Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. Here we introduce position restraints, or “anchors” as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.

Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors

The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly aligned by a standard pairwise alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the alignment. An alternative approach is the use of restraints, or anchors, to incorporate such position-matching explicitly during alignment. Here we introduce position anchoring in the alignment tool AlignMe as an aid to pairwise sequence alignment of membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of even a single anchor can dramatically improve the accuracy of the alignments, while maintaining the reproducibility and rigor of the overall alignment.

Organic–inorganic hybrid photocatalyst for carbon dioxide reduction

Efficient hybrid photocatalysts for carbon dioxide reduction were developed from dye-sensitized TiO2 nanoparticles and their catalytic performance was optimized by ternary organic/inorganic components. Thus, the hybrid system consists of (E)-2-cyano-3-(5′-(5′′-(p-(diphenylamino)phenyl)thiophen-2′′-yl)thiophen-2′-yl)-acrylic acid as a sensitizer and fac-[Re(4,4′-bis(diethoxyphosphorylmethyl)-2,2′-bipyridine)(CO)3Cl] as a reduction catalyst (ReP), both of which have been fixed onto TiO2 semiconductors (s-TiO2, h-TiO2, d-TiO2). Mott–Schottky analysis on flat-band potential (Efb) of TiO2 mesoporous films has verified that Efb can be finely modulated by volume variation of water (0 to 20 vol%). The increase of added water resulted in substantial positive shifts of Efb from −1.93 V at 0 vol% H2O, to −1.74 V (3 vol% H2O), to −1.56 V (10 vol% H2O), and to −1.47 V (20 vol% H2O). As a result, with addition of 3–10 vol% water in the photocatalytic reaction, conversion efficiency of CO2 to CO increased significantly reaching a TON value of ∼350 for 30 h. Catalytic activity enhancement is mainly attributed to (1) the optimum alignment of Efb by 3–10 vol% water with respect to the of the dye and Ered of ReP for smooth electron transfer from photo-excited dye to RePvia the TiO2 semiconductor and (2) the water-induced acceleration of chemical processes on the fixed ReP. In addition, the energy level was further tuned by variation of the dye and ReP amounts. We also found that the intrinsic properties of TiO2 sources (morphology, size, agglomeration) exert a great influence on the overall photocatalytic activity of this hybrid system. Implications of the present observations and reaction mechanisms are discussed in detail.

Comparative Study on Mechanical Properties of GMA Welded IRSM41 Mild Steel Plate Based on Grain Flow Direction

The purpose of this work was to study the mechanical properties of GMAW welded IRSM41 material based on the grain flow directions. It is a joining process that fuses the base metal to make the weld. The results were analyzed by means of the mechanical properties such as tensile strength, bend test, microstructure and hardness was carried out for both along and across the grain flow direction of the weldments. The important implication about grain flow is that some mechanical properties vary with respect to orientation of the grain flow. The strength and hardness are primarily varied based on the grain flow direction. The desirable properties associated with retarding crack propagation can see significant differences depending on the grain flow and the direction of the moving crack. So, properties like fatigue strength, impact toughness and ductility, which are measures of a material’s resistance to cracking (measured after fracture), can be significantly improved if the crack propagation direction and the grain flow are properly aligned. The optimum alignment occurs when the maximum principal stress (perpendicular to a potential crack or fracture) is aligned with the grain-flow lines. On testing the mechanical properties, it reveals that along the grain flow direction has 13.5% higher than the across the grain flow direction.

High Field Breakdown of Carbon Nanotube Network Transistors

We develop and employ a self-consistent electro-thermal model to study the high field breakdown of carbon nanotube (CNT) network thin film transistors (CN-TFTs). We investigate the effects of the CNT alignment angle and length distribution on the breakdown process caused by excessive self-heating. We examine relevant breakdown characteristics such as the peak current and corresponding voltage and power in relation to these two network parameters. We find that the breakdown behavior can significantly vary with respect to the CNT length and alignment distribution even when the network density is kept the same. Results suggest that an optimum alignment (∼ 65°) can be found for a network with constant CNT lengths to obtain higher current/power without setting off an early breakdown. When both CNT length and alignment angle are varied, we find that networks with higher average CNT length have lower optimum alignment such that doubling the average CNT length lowers the optimum alignment angle by half. Therefore these network parameters need to be carefully selected to achieve greater thermal reliability and higher electrical performance.

Coincidence-Based Scoring of Mappings in Ontology Alignment

Ontology Matching (OM) which targets finding a set of alignments across two ontologies, is a key enabler for the success of Semantic Web. In this paper, we introduce a new perspective on this problem. By interpreting ontologies as Typed Graphs embedded in a Metric Space,coincidenceof the structures of the two ontologies is formulated. Having such a formulation, we define a mechanism to score mappings. This scoring can then be used to extract a good alignment among a number of candidates. To do this, this paper introduces three approaches: The first one, straightforward and capable of finding the optimum alignment, investigates all possible alignments, but its runtime complexity limits its use to small ontologies only. To overcome this shortcoming, we introduce a second solution as well which employs a Genetic Algorithm (GA) and shows a good effectiveness for some certain test collections. Based on approximative approaches, a third solution is also provided which, for the same purpose, measures random walks in each ontology versus the other.