Towards more rational approaches of membrane protein stabilisation and novel structures of membrane-bound pyrophosphatase

Membrane proteins have a range of crucial biological functions and are targeted by most prescribed drugs despite lagging behind soluble proteins when it comes to their biochemical and biophysical characterisation. A major bottleneck in membrane protein research is protein instability upon extraction. Protein stabilisation strategies are typically expensive and labour-intensive. Therefore, I contributed to the development and evaluation of two new general-purpose tools, both designed for the streamlined and rational stabilisation of membrane proteins. The first tool, the integral membrane protein stability selector (IMPROvER), predicts stabilising point-mutations in membrane proteins using three individual approaches with additive prediction power. The second tool, a novel pre-prepared and easy-to-use screen for the high-throughput identification of stabilising lipids, facilitates the structural and functional analysis of stable and physiologically relevant protein sample. Both tools were successfully employed to stabilise a range of membrane proteins with different folds, topologies and modes of action at significantly reduced cost and work effort. Moreover, engineered or natively thermostable membrane-bound pyrophosphatases (M-PPase), were studied in more detail using conventional and time-resolved X-ray crystallography. Based on structural data obtained on a pyrophosphate-energised K+-independent H+-pump, I derived an updated model of ion-selectivity that is centred on a glutamate-serine interplay at the ion-gate. This is the first model that explains ion selectivity in all M PPase subclasses when considering functional asymmetry. Indeed, complementary time-resolved structural studies of a K+-dependent Na+-pump revealed asymmetric substrate binding to M-PPase active sites. These findings give valuable mechanistic insights into key processes of M-PPase biochemistry, which are of upmost importance for structure-guided drug discovery. Ultimately, tweaking M-PPase function has the potential to address existing and emerging challenges to human health and global food security as M-PPases play a vital role in the stress resistance of pathogens or salt and drought resistance in plants

A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution

Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A(2A)R). A(2A)R is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.Peer reviewe

IMPROvER : the Integral Membrane Protein Stability Selector

Identifying stabilising variants of membrane protein targets is often required for structure determination. Our new computational pipeline, the Integral Membrane Protein Stability Selector (IMPROvER) provides a rational approach to variant selection by employing three independent approaches: deep-sequence, model-based and data-driven. In silico tests using known stability data, and in vitro tests using three membrane protein targets with 7, 11 and 16 transmembrane helices provided measures of success. In vitro, individual approaches alone all identified stabilising variants at a rate better than expected by random selection. Low numbers of overlapping predictions between approaches meant a greater success rate was achieved (fourfold better than random) when approaches were combined and selections restricted to the highest ranked sites. The mix of information IMPROvER uses can be extracted for any helical membrane protein. We have developed the first general-purpose tool for selecting stabilising variants of alpha -helical membrane proteins, increasing efficiency and reducing workload. IMPROvER can be accessed at http://improver.ddns.net/IMPROvER/.Peer reviewe

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

The Role of Coastal Yedoma Deposits and Continental Shelf Sediments in the Arctic Ocean Silicon Cycle

The availability of silicon (Si) in the ocean plays an important role in regulating biogeochemical and ecological processes. The Si budget of the Arctic Ocean appears balanced, with inputs equivalent to outputs, though it is unclear how a changing climate might aggravate this balance. In this study, we focus on Si cycling in Arctic coastal areas and continental shelf sediments to better constrain the Arctic Ocean Si budget. We provide the first estimate of amorphous Si (ASi) loading from erosion of coastal Yedoma deposits (30–90 Gmol yr−1), demonstrating comparable rates to particulate Si loading from rivers (10–90 Gmol yr−1). We found a positive relationship between surface sediment ASi and organic matter content on continental shelves. Combining these values with published Arctic shelf sediment properties and burial rates we estimate 70 Gmol Si yr−1 is buried on Arctic continental shelves, equivalent to 4.5% of all Si inputs to the Arctic Ocean. Sediment dissolved Si fluxes increased with distance from river mouths along cruise transects of shelf regions influenced by major rivers in the Laptev and East Siberian seas. On an annual basis, we estimate that Arctic shelf sediments recycle approximately up to twice as much DSi (680 Gmol Si) as is loaded from rivers (340–500 Gmol Si)

The Permafrost Young Researchers Network (PYRN) is getting older: The past, present, and future of our evolving community

International audienceA lasting legacy of the International Polar Year (IPY) 2007–2008 was the promotion of the Permafrost Young Researchers Network (PYRN), initially an IPY outreach and education activity by the International Permafrost Association (IPA). With the momentum of IPY, PYRN developed into a thriving network that still connects young permafrost scientists, engineers, and researchers from other disciplines. This research note summarises (1) PYRN’s development since 2005 and the IPY’s role, (2) the first 2015 PYRN census and survey results, and (3) PYRN’s future plans to improve international and interdisciplinary exchange between young researchers. The review concludes that PYRN is an established network within the polar research community that has continually developed since 2005. PYRN’s successful activities were largely fostered by IPY. With >200 of the 1200 registered members active and engaged, PYRN is capitalising on the availability of social media tools and rising to meet environmental challenges while maintaining its role as a successful network honouring the legacy of IPY

Search for the dimuon decay of the Higgs boson in pppp collisions at s\sqrt{s} = 13 TeV with the ATLAS detector

International audienceA search for the dimuon decay of the Higgs boson was performed using data corresponding to an integrated luminosity of 36.1  fb-1 collected with the ATLAS detector in pp collisions at s=13  TeV at the Large Hadron Collider. No significant excess is observed above the expected background. The observed (expected) upper limit on the cross section times branching ratio is 3.0 (3.1) times the Standard Model prediction at the 95% confidence level for a Higgs boson mass of 125 GeV. When combined with the pp collision data at s=7  TeV and s=8  TeV, the observed (expected) upper limit is 2.8 (2.9) times the Standard Model prediction

Measurements of ttˉt\bar{t} differential cross-sections of highly boosted top quarks decaying to all-hadronic final states in pppp collisions at s=13 \sqrt{s}=13\, TeV using the ATLAS detector

Measurements are made of differential cross-sections of highly boosted pair-produced top quarks as a function of top-quark and $t\bar{t}$ system kinematic observables using proton--proton collisions at a center-of-mass energy of $\sqrt{s} = 13$ TeV. The data set corresponds to an integrated luminosity of $36.1$ fb$^{-1}$, recorded in 2015 and 2016 with the ATLAS detector at the CERN Large Hadron Collider. Events with two large-radius jets in the final state, one with transverse momentum $p_{\rm T} > 500$ GeV and a second with $p_{\rm T}>350$ GeV, are used for the measurement. The top-quark candidates are separated from the multijet background using jet substructure information and association with a $b$-tagged jet. The measured spectra are corrected for detector effects to a particle-level fiducial phase space and a parton-level limited phase space, and are compared to several Monte Carlo simulations by means of calculated $\chi^2$ values. The cross-section for $t\bar{t}$ production in the fiducial phase-space region is $292 \pm 7 \ \rm{(stat)} \pm 76 \rm{(syst)}$ fb, to be compared to the theoretical prediction of $384 \pm 36$ fb

Study of the material of the ATLAS inner detector for Run 2 of the LHC

International audienceThe ATLAS inner detector comprises three different sub-detectors: the pixel detector, the silicon strip tracker, and the transition-radiation drift-tube tracker. The Insertable B-Layer, a new innermost pixel layer, was installed during the shutdown period in 2014, together with modifications to the layout of the cables and support structures of the existing pixel detector. The material in the inner detector is studied with several methods, using a low-luminosity √s=13 TeV pp collision sample corresponding to around 2.0 nb−1 collected in 2015 with the ATLAS experiment at the LHC. In this paper, the material within the innermost barrel region is studied using reconstructed hadronic interaction and photon conversion vertices. For the forward rapidity region, the material is probed by a measurement of the efficiency with which single tracks reconstructed from pixel detector hits alone can be extended with hits on the track in the strip layers. The results of these studies have been taken into account in an improved description of the material in the ATLAS inner detector simulation, resulting in a reduction in the uncertainties associated with the charged-particle reconstruction efficiency determined from simulation