Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda.

Journal ArticleResearch Support, Non-U.S. Gov'tThe presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the R(free) ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics.STFC UKCCP4BBSR

Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors.

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.Wellcome TrustYorkshire Cancer ResearchBBSRCEPSRCMR

An order-disorder twin crystal of L-2-haloacid dehalogenase from Sulfolobus tokodaii.

Journal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tThe L-2-haloacid dehalogenase enzymes catalyse the hydrolytic cleavage of a halogen from the C2 position of short-chain haloacids. The recombinant dehalogenase from the thermophilic archaeon Sulfolobus tokodaii has been cloned, overexpressed and purified to homogeneity. The 24 kDa enzyme was crystallized using the microbatch method in the monoclinic space group C2, with unit-cell parameters a = 127.6, b = 58.1, c = 51.2 A, beta = 97.2 degrees . Data were collected to 1.9 A resolution using synchrotron radiation and the structure was solved by molecular replacement. Analysis of the data and the preliminary refined model showed that the crystal was an order-disorder twin by reticular merohedry with a twin index of 10. It was possible to de-twin the experimental data utilizing the symmetry of the molecular layers from which the crystal is built.Engineering and Physical Sciences Research CouncilNIHBBSRCNWDA project awar

The crystal structure of human microsomal triglyceride transfer protein

This is the final version. Available from National Academy of Sciences via the DOI in this record.Data deposition: The data have been deposited in the Protein Data Bank, www.wwpdb.org (PDB ID code 6I7S).Microsomal triglyceride transfer protein (MTP) plays an essential role in lipid metabolism, especially in the biogenesis of very low-density lipoproteins and chylomicrons via the transfer of neutral lipids and the assembly of apoB-containing lipoproteins. Our understanding of the molecular mechanisms of MTP has been hindered by a lack of structural information of this heterodimeric complex comprising an MTPα subunit and a protein disulfide isomerase (PDI) β-subunit. The structure of MTP presented here gives important insights into the potential mechanisms of action of this essential lipid transfer molecule, structure-based rationale for previously reported disease-causing mutations, and a means for rational drug design against cardiovascular disease and obesity. In contrast to the previously reported structure of lipovitellin, which has a funnel-like lipid-binding cavity, the lipid-binding site is encompassed in a β-sandwich formed by 2 β-sheets from the C-terminal domain of MTPα. The lipid-binding cavity of MTPα is large enough to accommodate a single lipid. PDI independently has a major role in oxidative protein folding in the endoplasmic reticulum. Comparison of the mechanism of MTPα binding by PDI with previously published structures gives insights into large protein substrate binding by PDI and suggests that the previous structures of human PDI represent the "substrate-bound" and "free" states rather than differences arising from redox state.Academy of FinlandAcademy of FinlandSigrid Juselius FoundationBiocenter Oul

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.Marie Curie Career Integration GrantIsrael Science FoundationIsraeli Cancer Associatio

Structural effects in UO2_2 thin films irradiated with fission-energy Xe ions

Uranium dioxide thin films have been successfully grown on LSAT (Al$_{10}$La$_3$O$_{51}$Sr$_{14}$Ta$_7$) substrates by reactive magnetron sputtering. Irradiation by 92 MeV $^{129}$Xe$^{23+}$ ions to simulate fission damage that occurs within nuclear fuels caused microstructural and crystallographic changes. Initially flat and continuous thin films were produced by magnetron sputtering with a root mean square roughness of 0.35 nm determined by AFM. After irradiation, this roughness increased to 60-70 nm, with the films developing discrete microstructural features: small grains (~3 $\mu$m), along with larger circular (up to 40 $\mu$m) and linear formations with non-uniform composition according to the SEM, AFM and EDX results. The irradiation caused significant restructuring of the UO$_2$ films that was manifested in significant filmsubstrate mixing, observed through EDX analysis. Diffusion of Al from the substrate into the film in unirradiated samples was also observed.Engineering and Physical Sciences Research Council (Grant ID: EP/ I036400/1), Radioactive Waste Management Ltd (formerly the Radioactive Waste Management Directorate of the UK Nuclear Decommissioning Authority, contract NPO004411A-EPS02), Russian Foundation for Basic Research (projects 13-03-90916), CSAR, Grand Accelélérateur National d’Ions Lourds (GANIL) Caen France, French Network EMIR, CIMAP-CIRIL, M.V.Lomonosov Moscow State University Program of Development, CKP FMI IPCE RA

Non-minimal coupling of the Higgs boson to curvature in an inflationary universe

In the absence of new physics around 10^10 GeV, the electroweak vacuum is at best metastable. This represents a major challenge for high scale in ationary models as, during the early rapid expansion of the universe, it seems difficult to understand how the Higgs vacuum would not decay to the true lower vacuum of the theory with catas- trophic consequences if inflation took place at a scale above 10^10 GeV. In this paper we show that the non-minimal coupling of the Higgs boson to curvature could solve this problem by generating a direct coupling of the Higgs boson to the inflationary potential thereby stabilizing the electroweak vacuum. For specific values of the Higgs field initial condition and of its non-minimal coupling, inflation can drive the Higgs field to the electroweak vacuum quickly during inflation

Magnetic dating of the Holocene monogenetic Tkarsheti volcano in the Kazbeki region (Great Caucasus)

The radiocarbon technique is widely used to date Late Pleistocene and Holocene lava flows. The significant difference with palaeomagnetic methods is that the 14C dating is performed on the organic matter carbonized by the rock formation or the paleosols found within or below the lava flow. On the contrary, the archaeomagnetic dating allows to date the moment when the lava is cooling down below the Curie temperatures. In the present study, we use the paleomagnetic dating to constrain the age of the Tkarsheti monogenetic volcano located within the Kazbeki Volcanic Province (Great Caucasus). A series of rock-magnetic experiments including the measurement of hysteresis curves, isothermal remanence, back-field and continuous thermomagnetic curves were applied. These experiments indicated that Pseudo-Single-Domain Ti-poor titanomagnetite is responsible for remanence. A characteristic remanent magnetization was obtained for all twenty analyzed samples yielding a stable single magnetization component observed upon both thermal and alternating field treatments. Comparison of the mean directions obtained (Inc = 48.6º, Dec = 6.4º, A95 = 4.0° and K = 67) with the SCHA.DIF.14k model yielded two main time intervals (4740–4650 or 4427– 4188 BC) as the best age estimate of the Lesser Tkarsheti lava flow. These results suggest an earlier age (between approximately 200 and 700 years) for this monogenetic lava flow than expected from the estimated age provided by a former 14C dating obtained in 1973 on woody remains. This first attempt to use the archaeomagnetic technique in the Caucasus indicates that the SCHA.DIF.14k geomagnetic model may be successfully used for dating purposes in the region.Projects BU0066U16 and BU235P18 (Junta de Castilla y Leon, Spain) and the European Regional Development Fund (ERDF). AG is grateful for financial support of CONACyT 252149 and UNAM-PAPIIT project 101717. MC-R and AC acknowledge the financial support given by the Junta de Castilla y León (project BU235P18) and the European Regional Development Fund (ERD)