2,540 research outputs found
THERMAL DENATURATION OF MONOMERIC AND TRIMERIC PHYCOCYANINS STUDIED BY STATIC AND SPECTROSCOPY POLARIZED TIME-RESOLVED FLUORESCENCE
C-Phycocyanin (PC) and allophycocyanin (APC). as well as the a-subunit of PC. have been
isolated from the blue-green alga (cyanobacterium). Spirulina platensis. The effects of partial thermal
denaturation of PC and of its state of aggregation have been studied by ps time-resolved, polarized
fluorescence spectroscopy. All measurements have been performed under low photon fluxes (< 10’ ’
photonsipulse x cm’) to minimize singlet-singlet annihilation processes. A complex decay is obtained
under most conditions, which can be fitted satisfactorily with a bi-exponential (7’ = 70400 ps. T? =
1000-3000 ps) for both the isotropic and the polarized part, but with different intensities and time
constants for the two decay curves. The data are interpreted in the frameworkof the model first developed
by Teak and Dale (Biochern. J. 116, 161 (1970)], which divides the spectroscopically different
chromophores in (predominantly) sensitizing (s) and fluorescing U, ones. If one assumes temperature
dependent losses in the energy transfer from the s to the f and between f chromophores. both the
biexponential nature of the isotropic fluorescence decay and the polarization data can be rationalized. In
the isotropic emission (corresponding to the population of excited states) the short lifetime is related to the
s-,f transfer. the longer one to the “free“ decay of the final acceptor(s) (= f). The polarized part is
dominated by an extremely short decay time. which is related to s+f transfer, as well as to resonance
transfer between the f-chromophores
Picosecond time-resolved, polarized fluorescence decay of phycobilisomes and constituent biliproteins isolated from Mastigocladus laminosus
FÖRSTER TRANSFER CALCULATIONS BASED ON CRYSTAL STRUCTURE DATA FROM Agmenellum quadruplicatum C-PHYCOCYANIN
Excitation energy transfer in C-phycocyanin is modeled using the Forster inductive resonance mechanism. Detailed calculations are carried out using coordinates and orientations of the chromophores derived from X-ray crystallographic studies of C-phycocyanin from two different species (Schirmer et al, J. Mol. Biol. 184, 257–277 (1985) and ibid., 188, 651-677 (1986)). Spectral overlap integrals are estimated from absorption and fluorescence spectra of C-phycocyanin of Mastigocladus laminosus and its separated subunits. Calculations are carried out for the β-subunit, αβ-monomer, (αβ)3-trimer and (αβ)0-hexamer species with the following chromophore assignments: β155 = 's’(sensitizer), β84 =‘f (fluorescer) and α84 =‘m’(intermediate):]:. The calculations show that excitation transfer relaxation occurs to 3=98% within 200 ps in nearly every case; however, the rates increase as much as 10-fold for the higher aggregates. Comparison with experimental data on fluorescence decay and depolarization kinetics from the literature shows qualitative agreement with these calculations. We conclude that Forster transfer is sufficient to account for all of the observed fluorescence properties of C-phycocyanin in aggregation states up to the hexamer and in the absence of linker polypeptides
Picosecond time-resolved fluorescence of phycobiliproteins
The α- and β-subunits of C-phycocyanin from Mastigocladus laminosus were prepared according to revised procedures. Both subunits are isolated as dimers, which can be dissociated into monomers with detergent mixtures. The fluorescence decay kinetics are similar for the respective monomers and dimers. In no case could they be fitted by only one (α-subunit) or two exponentials (β-subunit) which are predicted by theory for samples with a unique chromophore—protein arrangement containing one and two chromophores, respectively. It is suggested that there exists a heterogeneity among the chromophores of the subunits, which may persist in the highly aggregated complexes present in cyanobacterial antennas
Competing Patterns of Signaling Activity in Dictyostelium discoideum
Quantitative experiments are described on spatio-temporal patterns of
coherent chemical signaling activity in populations of {\it Dictyostelium
discoideum} amoebae. We observe competition between spontaneously firing
centers and rotating spiral waves that depends strongly on the overall cell
density. At low densities, no complete spirals appear and chemotactic
aggregation is driven by periodic concentric waves, whereas at high densities
the firing centers seen at early times nucleate and are apparently entrained by
spiral waves whose cores ultimately serve as aggregation centers. Possible
mechanisms for these observations are discussed.Comment: 10 pages, RevTeX, 4 ps figures, accepted in PR
On the interpretation of spin-polarized electron energy loss spectra
We study the origin of the structure in the spin-polarized electron energy
loss spectroscopy (SPEELS) spectra of ferromagnetic crystals. Our study is
based on a 3d tight-binding Fe model, with constant onsite Coulomb repulsion U
between electrons of opposite spin. We find it is not the total density of
Stoner states as a function of energy loss which determines the response of the
system in the Stoner region, as usually thought, but the densities of Stoner
states for only a few interband transitions. Which transitions are important
depends ultimately on how strongly umklapp processes couple the corresponding
bands. This allows us to show, in particular, that the Stoner peak in SPEELS
spectra does not necessarily indicate the value of the exchange splitting
energy. Thus, the common assumption that this peak allows us to estimate the
magnetic moment through its correlation with exchange splitting should be
reconsidered, both in bulk and surface studies. Furthermore, we are able to
show that the above mechanism is one of the main causes for the typical
broadness of experimental spectra. Finally, our model predicts that optical
spin waves should be excited in SPEELS experiments.Comment: 11 pages, 7 eps figures, REVTeX fil
Nonequilibrium effects in DNA microarrays: a multiplatform study
It has recently been shown that in some DNA microarrays the time needed to
reach thermal equilibrium may largely exceed the typical experimental time,
which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81,
012901 (2010)). In this paper we discuss how this breakdown of thermodynamic
equilibrium could be detected in microarray experiments without resorting to
real time hybridization data, which are difficult to implement in standard
experimental conditions. The method is based on the analysis of the
distribution of fluorescence intensities I from different spots for probes
carrying base mismatches. In thermal equilibrium and at sufficiently low
concentrations, log I is expected to be linearly related to the hybridization
free energy with a slope equal to , where is
the experimental temperature and R is the gas constant. The breakdown of
equilibrium results in the deviation from this law. A model for hybridization
kinetics explaining the observed experimental behavior is discussed, the
so-called 3-state model. It predicts that deviations from equilibrium yield a
proportionality of to . Here, is an
effective temperature, higher than the experimental one. This behavior is
indeed observed in some experiments on Agilent arrays. We analyze experimental
data from two other microarray platforms and discuss, on the basis of the
results, the attainment of equilibrium in these cases. Interestingly, the same
3-state model predicts a (dynamical) saturation of the signal at values below
the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl
Repurposing a photosynthetic antenna protein as a super-resolution microscopy label
Techniques such as Stochastic Optical Reconstruction Microscopy (STORM) and Structured Illumination Microscopy (SIM) have increased the achievable resolution of optical imaging, but few fluorescent proteins are suitable for super-resolution microscopy, particularly in the far-red and near-infrared emission range. Here we demonstrate the applicability of CpcA, a subunit of the photosynthetic antenna complex in cyanobacteria, for STORM and SIM imaging. The periodicity and width of fabricated nanoarrays of CpcA, with a covalently attached phycoerythrobilin (PEB) or phycocyanobilin (PCB) chromophore, matched the lines in reconstructed STORM images. SIM and STORM reconstructions of Escherichia coli cells harbouring CpcA-labelled cytochrome bd 1 ubiquinol oxidase in the cytoplasmic membrane show that CpcA-PEB and CpcA-PCB are suitable for super-resolution imaging in vivo. The stability, ease of production, small size and brightness of CpcA-PEB and CpcA-PCB demonstrate the potential of this largely unexplored protein family as novel probes for super-resolution microscopy
Virtual-crystal approximation that works: Locating a composition phase boundary in Pb(Zr_{1-x}Ti_3)O_3
We present a new method for modeling disordered solid solutions, based on the
virtual crystal approximation (VCA). The VCA is a tractable way of studying
configurationally disordered systems; traditionally, the potentials which
represent atoms of two or more elements are averaged into a composite atomic
potential. We have overcome significant shortcomings of the standard VCA by
developing a potential which yields averaged atomic properties. We perform the
VCA on a ferroelectric oxide, determining the energy differences between the
high-temperature rhombohedral, low-temperature rhombohedral and tetragonal
phases of Pb(Zr_{1-x}Ti_x)O_3 at x=0.5 and comparing these results to
superlattice calculations and experiment. We then use our new method to
determine the preferred structural phase at x=0.4. We find that the
low-temperature rhombohedral phase becomes the ground state at x=0.4, in
agreement with experimental findings.Comment: 5 pages, no figure
A generalized Tullock contest
We construct a generalized Tullock contest under complete information where contingent upon winning or losing, the payoff of a player is a linear function of prizes, own effort, and the effort of the rival. This structure nests a number of existing contests in the literature and can be used to analyze new types of contests. We characterize the unique symmetric equilibrium and show that small parameter modifications may lead to substantially different types of contests and hence different equilibrium effort levels
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