Stranded in isolation: structural role of isolated extended strands in proteins

Reasons for the formation of extended-strands (E-strands) in proteins are often associated with the formation of β -sheets. However E-strands, not part of β-sheets, commonly occur in proteins. This raises questions about the structural role and stability of such isolated E-strands. Using a dataset of 250 largely non-homologous and high-resolution (<2 Å) crystal structures of proteins, we have identified 518 isolated E-strands from 187 proteins. The two most distinguishing features of isolated E-strands from β-strands in β-sheets are the high preponderance of prolyl residues occuring in isolated E-strands and their high exposure to the surroundings. Removal of regions with polyproline conformation from the dataset did not significantly reduce the propensity of prolyl residues to occur in isolated E-strands. Isolated E-strands are often characterized by their main-chain amide and carbonyl groups involved in hydrogen bonding with polar side chains or water. They are often flanked by irregular loop structures and are less well conserved, than β-sheet forming β-strands, among homologous protein structures. It is suggested that isolated β-strands have many characteristics of loop segments but with repetitive (φ,ψ) values falling within the β-region of the Ramachandran map

Cell-Type Specific Transcriptomic Profiling to Dissect Mechanisms of Differential Dendritogenesis

The establishment, maintenance and modulation of cell-type specific neural architectures are critically important to the formation of functional neural networks. At the neuroanatomical level, differential patterns of dendritic arborization directly impact neural function and connectivity, however the molecular mechanisms underlying the specification of distinct dendrite morphologies remain incompletely understood. To address this question, we analyzed global gene expression from purified populations of wild-type class I and class IV Drosophila melanogaster dendritic arborization (da) sensory neurons compared to wild-type whole larval RNA using oligo DNA microarray expression profiling. Herein we present detailed experimental methods and bioinformatic anal- yses to correspond with our data reported in the Gene Expression Omnibus under accession number GSE46154. We further provide R code to facilitate data accession, perform quality controls, and conduct bioinformatic analyses relevant to this dataset. Our cell-type specific gene expression datasets provide a valuable resource for guiding further investigations designed to explore the molecular mechanisms underlying differential patterns of neuronal patterning

A road map for the generation of a near-infrared guide star catalog for thirty meter telescope observations

The near-infrared instruments in the upcoming Thirty Meter Telescope (TMT) will be assisted by a multi conjugate Adaptive Optics (AO) system. For the efficient operation of the AO system, during observations, a near-infrared guide star catalog which goes as faint as 22 mag in JVega band is essential and such a catalog does not exist. A methodology, based on stellar atmospheric models, to compute the expected near-infrared magnitudes of stellar sources from their optical magnitudes is developed. The method is applied and validated in JHKs bands for a magnitude range of JVega 16–22 mag. The methodology is also applied and validated using the reference catalog of PAN STARRS. We verified that the properties of the final PAN STARRS optical catalog will satisfy the requirements of TMT IRGSC and will be one of the potential sources for the generation of the final catalog. In a broader context, this methodology is applicable for the generation of a guide star catalog for any existing/upcoming near-infrared telescopes

The cohesin ring concatenates sister DNA molecules

Sister chromatid cohesion, which is essential for mitosis, is mediated by a multi-subunit protein complex called cohesin whose Scc1, Smc1, and Smc3 subunits form a tripartite ring structure. It has been proposed that cohesin holds sister DNAs together by trapping them inside its ring. To test this, we used site-specific cross-linking to create chemical connections at the three interfaces between the ring’s three constituent polypeptides, thereby creating covalently closed cohesin rings. As predicted by the ring entrapment model, this procedure produces dimeric DNA/cohesin structures that are resistant to protein denaturation. We conclude that cohesin rings concatenate individual sister minichromosome DNAs

Generation of a near infra-red guide star catalog for thirty-meter telescope observations

The requirements for the production of a near Infra-Red Guide Star Catalog (IRGSC) for Thirty Meter Telescope (TMT) observations are identified and presented. A methodology to compute the expected J band magnitude of stellar sources from their optical (g, r, i) magnitudes is developed. The computed and observed J magnitudes of sources in three test fields are compared and the methodology developed is found to be satisfactory for the magnitude range, JVega = 16–22 mag. From this analysis, we found that for the production of final TMT IRGSC (with a limiting magnitude of JVega = 22 mag), we need g, r, i bands optical data which go up to iAB ~ 23 mag. Fine tuning of the methodology developed, such as using Spectral Energy Distribution (SED) template fitting for optimal classification of stars in the fainter end, incorporating spectral libraries in the model, to reduce the scatter, and modification of the existing colour–temperature relation to increase the source density are planned for the subsequent phase of this work

A HARDWARE REDUCTION IN CELL SEARCH REGULATORY TRACKING SYSTEM

Following symbol timing, the fractional carrier frequency offset is believed and compensated utilizing an adaptive in loop, which enables for a high-precision compensation in a short interval. A manuscript architecture for efficient some time and frequency synchronization, put on the lengthy-term evolution standard, is suggested. For symbol timing, we advise using a symbol-folding method on the top from the sign-bit reduction technique, resulting in a manuscript formula for that cyclic prefix-type recognition in LTE. Within the frequency domain, for cell search, we propose an indication-bit reduction technique on the top from the matched filter way of the main synchronization signal recognition. Additionally, we advise the sign-bit maximum-likelihood sequence recognition formula for that secondary synchronization signal analysis. The fabricated and examined synchronizer core proves to possess an outstanding performance for those defined communication modes in LTE. The suggested architecture is fabricated inside a 130-nm CMOS technology occupying0.68 mm2 of plastic area

SMAP Soil Moisture Change as an Indicator of Drought Conditions

Soil moisture is considered a key variable in drought analysis. The soil moisture dynamics given by the change in soil moisture between two time periods can provide information on the intensification or improvement of drought conditions. The aim of this work is to analyze how the soil moisture dynamics respond to changes in drought conditions over multiple time intervals. The change in soil moisture estimated from the Soil Moisture Active Passive (SMAP) satellite observations was compared with the United States Drought Monitor (USDM) and the Standardized Precipitation Index (SPI) over the contiguous United States (CONUS). The results indicated that the soil moisture change over 13-week and 26-week intervals is able to capture the changes in drought intensity levels in the USDM, and the change over a four-week interval correlated well with the one-month SPI values. This suggested that a short-term negative soil moisture change may indicate a lack of precipitation, whereas a persistent long-term negative soil moisture change may indicate severe drought conditions. The results further indicate that the inclusion of soil moisture change will add more value to the existing drought-monitoring products

Designing libraries of chimeric proteins using SCHEMA recombination and RASPP

SCHEMA is a method for designing libraries of novel proteins by recombination of homologous sequences. The goal is to maximize the number of folded proteins while simultaneously generating significant sequence diversity. Here, we use the RASPP algorithm to identify optimal SCHEMA designs for shuffling contiguous elements of sequence. To exemplify the method, SCHEMA is used to recombine five fungal cellobiohydrolases (CBH1s) to produce a library of more than 390,000 novel CBH1 sequences

Motivated proteins: a web application for studying small three-dimensional protein motifs

<b>BACKGROUND:</b> Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are alphabeta-motifs, asx-motifs, asx-turns, beta-bulges, beta-bulge loops, beta-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns.We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. <b>DESCRIPTION:</b> The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. <b>CONCLUSION:</b> Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schem

Molecular basis of ion permeability in a voltage-gated sodium channel

Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+ ≈ Li+ ≫ K+, Ca2+, Mg2+) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones