Recent research highlights
Functionalised carbon nanomaterials as nucleants
Govada et al. 2016 Sci Rep 6:20053; Leese et al. 2016 Chem Sci 7:2916
Characterization and architecture of yeast SWR1 histone exchange complex
Chromatin remodeling alters chromatin structure to make DNA more accessible for DNA regulatory proteins those are involved in the transcription, replication and DNA repair. SWR1 is an ATP-dependent chromatin remodeling complex that catalyzes the exchange of the variant histone Htz1 with the canonical histone H2A in the nucleosome. SWR1 complex is composed of fourteen subunits with a molecular weight about 1.07 MDa. We expressed and purified SWR1 complex from insect cells and the recombinant material is active in both gel and FRET-based histone exchange assays. We used subunit deletions and serial truncation of the Swr1 main subunit to investigate interactions between subunits of the SWR1 complex. Finally, we present electron microscopy studies revealing the dynamic nature of the complex and a 21 Å resolution reconstruction of the intact complex provides details not apparent in previously reported structures, including a large central cavity of sufficient size to accommodate a nucleosome (Lin et al. (2017) Nucleic Acids Res.).
Mechanism for Nuclease Regulation in RecBCD
In Escherichia Coli, the helicase-nuclease protein complex RecBCD is responsible for processing double strand breaks for repair by homologous recombination. There is little structural information available about how the multiple activities of RecBCD are regulated. The group of Prof. Dale Wigley have solved a 3.8Å resolution cryo-EM structure of RecBCD with a DNA substrate that reveals a mechanism for nuclease activation within the complex. Interactions between the unwound 5’ ssDNA tail and RecD initiate conformational changes that transmit through all three subunits to release a blocking helix from the nuclease active site. A bacterial SH3-like domain plays a key role in the conformational changes that lead to activation (Wilkinson et al. (2016) eLife 5:e18227).
TssA forms a gp6‐like ring attached to the type VI secretion sheath
The type VI secretion system (T6SS) is a supra‐molecular bacterial complex that resembles phage tails. It is a killing machine which fires toxins into target cells upon contraction of its TssBC sheath. Here, we show that TssA1 is a T6SS component forming dodecameric ring structures whose dimensions match those of the TssBC sheath and which can accommodate the inner Hcp tube. The TssA1 ring complex binds the T6SS sheath and impacts its behaviour in vivo. In the phage, the first disc of the gp18 sheath sits on a baseplate wherein gp6 is a dodecameric ring. The Filloux and Freemont groups found remarkable sequence and structural similarities between TssA1 and gp6 C‐termini, and they propose that TssA1 could be a baseplate component of the T6SS. Furthermore, they identified similarities between TssK1 and gp8, the former interacting with TssA1 while the latter is found in the outer radius of the gp6 ring. These observations, combined with similarities between TssF and gp6N‐terminus or TssG and gp53, lead them to propose a comparative model between the phage baseplate and the T6SS (Planamente et al. (2016) EMBO J 35:1613).
A Salmonella toxin promotes persister formation through tRNA acetylation
All bacterial species form persisters, which are cells that stop replicating and are tolerant to many antibiotics. Persisters are likely to be a cause of many recurrent infections, but little is known about how they arise. Salmonella, which causes gastroenteritis and typhoid fever, forms large numbers of non-replicating persisters after being engulfed by immune cells called macrophages. At least 14 Toxin-Antitoxin modules of Salmonella are involved in the formation of persisters after uptake by macrophages. Work from the Helaine and Hare groups led to the characterization of one of these toxins of a new type. They solved its crystal structure and revealed that it blocks protein production by acetylation of aminoacyl-tRNAs (Cheverton et al. (2016) Mol Cell 16:30139).
Functionalised carbon nanomaterials as nucleants for macromolecular crystallization
Naomi Chayen and colleagues report the first large-scale systematic analysis of a series of carbon nanomaterials (CNMs) with different surface functionalization for their effectiveness in inducing crystal nucleation. Functionalised CNMs are particularly attractive as their reactions tend to create combinations of surface area, porosity and surface heterogeneity (created by topography and chemistry) which are important for crystal nucleation of proteins and other macromolecules. Sparsely functionalized ﬂat sheet geometries proved exceptionally eﬀective leading to a new class of nucleant, based on PEG grafted graphene-related materials that can be applied to promote the growth of 3D crystals for X-ray crystallography (Govada et al. (2016)Scientific Reports Nature publishing Group 6:20053; Leese et al. (2016) Chemical Science 7, 2916-2923).
Structure of UapA suggest role for homodimerisation in transport activity
The high resolution structure of the eukaryotic purine/H+ symporter, UapA, in complex with xanthine revealed that the protein forms a closely associated dimer. The structure revealed novel details on the precise molecular basis substrate binding and selectivity and also showed that dimerisation plays a key role in transporter function (Alguel et al. 2016 Nature Communications 7:11336).
Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family.
Bacteria from the Neisseriaceae family of human pathogens extract the haem group from haemoglobin as an important iron source. Work from Stephen Hare’s group has revealed the structure of one of the receptor components, HpuA, in complex with haemoglobin. These results demonstrate how bacteria are able to diversify the sequence of this protein to avoid antibody recognition and yet retain haemoglobin binding (Wong et al. 2015 Nature Communications 6:10172).
Structural basis of complement membrane attack complex formation
The group of Dr Doryen Bubeck solved the electron cryo-microscopy structure of human membrane attack complex (MAC) at 7.3 Å resolution. The structure reveals the stochiometry of the complete pore and identifies a network of interaction interfaces that determine its assembly mechanism. MAC adopts a 'split-washer' configuration where assembly precursors partially penetrate the lipid bilayer resulting in an irregular β-barrel pore. Nat Comms, 2016 vol. 7, 10587. Imperial News website coverage.
Perk tetramer crystal structure in ER stress signaling
The group of Dr Maruf Ali solved the crystal structure of human PERK luminal domain captured in a novel tetramer arrangement. Biochemical and cellular analysis suggests that tetramer arrangement maybe a key regulatory step in ER stress signaling. EMBO J, 2015 vol. 34 (11) pp. 1589-1600.
Novel allosteric model for Unfolded Protein Response (UPR) induction
The group of Dr Maruf Ali discovered a non-canonical interaction between the ATPase domain of ER hsp70 chaperone termed BiP, and the luminal domains of UPR sensor proteins Ire1 and Perk, that dissociates upon addition of authentic misfolded protein CH1, leading to them proposing an allosteric model for UPR induction (eLife 2015;4:e03522. DOI: 10.7554/eLife.03522, http://f1000.com/prime/725357434).
Regulation of bacterial RNAP by σ factors
The group of Xiaodong Zhang, in collaboration with researchers in China and the US, has determined the structure of bacterial RNA polymerase in complex with σ54. Their work reveals the molecular basis by which binding of σ54 to RNAP inhibits gene transcription in bacteria, and it is hoped that these insights will lead to the development of new strategies in the fight against antibiotic resistant bacteria (Yang et al. , Science 349:6250).
Regulation of the type VI secretion system
In work combining in vitro interaction assays, X-ray crystallography and molecular phylogeny, the groups of Alain Filloux and Paul Freemont uncovered a division among type VI secretion systems. The different subclasses are thought to have distinct mechanisms of secretion sheath disassembly (Förster et al. , JBC 289:33032).
Repair of DNA double-strand breaks
The group of Xiaodong Zhang and colleagues from the London Research Institute present a biochemical and structural characterization of the full-length tumor suppressor BRCA2, alone and in complex with RAD51. BRCA2 exists as a dimer and facilitates nucleation of RAD51 filaments at multiple sites on single-stranded DNA, which is important for the repair of DNA double-strand breaks (Shahid et al.  NSMB 21:962).
Lipoteichoic acid biosynthesis
The structures of the extracellular domains of LtaP and LtaS, two homologous enzymes responsible for the biosynthesis of lipoteichoic acid (LTA), an essential component of the Listeria monocytogenes cell wall, were determined in the labs of Angelika Gründling and Paul Freemont. Differences in the active site arrangement provided important clues on the molecular bases for the difference in enzyme specificity. A third structure containing an additional bound substrate molecule allowed proposing a revised mechanism for LTA biosynthesis and a model for the binding of the growing chain (Campeotto et al. , JBC 289:28054).
Alfonso De Simone and colleagues have used a combination of solid-state and solution NMR spectroscopy to characterise the structure and dynamics of α-synuclein interacting with lipid membranes (Fusco et al. , Nat Commun 5:3827). This is a central interaction for synaptic regulation as well as for the mechanisms leading to Parkinson's disease.
Phosphoregulation of Ire1 RNase splicing activity
Maruf Ali and colleagues have shown how Ire1, an essential mediator of the unfolded protein response within the endoplasmic reticulum, is regulated by phosphorylation of its kinase domain (Prischi et al. , Nat Commun 5:3554).
Specific DNA recognition by a type IV pilin
Vladimir Pelicic and colleagues have identified and characterised the specific DNA receptor that allows Neisseria and many other species to recognise their own DNA during natural transformation (Cehovin et al. , PNAS 110:3065).
Pore formation by a bacterial toxin
Doryen Bubeck and colleagues have determined the structure of a pore-forming bacterial toxin in complex with the human immune receptor, CD59 (Johnson et al. , Cell Rep 3:1369). This work provides a structural basis for how CD59 nucleates an early prepore state of this bacterial cytolysin.
Bacteria under nutrient starvation produce antibacterial peptides for survival. Konstantinos Beis’ group has recently determined the structure of the siderophore receptor FhuA in complex with the antibacterial peptide MccJ25 (Mathavan et al. , Nat Chem Biol 10:340). The structure explains how structurally unrelated peptides can hijack outer membrane receptors for internalization and subsequent cell death. This mechanism gives the peptide-producing bacteria higher chances for survival. The findings open the route to new antimicrobials to treat infections.
Viral RNA replication
The groups of Stephen Curry and Steve Matthews have recently reported the first structures of calicivirus VPg, unusual protein primers that are required for virus RNA replication (Leen et al. , J Virol 87:5318). Remarkably, because they become attached to the 5´end of the RNA genome, they also have an important role in initiating protein synthesis.
Naomi Chayen’s group and collaborators have designed a new way of obtaining crystals by imprinting polymers (MIPs) with protein molecules (Saridakis and Chayen , Trends Biotechnol, 31:515). The technique is currently in the process of being commercialised. The imprinting creates a fingerprint of the protein on the polymer and exhibits selectiv e re-bind ing of the protein, thereby enabling it to serve as a tailor-made nucleant. MIPs are effective in both screening and opti misation of crystallization. MIP-containing screening trials yielded hits for proteins that had not produced useful crystals or indeed any crystals at all in their absence or in the presence of traditional nucleants. At the optimization stage, the presence of MIPs led to faster formation of crystals and to major improvement in diffraction in some cases (Saridakis et al. , PNAS 108:11081).