Direct observation of (H8,H6)-Hr J-coupling correlations in oligonucleotides for unambiguous resonance assignments: use of J-scaling in two-dimensional correlated spectroscopy

Four-bond H8/H6-H1 scalar coupling correlations in two-dimensional correlated spectroscopy have been observed directly for the first time by using the J-scaled COSY [(1985) Chem. Phys. Lett. 116, 105-108] technique in a dinucleotide, cytidylyl(2'-5')guanosine (CpG). Unambiguous resonance assignment of nonexchangeable protons in CpG has been obtained using these H8/H6-H1' 4-bond correlations and the various 3- and 4-bond sugar ring proton correlations observed in the COSY and SUPER COSY experiments

N-Terminal myristoylation alters the calcium binding pathways in neuronal calcium sensor-1

Neuronal calcium sensor-1 (NCS-1) interacts with many membranes and cytosolic proteins, both in a Ca2+-dependent and in a Ca2+-independent manner, and its physiological role is governed by its N-terminal myristoylation. To understand the role of myristoylation in altering Ca2+ response and other basic biophysical properties, we have characterized the Ca2+ filling pathways in both myristoylated (myr) and non-myristoylated (non-myr) forms of NCS-1. We have observed that Ca2+ binds simultaneously to all three active EF-hands in non-myr NCS-1, whereas in the case of myr NCS-1, the process is sequential, where the second EF-hand is filled first, followed by the third and fourth EF-hands. In the case of myr NCS-1, the observed sequential Ca2+ binding process becomes more prominent in the presence of Mg2+. Besides, the analysis of 15N-relaxation data reveals that non-myr NCS-1 is more dynamic than myr NCS-1. The overall molecular tumbling correlation time increases by approximately 20% upon myristoylation. Comparing the apo forms of non-myr NCS-1 and myr NCS-1, we found the possibility of existence of some substates, which are structurally closer to the holo form of the protein. There are more such substates in the case of non-myr NCS-1 than in the case of the myr NCS-1, suggesting that the former accesses larger volumes of conformational substates compared with the latter. Further, the study reveals that the possibility of Ca2+ binding simultaneously to different parts of the protein is more favourable in non-myr NCS-1 than in myr NCS-1

Refined procedures for accurate determination of solution structures of nucleic acids by two dimensional nuclear magnetic resonance spectroscopy

New procedures have been described for accurate determination of solution structures of nucleic acids. These are two fold; new two dimensional nuclear magnetic resonance techniques and better approaches for interpretation of nuclear magnetic resonance data for structure determination purposes. The significant development in two dimensional nuclear magnetic resonance techniques for this purpose are ω1 -scaling and recording of pure phase spectra. Use ofω1-scaled correlated and nuclear Overhauser effect spectra for estimation of interproton distances and 1H-1H coupling constants has been described. Computer simulation procedures for exact determination of structure have been described. Experimental spectra demonstrating the application of new procedures have been presented

A tracked approach for automated NMR assignments in proteins (TATAPRO)

A novel automated approach for the sequence specific NMR assignments of 1HN, 13Cα, 13Cβ, 13C'/1Hα and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Cα, 13Cβ and 13C'/1Hα. The information derived from such correlations is used to create a 'master list' consisting of all possible sets of 1HN i, 15Ni, 13Cα i, 13Cβ i, 13C'i/1Hα i, 13Cα i-1, 13Cβ i-1 and 13C'i-1/ 1Hα i-1 chemical shifts. On the basis of an extensive statistical analysis of 13Cα and 13Cβ chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master list and also to translate the protein primary sequence into an array called pps array. The program then uses the master list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master list created for the test proteins

Application of Resonance Perturbation Theory to Dynamics of Magnetization in Spin Systems Interacting with Local and Collective Bosonic Reservoirs

We apply our recently developed resonance perturbation theory to describe the dynamics of magnetization in paramagnetic spin systems interacting simultaneously with local and collective bosonic environments. We derive explicit expressions for the evolution of the reduced density matrix elements. This allows us to calculate explicitly the dynamics of the macroscopic magnetization, including characteristic relaxation and dephasing time-scales. We demonstrate that collective effects (i) do not influence the character of the relaxation processes but merely renormalize the relaxation times, and (ii) significantly modify the dephasing times, leading in some cases to a complicated (time inhomogeneous) dynamics of the transverse magnetization, governed by an effective time-dependent magnetic field

Structural characterization of a novel KH-domain containing plant chloroplast endonuclease

Chlamydomonas reinhardtii is a single celled alga that undergoes apoptosis in response to UV-C irradiation. UVI31+, a novel UV-inducible DNA endonuclease in C. reinhardtii, which normally localizes near cell wall and pyrenoid regions, gets redistributed into punctate foci within the whole chloroplast, away from the pyrenoid, upon UV-stress. Solution NMR structure of the first putative UV inducible endonuclease UVI31+ revealed an alpha(1)-beta(1)-beta(2)-alpha(2)-alpha(3)-beta(3) fold similar to BolA and type II KH-domain ubiquitous protein families. Three alpha-helices of UVI31+ constitute one side of the protein surface, which are packed to the other side, made of three-stranded beta-sheet, with intervening hydrophobic residues. A twenty-three residues long polypeptide stretch (D54-H76) connecting beta(1) and beta(2) strands is found to be highly flexible. Interestingly, UVI31+ recognizes the DNA primarily through its beta-sheet. We propose that the catalytic triad residues involving Ser114, His95 and Thr116 facilitate DNA endonuclease activity of UVI31+. Further, decreased endonuclease activity of the S114A mutant is consistent with the direct participation of Ser114 in the catalysis. This study provides the first structural description of a plant chloroplast endonuclease that is regulated by UV-stress response

The Hawk-I UDS and GOODS Survey (HUGS): Survey design and deep K-band number counts

We present the results of a new, ultra-deep, near-infrared imaging survey executed with the Hawk-I imager at the ESO VLT, of which we make all the data public. This survey, named HUGS (Hawk-I UDS and GOODS Survey), provides deep, high-quality imaging in the K and Y bands over the CANDELS UDS and GOODS-South fields. We describe here the survey strategy, the data reduction process, and the data quality. HUGS delivers the deepest and highest quality K-band images ever collected over areas of cosmological interest, and ideally complements the CANDELS data set in terms of image quality and depth. The seeing is exceptional and homogeneous, confined to the range 0.38"-0.43". In the deepest region of the GOODS-S field, (which includes most of the HUDF) the K-band exposure time exceeds 80 hours of integration, yielding a 1-sigma magnitude limit of ~28.0 mag/sqarcsec. In the UDS field the survey matches the shallower depth of the CANDELS images reaching a 1-sigma limit per sq.arcsec of ~27.3mag in the K band and ~28.3mag in the Y-band, We show that the HUGS observations are well matched to the depth of the CANDELS WFC3/IR data, since the majority of even the faintest galaxies detected in the CANDELS H-band images are also detected in HUGS. We present the K-band galaxy number counts produced by combining the HUGS data from the two fields. We show that the slope of the number counts depends sensitively on the assumed distribution of galaxy sizes, with potential impact on the estimated extra-galactic background light (abridged).Comment: Accepted for publication on Astronomy and Astrophysic

GOODS-Herschel: star formation, dust attenuation, and the FIR-radio correlation on the main sequence of star-forming galaxies up to z=4

We use deep panchromatic data sets in the GOODS-N field, from GALEX to the deepest Herschel far-infrared (FIR) and VLA radio continuum imaging, to explore the evolution of star-formation activity and dust attenuation properties of star-forming galaxies to z sime 4, using mass-complete samples. Our main results can be summarized as follows: (i) the slope of the star-formation rate–M* correlation is consistent with being constant sime0.8 up to z sime 1.5, while its normalization keeps increasing with redshift; (ii) for the first time we are able to explore the FIR–radio correlation for a mass-selected sample of star-forming galaxies: the correlation does not evolve up to z sime 4; (iii) we confirm that galaxy stellar mass is a robust proxy for UV dust attenuation in star-forming galaxies, with more massive galaxies being more dust attenuated. Strikingly, we find that this attenuation relation evolves very weakly with redshift, with the amount of dust attenuation increasing by less than 0.3 mag over the redshift range [0.5–4] for a fixed stellar mass; (iv) the correlation between dust attenuation and the UV spectral slope evolves with redshift, with the median UV slope becoming bluer with redshift. By z sime 3, typical UV slopes are inconsistent, given the measured dust attenuations, with the predictions of commonly used empirical laws. (v) Finally, building on existing results, we show that gas reddening is marginally larger (by a factor of around 1.3) than the stellar reddening at all redshifts probed. Our results support a scenario where the ISM conditions of typical star-forming galaxies evolve with redshift, such that at z ≥ 1.5 Main Sequence galaxies have ISM conditions moving closer to those of local starbursts

Calibrating Extinction-Free Star Formation Rate Diagnostics with 33GHz Free-Free Emission in NGC6946

Abridged: Using free-free emission measured in the Ka-band (26-40GHz) for 10 star-forming regions in the nearby galaxy NGC6946, including its starbursting nucleus, we compare a number of SFR diagnostics that are typically considered to be unaffected by interstellar extinction: i.e., non-thermal radio (i.e., 1.4GHz), total infrared (IR; 8-1000um), and warm dust (i.e., 24um) emission, along with the hybrid (obscured + unobscured) indicators of H\alpha+24um and UV+IR. The 33GHz free-free emission is assumed to provide the most accurate measure of the current SFR. Among the extranuclear star-forming regions, the 24um, H\alpha+24um and UV+IR SFR calibrations are in good agreement with the 33GHz free-free SFRs. However, each of the SFR calibrations relying on some form of dust emission overestimate the nuclear SFR by a factor of ~2. This is more likely the result of excess dust heating through an accumulation of non-ionizing stars associated with an extended episode of star formation in the nucleus rather than increased competition for ionizing photons by dust. SFR calibrations using the non-thermal radio continuum yield values which only agree with the free-free SFRs for the nucleus, and underestimate the SFRs from the extranuclear star-forming regions by a factor of ~2. This result likely arises from the CR electrons decaying within the starburst region with negligible escape compared to the young extranuclear star-forming regions. Finally, we find that the SFRs estimated using the total 33GHz emission agree well with the free-free SFRs due to the large thermal fractions present at these frequencies even when local diffuse backgrounds are not removed. Thus, rest-frame 33GHz observations may act as a reliable method to measure the SFRs of galaxies at increasingly high redshift without the need of ancillary radio data to account for the non-thermal emission.Comment: 18 pages, 7 Figures, Accepted for publication in Ap