A New Algorithm for Self-Consistent 3-D Modeling of Collisions in Dusty Debris Disks

We present a new "collisional grooming" algorithm that enables us to model images of debris disks where the collision time is less than the Poynting Robertson time for the dominant grain size. Our algorithm uses the output of a collisionless disk simulation to iteratively solve the mass flux equation for the density distribution of a collisional disk containing planets in 3 dimensions. The algorithm can be run on a single processor in ~1 hour. Our preliminary models of disks with resonant ring structures caused by terrestrial mass planets show that the collision rate for background particles in a ring structure is enhanced by a factor of a few compared to the rest of the disk, and that dust grains in or near resonance have even higher collision rates. We show how collisions can alter the morphology of a resonant ring structure by reducing the sharpness of a resonant ring's inner edge and by smearing out azimuthal structure. We implement a simple prescription for particle fragmentation and show how Poynting-Robertson drag and fragmentation sort particles by size, producing smaller dust grains at smaller circumstellar distances. This mechanism could cause a disk to look different at different wavelengths, and may explain the warm component of dust interior to Fomalhaut's outer dust ring seen in the resolved 24 micron Spitzer image of this system.Comment: 30 pages, 9 figure

Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation.

The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation

Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases.

Dipeptidyl-peptidase VI from Bacillus sphaericus and YkfC from Bacillus subtilis have both previously been characterized as highly specific γ-D-glutamyl-L-diamino acid endopeptidases. The crystal structure of a YkfC ortholog from Bacillus cereus (BcYkfC) at 1.8 Å resolution revealed that it contains two N-terminal bacterial SH3 (SH3b) domains in addition to the C-terminal catalytic NlpC/P60 domain that is ubiquitous in the very large family of cell-wall-related cysteine peptidases. A bound reaction product (L-Ala-γ-D-Glu) enabled the identification of conserved sequence and structural signatures for recognition of L-Ala and γ-D-Glu and, therefore, provides a clear framework for understanding the substrate specificity observed in dipeptidyl-peptidase VI, YkfC and other NlpC/P60 domains in general. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. A conserved tyrosine in the SH3b domain of the YkfC subfamily is correlated with the presence of a conserved acidic residue in the NlpC/P60 domain and both residues interact with the free amine group of the alanine. This structural feature allows the definition of a subfamily of NlpC/P60 enzymes with the same N-terminal substrate requirements, including a previously characterized cyanobacterial L-alanine-γ-D-glutamate endopeptidase that contains the two key components (an NlpC/P60 domain attached to an SH3b domain) for assembly of a YkfC-like active site

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function.

Proteins that contain the DUF2874 domain constitute a new Pfam family PF11396. Members of this family have predominantly been identified in microbes found in the human gut and oral cavity. The crystal structure of one member of this family, BVU2987 from Bacteroides vulgatus, has been determined, revealing a β-lactamase inhibitor protein-like structure with a tandem repeat of domains. Sequence analysis and structural comparisons reveal that BVU2987 and other DUF2874 proteins are related to β-lactamase inhibitor protein, PepSY and SmpA_OmlA proteins and hence are likely to function as inhibitory proteins

A Fast Radio Burst in a Compact Galaxy Group at zz~1

FRB 20220610A is a high-redshift Fast Radio Burst (FRB) that has not been observed to repeat. Here, we present rest-frame UV and optical $\textit{Hubble Space Telescope}$ observations of the field of FRB 20220610A. The imaging reveals seven extended sources, one of which we identify as the most likely host galaxy with a spectroscopic redshift of $z$=1.017. We spectroscopically confirm at least three additional sources to be at the same redshift, and identify the system as a compact galaxy group with possible signs of interaction among group members. We determine the host of FRB 20220610A to be a star-forming galaxy with stellar mass of $\approx10^{9.7}\,M_{\odot}$, mass-weighted age of $\approx2.6$~Gyr, and star formation rate (integrated over the last 100 Myr) of $\approx1.7$~M$_{\odot}$~yr$^{-1}$. These host properties are commensurate with the star-forming field galaxy population at z~1 and trace their properties analogously to the population of low-$z$ FRB hosts. Based on estimates of the total stellar mass of the galaxy group, we calculate a fiducial contribution to the observed Dispersion Measure (DM) from the intragroup medium of $\approx 110-220$ $\rm pc \, cm^{-3}$ (rest-frame). This leaves a significant excess of $500^{+272}_{-109}$ $\rm pc \, cm^{-3}$ (in the observer frame), with additional sources of DM possibly originating from the circumburst environment, host galaxy interstellar medium, and/or foreground structures along the line of sight. Given the low occurrence rates of galaxies in compact groups, the discovery of an FRB in such a group demonstrates a rare and novel environment in which FRBs can occur.Comment: 24 pages, 8 figures, 2 tables, submitte

The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

The crystal structure of SSO2064, the first structural representative of Pfam family PF01796 (DUF35), reveals a two-domain architecture comprising an N-terminal zinc-ribbon domain and a C-terminal OB-fold domain. Analysis of the domain architecture, operon organization and bacterial orthologs combined with the structural features of SSO2064 suggests a role involving acyl-CoA binding for this family of proteins

Mapping Obscured Star Formation in the Host Galaxy of FRB 20201124A

We present high-resolution 1.5--6 GHz Karl G. Jansky Very Large Array (VLA) and $\textit{Hubble Space Telescope}$ ($\textit{HST}$) optical and infrared observations of the extremely active repeating fast radio burst (FRB) FRB$\,$20201124A and its barred spiral host galaxy. We constrain the location and morphology of star formation in the host and search for a persistent radio source (PRS) coincident with FRB$\,$20201124A. We resolve the morphology of the radio emission across all frequency bands and measure a star formation rate SFR $\approx 8.9\,M_{\odot}$ yr$^{-1}$, a factor of $\approx 4-6$ larger than optically-inferred SFRs, demonstrating dust-obscured star formation throughout the host. Compared to a sample of all known FRB hosts with radio emission, the host of FRB$\,$20201124A has the most significant obscured star formation. While ${\it HST}$ observations show the FRB to be offset from the bar or spiral arms, the radio emission extends to the FRB location. We propose that the FRB progenitor could have formed $\textit{in situ}$ (e.g., a magnetar central engine born from the explosion of a massive star). It is still plausible, although less likely, that the progenitor of FRB$\,$20201124A migrated from the central bar of the host, e.g., via a runaway massive star. We further place a limit on the luminosity of a putative PRS at the FRB position of $L_{\rm 6.0 \ GHz}$$\lesssim$2.6$\times$$10^{27}$erg s$^{-1}$Hz$^{-1}$, two orders of magnitude below any PRS known to date. However, this limit is still broadly consistent with both magnetar nebulae and hypernebulae models assuming a constant energy injection rate of the magnetar and an age of$\gtrsim 10^{5}$ yr in each model, respectively.Comment: 21 pages, 6 figures, 3 tables, Submitte

Structure of the first representative of Pfam family PF09410 (DUF2006) reveals a structural signature of the calycin superfamily that suggests a role in lipid metabolism

The first structural representative of the domain of unknown function DUF2006 family, also known as Pfam family PF09410, comprises a lipocalin-like fold with domain duplication. The finding of the calycin signature in the N-terminal domain, combined with remote sequence similarity to two other protein families (PF07143 and PF08622) implicated in isoprenoid metabolism and the oxidative stress response, support an involvement in lipid metabolism. Clusters of conserved residues that interact with ligand mimetics suggest that the binding and regulation sites map to the N-terminal domain and to the interdomain interface, respectively.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79347/1/S1744309109037749.pd

The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes

The crystal structure of the prephenate dehydrogenase component of the bifunctional H. influenzae TyrA reveals unique structural differences between bifunctional and monofunctional TyrA enzymes