Journal articles: 'Domain structure'

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Daminov, Mirzogid Islomovich, Mirzo Zokirovich Sharipov, Rustam Khalilovich Shamsiev, and Dilshod Ergashovich Khaitov. "DOMAIN STRUCTURE AND SOME PROPERTIES OF RARE-EARTH GRANITE FERRITES." Scientific Reports of Bukhara State University 4, no. 3 (June 26, 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, and Jeffrey J. Gray. "Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains." Structure 16, no. 4 (April 2008): 513–27. http://dx.doi.org/10.1016/j.str.2008.01.012.

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Urs, Usha K., Ramachandran Murali, and 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, no. 12 (December 1, 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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Zhou, Xiaogen, Jun Hu, Chengxin Zhang, Guijun Zhang, and Yang Zhang. "Assembling multidomain protein structures through analogous global structural alignments." Proceedings of the National Academy of Sciences 116, no. 32 (July 24, 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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Biggin, Phil C., Tarmo Roosild, and Senyon Choe. "Potassium channel structure: domain by domain." Current Opinion in Structural Biology 10, no. 4 (August 2000): 456–61. http://dx.doi.org/10.1016/s0959-440x(00)00114-7.

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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, and Mark J. van Raaij. "Crystallographic Structure of Porcine Adenovirus Type 4 Fiber Head and Galectin Domains." Journal of Virology 84, no. 20 (August 4, 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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Chzhan, A. V., V. N. Vasiliev, T. N. Isaeva, and G. S. Patrin. "Research of Features Magnetic Permeability and Domain Structures in Fe₂O₃:GA Crystals near the Morin Transition." Solid State Phenomena 152-153 (April 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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Michiue, Yuichi, Akiji Yamamoto, Mitsuko Onoda, Akira Sato, Takaya Akashi, Hisanori Yamane, and 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, no. 2 (March 16, 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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Shcherbakov, V. P., and S. A. Tarashchan. "Domain structure of titanomagnetite grains with closure domains." Physics of the Earth and Planetary Interiors 65, no. 1-2 (January 1990): 177–87. http://dx.doi.org/10.1016/0031-9201(90)90085-c.

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Tsukahara, S. "Atomic Structure-Sensitive Magnetic Domain Structures of Thin Films." Proceedings, annual meeting, Electron Microscopy Society of America 43 (August 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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Inoshita, Takumi, Yasuhide Inoue, Yoichi Horibe, and Yasumasa Koyama. "Features of the ferroelectric domain structure in the multiferroic material YbMnO3." MRS Advances 1, no. 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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Kwon, Gihan, Oleksandr Kokhan, Ali Han, Karena W. Chapman, Peter J. Chupas, Pingwu Du, and 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, no. 6 (December 1, 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, and Wim P. Burmeister. "The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction." Viruses 14, no. 10 (October 7, 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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Lee, W. T., E. K. H. Salje, and U. Bismayer. "Domain-wall structure and domain-wall strain." Journal of Applied Physics 93, no. 12 (June 15, 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, and Sergey V. Korenev. "Domain structure of CoIr nanoalloys." Powder Diffraction 32, S1 (April 11, 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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Surtees, Jennifer A., and Barbara E. Funnell. "P1 ParB Domain Structure Includes Two Independent Multimerization Domains." Journal of Bacteriology 181, no. 19 (October 1, 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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Ha, N. T. T., M. T. Lan, N. V. Hong, and P. K. Hung. "Structural transformation and dynamical heterogeneity in Germania melt under compression: molecular dynamic simulation." Canadian Journal of Physics 99, no. 12 (December 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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Joseph, Raji E., Nathaniel D. Ginder, Julie A. Hoy, Jay C. Nix, D. Bruce Fulton, Richard B. Honzatko, and 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, no. 2 (January 25, 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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Rotem, S., C. Katz, and A. Friedler. "Insights into the structure and protein–protein interactions of the pro-apoptotic protein ASPP2." Biochemical Society Transactions 35, no. 5 (October 25, 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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Fodor, Anthony A., and Richard W. Aldrich. "Statistical Limits to the Identification of Ion Channel Domains by Sequence Similarity." Journal of General Physiology 127, no. 6 (May 30, 2006): 755–66. http://dx.doi.org/10.1085/jgp.200509419.

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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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Leung, Josephine, Lici Schurig-Briccio, Mutsuo Yamaguchi, Arne Moeller, Jeffrey Speir, Robert Gennis, and Charles Stout. "Transhydrogenase coupling proton translocation and hydride transfer." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 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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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, no. 52 (December 9, 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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Shishkina, Ekaterina, Vladimir Yuzhakov, Maksim Nebogatikov, Elena Pelegova, Eduard Linker, Lyudmila Ivleva, and Vladimir Shur. "As-Grown Domain Structure in Calcium Orthovanadate Crystals." Crystals 11, no. 12 (December 3, 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, no. 1_Supplement (May 1, 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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Poměnková, J., and R. Maršálek. " Time and frequency domain in the business cycle structure." Agricultural Economics (Zemědělská ekonomika) 58, No. 7 (July 23, 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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Ohyama, Takako, Hazuki Takahashi, Harshita Sharma, Toshio Yamazaki, Stefano Gustincich, Yoshitaka Ishii, and Piero Carninci. "An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs." Nucleic Acids Research 48, no. 16 (July 22, 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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Siponen, Marina, Silvia Spinelli, Stéphanie Blangy, Sylvain Moineau, Christian Cambillau, and Valérie Campanacci. "Crystal Structure of a Chimeric Receptor Binding Protein Constructed from Two Lactococcal Phages." Journal of Bacteriology 191, no. 10 (March 13, 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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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, no. 5 (December 17, 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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Li, Hongyang, Yali Xie, Huali Yang, Haixu Hu, Mengchao Li, and Run-Wei Li. "The Effect of Size and Strain on Micro Stripe Magnetic Domain Structure of CoFeB Thin Films." Metals 13, no. 4 (March 30, 2023): 678. http://dx.doi.org/10.3390/met13040678.

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The prerequisite for flexible magnetic electronic devices is the knowledge of the preparation technology of flexible magnetic films and the evolution of the film properties under strain. In this work, CoFeB amorphous ferromagnetic films with stripe domains were prepared on flexible polyimide (PI) substrates by oblique sputtering. The results show that oblique sputtering induces the formation of columnar crystal structure in CoFeB films, which increases the perpendicular magnetic anisotropy of the films, thus leading to the appearance of stripe magnetic domain structures. On this basis, the CoFeB films with stripe domains were processed on a microscopic scale to investigate the size effect and strain regulation on the microscopic domain structure of the magnetic films. The characterization of the magnetic domain structure shows that the stripe domain contrast is reduced by the striped structure prepared by lithography. The triangular, circular and ring patterns deflect the alignment of the stripe domain to different degrees. The experimental results show that the deflection of the stripe domains is caused by the anisotropy of the shapes produced by the different patterns and that the size of the microstructure needs to be close to the period of the stripe domains for the size effect to be significant. In addition, the strain-induced magnetoelastic anisotropy effectively rotates the orientation of the stripe domains, and the variation in domain contrast demonstrates that tensile/compressive strains vary the magnitude of the out-of-plane stray field of the film. Our results provide some insight into the modulation of the physical properties of flexible magnetic films.

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

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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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Hallin, Erik I., Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda, Clive R. Bramham, and Petri Kursula. "Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc." PLOS ONE 16, no. 5 (May 14, 2021): e0251459. http://dx.doi.org/10.1371/journal.pone.0251459.

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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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Akhmatkhanov, Andrey, Constantine Plashinnov, Maxim Nebogatikov, Evgenii Milov, Ilya Shnaidshtein, and Vladimir Shur. "In Situ Imaging of Domain Structure Evolution in LaBGeO5 Single Crystals." Crystals 10, no. 7 (July 6, 2020): 583. http://dx.doi.org/10.3390/cryst10070583.

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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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Kostyukova, Alla, Elizaveta Tiktopulo, Inna Krieger, K. Maeda, and 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, and Zhi-Xin Wang. "Structure ofDrosophilaMad MH2 domain." Acta Crystallographica Section F Structural Biology and Crystallization Communications 64, no. 11 (October 31, 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, no. 3 (January 1, 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, and Yuichiro Maéda. "Domain structure of tropomodulin." European Journal of Biochemistry 267, no. 21 (November 2000): 6470–75. http://dx.doi.org/10.1046/j.1432-1327.2000.01738.x.

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Zamakhov, Ilya M., Viktor A. Anashkin, Andrey V. Moiseenko, Victor N. Orlov, Natalia N. Vorobyeva, Olga S. Sokolova, and Alexander A. Baykov. "The Structure and Nucleotide-Binding Characteristics of Regulated Cystathionine β-Synthase Domain-Containing Pyrophosphatase without One Catalytic Domain." International Journal of Molecular Sciences 24, no. 24 (December 5, 2023): 17160. http://dx.doi.org/10.3390/ijms242417160.

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Regulatory adenine nucleotide-binding cystathionine β-synthase (CBS) domains are widespread in proteins; however, information on the mechanism of their modulating effects on protein function is scarce. The difficulty in obtaining structural data for such proteins is ascribed to their unusual flexibility and propensity to form higher-order oligomeric structures. In this study, we deleted the most movable domain from the catalytic part of a CBS domain-containing bacterial inorganic pyrophosphatase (CBS-PPase) and characterized the deletion variant both structurally and functionally. The truncated CBS-PPase was inactive but retained the homotetrameric structure of the full-size enzyme and its ability to bind a fluorescent AMP analog (inhibitor) and diadenosine tetraphosphate (activator) with the same or greater affinity. The deletion stabilized the protein structure against thermal unfolding, suggesting that the deleted domain destabilizes the structure in the full-size protein. A “linear” 3D structure with an unusual type of domain swapping predicted for the truncated CBS-PPase by Alphafold2 was confirmed by single-particle electron microscopy. The results suggest a dual role for the CBS domains in CBS-PPase regulation: they allow for enzyme tetramerization, which impedes the motion of one catalytic domain, and bind adenine nucleotides to mitigate or aggravate this effect.

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Li, Jie-Fang, Xunhu Dai, Albert Chow, and Dwight Viehland. "Polarization switching mechanisms and electromechanical properties of La-modified lead zirconate titanate ceramics." Journal of Materials Research 10, no. 4 (April 1995): 926–38. http://dx.doi.org/10.1557/jmr.1995.0926.

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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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Gross, Katherine, Kurt Westerholt, Maria E. Gómez, and 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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Žoldák, Gabriel, Thomas A. Knappe, Anne-Juliane Geitner, Christian Scholz, Holger Dobbek, Franz X. Schmid, and Roman P. Jakob. "Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst—A Structural and Functional Analysis." Molecules 29, no. 7 (March 23, 2024): 1440. http://dx.doi.org/10.3390/molecules29071440.

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Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.

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Laco, Gary S., and Yves Pommier. "Role of a tryptophan anchor in human topoisomerase I structure, function and inhibition." Biochemical Journal 411, no. 3 (April 14, 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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Wang, Li, Qi Qiao, Ryan Ferrao, Chen Shen, John M. Hatcher, Sara J. Buhrlage, Nathanael S. Gray, and Hao Wu. "Crystal structure of human IRAK1." Proceedings of the National Academy of Sciences 114, no. 51 (December 5, 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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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, and V. Ya Shur. "Domain structure evolution during polarization reversal in calcium orthovanadate single crystals." Journal of Applied Physics 132, no. 18 (November 14, 2022): 184101. http://dx.doi.org/10.1063/5.0120792.

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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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Thangavelu, Bharani, Alexander G. Pavlovsky, and Ronald Viola. "Structure of homoserineO-acetyltransferase fromStaphylococcus aureus: the first Gram-positive ortholog structure." Acta Crystallographica Section F Structural Biology Communications 70, no. 10 (September 25, 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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Varlioglu, Mesut, Ulrich Lienert, Jun-Sang Park, Jacob L. Jones, and Ersan Üstündag. "Thermal and Electric Field-Dependent Evolution of Domain Structures in Polycrystalline BaTiO3 Using the 3D-XRD Technique." Texture, Stress, and Microstructure 2010 (November 7, 2010): 1–10. http://dx.doi.org/10.1155/2010/910793.

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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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Robinson, Victoria L., Ti Wu, and Ann M. Stock. "Structural Analysis of the Domain Interface in DrrB, a Response Regulator of the OmpR/PhoB Subfamily." Journal of Bacteriology 185, no. 14 (July 15, 2003): 4186–94. http://dx.doi.org/10.1128/jb.185.14.4186-4194.2003.

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ABSTRACT The N-terminal regulatory domains of bacterial response regulator proteins catalyze phosphoryl transfer and function as phosphorylation-dependent regulatory switches to control the output activities of C-terminal effector domains. Structures of numerous isolated regulatory and effector domains have been determined. However, a detailed understanding of regulatory interactions among these domains has been limited by the relative paucity of structural data for intact multidomain response regulator proteins. The first multidomain structures determined, those of transcription factor NarL and methylesterase CheB, both revealed extensive interdomain interfaces. The regulatory domains obstruct access to the functional sites of the effector domains, indicating a regulatory mechanism based on inhibition. In contrast, the recently determined structure of the OmpR/PhoB homologue DrrD revealed no significant interdomain interface, suggesting that the domains are tethered by a flexible linker and lack a fixed orientation relative to each other. To address the generality of this feature, we have determined the 1.8-Å resolution crystal structure of Thermotoga maritima DrrB, providing a second structure of a multidomain response regulator of the OmpR/PhoB subfamily. The structure reveals an extensive domain interface of 751 Å2 and therefore differs greatly from that observed in DrrD. Residues that are crucial players in defining the activation state of the regulatory domain contribute to this interface, implying that conformational changes associated with phosphorylation will influence these intramolecular contacts. The DrrB and DrrD structures are suggestive of different signaling mechanisms, with intramolecular communication between N- and C-terminal domains making substantially different contributions to effector domain regulation in individual members of the OmpR/PhoB family.

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Liu, Xiaoming, Mengyuan Cao, Guan Yang, Jie Liu, Yang Liu, and Hang Wang. "Harnessing Causal Structure Alignment for Enhanced Cross-Domain Named Entity Recognition." Electronics 13, no. 1 (December 22, 2023): 67. http://dx.doi.org/10.3390/electronics13010067.

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Cross-domain named entity recognition (NER) is a crucial task in various practical applications, particularly when faced with the challenge of limited data availability in target domains. Existing methodologies primarily depend on feature representation or model parameter sharing mechanisms to enable the transfer of entity recognition capabilities across domains. However, these approaches often ignore the latent causal relationships inherent in invariant features. To address this limitation, we propose a novel framework, the Causal Structure Alignment-based Cross-Domain Named Entity Recognition (CSA-NER) framework, designed to harness the causally invariant features within causal structures to enhance the cross-domain transfer of entity recognition competence. Initially, CSA-NER constructs a causal feature graph utilizing causal discovery to ascertain causal relationships between entities and contextual features across source and target domains. Subsequently, it performs graph structure alignment to extract causal invariant knowledge across domains via the graph optimal transport (GOT) method. Finally, the acquired causal invariant knowledge is refined and utilized through the integration of Gated Attention Units (GAUs). Comprehensive experiments conducted on five English datasets and a specific CD-NER dataset exhibit a notable improvement in the average performance of the CSA-NER model in comparison to existing cross-domain methods. These findings underscore the significance of unearthing and employing latent causal invariant knowledge to effectively augment the entity recognition capabilities in target domains, thereby contributing a robust methodology to the broader realm of cross-domain natural language processing.

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Novokhatny, V. V., K. C. Ingham, and L. V. Medved. "Domain structure and domain-domain interactions of recombinant tissue plasminogen activator." Journal of Biological Chemistry 266, no. 20 (July 1991): 12994–3002. http://dx.doi.org/10.1016/s0021-9258(18)98794-6.

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Vysotchin, A., L. V. Medved, and K. C. Ingham. "Domain structure and domain-domain interactions in human coagulation factor IX." Journal of Biological Chemistry 268, no. 12 (April 1993): 8436–46. http://dx.doi.org/10.1016/s0021-9258(18)52895-7.

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Perkins, S. J., H. E. Gilbert, M. Aslam, J. Hannan, V. M. Holers, and T. H. J. Goodship. "Solution structures of complement components by X-ray and neutron scattering and analytical ultracentrifugation." Biochemical Society Transactions 30, no. 6 (November 1, 2002): 996–1001. http://dx.doi.org/10.1042/bst0300996.

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The short consensus/complement repeat (SCR) domain (also known as the complement control protein domain) is the most abundant domain type in the complement system. Crystal and NMR structures for proteins that contain single and multiple SCR domains have now been published. These contain inter-SCR linkers of between three and eight residues, and the structures show much variability in inter-SCR orientations. X-ray and neutron scattering, combined with analytical ultracentrifugation and constrained modelling based on known subunit structures will yield a medium-resolution structure for the protein of interest. The fewer parameters that are associated with the structure of interest, the more defined the structure of interest becomes. These solution studies have been applied to several SCR-containing proteins in the complement system, most notably Factor H with 20 SCR domains, a complement receptor type 2 fragment with two SCR domains, and rat complement receptor-related protein (Crry) which contains five SCR domains. The results show great conformational variability in the inter-SCR orientation, and these will be reviewed. Even though the rotational orientation cannot be modelled, it is nonetheless possible to measure the degree of extension of the multi-SCR proteins and, from this, to obtain functionally useful results.

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Journal articles on the topic 'Domain structure'

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