Structure of the response regulator VicR DNA-binding domain

The structure of the DNA-binding domain of the response regulator VicR from E. faecalis has been solved at 1.9 Å resolution. It is very similar to the related domains from PhoB and OmpR, but differs in two loops that may affect transcription activation or DNA–protein interactions

Structures of alternatively spliced isoforms of human ketohexokinase

The structures of the two alternatively spliced isoforms of human ketohexokinase, hepatic KHK-C and peripheral KHK-A, and of the ternary complex of KHK-A with the substrate fructose and AMP-PNP have been solved. The differences between KHK-A and KHK-C resulting from the spliced region are subtle and affect thermostability and probably flexibility; the mutations causing fructosuria were modelled

Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus

The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed

Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus. Corrigendum

A corrigendum to the paper by Carr et al. (2006), Acta Cryst. F62, 1164–1167

Purification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans

Two manganese superoxide dismutase enzymes isolated from the eukaryote C. elegans have been characterized and their structures determined. The closely related structures reveal a striking similarity to manganese superoxide dismutase found in humans

Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging

Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 degrees C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery.Peer reviewe

Electron-deuteron scattering in a current-conserving description of relativistic bound states: formalism and impulse approximation calculations

The electromagnetic interactions of a relativistic two-body bound state are formulated in three dimensions using an equal-time (ET) formalism. This involves a systematic reduction of four-dimensional dynamics to a three-dimensional form by integrating out the time components of relative momenta. A conserved electromagnetic current is developed for the ET formalism. It is shown that consistent truncations of the electromagnetic current and the $NN$ interaction kernel may be made, order-by-order in the coupling constants, such that appropriate Ward-Takahashi identities are satisfied. A meson-exchange model of the $NN$ interaction is used to calculate deuteron vertex functions. Calculations of electromagnetic form factors for elastic scattering of electrons by deuterium are performed using an impulse-approximation current. Negative-energy components of the deuteron's vertex function and retardation effects in the meson-exchange interaction are found to have only minor effects on the deuteron form factors.Comment: 42 pages, RevTe

'This was a Conradian world I was entering': Postcolonial river-journeys beyond the Black Atlantic in Caryl Phillips's work

Caryl Phillips has been accused of replicating the stereotyped view of a timeless, ahistorical Africa that Paul Gilroy puts forward in his paradigm of the Black Atlantic. Yet this article shows that Crossing the River and Phillips’s essays about Africa suggest ways in which Gilroy’s important paradigm of the black Atlantic could be broadened to become more inclusive of writing about Africa. Phillips draws inspiration from writers such as V S Naipaul, Chinua Achebe, and especially Joseph Conrad, to update the literary journey upriver and make it relevant to contemporary West African issues. A complex interplay of racial identities occurs when people from the African diaspora travel to Africa; this is a key preoccupation for Phillips when he rewrites Conrad. During the course of his river-journeys, Phillips meditates upon the complexities of being a black Westerner in Africa, examines the memory of slavery, colonialism and postcolonial unrest, problematises diasporan attempts to ‘return’ to Africa, and recognises the longstanding modernity of African countries

Rewriting Nature’s Assembly Manual for a ssRNA Virus

Satellite Tobacco Necrosis Virus (STNV) is one of the smallest viruses known. Its genome encodes only its coat protein (CP) subunit relying on the polymerase of its helper virus TNV for replication. The genome contains a cryptic set of dispersed assembly signals in the form of stem-loops that each present a minimal CP binding motif -A.X.X.A- in the loops. The genomic fragment encompassing nucleotides 1-127 is predicted to contain five such Packaging Signals (PSs). We have used mutagenesis to determine the critical assembly features in this region. These include the CP binding motif, the relative placement of PS stem-loops, their number and their folding propensity. CP binding has an electrostatic contribution but assembly nucleation is dominated by the recognition of the folded PSs in the RNA fragment. Mutation to remove all –A.X.X.A- motifs in PSs throughout the genome yields an RNA that is unable to assemble efficiently. In contrast, when a synthetic 127nt fragment encompassing improved PSs is swapped onto the RNA otherwise lacking CP recognition motifs assembly is partially restored although the virus-like particles created are incomplete, implying that PSs outside this region are required for correct assembly. Swapping this improved region into the wild-type STNV1 sequence results in a better assembly substrate than the viral RNA, producing complete capsids and outcompeting the wild-type genome in head-to-head competition. These data confirm details of the PS-mediated assembly mechanism for STNV, and identify an efficient approach for production of stable viruslike particles encapsidating non-native RNAs or other cargoes