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Journal articles on the topic 'Asymmetrical dimers'

Author: Grafiati
Published: 19 February 2023

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1

Kaur, Sandeep, Hitesh Sharma, and Isha Mudahar. "Substitutional Doping of Asymmetrical Small Fullerene Dimers." Advanced Science Letters 24, no. 2 (February 1, 2018): 888–92. http://dx.doi.org/10.1166/asl.2018.10867.

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2

Javitch, Jonathan A. "Asymmetrical function of dopamine D2 receptor dimers." Biophysical Journal 96, no. 3 (February 2009): 373a. http://dx.doi.org/10.1016/j.bpj.2008.12.2803.

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3

Choi, Jaeyeong, Marie Wahlgren, Vilhelm Ek, Ulla Elofsson, Jonas Fransson, Lars Nilsson, Ann Terry, and Christopher A. G. Söderberg. "Characterization of binding between model protein GA-Z and human serum albumin using asymmetrical flow field-flow fractionation and small angle X-ray scattering." PLOS ONE 15, no. 11 (November 24, 2020): e0242605. http://dx.doi.org/10.1371/journal.pone.0242605.

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Protein-based drugs often require targeted drug delivery for optimal therapy. A successful strategy to increase the circulation time of the protein in the blood is to link the therapeutic protein with an albumin-binding domain. In this work, we characterized such a protein-based drug, GA-Z. Using asymmetrical flow field-flow fractionation coupled with multi-angle light scattering (AF4-MALS) we investigated the GA-Z monomer-dimer equilibrium as well as the molar binding ratio of GA-Z to HSA. Using small angle X-ray scattering, we studied the structure of GA-Z as well as the complex between GA-Z and HSA. The results show that GA-Z is predominantly dimeric in solution at pH 7 and that it binds to monomeric as well as dimeric HSA. Furthermore, GA-Z binds to HSA both as a monomer and a dimer, and thus, it can be expected to stay bound also upon dilution following injection in the blood stream. The results from SAXS and binding studies indicate that the GA-Z dimer is formed between two target domains (Z-domains). The results also indicate that the binding of GA-Z to HSA does not affect the ratio between HSA dimers and monomers, and that no higher order oligomers of the complex are seen other than those containing dimers of GA-Z and dimers of HSA.
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4

Schubert, Ina, Wilfried Sigle, Peter A. van Aken, Christina Trautmann, and Maria Eugenia Toimil-Molares. "STEM-EELS analysis of multipole surface plasmon modes in symmetry-broken AuAg nanowire dimers." Nanoscale 7, no. 11 (2015): 4935–41. http://dx.doi.org/10.1039/c4nr06578f.

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5

Lee, Ji-Hye, Intekhab Alam, Kang Rok Han, Sunyoung Cho, Sungho Shin, Seokha Kang, Jai Myung Yang, and Kyung Hyun Kim. "Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase." Journal of General Virology 92, no. 7 (July 1, 2011): 1607–16. http://dx.doi.org/10.1099/vir.0.031104-0.

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Norovirus is one of the leading agents of gastroenteritis and is a major public health concern. In this study, the crystal structures of recombinant RNA-dependent RNA polymerase (RdRp) from murine norovirus-1 (MNV-1) and its complex with 5-fluorouracil (5FU) were determined at 2.5 Å resolution. Crystals with C2 symmetry revealed a dimer with half a dimer in the asymmetrical unit, and the protein exists predominantly as a monomer in solution, in equilibrium with a smaller population of dimers, trimers and hexamers. MNV-1 RdRp exhibited polymerization activity with a right-hand fold typical of polynucleotide polymerases. The metal ion modelled in close proximity to the active site was found to be coordinated tetrahedrally to the carboxyl groups of aspartate clusters. The orientation of 5FU observed in three molecules in the asymmetrical unit was found to be slightly different, but it was stabilized by a network of favourable interactions with the conserved active-site residues Arg185, Asp245, Asp346, Asp347 and Arg395. The information gained on the structural and functional features of MNV-1 RdRp will be helpful in understanding replication of norovirus and in designing novel therapeutic agents against this important pathogen.
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6

Du, Guangqing, Yu Lu, Dayantha Lankanath, Xun Hou, and Feng Chen. "Theoretical Study on Symmetry-Broken Plasmonic Optical Tweezers for Heterogeneous Noble-Metal-Based Nano-Bowtie Antennas." Nanomaterials 11, no. 3 (March 17, 2021): 759. http://dx.doi.org/10.3390/nano11030759.

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Plasmonic optical tweezers with a symmetry-tunable potential well were investigated based on a heterogeneous model of nano-bowtie antennas made of different noble substances. The typical noble metals Au and Ag are considered as plasmonic supporters for excitation of hybrid plasmonic modes in bowtie dimers. It is proposed that the plasmonic optical trapping force around a quantum dot exhibits symmetry-broken characteristics and becomes increasingly asymmetrical with increasing applied laser electric field. Here, it is explained by the dominant plasmon hybridization of the heterogeneous Au–Ag dimer, in which the plasmon excitations can be inconsistently modified by tuning the applied laser electric field. In the spectrum regime, the wavelength-dependent plasmonic trapping potential exhibits a two-peak structure for the heterogeneous Au–Ag bowtie dimer compared to a single-peak trapping potential of the Au–Au bowtie dimer. In addition, we comprehensively investigated the influence of structural parameter variables on the plasmonic potential well generated from the heterogeneous noble nano-bowtie antenna with respect to the bowtie edge length, edge/tip rounding, bowtie gap, and nanosphere size. This work could be helpful in improving our understanding of wavelength and laser field tunable asymmetric nano-tweezers for flexible and non-uniform nano-trapping applications of particle-sorting, plasmon coloring, SERS imaging, and quantum dot lighting.
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7

Rolfsson, Ottar, Katerina Toropova, Victoria Morton, Simona Francese, Gabriella Basnak, Gary S. Thompson, Stephen W. Homans, et al. "RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2." Computational and Mathematical Methods in Medicine 9, no. 3-4 (2008): 339–49. http://dx.doi.org/10.1080/17486700802168445.

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Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo-electron microscopy (cryo-EM), we have been able to show that quasi-equivalent conformer switching in the coat protein (CP) of an RNA bacteriophage (MS2) is controlled by a sequence-specific RNA–protein interaction. The RNA component of this complex is an RNA stem-loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of theT = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi-equivalent conformers seen in the 3D structure of the virion. An icosahedrally-averaged single particle cryo-EM reconstruction of the wild-type phage (to ∼9 Å resolution) has revealed icosahedrally ordered density encompassing up to 90% of the single-stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5-fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in theT = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi-equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA-mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.
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8

Mallick, Suman, Tao Cheng, Lu Chen, Miao Meng, Yu Yu Zhang, and Chun Y. Liu. "A study of asymmetrical mixed-valent Mo2–Mo2 complexes in the class III regime." Dalton Transactions 46, no. 17 (2017): 5711–23. http://dx.doi.org/10.1039/c6dt04915j.

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With thiolated oxalato bridging ligands, three strongly coupled, asymmetrical Mo2 dimers have been studied. In these strongly mixed-valence systems, the charge is unevenly distributed and electron transfer between the two bridged Mo2 centers occurs, as indicated by the LMCT absorption and supported by the DFT calculations.
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9

Al-Hamdani, Uhood Jabbar, Hanna S. Abbo, Ebtahal Hamid Shaheeb, and Salam J. J. Titinchi. "Symmetrical and asymmetrical liquid crystal dimers: synthesis, characterisation and mesomorphic behaviour." Liquid Crystals 46, no. 15 (June 20, 2019): 2291–300. http://dx.doi.org/10.1080/02678292.2019.1626925.

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10

Kaur, Sandeep, Amrish Sharma, Hitesh Sharma, and Isha Mudahar. "Structural and magnetic properties of small symmetrical and asymmetrical sized fullerene dimers." Materials Research Express 5, no. 1 (January 18, 2018): 016105. http://dx.doi.org/10.1088/2053-1591/aaa567.

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11

Purdy, Andrew P., and Ray J. Butcher. "Tetrakis[μ2-1,1,1,3,3,3-hexafluoro-2-(trifluoromethyl)propan-2-olato]tetrakis(μ3-2-methylpropan-2-olato)octacopper(I)." Acta Crystallographica Section E Crystallographic Communications 77, no. 6 (May 28, 2021): 668–71. http://dx.doi.org/10.1107/s2056989021005429.

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The title compound, [Cu8(C4H9O)4(C4F9O)4], crystallizes in the monoclinic space group, P21/n and contains a self-assembly of two C16H18Cu4F18O4 units linked by bridging tert-butyl groups [Cu—O bonds of length 2.3779 (15) and 2.4248 (15) Å], generating a centrosymmetric dimer. The asymmetrical unit, C16H18Cu4F18O4, contains an almost square-planar arrangement of the four Cu atoms linked by bridging tert-butyl and perfluorinated tert-butyl groups with Cu—Cu distances ranging from 2.7108 (4) to 2.7612 (4) Å and Cu —Cu—Cu angle values close to 90° [ranging from 89.459 (10)° to 90.025 (11)°]. These dimers are further linked by weak C—H...F and F...F interactions. As is commonly encountered in perfluorinated tert-butyl groups, one of the CF3 groups is disordered and was refined with two equivalent conformations with occupancies of 0.74 (3) and 0.26 (3).
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12

Santana, Samuel, and Esov S. Velázquez. "Variational mean spherical scaling approximation for nonspherical ions: The case of asymmetrical dimers." Journal of Chemical Physics 119, no. 2 (July 8, 2003): 972–77. http://dx.doi.org/10.1063/1.1578631.

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13

Lohmeier, Martin, H. A. van der Vegt, R. G. van Silfhout, E. Vlieg, J. M. C. Thornton, J. E. Macdonald, and P. M. L. O. Scholte. "Asymmetrical dimers on the Ge(001)-2 × 1-Sb surface observed using X-ray diffraction." Surface Science 275, no. 3 (September 1992): 190–200. http://dx.doi.org/10.1016/0039-6028(92)90793-6.

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14

Dey, Sumitra, and Ahmed Hassan. "Asymmetric Carbon Nanotube Dimers for Novel Sensing Applications." Applied Computational Electromagnetics Society 35, no. 11 (February 4, 2021): 1320–21. http://dx.doi.org/10.47037/2020.aces.j.351129.

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In this work, we study the use of asymmetric carbon nanotube (CNT) dimers for the contactless detection of foreign nano-particles. Asymmetric CNT dimers create a unique field distribution, through the electromagnetic coupling, which in turn generates two distinct resonances representing the bonding and anti-bonding modes. The presence of a foreign nano-particle (NP) in the vicinity of the CNT dimer perturbs the dimer’s field distribution and causes the bonding and anti-bonding resonances to shift by unequal amounts depending on the NP location. By studying the difference in the shift of the bonding and the anti-bonding resonances, we show that the NP relative location can be reconstructed. The computational experiments performed in this work show how asymmetric CNT dimers can be used for novel sensing applications.
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15

Miyazaki, Naoyuki, Lakha Salaipeth, Satoko Kanematsu, Kenji Iwasaki, and Nobuhiro Suzuki. "Megabirnavirus structure reveals a putative 120-subunit capsid formed by asymmetrical dimers with distinctive large protrusions." Journal of General Virology 96, no. 8 (August 1, 2015): 2435–41. http://dx.doi.org/10.1099/vir.0.000182.

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16

He, Tianwei, Alain R. Puente Santiago, and Aijun Du. "Atomically embedded asymmetrical dual-metal dimers on N-doped graphene for ultra-efficient nitrogen reduction reaction." Journal of Catalysis 388 (August 2020): 77–83. http://dx.doi.org/10.1016/j.jcat.2020.05.009.

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17

Seida, Pamela R., Jeanne W. Bundens, and Michelle M. Francl. "Ab initio MO study of the symmetrical and asymmetrical isomers of bridging alkynylaluminum and alkynylberyllium dimers." International Journal of Quantum Chemistry 95, no. 6 (2003): 806–9. http://dx.doi.org/10.1002/qua.10690.

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18

Soos, M. A., J. Whittaker, R. Lammers, A. Ullrich, and K. Siddle. "Receptors for insulin and insulin-like growth factor-I can form hybrid dimers. Characterisation of hybrid receptors in transfected cells." Biochemical Journal 270, no. 2 (September 1, 1990): 383–90. http://dx.doi.org/10.1042/bj2700383.

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We have demonstrated the formation of hybrid insulin/insulin-like growth factor-I(IGF-I) receptors in transfected rodent fibroblasts, which overexpress human receptors, by examining reactivity with species- and receptor-specific monoclonal antibodies. In NIH 3T3 and Rat 1 fibroblasts, endogenous IGF-I receptors were unreactive with anti-(human insulin receptor)monoclonal antibodies (47-9, 25-49, 83-14, 83-7, 18-44). However, in transfected cells expressing high levels of insulin receptors, 60-80% of high-affinity IGF-I receptors reacted with these antibodies, as assessed either by inhibition of ligand binding in intact cells or by precipitation of solubilized receptors. Conversely, endogenous insulin receptors in NIH 3T3 cells were unreactive with anti-(IGF-I receptor) antibodies alpha IR-3 and 16-13. However, approx. 50% of high-affinity insulin receptors reacted with these antibodies in cells expressing high levels of human IGF-I receptors. The hybrid receptors in transfected cells bound insulin or IGF-I with high affinity. However, responses to these ligands were asymmetrical, in that binding of IGF-I inhibited subsequent binding of insulin, but prior binding of insulin did not affect the affinity for IGF-I. The existence of hybrid receptors in normal tissues could have important implications for metabolic regulation by insulin and IGF-I.
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19

Griffiths, Scott, Carl H. Mesarich, Benedetta Saccomanno, Abraham Vaisberg, Pierre J. G. M. De Wit, Russell Cox, and Jérôme Collemare. "Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization." Proceedings of the National Academy of Sciences 113, no. 25 (June 6, 2016): 6851–56. http://dx.doi.org/10.1073/pnas.1603528113.

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Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungusCladosporium fulvum. A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families.
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20

Jiang, Wangshu, Glareh Askarieh, Alexander Shkumatov, My Hedhammar, and Stefan D. Knight. "Structure of the N-terminal domain of Euprosthenops australis dragline silk suggests that conversion of spidroin dope to spider silk involves a conserved asymmetric dimer intermediate." Acta Crystallographica Section D Structural Biology 75, no. 7 (June 26, 2019): 618–27. http://dx.doi.org/10.1107/s2059798319007253.

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Spider silk is a biomaterial with exceptional mechanical toughness, and there is great interest in developing biomimetic methods to produce engineered spider silk-based materials. However, the mechanisms that regulate the conversion of spider silk proteins (spidroins) from highly soluble dope into silk are not completely understood. The N-terminal domain (NT) of Euprosthenops australis dragline silk protein undergoes conformational and quaternary-structure changes from a monomer at a pH above 7 to a homodimer at lower pH values. Conversion from the monomer to the dimer requires the protonation of three conserved glutamic acid residues, resulting in a low-pH `locked' dimer stabilized by symmetric electrostatic interactions at the poles of the dimer. The detailed molecular events during this transition are still unresolved. Here, a 2.1 Å resolution crystal structure of an NT T61A mutant in an alternative, asymmetric, dimer form in which the electrostatic interactions at one of the poles are dramatically different from those in symmetrical dimers is presented. A similar asymmetric dimer structure from dragline silk of Nephila clavipes has previously been described. It is suggested that asymmetric dimers represent a conserved intermediate state in spider silk formation, and a revised `lock-and-trigger' mechanism for spider silk formation is presented.
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21

MOLINA, MARIO I. "THE MAGNETOINDUCTIVE DIMER." Modern Physics Letters B 27, no. 27 (October 15, 2013): 1350196. http://dx.doi.org/10.1142/s0217984913501960.

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In this paper, we examine a nonlinear magnetoinductive dimer and compute its linear and nonlinear symmetric, antisymmetric and asymmetric modes in closed-form, in the rotating-wave approximation. A linear stability analysis of these modes reveals that the asymmetric mode is always stable, for any allowed value of the coupling parameter and for both, hard and soft nonlinearity. An exact numerical computation of the dimer dynamics reveals a magnetic energy self-trapping whose threshold increases for increasing dimer coupling, decreases for increasing nonlinearity response and is robust against asymmetrical nonlinear responses and resonant frequencies mismatch.
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22

Duanmu, M., K. Li, R. L. Horne, P. G. Kevrekidis, and N. Whitaker. "Linear and nonlinear parity-time-symmetric oligomers: a dynamical systems analysis." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 371, no. 1989 (April 28, 2013): 20120171. http://dx.doi.org/10.1098/rsta.2012.0171.

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In the present work, we focus on the cases of two-site (dimer) and three-site (trimer) configurations, i.e. oligomers, respecting the parity-time ( ) symmetry, i.e. with a spatially odd gain–loss profile. We examine different types of solutions of such configurations with linear and nonlinear gain/loss profiles. Solutions beyond the linear -symmetry critical point as well as solutions with asymmetric linearization eigenvalues are found in both the nonlinear dimer and trimer. The latter feature is absent in linear -symmetric trimers, while both of them are absent in linear -symmetric dimers. Furthermore, nonlinear gain/loss terms enable the existence of both symmetric and asymmetric solution profiles (and of bifurcations between them), while only symmetric solutions are present in the linear -symmetric dimers and trimers. The linear stability analysis around the obtained solutions is discussed and their dynamical evolution is explored by means of direct numerical simulations. Finally, a brief discussion is also given of recent progress in the context of -symmetric quadrimers.
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23

Bloomfield, Hannah R., and Jamie S. Ritch. "A new polymorph of phenylselenium trichloride." Acta Crystallographica Section C Structural Chemistry 75, no. 11 (October 4, 2019): 1471–74. http://dx.doi.org/10.1107/s2053229619013019.

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A second polymorph of phenylselenium trichloride, PhSeCl3 or C6H5Cl3Se, is disclosed, which is comprised of asymmetric chlorine-bridged noncovalent dimer units rather than polymeric chains. These dimers are each weakly bound to an adjacent dimer through noncovalent Se...Cl bonding interactions. Phenyl rings within each dimer are oriented in a syn fashion. Density functional theory (DFT) calculations reveal that the putative anti isomer is within 5 kJ mol−1 of the experimentally observed form. This structure represents the first additional polymorph discovered for an organoselenium trihalide compound.
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24

WU, Tzong-Yuan, Chun-I. LIU, and Yen-Chung CHANG. "A study of the oligomeric state of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-preferring glutamate receptors in the synaptic junctions of porcine brain." Biochemical Journal 319, no. 3 (November 1, 1996): 731–39. http://dx.doi.org/10.1042/bj3190731.

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The number of the subunits in an α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-preferring L-glutamate receptor in the synaptic junctions of porcine brain was investigated in this study. Upon incubation of the synaptic junctions with three cross-linking reagents, dimethyl adipimidate (DMA), dimethyl suberimidate (DMS) and N-succinimidyl-(4-azidophenyl)-1,3´-dithiopropionate (SADP), AMPA receptor subunits in higher-molecular-mass aggregates were detected by immunoblotting. These aggregates migrated as proteins of approx. 200, 300 and 400 kDa. The number and identity of the subunits in a solubilized AMPA receptor were also investigated here. Two samples, W1 and W2, enriched in AMPA receptors were prepared from synaptic junctions by a combination of detergent-solubilization, anion-exchange chromatography and wheatgerm agglutinin affinity chromatography. Hydrodynamic behaviour analyses revealed that the majority of the AMPA receptors in either one of these samples were asymmetrical detergent-surrounded particles with a protein mass around 350 kDa. SDS/PAGE analysis revealed that the majority of AMPA receptors in the W1 sample were comprised of dimers of 106 kDa subunits which were covalently linked by disulphide bonds. Cross-linking these receptors with SADP yielded a new band of approx. 400 kDa. The results obtained here, either from the studies of AMPA receptors embedding in synaptic junctions or from those of detergent-solubilized and partially purified receptors, suggest that AMPA receptors contain a basic core structure comprising of four 106 kDa subunits.
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25

de Azevedo, W. F., R. J. Ward, F. R. Lombardi, J. R. Giglio, A. M. Soares, M. R. M. Fontes, and R. K. Arni. "Crystal structure of myotoxin-11: a myotoxic phospholipase A2 - homologue from bothrops moojenivenom." Protein & Peptide Letters 4, no. 5 (October 1997): 329–34. http://dx.doi.org/10.2174/092986650405221017153439.

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Abstract: The crystal structure ofMyotoxin-II (MjTX-II), a Lys49 PLAi-homologue from Bothrops moojeni venom has been determined and refined at 2.0 A to a crystallographic residual of 19.7% (Ru.0=28.1%). MjTX-II is a dimer in the crystal, with the monomers in the asymmetric unit related by a two-fold symmetry axis running through the dimer interface. The dimers of MjTX-II and the Lys49 PLA2 from B. asper venom are similar, however the relative orientations of the monomers suggests a flexible dimer interface, which serves as a hinge between the two molecules.
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26

Bouillet, Sophie, Ti Wu, Shaoxing Chen, Ann M. Stock, and Rong Gao. "Structural asymmetry does not indicate hemiphosphorylation in the bacterial histidine kinase CpxA." Journal of Biological Chemistry 295, no. 23 (February 24, 2020): 8106–17. http://dx.doi.org/10.1074/jbc.ra120.012757.

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Histidine protein kinases (HKs) are prevalent prokaryotic sensor kinases that are central to phosphotransfer in two-component signal transduction systems, regulating phosphorylation of response regulator proteins that determine the output responses. HKs typically exist as dimers and can potentially autophosphorylate at each conserved histidine residue in the individual protomers, leading to diphosphorylation. However, analyses of HK phosphorylation in biochemical assays in vitro suggest negative cooperativity, whereby phosphorylation in one protomer of the dimer inhibits phosphorylation in the second protomer, leading to ∼50% phosphorylation of the available sites in dimers. This negative cooperativity is often correlated with an asymmetric domain arrangement, a common structural characteristic of autophosphorylation states in many HK structures. In this study, we engineered covalent dimers of the cytoplasmic domains of Escherichia coli CpxA, enabling us to quantify individual species: unphosphorylated, monophosphorylated, and diphosphorylated dimers. Together with mathematical modeling, we unambiguously demonstrate no cooperativity in autophosphorylation of CpxA despite its asymmetric structures, indicating that these asymmetric domain arrangements are not linked to negative cooperativity and hemiphosphorylation. Furthermore, the modeling indicated that many parameters, most notably minor amounts of ADP generated during autophosphorylation reactions or present in ATP preparations, can produce ∼50% total phosphorylation that may be mistakenly attributed to negative cooperativity. This study also establishes that the engineered covalent heterodimer provides a robust experimental system for investigating cooperativity in HK autophosphorylation and offers a useful tool for testing how symmetric or asymmetric structural features influence HK functions.
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27

TÜRKMENOĞLU, MUSTAFA, and ŞENAY KATIRCIOĞLU. "ADSORPTION AND DISSOCIATION OF PH3 ON SiGe(100) (2 × 1) SURFACE." Surface Review and Letters 15, no. 03 (June 2008): 307–17. http://dx.doi.org/10.1142/s0218625x08011408.

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The most stable structures for the adsorption and dissociation of phosphine ( PH 3) on SiGe (100) (2 × 1) surface have been investigated by relative total energy calculations based on density functional theory. According to the optimization calculations, PH 3 is adsorbed on the Si (down) and Ge (down) site of the Ge – Si and Ge – Ge dimers on SiGe surface, respectively. The PH 2 and H products have been found to be thermodynamically favored in the dissociation path of PH 3 on SiGe surface when the system is thermally activated. Although PH 3 is adsorbed on the Ge – Ge and Ge – Si dimers directly, it dissociates on the SiGe surface by passing through a transition state. The asymmetric Ge – Si and Ge – Ge dimers on SiGe surface are found to be approximately symmetric after the dissociation of PH 3 on the surface. The present work has showed that PH 2 prefers to be adsorbed on Ge site of the Ge – Si dimer. Therefore, the adsorption of PH 2 on Ge site of the Ge – Si dimer, while PH 3 being dissociated on the Si site, has indicated the migration of PH 2 on SiGe surface.
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28

Chen, Yujie, Joshua M. Tokuda, Traci Topping, Steve P. Meisburger, Suzette A. Pabit, Lisa M. Gloss, and Lois Pollack. "Asymmetric unwrapping of nucleosomal DNA propagates asymmetric opening and dissociation of the histone core." Proceedings of the National Academy of Sciences 114, no. 2 (December 27, 2016): 334–39. http://dx.doi.org/10.1073/pnas.1611118114.

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The nucleosome core particle (NCP) is the basic structural unit for genome packaging in eukaryotic cells and consists of DNA wound around a core of eight histone proteins. DNA access is modulated through dynamic processes of NCP disassembly. Partly disassembled structures, such as the hexasome (containing six histones) and the tetrasome (four histones), are important for transcription regulation in vivo. However, the pathways for their formation have been difficult to characterize. We combine time-resolved (TR) small-angle X-ray scattering and TR-FRET to correlate changes in the DNA conformations with composition of the histone core during salt-induced disassembly of canonical NCPs. We find that H2A–H2B histone dimers are released sequentially, with the first dimer being released after the DNA has formed an asymmetrically unwrapped, teardrop-shape DNA structure. This finding suggests that the octasome-to-hexasome transition is guided by the asymmetric unwrapping of the DNA. The link between DNA structure and histone composition suggests a potential mechanism for the action of proteins that alter nucleosome configurations such as histone chaperones and chromatin remodeling complexes.
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29

Savich, Carolyn Z., and Joseph M. Tanski. "Crystallographic and spectroscopic characterization of racemic Mosher's Acid." Acta Crystallographica Section E Crystallographic Communications 76, no. 7 (June 26, 2020): 1143–45. http://dx.doi.org/10.1107/s2056989020008403.

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The title compound, C10H9F3O3, represents the structure of racemic Mosher's Acid (systematic name: 3,3,3-trifluoro-2-methoxy-2-phenylpropanoic acid), a carboxylic acid that when resolved can be employed as a chiral derivatizing agent. The compound contains a carboxylic acid group, a methoxy group and a trifluoromethyl substituent on an asymmetric benzylic carbon atom. The two independent molecules in the asymmetric unit form a non-centrosymmetric homochiral dimer via intermolecularly hydrogen-bonded head-to-tail dimers with graph-set notation R 2 2(8) and donor–acceptor hydrogen-bonding distances of 2.6616 (13) and 2.6801 (13) Å.
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30

Ma, Fuduo, Sijia Wang, David T. Wu, and Ning Wu. "Electric-field–induced assembly and propulsion of chiral colloidal clusters." Proceedings of the National Academy of Sciences 112, no. 20 (May 4, 2015): 6307–12. http://dx.doi.org/10.1073/pnas.1502141112.

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Chiral molecules with opposite handedness exhibit distinct physical, chemical, or biological properties. They pose challenges as well as opportunities in understanding the phase behavior of soft matter, designing enantioselective catalysts, and manufacturing single-handed pharmaceuticals. Microscopic particles, arranged in a chiral configuration, could also exhibit unusual optical, electric, or magnetic responses. Here we report a simple method to assemble achiral building blocks, i.e., the asymmetric colloidal dimers, into a family of chiral clusters. Under alternating current electric fields, two to four lying dimers associate closely with a central standing dimer and form both right- and left-handed clusters on a conducting substrate. The cluster configuration is primarily determined by the induced dipolar interactions between constituent dimers. Our theoretical model reveals that in-plane dipolar repulsion between petals in the cluster favors the achiral configuration, whereas out-of-plane attraction between the central dimer and surrounding petals favors a chiral arrangement. It is the competition between these two interactions that dictates the final configuration. The theoretical chirality phase diagram is found to be in excellent agreement with experimental observations. We further demonstrate that the broken symmetry in chiral clusters induces an unbalanced electrohydrodynamic flow surrounding them. As a result, they rotate in opposite directions according to their handedness. Both the assembly and propulsion mechanisms revealed here can be potentially applied to other types of asymmetric particles. Such kinds of chiral colloids will be useful for fabricating metamaterials, making model systems for both chiral molecules and active matter, or building propellers for microscale transport.
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31

MacPherson, Kirsty H. R., Paul D. Carr, Denis Verger, Terry Kwok, Barrie E. Davidson, and David L. Ollis. "Crystallization of the N-terminal domain of the Escherichia coli regulatory protein TyrR." Acta Crystallographica Section D Biological Crystallography 55, no. 11 (November 1, 1999): 1923–24. http://dx.doi.org/10.1107/s0907444999010902.

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The N-terminal domain of the regulatory protein TyrR from Escherichia coli forms a dimer in solution and has been purified and crystallized. The crystals belong to space group C2 with unit-cell parameters a = 134.5, b = 72.1, c = 96.7 Å, β = 98.5°. The crystals diffract to 2.8 Å. Assuming a molecular weight of 23219 Da, a Vm of 2.5 Å3 Da−1 is obtained for two dimers in the asymmetric unit.
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32

Byrne, CJ, IK Morris, and AD Ward. "The Synthesis of the Dimer and Trimer Ether-Linked Components of Hematoporphyrin Derivative." Australian Journal of Chemistry 43, no. 11 (1990): 1889. http://dx.doi.org/10.1071/ch9901889.

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The preparation is described of all of the likely dimer and trimer ether-linked components of the anticancer material known as hematoporphyrin derivative. The hydroxyethyl side chain of one porphyrin, related to hematoporphyrin, reacts readily with a bromoethyl system derived from the same, or similar, hematoporphyrin -derived porphyrin to form a diporphyrin ether. The coupling reaction can be controlled to occur in situ, allowing the preparation of a symmetrical ether-linked dimer , or separately to provide an asymmetrically substituted porphyrin dimer . The bromoethyl groups can be formed from either the hydroxyethyl groups or, more slowly, from a vinyl side chain by using hydrogen bromide in dichloromethane. Ether-linked porphyrin trimers can be prepared by reacting a dibromoethyl system with 2 equiv. of a hydroxyethyl -containing porphyrin or by further reaction of an initially formed dimer. Hydroxyethyl side chains in the dimers and trimers are best obtained by reduction of an acetyl group. Some spectral properties of the products are described.
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33

Abosadiya, Hamza M., Siti Aishah Hasbullah, Bohari M. Yamin, and Adibatul H. Fadzil. "1-(4-Chlorobutanoyl)-3-(3-chlorophenyl)thiourea." Acta Crystallographica Section E Structure Reports Online 70, no. 6 (May 17, 2014): o675. http://dx.doi.org/10.1107/s1600536814009295.

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The two independent molecules in the asymmetric unit of the title compound, C11H12Cl2N2OS, exhibit different conformations, with the benzene ring and the N2CS thiourea group forming dihedral angles of 87.40 (18) and 69.42 (15)°. An intramolecular N—H...O hydrogen bond is present in each molecule. Two further N—H...O hydrogen bonds link the independent molecules into a dimer. In the crystal, the dimers are linked by N—H...S and C—H...S hydrogen bonds, forming chains parallel to thecaxis.
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34

Manoj, N., V. R. Srinivas, and K. Suguna. "Structure of basic winged-bean lectin and a comparison with its saccharide-bound form." Acta Crystallographica Section D Biological Crystallography 55, no. 4 (April 1, 1999): 794–800. http://dx.doi.org/10.1107/s090744499900044x.

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The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 Å resolution. The final R factor is 19.7% for all data in the resolution range 8.0–2.3 Å. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-α-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 Å of the main-chain atoms of the variable loop.
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35

Gross, David C. "Asymmetric distannoxane dimers." Inorganic Chemistry 28, no. 12 (June 1989): 2355–59. http://dx.doi.org/10.1021/ic00311a021.

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36

Kim, Minsik, Hee Jung Kim, Sang Hyeon Son, Hye Jin Yoon, Youngbin Lim, Jong Woo Lee, Yeong-Jae Seok, et al. "Noncanonical DNA-binding mode of repressor and its disassembly by antirepressor." Proceedings of the National Academy of Sciences 113, no. 18 (April 20, 2016): E2480—E2488. http://dx.doi.org/10.1073/pnas.1602618113.

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DNA-binding repressors are involved in transcriptional repression in many organisms. Disabling a repressor is a crucial step in activating expression of desired genes. Thus, several mechanisms have been identified for the removal of a stably bound repressor (Rep) from the operator. Here, we describe an uncharacterized mechanism of noncanonical DNA binding and induction by a Rep from the temperate Salmonella phage SPC32H; this mechanism was revealed using the crystal structures of homotetrameric Rep (92–198) and a hetero-octameric complex between the Rep and its antirepressor (Ant). The canonical method of inactivating a repressor is through the competitive binding of the antirepressor to the operator-binding site of the repressor; however, these studies revealed several noncanonical features. First, Ant does not compete for the DNA-binding region of Rep. Instead, the tetrameric Ant binds to the C-terminal domains of two asymmetric Rep dimers. Simultaneously, Ant facilitates the binding of the Rep N-terminal domains to Ant, resulting in the release of two Rep dimers from the bound DNA. Second, the dimer pairs of the N-terminal DNA-binding domains originate from different dimers of a Rep tetramer (trans model). This situation is different from that of other canonical Reps, in which two N-terminal DNA-binding domains from the same dimeric unit form a dimer upon DNA binding (cis model). On the basis of these observations, we propose a noncanonical model for the reversible inactivation of a Rep by an Ant.
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37

Manoj, N., V. R. Srinivas, B. Satish, Netai C. Singha, and K. Suguna. "Crystallization and preliminary crystallographic analysis of winged bean acidic lectin." Acta Crystallographica Section D Biological Crystallography 55, no. 2 (February 1, 1999): 564–65. http://dx.doi.org/10.1107/s0907444998013018.

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The acidic lectin (WBAII) from the winged bean (Psophocarpus tetragonolobus) binds to the H-antigenic determinant on human erythrocytes and to the T-antigenic disaccharide Gal-β1,3-GalNAc. Two crystal forms of WBAII were obtained in the presence of methyl-α-D-galactose. Form I belongs to space group R3 with unit-cell dimensions a = b = 182.11, c = 44.99 Å and has one dimer in the asymmetric unit. Form II belongs to space group C2 with unit-cell dimensions a = 135.36, b = 127.25, c = 139.98 Å, β = 95.9° and has four dimers in the asymmetric unit. Intensity data were collected to 3.0 Å and to 3.5 Å from crystals of form I and II, respectively. The structures were solved by the molecular-replacement method using the coordinates of the basic form of winged bean lectin.
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38

Begum, M. S., M. B. H. Howlader, M. C. Sheikh, R. Miyatake, and E. Zangrando. "Crystal structure ofS-hexyl (E)-3-(2-hydroxybenzylidene)dithiocarbazate." Acta Crystallographica Section E Crystallographic Communications 72, no. 3 (February 6, 2016): 290–92. http://dx.doi.org/10.1107/s2056989016001857.

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The title compound, C14H20N2OS2[systematic name:S-hexyl (E)-2-(2-hydroxybenzylidene)hydrazine-1-carbodithioate], crystallizes with four independent molecules (A–D) in the asymmetric unit. All four molecules adopt anEconformation with respect to the C=N bond of the benzylidene moiety and have an intramolecular O—H...N hydrogen bond generating anS(6) ring motif. In the crystal, theAandDmolecules are connected by a pair N—H...S hydrogen bonds, forming a dimer with anR22(8) ring motif. In the case of moleculesBandC, they are linked to themselves by pairs of N—H...S hydrogen bonds, formingB–BandC–Cinversion dimers withR22(8) ring motifs.
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39

Faizi, Md Serajul Haque, Musheer Ahmad, and Irina A. Golenya. "Crystal structure of 4-[4-(ethoxycarbonyl)piperazin-1-yl]benzoic acid." Acta Crystallographica Section E Crystallographic Communications 72, no. 9 (August 9, 2016): 1267–69. http://dx.doi.org/10.1107/s2056989016012482.

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The asymmetric unit of the title compound, C14H18N2O4, contains two independent molecules (AandB) which have essentially the same conformation. The piperazine rings adopts chair conformations with the N atoms out of plane. The dihedral angles formed by the four approximately planar C atoms of the piperazine ring and the benzene ring is 30.8 (5)° in moleculeAand 30.6 (5)° in moleculeB. In the crystal, moleculesAandBare connected by a pair of O—H...O hydrogen bonds, forming a dimer with graph-set notationR22(8). Weak C—H...O hydrogen bonds connect the dimers, forming zigzag chains along [001].
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40

Hwang, In Hong, Pan-Gi Kim, Cheal Kim, and Youngmee Kim. "Bis(μ-2-carboxymethyl-2-hydroxybutanedioato)bis[diaquamanganese(II)]–1,2-bis(pyridin-4-yl)ethane–water (1/1/2)." Acta Crystallographica Section E Structure Reports Online 68, no. 8 (July 25, 2012): m1116—m1117. http://dx.doi.org/10.1107/s1600536812032771.

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The asymmetric unit of the title compound, [Mn2(C6H6O7)2(H2O)4]·C12H12N2·2H2O, comprises half of a centrosymmetric dimer, half of a 1,2-bis(pyridin-4-yl)ethane and one water molecule. Two citrate ligands bridge two MnIIions, the MnIIion being coordinated by four O atoms from the citrate(2−) ligands and two water O atoms, forming a distorted octahedral environment. In the crystal, O—H...O hydrogen bonds link the centrosymmetric dimers and lattice water molecules into a three-dimensional structure which is further stabilized by intermolecular π–π interactions [centroid–centroid distance = 3.792 (2) Å].
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41

Visudtiphole, Virak, Matthew B. Thomas, David A. Chalton, and Jeremy H. Lakey. "Refolding of Escherichia coli outer membrane protein F in detergent creates LPS-free trimers and asymmetric dimers." Biochemical Journal 392, no. 2 (November 22, 2005): 375–81. http://dx.doi.org/10.1042/bj20051257.

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The Escherichia coli OmpF (outer-membrane protein F; matrix porin) is a homotrimeric β-barrel and a member of the bacterial porin superfamily. It is the best characterized porin protein, but has resisted attempts to refold it efficiently in vitro. In the present paper, we report the discovery of detergent-based folding conditions, including dodecylglucoside, which can create pure samples of trimeric OmpF. Whereas outer membrane LPS (lipopolysaccharide) is clearly required for in vivo folding, the artificially refolded and LPS-free trimer has properties identical with those of the outer-membrane-derived form. Thus LPS is not required either for in vitro folding or for structural integrity. Dimeric forms of OmpF have been observed in vivo and are proposed to be folding intermediates. In vitro, dimers occur transiently in refolding of trimeric OmpF and, in the presence of dodecylmaltoside, pure dimer can be prepared. This form has less β-structure by CD and shows lower thermal stability than the trimer. Study of these proteins at the single-molecule level is possible because each OmpF subunit forms a distinct ion channel. Whereas each trimer contains three channels of equal conductance, each dimer always contains two distinct channel sizes. This provides clear evidence that the two otherwise identical monomers adopt different structures in the dimer and indicates that the asymmetric interaction, characteristic of C3 symmetry, is formed at the dimer stage. This asymmetric dimer may be generally relevant to the folding of oligomeric proteins with odd numbers of subunits such as aspartate transcarbamoylase.
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42

Vogt, Marian S., Simon L. Völpel, Sonja-Verena Albers, Lars-Oliver Essen, and Ankan Banerjee. "Crystal structure of an Lrs14-like archaeal biofilm regulator fromSulfolobus acidocaldarius." Acta Crystallographica Section D Structural Biology 74, no. 11 (October 29, 2018): 1105–14. http://dx.doi.org/10.1107/s2059798318014146.

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The small winged helix–turn–helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeoteSulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices. Conserved anchor interactions between helices H0 and H4 of AbfR2 further contribute to dimer stabilization. The combined structural and bioinformatic analysis reveals cluster-specific structural differences between different members of the Lrs14 protein family.
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43

Dong, A., L. Zhou, X. Zhang, S. Stickel, R. J. Roberts, and X. Cheng. "Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions." Biological Chemistry 385, no. 5 (May 14, 2004): 373–79. http://dx.doi.org/10.1515/bc.2004.041.

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Abstract We have determined the structure of a mutant (Q237W) of HhaI DNA methyltransferase, complexed with the methyl-donor product AdoHcy. The Q237W mutant proteins were crystallized in the monoclinic space group C2 with two molecules in the crystallographic asymmetric unit. Protein-protein interface calculations in the crystal lattices suggest that the dimer interface has the specific characteristics for homodimer protein-protein interactions, while the two active sites are spatially independent on the outer surface of the dimer. The solution behavior suggests the formation of HhaI dimers as well. The same HhaI dimer interface is also observed in the previously characterized binary (M.HhaIAdoMet) and ternary (M.HhaIDNAAdoHcy) complex structures, crystallized in different space groups. The dimer is characterized either by a noncrystallographic two-fold symmetry or a crystallographic symmetry. The dimer interface involves three segments: the aminoterminal residues 28, the carboxyterminal residues 313327, and the linker (amino acids 179184) between the two functional domains the catalytic methylation domain and the DNA target recognition domain. Both the amino- and carboxy-terminal segments are part of the methylation domain. We also examined proteinprotein interactions of other structurally characterized DNA MTases, which are often found as a 2-fold related dimer with the largest dimer interface area for the group-β MTases. A possible evolutionary link between the Type I and Type II restriction-modification systems is discussed.
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44

Zhang, Ya-Jie, Yan Sun, Shu-Mei Gao, Xiao-Qing Jiang, and Yu-Heng Deng. "3,3,3′,3′-Tetramethyl-6,6′-bis[(pyridin-4-yl)methoxy]-1,1′-spirobiindane monohydrate." Acta Crystallographica Section E Structure Reports Online 68, no. 6 (May 16, 2012): o1763—o1764. http://dx.doi.org/10.1107/s1600536812021289.

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The asymmetric unit in the title compound, C33H34N2O2·H2O, consists of a V-shaped molecule and a water molecule to which it is hydrogen bonded. The angle between the mean planes of the two spiro-connected indane groups is 77.06 (5)°. The two five-membered rings of the indane groups have envelope conformations with the methylene atoms adjacent to the spiro C atom forming the flaps. They have deviations from the mean plane of the other four atoms in the rings of 0.374 (4) and 0.362 (4) Å. In the crystal, molecules are linked to form inversion dimers via O—H...N hydrogen bonds involving the pyridine N atoms and the solvent water molecule. The dimers are linked into a chain along the b axis by π–π stacking interactions between a pyridine ring and its centrosymmetrically related ring in an adjacent dimer. The centroid–centroid distance between the planes is 3.7756 (17) Å, the perpendicular distance is 3.4478 (11) Å and the offset is 1.539 Å.
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45

Cheng, Jen-Hao, Chien-Chih Huang, Yen-Hua Huang, and Cheng-Yang Huang. "Structural Basis for pH-Dependent Oligomerization of Dihydropyrimidinase from Pseudomonas aeruginosa PAO1." Bioinorganic Chemistry and Applications 2018 (January 30, 2018): 1–8. http://dx.doi.org/10.1155/2018/9564391.

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Dihydropyrimidinase, a dimetalloenzyme containing a carboxylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase, dihydroorotase, hydantoinase, and imidase. Unlike all known dihydropyrimidinases, which are tetrameric, pseudomonal dihydropyrimidinase forms a dimer at neutral pH. In this paper, we report the crystal structure of P. aeruginosa dihydropyrimidinase at pH 5.9 (PDB entry 5YKD). The crystals of P. aeruginosa dihydropyrimidinase belonged to space group C2221 with cell dimensions of a = 108.9, b = 155.7, and c = 235.6 Å. The structure of P. aeruginosa dihydropyrimidinase was solved at 2.17 Å resolution. An asymmetric unit of the crystal contained four crystallographically independent P. aeruginosa dihydropyrimidinase monomers. Gel filtration chromatographic analysis of purified P. aeruginosa dihydropyrimidinase revealed a mixture of dimers and tetramers at pH 5.9. Thus, P. aeruginosa dihydropyrimidinase can form a stable tetramer both in the crystalline state and in the solution. Based on sequence analysis and structural comparison of the dimer-dimer interface between P. aeruginosa dihydropyrimidinase and Thermus sp. dihydropyrimidinase, different oligomerization mechanisms are proposed.
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46

Mague, Joel T., Shaaban K. Mohamed, Mehmet Akkurt, Alaa A. Hassan, and Mustafa R. Albayati. "Crystal structure of 2-[(E)-2-(2-chlorobenzylidene)hydrazin-1-yl]-4-phenyl-1,3-thiazole." Acta Crystallographica Section E Structure Reports Online 70, no. 9 (August 1, 2014): o907—o908. http://dx.doi.org/10.1107/s1600536814016298.

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The asymmetric unit of the title compound, C16H12ClN3S, contains two independent molecules whose conformations differ primarily in the orientations of the phenyl and chlorobenzene rings with respect to the thiazole ring. In the first molecule, the dihedral angles are 3.0 (1) and 9.2 (1)°, respectively, for the phenyl ring and the chlorobenzene ring, while in the second molecule, the corresponding angles are 18.6 (1) and 23.4 (1)°. In the crystal, the two independent molecules are associatedviacomplementary N—H...N hydrogen bonds into a dimer. These dimers are associated through weak C—H...Cl and C—H...S interactions into supramolecular chains propagating along thea-axis direction.
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47

El-Hiti, Gamal A., Keith Smith, Amany S. Hegazy, Saud A. Alanazi, and Benson M. Kariuki. "Crystal structure of 2,2-dimethyl-N-(5-methylpyridin-2-yl)propanamide." Acta Crystallographica Section E Crystallographic Communications 71, no. 6 (May 23, 2015): o419—o420. http://dx.doi.org/10.1107/s2056989015009378.

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There are two molecules in the asymmetric unit of the title compound, C11H16N2O. The pyridine rings and amide groups overlap almost perfectly (r.m.s. overlay fit = 0.053 Å), but the tertiary butyl groups have different orientations: in one molecule, one of the methyl C atoms issynto the amide O atom [O—C—C—C = −0.8 (3)°] and in the other the equivalent torsion angle is 31.0 (2)°. In the crystal, the two independent molecules are linked by a pair of N—H...N hydrogen bonds in the form of anR22(8) loop to form a dimer. A C—H...O interaction connects the dimers into [100] chains.
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48

Shi, Hao. "(1R,4S,8R,12S,13S,14R,16S,17R,19R)-14-Hydroxy-7,7,17-trimethyl-2,9,18-trioxo-3,10-dioxapentacyclo[14.2.1.01,13.04,12.08,12]nonadec-19-yl acetate." Acta Crystallographica Section E Structure Reports Online 63, no. 11 (October 31, 2007): o4495. http://dx.doi.org/10.1107/s1600536807053317.

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The title compound, C22H28O8, was prepared from the natural diterpenoid macrocalyxin J by two steps. It is built up from five fused rings: three six-membered rings and two five-membered rings. Two molecules are present in the asymmetric unit; both independent molecules have the same absolute configuration, and the absolute configuration was deduced from the chirality of macrocalyxin A, which was isolated from the same plant (i.e. Rabdosia macrocalyx) as macrocalyxin J. The two molecules are linked by O—H...O hydrogen bonds, building a pseudo-dimer. Further O—H...O hydrogen bonds link these dimers to form a chain parallel to the a axis.
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49

Kobayashi, Fumiya, Atsushi Koga, Ryo Ohtani, Shinya Hayami, and Masaaki Nakamura. "Crystal structure of [2-({2-[(2-azanidylbenzylidene)amino]benzylidene}amino)-4-chlorophenolato]nickel(II)." Acta Crystallographica Section E Crystallographic Communications 73, no. 4 (March 31, 2017): 637–39. http://dx.doi.org/10.1107/s2056989017004613.

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The title complex, [Ni(C20H14ClN3O)], with an asymmetrically chloride-appended Schiff base ligand has been synthesized and structurally characterized at 100 K. In the compound, the central nickel(II) ion has a square-planar coordination geometry with N3O donors of the π-conjugated tetradentate Schiff base ligand. In the crystal, the complexes are connected into an inversion dimerviaan Ni...Ni interaction [3.1753 (5) Å] and a pair of π–π interactions [centroid–centroid distance = 3.8416 (16) Å]. The dimers are linkedviaa C—H...Cl hydrogen bond, forming a chain along thec-axis direction. The dimer chains interact with each other through π–π interactions [centroid–centroid distance = 3.8736 (16) Å], forming a layer expanding parallel to theacplane.
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50

Raja, R., J. Govindaraj, M. Suresh, R. Raghunathan, and A. SubbiahPandi. "Crystal structure of ethyl 1′,5-dimethyl-2′′,3-dioxo-3H-dispiro[benzo[b]thiophene-2,3′-pyrrolidine-2′,3′′-indoline]-4′-carboxylate." Acta Crystallographica Section E Crystallographic Communications 71, no. 3 (February 7, 2015): o152—o153. http://dx.doi.org/10.1107/s2056989015001528.

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The title compound, C23H22N2O4S, crystallized with two independent molecules (AandB) in the asymmetric unit. They have very similar conformations with the pyrrolidine ring having a twisted conformation, on the Cspiro—Cspirobond, in both molecules. In moleculeA, the mean planes of the benzothiophene and indoline ring systems are inclined to the mean plane of the pyrrolidine ring by 87.59 (10) and 84.51 (11)°, respectively, and to one another by 72.69 (7)°. The corresponding angles in moleculeBare 87.15 (10), 84.58 (10) and 72.07 (7)°, respectively. In the crystal, theAandBmolecules are linked to one another by two N—H...O hydrogen bonds, forming a dimer. These dimers are linkedviaC—H...O hydrogen bonds, forming a three-dimensional structure.
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