Potential functions of LEA proteins from the brine shrimp Artemia franciscana - Anhydrobiosis meets bioinformatics.

Late embryogenesis abundant (LEA) proteins are a large group of anhydrobiosis-associated intrinsically disordered proteins (IDP), which are commonly found in plants and some animals. The brine shrimp Artemiafranciscana is the only known animal that expresses LEA proteins from three, and not only one, different groups in its anhydrobiotic life stage. The reason for the higher complexity in the A. franciscana LEA proteome (LEAome), compared with other anhydrobiotic animals, remains mostly unknown. To address this issue, we have employed a suite of bioinformatics tools to evaluate the disorder status of the ArtemiaLEAome and to analyze the roles of intrinsic disorder in functioning of brine shrimp LEA proteins. We show here that A. franciscanaLEA proteins from different groups are more similar to each other than one originally expected, while functional differences among members of group 3 are possibly larger than commonly anticipated. Our data show that although these proteins are characterized by a large variety of forms and possible functions, as a general strategy, A. franciscana utilizes glassy matrix forming LEAs concurrently with proteins that more readily interact with binding partners. It is likely that the function(s) of both types, the matrix-forming and partner-binding LEA proteins, are regulated by changing water availability during desiccation

Shot Noise in Mesoscopic Diffusive Andreev Wires

We study shot noise in mesoscopic diffusive wires between a normal and a superconducting terminal. We particularly focus on the regime, in which the proximity-induced reentrance effect is important. We will examine the difference between a simple Boltzmann-Langevin description, which neglects induced correlations beyond the simple conductivity correction, and a full quantum calculation. In the latter approach, it turns out that two Andreev pairs propagating coherently into the normal metal are anti-correlated for E<E_c, where E_c=D/L^2 is the Thouless energy. In a fork geometry the flux-sensitive suppression of the effective charge was confirmed experimentally.Comment: 12 pages, proceedings of the NATO ARW MQO, Bled, Sloveni

Energy dependent counting statistics in diffusive superconducting tunnel junctions

We present an investigation of the energy dependence of the full charge counting statistics in diffusive normal-insulating-normal-insulating-superconducting junctions. It is found that the current in general is transported via a correlated transfer of pairs of electrons. Only in the case of strongly asymmetric tunnel barriers or energies much larger than the Thouless energy is the pair transfer uncorrelated. The second cumulant, the noise, is found to depend strongly on the applied voltage and temperature. For a junction resistance dominated by the tunnel barrier to the normal reservoir, the differential shot noise shows a double peak feature at voltages of the order of the Thouless energy, a signature of an ensemble averaged electron-hole resonance.Comment: 8 pages, 5 figure

Reflectionless tunneling in ballistic normal-metal--superconductor junctions

We investigate the phenomenon of reflectionless tunneling in ballistic normal-metal--superconductor (NS) structures, using a semiclassical formalism. It is shown that applied magnetic field and superconducting phase difference both impair the constructive interference leading to this effect, but in a qualitatively different way. This is manifested both in the conductance and in the shot noise properties of the system considered. Unlike diffusive systems, the features of the conductance are sharp, and enable fine spatial control of the current, as well as single channel manipulations. We discuss the possibility of conducting experiments in ballistic semiconductor-superconductor structures with smooth interfaces and some of the phenomena, specific to such structures, that could be measured. A general criterion for the barrier at NS interfaces, though large, to be effectively transparent to pair current is obtained.Comment: published versio

Quasiclassical theory of superconductivity: a multiple interface geometry

The purpose of the paper is to suggest a new method which allows one to study multiple coherent reflection/transmissions by partially transparent interfaces (e.g. in multi-layer mesoscopic structures or grain boundaries in high-Tc's) in the framework of the quasiclassical theory of superconductivity. It is argued that typically the trajectory of the particle is a simply connected tree (no loops) with knots, i.e. the points where interface scattering events occur and ballistic pieces of the trajectory are mixed. A linear boundary condition for the 2-component trajectory "wave function" which factorizes matrix (retarded) Green's function, is formulated for an arbitrary interface, specular or diffusive. To show the usage of the method, the current response to the vector potential (the total superfluid density rho_s) of a SS' sandwich with the different signs of the order parameter in S and S', is calculated. In this model, a few percent of reflection by the SS' interface transforms the paramagnetic response (rho_s < 0) created by the zero-energy Andreev bound states near an ideal interface (see Fauchere et al. PRL, 82, 3336 (1999), cond-mat/9901112), into the usual diamagnetic one (rho_s >0).Comment: Extended abstract submitted to "Electron Transport in Mesoscopic Systems", Satellite conference to LT22, Goteborg, 12-15 August, 1999. 2 pages Minor changes + the text height problem fixe

Incorporating Distant Sequence Features and Radial Basis Function Networks to Identify Ubiquitin Conjugation Sites

Ubiquitin (Ub) is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3) enzymes. Three major enzymes participate in ubiquitin conjugation. They are – E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF) network to identify protein ubiquitin conjugation (ubiquitylation) sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub) sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (−20∼+20) revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information), which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence features of Ub sites can improve predictive performance. Additionally, the independent test demonstrates that the proposed method can outperform other ubiquitylation prediction tools

Prediction of Amyloidogenic and Disordered Regions in Protein Chains

The determination of factors that influence protein conformational changes is very important for the identification of potentially amyloidogenic and disordered regions in polypeptide chains. In our work we introduce a new parameter, mean packing density, to detect both amyloidogenic and disordered regions in a protein sequence. It has been shown that regions with strong expected packing density are responsible for amyloid formation. Our predictions are consistent with known disease-related amyloidogenic regions for eight of 12 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Our findings support the concept that the mechanism of amyloid fibril formation is similar for different peptides and proteins. Moreover, we have demonstrated that regions with weak expected packing density are responsible for the appearance of disordered regions. Our method has been tested on datasets of globular proteins and long disordered protein segments, and it shows improved performance over other widely used methods. Thus, we demonstrate that the expected packing density is a useful value with which one can predict both intrinsically disordered and amyloidogenic regions of a protein based on sequence alone. Our results are important for understanding the structural characteristics of protein folding and misfolding

Global Analysis of Proline-Rich Tandem Repeat Proteins Reveals Broad Phylogenetic Diversity in Plant Secretomes

Cell walls, constructed by precisely choreographed changes in the plant secretome, play critical roles in plant cell physiology and development. Along with structural polysaccharides, secreted proline-rich Tandem Repeat Proteins (TRPs) are important for cell wall function, yet the evolutionary diversity of these structural TRPs remains virtually unexplored. Using a systems-level computational approach to analyze taxonomically diverse plant sequence data, we identified 31 distinct Pro-rich TRP classes targeted for secretion. This analysis expands upon the known phylogenetic diversity of extensins, the most widely studied class of wall structural proteins, and demonstrates that extensins evolved before plant vascularization. Our results also show that most Pro-rich TRP classes have unexpectedly restricted evolutionary distributions, revealing considerable differences in plant secretome signatures that define unexplored diversity