Crystal structures of trypanosoma brucei oligopeptidase B broaden the paradigm of catalytic regulation in prolyl oligopeptidase family enzymes

Oligopeptidase B cleaves after basic amino acids in peptides up to 30 residues. As a virulence factor in bacteria and trypanosomatid pathogens that is absent in higher eukaryotes, this is a promising drug target. Here we present ligand-free open state and inhibitor-bound closed state crystal structures of oligopeptidase B from Trypanosoma brucei, the causative agent of African sleeping sickness. These (and related) structures show the importance of structural dynamics, governed by a fine enthalpic and entropic balance, in substrate size selectivity and catalysis. Peptides over 30 residues cannot fit the enzyme cavity, preventing the complete domain closure required for a key propeller Asp/Glu to fix the catalytic His and Arg in the catalytically competent conformation. This size exclusion mechanism protects larger peptides and proteins from degradation. Similar bacterial prolyl endopeptidase and archael acylaminoacyl peptidase structures demonstrate this mechanism is conserved among oligopeptidase family enzymes across all three domains of life

Digging for red nuggets: Discovery of hot haloes surrounding massive, compact, relic galaxies

We present the results of Chandra X-ray observations of the isolated, massive, compact, relic galaxies MRK 1216 and PGC 032873. Compact massive galaxies observed at z > 2, also called red nuggets, formed in quick dissipative events and later grew by dry mergers into the local giant ellipticals. Due to the stochastic nature of mergers, a few of the primordial massive galaxies avoided the mergers and remained untouched over cosmic time.We find that the hot atmosphere surrounding MRK 1216 extends far beyond the stellar population and has a 0.5-7 keV X-ray luminosity of LX = (7.0 ± 0.2) × 1041 erg s-1, which is similar to the nearby X-ray bright giant ellipticals. The hot gas has a short central cooling time of ~50 Myr and the galaxy has an ~13-Gyr-old stellar population. The presence of an X-ray atmosphere with a short nominal cooling time and the lack of young stars indicate the presence of a sustained heating source, which prevented star formation since the dissipative origin of the galaxy 13 Gyr ago. The central temperature peak and the presence of radio emission in the core of the galaxy indicate that the heating source is radio-mechanical active galactic nucleus (AGN) feedback. Given that both MRK 1216 and PGC 032873 appear to have evolved in isolation, the order of magnitude difference in their current X-ray luminosity could be traced back to a difference in the ferocity of the AGN outbursts in these systems. Finally, we discuss the potential connection between the presence of hot haloes around such massive galaxies and the growth of super-/overmassive black holes via chaotic cold accretion. © 2018 The Author(s) Published by Oxford University Press on behalf of the Royal Astronomical Society

Tracing the origin of the AGN fuelling reservoir in MCG–6-30-15

The active galaxy MCG–6-30-15 has a 400 pc diameter stellar kinematically distinct core, counter-rotating with respect to the main body of the galaxy. Our previous high spatial resolution (0.1 arcsec) H-band observations of this galaxy mapped the stellar kinematics and [Fe II] 1.64 μm gas dynamics though mainly restricted to the spatial region of the counter-rotating core. In this work, we probe the stellar kinematics on a larger field of view and determine the ionized and molecular gas dynamics to study the formation of the counter-rotating core and the implications for active galactic nucleus (AGN) fuelling. We present integral field spectroscopy observations with SINFONI in the H and K bands in the central 1.2 kpc and with VIMOS HR-blue in the central 4 kpc of the galaxy. Ionized gas outflows of v_out ∼ 100 km s⁻¹ are traced by the [Ca VIII] 2.32 μm coronal line and extend out to at least a radius of r ∼ 140 pc. The molecular gas, traced by the H₂ 2.12 μm emission, is also counter-rotating with respect to the main body of the galaxy, indicating that the formation of the distinct core was associated with inflow of external gas into the centre of MCG–6-30-15. The molecular gas traces the available gas reservoir for AGN fuelling and is detected as close as r ∼ 50–100 pc. External gas accretion is able to significantly replenish the fuelling reservoir suggesting that the event which formed the counter-rotating core was also the main mechanism providing gas for AGN fuelling.PG acknowledges support from STFC (grant reference ST/J003697/2). This research has made use of the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. In this work, we used data obtained as part of the Two Micron All Sky Survey (2MASS), a joint project of the University of Massachusetts and the Infrared Processing and Analysis Center/California Institute of Technology, funded by the National Aeronautics and Space Administration and the National Science Foundation. This research has made use of NASA’s Astrophysics Data System

Improved measurements of turbulence in the hot gaseous atmospheres of nearby giant elliptical galaxies

We present significantly improved measurements of turbulent velocities in the hot gaseous haloes of nearby giant elliptical galaxies. Using deep XMM-Newton Reflection Grating Spectrometer (RGS) observations and a combination of resonance scattering and direct line broadening methods, we obtain well bounded constraints for 13 galaxies. Assuming that the turbulence is isotropic, we obtain a best-fitting mean 1D turbulent velocity of similar to 110 km s(-1). This implies a typical 3D Mach number similar to 0.45 and a typical non-thermal pressure contribution of similar to 6 per cent in the cores of nearby massive galaxies. The intrinsic scatter around these values is modest-consistent with zero, albeit with large statistical uncertainty-hinting at a common and quasi-continuous mechanism sourcing the velocity structure in these objects. Using conservative estimates of the spatial scales associated with the observed turbulent motions, we find that turbulent heating can be sufficient to offset radiative cooling in the inner regions of these galaxies (< 10 kpc, typically 2-3 kpc). The full potential of our analysis methods will be enabled by future X-ray micro-calorimeter observations

The mass distribution of the unusual merging cluster Abell 2146 from strong lensing

Abell 2146 consists of two galaxy clusters that have recently collided close to the plane of the sky, and it is unique in showing two large shocks on $\textit{Chandra X-ray Observatory}$ images. With an early stage merger, shortly after first core passage, one would expect the cluster galaxies and the dark matter to be leading the X-ray emitting plasma. In this regard, the cluster Abell 2146-A is very unusual in that the X-ray cool core appears to lead, rather than lag, the brightest cluster galaxy (BCG) in their trajectories. Here we present a strong-lensing analysis of multiple-image systems identified on $\textit{Hubble Space Telescope}$ images. In particular, we focus on the distribution of mass in Abell 2146-A in order to determine the centroid of the dark matter halo. We use object colours and morphologies to identify multiple-image systems; very conservatively, four of these systems are used as constraints on a lens mass model. We find that the centroid of the dark matter halo, constrained using the strongly lensed features, is coincident with the BCG, with an offset of ≈2 kpc between the centres of the dark matter halo and the BCG. Thus from the strong-lensing model, the X-ray cool core also leads the centroid of the dark matter in Abell 2146-A, with an offset of ≈30 kpc.JEC acknowledges support from The University of Texas at Dallas, and NASA through a Fellowship of the Texas Space Grant Consortium. Based on observations made with the NASA/ESA HST, obtained through programme 12871 through the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. Additional funding supporting JEC, LJK, and DIC came from a grant from the Space Telescope Science Institute under the same programme 12871. Additional funding supporting JEC and LJK came from a grant from the National Science Foundation, number 1517954. This work was supported in part by World Premier International Research Center Initiative (WPI Initiative), MEXT, Japan, and JSPS KAKENHI Grant Number 26800093 and 15H05892

HST imaging of the dusty filaments and nucleus swirl in NGC4696 at the centre of the Centaurus Cluster

Narrow-band HST imaging has resolved the detailed internal structure of the 10 kpc diameter H alpha+[NII] emission line nebulosity in NGC4696, the central galaxy in the nearby Centaurus cluster, showing that the dusty, molecular, filaments have a width of about 60pc. Optical morphology and velocity measurements indicate that the filaments are dragged out by the bubbling action of the radio source as part of the AGN feedback cycle. Using the drag force we find that the magnetic field in the filaments is in approximate pressure equipartition with the hot gas. The filamentary nature of the cold gas continues inward, swirling around and within the Bondi accretion radius of the central black hole, revealing the magnetic nature of the gas flows in massive elliptical galaxies. HST imaging resolves the magnetic, dusty, molecular filaments at the centre of the Centaurus cluster to a swirl around and within the Bondi radius.This is the accepted manuscript. It is currently embargoed pending publication

PISA analysis of the peptidase and propeller domain interface in the open and closed states of TbOPB, ApPREP and ApAAP.

<p>PDB codes for the analyses are shown. These are the same as those used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079349#pone-0079349-g003" target="_blank">Fig. 3</a>.</p

Comparison of the catalytic site in open and closed structures of prolyl oligopeptidase family enzymes.

<p>A: Detailed view of the active site of TbOPB in the open and closed state. Open and closed states are superposed to clearly show the localised structural changes that occur upon substrate binding/domain closure. Open state residues are coloured grey, closed state residues are coloured green, and the bound Antipain is coloured magenta. In the open state, the propeller domain Glu172 is a long distance from the active site residues. Arg650 is in a catalytically incompetent conformation in which it binds to the catalytic triad Asp648, displacing the catalytic triad His683 and the His loop from the active site, rupturing the catalytic triad and inactivating the enzyme. Upon domain closure, Glu172 is brought into the active site, where it pulls Arg650 into the catalytically competent position, away from the catalytic triad Asp648, which allows His683 and the His loop to swing into the active site, where His683 can complete the catalytic triad and activate the enzyme. B: ApPREP open (PDB code 3IUN) and closed (PDB code 3IVM) structures. C: ApAAP open (PDB code 3O4J) and closed (PDB code 2HU8) structures. Open and closed states are coloured, superposed, and shown in the same orientation as (A) to facilitate comparison between the different PREP family enzymes. Very similar global and local conformational changes are apparent in these structures, supporting a conserved mechanism of catalytic regulation in different PREP family enzymes. Residues in the open and closed structures are labeled in italic and bold type, respectively.</p

Data collection, phasing and refinement statistics.

<p>Numbers in parentheses refer to values in the highest resolution shell.</p>a<p><i>R</i>_sym = Σ_jΣ_h|<i>I</i>_h,j−<<i>I</i>_h>|/Σ_jΣ_h<<i>I</i>_h> where <i>I</i>_h,j is the jth observation of reflection h, and <<i>I</i>_h> is the mean intensity of that reflection.</p>b<p><i>R</i>_cryst = Σ||<i>F</i>_obs|−|<i>F</i>_calc||/Σ|<i>F</i>_obs| where <i>F</i>_obs and <i>F</i>_calc are the observed and calculated structure factor amplitudes, respectively.</p>c<p><i>R</i>_free is equivalent to <i>R</i>_cryst for a 4% subset of reflections not used in the refinement.</p

The catalytic site of TbOPB.

<p>A: Electron density of the active site of the TbOPB-Antipain closed state complex, contoured at the 0.8 σ level, where σ represents the RMS electron density for the unit cell. Contours more than 1.4 Å from any of the displayed atoms have been removed for clarity. TbOPB carbon atoms are coloured green, and Antipain carbon atoms are coloured magenta. B: Detailed view of the active site of the TbOPB-Antipain closed state complex. The catalytic triad Asp648, His683, and Ser563 form a charge relay. Ser563 forms a covalent hemiacetal transition state analogue complex with Antipain. The oxyanion is stabilized by Ala564 and Tyr482. The P1 Arg is bound to Glu607, Glu655, Arg650, and has a π-stacking interaction with Phe589. The P2 carbonyl is hydrogen bonded to Arg650. The LmOPB-antipain structure (PDB code 2XE4) determined previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0079349#pone.0079349-McLuskey1" target="_blank">[19]</a> is superimposed and is shown in line representation. The P3 Arg interacts with Ser523 and Leu617, whilst in TbOPB interactions are with Asp214 and Lys208 of the propeller domain. The P4 Phe does not make any specific interactions with enzyme residues in either TbOPB or LmOPB. TbOPB and LmOPB residues are labeled in bold and italic type, respectively.</p