Structural diversity in the AdoMet radical enzyme superfamily

AdoMet radical enzymes are involved in processes such as cofactor biosynthesis, anaerobic metabolism, and natural product biosynthesis. These enzymes utilize the reductive cleavage of S-adenosylmethionine (AdoMet) to afford l-methionine and a transient 5′-deoxyadenosyl radical, which subsequently generates a substrate radical species. By harnessing radical reactivity, the AdoMet radical enzyme superfamily is responsible for an incredible diversity of chemical transformations. Structural analysis reveals that family members adopt a full or partial Triose-phosphate Isomerase Mutase (TIM) barrel protein fold, containing core motifs responsible for binding a catalytic [4Fe–4S] cluster and AdoMet. Here we evaluate over twenty structures of AdoMet radical enzymes and classify them into two categories: ‘traditional’ and ‘ThiC-like’ (named for the structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase (ThiC)). In light of new structural data, we reexamine the ‘traditional’ structural motifs responsible for binding the [4Fe–4S] cluster and AdoMet, and compare and contrast these motifs with the ThiC case. We also review how structural data combine with biochemical, spectroscopic, and computational data to help us understand key features of this enzyme superfamily, such as the energetics, the triggering, and the molecular mechanisms of AdoMet reductive cleavage. This article is part of a Special Issue entitled: Radical SAM Enzymes and Radical Enzymology.Wellcome Trust (London, England) (091162/Z/10/Z)National Science Foundation (U.S.) (NSF Grant MCB-0543833)Howard Hughes Medical Institute (Investigator

Comet 9P/Tempel 1: Interpretation with the Deep Impact Results

According to our common understandings, the original surface of a short-period comet nucleus has been lost by sublimation processes during its close approaches to the Sun. Sublimation results in the formation of a dust mantle on the retreated surface and in chemical differentiation of ices over tens or hundreds of meters below the mantle. In the course of NASA's Deep Impact mission, optical and infrared imaging observations of the ejecta plume were conducted by several researchers, but their interpretations of the data came as a big surprise: (1) The nucleus of comet 9P/Tempel 1 is free of a dust mantle, but maintains its pristine crust of submicron-sized carbonaceous grains; (2) Primordial materials are accessible already at a depth of several tens of cm with abundant silicate grains of submicrometer sizes. In this study, we demonstrate that a standard model of cometary nuclei explains well available observational data: (1) A dust mantle with a thickness of ~1-2 m builds up on the surface, where compact aggregates larger than tens of micrometers dominate; (2) Large fluffy aggregates are embedded in chemically differentiated layers as well as in the deepest part of the nucleus with primordial materials. We conclude that the Deep Impact results do not need any peculiar view of a comet nucleus.Comment: 11 pages, 1 figure, 1 table. ApJ letters, 673, L199-20

Primary Beam Shape Calibration from Mosaicked, Interferometric Observations

Image quality in mosaicked observations from interferometric radio telescopes is strongly dependent on the accuracy with which the antenna primary beam is calibrated. The next generation of radio telescope arrays such as the Allen Telescope Array (ATA) and the Square Kilometer Array (SKA) have key science goals that involve making large mosaicked observations filled with bright point sources. We present a new method for calibrating the shape of the telescope's mean primary beam that uses the multiple redundant observations of these bright sources in the mosaic. The method has an analytical solution for simple Gaussian beam shapes but can also be applied to more complex beam shapes through $\chi^2$ minimization. One major benefit of this simple, conceptually clean method is that it makes use of the science data for calibration purposes, thus saving telescope time and improving accuracy through simultaneous calibration and observation. We apply the method both to 1.43 GHz data taken during the ATA Twenty Centimeter Survey (ATATS) and to 3.14 GHz data taken during the ATA's Pi Gigahertz Sky Survey (PiGSS). We find that the beam's calculated full width at half maximum (FWHM) values are consistent with the theoretical values, the values measured by several independent methods, and the values from the simulation we use to demonstrate the effectiveness of our method on data from future telescopes such as the expanded ATA and the SKA. These results are preliminary, and can be expanded upon by fitting more complex beam shapes. We also investigate, by way of a simulation, the dependence of the accuracy of the telescope's FWHM on antenna number. We find that the uncertainty returned by our fitting method is inversely proportional to the number of antennas in the array.Comment: Accepted by PASP. 8 pages, 8 figure

Cosmological Limits on the Neutrino Mass from the Lya Forest

The Lya forest in quasar spectra probes scales where massive neutrinos can strongly suppress the growth of mass fluctuations. Using hydrodynamic simulations with massive neutrinos, we successfully test techniques developed to measure the mass power spectrum from the forest. A recent observational measurement in conjunction with a conservative implementation of other cosmological constraints places upper limits on the neutrino mass: m_nu < 5.5 eV for all values of Omega_m, and m_nu < 2.4 (Omega_m/0.17 -1) eV, if 0.2 < Omega_m <0.5 as currently observationally favored (both 95 % C.L.).Comment: 4 pages, 2 ps figures, REVTex, submitted to Phys. Rev. Let

Proteins in Ionic Liquids: Reactions, Applications and Futures

Biopolymer processing and handling is greatly facilitated by the use of ionic liquids, given the increased solubility, and in somecases, structural stability imparted to these molecules. Focussing on proteins, we highlight here not just the key drivers behind protein-ionic liquid interactions that facilitate these functionalities, but address relevant current and potential applications of protein-ionic liquid interactions, including areas of future interest

Protoclusters associated with z > 2 radio galaxies. I. Characteristics of high redshift protoclusters

[Abridged] We present the results of a large program conducted with the Very Large Telescope and Keck telescope to search for forming clusters of galaxies near powerful radio galaxies at 2.0 < z < 5.2. We obtained narrow- and broad-band images of nine radio galaxies and their surroundings. The imaging was used to select candidate Lyman alpha emitting galaxies in ~3x3 Mpc^2 areas near the radio galaxies. A total of 337 candidate emitters were found with a rest-frame Lyman alpha equivalent width of EW_0 > 15 A and Sigma = EW_0/Delta EW_0 > 3. Follow-up spectroscopy confirmed 168 Lyman alpha emitters near eight radio galaxies. The success rate of our selection procedure is 91%. At least six of our eight fields are overdense in Lyman alpha emitters by a factor 3-5. Also, the emitters show significant clustering in velocity space. In the overdense fields, the width of the velocity distributions of the emitters is a factor 2-5 smaller than the width of the narrow-band filters. Taken together, we conclude that we have discovered six forming clusters of galaxies (protoclusters). We estimate that roughly 75% of powerful (L_2.7GHz > 10^33 erg/s/Hz/sr) high redshift radio galaxies reside in a protocluster, with a sizes of at least 1.75 Mpc. We estimate that the protoclusters have masses in the range 2-9 x 10^14 Msun and they are likely to be progenitors of present-day (massive) clusters of galaxies. For the first time, we have been able to estimate the velocity dispersion of cluster progenitors from z~5 to ~2. The velocity dispersion of the emitters increases with cosmic time, in agreement with the dark matter velocity dispersion in numerical simulations of forming massive clusters.Comment: 30 pages, 20 figures. Published in A&A. The article with high resolution figures is available at http://www.ast.cam.ac.uk/~venemans/research/datapaper/index.htm

Structural elements of an NRPS cyclization domain and its intermodule docking domain

Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA–F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and L-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes L-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-Å resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-Å-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct

Structural elements of an NRPS cyclization domain and its intermodule docking domain

Epothilones are thiazole-containing natural products with anticancer activity that are biosynthesized by polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) enzymes EpoA-F. A cyclization domain of EpoB (Cy) assembles the thiazole functionality from an acetyl group and l-cysteine via condensation, cyclization, and dehydration. The PKS carrier protein of EpoA contributes the acetyl moiety, guided by a docking domain, whereas an NRPS EpoB carrier protein contributes l-cysteine. To visualize the structure of a cyclization domain with an accompanying docking domain, we solved a 2.03-A resolution structure of this bidomain EpoB unit, comprising residues M1-Q497 (62 kDa) of the 160-kDa EpoB protein. We find that the N-terminal docking domain is connected to the V-shaped Cy domain by a 20-residue linker but otherwise makes no contacts to Cy. Molecular dynamic simulations and additional crystal structures reveal a high degree of flexibility for this docking domain, emphasizing the modular nature of the components of PKS-NRPS hybrid systems. These structures further reveal two 20-A-long channels that run from distant sites on the Cy domain to the active site at the core of the enzyme, allowing two carrier proteins to dock with Cy and deliver their substrates simultaneously. Through mutagenesis and activity assays, catalytic residues N335 and D449 have been identified. Surprisingly, these residues do not map to the location of the conserved HHxxxDG motif in the structurally homologous NRPS condensation (C) domain. Thus, although both C and Cy domains have the same basic fold, their active sites appear distinct

The Reactome BioMart

Reactome is an open source, expert-authored, manually curated and peer-reviewed database of reactions, pathways and biological processes. We provide an intuitive web-based user interface to pathway knowledge and a suite of data analysis tools. The Reactome BioMart provides biologists and bioinformaticians with a single web interface for performing simple or elaborate queries of the Reactome database, aggregating data from different sources and providing an opportunity to integrate experimental and computational results with information relating to biological pathways. Database URL: http://www.reactome.org