-head competition on the mechanical response of skeletal muscle under equilibrium conditions is considered. For this purpose, the recent multiple site equilibrium cross-bridge model of Schoenberg (Schoenberg, M., 1985, Biophys. J., 48:467-475) is extended in accordance wit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(86)83528-7
更新日期:1986-11-01 00:00:00
abstract::A nitroxide spin label attached to the C-terminus of the channel forming peptide alamethicin produces an enhancement of the nuclear spin-lattice relaxation rates of peptide protons as a result of both intermolecular and intramolecular magnetic dipole-dipole interactions. The intermolecular contribution provides eviden...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80667-8
更新日期:1994-11-01 00:00:00
abstract::Isopycnic banding of Chinese hamster line CHO cells in Ficoll gradients shows that a population in balanced, exponential growth is very homogeneous with respect to density, the coefficient of variation of the density distribution spectrum being less than 5% of the mean reduced density (i.e. density minus one). Similar...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(70)86325-1
更新日期:1970-07-01 00:00:00
abstract::We continue in this paper the presentation of theoretical and experimental methods for the joint refinement of neutron and x-ray lamellar diffraction data for the analysis of fluid (L alpha phase) bilayer structure (Wiener, M. C., and S. H. White. 1991 a, b, c. Biophys. J. 59:162-173 and 174-185; Biochemistry. 30:6997...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81848-9
更新日期:1992-02-01 00:00:00
abstract::Viral infection begins with the binding of a virus to a specific target on the surface of the host cell, followed by viral genome delivery into the host and a continuation of the infection process. Before binding occurs, the virus must first find its receptor by a process whose details are largely unknown. We applied ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.014
更新日期:2011-06-22 00:00:00
abstract::Diffusional encounters between a dumbbell model of a cleft enzyme and a dumbbell model of an elongated ligand are simulated by Brownian dynamics. The simulations take into account electrostatic and hydrodynamic interactions between the molecules. It is shown that the primary effect of inclusion of hydrodynamic interac...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79874-5
更新日期:1995-07-01 00:00:00
abstract::Sarcomere lengths, cell widths, indices of stiffness, and striation pattern uniformity were determined from radially compressed isolated adult cardiac myocytes from the rat. Single cells were bathed in a series of relaxing solutions containing 0-15% concentrations of nonpenetrating long chain polymers PVP-40 and dextr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82467-X
更新日期:1990-11-01 00:00:00
abstract::Coarse-grained (CG) models of biomolecules have recently attracted considerable interest because they enable the simulation of complex biological systems on length-scales and timescales that are inaccessible for atomistic molecular dynamics simulation. A CG model is defined by a map that transforms an atomically detai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.139626
更新日期:2008-12-01 00:00:00
abstract::Choice of network topology for gene regulation has been a question of interest for a long time. How do simple and more complex topologies arise? In this work, we analyze the topology of the marRAB operon in Escherichia coli, which is associated with control of expression of genes associated with conferring resistance ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.08.017
更新日期:2015-10-06 00:00:00
abstract::Recent suggestions of nanoscale heat confinement on the surface of synthetic and biogenic magnetic nanoparticles during heating by radio frequency-alternating magnetic fields have generated intense interest because of the potential utility of this phenomenon for noninvasive control of biomolecular and cellular functio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.01.028
更新日期:2020-03-24 00:00:00
abstract::A variety of experiments suggest that membrane proteins are important targets of anesthetic molecules, and that ion channels interact differently with anesthetics in their open and closed conformations. The availability of an open and a closed structural model for the KirBac1.1 potassium channel has made it possible t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.119958
更新日期:2008-06-01 00:00:00
abstract::The structure and dynamics of a large segment of Ste2p, the G-protein-coupled alpha-factor receptor from yeast, were studied in dodecylphosphocholine (DPC) micelles using solution NMR spectroscopy. We investigated the 73-residue peptide EL3-TM7-CT40 consisting of the third extracellular loop 3 (EL3), the seventh trans...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.103770
更新日期:2007-07-15 00:00:00
abstract::A sample preparation method using spherical glass ampoules has been used to achieve 1.5-Hz resolution in 1H magic-angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of aqueous multilamellar dispersions of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (P...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77205-X
更新日期:1999-01-01 00:00:00
abstract::Numerous isotypes of the structural protein tubulin have now been characterized in various organisms and their expression offers a plausible explanation for observed differences affecting microtubule function in vivo. While this is an attractive hypothesis, there are only a handful of studies demonstrating a direct in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.132233
更新日期:2008-08-01 00:00:00
abstract::Recent experimental evidence from a number of preparations indicates that sodium channel inactivation may be intrinsically voltage sensitive. Intrinsically voltage sensitive inactivation should produce a charge movement. Crayfish giant axons provide a unique opportunity to reexamine the slower components of gating cur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84434-8
更新日期:1983-03-01 00:00:00
abstract::The three phases of dipalmitoylphosphatidylcholine-water dispersions, occurring below the main transition are studied by a moment analysis of 1H-nuclear magnetic resonance (NMR) spectra. The subtransition, recently detected by Chen, S. C., J. M. Sturtevant, and B. J. Gaffney, 1980, Pro. Natl. Acad. Sci. USA, 77:5060-5...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(83)84396-3
更新日期:1983-06-01 00:00:00
abstract::Two different stereoisomers of the dioxolane-linked gramicidin A (gA) channels were individually synthesized (the SS and RR dimers;. Science. 244:813-817). The structural differences between these dimers arise from different chiralities within the dioxolane linker. The SS dimer mimics the helicity and the inter- and i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77084-0
更新日期:1999-11-01 00:00:00
abstract::We have measured the fluorescence spectra of a single fluorophore attached to a single protein molecule in aqueous solution using a total internal reflection fluorescence microscope. The most reactive cysteine residue of myosin subfragment-1 (S1) was labeled with tetramethylrhodamine. The spectral shift induced by a c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76708-7
更新日期:2000-03-01 00:00:00
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...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77962-7
更新日期:1998-05-01 00:00:00
abstract::Critical to biological processes such as secretion and transport, protein-lipid interactions within the membrane and at the membrane-water interface still raise many questions. Here we examine the role of lipid headgroups in these interactions by using gramicidin A (gA) channels in planar bilayers as a probe. We show ...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.120261
更新日期:2008-02-15 00:00:00
abstract::Isothermal (27 degrees C) phase behavior of dimyristoyl phosphatidyl choline-cholesterol mixtures at various osmotic pressures and cholesterol contents was investigated by means of isothermal sorption microcalorimetry and (2)H-nuclear magnetic resonance. The calorimetric method allows for simultaneous measurement of t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)73963-5
更新日期:2002-10-01 00:00:00
abstract::From the study of the kinetics of the fluorescence self-quenching of pyrene in multilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) in the fluid phase we obtain the molecular diffusion parameters, diffusion coefficients, and activation energies for lateral diffusion for three probes: 1-palmitoy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76062-6
更新日期:2001-02-01 00:00:00
abstract::Human apolipoprotein E (apoE) is a 299-amino-acid protein with a molecular weight of 34 kDa. The difference between the apoE3 and apoE4 isoforms is a single residue substitution involving a Cys-Arg replacement at residue 112. ApoE4 is positively associated with atherosclerosis and late-onset and sporadic Alzheimer's d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.046813
更新日期:2005-01-01 00:00:00