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Journal articles on the topic 'Helix 38'

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Published: 4 June 2021
Last updated: 1 February 2022

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1

Moroz, P. E. "Novel stellarator configuration with double helix centre post." Nuclear Fusion 38, no. 6 (June 1998): 795–806. http://dx.doi.org/10.1088/0029-5515/38/6/302.

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2

Sonief, Achmad As'ad, Arda Nur Fauzan, Fachry Azlan, and Muhammad Aziz Bashori. "Chatter Vibration Comparison Between Normal Helix Angle and Variable Helix Angle in End Milling Process Based on Spectrum Analysis." Jurnal Rekayasa Mesin 11, no. 3 (December 15, 2020): 531–36. http://dx.doi.org/10.21776/ub.jrm.2020.011.03.25.

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Chatter vibration in machining processes is often found in cutting processes which will decrease the machining efficiency and the surface quality of the products. Chatter is a relative vibration of the cutting tool and workpiece caused by the fluctuation of cutting force that is concerned to be a self-excited vibration. The variable Helix Angle Cutting tool which has pitch angle variation will also inflict different tooth passing frequencies on the flute that stand contiguous and trim the resonance frequency. This research aims to compare chatter vibrations that occurred between Normal Helix Angle and Variable Helix Angle cutting tool based on spectrum analysis on cutting parameter variety (depth of cut; rotation speed; feed rate milling). The outcome is spectrum analysis can detect the chatter phenomenon, measure the natural frequency (38-42 Hz), and also compare chatter vibrations between two tools appropriately.
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3

Rastelli, E., S. Sedazzari, and A. Tassi. "The helix-fan transition in the square planar model." Journal of Physics: Condensed Matter 5, no. 38 (September 20, 1993): 7121–30. http://dx.doi.org/10.1088/0953-8984/5/38/008.

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4

Rakauskaite, Rasa, and Jonathan D. Dinman. "An Arc of Unpaired “Hinge Bases” Facilitates Information Exchange among Functional Centers of the Ribosome." Molecular and Cellular Biology 26, no. 23 (September 25, 2006): 8992–9002. http://dx.doi.org/10.1128/mcb.01311-06.

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ABSTRACT Information must be shared and functions coordinated among the spatially distinct functional centers of the ribosome. To address these issues, a yeast-based genetic system enabling generation of stable strains expressing only mutant forms of rRNA was devised. The B1a bridge (helix 38) has been implicated in the subtle modulation of numerous ribosomal functions. Base-specific mutations were introduced into helix 38 at sites affecting the B1a bridge and where it contacts the aminoacyl-tRNA (aa-tRNA) D-loop. Both sets of mutants promoted increased affinities for aa-tRNA but had different effects in their responses to two A-site-specific drugs and on suppression nonsense codons. Structural analyses revealed an arc of nucleotides in 25S rRNA that link the B1a bridge, the peptidyltransferase center, the GTPase-associated center, and the sarcin/ricin loop. We propose that a series of regularly spaced “hinge bases” provide fulcrums around which rigid helices can reorient themselves depending on the occupancy status of the A-site.
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5

Maeda, Yasushi, Takuya Matsumoto, Hiroyuki Tanaka, and Tomoji Kawai. "Imaging of the DNA (deoxyribonucleic acid) Double Helix Structure by Noncontact Atomic Force Microscopy." Japanese Journal of Applied Physics 38, Part 2, No. 11A (November 1, 1999): L1211—L1212. http://dx.doi.org/10.1143/jjap.38.l1211.

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6

Perera, Rushika, Chanakha Navaratnarajah, and Richard J. Kuhn. "A Heterologous Coiled Coil Can Substitute for Helix I of the Sindbis Virus Capsid Protein." Journal of Virology 77, no. 15 (August 1, 2003): 8345–53. http://dx.doi.org/10.1128/jvi.77.15.8345-8353.2003.

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ABSTRACT Alphavirus core assembly proceeds along an assembly pathway involving a dimeric assembly intermediate. Several regions of the alphavirus capsid protein have been implicated in promoting and stabilizing this dimerization, including a putative heptad repeat sequence named helix I. This sequence, which spans residues 38 to 55 of the Sindbis virus capsid protein, was implicated in stabilizing dimeric contacts initiated through the C-terminal two-thirds of the capsid protein and nucleic acid. The studies presented here demonstrate that helix I can be functionally replaced by the corresponding sequence of a related alphavirus, western equine encephalitis virus, and also by an unrelated sequence from the yeast transcription activator, GCN4, that was previously shown to form a dimeric coiled coil. Replacing helix I with the entire leucine zipper domain of GCN4 (residues 250 to 281) produced a virus with the wild-type phenotype as determined by plaque assay and one-step growth analysis. However, replacement of helix I with a GCN4 sequence that favored trimer formation produced a virus that exhibited ∼40-fold reduction in virus replication compared to the wild-type Sindbis virus. Changing residues within the Sindbis virus helix I sequence to favor trimer formation also produced a virus with reduced replication. Peptides corresponding to helix I inhibited core-like particle assembly in vitro. On the basis of these studies, it is proposed that helix I favors capsid protein-capsid protein interactions through the formation of dimeric coiled-coil interactions and may stabilize assembly intermediates in the alphavirus nucleocapsid core assembly pathway.
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7

Kanno, Takashi, Hiroyuki Tanaka, Tomohiko Nakamura, Hitoshi Tabata, and Tomoji Kawai. "Real Space Observation of Double-Helix DNA Structure Using a Low Temperature Scanning Tunneling Microscopy." Japanese Journal of Applied Physics 38, Part 2, No. 6A/B (June 15, 1999): L606—L607. http://dx.doi.org/10.1143/jjap.38.l606.

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8

Andre Hardinsi, Festo, Oyong Novareza, and Achmad As'ad Sonief. "OPTIMIZATION OF VARIABEL HELIX ANGLE PARAMETERS IN CNC MILLING OF CHATTER AND SURFACE ROUGHNES USING TAGUCHI METHOD." Journal of Engineering and Management in Industrial System 9, no. 1 (May 30, 2021): 35–44. http://dx.doi.org/10.21776/ub.jemis.2021.009.01.4.

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In the manufacturing industries, the main problem in process of operating CNC milling machine was chatter effect (self-excited vibration) which increases the quality of the surface roughness. In this study is to determine optimal value of parameters for chatter and surface roughness. The chatter measured using accelerometer MPU-6050 with Arduino by software LabVIEW-2019 based on peaks-FFT value and the surface roughness measured by SJ-301 tester. The research parameters like variable helix angle, spindle speed, feed rate, and depth of cut using stainless steel 304 by Taguchi method. The optimum parameters value obtained are variable helix 35/38 degrees, spindle speed 3000 RPM, feed rate 150 mm/min and depth of cut 0.4 mm. Based on ANOVA value, the variable helix angle and depth of cut are found to be significant for chatter and surface roughness. The depth of cut was high contribution by ANOVA chatter by 93.84% and surface roughness by 91.93%.
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9

Perera, Rushika, Katherine E. Owen, Timothy L. Tellinghuisen, Alexander E. Gorbalenya, and Richard J. Kuhn. "Alphavirus Nucleocapsid Protein Contains a Putative Coiled Coil α-Helix Important for Core Assembly." Journal of Virology 75, no. 1 (January 1, 2001): 1–10. http://dx.doi.org/10.1128/jvi.75.1.1-10.2001.

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ABSTRACT The alphavirus nucleocapsid core is formed through the energetic contributions of multiple noncovalent interactions mediated by the capsid protein. This protein consists of a poorly conserved N-terminal region of unknown function and a C-terminal conserved autoprotease domain with a major role in virion formation. In this study, an 18-amino-acid conserved region, predicted to fold into an α-helix (helix I) and embedded in a low-complexity sequence enriched with basic and Pro residues, has been identified in the N-terminal region of the alphavirus capsid proteins. In Sindbis virus, helix I spans residues 38 to 55 and contains three conserved leucine residues, L38, L45, and L52, conforming to the heptad amino acid organization evident in leucine zipper proteins. Helix I consists of an N-terminally truncated heptad and two complete heptad repeats with β-branched residues and conserved leucine residues occupying the a andd positions of the helix, respectively. Complete or partial deletion of helix I, or single-site substitutions at the conserved leucine residues (L45 and L52), caused a significant decrease in virus replication. The mutant viruses were more sensitive to elevated temperature than wild-type virus. These mutant viruses also failed to accumulate cores in the cytoplasm of infected cells, although they did not have defects in protein translation or processing. Analysis of these mutants using an in vitro assembly system indicated that the majority were defective in core particle assembly. Furthermore, mutant proteins showed a trans-dominant negative phenotype in in vitro assembly reactions involving mutant and wild-type proteins. We propose that helix I plays a central role in the assembly of nucleocapsid cores through coiled coil interactions. These interactions may stabilize subviral intermediates formed through the interactions of the C-terminal domain of the capsid protein and the genomic RNA and contribute to the stability of the virion.
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10

Tsueshita, Takaya, Salil Gandhi, Hayat Önyüksel, and Israel Rubinstein. "Phospholipids modulate the biophysical properties and vasoactivity of PACAP-(1—38)." Journal of Applied Physiology 93, no. 4 (October 1, 2002): 1377–83. http://dx.doi.org/10.1152/japplphysiol.00277.2002.

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The purpose of this study was to elucidate the interactions between pituitary adenylate cyclase-activating peptide (PACAP)-(1—38) and phospholipids in vitro and to determine whether these phenomena modulate, in part, the vasorelaxant effects of the peptide in the intact peripheral microcirculation. We found that the critical micellar concentration of PACAP-(1—38) was 0.4–0.9 μM. PACAP-(1—38) significantly increased the surface tension of a dipalmitoylphosphatidylcholine monolayer and underwent conformational transition from predominantly random coil in saline to α-helix in the presence of distearoyl-phosphatidylethanolamine-polyethylene glycol (molecular mass of 2,000 Da) sterically stabilized phospholipid micelles (SSM) ( P < 0.05). Using intravital microscopy, we found that aqueous PACAP-(1—38) evoked significant concentration-dependent vasodilation in the intact hamster cheek pouch that was significantly potentiated when PACAP-(1—38) was associated with SSM ( P < 0.05). The vasorelaxant effects of aqueous PACAP-(1—38) were mediated predominantly by PACAP type 1 (PAC1) receptors, whereas those of PACAP-(1—38) in SSM predominantly by PACAP/vasoactive intestinal peptide type 1 and 2 (VPAC1/VPAC2) receptors. Collectively, these data indicate that PACAP-(1—38) self-associates and interacts avidly with phospholipids in vitro and that these phenomena amplify peptide vasoactivity in the intact peripheral microcirculation.
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11

Pan, Xingjie, Michael C. Thompson, Yang Zhang, Lin Liu, James S. Fraser, Mark J. S. Kelly, and Tanja Kortemme. "Expanding the space of protein geometries by computational design of de novo fold families." Science 369, no. 6507 (August 27, 2020): 1132–36. http://dx.doi.org/10.1126/science.abc0881.

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Naturally occurring proteins vary the precise geometries of structural elements to create distinct shapes optimal for function. We present a computational design method, loop-helix-loop unit combinatorial sampling (LUCS), that mimics nature’s ability to create families of proteins with the same overall fold but precisely tunable geometries. Through near-exhaustive sampling of loop-helix-loop elements, LUCS generates highly diverse geometries encompassing those found in nature but also surpassing known structure space. Biophysical characterization showed that 17 (38%) of 45 tested LUCS designs encompassing two different structural topologies were well folded, including 16 with designed non-native geometries. Four experimentally solved structures closely matched the designs. LUCS greatly expands the designable structure space and offers a new paradigm for designing proteins with tunable geometries that may be customizable for novel functions.
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12

Fekete, Gyula László, and Júlia Edit Fekete. "Chondrodermatitis Nodularis Helicis." Acta Medica Marisiensis 59, no. 1 (February 1, 2013): 55–56. http://dx.doi.org/10.2478/amma-2013-0013.

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Abstract Chondrodermatitis nodularis helicis is a rare and well defined clinical condition, characterized by the appearance of painful nodule or nodules located on the helix. Affects mainly white men, aged 50 and more. The pathogenesis of the disease is unclear. The used treatments gives excellent results, but the disease tends to relapse. We present a clinical case of a young man of 38 years of age with a painful nodule located on the left ear.
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13

Kwon, Yo Han, Sang-Wook Woo, Hye-Ran Jung, Hyung Kyun Yu, Kitae Kim, Byung Hun Oh, Soonho Ahn, et al. "Batteries: Cable-Type Flexible Lithium Ion Battery Based on Hollow Multi-Helix Electrodes (Adv. Mater. 38/2012)." Advanced Materials 24, no. 38 (September 25, 2012): 5145. http://dx.doi.org/10.1002/adma.201290232.

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14

Oliveira, Marli Lourdes de, Leila Maria Beltramini, Salvatore Giovanni de Simone, Maria Helena Nasser Brumano, Rosemeire Aparecida Silva-Lucca, Marcelo Kiyoshi Kian Nakaema, Christiano Vieira Pires, and Maria Goreti de Almeida Oliveira. "Purification and partial characterization of a lectin from Caesalpinia tinctoria Domb, ex Dc fruits." Brazilian Journal of Plant Physiology 15, no. 2 (August 2003): 119–22. http://dx.doi.org/10.1590/s1677-04202003000200008.

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A lectin was isolated from the pod saline extract of Caesalpinia tinctoria by dialoconcentration on Centripep-10 and affinity chromatography on chitin column. The purified lectin was partially characterized with respect to its biochemical and structural properties. It contains 8.3 % of carbohydrate and exhibited an agglutinating activity against human erythrocytes (ABO groups). Its amino acid composition was characterized by a great number of acidic and hydrophobic residues and the estimated molecular mass was 12.5 kDa. The presence of only one N-terminal amino acid sequence (D¹-V-P-A-Y-V-Y-V-H-F10-G-F-G-E-E-H-R -D-V-F20-D), showed the homogeneity of the purified lectin. The far-ultraviolet circular dichroism (CD) spectrum of lectin indicated that it contains 10 % a-helix, 38 % b-sheet, 28 % unordered form and 6 % of P II (poly-L-proline II helix conformation).
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15

Rampioni, Giordano, Fabio Polticelli, Iris Bertani, Karima Righetti, Vittorio Venturi, Elisabetta Zennaro, and Livia Leoni. "The Pseudomonas Quorum-Sensing Regulator RsaL Belongs to the Tetrahelical Superclass of H-T-H Proteins." Journal of Bacteriology 189, no. 5 (December 15, 2006): 1922–30. http://dx.doi.org/10.1128/jb.01552-06.

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ABSTRACT In the opportunistic human pathogen Pseudomonas aeruginosa, quorum sensing (QS) is crucial for virulence. The RsaL protein directly represses the transcription of lasI, the synthase gene of the main QS signal molecule. On the basis of sequence homology, RsaL cannot be predicted to belong to any class of characterized DNA-binding proteins. In this study, an in silico model of the RsaL structure was inferred showing that RsaL belongs to the tetrahelical superclass of helix-turn-helix proteins. The overall structure of RsaL is very similar to the N-terminal domain of the lambda cI repressor and to the POU-specific domain of the mammalian transcription factor Oct-1 (Oct-1 POUs). Moreover, residues of Oct-1 POUs important for structural stability and/or DNA binding are conserved in the same positions in RsaL and in its homologs found in GenBank. These residues were independently replaced with Ala, and the activities of the mutated variants of RsaL were compared to that of the wild-type counterpart in vivo by complementation assays and in vitro by electrophoretic mobility shift assays. The results validated the RsaL in silico model and showed that residues Arg 20, Gln 38, Ser 42, Arg 43, and Glu 45 are important for RsaL function. Our data indicate that RsaL could be the founding member of a new protein family within the tetrahelical superclass of helix-turn-helix proteins. Finally, the minimum DNA sequence required for RsaL binding on the lasI promoter was determined, and our data support the hypothesis that RsaL binds DNA as a dimer.
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16

Rozek, Annett, James T. Sparrow, Karl H. Weisgraber, and Robert J. Cushley. "Sequence-specific 1H NMR resonance assignments and secondary structure of human apolipoprotein C-I in the presence of sodium dodecyl sulfate." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 267–75. http://dx.doi.org/10.1139/o98-053.

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Apolipoprotein (apo) C-I is a 57-residue exchangeable plasma protein distributed mainly in high and very low density lipoprotein. In this report we present the nuclear magnetic resonance spectra of native apoC-I and synthetic apoC-I, containing selected 15N-labelled amino acids, in the presence of sodium dodecyl sulfate. The proton resonances of apoC-I are assigned and the secondary structure is estimated from the difference of measured alpha-proton chemical shifts to random coil values and the observed NOE interactions. According to these data apoC-I forms two helices, Val-4-Lys-30 and Leu-34-Lys-52, linked by an unstructured region Gln-31-Glu-33. The N-terminal segments of each helix, Val-4-Gly-15 and Leu-34-Met-38, appear to be more flexible than the helical core regions Asn-16-Lys-30 and Arg-39-Lys-52.Key words: 15N-filtered NOESY, chemical shift index, amphipathic helix, lecithin:cholesterol acyltransferase.
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17

Kovalev, Mikhail, and He Yanhai. "China's experience in the digital organization of the triple helix of «state – science – business»." Science and Innovations 6 (June 2021): 38–45. http://dx.doi.org/10.29235/1818-9857-2021-6-38-45.

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Проанализирован и обобщен опыт Китая в организации взаимодействия государства, науки и бизнеса с помощью средств цифровизации. Показано, как цифровые технологии повлияли на эффективность национальной инновационной системы (НИС) и общую результативность инновационной деятельности.
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18

Kochan, Z., J. Karbowska, G. Bukato, M. M. Zydowo, E. Bertoli, F. Tanfani, and J. Swierczyński. "A comparison of the secondary structure of human brain mitochondrial and cytosolic ‘malic’ enzyme investigated by Fourier-transform infrared spectroscopy." Biochemical Journal 309, no. 2 (July 15, 1995): 607–11. http://dx.doi.org/10.1042/bj3090607.

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The secondary structure of human brain cytosolic and mitochondrial ‘malic’ enzymes purified to homogeneity has been investigated by Fourier-transform IR spectroscopy. The absorbance IR spectra of these two isoenzymes were slightly different, but calculated secondary-structure compositions were essentially similar (38% alpha-helix, 38-39% beta-sheet, 14% beta-turn and 9-10% random structure). These proportions were not affected by succinate, a positive effector of mitochondrial ‘malic’ enzyme activity. IR spectra indicate that the tertiary structures of human brain cytosolic and mitochondrial ‘malic’ enzymes are slightly different, and addition of succinate does not cause conformational changes to the tertiary structure of the mitochondrial enzyme. Thermal-denaturation patterns of the cytosolic and mitochondrial enzymes, obtained from spectra recorded at different temperatures in the absence or presence of Mg2+, suggest that the tertiary structure of both isoenzymes is stabilized by bivalent cations and that the cytosolic enzyme possesses a more compact tertiary structure.
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19

Liu, Gang, Ming Chen, Lu Lu Jing, Z. G. Hu, X. F. Zhu, Z. W. Li, and H. Xu. "The Development of Special Drills for High-Efficient Drilling Austenitic Stainless Steel Part I: Drill Comparison and Experiment Research." Key Engineering Materials 315-316 (July 2006): 195–99. http://dx.doi.org/10.4028/www.scientific.net/kem.315-316.195.

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Austenitic stainless steel is a kind of difficult-to-cut material widely utilized in various industry fields. But cutting tools is the uppermost obstacle in the application of high efficient and precise machining of austenitic stainless steel. Drill is the one of the most complicated universal cutting tools, whose geometry structure influences greatly on drilling performance. So the development of special drills is imperative for high-efficient drilling. This paper presented the optimal geometrical characteristics of the special drills, with138° point angle and 38° helix angle, for high-efficient drilling austenitic stainless steel. The drilling performance has been evaluated completely and comprehensively through the experiments including measuring cutting deformation coefficient, thrust force, torque, cutting temperature near the cutting point, cutting tool life, drill wear mechanism and so on. The special drill indicated appreciated cutting performance during drilling austenitic stainless steel with high efficiency. Compared to the commercial available standard drill with 118° point angle and 32° helix angle, the cutting tool life of the special drill was 1.6 times of the standard drill and the special drill yielded good performance of chip evacuation, good wear resistance and great drilling quality.
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20

Cambot, Marie, Sandra Aresta, Brigitte Kahn-Perlès, Jean de Gunzburg, and Paul-Henri Roméo. "Human Immune Associated Nucleotide 1: a member of a new guanosine triphosphatase family expressed in resting T and B cells." Blood 99, no. 9 (May 1, 2002): 3293–301. http://dx.doi.org/10.1182/blood.v99.9.3293.

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Abstract TAL-1 is a basic helix-loop-helix oncoprotein that is expressed in up to 30% of T-cell acute lymphoblastic leukemias but not in the T lineage. We have cloned a complementary DNA, called Human Immune Associated Nucleotide 1 (hIAN1), whose messenger RNA (mRNA) level expression is inversely correlated to the TAL-1 mRNA level in human leukemic T-cell lines. The hIAN1 encodes a 38-kd protein that belongs to a novel family of proteins conserved from plants to humans and characterized by motifs related to, but highly divergent from, the consensus motifs found in guanosine triphosphate (GTP)–binding proteins. Despite these divergent amino acids at positions involved in GTP/guanosine diphosphate (GDP) binding and guanosine triphosphatase (GTPase) activities, we found that hIAN1 specifically binds GDP (Kd = 0.47 μM) and GTP (Kd = 6 μM) and exhibits intrinsic GTPase activity. Among mature hematopoietic cells, hIAN1 is specifically expressed in resting T and B lymphocytes, and its expression level tremendously decreased at the protein but not the mRNA level during B- or T-lymphocyte activation, suggesting a specific role for this new type of GTPase during the immune response.
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21

Kimura, Shunsaku, Yoshiko Miura, Tomoyuki Morita, Shiro Kobayashi, and Yukio Imanishi. "Preparation and functions of self-assembled monolayers of helix peptides." Journal of Polymer Science Part A: Polymer Chemistry 38, S1 (2000): 4826–31. http://dx.doi.org/10.1002/1099-0518(200012)38:1+<4826::aid-pola200>3.0.co;2-m.

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22

Itahana, Koji, Ying Zou, Yoko Itahana, Jose-Luis Martinez, Christian Beausejour, Jacqueline J. L. Jacobs, Maarten van Lohuizen, Vimla Band, Judith Campisi, and Goberdhan P. Dimri. "Control of the Replicative Life Span of Human Fibroblasts by p16 and the Polycomb Protein Bmi-1." Molecular and Cellular Biology 23, no. 1 (January 1, 2003): 389–401. http://dx.doi.org/10.1128/mcb.23.1.389-401.2003.

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ABSTRACT The polycomb protein Bmi-1 represses the INK4a locus, which encodes the tumor suppressors p16 and p14ARF. Here we report that Bmi-1 is downregulated when WI-38 human fibroblasts undergo replicative senescence, but not quiescence, and extends replicative life span when overexpressed. Life span extension by Bmi-1 required the pRb, but not p53, tumor suppressor protein. Deletion analysis showed that the RING finger and helix-turn-helix domains of Bmi-1 were required for life span extension and suppression of p16. Furthermore, a RING finger deletion mutant exhibited dominant negative activity, inducing p16 and premature senescence. Interestingly, presenescent cultures of some, but not all, human fibroblasts contained growth-arrested cells expressing high levels of p16 and apparently arrested by a p53- and telomere-independent mechanism. Bmi-1 selectively extended the life span of these cultures. Low O2 concentrations had no effect on p16 levels or life span extension by Bmi-1 but reduced expression of the p53 target, p21. We propose that some human fibroblast strains are more sensitive to stress-induced senescence and have both p16-dependent and p53/telomere-dependent pathways of senescence. Our data suggest that Bmi-1 extends the replicative life span of human fibroblasts by suppressing the p16-dependent senescence pathway.
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23

Niño-Gómez, Doris C., Claudia M. Rivera-Hoyos, Edwin D. Morales-Álvarez, Edgar A. Reyes-Montaño, Nury E. Vargas-Alejo, Ingrid N. Ramírez-Casallas, Kübra Erkan Türkmen, et al. "“In Silico” Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger." Enzyme Research 2017 (November 20, 2017): 1–23. http://dx.doi.org/10.1155/2017/9746191.

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Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.
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24

Gautier, Antoine, John P Kirkpatrick, and Daniel Nietlispach. "Innentitelbild: Solution-State NMR Spectroscopy of a Seven-Helix Transmembrane Protein Receptor: Backbone Assignment, Secondary Structure, and Dynamics (Angew. Chem. 38/2008)." Angewandte Chemie 120, no. 38 (September 8, 2008): 7252. http://dx.doi.org/10.1002/ange.200890240.

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25

Song, Kai, Yu Li, Huawei He, Lina Liu, Ping Zhao, Qingyou Xia, and Yejing Wang. "A Novel Adenosine Kinase from Bombyx mori: Enzymatic Activity, Structure, and Biological Function." International Journal of Molecular Sciences 20, no. 15 (July 31, 2019): 3732. http://dx.doi.org/10.3390/ijms20153732.

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Adenosine kinase (ADK) is the first enzyme in the adenosine remediation pathway that catalyzes adenosine phosphorylation into adenosine monophosphate, thus regulating adenosine homeostasis in cells. To obtain new insights into ADK from Bombyx mori (BmADK), we obtained recombinant BmADK, and analyzed its activity, structure, and function. Gel-filtration showed BmADK was a monomer with molecular weight of approximately 38 kDa. Circular dichroism spectra indicated BmADK had 36.8% α-helix and 29.9% β-strand structures, respectively. The structure of BmADK was stable in pH 5.0–11.0, and not affected under 30 °C. The melting temperature and the enthalpy and entropy changes in the thermal transition of BmADK were 46.51 ± 0.50 °C, 253.43 ± 0.20 KJ/mol, and 0.79 ± 0.01 KJ/(mol·K), respectively. Site-directed mutagenesis demonstrated G68, S201, E229, and D303 were key amino acids for BmADK structure and activity. In particular, S201A mutation significantly increased the α-helix content of BmADK and its activity. BmADK was located in the cytoplasm and highly expressed in the silk gland during the pre-pupal stage. RNA interference revealed the downregulation of BmADK decreased ATG-8, Caspase-9, Ec-R, E74A, and Br-C expression, indicating it was likely involved in 20E signaling, apoptosis, and autophagy to regulate silk gland degeneration and silkworm metamorphosis. Our study greatly expanded the knowledge on the activity, structure, and role of ADK.
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26

Sandmöller, A., H. Meents, and H. H. Arnold. "A novel E1A domain mediates skeletal-muscle-specific enhancer repression independently of pRB and p300 binding." Molecular and Cellular Biology 16, no. 10 (October 1996): 5846–56. http://dx.doi.org/10.1128/mcb.16.10.5846.

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The adenovirus E1A oncoprotein completely blocks muscle differentiation and specifically inhibits the transactivating function of myogenic basic helix-loop-helix (bHLH) transcription factors. This inhibition is dependent on the conserved region CR1 of E1A, which also constitutes part of the binding sites for the pocket proteins pRB, p107, and p130 and the transcriptional coactivators p300 and CBP. Here we report a detailed mutational analysis of E1A and the identification of a muscle inhibition motif within CR1. This motif encompasses amino acids 38 to 62 and inhibits Myf-5- or MyoD-mediated activation of myogenin and the muscle creatine kinase gene. Overexpression of this E1A region also inhibits the conversion of 10T1/2 fibroblasts to the myogenic lineage. The sequence motif EPDNEE (amino acids 55 to 60) within CR1 appears to be particularly important, because point mutations of this sequence diminish the E1A inhibitory activity. Interactions of E1A with pRB and with p300 do not seem to be necessary for the muscle-specific enhancer repression, because E1A mutants which lack these interactions still inhibit Myf-5- and MyoD-mediated transactivation. Moreover, overexpression of p300 fails to overcome muscle-specific inhibition by wild-type E1A and mutant E1A protein which lacks pRB binding. Since we have no evidence for direct E1A interaction with bHLH proteins, we propose that E1A may target a necessary cofactor of the muscle-specific bHLH transcription complex.
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27

Brooks, S. A., M. Lymboura, U. Schumacher, and A. J. Leathem. "Histochemistry to detect Helix pomatia lectin binding in breast cancer: methodology makes a difference." Journal of Histochemistry & Cytochemistry 44, no. 5 (May 1996): 519–24. http://dx.doi.org/10.1177/44.5.8627008.

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A number of studies have shown that altered cellular glycosylation, as detected by binding of Helix pomatia lectin to paraffin sections, is associated with metastatic disease and consequent poor patient prognosis in breast and other cancers. In a 24-year retrospective study, sections of 373 primary breast cancers were stained for binding of the lectin using two different histochemical techniques: a direct method (using peroxidase-conjugated lectin) and an indirect method (using native, unconjugated lectin). Similar percentages of cases were positive (79%) and negative (21%) for lectin binding with either technique, but there was enormous inconsistency when individual cases were examined. A total of 38/373 (10.2%) cases that were negative by the indirect method were positive by the direct method, and 37/373 (9.9%) cases that were negative by the direct method were positive by the indirect method. Life tables calculated for lectin staining vs nonstaining cases showed a very strong correlation between lectin binding and long-term survival (p < 0.0001) when staining was performed by the indirect method, but only very weak correlation with prognosis (p < 0.03, borderline significance) when the direct technique was employed. SDS-PAGE revealed that there were differences in breast cancer glycoproteins recognized by native lectin and peroxidase-conjugated lectin immobilized on Sepharose 4B affinity beads. Helix pomatia lectin binding appears to be an intriguing and potentially valuable marker of biological behavior in breast cancer. This study emphasizes the importance of selecting an appropriate immunohistochemical technique for its visualization.
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28

Guo, Shi Hui, Chun Lei Wang, Hong Yi Yang, Na Na Zhang, Xin Zhuang, and Dai Zong Cui. "Prediction of Antigenic Epitopes for Coat Protein of Potato virus Y." Advanced Materials Research 183-185 (January 2011): 1204–8. http://dx.doi.org/10.4028/www.scientific.net/amr.183-185.1204.

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Potato virus Y (PVY) is one of the most important viruses that infect Solanaceous crops. In the study, the antigenic epitopes were predicted using computer-assisted analysis, and many potential regions of antigenic epitopes were located. Many properties of coat protein, such as the antigenic index, α-helix, β-sheet, β-turn, coil structure, hydrophilicity, surface probability, and flexibility, were analyzed with several algorithms in some softwares. Based on the rules for location the antigenic epitopes in the regions including β-turns and coil structures with the high hydrophilicity and surface probability, the predicted epitopes were located in the region of amino acid position 8-22, 24-38, 45-55, 240-255, respectively. It is helpful to prepare the antiserum of PVY based on the prediction result of antigenic epitope.
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29

Herler, M., A. Bubert, M. Goetz, Y. Vega, J. A. Vazquez-Boland, and W. Goebel. "Positive Selection of Mutations Leading to Loss or Reduction of Transcriptional Activity of PrfA, the Central Regulator ofListeria monocytogenes Virulence." Journal of Bacteriology 183, no. 19 (October 1, 2001): 5562–70. http://dx.doi.org/10.1128/jb.183.19.5562-5570.2001.

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ABSTRACT Transcription factor PrfA controls the expression of virulence genes essential for Listeria monocytogenes pathogenesis. To gain insight into the structure-function relationship of PrfA, we devised a positive-selection system to isolate mutations reducing or abolishing transcriptional activity. The system is based on the observation that the listerial iap gene, encoding the p60 protein, is lethal if overexpressed in Bacillus subtilis. A plasmid in which the iap gene is placed under the control of the PrfA-dependent hlypromoter was constructed and introduced into B. subtilis. This strain was rapidly killed when expression ofiap was induced by introduction of a second plasmid carrying prfA. Two classes of B. subtilissurvivor mutants were identified: one carried mutations iniap, and the second carried mutations inprfA. Sequence analysis of the defectiveprfA genes identified mutations in three regions of the PrfA protein: region A, between amino acids 58 and 67 in the β-roll domain of PrfA; region B, between amino acids 169 and 193, which corresponds to the DNA-binding helix-turn-helix motif; and region C, comprising the 38 C-terminal amino acids of PrfA, which form a leucine zipper-like structure. PrfA proteins with mutations in regions B and C were unable to bind to the PrfA-binding site in the target DNA, while mutations in region A resulted in a protein still binding the target DNA but unable to form a stable complex with RNA polymerase and initiate transcription in vitro.
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30

Koschel, Matthias, Reiner Thomssen, and Volker Bruss. "Extensive Mutagenesis of the Hepatitis B Virus Core Gene and Mapping of Mutations That Allow Capsid Formation." Journal of Virology 73, no. 3 (March 1, 1999): 2153–60. http://dx.doi.org/10.1128/jvi.73.3.2153-2160.1999.

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ABSTRACT We generated a large number of mutations in the hepatitis B virus (HBV) core gene inserted into a bacterial expression vector. The new mutagenesis procedure generated deletions and insertions (as sequence repeats) of various lengths at random positions between M1 and E145 but not substitutions. The R-rich 30-amino-acid C-terminal domain was not analyzed. A total of 50,000 colonies were tested with a polyclonal human serum for the expression of hepatitis B core or e antigen. A total of 110 mutants randomly chosen from 1,500 positive colonies were genotyped. Deletions and insertions were clustered in four regions: D2 to E14, corresponding to the N-terminal loop in a model for the core protein fold (B. Bottcher, S. A. Wynne, and R. A. Crowther, Nature 386:88–91, 1997); V27 to P50 (second loop); L60 to V86 (upper half of the alpha helix forming the N-terminal part of the spike and the tip of the spike); and V124 to L140 (C-terminal part of the C-terminal helix and downstream loop). Deletions or insertions in the remaining parts of the molecule forming the compact center of the fold seemed to destabilize the protein. Of the 110 mutations, 38 allowed capsid formation in Escherichia coli. They mapped exclusively to nonhelical regions of the proposed fold. The mutations form a basis for subsequent analysis of further functions of the HBV core protein in the viral life cycle.
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31

Jurata, L. W., and G. N. Gill. "Functional analysis of the nuclear LIM domain interactor NLI." Molecular and Cellular Biology 17, no. 10 (October 1997): 5688–98. http://dx.doi.org/10.1128/mcb.17.10.5688.

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LIM homeodomain and LIM-only (LMO) transcription factors contain two tandemly arranged Zn2+-binding LIM domains capable of mediating protein-protein interactions. These factors have restricted patterns of expression, are found in invertebrates as well as vertebrates, and are required for cell type specification in a variety of developing tissues. A recently identified, widely expressed protein, NLI, binds with high affinity to the LIM domains of LIM homeodomain and LMO proteins in vitro and in vivo. In this study, a 38-amino-acid fragment of NLI was found to be sufficient for the association of NLI with nuclear LIM domains. In addition, NLI was shown to form high affinity homodimers through the amino-terminal 200 amino acids, but dimerization of NLI was not required for association with the LIM homeodomain protein Lmxl. Chemical cross-linking analysis revealed higher-order complexes containing multiple NLI molecules bound to Lmx1, indicating that dimerization of NLI does not interfere with LIM domain interactions. Additionally, NLI formed complexes with Lmx1 on the rat insulin I promoter and inhibited the LIM domain-dependent synergistic transcriptional activation by Lmx1 and the basic helix-loop-helix protein E47 from the rat insulin I minienhancer. These studies indicate that NLI contains at least two functionally independent domains and may serve as a negative regulator of synergistic transcriptional responses which require direct interaction via LIM domains. Thus, NLI may regulate the transcriptional activity of LIM homeodomain proteins by determining specific partner interactions.
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32

Peterson, A. J., M. Kyba, D. Bornemann, K. Morgan, H. W. Brock, and J. Simon. "A domain shared by the Polycomb group proteins Scm and ph mediates heterotypic and homotypic interactions." Molecular and Cellular Biology 17, no. 11 (November 1997): 6683–92. http://dx.doi.org/10.1128/mcb.17.11.6683.

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The Sex comb on midleg (Scm) and polyhomeotic (ph) proteins are members of the Polycomb group (PcG) of transcriptional repressors. PcG proteins maintain differential patterns of homeotic gene expression during development in Drosophila flies. The Scm and ph proteins share a homology domain with 38% identity over a length of 65 amino acids, termed the SPM domain, that is located at their respective C termini. Using the yeast two-hybrid system and in vitro protein-binding assays, we show that the SPM domain mediates direct interaction between Scm and ph. Binding studies with isolated SPM domains from Scm and ph show that the domain is sufficient for these protein interactions. These studies also show that the Scm-ph and Scm-Scm domain interactions are much stronger than the ph-ph domain interaction, indicating that the isolated domain has intrinsic binding specificity determinants. Analysis of site-directed point mutations identifies residues that are important for SPM domain function. These binding properties, predicted alpha-helical secondary structure, and conservation of hydrophobic residues prompt comparisons of the SPM domain to the helix-loop-helix and leucine zipper domains used for homotypic and heterotypic protein interactions in other transcriptional regulators. In addition to in vitro studies, we show colocalization of the Scm and ph proteins at polytene chromosome sites in vivo. We discuss the possible roles of the SPM domain in the assembly or function of molecular complexes of PcG proteins.
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33

Leonidas, Demetres D., Spyros E. Zographos, Katerina E. Tsitsanou, Vassiliki T. Skamnaki, George Stravodimos, and Efthimios Kyriakis. "Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators." Acta Crystallographica Section F Structural Biology Communications 77, no. 9 (August 26, 2021): 303–11. http://dx.doi.org/10.1107/s2053230x21008542.

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The crystal structures of free T-state and R-state glycogen phosphorylase (GP) and of R-state GP in complex with the allosteric activators IMP and AMP are reported at improved resolution. GP is a validated pharmaceutical target for the development of antihyperglycaemic agents, and the reported structures may have a significant impact on structure-based drug-design efforts. Comparisons with previously reported structures at lower resolution reveal the detailed conformation of important structural features in the allosteric transition of GP from the T-state to the R-state. The conformation of the N-terminal segment (residues 7–17), the position of which was not located in previous T-state structures, was revealed to form an α-helix (now termed α0). The conformation of this segment (which contains Ser14, phosphorylation of which leads to the activation of GP) is significantly different between the T-state and the R-state, pointing in opposite directions. In the T-state it is packed between helices α4 and α16 (residues 104–115 and 497–508, respectively), while in the R-state it is packed against helix α1 (residues 22′–38′) and towards the loop connecting helices α4′ and α5′ of the neighbouring subunit. The allosteric binding site where AMP and IMP bind is formed by the ordering of a loop (residues 313–326) which is disordered in the free structure, and adopts a conformation dictated mainly by the type of nucleotide that binds at this site.
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34

Pernod, Ketty, Laure Schaeffer, Johana Chicher, Eveline Hok, Christian Rick, Renaud Geslain, Gilbert Eriani, Eric Westhof, Michael Ryckelynck, and Franck Martin. "The nature of the purine at position 34 in tRNAs of 4-codon boxes is correlated with nucleotides at positions 32 and 38 to maintain decoding fidelity." Nucleic Acids Research 48, no. 11 (April 8, 2020): 6170–83. http://dx.doi.org/10.1093/nar/gkaa221.

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Abstract Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.
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35

Hao, Guixia, and Thomas J. Burr. "Regulation of Long-Chain N-Acyl-Homoserine Lactones in Agrobacterium vitis." Journal of Bacteriology 188, no. 6 (March 15, 2006): 2173–83. http://dx.doi.org/10.1128/jb.188.6.2173-2183.2006.

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ABSTRACT Homologs of quorum-sensing luxR and luxI regulatory genes, avsR and avsI, were identified in Agrobacterium vitis strain F2/5. Compared to other LuxI proteins from related species, the deduced AvsI shows the greatest identity to SinI (71%) from Sinorhizobium meliloti Rm1021. AvsR possesses characteristic autoinducer binding and helix-turn-helix DNA binding domains and shares a high level of identity with SinR (38%) from Rm1021. Site-directed mutagenesis of avsR and avsI was performed, and both genes are essential for hypersensitive-like response (HR) and necrosis. Two hypothetical proteins (ORF1 and ORF2) that are positioned downstream of avsR-avsI are also essential for the phenotypes. Profiles of N-acyl-homoserine lactones (AHLs) isolated from the wild type and mutants revealed that disruption of avsI, ORF1, or ORF2 abolished the production of long-chain AHLs. Disruption of avsR reduces long-chain AHLs. Expression of a cloned avsI gene in A. tumefaciens strain NT1 resulted in synthesis of long-chain AHLs. The necrosis and HR phenotypes of the avsI and avsR mutants were fully complemented with cloned avsI. The addition of synthetic AHLs (C16:1 and 3-O-C16:1) complemented grape necrosis in the avsR, avsI, ORF1, and ORF2 mutants. It was determined by reverse transcriptase PCR that the expression level of avsI is regulated by avsR but not by aviR or avhR, two other luxR homologs which were previously shown to be associated with induction of a tobacco hypersensitive response and grape necrosis. We further verified that avsR regulates avsI by measuring the expression of an avsI::lacZ fusion construct.
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36

CLEAVER, E. James, and J. Christopher STATES. "The DNA damage-recognition problem in human and other eukaryotic cells: the XPA damage binding protein." Biochemical Journal 328, no. 1 (November 15, 1997): 1–12. http://dx.doi.org/10.1042/bj3280001.

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The capacity of human and other eukaryotic cells to recognize a disparate variety of damaged sites in DNA, and selectively excise and repair them, resides in a deceptively small simple protein, a 38-42 kDa zinc-finger binding protein, XPA (xeroderma pigmentosum group A), that has no inherent catalytic properties. One key to its damage-recognition ability resides in a DNA-binding domain which combines a zinc finger and a single-strand binding region which may infiltrate small single-stranded regions caused by helix-destabilizing lesions. Another is the augmentation of its binding capacity by interactions with other single-stranded binding proteins and helicases which co-operate in the binding and are unloaded at the binding site to facilitate further unwinding of the DNA and subsequent catalysis. The properties of these reactions suggest there must be considerable conformational changes in XPA and associated proteins to provide a flexible fit to a wide variety of damaged structures in the DNA.
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37

Gautier, Antoine, John P Kirkpatrick, and Daniel Nietlispach. "Inside Cover: Solution-State NMR Spectroscopy of a Seven-Helix Transmembrane Protein Receptor: Backbone Assignment, Secondary Structure, and Dynamics (Angew. Chem. Int. Ed. 38/2008)." Angewandte Chemie International Edition 47, no. 38 (September 8, 2008): 7142. http://dx.doi.org/10.1002/anie.200890186.

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38

Siddiqui, K. S., M. Rangarajan, B. S. Hartley, A. Kitmitto, M. Panico, I. P. Blench, and H. R. Morris. "Arthrobacter d-xylose isomerase: partial proteolysis with thermolysin." Biochemical Journal 289, no. 1 (January 1, 1993): 201–8. http://dx.doi.org/10.1042/bj2890201.

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The pattern and kinetics of partial proteolysis of Arthrobacter D-xylose isomerase tetramer was studied in order to determine the flexibility of surface loops that may control its stability. It was completely resistant to trypsin, chymotrypsin and elastase at 37 degrees C, but thermolysin cleaved specifically and quantitatively at Thr-347-Leu-348 between helices 10 and 11 to remove 47 residues from the C-terminus of each 43.3 kDa subunit. At high temperatures, helices 9 and 10 were removed from each 38 kDa subunit to give a 36 kDa tetramer. The kinetics of nicking by thermolysin indicated that the Thr-347-Leu-348 loop is locked at low temperatures, but ‘melts’ at 25 degrees C and is fully flexible above 34 degrees C. The flexibility appears to be associated with binding of Ca2+ ions at the active site, since Co2+, Mg2+ and xylitol protect in proportion to their ability to displace Ca2+. The missing C-terminal helices make many intersubunit contacts that appear in the structure to stabilize the tetramer, but the properties of the purified nicked proteins are almost indistinguishable from the native enzyme. Both the 38 kDa tetramer and the 36 kDa tetramer are identically active and dissociate similarly in urea or SDS to fully active dimers, but the nicked dimers are slightly less stable to urea at 62 degrees C. In the Mg2+ form the thermostability of the 38 kDa tetramer is identical with that of the native enzyme, but the 36 kDa tetramer has a slightly lower ‘melting point’ (70 degrees C versus 80 degrees C), which may be due to unravelling from the end of helix 8. Since elimination of all the C-terminal helices and many intersubunit contacts has so little effect, one can conclude that the ‘weak point’ that controls the protein's thermostability lies within the N-terminal beta-barrel domain.
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39

McDonald, J. R., M. P. Walsh, W. D. McCubbin, K. Oikawa, and C. M. Kay. "Physicochemical properties of a novel Mr-21 000 Ca2+-binding protein of bovine brain." Biochemical Journal 232, no. 2 (December 1, 1985): 569–75. http://dx.doi.org/10.1042/bj2320569.

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The physicochemical properties of a novel Mr-21 000 Ca2+-binding protein isolated from bovine brain were investigated. The protein exhibited a partial specific volume of 0.724 ml/g, a degree of hydration of 0.47 g of water/g of protein and a mean residue weight of 119. Sedimentation equilibrium analysis revealed Mr = 22 600 in the absence of Ca2+; Ca2+ binding appeared to induce dimerization of the molecule. Size-exclusion chromatography indicated a compacting of the molecule on binding of Ca2+: the Stokes radius decreased from 2.75 nm in the absence of Ca2+ to 2.56 nm in its presence. Far-u.v.c.d. spectroscopy showed the apoprotein to be composed of 44% α-helix, 18% β-pleated sheet and 38% random coil. Addition of either KCl (0.1 M) plus Mg2+ (1 mM), or Ca2+ (2 mM), changed the conformation to 49% α-helix, 18% β-pleated sheet and 33% random coil. Near-u.v.c.d. and u.v. difference spectroscopy both indicated perturbations in the environments of all three types of aromatic amino acids on binding of Ca2+. Ca2+ binding also resulted in a 30% enhancement in the tryptophan fluorescence emission intensity. Ca2+ titration of the far-u.v.c.d. and fluorescence enhancement provided KD values of 9.91 microM and 4.68 microM respectively. Finally, the protein was shown to bind Zn2+ with KD = 1.44 microM (no Mg2+) and 1.82 microM (+ Mg2+). These observations strongly support the possibility that this novel Ca2+-binding protein resembles calmodulin and related Ca2+-binding proteins and undergoes a conformational change on binding of Ca2+ which reflects a physiological role in Ca2+-mediated regulation of brain function.
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40

Mamula, Olimpia, Alex von Zelewsky, Thomas Bark, and Gérald Bernardinelli. "Stereoselective Synthesis of Coordination Compounds: Self-Assembly of a Polymeric Double Helix with Controlled Chirality." Angewandte Chemie International Edition 38, no. 19 (October 4, 1999): 2945–48. http://dx.doi.org/10.1002/(sici)1521-3773(19991004)38:19<2945::aid-anie2945>3.0.co;2-d.

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41

Peshavaria, M., E. Henderson, A. Sharma, C. V. Wright, and R. Stein. "Functional characterization of the transactivation properties of the PDX-1 homeodomain protein." Molecular and Cellular Biology 17, no. 7 (July 1997): 3987–96. http://dx.doi.org/10.1128/mcb.17.7.3987.

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Pancreas formation is prevented in mice carrying a null mutation in the PDX-1 homeoprotein, demonstrating a key role for this factor in development. PDX-1 can also bind to and activate transcription from cis-acting regulatory sequences in the insulin and somatostatin genes, which are expressed in pancreatic islet beta and delta cells, respectively. In this study, we compared the functional properties of PDX-1 with those of the closely related Xenopus homeoprotein XIHbox8. Analysis of chimeras between PDX-1, XIHbox8, and the DNA-binding domain of the Saccharomyces cerevisiae transcription factor GAL4 revealed that their transactivation domain was contained within the N-terminal region (amino acids 1 to 79). Detailed mutagenesis of this region indicated that transactivation is mediated by three highly conserved sequences, spanning amino acids 13 to 22 (subdomain A), 32 to 38 (subdomain B), and 60 to 73 (subdomain C). These sequences were also required by PDX-1 to synergistically activate insulin enhancer-mediated transcription with another key insulin gene activator, the E2A-encoded basic helix-loop-helix E2-5 and E47 proteins. These results indicated that N-terminal sequences conserved between the mammalian PDX-1 and Xenopus XIHbox8 proteins are important in transcriptional activation. Stable expression of the PDX-1 deltaABC mutant in the insulin- and PDX-1-expressing betaTC3 cell line resulted in a threefold reduction in the rate of endogenous insulin gene transcription. Strikingly, the level of the endogenous PDX-1 protein was reduced to very low levels in these cells. These results suggest that PDX-1 is not absolutely essential for insulin gene expression in betaTC3 cells. We discuss the possible significance of these findings for insulin gene transcription in islet beta cells.
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42

Savich, Yahor, Benjamin P. Binder, Andrew R. Thompson, and David D. Thomas. "Myosin lever arm orientation in muscle determined with high angular resolution using bifunctional spin labels." Journal of General Physiology 151, no. 8 (June 21, 2019): 1007–16. http://dx.doi.org/10.1085/jgp.201812210.

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Despite advances in x-ray crystallography, cryo-electron microscopy (cryo-EM), and fluorescence polarization, none of these techniques provide high-resolution structural information about the myosin light chain domain (LCD; lever arm) under ambient conditions in vertebrate muscle. Here, we measure the orientation of LCD elements in demembranated muscle fibers by electron paramagnetic resonance (EPR) using a bifunctional spin label (BSL) with an angular resolution of 4°. To achieve stereoselective site-directed labeling with BSL, we engineered a pair of cysteines in the myosin regulatory light chain (RLC), either on helix E or helix B, which are roughly parallel or perpendicular to the myosin lever arm, respectively. By exchanging BSL-labeled RLC onto oriented muscle fibers, we obtain EPR spectra from which the angular distributions of BSL, and thus the lever arm, can be determined with high resolution relative to the muscle fiber axis. In the absence of ATP (rigor), each of the two labeled helices exhibits both ordered (σ ∼9–11°) and disordered (σ &gt; 38°) populations. Using these angles to determine the orientation of the lever arm (LCD combined with converter subdomain), we observe that the oriented population corresponds to a lever arm that is perpendicular to the muscle fiber axis and that the addition of ATP in the absence of Ca2+ (inducing relaxation) shifts the orientation to a much more disordered orientational distribution. Although the detected orientation of the myosin light chain lever arm is ∼33° different than predicted from a standard “lever arm down” model based on cryo-EM of actin decorated with isolated myosin heads, it is compatible with, and thus augments and clarifies, fluorescence polarization, x-ray interference, and EM data obtained from muscle fibers. These results establish feasibility for high-resolution detection of myosin LCD rotation during muscle contraction.
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43

Cho, Yong-Soon, Jiho Yoo, Soomin Park, and Hyun-Soo Cho. "The structures of the kinase domain and UBA domain of MPK38 suggest the activation mechanism for kinase activity." Acta Crystallographica Section D Biological Crystallography 70, no. 2 (January 31, 2014): 514–21. http://dx.doi.org/10.1107/s1399004713027806.

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Murine protein serine/threonine kinase 38 (MPK38) is the murine orthologue of human maternal embryonic leucine-zipper kinase (MELK), which belongs to the SNF1/AMPK family. MELK is considered to be a promising drug target for anticancer therapy because overexpression and hyperactivation of MELK is correlated with several human cancers. Activation of MPK38 requires the extended sequence (ExS) containing the ubiquitin-associated (UBA) linker and UBA domain and phosphorylation of the activation loop. However, the activation mechanism of MPK38 is unknown. This paper reports the crystal structure of MPK38 (T167E), which mimics a phosphorylated state of the activation loop, in complex with AMP-PNP. In the MPK38 structure, the UBA linker forces an inward movement of the αC helix. Phosphorylation of the activation loop then induces movement of the activation loop towards the C-lobe and results in interlobar cleft closure. These processes generate a fully active state of MPK38. This structure suggests that MPK38 has a similar molecular mechanism regulating activation as in other kinases of the SNF1/AMPK family.
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44

HELMERHORST, Eva J., Wim VAN 'T HOF, Enno C. I. VEERMAN, Ina SIMOONS-SMIT, and Arie V. NIEUW AMERONGEN. "Synthetic histatin analogues with broad-spectrum antimicrobial activity." Biochemical Journal 326, no. 1 (August 15, 1997): 39–45. http://dx.doi.org/10.1042/bj3260039.

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Histatins are salivary histidine-rich cationic peptides, ranging from 7 to 38 amino acid residues in length, that exert a potent killing effect in vitro on Candida albicans. Starting from the C-terminal fungicidal domain of histatin 5 (residues 11–24, called dh-5) a number of substitution analogues were chemically synthesized to study the effect of amphipathicity of the peptide in helix conformation on candidacidal activity. Single substitutions in dh-5 at several positions did not have any effect on fungicidal activity. However, multi-site substituted analogues (dhvar1 and dhvar2) exhibited a 6-fold increased activity over dh-5. In addition, dhvar1 and dhvar2 inhibited the growth of the second most common yeast found in clinical isolates, Torulopsis glabrata, of oral- and non-oral pathogens such as Prevotella intermedia and Streptococcus mutans, and of a methicillin-resistant Staphylococcus aureus. In their broad-spectrum activity, dhvar1 and dhvar2 were comparable to magainins (PGLa and magainin 2), antimicrobial peptides of amphibian origin. Both the fungicidal and the haemolytic activities of dhvar1, dhvar2 and magainins increased at decreasing ionic strength.
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45

Sengupta, Jayati, Cyril Bussiere, Jesper Pallesen, Matthew West, Arlen W. Johnson, and Joachim Frank. "Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit." Journal of Cell Biology 189, no. 7 (June 28, 2010): 1079–86. http://dx.doi.org/10.1083/jcb.201001124.

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The nucleocytoplasmic shuttling protein Nmd3 is an adaptor for export of the 60S ribosomal subunit from the nucleus. Nmd3 binds to nascent 60S subunits in the nucleus and recruits the export receptor Crm1 to facilitate passage through the nuclear pore complex. In this study, we present a cryoelectron microscopy (cryo-EM) reconstruction of the 60S subunit in complex with Nmd3 from Saccharomyces cerevisiae. The density corresponding to Nmd3 is directly visible in the cryo-EM map and is attached to the regions around helices 38, 69, and 95 of the 25S ribosomal RNA (rRNA), the helix 95 region being adjacent to the protein Rpl10. We identify the intersubunit side of the large subunit as the binding site for Nmd3. rRNA protection experiments corroborate the structural data. Furthermore, Nmd3 binding to 60S subunits is blocked in 80S ribosomes, which is consistent with the assigned binding site on the subunit joining face. This cryo-EM map is a first step toward a molecular understanding of the functional role and release mechanism of Nmd3.
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46

Love, Cassandra L., Dereje Jima, Zhen Sun, Rodney R. Miles, Cherie H. Dunphy, William W. L. Choi, Wing Y. Au, et al. "ID3 Is a Novel Tumor Suppressor Gene in Burkitt Lymphom." Blood 120, no. 21 (November 16, 2012): 898. http://dx.doi.org/10.1182/blood.v120.21.898.898.

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Abstract Abstract 898 Burkitt Lymphoma (BL) is a highly proliferative form of non-Hodgkin lymphoma and is characterized by translocation of the C-MYC gene to the immunoglobulin gene loci resulting in deregulation. The role of collaborating gene mutations in BL is largely unknown. We performed whole exome sequencing and gene expression profiling of 57 Burkitt lymphoma and 94 DLBCL exomes. Mutational analysis revealed that ID3 is recurrently mutated in 38% of Burkitt lymphoma samples. ID3 mutations did not occur in any of the 94 DLBCL cases. ID3 gene expression was also found to be a distinguishing feature of Burkitt lymphomas (P<10−6), compared to DLBCL. We found a total of 27 distinct mutations in the ID3 genes among the 22 BL cases. These included five frameshift, four nonsense, and 18 missense mutations. We validated 16 of these events with Sanger sequencing with over 90% concordance. All of these mutations were located in the highly conserved helix-loop-helix region located on Exon 1. We explored the biological significance of ID3 mutations by initially comparing the gene expression profiles of BL cases that had mutated and wild-type ID3. Gene set enrichment analysis showed that those samples with mutated ID3 had higher expression of genes that were involved in cell cycle regulation, specifically those involved in the G1-S transition (P=0.01). In order to experimentally investigate the functional consequences of ID3 mutation, we generated mutant constructs corresponding to six different ID3 mutations observed in BLs. These mutant constructs were cloned into lentiviral vectors and overexpressed in BL cells that were wild type for ID3. We then performed cell cycle analysis for these wild type cells expressing GFP controls or the mutant constructs. We found that BL cells expressing each of the six mutant constructs demonstrated significant cell cycle progression from G1 to S phase compared to wild-type (P=0.01). Separately, we tested the effects of expressing mutant ID3 in cell proliferation assays and found that cells expressing mutant ID3 were considerably more proliferative than those expressing wild type (P=0.03). Conversely, we over-expressed the wild type form of ID3 in BL cells that had mutated ID3. These experiments completely rescued the observed phenotypes of the mutant ID3 constructs, with reduced cell cycle progression through increased G1 phase and decreased S-phase (P=0.04). We also noted decreased cell proliferation in these cells (P=0.03). These experiments support a role for ID3 as a novel tumor suppressor gene in Burkitt lymphoma. ID3 is a basic helix loop helix (bHLH) protein that binds to other E-proteins, blocking their ability to bind DNA. ID3 has been shown to be involved in a variety of biological processes including development and T and B cell differentiation. ID3 knockout mice have been shown to develop T cell as well as B cell lymphomas. Our data implicates this gene for the first time as a tumor suppressor in human cancer. Disclosures: No relevant conflicts of interest to declare.
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47

Garibaldi, A., D. Bertetti, J. Rossi, and M. L. Gullino. "First Report of Powdery Mildew Incited by Erysiphe heraclei on English Ivy (Hedera helix) in Italy." Plant Disease 92, no. 2 (February 2008): 313. http://dx.doi.org/10.1094/pdis-92-2-0313a.

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Hedera helix L. (Araliaceae) is a common ornamental species that is able to grow in shaded areas and is often used in parks and gardens. During the fall of 2006, severe outbreaks of a previously unknown powdery mildew were observed in several gardens in Liguria (northern Italy). Both surfaces of young leaves of affected plants were covered with dense, white mycelia and conidia. As the disease progressed, infected leaves turned yellow and dropped. Mycelia and conidia were also observed on young stems. Conidia were hyaline, cylindrical, borne singly, and measured 38 to 51 × 12 to 18 (average 42 × 16) μm. Single germ tubes, moderately long (average 26 μm), developed at the end of conidia. Appressoria of germ tubes and hyphae were lobed (three to four lobes). Conidiophores, 68 to 82 × 7 to 8 (average75 × 8) μm, showed foot cells measuring 39 to 60 × 7 to 8 (average 52 × 8) μm, followed by one shorter cell measuring 19 to 28 × 8 to 9 (average 23 × 9) μm. Fibrosin bodies were absent. Chasmothecia were numerous, spherical, amber-colored then brown at maturity, with diameters ranging from 97 to 140 (average 120) μm, containing four asci shortly stalked, 57 to 72 × 32 to 51 (average 65 × 41 μm). Ascospores were ellipsoid and measured 24 to 34 × 15 to 20 (average 30 × 17) μm. The internal transcribed spacer (ITS) region of rDNA was amplified using the primers ITS4/ITS6 and sequenced. BLASTn analysis (1) of the 613-bp fragment showed an E-value of 0.0 with Erysiphe heraclei. The nucleotide sequence has been assigned GenBank Accession No. EU 010381. In GenBank, our nucleotide sequence shows an E-value of 0.0 also with E. betae. However, the comparison of appressorium shape and germ tube length observed on our microorganism with those described for E. betae by Braun (2) suggests that the causal agent of the powdery mildew reported on ivy is E. heraclei. Furthermore, symptoms described on our host, appressorium shape and the length of conidiophores, are different from those of Oidium araliacearum described by Braun (2) on Araliaceae. Inoculations were made by gently pressing diseased leaves onto leaves of five healthy H. helix plants. Three noninoculated plants served as controls. Inoculated and noninoculated plants were maintained in a greenhouse at temperatures between 21 and 25°C. After 15 days, typical powdery mildew colonies developed on inoculated plants. Noninoculated plants did not show symptoms. The pathogenicity test was carried out twice. To our knowledge, this is the first report of the presence of powdery mildew on H. helix caused by E. heraclei in Italy. A powdery mildew caused by E. cichoracearum was previously reported on H. canariensis var. azorica in Italy (3), while a powdery mildew on H. helix caused by O. araliacearum and Golovinomyces orontii, respectively, were observed in the United States (4) and Germany. Herbarium specimens of this disease are available at AGROINNOVA Collection, University of Torino, Italy. References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) U. Braun. A Monograph of the Erysiphaceae (Powdery Mildews). Cramer, Berlin, Germany, 1987. (3) C. Nali. Plant Dis. 83:198, 1999. (4) G. S. Saenz and S. T. Koike. Plant Dis. 82:127, 1998.
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48

Ferreira, Lize V., Silvia A. L. Souza, Luciana R. Montenegro, Ivo J. P. Arnhold, Titania Pasqualini, Juan Jorge Heinrich, Ana Claudia Keselman, Berenice B. Mendonça, and Alexander A. L. Jorge. "Variabilidade do fenótipo de pacientes com síndrome de Noonan com e sem mutações no gene PTPN11." Arquivos Brasileiros de Endocrinologia & Metabologia 51, no. 3 (April 2007): 450–56. http://dx.doi.org/10.1590/s0004-27302007000300014.

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INTRODUÇÃO: Aproximadamente 50% dos pacientes com síndrome de Noonan (SN) apresentam mutações em heterozigose no gene PTPN11. OBJETIVO: Avaliar a freqüência de mutações no PTPN11 em pacientes com SN e analisar a correlação fenótipo-genótipo. PACIENTES: 33 pacientes com SN. MÉTODO: Extração de DNA de leucócitos periféricos e seqüenciamento dos 15 exons do PTPN11. RESULTADOS: Nove diferentes mutações missense no PTPN11, incluindo a mutação P491H, ainda não descrita, foram encontradas em 16 dos 33 pacientes. As características clínicas mais freqüentes dos pacientes com SN foram: pavilhão auricular com rotação incompleta e espessamento da helix (85%), baixa estatura (79%), prega cervical (77%) e criptorquidismo nos meninos (60%). O Z da altura foi de -2,7 ± 1,2 e o do IMC foi de -1 ± 1,4. Os pacientes com mutação no PTPN11 apresentaram maior freqüência de estenose pulmonar do que os pacientes sem mutação (38% vs. 6%, p< 0,05). Pacientes com ou sem mutação no PTPN11 não diferiram em relação à média do Z da altura, Z do IMC, freqüência de alterações torácicas, características faciais, criptorquidia, retardo mental, dificuldade de aprendizado, pico de GH ao teste de estímulo e Z de IGF-1 ou IGFBP-3. CONCLUSÃO: Identificamos mutações no PTPN11 em 48,5% dos pacientes com SN, os quais apresentaram maior freqüência de estenose pulmonar.
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49

Matveyenko, Leonid I., Phil J. Diamond, and David A. Graham. "Dynamics of the superfine structure in the Orion KL jet." Symposium - International Astronomical Union 206 (2002): 96–99. http://dx.doi.org/10.1017/s0074180900222158.

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We have studied the superfine structure of the active H2O maser region in Orion KL with an angular resolution of ≤ 0.3 × 0.7 mas. The high level of H2O maser emission from 1979-1988 was due to an accretion disk, which is divided into five groups of protoplanetary rings. The peak brightness temperatures of the structures was Tpeak = 1013-14 K. The region is located in the OMC-1 molecular cloud, VLSR ⋍ 7.74 km/s. The cloud amplifies by more than two orders of magnitude the emission from the structures, whose radial velocities are within the maser window ±0.3 km/s. Due to this, the velocity of the H2O super maser emission is constant. In the quiescent period of 1995 a 6 AU jet was discovered, PA = −32°, Tb ⋍ 1011K. In 1998 the jet's brightness temperature increased by more than 3 orders of magnitude. Initially the jet's position angle was PA = −45°, and then changed to PA = −38°. During the period of decreasing emission in 1999 the jet had changed its form and became a helix, that suggests the precession of the rotation axes. In the central part of the jet there is a compact bright source - “the ejector” - with Tejc = 1017 K.
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50

Gong, Huansheng, Anne Murphy, Christopher R. McMaster, and David M. Byers. "Neutralization of Acidic Residues in Helix II Stabilizes the Folded Conformation of Acyl Carrier Protein and Variably Alters Its Function with Different Enzymes." Journal of Biological Chemistry 282, no. 7 (December 18, 2006): 4494–503. http://dx.doi.org/10.1074/jbc.m608234200.

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Acyl carrier protein (ACP), a small protein essential for bacterial growth and pathogenesis, interacts with diverse enzymes during the biosynthesis of fatty acids, phospholipids, and other specialized products such as lipid A. NMR and hydrodynamic studies have previously shown that divalent cations stabilize native helical ACP conformation by binding to conserved acidic residues at two sites (A and B) at either end of the “recognition” helix II. To examine the roles of these amino acids in ACP structure and function, site-directed mutagenesis was used to replace individual site A (Asp-30, Asp-35, Asp-38) and site B (Glu-47, Glu-53, Asp-56) residues in recombinant Vibrio harveyi ACP with the corresponding amides, along with combined mutations at each site (SA, SB) or both sites (SA/SB). Like native V. harveyi ACP, all individual mutants were unfolded at neutral pH but adopted a helical conformation in the presence of millimolar Mg2+ or upon fatty acylation. Mg2+ binding to sites A or B independently stabilized native ACP conformation, whereas mutant SA/SB was folded in the absence of Mg2+, suggesting that charge neutralization is largely responsible for ACP stabilization by divalent cations. Asp-35 in site A was critical for holo-ACP synthase activity, while acyl-ACP synthetase and UDP-N-acetylglucosamine acyltransferase (LpxA) activities were more affected by mutations in site B. Both sites were required for fatty acid synthase activity. Overall, our results indicate that divalent cation binding site mutations have predicted effects on ACP conformation but unpredicted and variable consequences on ACP function with different enzymes.
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