Anthozoa red fluorescent protein in biosensing

The identification and cloning of a red fluorescent protein (DsRed) obtained from Anthozoa corals has provided an alternative to commonly used green fluorescent proteins (GFPs) in bioanalytical and biomedical research. DsRed in tandem with GFPs has enhanced the feasibility of multicolor labeling studies. Properties of DsRed, for example high photostability, red-shifted fluorescence emission, and stability to pH changes have proven valuable in its use as a fluorescent tag in cell-biology applications. DsRed has some limitations, however. Its slow folding and tendency to form tetramers have been a hurdle. Several different mutational studies have been performed on DsRed to overcome these problems. In this paper, applications of DsRed in biosensing, specifically in FRET/BRET assays, whole-cell assays, and in biosensors, is discussed. In the future, construction of DsRed mutants with unique characteristics will further expand its applications in bioanalysis.     

Calculations of the free energy of interaction of the c-Fos-c-Jun coiled coil: effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein-protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson-Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos-c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos-c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.     

Mass Spectrometric Analysis of Cyclotides from Clitoria ternatea: Xxx-Pro Bond Fragmentation as Convenient Diagnostic of Pro Residue Positioning

Cyclotides, a class of macrocyclic plant peptides, characterized by a cyclic backbone and three inter-locking disulfide bonds, may be divided into two major structural subfamilies, Möbius and Bracelet, based on the presence or absence of a specific proline residue. The present study describes the suite of cyclotides obtained from Clitoria ternatea, characterized by LC−MS and MS/MS techniques. Notable variations in product ion distributions were observed in cyclotides belonging to different structural subfamilies based on the number and positions of proline residues. For instance, Cter M which is an abundant Möbius cyclotide in this plant containing three proline residues, displayed distinct b- and y- ion characteristics in the MS/MS spectra compared to Cliotide T1, another commonly identified cyclotide but belonging to the Bracelet subfamily having two proline residues. The distinct fragmentation pattern of prototypical cyclotides of each structural subfamily, determined by Xxx-Pro bond fragmentation, was used to rapidly identify and sequence a novel cyclotide ctr pep 30 from this plant.     

Crystallization and glass transition kinetics in Cu ion substituted Cux-Ag1 − xI-Ag2O-V2O5 superionic glasses

Crystallization kinetics and thermal properties in superionic glasses Cu_xAg_1 − xI-Ag₂O-V₂O₅ for x = 0.1-0.3 have been thoroughly investigated. X-ray diffraction and differential scanning calorimetry measurements confirm the precipitation of at least three compounds during crystallization, viz. AgI, Ag₄V₂O₇ and Ag₈I₄V₂O₇. The activation energies for structural relaxation (E_s) and crystallization (E_c) obtained using Moynihan and Kissinger formulation exhibit interesting trends with CuI substitution. The E_s value decreases with CuI substitution in the system. Further, the E_c values corresponding to precipitation of Ag₄V₂O₇ and Ag₈I₄V₂O₇ exhibit increasing trend, whereas, for that of AgI precipitation a decreasing trend with CuI content. The Avrami parameter calculated from Augis-Bennett method and Ozawa equation suggests predominantly surface crystallization in the glassy system. The electrical conductivity-temperature (σ-T) cycles interestingly demonstrate increasing precipitation of AgI with CuI content in the glass matrix.     

Dynamical mean-field theory for molecules and nanostructures

Dynamical mean-field theory (DMFT) has established itself as a reliable and well-controlled approximation to study correlation effects in bulk solids and also two-dimensional systems. In combination with standard density-functional theory (DFT), it has been successfully applied to study materials in which localized electronic states play an important role. It was recently shown that this approach can also be successfully applied to study correlation effects in nanostructures. Here, we provide some details on our recently proposed DFT+DMFT approach to study the magnetic properties of nanosystems [V. Turkowski, A. Kabir, N. Nayyar, and T. S. Rahman, J. Phys.: Condens. Matter 22, 462202 (2010)] and apply it to examine the magnetic properties of small FePt clusters. We demonstrate that DMFT produces meaningful results even for such small systems. For benchmarking and better comparison with results obtained using DFT+U, we also include the case of small Fe clusters. As in the case of bulk systems, the latter approach tends to overestimate correlation effects in nanostructures. Finally, we discuss possible ways to further improve the nano-DFT+DMFT approximation and to extend its application to molecules and nanoparticles on substrates and to nonequilibrium phenomena.     

Photovoltaics literature survey (no. 85)

In order to help keep readers up‐to‐date in the field each issue of Progress in Photovoltaics will contain a list of recently published journal articles most relevant to its aims and scope. This list is drawn from an extremely wide range of journals, including IEEE Transactions on Electron Devices, Journal of Applied Physics, Applied Physics Letters, Progress in Photovoltaics and Solar Energy Materials and Solar Cells. To assist the reader, the list is separated into broad categories, but please note that these classifications are by no means strict. Also note that inclusion in the list is not an endorsement of a paper's quality. If you have any suggestions please email Santosh Shrestha at s.shrestha@unsw.edu.au .