Articoli di riviste: "Domain structure"

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Daminov, Mirzogid Islomovich, Mirzo Zokirovich Sharipov, Rustam Khalilovich Shamsiev e Dilshod Ergashovich Khaitov. "DOMAIN STRUCTURE AND SOME PROPERTIES OF RARE-EARTH GRANITE FERRITES". Scientific Reports of Bukhara State University 4, n. 3 (26 giugno 2020): 3–9. http://dx.doi.org/10.52297/2181-1466/2020/4/3/12.

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The crystals of rare-earth garnet ferrites have a complex domain structure, the form of which substantially depends on the crystallographic orientation of the under study sample. Due to the cubic symmetry of rare-earth garnet ferrites, 70, 110, and 180-degree domains can exist in them, and depending on the crystallographic orientation of the sample, the spontaneous magnetization vector in the realized domain configuration can lie in the plane of the sample (“Cotton” domains) perpendicular to the plane of the sample ("Faraday" domains), and make up a certain angle with its plane. According to known data, in all cases, the boundaries between neighboring domains in rare-earth garnet ferrites are the domain walls of the Bloch type

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Berrondo, Monica, Marc Ostermeier e Jeffrey J. Gray. "Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains". Structure 16, n. 4 (aprile 2008): 513–27. http://dx.doi.org/10.1016/j.str.2008.01.012.

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Biggin, Phil C., Tarmo Roosild e Senyon Choe. "Potassium channel structure: domain by domain". Current Opinion in Structural Biology 10, n. 4 (agosto 2000): 456–61. http://dx.doi.org/10.1016/s0959-440x(00)00114-7.

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Urs, Usha K., Ramachandran Murali e H. M. Krishna Murthy. "Structure of Taq DNA polymerase shows a new orientation for the structure-specific nuclease domain". Acta Crystallographica Section D Biological Crystallography 55, n. 12 (1 dicembre 1999): 1971–77. http://dx.doi.org/10.1107/s0907444999011324.

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Thermus aquaticus DNA polymerase I consists of the polymerase, the structure-specific nuclease and the vestigial editing nuclease domains. Three-dimensional structures of the native enzyme and its complex with DNA have already been reported. The structure of a complex with an inhibitory antibody has also been determined. The structure of the native enzyme in a different crystal form determined at 2.6 Å is reported here. Optimized anomalous diffraction measurements made at the holmium L III edge were valuable in validating solutions obtained through molecular replacement. The structure of the polymerase domain is similar to those reported previously, while the relative orientation of the structure-specific nuclease domain is significantly different from those of the native enzyme and the DNA complex; it is, however, identical to that observed in the structure of the Fab complex. In the structures of the native enzyme and of the DNA complex reported previously, the active site of the structure-specific nuclease domain is too far from that of the polymerase domain, making it difficult to propose a structural model for the in vivo primer-excision and nick-translation activities of the enzyme. In the present structure, the two active sites are considerably closer. Taken together, the reported structure of the native enzyme, that of the Fab complex and the present structure imply that the different orientation of the structure-specific nuclease domain is probably a consequence of intrinsically high relative mobility between these two domains in this enzyme.

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Guardado-Calvo, Pablo, Eva M. Muñoz, Antonio L. Llamas-Saiz, Gavin C. Fox, Richard Kahn, David T. Curiel, Joel N. Glasgow e Mark J. van Raaij. "Crystallographic Structure of Porcine Adenovirus Type 4 Fiber Head and Galectin Domains". Journal of Virology 84, n. 20 (4 agosto 2010): 10558–68. http://dx.doi.org/10.1128/jvi.00997-10.

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ABSTRACT Adenovirus isolate NADC-1, a strain of porcine adenovirus type 4, has a fiber containing an N-terminal virus attachment region, shaft and head domains, and a C-terminal galectin domain connected to the head by an RGD-containing sequence. The crystal structure of the head domain is similar to previously solved adenovirus fiber head domains, but specific residues for binding the coxsackievirus and adenovirus receptor (CAR), CD46, or sialic acid are not conserved. The structure of the galectin domain reveals an interaction interface between its two carbohydrate recognition domains, locating both sugar binding sites face to face. Sequence evidence suggests other tandem-repeat galectins have the same arrangement. We show that the galectin domain binds carbohydrates containing lactose and N-acetyl-lactosamine units, and we present structures of the galectin domain with lactose, N-acetyl-lactosamine, 3-aminopropyl-lacto-N-neotetraose, and 2-aminoethyl-tri(N-acetyl-lactosamine), confirming the domain as a bona fide galectin domain.

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Shcherbakov, V. P., e S. A. Tarashchan. "Domain structure of titanomagnetite grains with closure domains". Physics of the Earth and Planetary Interiors 65, n. 1-2 (gennaio 1990): 177–87. http://dx.doi.org/10.1016/0031-9201(90)90085-c.

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Zhou, Xiaogen, Jun Hu, Chengxin Zhang, Guijun Zhang e Yang Zhang. "Assembling multidomain protein structures through analogous global structural alignments". Proceedings of the National Academy of Sciences 116, n. 32 (24 luglio 2019): 15930–38. http://dx.doi.org/10.1073/pnas.1905068116.

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Most proteins exist with multiple domains in cells for cooperative functionality. However, structural biology and protein folding methods are often optimized for single-domain structures, resulting in a rapidly growing gap between the improved capability for tertiary structure determination and high demand for multidomain structure models. We have developed a pipeline, termed DEMO, for constructing multidomain protein structures by docking-based domain assembly simulations, with interdomain orientations determined by the distance profiles from analogous templates as detected through domain-level structure alignments. The pipeline was tested on a comprehensive benchmark set of 356 proteins consisting of 2–7 continuous and discontinuous domains, for which DEMO generated models with correct global fold (TM-score > 0.5) for 86% of cases with continuous domains and for 100% of cases with discontinuous domain structures, starting from randomly oriented target-domain structures. DEMO was also applied to reassemble multidomain targets in the CASP12 and CASP13 experiments using domain structures excised from the top server predictions, where the full-length DEMO models showed a significantly improved quality over the original server models. Finally, sparse restraints of mass spectrometry-generated cross-linking data and cryo-EM density maps are incorporated into DEMO, resulting in improvements in the average TM-score by 6.3% and 12.5%, respectively. The results demonstrate an efficient approach to assembling multidomain structures, which can be easily used for automated, genome-scale multidomain protein structure assembly.

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Tsukahara, S. "Atomic Structure-Sensitive Magnetic Domain Structures of Thin Films". Proceedings, annual meeting, Electron Microscopy Society of America 43 (agosto 1985): 206–9. http://dx.doi.org/10.1017/s0424820100117960.

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Transmission electron microscopy, TEM, that can serve for observation of both atomic and magnetic structures is useful to investigate structure sensitive magnetic properties. It is most effective when it is applied to thin films for which direct interpretation of the results is possible without considering additional effects through specimen handling for TEM use and modification of dimension dependent magnetic properties.Transmission Lorentz microscopy, TLM, to observe magnetic domains has been known for a quarter century. Among TLM modes the defocused mode has been most popular due to its simple way of operation. Recent development of TEM made it possible that an average instrument commercially available could be easily operated at any TLM modes to produce high quality images. This paper mainly utilizes the Foucault mode to investigate domain walls and magnetization ripples as the finest details of domain structure.

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Chzhan, A. V., V. N. Vasiliev, T. N. Isaeva e G. S. Patrin. "Research of Features Magnetic Permeability and Domain Structures in Fe₂O₃:GA Crystals near the Morin Transition". Solid State Phenomena 152-153 (aprile 2009): 29–32. http://dx.doi.org/10.4028/www.scientific.net/ssp.152-153.29.

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Specially picked up web-chamber is used for visualization of domain structure in hematite. An analysis of domain configuration shows, that domain structure of hematite in a basal plane represents multilayered structure which contains domains both in paralleled thickness and in the parallel basal planes. The temperature features of magnetic permeability and domain structures in Fe2O3:Ga crystals near the Morin transition are investigated. Observable changes of magnetic permeability and changes in domain structure confirm that transition from АFM to WFM occurs in the hematite with Ga impurity as transition of the first sort. Results of research of antiferromagnetic and weakly ferromagnetic resonances (AFMR and WFMR) in these compounds are presented.

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Inoshita, Takumi, Yasuhide Inoue, Yoichi Horibe e Yasumasa Koyama. "Features of the ferroelectric domain structure in the multiferroic material YbMnO3". MRS Advances 1, n. 9 (2016): 591–96. http://dx.doi.org/10.1557/adv.2016.154.

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ABSTRACTThe multiferroic material YbMnO3 has been reported to exhibit both ferroelectric and antiferromagnetic orders in the ground state. Of these two orders, the ferroelectric order is associated with the P63/mmc-to-P63cm structural transition, which occurs around 1270 K. The interesting feature of the ferroelectric state is that a cloverleaf domain structure with a pseudo-six-fold symmetry is observed in transmission electron microscopy images with the beam incidence parallel to the hexagonal axis. To understand the origin of the formation of the cloverleaf domain structure, we have examined the crystallographic features of the ferroelectric state in YbMnO3 by transmission electron microscopy. In this study, particularly, we adopted the experimental condition that electron beam incidences are perpendicular to the hexagonal axis. It was, as a result, found that there existed various ferroelectric domain structures including the cloverleaf domain structure under the present condition. The notable feature of domain structures found in this study is that each domain structure basically consists of six domains, whose domain boundaries are terminated at one point. Because this feature makes us reminiscent of a discommensurate structure in an incommensurate state, we took high-resolution electron micrographs of areas including domain boundaries. Their analysis indicated that a domain boundary could be identified as a discommensuration with a phase slip of π/3. It is thus understood that the cloverleaf domain structure should be one of domain morphologies for a discommensurate structure, which is related to the break of the translational symmetry.

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Michiue, Yuichi, Akiji Yamamoto, Mitsuko Onoda, Akira Sato, Takaya Akashi, Hisanori Yamane e Takashi Goto. "Incommensurate crystallographic shear structure of Ba x Bi2 − 2x Ti4 − x O11 − 4x (x = 0.275)". Acta Crystallographica Section B Structural Science 61, n. 2 (16 marzo 2005): 145–53. http://dx.doi.org/10.1107/s0108768105001655.

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The title compound generates diffraction patterns which are indexable within the framework of the higher-dimensional description of incommensurate structures. However, it is difficult to discriminate the main reflections from the satellite ones. This paper has clarified that the structure can be treated as a strongly modulated structure with sawtooth-like modulation functions and is classified as an incommensurate crystallographic shear (CS) structure. The structure consists of domains isostructural to β-Bi2Ti4O11 and domain boundaries composed of TiO6 octahedra. Ba and Bi ions are accommodated in the cavities between TiO6 octahedra in the domain. Domain boundaries are aperiodically inserted, in contrast to the usual CS structures, forming an incommensurate structure.

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Lee, W. T., E. K. H. Salje e U. Bismayer. "Domain-wall structure and domain-wall strain". Journal of Applied Physics 93, n. 12 (15 giugno 2003): 9890–97. http://dx.doi.org/10.1063/1.1573749.

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Filatov, Evgeny Yu, Svetlana V. Cherepanova, Ilia V. Kochetygov, Yury V. Shubin e Sergey V. Korenev. "Domain structure of CoIr nanoalloys". Powder Diffraction 32, S1 (11 aprile 2017): S155—S159. http://dx.doi.org/10.1017/s0885715617000367.

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X-ray diffraction (XRD) pattern of nanosized equimolar solid solution CoIr prepared by thermolysis of [Co(NH3)6][Ir(C2O4)3] contains peaks characteristic of both face-centered cubic (fcc) and hexagonal close-packed (hcp) structure. Moreover, 101 peak of hcp modification is substantially wider than 100 and 002 peaks, 102 and 103 are very broad and almost invisible. Peak 200 of fcc structure is wider than the other peaks of this modification and slightly shifted toward lower angles. It was shown by simulation of XRD patterns that particles of CoIr alloy are nanoheterogeneous and consist of lamellar domains having fcc and hcp structures. The best fit was obtained for the following model parameters: an average crystallites size is about 10 nm, average thicknesses of the fcc and hcp domains are 1.7 and 1.1 respectively. The presence of domain structure was confirmed by transmission electron microscopy data.

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Kwon, Gihan, Oleksandr Kokhan, Ali Han, Karena W. Chapman, Peter J. Chupas, Pingwu Du e David M. Tiede. "Oxyanion induced variations in domain structure for amorphous cobalt oxide oxygen evolving catalysts, resolved by X-ray pair distribution function analysis". Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 71, n. 6 (1 dicembre 2015): 713–21. http://dx.doi.org/10.1107/s2052520615022180.

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Amorphous thin film oxygen evolving catalysts, OECs, of first-row transition metals show promise to serve as self-assembling photoanode materials in solar-driven, photoelectrochemical `artificial leaf' devices. This report demonstrates the ability to use high-energy X-ray scattering and atomic pair distribution function analysis, PDF, to resolve structure in amorphous metal oxide catalyst films. The analysis is applied here to resolve domain structure differences induced by oxyanion substitution during the electrochemical assembly of amorphous cobalt oxide catalyst films, Co-OEC. PDF patterns for Co-OEC films formed using phosphate, Pi, methylphosphate, MPi, and borate, Bi, electrolyte buffers show that the resulting domains vary in size following the sequence Pi < MPi < Bi. The increases in domain size for CoMPi and CoBi were found to be correlated with increases in the contributions from bilayer and trilayer stacked domains having structures intermediate between those of the LiCoOO and CoO(OH) mineral forms. The lattice structures and offset stacking of adjacent layers in the partially stacked CoMPi and CoBi domains were best matched to those in the LiCoOO layered structure. The results demonstrate the ability of PDF analysis to elucidate features of domain size, structure, defect content and mesoscale organization for amorphous metal oxide catalysts that are not readily accessed by other X-ray techniques. PDF structure analysis is shown to provide a way to characterize domain structures in different forms of amorphous oxide catalysts, and hence provide an opportunity to investigate correlations between domain structure and catalytic activity.

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Hutin, Stephanie, Wai Li Ling, Nicolas Tarbouriech, Guy Schoehn, Clemens Grimm, Utz Fischer e Wim P. Burmeister. "The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction". Viruses 14, n. 10 (7 ottobre 2022): 2206. http://dx.doi.org/10.3390/v14102206.

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Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323–785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.

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Poměnková, J., e R. Maršálek. " Time and frequency domain in the business cycle structure". Agricultural Economics (Zemědělská ekonomika) 58, No. 7 (23 luglio 2012): 332–46. http://dx.doi.org/10.17221/113/2011-agricecon.

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 The presented paper deals with the identification of cyclical behaviour of business cycle from the time and frequency domain perspective. Herewith, methods for obtaining the growth business cycle are investigated – the first order difference, the unobserved component models, the regression curves and filtration using the Baxter-King, Christiano-Fitzgerald and Hodrick-Prescott filter. In the case of the time domain, the analysis identification of cycle lengths is based on the dating process of the growth business cycle. Thus, the right and left variant of the naive techniques and the Bry-Boschan algorithm are applied. In the case of the frequency domain, the analysis of the cyclical structure trough spectrum estimate via the periodogram and the autoregressive process are suggested. Results from both domain approaches are compared. On their bases, recommendations for the cyclical structure identification of the growth business cycle of the Czech Republic are formulated. In the time domain analysis, the evaluation of the unity results of detrending techniques from the identification turning point points of view is attached. The analyses are done on the quarterly data of the GDP, the total industry excluding construction, the gross capital formation in 1996–2008 and on the final consumption expenditure in 1995–2008.    

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Surtees, Jennifer A., e Barbara E. Funnell. "P1 ParB Domain Structure Includes Two Independent Multimerization Domains". Journal of Bacteriology 181, n. 19 (1 ottobre 1999): 5898–908. http://dx.doi.org/10.1128/jb.181.19.5898-5908.1999.

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ABSTRACT ParB is one of two P1-encoded proteins that are required for active partition of the P1 prophage in Escherichia coli. To probe the native domain structure of ParB, we performed limited proteolytic digestions of full-length ParB, as well as of several N-terminal and C-terminal deletion fragments of ParB. The C-terminal 140 amino acids of ParB form a very trypsin-resistant domain. In contrast, the N terminus is more susceptible to proteolysis, suggesting that it forms a less stably folded domain or domains. Because native ParB is a dimer in solution, we analyzed the ability of ParB fragments to dimerize, using both the yeast two-hybrid system and in vitro chemical cross-linking of purified proteins. These studies revealed that the C-terminal 59 amino acids of ParB, a region within the protease-resistant domain, are sufficient for dimerization. Cross-linking and yeast two-hybrid experiments also revealed the presence of a second self-association domain within the N-terminal half of ParB. The cross-linking data also suggest that the C terminus is inhibitory to multimerization through the N-terminal domain in vitro. We propose that the two multimerization domains play distinct roles in partition complex formation.

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Rotem, S., C. Katz e A. Friedler. "Insights into the structure and protein–protein interactions of the pro-apoptotic protein ASPP2". Biochemical Society Transactions 35, n. 5 (25 ottobre 2007): 966–69. http://dx.doi.org/10.1042/bst0350966.

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ASPP (apoptosis-stimulating protein of p53) 2 is a pro-apoptotic protein that stimulates the p53-mediated apoptotic response. Here, we provide an overview of the structure and protein–protein interactions of ASPP2. The C-terminus of ASPP2 contains Ank (ankyrin) repeats and an SH3 domain (Src homology 3 domain). The Ank–SH3 domains mediate interactions between ASPP2 and numerous proteins involved in apoptosis such as p53 and Bcl-2. The proline-rich domain of ASPP2 is unfolded in its native state, but was not shown to mediate intermolecular interactions. Instead, it makes an intramolecular domain–domain interaction with the Ank–SH3 C-terminal domains of ASPP2. This intramolecular interaction between the unstructured proline-rich domain and the structured Ank–SH3 domains in ASPP2, which is possible due to the unfolded nature of the proline-rich domain, is proposed to have an important role in regulating the intermolecular interactions of ASPP2 with its partner proteins.

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Kostyukova, Alla, Elizaveta Tiktopulo, Inna Krieger, K. Maeda e Y. Maeda. "1H1815 Tropomodulin domain structure". Seibutsu Butsuri 40, supplement (2000): S65. http://dx.doi.org/10.2142/biophys.40.s65_2.

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Hao, Rui, Lei Chen, Jia-Wei Wu e Zhi-Xin Wang. "Structure ofDrosophilaMad MH2 domain". Acta Crystallographica Section F Structural Biology and Crystallization Communications 64, n. 11 (31 ottobre 2008): 986–90. http://dx.doi.org/10.1107/s1744309108033034.

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Ison, J. C. "Exploring protein domain structure". Briefings in Bioinformatics 1, n. 3 (1 gennaio 2000): 305–12. http://dx.doi.org/10.1093/bib/1.3.305.

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Kostyukova, Alla, Kayo Maeda, Emiko Yamauchi, Inna Krieger e Yuichiro Maéda. "Domain structure of tropomodulin". European Journal of Biochemistry 267, n. 21 (novembre 2000): 6470–75. http://dx.doi.org/10.1046/j.1432-1327.2000.01738.x.

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Shishkina, Ekaterina, Vladimir Yuzhakov, Maksim Nebogatikov, Elena Pelegova, Eduard Linker, Lyudmila Ivleva e Vladimir Shur. "As-Grown Domain Structure in Calcium Orthovanadate Crystals". Crystals 11, n. 12 (3 dicembre 2021): 1508. http://dx.doi.org/10.3390/cryst11121508.

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An as-grown domain structure in nominally pure and Mn-doped calcium orthovanadate (CVO) crystals was studied by several methods of domain imaging: optical microscopy, piezoelectric force microscopy, and Cherenkov-type second harmonic generation. The combination of imaging methods provided an opportunity for comprehensive study of the domain structure on the polar surface and in the bulk of the samples. It was shown that, in nominally pure CVO crystals, an irregular 3D maze of rounded domains, with charged walls, essentially tilted from the polar direction, was present. It was proposed that the domain structure was formed just below the phase transition temperature and persisted during subsequent cooling. Such behavior is due to effective bulk screening of the depolarization field and a low value of the pyroelectric field which appears during cooling. The revealed formation of triangular domains and flat fragments of domain walls in Mn-doped CVO was attributed to polarization reversal under the action of the polar component of the pyroelectric field, above the threshold value for domain switching. This fact represents the first observation of the domain switching in CVO crystals.

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Zeng, Wei-ping. "Structure-functional analysis of Foxp3 (IRC4P.478)". Journal of Immunology 192, n. 1_Supplement (1 maggio 2014): 60.5. http://dx.doi.org/10.4049/jimmunol.192.supp.60.5.

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Abstract Foxp3 is responsible for the major immunological features of Treg cells, including hypoproliferation in vitro, immune suppression of conventional T cells and resistance to Th2 cell differentiation. In addition to the Forkhead domain, the Foxp3 protein contains the N-terminal, zinc finger and leucine zipper domains. To understand how these domains contribute to Foxp3 functions, we systematically compared the roles of these domains in determining the 3 major immunological features of Treg cells. We designed a bridge-mediated mutagenesis method to generate Foxp3 mutants with complete deletion of each of the domains. CD4 T cells expressing the Foxp3 mutant with deletion of the N-terminal, leucine zipper or the forkhead domain showed robust TCR dependent proliferation in vitro, differentiated into Th2 cells, and lost immune suppressive activities in vitro and in vivo, demonstrating a complete loss of all 3 functions of Foxp3. In contrast, deletion of the zinc finger domain only partially impaired these functions of Foxp3. This result suggests that mutations in the zinc finger domain could lead to nonlethal autoimmune and allergic diseases, in which reduction rather than complete loss of Foxp3 functions is expected. In any case, deletion of a particular domain showed similar effects on all 3 functions of Foxp3. Therefore defining each of the immunological features of Treg cells requires intact Foxp3 proteins.

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Gross, Katherine, Kurt Westerholt, Maria E. Gómez e Hartmut Zabel. "Domain Structure and Magnetoresistance in Co2MnGe Zigzag Structures". Physics Procedia 75 (2015): 1072–79. http://dx.doi.org/10.1016/j.phpro.2015.12.177.

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Siponen, Marina, Silvia Spinelli, Stéphanie Blangy, Sylvain Moineau, Christian Cambillau e Valérie Campanacci. "Crystal Structure of a Chimeric Receptor Binding Protein Constructed from Two Lactococcal Phages". Journal of Bacteriology 191, n. 10 (13 marzo 2009): 3220–25. http://dx.doi.org/10.1128/jb.01637-08.

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ABSTRACT Lactococcus lactis, a gram-positive bacterium widely used by the dairy industry to manufacture cheeses, is subject to infection by a diverse population of virulent phages. We have previously determined the structures of three receptor binding proteins (RBPs) from lactococcal phages TP901-1, p2, and bIL170, each of them having a distinct host range. Virulent phages p2 and bIL170 are classified within the 936 group, while the temperate phage TP901-1 is a member of the genetically distinct P335 polythetic group. These RBPs comprise three domains: the N-terminal domain, binding to the virion particle; a β-helical linker domain; and the C-terminal domain, bearing the receptor binding site used for host recognition. Here, we have designed, expressed, and determined the structure of an RBP chimera in which the N-terminal and linker RBP domains of phage TP901-1 (P335) are fused to the C-terminal RBP domain of phage p2 (936). This chimera exhibits a stable structure that closely resembles the parental structures, while a slight displacement of the linker made RBP domain adaptation efficient. The receptor binding site is structurally indistinguishable from that of native p2 RBP and binds glycerol with excellent affinity.

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Ha, N. T. T., M. T. Lan, N. V. Hong e P. K. Hung. "Structural transformation and dynamical heterogeneity in Germania melt under compression: molecular dynamic simulation". Canadian Journal of Physics 99, n. 12 (dicembre 2021): 1086–94. http://dx.doi.org/10.1139/cjp-2020-0493.

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The structural transformation and dynamical heterogeneity in Germania (GeO2) are investigated via molecular dynamics (MD) simulation. The MD model with 5499 atoms was constructed under pressure up to 150 GPa and at a temperature of 3500 K. The structural transformation mechanism has been studied by observing domain structures and boundary oxygen atoms. The simulation result reveals that GeO2 consists of separate domains and boundaries in its melt structure. Under compression, the structure of GeO2 changes gradually and represents many types of structures. The melt structure exhibits many structural domains Dx, and polymorphism appears at pressures of 12 and 20 GPa. The change of tetrahedral structure to octahedral structure in germanium coordination occurred in parallel with the process of merging and splitting of domain structure. Moreover, the existence of high- and low-density phases in GeO2 melt is indicated. The high-density phase is D6 domain and boundary oxygen while the low-density phase is D4 and D5 domain. The compression mechanism in GeO2 melt mainly is a reduction of average Voronoi volume of oxygen and Voronoi volume of D6, boundary atoms oxygen. Furthermore, we find the dynamical heterogeneity at ambient pressure. The separate “fast” regions and “slow” regions in GeO2 are detected via link-cluster function.

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Leung, Josephine, Lici Schurig-Briccio, Mutsuo Yamaguchi, Arne Moeller, Jeffrey Speir, Robert Gennis e Charles Stout. "Transhydrogenase coupling proton translocation and hydride transfer". Acta Crystallographica Section A Foundations and Advances 70, a1 (5 agosto 2014): C1495. http://dx.doi.org/10.1107/s2053273314085040.

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Nicotinamide nucleotide transhydrogenase (TH) is a homodimeric 200 kDa membrane protein that is associated with glucose homeostasis in diabetes: mice with mutations or deletions in the TH-encoding gene exhibit glucose intolerance and impaired secretion of insulin [1-2]. TH couples hydride transfer between nicotinamide nucleotides to proton translocation between the matrix (in) and the intermembrane space (out) of mitochondria (or between the cytosol and the periplasm in prokaryotes) [3]: NADH + NADP + H+(out) ⇌ NAD + NADPH + H+(in). Each TH monomer contains three domains: a soluble 40 kDa NAD(H)-binding domain (domain I), a 40kDa membrane-intercalated proton channel (domain II), and a soluble 20 kDa NADP(H)-binding domain (domain III), which is connected to domain II. Hydride transfer between nucleotides occurs between domain I and domain III; and proton translocation is carried out in domain II [3]. The mechanism of TH is unknown due to the lack of structures of the transmembrane domain and the intact enzyme. We have solved three crystal structures of the membrane-intercalated domain II of Thermus thermophilus TH at 2.8-3.0 Å using selenomethionine derivatives and mercury derivatives of crystals obtained in the lipidic cubic phase. Four crystal structures of the soluble domains have also been obtained at 1.8-2.4 Å. Using the higher resolution structures of the subunits, we have determined the structure of the entire TH complex at 6.9 Å by crystallography, and 18 Å by single-particle cryogenic electron microscopy. The intact TH structure reveals that domain III subunits violate the local 2-fold symmetry: one has its NADP(H) binding site 'face-up' to interact with domain I for hydride transfer; the other 'face-down' to interact with domain II for proton translocation. An alternating mechanism of the NADP(H) binding domains provides insights into how TH couples hydride transfer to proton motive force.

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29

Ohyama, Takako, Hazuki Takahashi, Harshita Sharma, Toshio Yamazaki, Stefano Gustincich, Yoshitaka Ishii e Piero Carninci. "An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs". Nucleic Acids Research 48, n. 16 (22 luglio 2020): 9346–60. http://dx.doi.org/10.1093/nar/gkaa598.

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Abstract Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive transcriptome analysis has revealed that retrotransposon elements (REs) are transcribed and enriched in lncRNA sequences. However, the functions of lncRNAs and the molecular roles of the embedded REs are largely unknown. The secondary and tertiary structures of lncRNAs and their embedded REs are likely to have essential functional roles, but experimental determination and reliable computational prediction of large RNA structures have been extremely challenging. We report here the nuclear magnetic resonance (NMR)-based secondary structure determination of the 167-nt inverted short interspersed nuclear element (SINE) B2, which is embedded in antisense Uchl1 lncRNA and upregulates the translation of sense Uchl1 mRNAs. By using NMR ‘fingerprints’ as a sensitive probe in the domain survey, we successfully divided the full-length inverted SINE B2 into minimal units made of two discrete structured domains and one dynamic domain without altering their original structures after careful boundary adjustments. This approach allowed us to identify a structured domain in nucleotides 31–119 of the inverted SINE B2. This approach will be applicable to determining the structures of other regulatory lncRNAs.

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30

Joseph, Raji E., Nathaniel D. Ginder, Julie A. Hoy, Jay C. Nix, D. Bruce Fulton, Richard B. Honzatko e Amy H. Andreotti. "Structure of the interleukin-2 tyrosine kinase Src homology 2 domain; comparison between X-ray and NMR-derived structures". Acta Crystallographica Section F Structural Biology and Crystallization Communications 68, n. 2 (25 gennaio 2012): 145–53. http://dx.doi.org/10.1107/s1744309111049761.

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The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy,cis–trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and thecisform of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts thecisconformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolylcis–transisomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerizationversusdomain-swapped dimerization, respectively.

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31

Birrane, Gabriel, Anne P. Beigneux, Brian Dwyer, Bettina Strack-Logue, Kristian Kølby Kristensen, Omar L. Francone, Loren G. Fong et al. "Structure of the lipoprotein lipase–GPIHBP1 complex that mediates plasma triglyceride hydrolysis". Proceedings of the National Academy of Sciences 116, n. 5 (17 dicembre 2018): 1723–32. http://dx.doi.org/10.1073/pnas.1817984116.

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Lipoprotein lipase (LPL) is responsible for the intravascular processing of triglyceride-rich lipoproteins. The LPL within capillaries is bound to GPIHBP1, an endothelial cell protein with a three-fingered LU domain and an N-terminal intrinsically disordered acidic domain. Loss-of-function mutations in LPL or GPIHBP1 cause severe hypertriglyceridemia (chylomicronemia), but structures for LPL and GPIHBP1 have remained elusive. Inspired by our recent discovery that GPIHBP1’s acidic domain preserves LPL structure and activity, we crystallized an LPL–GPIHBP1 complex and solved its structure. GPIHBP1’s LU domain binds to LPL’s C-terminal domain, largely by hydrophobic interactions. Analysis of electrostatic surfaces revealed that LPL contains a large basic patch spanning its N- and C-terminal domains. GPIHBP1’s acidic domain was not defined in the electron density map but was positioned to interact with LPL’s large basic patch, providing a likely explanation for how GPIHBP1 stabilizes LPL. The LPL–GPIHBP1 structure provides insights into mutations causing chylomicronemia.

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32

Whelan, Fiona, Aleix Lafita, Samuel C. Griffiths, Rachael E. M. Cooper, Jean L. Whittingham, Johan P. Turkenburg, Iain W. Manfield et al. "Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection". Proceedings of the National Academy of Sciences 116, n. 52 (9 dicembre 2019): 26540–48. http://dx.doi.org/10.1073/pnas.1911776116.

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Streptococcusgroups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the β-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin β-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain.

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33

Novokhatny, V. V., K. C. Ingham e L. V. Medved. "Domain structure and domain-domain interactions of recombinant tissue plasminogen activator". Journal of Biological Chemistry 266, n. 20 (luglio 1991): 12994–3002. http://dx.doi.org/10.1016/s0021-9258(18)98794-6.

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34

Vysotchin, A., L. V. Medved e K. C. Ingham. "Domain structure and domain-domain interactions in human coagulation factor IX." Journal of Biological Chemistry 268, n. 12 (aprile 1993): 8436–46. http://dx.doi.org/10.1016/s0021-9258(18)52895-7.

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35

Fodor, Anthony A., e Richard W. Aldrich. "Statistical Limits to the Identification of Ion Channel Domains by Sequence Similarity". Journal of General Physiology 127, n. 6 (30 maggio 2006): 755–66. http://dx.doi.org/10.1085/jgp.200509419.

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Abstract (sommario):

The study of ion channel function is constrained by the availability of structures for only a small number of channels. A commonly used bioinformatics technique is to assert, based on sequence similarity, that a domain within a channel of interest has the same structure as a reference domain for which the structure is known. This technique, while useful, is often employed when there is only a slight similarity between the channel of interest and the domain of known structure. In this study, we exploit recent advances in structural genomics to calculate the sequence-based probability of the presence of putative domains in a number of ion channels. We find strong support for the presence of many domains that have been proposed in the literature. For example, eukaryotic and prokaryotic CLC proteins almost certainly share a common structure. A number of proposed domains, however, are not as well supported. In particular, for the COOH terminus of the BK channel we find a number of literature proposed domains for which the assertion of common structure based on common sequence has a nontrivial probability of error.

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36

Akhmatkhanov, Andrey, Constantine Plashinnov, Maxim Nebogatikov, Evgenii Milov, Ilya Shnaidshtein e Vladimir Shur. "In Situ Imaging of Domain Structure Evolution in LaBGeO5 Single Crystals". Crystals 10, n. 7 (6 luglio 2020): 583. http://dx.doi.org/10.3390/cryst10070583.

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Abstract (sommario):

LaBGeO5 (LBGO) crystals are unique ferroelectric materials for manufacturing highly efficient UV laser sources based on frequency conversion. This is due to their low cut-off wavelength, high nonlinear-optical coefficients, and non-hygroscopicity. Periodical poling requires a deep study of domain kinetics in these crystals. Domain imaging by Cherenkov second harmonic generation microscopy was used to reveal the main processes of domain structure evolution: (1) growth and merging of isolated domains, (2) growth of stripe domains formed on the artificial linear surface defects, and (3) domain shrinkage. In a low field, growth of triangular domains and fast shape recovery after merging were observed, while in a high field, the circular domains grew independently after merging. The revealed essential wall motion anisotropy decreased with the field. The anisotropy led to significant shape transformations during domain shrinkage in low field. The formation of short-lived triangular domains rotated by 180 degrees with respect to the growing isolated domains was observed. The obtained results were explained within the kinetic approach to domain structure evolution based on the analogy between the growth of crystals and ferroelectric domains, taking into account the gradual transition from determined nucleation in low field to the stochastic one in high field.

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37

Wang, Li, Qi Qiao, Ryan Ferrao, Chen Shen, John M. Hatcher, Sara J. Buhrlage, Nathanael S. Gray e Hao Wu. "Crystal structure of human IRAK1". Proceedings of the National Academy of Sciences 114, n. 51 (5 dicembre 2017): 13507–12. http://dx.doi.org/10.1073/pnas.1714386114.

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Interleukin 1 (IL-1) receptor-associated kinases (IRAKs) are serine/threonine kinases that play critical roles in initiating innate immune responses against foreign pathogens and other types of dangers through their role in Toll-like receptor (TLR) and interleukin 1 receptor (IL-1R) mediated signaling pathways. Upon ligand binding, TLRs and IL-1Rs recruit adaptor proteins, such as myeloid differentiation primary response gene 88 (MyD88), to the membrane, which in turn recruit IRAKs via the death domains in these proteins to form the Myddosome complex, leading to IRAK kinase activation. Despite their biological and clinical significance, only the IRAK4 kinase domain structure has been determined among the four IRAK family members. Here, we report the crystal structure of the human IRAK1 kinase domain in complex with a small molecule inhibitor. The structure reveals both similarities and differences between IRAK1 and IRAK4 and is suggestive of approaches to develop IRAK1- or IRAK4-specific inhibitors for potential therapeutic applications. While the IRAK4 kinase domain is capable of homodimerization in the unphosphorylated state, we found that the IRAK1 kinase domain is constitutively monomeric regardless of its phosphorylation state. Additionally, the IRAK1 kinase domain forms heterodimers with the phosphorylated, but not unphosphorylated, IRAK4 kinase domain. Collectively, these data indicate a two-step kinase activation process in which the IRAK4 kinase domain first homodimerizes in the Myddosome, leading to its trans-autophosphorylation and activation. The phosphorylated IRAK4 kinase domain then forms heterodimers with the IRAK1 kinase domain within the Myddosome, leading to its subsequent phosphorylation and activation.

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38

Laco, Gary S., e Yves Pommier. "Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition". Biochemical Journal 411, n. 3 (14 aprile 2008): 523–30. http://dx.doi.org/10.1042/bj20071436.

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Human Top1 (topoisomerase I) relaxes supercoiled DNA during cell division and transcription. Top1 is composed of 765 amino acids and contains an unstructured N-terminal domain of 200 amino acids, and a structured functional domain of 565 amino acids that binds and relaxes supercoiled DNA. In the present study we examined the region spanning the junction of the N-terminal domain and functional domain (junction region). Analysis of several published Top1 structures revealed that three tryptophan residues formed a network of aromatic stacking interactions and electrostatic interactions that anchored the N-terminus of the functional domain to sub-domains containing the nose cone and active site. Mutation of the three tryptophan residues (Trp203/Trp205/Trp206) to an alanine residue, either individually or together, in silico revealed that the individual tryptophan residue's contribution to the tryptophan ‘anchor’ was additive. When the three tryptophan residues were mutated to alanine in vitro, the resulting mutant Top1 differed from wild-type Top1 in that it lacked processivity, exhibited resistance to camptothecin and was inactivated by urea. The results indicated that the tryptophan anchor stabilized the N-terminus of the functional domain and prevented the loss of Top1 structure and function.

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39

Shishkina, E. V., M. A. Chuvakova, V. V. Yuzhakov, A. R. Akhmatkhanov, E. V. Pelegova, M. S. Nebogatikov, A. D. Ushakov, E. A. Linker, L. I. Ivleva e V. Ya Shur. "Domain structure evolution during polarization reversal in calcium orthovanadate single crystals". Journal of Applied Physics 132, n. 18 (14 novembre 2022): 184101. http://dx.doi.org/10.1063/5.0120792.

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Abstract (sommario):

We have switched polarization in calcium orthovanadate single crystal with as-grown domain structure consisting of isolated domains with charged domain walls (CDWs) located in the bulk using pretreatment by ac field and subsequent switching in dc field at the elevated temperature. The formation of the domain ledges at the CDW in the bulk and their growth in the polar direction has been revealed. The isolated domains with optically well-defined walls appeared when the ledge tops reached the surface, their shape and sizes remaining constant during further switching. Unlike usual continuous domain wall motion, we have observed the discrete switching by arising of the isolated domains without any input of the traditional domain nucleation at the polar surface. The obtained results have been explained under the assumption that at the used experimental conditions, the applied field is above the threshold value for ledge nucleation at CDW in the bulk, but below the threshold for domain wall motion at the surface. Thus, we have obtained the discrete switching by ledge growth without any sideways motion of the domain walls and domain coalescence. The nonuniform evolution of the domain structure at the surface is due to the dependence of the switching rate on the distance from CDW to the polar surface, which is random in the studied domain structure.

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40

Deshpande, Chandrika N., Aaron P. McGrath, Josep Font, Amy P. Guilfoyle, Megan J. Maher e Mika Jormakka. "Structure of an atypical FeoB G-domain reveals a putative domain-swapped dimer". Acta Crystallographica Section F Structural Biology and Crystallization Communications 69, n. 4 (29 marzo 2013): 399–404. http://dx.doi.org/10.1107/s1744309113005939.

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Abstract (sommario):

FeoB is a transmembrane protein involved in ferrous iron uptake in prokaryotic organisms. FeoB comprises a cytoplasmic soluble domain termed NFeoB and a C-terminal polytopic transmembrane domain. Recent structures of NFeoB have revealed two structural subdomains: a canonical GTPase domain and a five-helix helical domain. The GTPase domain hydrolyses GTP to GDP through a well characterized mechanism, a process which is required for Fe2+transport. In contrast, the precise role of the helical domain has not yet been fully determined. Here, the structure of the cytoplasmic domain of FeoB fromGallionella capsiferriformansis reported. Unlike recent structures of NFeoB, theG. capsiferriformansNFeoB structure is highly unusual in that it does not contain a helical domain. The crystal structures of both apo and GDP-bound protein forms a domain-swapped dimer.

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41

Aoyagi, Kenta, Takanori Kiguchi, Yoshitaka Ehara, Hiroshi Funakubo e Toyohiko J. Konno. "TEM Observation on Ferroelectric Domain Structures of PbTiO₃ Epitaxial Films". Key Engineering Materials 485 (luglio 2011): 179–82. http://dx.doi.org/10.4028/www.scientific.net/kem.485.179.

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Abstract (sommario):

The ferroelectric domain structure of PbTiO3(PTO) films was investigated by using transmission electron microscopy (TEM). In the film with PTO/SrTiO3(STO) structure, 180º domains are formed near the SrTiO3(STO) substrate and the domain length of 180º domains is 100 nm. However, 180º domains are not formed in the film with Pt/PTO/SrRuO3(SRO)/STO structure. These results show that 180º domains are formed in order to minimize depolarizing field energy, and that the domain length of 180º domains is determined by the competition among the depolarizing field energy, domain wall energy, Coulomb interaction and elastic interaction.

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42

Thangavelu, Bharani, Alexander G. Pavlovsky e Ronald Viola. "Structure of homoserineO-acetyltransferase fromStaphylococcus aureus: the first Gram-positive ortholog structure". Acta Crystallographica Section F Structural Biology Communications 70, n. 10 (25 settembre 2014): 1340–45. http://dx.doi.org/10.1107/s2053230x14018664.

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HomoserineO-acetyltransferase (HTA) catalyzes the formation of L-O-acetyl-homoserine from L-homoserine through the transfer of an acetyl group from acetyl-CoA. This is the first committed step required for the biosynthesis of methionine in many fungi, Gram-positive bacteria and some Gram-negative bacteria. The structure of HTA fromStaphylococcus aureus(SaHTA) has been determined to a resolution of 2.45 Å. The structure belongs to the α/β-hydrolase superfamily, consisting of two distinct domains: a core α/β-domain containing the catalytic site and a lid domain assembled into a helical bundle. The active site consists of a classical catalytic triad located at the end of a deep tunnel. Structure analysis revealed some important differences forSaHTA compared with the few known structures of HTA.

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43

Hallin, Erik I., Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda, Clive R. Bramham e Petri Kursula. "Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc". PLOS ONE 16, n. 5 (14 maggio 2021): e0251459. http://dx.doi.org/10.1371/journal.pone.0251459.

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Abstract (sommario):

Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid structures in a process requiring the N-terminal domain and contains two C-terminal lobes that are structural homologues to retroviral capsids. Drosophila has two isoforms of Arc, dArc1 and dArc2, with low sequence similarity to mammalian Arc, but lacking a large N-terminal domain. Both dArc isoforms are related to the Ty3/gypsy retrotransposon capsid, consisting of N- and C-terminal lobes. Structures of dArc1, as well as capsids formed by both dArc isoforms, have been recently determined. We carried out structural characterization of the four individual dArc lobe domains. As opposed to the corresponding mammalian Arc lobe domains, which are monomeric, the dArc lobes were all oligomeric in solution, indicating a strong propensity for homophilic interactions. A truncated N-lobe from dArc2 formed a domain-swapped dimer in the crystal structure, resulting in a novel dimer interaction that could be relevant for capsid assembly or other dArc functions. This domain-swapped structure resembles the dimeric protein C of flavivirus capsids, as well as the structure of histones dimers, domain-swapped transcription factors, and membrane-interacting BAK domains. The strong oligomerization properties of the isolated dArc lobe domains explain the ability of dArc to form capsids in the absence of any large N-terminal domain, in contrast to the mammalian protein.

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44

Li, Jie-Fang, Xunhu Dai, Albert Chow e Dwight Viehland. "Polarization switching mechanisms and electromechanical properties of La-modified lead zirconate titanate ceramics". Journal of Materials Research 10, n. 4 (aprile 1995): 926–38. http://dx.doi.org/10.1557/jmr.1995.0926.

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Abstract (sommario):

The electromechanical properties of (Pb1−xLax)(ZryTi1−y)O3 [PLZT x/y/(1 - y)] have been investigated in the compositional range 0 < x < 0.10 for y = 0.65 (rhombohedral PLZT) and 0 < x < 0.18 for y = 0.40 (tetragonal PLZT). Both field-induced strains (∊-E) associated with polarization switching and piezoelectric responses (d33) were studied. Transmission electron microscopy (TEM) and dielectric investigations were also performed. Room temperature TEM investigations revealed common trends in the domain structure with increasing La content for both PLZT x/65/35 and x/40/60, including a micron-sized domain structure, a subdomain tweed-like structure, and a nanopolar domain state. Changes in the field-induced strains and piezoelectric properties were then related to these microstructural trends. The dominant electromechanical coupling mechanism in the micron-sized domain state was found to be piezoelectricity. However, an electrostrictive coupling became apparent with the appearance of the subdomain tweed-like structures, and became stronger in the nanopolar domain state. It is believed that polarization switching can-occur through 70°or 110°domains, the subdomain tweed-like structure, or nanopolar domains depending on La content.

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45

Arnaud-Arnould, Mary, Marine Tauziet, Olivier Moncorgé, Caroline Goujon e Mickaël Blaise. "Crystal structure of the TLDc domain of human NCOA7-AS". Acta Crystallographica Section F Structural Biology Communications 77, n. 8 (28 luglio 2021): 230–37. http://dx.doi.org/10.1107/s2053230x21006853.

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Abstract (sommario):

The TLDc [Tre2/Bub2/Cdc16 (TBC), lysin motif (LysM), domain catalytic] domain is associated with oxidation-resistance related functions and is well conserved among eukaryotes. Seven proteins possess a TLDc domain in humans, notably proteins belonging to the oxidation resistance protein (OXR), nuclear receptor coactivator 7 (NCOA7) and TBC1 domain family member 24 (TBC1D24) families. Although the mechanism is unknown, a protective role of TLDc proteins against oxidative stress, notably in the brain, has been demonstrated. Neurobiological disorders caused by mutations in the TLDc domain have also been reported. The human NCOA7 gene encodes several mRNA isoforms; among these, isoform 4, named NCOA7-AS, is up-regulated by type 1 interferon in response to viral infection. NCOA7 and NCOA7-AS both interact with several subunits of the vacuolar proton pump V-ATPase, which leads to increased acidification of the endolysosomal system and consequently impairs infection by viruses that enter their host cells through the endosomal pathway, such as influenza A virus and hepatitis C virus. Similarly to full-length NCOA7, NCOA7-AS possesses a TLDc domain in its C-terminus. Structures of TLDc domains have been reported from zebrafish and fly but not from humans. Here, the expression, purification and crystallization of the TLDc domain from NCOA7 and NCOA7-AS is reported. The crystal structure solved at 1.8 Å resolution is compared with previously solved three-dimensional structures of TLDc domains.

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46

Liebschner, Dorothee, Krzysztof Brzezinski, Miroslawa Dauter, Zbigniew Dauter, Marta Nowak, Józef Kur e Marcin Olszewski. "Dimeric structure of the N-terminal domain of PriB protein fromThermoanaerobacter tengcongensissolvedab initio". Acta Crystallographica Section D Biological Crystallography 68, n. 12 (9 novembre 2012): 1680–89. http://dx.doi.org/10.1107/s0907444912041637.

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PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacteriumThermoanaerobacter tengcongensis(TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain ofT. tengcongensisshows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains,TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains ofTtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

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47

Varlioglu, Mesut, Ulrich Lienert, Jun-Sang Park, Jacob L. Jones e Ersan Üstündag. "Thermal and Electric Field-Dependent Evolution of Domain Structures in Polycrystalline BaTiO3 Using the 3D-XRD Technique". Texture, Stress, and Microstructure 2010 (7 novembre 2010): 1–10. http://dx.doi.org/10.1155/2010/910793.

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Abstract (sommario):

The evolution of ferroelectric domain structures inside a single grain embedded in a polycrystalline BaTiO3 ceramic was investigated under temperature and electric field using the three-dimensional X-ray diffraction (3D-XRD) method. The orientation of domains within the grain was studied during the phase transformation from the cubic to tetragonal crystal structure. The peak widths broadened from 0.10 ± 0.01∘ to 0.29±0.08∘ along the azimuthal direction during cooling. Four individual tetragonal domain structures were developed from the cubic grain. A twinning model based on {101} habit planes is discussed. While the twinning model predicts 89.47∘ misorientation between 90∘ domains and 1.049∘ misorientation between domain variants, the measured misorientations neither support the twinning model nor are the domain structures mutually orthogonal. The average misorientation of the domain structures at room temperature with respect to the cubic grain was about 0.3∘. Upon application of an electric field, the volume fractions of the domain structures changed systematically favoring growth of domain structures with small polarization angle with respect to applied field direction. No rotation of domain structures was observed upon application of an electric field which is consistent with domain boundary migration.

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48

Szczepanowski, Roman H., Renata Filipek e Matthias Bochtler. "Crystal Structure of a Fragment of Mouse Ubiquitin-activating Enzyme". Journal of Biological Chemistry 280, n. 23 (16 marzo 2005): 22006–11. http://dx.doi.org/10.1074/jbc.m502583200.

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Abstract (sommario):

Protein ubiquitination requires the sequential activity of three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin-ligase (E3). The ubiquitin-transfer machinery is hierarchically organized; for every ubiquitin-activating enzyme, there are several ubiquitin-conjugating enzymes, and most ubiquitin-conjugating enzymes can in turn interact with multiple ubiquitin ligases. Despite the central role of ubiquitin-activating enzyme in this cascade, a crystal structure of a ubiquitin-activating enzyme is not available. The enzyme is thought to consist of an adenylation domain, a catalytic cysteine domain, a four-helix bundle, and possibly, a ubiquitin-like domain. Its adenylation domain can be modeled because it is clearly homologous to the structurally known adenylation domains of the activating enzymes for the small ubiquitin-like modifier (SUMO) and for the protein encoded by the neuronal precursor cell-expressed, developmentally down-regulated gene 8 (NEDD8). Low sequence similarity and vastly different domain lengths make modeling difficult for the catalytic cysteine domain that results from the juxtaposition of two catalytic cysteine half-domains. Here, we present a biochemical and crystallographic characterization of the two half-domains and the crystal structure of the larger, second catalytic cysteine half-domain of mouse ubiquitin-activating enzyme. We show that the domain is organized around a conserved folding motif that is also present in the NEDD8- and SUMO-activating enzymes, and we propose a tentative model for full-length ubiquitin-activating enzyme.

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49

Frank, Aaron T., Caleen B. Ramsook, Henry N. Otoo, Cho Tan, Gregory Soybelman, Jason M. Rauceo, Nand K. Gaur, Stephen A. Klotz e Peter N. Lipke. "Structure and Function of Glycosylated Tandem Repeats from Candida albicans Als Adhesins". Eukaryotic Cell 9, n. 3 (9 ottobre 2009): 405–14. http://dx.doi.org/10.1128/ec.00235-09.

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ABSTRACT Tandem repeat (TR) regions are common in yeast adhesins, but their structures are unknown, and their activities are poorly understood. TR regions in Candida albicans Als proteins are conserved glycosylated 36-residue sequences with cell-cell aggregation activity (J. M. Rauceo, R. De Armond, H. Otoo, P. C. Kahn, S. A. Klotz, N. K. Gaur, and P. N. Lipke, Eukaryot. Cell 5:1664–1673, 2006). Ab initio modeling with either Rosetta or LINUS generated consistent structures of three-stranded antiparallel β-sheet domains, whereas randomly shuffled sequences with the same composition generated various structures with consistently higher energies. O- and N-glycosylation patterns showed that each TR domain had exposed hydrophobic surfaces surrounded by glycosylation sites. These structures are consistent with domain dimensions and stability measurements by atomic force microscopy (D. Alsteen, V. Dupres, S. A. Klotz, N. K. Gaur, P. N. Lipke, and Y. F. Dufrene, ACS Nano 3:1677–1682, 2009) and with circular dichroism determination of secondary structure and thermal stability. Functional assays showed that the hydrophobic surfaces of TR domains supported binding to polystyrene surfaces and other TR domains, leading to nonsaturable homophilic binding. The domain structures are like “classic” subunit interaction surfaces and can explain previously observed patterns of promiscuous interactions between TR domains in any Als proteins or between TR domains and surfaces of other proteins. Together, the modeling techniques and the supporting data lead to an approach that relates structure and function in many kinds of repeat domains in fungal adhesins.

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Kim, H. J., Y. Xu, A. Petri, K. Vanhoorelbeke, J. T. B. Crawley e J. Emsley. "Crystal structure of ADAMTS13 CUB domains reveals their role in global latency". Science Advances 7, n. 16 (aprile 2021): eabg4403. http://dx.doi.org/10.1126/sciadv.abg4403.

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ADAMTS13 is a plasma metalloprotease that is essential for the regulation of von Willebrand factor (VWF) function, mediator of platelet recruitment to sites of blood vessel damage. ADAMTS13 function is dynamically regulated by structural changes induced by VWF binding that convert it from a latent to active conformation. ADAMTS13 global latency is manifest by the interaction of its C-terminal CUB1-2 domains with its central Spacer domain. We resolved the crystal structure of the ADAMTS13 CUB1-2 domains revealing a previously unreported configuration for the tandem CUB domains. Docking simulations between the CUB1-2 domains with the Spacer domain in combination with enzyme kinetic functional characterization of ADAMTS13 CUB domain mutants enabled the mapping of the CUB1-2 domain site that binds the Spacer domain. Together, these data reveal the molecular basis of the ADAMTS13 Spacer-CUB interaction and the control of ADAMTS13 global latency.

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