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Academic literature on the topic 'ArnA Protein'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "ArnA Protein"

Kopp, Ulla C., Donna M. Farley, Michael Z. Cicha, and Lori A. Smith. "Activation of renal mechanosensitive neurons involves bradykinin, protein kinase C, PGE2, and substance P." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 278, no. 4 (April 1, 2000): R937—R946. http://dx.doi.org/10.1152/ajpregu.2000.278.4.r937.

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Increased renal pelvic pressure or bradykinin increases afferent renal nerve activity (ARNA) via PGE2-induced release of substance P. Protein kinase C (PKC) activation increases ARNA, and PKC inhibition blocks the ARNA response to bradykinin. We now examined whether bradykinin mediates the ARNA response to increased renal pelvic pressure by activating PKC. In anesthetized rats, the ARNA responses to increased renal pelvic pressure were blocked by renal pelvic perfusion with the bradykinin B2-receptor antagonist HOE 140 and the PKC inhibitor calphostin C by 76 ± 8% ( P < 0.02) and 81 ± 5% ( P < 0.01), respectively. Renal pelvic perfusion with 4β-phorbol 12,13-dibutyrate (PDBu) to activate PKC increased ARNA 27 ± 4% and renal pelvic release of PGE2 from 500 ± 59 to 1,113 ± 183 pg/min and substance P from 10 ± 2 to 30 ± 2 pg/min (all P < 0.01). Indomethacin abolished the increases in substance P release and ARNA. The PDBu-mediated increase in ARNA was also abolished by the substance P-receptor antagonist RP 67580. We conclude that bradykinin contributes to the activation of renal pelvic mechanosensitive neurons by activating PKC. PKC increases ARNA via a PGE2-induced release of substance P.

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Marcos, Caroline Maria, Haroldo Cesar de Oliveira, Patricia Akemi Assato, Cleverton Roberto de Andrade, Ana Marisa Fusco-Almeida, and Maria José Soares Mendes-Giannini. "Paracoccidioides brasiliensis 14-3-3 protein is important for virulence in a murine model." Medical Mycology 57, no. 7 (November 24, 2018): 900–904. http://dx.doi.org/10.1093/mmy/myy112.

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AbstractThe Paracoccidioides brasiliensis strain downregulated the expression of adhesin Pb14-3-3 (Pb14-3-3 aRNA) was evaluated in a murine model of paracoccidioidomycosis (PCM). Pb14-3-3 aRNA displays attenuated virulence and triggered the formation of fewer granulomas by lowering the fungal burden in the lungs. Additionally, the Pb14-3-3 aRNA showed more elongated yeast cells and less ability to induce pneumocytes apoptosis in vitro. Our results show that 14-3-3 is an important virulence factor in P. brasiliensis-induced pulmonary infection.

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Kopp, U. C., and L. A. Smith. "A role for protein kinase C in bradykinin-mediated activation of renal pelvic sensory receptors." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 269, no. 2 (August 1, 1995): R331—R338. http://dx.doi.org/10.1152/ajpregu.1995.269.2.r331.

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In anesthetized rats, activation of renal pelvic sensory receptors by bradykinin results in an increase in afferent renal nerve activity (ARNA) that is dependent on intact renal prostaglandin synthesis. Since bradykinin is a known activator of the phosphoinositide system, we examined whether the increase in ARNA produced by bradykinin involved activation of protein kinase C (PKC). Renal pelvic perfusion with the phorbol ester 4 beta-phorbol 12,13-dibutyrate (PDBu, 1 microM) increased ARNA (31 +/- 3%, P < 0.01) in rats fed a normal diet but not in rats fed an essential fatty acid-deficient (EFAD) diet. Renal pelvic perfusion with the PKC inhibitors calphostin C (1 microM), staurosporine (20 nM), and H-7 (40 microM) reduced the ARNA responses to bradykinin (20 microM) by 69 +/- 10, 76 +/- 10, and 77 +/- 10%, respectively (all P < 0.01). Pretreatment with PDBu (1 microM), known to cause a feedback inhibition of bradykinin-mediated activation of the phosphoinositide system, reduced the ARNA response to bradykinin by 73 +/- 6% (P < 0.01). Pretreatment with 4 alpha-phorbol 12,13-didecanoate was without effect. These findings suggest that activation of PKC contributes importantly to the activation of renal pelvic sensory receptors by bradykinin, likely via release of arachidonic acid.

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Fischer, Utz, Simon Hertlein, and Clemens Grimm. "The structure of apo ArnA features an unexpected central binding pocket and provides an explanation for enzymatic cooperativity." Acta Crystallographica Section D Biological Crystallography 71, no. 3 (February 26, 2015): 687–96. http://dx.doi.org/10.1107/s1399004714026686.

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The bacterial protein ArnA is an essential enzyme in the pathway leading to the modification of lipid A with the pentose sugar 4-amino-4-deoxy-L-arabinose. This modification confers resistance to polymyxins, which are antibiotics that are used as a last resort to treat infections with multiple drug-resistant Gram-negative bacteria. ArnA contains two domains with distinct catalytic functions: a dehydrogenase domain and a transformylase domain. The protein forms homohexamers organized as a dimer of trimers. Here, the crystal structure of apo ArnA is presented and compared with its ATP- and UDP-glucuronic acid-bound counterparts. The comparison reveals major structural rearrangements in the dehydrogenase domain that lead to the formation of a previously unobserved binding pocket at the centre of each ArnA trimer in its apo state. In the crystal structure, this pocket is occupied by a DTT molecule. It is shown that formation of the pocket is linked to a cascade of structural rearrangements that emerge from the NAD+-binding site. Based on these findings, a small effector molecule is postulated that binds to the central pocket and modulates the catalytic properties of ArnA. Furthermore, the discovered conformational changes provide a mechanistic explanation for the strong cooperative effect recently reported for the ArnA dehydrogenase function.

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Kopp, Ulla C., Olaf Grisk, Michael Z. Cicha, Lori A. Smith, Antje Steinbach, Torsten Schlüter, Nicole Mähler, and Tomas Hökfelt. "Dietary sodium modulates the interaction between efferent renal sympathetic nerve activity and afferent renal nerve activity: role of endothelin." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 297, no. 2 (August 2009): R337—R351. http://dx.doi.org/10.1152/ajpregu.91029.2008.

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Increasing efferent renal sympathetic nerve activity (ERSNA) increases afferent renal nerve activity (ARNA), which in turn decreases ERSNA via activation of the renorenal reflexes in the overall goal of maintaining low ERSNA. We now examined whether the ERSNA-induced increases in ARNA are modulated by dietary sodium and the role of endothelin (ET). The ARNA response to reflex increases in ERSNA was enhanced in high (HNa)- vs. low-sodium (LNa) diet rats, 7,560 ± 1,470 vs. 900 ± 390%·s. The norepinephrine (NE) concentration required to increase PGE2 and substance P release from isolated renal pelvises was 10 pM in HNa and 6,250 pM in LNa diet rats. In HNa diet pelvises 10 pM NE increased PGE2 release from 67 ± 6 to 150 ± 13 pg/min and substance P release from 6.7 ± 0.8 to 12.3 ± 1.8 pg/min. In LNa diet pelvises 6,250 pM NE increased PGE2 release from 64 ± 5 to 129 ± 22 pg/min and substance P release from 4.5 ± 0.4 to 6.6 ± 0.7 pg/min. In the renal pelvic wall, ETB-R are present on unmyelinated Schwann cells close to the afferent nerves and ETA-R on smooth muscle cells. ETA-receptor (R) protein expression in the renal pelvic wall is increased in LNa diet. In HNa diet, renal pelvic administration of the ETB-R antagonist BQ788 reduced ERSNA-induced increases in ARNA and NE-induced release of PGE2 and substance P. In LNa diet, the ETA-R antagonist BQ123 enhanced ERSNA-induced increases in ARNA and NE-induced release of substance P without altering PGE2 release. In conclusion, activation of ETB-R and ETA-R contributes to the enhanced and suppressed interaction between ERSNA and ARNA in conditions of HNa and LNa diet, respectively, suggesting a role for ET in the renal control of ERSNA that is dependent on dietary sodium.

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Robichon, Carine, Jianying Luo, Thomas B. Causey, Jack S. Benner, and James C. Samuelson. "Engineering Escherichia coli BL21(DE3) Derivative Strains To Minimize E. coli Protein Contamination after Purification by Immobilized Metal Affinity Chromatography." Applied and Environmental Microbiology 77, no. 13 (May 20, 2011): 4634–46. http://dx.doi.org/10.1128/aem.00119-11.

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ABSTRACTRecombinant His-tagged proteins expressed inEscherichia coliand purified by immobilized metal affinity chromatography (IMAC) are commonly coeluted with nativeE. coliproteins, especially if the recombinant protein is expressed at a low level. TheE. colicontaminants display high affinity to divalent nickel or cobalt ions, mainly due to the presence of clustered histidine residues or biologically relevant metal binding sites. To improve the final purity of expressed His-tagged protein, we engineeredE. coliBL21(DE3) expression strains in which the most recurring contaminants are either expressed with an alternative tag or mutated to decrease their affinity to divalent cations. The current study presents the design, engineering, and characterization of twoE. coliBL21(DE3) derivatives, NiCo21(DE3) and NiCo22(DE3), which express the endogenous proteins SlyD, Can, ArnA, and (optionally) AceE fused at their C terminus to a chitin binding domain (CBD) and the protein GlmS, with six surface histidines replaced by alanines. We show that eachE. coliCBD-tagged protein remains active and can be efficiently eliminated from an IMAC elution fraction using a chitin column flowthrough step, while the modification of GlmS results in loss of affinity for nickel-containing resin. The “NiCo” strains uniquely complement existing methods for improving the purity of recombinant His-tagged protein.

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Sonawane, Kailas D., Rishikesh S. Parulekar, Radhika S. Malkar, Pranhita R. Nimbalkar, Sagar H. Barage, and Deepak B. Jadhav. "Homology modeling and molecular docking studies of ArnA protein from Erwinia amylovora: role in polymyxin antibiotic resistance." Journal of Plant Biochemistry and Biotechnology 24, no. 4 (November 20, 2014): 425–32. http://dx.doi.org/10.1007/s13562-014-0293-3.

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Liu, Yifei. "Preparation of SARS-CoV-2 Polymerase Nsp12 and Optimization of Expression Conditions." Sustainability in Environment 8, no. 1 (January 23, 2023): p26. http://dx.doi.org/10.22158/se.v8n1p26.

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he core component of transcription and replication of SARS-CoV-2 is Nsp12, a non-structural protein that function as an RNA-dependent RNA polymerase. Nsp12 is a key drug target for the development of anti-coronavirus drugs. The purpose of this study was to explore and optimize the expression conditions of Nsp12 of SARS-CoV-2 with the aim of establishing expression conditions to obtain high-purity Nsp12 protein. This study compared the “ice-water bath cooling” and “shaking table cooling” methods and explored the differences in cooling rates and protein expression and properties using the two cooling methods. The shaking table cooling method resulted in reduced amounts of ArnA protein in the Nsp12 protein samples compared with levels from the ice-water bath cooling method. The shaking table method enabled purification of high-quality Nsp12 protein and ensured stable output of the protein. These methods will enable subsequent exploration of the SARS-CoV-2 replication mechanism, the development of specific drugs and drug screening for anti-SARS-CoV-2 pneumonitis.

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Ma, Ming-Chieh, Ho-Shiang Huang, Chiang-Ting Chien, Ming-Shiou Wu, and Chau-Fong Chen. "Temporal decrease in renal sensory responses in rats after chronic ligation of the bile duct." American Journal of Physiology-Renal Physiology 283, no. 1 (July 1, 2002): F164—F172. http://dx.doi.org/10.1152/ajprenal.00231.2001.

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Renal responses to renal sensory receptor activation were examined in rats after 1 and 4 wk of common bile duct ligation (CBDL). Compared with sham-operated rats (Sham), urine and sodium excretion after acute saline loading was significantly reduced at both times after CBDL. The blunted excretory responses in CBDL rats, accompanied by less activation of afferent renal nerve activity (ARNA), were already apparent at 1 wk and became severe at 4 wk. The defect in ARNA activation in CBDL rats was further studied using specific stimuli to activate renal sensory receptors. Graded increases in intrapelvic pressure or renal pelvic perfusion of substance P (SP) elicited an increase in ARNA in Sham rats, these responses being temporally attenuated in CBDL rats. Despite no significant change in renal pelvic SP release, no renorenal reflex was demonstrable in 4-wk CBDL rats. Immunoblotting showed that expression of renal pelvic neurokinin 1 (NK-1) receptors was 32 and 47% lower in 1- and 4-wk CBDL rats, respectively, than in Sham rats, this decrease correlating well with plasma SP levels. The quantitative real-time RT-PCR showed similar levels of NK-1 receptor mRNA in the renal pelvis in the Sham and 4-wk CBDL groups. We conclude that impairment of renal excretory and sensory responses increases with the duration of cirrhosis. An impaired renorenal reflex in cirrhotic rats is involved in the defective activation of the renal sensory receptors could be due, in part, to the low expression of NK-1 receptors, which is dependent on the duration of CBDL. The decrease in NK-1 receptor protein levels is not due to a decrease in mRNA levels.

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Hernández, Orville, Agostinho J. Almeida, Angel Gonzalez, Ana Maria Garcia, Diana Tamayo, Luz Elena Cano, Angela Restrepo, and Juan G. McEwen. "A 32-Kilodalton Hydrolase Plays an Important Role in Paracoccidioides brasiliensis Adherence to Host Cells and Influences Pathogenicity." Infection and Immunity 78, no. 12 (September 27, 2010): 5280–86. http://dx.doi.org/10.1128/iai.00692-10.

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ABSTRACT One of the most crucial events during infection with the dimorphic fungus Paracoccidioides brasiliensis is adhesion to pulmonary epithelial cells, a pivotal step in the establishment of disease. In this study, we have evaluated the relevance of a 32-kDa protein, a putative adhesion member of the haloacid dehalogenase (HAD) superfamily of hydrolases, in the virulence of this fungus. Protein sequence analyses have supported the inclusion of PbHad32p as a hydrolase and have revealed a conserved protein only among fungal dimorphic and filamentous pathogens that are closely phylogenetically related. To evaluate its role during the host-pathogen interaction, we have generated mitotically stable P. brasiliensis HAD32 (PbHAD32) antisense RNA (aRNA) strains with consistently reduced gene expression. Knockdown of PbHAD32 did not alter cell vitality or viability but induced morphological alterations in yeast cells. Moreover, yeast cells with reduced PbHAD32 expression were significantly affected in their capacity to adhere to human epithelial cells and presented decreased virulence in a mouse model of infection. These data support the hypothesis that PbHad32p binds to extracellular matrix (ECM) proteins and modulates the initial immune response for evasion of host defenses. Our findings point to PbHAD32 as a novel virulence factor active during the initial interaction with host cells in P. brasiliensis.

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Dissertations / Theses on the topic "ArnA Protein"

Gowher, Ali. "Characterization of protein factors targeting RNA into human mitochondria." Phd thesis, Université de Strasbourg, 2013. http://tel.archives-ouvertes.fr/tel-01071841.

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The import of yeast tRNALys (tRK1) into human mitochondria in the presence of cytosolic extract suggests that human cell possesses machinery for tRK1 import. Here, we show that precursor of mitochondrial lysyl-tRNA synthetase (preKARS2) interact with tRK1 and its derivatives containing tRK1 import determinants, and facilitates their import into isolated mitochondria and in vivo, when preKARS2 was overexpressed or downregulated. tRK1 import efficiency increased upon addition of glycolytic enzyme enolase, previously found as an actor of RNA import in yeast. We found that tRK1 and its derivatives translocate into mitochondrial matrix in polynucleotide phosphorylase (PNPase) dependent manner. Furthermore, a point mutation preventing trimerization of PNPase affect import of 5S rRNA and MRP RNA into mitochondria and subsequently mitochondrial translation. Overexpression of the wild-type PNPase induced an increase of 5S rRNA import into mitochondria and rescued translation.

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Corsi, Flavia. "Towards the in silico reconstruction of protein interaction networks : identification of DNA- and RNA-protein interfaces, and construction of a database of multiple interactions of proteins." Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS452.pdf.

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Cette thèse porte sur la caractérisation et la prédiction des interfaces protéine-ADN et -ARN, et des comparaisons avec les interfaces protéine-protéine. Nous avons créé un ensemble non-redondant et représentatif de 187 complexes protéine-ADN à haute résolution, comprenant aussi les conformations non liées de 82 protéines. Cette base de données peut servir de référence dans le domaine. Nous avons mené une analyse exhaustive des propriétés de séquence et structurels des interfaces protéine-ADN/ARN et nous les avons comparé avec les propriétés des interfaces protéine-protéine et celles des régions protéiques non-interagissantes. Nous avons développé JET2DNA et JET2RNA, nouvelles méthodes pour la prediction des sites de liaison protéine-ADN/ARN à la surface des protéines. En combinant quatre descripteurs biologiquement pertinents, elles surpassent des méthodes par apprentissage machine. Elles permettent aussi de découvrir des sites de liaison alternatifs avec l'ADN/ARN et de déchiffrer leurs propriétés. Afin de donner un aperçu global de la plasticité des protéines interagissant avec l'ADN, nous avons construit la base de données protéine-(protéine)-ADN (P(P)DNAdb). Elle inclut les 187 complexes protéine-ADN de notre ensemble de référence, les forme libres des protéines et les structures des autres complexes où ces protéines, ou des homologues proches, sont impliqués. L'utilisateur peut accéder aux propriétés des interfaces, visualiser les changements de conformation associés à la liaison avec des partenaires différents et localiser les résidus interagissants avec l'ADN dans les autres structures de la même protéine
This thesis focuses on the characterization and prediction of DNA- and RNA-binding sites on protein structures, with some comparisons with protein-protein ones. We compiled and manually curated a non-redundant and representative set of 187 high resolution protein-DNA complexes, with the available 82 protein unbound conformations, that could be used as a reference benchmark. We conducted a comprehensive analysis of sequence- and structure-based properties of protein-DNA/RNA interfaces and compared them with respect to protein-protein interfaces and to non-interacting protein regions. We developed JET2DNA and JET2RNA, new methods for predicting DNA- and RNA-binding sites on protein surfaces. Combining four biologically meaningful descriptors, they outperform other machine-learning methods, in terms of predictive power and robustness to conformational changes. Our tools demonstrated to be instrumental in discovering alternative DNA/RNA-binding sites and in deciphering their properties. This could be very helpful for drug design and repurposing. To give a comprehensive view of plasticity of DNA-binding proteins and structural information on their multiple interactions, we constructed the Protein-(Protein)-DNA database (P(P)DNAdb). It comprises the 187 protein-DNA complexes in our benchmark, protein unbound forms and structures of other complexes where the proteins, or closed homologs, were in contact with other proteins. The user can access properties of the interfaces, visualize conformational changes associated to the binding of different partners and the location of the DNA-binding residues on the unbound structures and on the complexes with the other protein partners

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CARUCCI, FEDERICA. "Agronomic strategies for Sustainable Management of Durum Wheat Cultivation in Mediterranean Area." Doctoral thesis, Università di Foggia, 2021. https://hdl.handle.net/11369/425190.

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L’azoto è un elemento nutritivo fondamentale per la produzione di cereali, tu5avia ha un signi!cativo impa5o ambientale. Nel presente elaborato vengono valutate diverse pratiche agronomiche al !ne di incrementare la sostenibilità della coltivazione del frumento duro, e migliorare la sua produ5ività e qualità. Gli studi sono stati tu5i condo5i nell’area del Mediterraneo, de!nita come una delle regioni maggiormente colpita dai cambiamenti climatici in corso. In quest’area, quindi, la gestione sostenibile dell’azoto diventa ancora più importante. L'obie5ivo generale è stato perseguito valutando le risposte di diversi genotipi di frumento duro alla gestione sostenibile della fertilizzazione azotata sia in sistemi produ5ivi biologici che a basso input. De!nire il sistema produ5ivo agricolo che da solo sia in grado di garantire alla popolazione mondale un'alimentazione sicura e sostenibile è impossibile. Tu5avia, per garantire contemporaneamente l’accesso al cibo e la sostenibilità ambientale, sarà necessario ricorrere a sistemi agricoli innovativi, compresi quelli a basso input e biologici. In conclusione, i risultati descri5i in questo elaborato hanno contribuito a far progredire il grado di conoscenza sulla sostenibilità, sulla produ5ività e su diversi aspe5i qualitativi del frumento duro in ambiente mediterraneo. Tu5avia, molte questioni signi!cative restano da indagare e saranno ogge5o di futuri studi.
Nitrogen is the most requested element in cereal systems and has the most signi!cant impact on the environment. This Ph.D. dissertation deals with di$erent agronomic strategies to improve the sustainability of durum wheat cultivation, together with its productivity and quality. Studies were conducted in the Mediterranean area, de!ned as one of the regions most vulnerable to climatic changes. Since, in this area the e'ciently use of nitrogen is more critical. The main objective was pursued evaluating the responses of di$erent durum wheat genotypes to the sustainable management of nitrogen fertilizers in organic and low-input systems. De!ne the best farming system that alone can satisfy the world safe and sustainable feeding is impossible. However, innovative farming systems, including low-input and organic ones, will be necessary for both food access and ecosystem security. In conclusion, the results described in this Ph.D. advance the current state of the knowledge about improving the sustainability, productivity and di$erent quality aspects of durum wheat under Mediterranean conditions. However, several signi!cant issues remain to be investigated in future research.

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Uchikawa, Emiko. "A structural approach of RNA-protein recognition and kinetics of binding in two examples : tRNA aminoacylation by arginyl-tRNA synthetase and 7SK stabilization by LaRP7." Strasbourg, 2011. http://www.theses.fr/2011STRA6052.

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Dans la cellule, les interactions ARN-protéines jouent un rôle fondamental dans divers processus impliqués dans la régulation de l'expression du message génétique. Si l'épissage de l'ARN pré-messager, la polyadénylation, le transport et l'adressage, la stabilité et la traduction sont des régulations de type post-transcriptionnel, les interactions ARN-protéines ont également un rôle-clé dans le domaine de la transcription. Effectivement, en addition aux capacités de codage, qui font de l'ADN et de l'ARN des supports de l'information génétique, la grande variabilité de structures et la flexibilité de l'ARN créent de nombreux sites uniques et le potentiel pour des régulations complexes. Les protéines se liant à l'ARN utilisent une bibliothèque de motifs structuraux pour reconnaître la séquence et la structure de leurs ARN cibles, ce qui conduit à un large éventail d'interactions, de labiles à stables. Ce manuscrit décrit nos travaux consistant à révéler les détails d'interactions RNA-protéines au niveau moléculaires, dans différents exemples concernant deux champs de la biologie cellulaire, la traduction et la transcription du code génétique. Nos cibles ont été choisies afin d'apporter des informations sur des interactions critiques pour la survie cellulaire et représentent différents modes de liaison de protéines à des ARN. Nous avions pour but d'utiliser la cristallographie aux rayons X, qui est une méthode fiable et reconnue pour la finesse des informations à l'échelle atomique que l'on peut en obtenir, et nous avons développé pour chaque cible un protocole de purification conduisant à une préparation homogène et cristallisable. Nous décrivons également les divers tests biophysiques et biochimiques ayant été utilisés pour caractériser nos échantillons
In the cell, RNA-protein interactions are fundamental to many processes involved in the regulation of gene expression, including pre-mRNA splicing, polyadenylation, editing, transport, cytoplasmic targeting, mRNA turnove and translation. In addition to these post-transcriptional processes, RNA-prote in interactions may also play a key rôle in transcription. Indeed, in addition to its coding capacity, which makes both DNA and RNA recipients of the genetic message, the high variability and conformationnal flexibility of RNA structure creates a number of unique binding sites and the potential for complex regulation by RNA binding proteins. These use a large Iibrary of structural modules in order to recognize RNAs in a combination of sequence- or structure-dependent ways, leading to a wide range of transient to more stable interactions. This manuscript describes our endeavour to reveal the details of RNAprotein interactions at the molecular level in several examples taken in two different fields of cell biology, transcription and translation. Our targets were chosen to better understand the molecular foundation of interactions critical for the cell survival, and represent different binding modes ofproteins to RNA. Aiming to use X-ray crystallography, a well-accepted and reliable mean to analyze recognition details at atomic resolution, we developed for each target a purification protocolleading to homogeneous preparations that were used for crystallization and subjected to various anai}'ses, including functional assays and biophysical characterization

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Fischer, Tiffany Brink. "A structural and energetic description of protein-protein interactions in atomic detail." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4775.

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Here, we present the program QContacts, which implements Voronoi polyhedra to determine atomic and residue contacts across the interface of a protein-protein interaction. While QContacts also describes hydrogen bonds, ionic pair and salt bridge interactions, we focus on QContactsÃ¢ÂÂ identification of atomic contacts in a protein interface compared against the current methods. Initially, we investigated in detail the differences between QContacts, radial cutoff and Change in Solvent Accessible Surface Area (delta-SASA) methods in identifying pair-wise contacts across the binding interface. The results were assessed based on a set of 71 double cycle mutants. QContacts excelled at identifying knob-in-hole contacts. QContacts, closest atom radial cutoff and the delta-SASA methods performed well at picking out direct contacts; however, QContacts was the most accurate in excluding false positives. The significance of the differences identified between QContacts and previous methods was assessed using pair-wise contact frequencies in a broader set of 592 protein interfaces. The inaccuracies introduced by commonly used radial cutoff methods were found to produce misleading bias in the residue frequencies. This bias could compromise pair-wise potentials that are based on such frequencies. Here we show that QContacts provides a more accurate description of protein interfaces at atomic resolution than other currently available methods. QContacts is available in a web-based form at http://tsailab.tamu.edu/qcons (Fischer et al., 2006).

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Jarrige, Domitille. "Déchiffrer le "code OPR" pour une meilleure compréhension du rôle physiologique des protéines OPR." Electronic Thesis or Diss., Sorbonne université, 2019. http://www.theses.fr/2019SORUS632.

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À la suite de l’endosymbiose, le génome chloroplastique a rétréci et dépend maintenant du génome nucléaire pour son expression. Chez Chlamydomonas reinhardtii, les protéines Octotricopeptide repeat (OPR), codées dans le noyau, contrôlent l’expression d’ARNm chloroplastiques spécifiques. La répétition OPR est un motif dégénéré de 38 acides aminés, qui forme un tandem d’hélices α antiparallèles qui lient l’ARN. Une répétition OPR est prédite pour interagir avec un nucléotide spécifique grâce à des résidus variables à des positions précises. La succession de répétitions permet aux protéines OPR de se lier à une séquence donnée. En partant d’un « code OPR » théorique, j’ai cherché à étudier cette spécificité de reconnaissance. J’ai mute in vivo les cibles chloroplastiques de facteurs OPR pour empêcher l’interaction OPR/ARN, puis j’ai tenté de la restaurer en mutant les résidus conférant la spécificité dans les répétitions correspondantes. Étonnamment, les interactions OPR/ARN sont très résilientes, ce qui a complétement changé notre vision de ces interactions in vivo. Des études fonctionnelles complémentaires que j’ai réalisées sur les facteurs OPR MDB1 and MTHI1 ont révélé que l’expression des gènes chloroplastiques dépend probablement de systèmes de facteurs nucléaires. En coopérant ces facteurs auraient une affinité combinée plus forte et seraient ainsi plus résilients
Following endosymbiosis, the chloroplast genome shrunk and became reliant on the host genome for its expression. In Chlamydomonas reinhardtii, Octotricopeptide repeat proteins (OPR), encoded in the nucleus, control the expression of a specific organellar mRNA. The OPR repeat is a degenerate motif of 38 amino-acids, folding into a tandem of antiparallel α-helices which can bind to RNA. An individual OPR repeat is predicted to interact with one given nucleotide thanks to specificity-conferring residues at defined positions within the repeat. OPR proteins contain tracks of successive OPR motifs, thus they can bind to a specific RNA “target” sequence and act on it. I aimed to study this specificity, called the “OPR code”, starting with a draft code based on known OPR protein/mRNA couples. I mutated in vivo the chloroplast targets of some OPR factors to disrupt the OPR/RNA interaction, and then tried to restore it by mutating the specificity-conferring residues in the corresponding repeats. Surprisingly, OPR/RNA interactions seem very resilient, challenging our view of how the specificity is established in vivo. Complementary functional studies that I performed on the OPR factors MDB1 and MTHI1 revealed that chloroplast gene expression might rely on complex networks of nuclear factors. By cooperating those putative systems would be both more specific and more resilient

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Li, Yi. "Study of Arnt-interacting proteins on Arnt-dependent signaling pathways." Scholarly Commons, 2006. https://scholarlycommons.pacific.edu/uop_etds/2786.

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In an effort to better understand the Ah receptor nuclear translocator (Arnt)-dependent signaling mechanisms, we employed a phage display system to identify Arnt-interacting peptides. Human liver cDNA library was utilized to screen for Arnt-interacting peptides using an Arnt construct fused to thioredoxin (TH-ArntCΔ418). Two clones, namely Ainp1 and Ainp2 (Arnt-interacting peptide), were identified and subsequently characterized. Ainp2 interacted with TH-ArntCΔ418 in the GST pull-down, TALON co-precipitation, and mammalian two-hybrid assays. Northern blot results revealed that Ainp2 is predominantly expressed in human liver. The putative full-length Ainp2 cDNA sequence was subsequently cloned using RACE PCR. Endogenous expression of Ainp2 was found in Jurkat cells and human fetal/adult liver medleys. Results from the transient transfection studies using a DRE- or ERE-driven reporter plasmid and the real-time QPCR experiments examining the endogenous CYP1A1 or GREB-1 expression demonstrated that Ainp2 enhances the 3MC-induced AhR signaling pathway in HepG2 cells, while suppresses the E2-induced ER signaling pathway in MCF-7 cells. These results suggested that Ainp2 plays a role in the Arnt-dependent signaling pathways. The suppressive effect of Ainp2 in the ER signaling pathway was not observed in Arnt-knockdown cells. Additionally, co-precipitation data showed that Ainp2 did not interact with ER α and ER β, suggesting that Ainp2 suppresses the ER signaling via an Arnt-mediated mechanism. The phage display technique also revealed another potential Arnt-interacting peptide Ainp1, which contains an open reading frame of 58 amino acids. The GST pull-down and mammalian two-hybrid assays showed that Ainp1 interacts with TH-ArntCΔ418. Northern blot results demonstrated that Ainp1 is ubiquitously present in all the tested tissues, including brain, placenta, skeletal muscle, heart, kidney, pancreas, liver, lung, spleen, and colon.

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Takeuchi, Akiko Krol Alain Allmang-Cura Christine. "RNA-protein interaction in the selenoprotein synthesis machinery." Strasbourg : Université de Strasbourg, 2009. http://eprints-scd-ulp.u-strasbg.fr:8080/1133/01/TAKEUCHI_Akiko_2009.pdf.

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Thèse de doctorat : Sciences du Vivant. Aspects moléculaire et cellulaire de la Biologie : Strasbourg : 2009.
Thèse soutenue sur un ensemble de travaux. Titre provenant de l'écran-titre. Bibliogr. 11 p.

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Takeuchi, Akiko. "RNA-protein interaction in the selenoprotein synthesis machinery." Strasbourg, 2009. http://www.theses.fr/2009STRA6054.

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La sélénocystéine est incorporée co-traductionnellement dans les sélénoprotéines en réponse à un codon UGA habituellement l’un des 3 codons stop. La protéine SBP2 joue un rôle majeur dans ce mécanisme de recodage en se liant à une structure en tige-boucle (SECIS) située dans la région 3’UTR de l’ARNm des sélénoprotéines. Nous avons isolé et caractérisé fonctionnellement SBP2 de Drosophila melanogaster. Par comparison avec SBP2 humaine, nous avons identifié un domaine de liaison à l’ARN additionnel essentiel à la liaison au SECIS et à la sous-unité ribosomique 60S et permettant une sélectivité structurale du SECIS. Des prédictions structurales et des analyses biophysiques ont établi que SBP2 était une protéine globalement désordonnée ou “Intrinsically Disordered Protein” qui ne se replie qu’en présence de partenaires. Enfin, nous avons établi que l’assemblage des mRNP de sélénoprotéines faisait appel à des facteurs communs et présentait de multiples similarités avec celui des sn/snoRNP
The 21st amino acid selenocysteine is encoded by a UGA codon that usually signifies translational termination. Selenoprotein synthesis therefore requires specialized factors. Among these is SBP2 that binds the SECIS, a stem-loop structure in the 3’UTR of selenoprotein mRNAs. In structural analyses of SBP2, we isolated and functionally characterized Drosophila melanogaster SBP2. By comparing it with human SBP2, we identified an additional RNA binding domain that is essential for SECIS and 60S ribosomal subunit binding, and also enables SECIS structure selectivity. In addition, computational and biophysical analyses established that SBP2 is globally unfolded, supporting our hypothesis that SBP2 is an Intrinsically Disordered Protein and becomes folded in the presence of partners yet to be identified. Finally, we searched for potential partners of SBP2 and our results showed that the molecular assembly of selenoprotein mRNPs has many similarities with that of sn/snoRNPs

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Mendez, Giraldez Raul. "Critical assessment of predicted interactions at atomic resolution." Doctoral thesis, Universite Libre de Bruxelles, 2007. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210664.

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Molecular Biology has allowed the characterization and manipulation of the molecules of life in the wet lab. Also the structures of those macromolecules are being continuously elucidated. During the last decades of the past century, there was an increasing interest to study how the different genes are organized into different organisms (‘genomes’) and how those genes are expressed into proteins to achieve their functions. Currently the sequences for many genes over several genomes have been determined. In parallel, the efforts to have the structure of the proteins coded by those genes go on. However it is experimentally much harder to obtain the structure of a protein, rather than just its sequence. For this reason, the number of protein structures available in databases is an order of magnitude or so lower than protein sequences. Furthermore, in order to understand how living organisms work at molecular level we need the information about the interaction of those proteins. Elucidating the structure of protein macromolecular assemblies is still more difficult. To that end, the use of computers to predict the structure of these complexes has gained interest over the last decades.

The main subject of this thesis is the evaluation of current available computational methods to predict protein – protein interactions and build an atomic model of the complex. The core of the thesis is the evaluation protocol I have developed at Service de Conformation des Macromolécules Biologiques et de Bioinformatique, Université Libre de Bruxelles, and its computer implementation. This method has been massively used to evaluate the results on blind protein – protein interaction prediction in the context of the world-wide experiment CAPRI, which have been thoroughly reviewed in several publications [1-3]. In this experiment the structure of a protein complex (‘the target’) had to be modeled starting from the coordinates of the isolated molecules, prior to the release of the structure of the complex (this is commonly referred as ‘docking’).

The assessment protocol let us compute some parameters to rank docking models according to their quality, into 3 main categories: ‘Highly Accurate’, ‘Medium Accurate’, ‘Acceptable’ and ‘Incorrect’. The efficiency of our evaluation and ranking is clearly shown, even for borderline cases between categories. The correlation of the ranking parameters is analyzed further. In the same section where the evaluation protocol is presented, the ranking participants give to their predictions is also studied, since often, good solutions are not easily recognized among the pool of computer generated decoys.

An overview of the CAPRI results made per target structure and per participant regarding the computational method they used and the difficulty of the complex. Also in CAPRI there is a new ongoing experiment about scoring previously and anonymously generated models by other participants (the ‘Scoring’ experiment). Its promising results are also analyzed, in respect of the original CAPRI experiment. The Scoring experiment was a step towards the use of combine methods to predict the structure of protein – protein complexes. We discuss here its possible application to predict the structure of protein complexes, from a clustering study on the different results.

In the last chapter of the thesis, I present the preliminary results of an ongoing study on the conformational changes in protein structures upon complexation, as those rearrangements pose serious limitations to current computational methods predicting the structure protein complexes. Protein structures are classified according to the magnitude of its conformational re-arrangement and the involvement of interfaces and particular secondary structure elements is discussed. At the end of the chapter, some guidelines and future work is proposed to complete the survey.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished

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Books on the topic "ArnA Protein"

Roterman-Konieczna, Irena, ed. Identification of Ligand Binding Site and Protein-Protein Interaction Area. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-5285-6.

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L, Hatfield Dolph, Lee Byeong J, and Pirtle Robert M, eds. Transfer RNA in protein synthesis. Boca Raton: CRC Press, 1992.

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Måns, Ehrenberg, ed. Structural aspects of protein synthesis. 2nd ed. New Jersey: World Scientific, 2013.

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Structural aspects of protein synthesis. Singapore: World Scientific, 2005.

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N, Khan Masood, and Findlay John W. A, eds. Ligand-binding assays: Development, validation, and implementation in the drug development arena. Hoboken, N.J: Wiley, 2009.

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Reynolds, Lindsey. DNA binding and structural studies of truncated forms of the AreA protein from Aspergillus nidulans. Portsmouth: University of Portsmouth, Dept. of Cell and Molecular Biology, 1998.

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S, Eggleston D., Prescott C. D, Pearson N. D. 1962-, and SmithKline Beecham Pharmaceuticals Research Symposia (8th : 1997 : Robinson College, Cambridge), eds. The many faces of RNA. San Diego, CA: Academic Press, 1998.

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N, Khan Masood, and Findlay John W. A, eds. Ligand-binding assays: Development, validation, and implementation in the drug development arena. Hoboken, N.J: Wiley, 2010.

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Matt, Werner, and Woods Isa, eds. Bay Area underground: Photos of protests and social movements, 2008-2012. Berkeley, Calif: Thought Pub., 2013.

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1952-, Baud Michiel, and Rutten Rosanne, eds. Popular intellectuals and social movements: Framing protest in Asia, Africa, and Latin America. Cambridge: Cambridge University Press, 2004.

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Book chapters on the topic "ArnA Protein"

Marchewka, Damian, Wiktor Jurkowski, Mateusz Banach, and Irena Roterman-Konieczna. "Prediction of Protein-Protein Binding Interfaces." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 105–33. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_6.

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Chemelle, Julie-Anne, Emmmanuel Bettler, Christophe Combet, Raphaël Terreux, Christophe Geourjon, and Gilbert Deléage. "SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 1–23. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_1.

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Huang, Bingding. "Identification of Pockets on Protein Surface to Predict Protein–Ligand Binding Sites." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 25–39. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_2.

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Banach, Mateusz, Leszek Konieczny, and Irena Roterman-Konieczna. "Can the Structure of the Hydrophobic Core Determine the Complexation Site?" In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 41–54. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_3.

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Alejster, Paweł, Mateusz Banach, Wiktor Jurkowski, Damian Marchewka, and Irena Roterman-Konieczna. "Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 55–86. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_4.

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Janin, Joël. "Docking Predictions of Protein-Protein Interactions and Their Assessment: The CAPRI Experiment." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 87–104. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_5.

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Belloum, Adam S. Z., Reginald Cushing, Spiros Koulouzis, Vladimir Korkhov, Dmitry Vasunin, Victor Guevara-Masis, Zhiming Zhao, and Marian Bubak. "Support for Cooperative Experiments in e-Science: From Scientific Workflows to Knowledge Sharing." In Identification of Ligand Binding Site and Protein-Protein Interaction Area, 135–59. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5285-6_7.

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Zolkiewski, Michal, and Hui-Chuan Wu. "Emerging Area: TorsinA, a Novel ATP-Dependent Factor Linked to Dystonia." In Protein Chaperones and Protection from Neurodegenerative Diseases, 359–83. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118063903.ch11.

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Yong, K. P., K. S. Sim, H. Y. Ting, W. K. Lim, K. L. Mok, and A. H. M. Yatim. "Latex Glove Protein Estimation Using Maximum Minimum Area Variation." In IFMBE Proceedings, 682–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-21729-6_166.

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Suckling, Keith E. "Enzymology and protein chemistry in the wider area of biology." In Enzyme Chemistry, 352–73. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-1832-0_9.

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Conference papers on the topic "ArnA Protein"

Chu, Benjamin, Dean Ho, Hyeseung Lee, Karen Kuo, and Carlo Montemagno. "Protein-Functionalized Proton Exchange Membranes." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46018.

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Protein-functionalized biomimetic membranes, based upon a triblock copolymer simulating a natural lipid bilayer in a single chain, serves as a core technology for applications in bioenergetics. Monolayers of block copolymer, which simulates the hydrophilic-hydrophobic-hydrophilic chain of a natural cell membrane, can be formed by Langmuir-Blodgett (LB) deposition and provides a favorable environment for protein refolding. Large-scale membrane formation is achieved using LB deposition on a variety of substrates, such as gold, quartz, silicon, and Nafion®. We have successfully inserted membrane proteins, such as the light-activated proton pump, bacteriorhodopsin (BR) and the pH/voltage-gateable porin, Outermembrane Protein F (OmpF), into large-area LB monolayers. We have also established sustained protein functionality in films through the measurement of light-activated proton transport.

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Ho, D., B. Chu, H. Lee, K. Kuo, and C. D. Montemagno. "Fabrication of Hybrid Bionanodevices Based on Coupled Protein Functionality." In ASME 2004 3rd Integrated Nanosystems Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/nano2004-46012.

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Block copolymer-based membrane technology represents a versatile class of nanoscale materials in which biomolecules, such as membrane proteins, can be reconstituted. Among its many advantages over conventional lipid-based membrane systems, block copolymers can mimic natural cell biomembrane environments in a single chain, enabling large-area membrane fabrication using methods like Langmuir-Blodgett deposition, or spontaneous protein-functionalized nanovesicle formation. Based on this unique membrane property, a wide variety of membrane proteins possessing unique functionalities including pH/voltage gatable porosity, photon-activated proton pumping, and gradient-dependent production of electricity have been successfully inserted into these biomimetic systems.

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Edmiston, Paul L., Laurie L. Wood, John E. Lee, and S. Scott Saavedra. "Molecular Orientation in Protein Films Deposited on Substrates Coated with Langmuir-Blodgett and Self-Assembled Monolayers." In Organic Thin Films for Photonic Applications. Washington, D.C.: Optica Publishing Group, 1997. http://dx.doi.org/10.1364/otfa.1997.the.9.

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Formation and characterization of organic thin film assemblies intended for use in biomolecular devices, such as biosensors, is currently a very active area of research. We have been investigating techniques for creating macroscopically ordered protein films formed by covalent bonding between a unique site on the protein and an appropriately derivatized substrate surface. Assemblies consisting of heme proteins immobilized on substrates coated with self-assembled monolayers and Langmuir-Blodgett are being examined. Macroscopic film order is probed using a combination of total internal reflectance fluorescence and planar integrated optical waveguide-attenuated total reflection spectroscopies, from which the orientation distribution of heme tilt angles in the protein film is determined.

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Babaei, Elham, Samuel Mathew, Mirali Seyed Shariatdoust, Demelza Wright, Laura Itzhaki, Ivet Bahar, Shang-Hua Yang, and Reuven Gordon. "Analysis of single unmodified proteins and their interactions with nanoaperture optical tweezers: PR65 case study." In Optical Manipulation and Its Applications. Washington, D.C.: Optica Publishing Group, 2023. http://dx.doi.org/10.1364/oma.2023.am3d.5.

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There is a new class of technologies emerging for observing unmodified proteins in action and at the single molecule level. This presentation will give an introduction to the double-nanohole nanoaperture optical tweezer approach and overview the developments from ours and other groups working in the area. Particularly, I will focus on the analysis of the A sub-unit of protein phosphatase PP2A: PR65.

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Dyr, J. E., H. Fořtová, J. Suttnar, Z. Vorlová, and F. Kornalxk. "ISOLATION OF HUMAN PROTEIN C AND ITS SNAKE VENOM ACTIVATORS BY ION EXCHANGE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644896.

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Simple and efficient methods for the purification of functionally active clotting factors in good yields are still missing. The purpose of the present study was to design a chromatographic procedure for the isolation of protein C (PC) and its snake venom activators taking advantage of the high resolution, high speed of analysis and sensitive detection of high performance liquid chromatography.PC was purified from a human plasma concentrate containing vitamin Kdependent proteins using a Mono Q anion exchanger. Electrophoretic titration curve was used to serve as a guide for finding approximate conditions for separations. Elution profiles for vitamin K-dependent proteins were determined. PC was assayed by both immunological and functional methods. For the latter methods, protein C activators (PCA) were isolated from snake venoms of Agkistrodon c, -contortrix (ACC) and Agkistrodon c, mokasen.Both venoms (pooled samples)were found to contain at least two different PCA. AtpH 6.5> by simple one step procedures either an acidic PCA (on a Mono Q) or a basic PCA (on a Mono S) was isolated. A great diversity was found among venom samples from specimen originating from a small geographic area near Philadelphia (USA). In six out of the nine analysed ACC venoms only the acidic PCA was present.In conclusion, an optimum separationof protein C onthe Mono Q at pH 8.0 was proposed (usual recovery 90-95%).Optimalization of the salt gradient was considerably more effective than the pH changes. A great individual variability has to be taken into account when snake venoms are used as a source of protein C activators.

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Sharifimehr, Shahrzad, Supratim Ghosh, and Ramaswami Sammynaiken. "Development of Protein–polyphenol Conjugates via Free Radical Grafting Method: Evaluation of Physicochemical and Functional Properties." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/bpzg5215.

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Lipid oxidation is a common phenomenon in emulsions that can be controlled by different techniques. Since proteins are beneficial emulsifiers but with low antioxidant ability, they are used in combination with an antioxidant compound such as polyphenols. Strong interaction between the protein and the polyphenol makes this combination more effective. In this study, soluble fraction of faba protein concentrate (FPC) was conjugated with tannic acid via the free radical grafting, and the structural and functional characteristics of the conjugates were determined in comparison with the mixture of the protein and tannic acid, and the pure protein. After dialysis, the amount of protein and polyphenol from the conjugated materials was significantly reduced, indicating that the unreacted peptides and polyphenol left the solutions. The reduction of the free amino and thiol groups in the protein specified the establishment of a strong interaction between the protein and tannic acid remaining in the solution. Moreover, the conjugate showed high ABTS, hydroxyl radical scavenging activity and ferric reducing power than the protein alone. As the purpose of making the conjugate was to be used as a multilayer film around the oil droplets, the film formation ability of the conjugates was investigated using Langmuir-Blodgett technique. Depending on the size of the trough and the nature of the compounds being used, the concentration and surface pressure required to form a strong film will vary. All samples showed an extended gas state of the film that changed abruptly and directly into a solid state below a critical surface area. Such LB film of the protein-tannic acid conjugate will be used to test its free radical scavenging ability so that its ability to prevent lipid oxidation in emulsions can be predicted.

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Schoenborn, Benno P. "Area detectors for neutron protein crystallography." In San Diego '92, edited by John M. Carpenter, David B. Cline, Richard C. Lanza, and David F. R. Mildner. SPIE, 1993. http://dx.doi.org/10.1117/12.138663.

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Radt, Benno, Jesper Serbin, Björn I. Lange, Reginald Birngruber, and Gereon Hüttmann. "Laser generated micro- and nanoeffects: inactivation of proteins coupled to gold nanoparticles with nano- and picosecond pulses." In European Conference on Biomedical Optics. Washington, D.C.: Optica Publishing Group, 2001. http://dx.doi.org/10.1364/ecbo.2001.4433_16.

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Background: Protein denaturation in the fs-ns time regime is of fundamental interest for high precision applications in laser tissue interaction. Conjugates of colloidal gold coupled to proteins are presented as a model system for investigating ultrafast protein denaturation. It is expected that irradiation of such conjugates in tissue using pico-up to nanosecond laser pulses could result in effects with a spatial confinement in the regime of single macromolecules up to organelles. Materials and Methods: Experiments were done with bovine intestinal alkaline phosphatase (aP) coupled to 15 nm colloidal Gold. This complex was irradiated at 527 nm/ 532 nm with a variable number of pico- and nanosecond pulses. The radiant exposure per pulse was varied from 2 to 50 mJ/cm2 in the case of the picosecond pulses and 10 to 500 mJ/cm2 in the case of the nanosecond pulses. Denaturation was detected as a loss of protein function with the help of the fluorescence substrate 4MUP. Results and Discussion: Irradiation did result in a steady decrease of the aP activity with increasing radiant exposures and increasing number of pulses. Inactivations up to 80% using 35 ps pulses at 527 nm with 50 mJ/cm2 and a complete inactivation induced by 16 ns pulses at 450 mJ/cm2 are discussed. The induced temperature in the particles and the surrounding water was calculated using Mie’s formulas for the absorption of the nanometer gold particles and an analytical solution of the for heat diffusion. The calculated temperatures suggest that picosecond pulses heat a molecular scaled area whereas nanosecond pulses could be used for targeting larger cellular compartiments. It is difficult to identify one of the possible damage mechanisms, i.e. thermal denaturation or formation of micro bubbles, from the dependance of the inactivation on pulse energy and number of applied pulses. Therefore experiments are needed to further elucidate the damage mechanisms. The observed inactivation dependencies on applied energy and radiant power can not be explained with one or two photon photochemistry. In conclusion, denaturing proteins irreversibly via nanoabsorbers using pico-/ nanosecond laser pulses is possible. The expected confinement of the heat to the nanoabsorbers suggests that denaturation of proteins with nanometer precision could be possible with this approach. However, the mechanism of protein inactivation, which is part of present investigations, is crucial for the precision of such nanoeffects.

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Kaugarenia, Nastassia, Sophie Beaubier, Erwann Durand, François Lesage, Xavier Framboisier, Arnaud Aymes, Pierre Villeneuve, and Romain Kapel. "Optimization of Potent Mineral Chelating Peptides Production from Rapeseed Meal Proteins Proteolysis and Peptide Characterizations." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/ougk6662.

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Preventing lipid oxidation and microbial spoilage are both major concerns in sectors such as food and cosmetic industries. Biopeptides, arouse great interest to substitute synthetic antioxidants. Some plant proteins, like 2S rapeseed albumins are known presenting antimicrobial properties. In this context, we aimed to valorize total rapeseed meal proteins with controlled enzymatic proteolysis to generate mineral chelating peptides from the 11S globulins fraction while keeping intact the albumins fraction. To do so, screening of proteases on total rapeseed protein isolate was implemented highlighting a globulin-selective hydrolysis with Prolyve®. Ultrafiltration was then used to purified albumins and enrich the peptide fraction. The fraction obtained showed a noteworthy metal chelating activity. Then, the selected proteolysis was optimized in order to maximize the albumins purity and yield. For that, enzymatic mechanism identification in a wide operating conditions area was led to define the DoE. Then, simulation of hydrolysis kinetics was driven to predict protein fractions concentration at any time and any set of operation conditions. The obtained models were implemented in a genetic-evolutionary algorithm to generate the Pareto Front and Domain, presenting the targeted economical compromises. One solution was chosen and the identified corresponding operating conditions proved the metal chelating activity conservation (EC50 = 247 ± 27 µg) for three times faster production at the same enzyme cost. Finally, peptide activity was investigated in oil-in-water emulsion systems and compared with EDTA. Results showed that peptides could be as effective as EDTA to avoid primary and secondary lipid oxidation products formation.This work demonstrates an original total valorization of both rapeseed meal proteins in food applications. First, antioxidant peptides produced from the globulin fraction, could be used as food preservative in oil-in-water emulsion systems, but also as preventing agents for micronutrient deficiencies. And, the purified albumin fraction could be used to prevent microbial spoilage.

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Ross, Stephan W., Istvan Naday, Miklos Kanyo, Mary L. Westbrook, Edwin M. Westbrook, Walter C. Phillips, Martin J. Stanton, and Robert A. Street. "Amorphous silicon area detectors for protein crystallography." In IS&T/SPIE's Symposium on Electronic Imaging: Science & Technology, edited by Morley M. Blouke. SPIE, 1995. http://dx.doi.org/10.1117/12.206516.

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Reports on the topic "ArnA Protein"

Matthews, Lisa, Guanming Wu, Robin Haw, Timothy Brunson, Nasim Sanati, Solomon Shorser, Deidre Beavers, Patrick Conley, Lincoln Stein, and Peter D'Eustachio. Illuminating Dark Proteins using Reactome Pathways. Reactome, October 2022. http://dx.doi.org/10.3180/poster/20221027matthews.

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Diseases are often the consequence of proteins or protein complexes that are non-functional or that function improperly. An active area of research has focused on the identification of molecules that can interact with defective proteins and restore their function. While 22% percent of human proteins are estimated to be druggable, less than fifteen percent are targeted by FDA-approved drugs, and the vast majority of untargeted proteins are understudied or so-called "dark" proteins. Elucidation of the function of these dark proteins, particularly those in commonly drug-targeted protein families, may offer therapeutic opportunities for many diseases. Reactome is the most comprehensive, open-access pathway knowledgebase covering 2585 pathways and including 14246 reactions, 11088 proteins, 13984 complexes, and 1093 drugs. Placing dark proteins in the context of Reactome pathways provides a framework of reference for these proteins facilitating the generation of hypotheses for experimental biologists to develop targeted experiments, unravel the potential functions of these proteins, and then design drugs to manipulate them. To this end, we have trained a random forest with 106 protein/gene pairwise features collected from multiple resources to predict functional interactions between dark proteins and proteins annotated in Reactome and then developed three scores to measure the interactions between dark proteins and Reactome pathways based on enrichment analysis and fuzzy logic simulations. Literature evidence via manual checking and systematic NLP-based analysis support predicted interacting pathways for dark proteins. To visualize dark proteins in the context of Reactome pathways, we have also developed a new website, idg.reactome.org, by extending the Reactome web application with new features illustrating these proteins together with tissue-specific protein and gene expression levels and drug interactions.

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Ghanim, Murad, Joe Cicero, Judith K. Brown, and Henryk Czosnek. Dissection of Whitefly-geminivirus Interactions at the Transcriptomic, Proteomic and Cellular Levels. United States Department of Agriculture, February 2010. http://dx.doi.org/10.32747/2010.7592654.bard.

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Our project focuses on gene expression and proteomics of the whitefly Bemisia tabaci (Gennadius) species complex in relation to the internal anatomy and localization of expressed genes and virions in the whitefly vector, which poses a major constraint to vegetable and fiber production in Israel and the USA. While many biological parameters are known for begomovirus transmission, nothing is known about vector proteins involved in the specific interactions between begomoviruses and their whitefly vectors. Identifying such proteins is expected to lead to the design of novel control methods that interfere with whitefly-mediated begomovirus transmission. The project objectives were to: 1) Perform gene expression analyses using microarrays to study the response of whiteflies (B, Q and A biotypes) to the acquisition of begomoviruses (Tomato yellow leaf curl (TYLCV) and Squash leaf curl (SLCV). 2) Construct a whitefly proteome from whole whiteflies and dissected organs after begomovirus acquisition. 3) Validate gene expression by q-RTPCR and sub-cellular localization of candidate ESTs identified in microarray and proteomic analyses. 4) Verify functionality of candidate ESTs using an RNAi approach, and to link these datasets to overall functional whitefly anatomical studies. During the first and second years biological experiments with TYLCV and SLCV acquisition and transmission were completed to verify the suitable parameters for sample collection for microarray experiments. The parameters were generally found to be similar to previously published results by our groups and others. Samples from whole whiteflies and midguts of the B, A and Q biotypes that acquired TYLCV and SLCV were collected in both the US and Israel and hybridized to B. tabaci microarray. The data we analyzed, candidate genes that respond to both viruses in the three tested biotypes were identified and their expression that included quantitative real-time PCR and co-localization was verified for HSP70 by the Israeli group. In addition, experiments were undertaken to employ in situ hybridization to localize several candidate genes (in progress) using an oligonucleotide probe to the primary endosymbiont as a positive control. A proteome and corresponding transcriptome to enable more effective protein identification of adult whiteflies was constructed by the US group. Further validation of the transmission route of begomoviruses, mainly SLCV and the involvement of the digestive and salivary systems was investigated (Cicero and Brown). Due to time and budget constraints the RNAi-mediated silencing objective to verify gene function was not accomplished as anticipated. HSP70, a strong candidate protein that showed over-expression after TYLCV and SLCV acquisition and retention by B. tabaci, and co-localization with TYLCV in the midgut, was further studies. Besides this protein, our joint research resulted in the identification of many intriguing candidate genes and proteins that will be followed up by additional experiments during our future research. To identify these proteins it was necessary to increase the number and breadth of whitefly ESTs substantially and so whitefly cDNAs from various libraries made during the project were sequenced (Sanger, 454). As a result, the proteome annotation (ID) was far more successful than in the initial attempt to identify proteins using Uniprot or translated insect ESTs from public databases. The extent of homology shared by insects in different orders was surprisingly low, underscoring the imperative need for genome and transcriptome sequencing of homopteran insects. Having increased the number of EST from the original usable 5500 generated several years ago to >600,000 (this project+NCBI data mining), we have identified about one fifth of the whitefly proteome using these new resources. Also we have created a database that links all identified whitefly proteins to the PAVEdb-ESTs in the database, resulting in a useful dataset to which additional ESTS will be added. We are optimistic about the prospect of linking the proteome ID results to the transcriptome database to enable our own and other labs the opportunity to functionally annotate not only genes and proteins involved in our area of interest (whitefly mediated transmission) but for the plethora of other functionalities that will emerge from mining and functionally annotating other key genes and gene families in whitefly metabolism, development, among others. This joint grant has resulted in the identification of numerous candidate proteins involved in begomovirus transmission by B. tabaci. A next major step will be to capitalize on validated genes/proteins to develop approaches to interfere with the virus transmission.

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Wender, Stephen, Dale Tupa, Elena Guardincerri, and Yuri Batygin. Development of Low-Power H- Proton Beam Capability in Area-A. Office of Scientific and Technical Information (OSTI), March 2023. http://dx.doi.org/10.2172/1968183.

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Dickman, Martin B., and Oded Yarden. Regulation of Early Events in Hyphal Elongation, Branching and Differentiation of Filamentous Fungi. United States Department of Agriculture, 2000. http://dx.doi.org/10.32747/2000.7580674.bard.

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In filamentous fungi, hyphal elongation, branching and morphogenesis are in many cases the key to successful saprophytic and pathogenic fungal proliferation. The understanding of the fungal morphogenetic response to environmental cues is in its infancy. Studies concerning the regulation of fungal growth and development (some of which have been obtained by the participating collaborators in this project) point to the fact that ser/thr protein kinases and phosphatases are (i) involved in the regulation of such processes and (ii) share common structural and functional features between saprophytes and pathogens. It is our objective to combine a pharmaceutical and a genetic approach in order to identify, characterize and functionally dissect some of the regulatory factors involved in hyphal growth, branching and differentiation. Using an immunohistochemical approach, a ser/thr protein kinase involved in hyphal elongation in both Neurospora crassa and Colletotrichum trifolii has been localized in order to identify the physical arena of regulation of hyphal elongation. The analysis of additional kinases and phosphatases (e.g. Protein kinase C, cAMP-dependent kinase, lipid-activated protein kinase, components of the type 2A protein phosphatase) as well as a RAS-related gene (an additional key participant in signal transduction) has been performed. In order to succeed in advancing the goals of this project, we have taken advantage of available elongation/branching mutants in N. crassa and continuously combined the accumulated information obtained while studying the two systems in order to dissect the elements involved in these processes. The various inhibitors/effectors analyzed can serve as a basis for modification to be used as anti-fungal compounds. Understanding the regulation of hyphal proliferation is a key requirement for identifying novel target points for either curbing fungal growth (as in the case of pathogenesis) or affecting growth patterns in various biotechnological processes. The major objective of our joint project was to advance our understanding of regulation of hyphal growth, especially during early events of fungal germination. Towards achieving this goal, we have coupled the analysis of a genetically tractable organism (N. crassa) with a plant pathogen o economic importance (C. trifolii). As the project progressed we believe that the results obtained have provided a reinforcement to our basic approach which called for combining the two fungal systems for a joint research project. On the one hand, we feel that much of the advance made was possible due to the amenability of N. crassa to genetic manipulations. The relevance of some of the initial findings obtained in Neurospora have been proven to be relevant to the plant pathogen while unique features of the pathogen have been identified in Colletotrichum. Most of the results obtained from this research project have been published. Thus, the main volume of this report is comprised of the relevant publications describing the research and results obtained.

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Chamovitz, Daniel A., and Xing-Wang Deng. Developmental Regulation and Light Signal Transduction in Plants: The Fus5 Subunit of the Cop9 Signalosome. United States Department of Agriculture, September 2003. http://dx.doi.org/10.32747/2003.7586531.bard.

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Plants adjust their growth and development in a manner optimal for the prevailing light conditions. The molecular mechanisms by which light signals are transduced and integrated with other environmental and developmental signals are an area of intense research. (Batschauer, 1999; Quail, 2002) One paradigm emerging from this work is the interconnectedness of discrete physiological responses at the biochemical level, for instance, between auxin and light signaling (Colon-Carmona et al., 2000; Schwechheimer and Deng, 2001; Tian and Reed, 1999) and between light signaling and plant pathogen interactions (Azevedo et al., 2002; Liu et al., 2002). The COP9 signalosome (CSN) protein complex has a central role in the light control of plant development. Arabidopsis mutants that lack this complex develop photomorphogenically even in the absence of light signals (reviewed in (Karniol and Chamovitz, 2000; Schwechheimer and Deng, 2001). Thus the CSN was hypothesized to be a master repressor of photomorphogenesis in darkness, and light acts to bypass or eliminate this repression. However, the CSN regulates more than just photomorphogenesis as all mutants lacking this complex die near the end of seedling development. Moreover, an essentially identical complex was subsequently discovered in animals and yeast, organisms whose development is not light responsive, exemplifying how plant science can lead the way to exciting discoveries in biomedical model species (Chamovitz and Deng, 1995; Freilich et al., 1999; Maytal-Kivity et al., 2002; Mundt et al., 1999; Seeger et al., 1998; Wei et al., 1998). Our long-term objective is to determine mechanistically how the CSN controls plant development. We previously that this complex contains eight subunits (Karniol et al., 1998; Serino et al., 1999) and that the 27 ilia subunit is encoded by the FUS5/CSN7 locus (Karniol et al., 1999). The CSN7 subunit also has a role extraneous to the COP9 signalosome, and differential kinase activity has been implicated in regulating CSN7 and the COP9 signalosome (Karniol et al., 1999). In the present research, we further analyzed CSN7, both in terms of interacting proteins and in terms of kinases that act on CSN7. Furthermore we completed our analysis of the CSN in Arabidopsis by analyzing the remaining subunits. Outline of Original Objectives and Subsequent Modifications The general goal of the proposed research was to study the CSN7 (FUS5) subunit of the COP9 signalosome. To this end we specifically intended to: 1. Identify the residues of CSN7 that are phosphorylated. 2. Monitor the phosphorylation of CSN7 under different environmental conditions and under different genetic backgrounds. 3. Generate transgenic plants with altered CSN7 phosphorylation sites. 4. Purify CSN7 kinase from cauliflower. 5. Clone the Arabidopsis cDNA encoding CSN7 kinase 6. Isolate and characterize additional CSN7 interacting proteins. 7. Characterize the interaction of CSN7 and the COP9 signalosome with the HY5-COP1 transcriptional complex. Throughout the course of the research, emphasis shifted from studying CSN7 phosphorylation (Goals 1-3), to studying the CSN7 kinase (Goal 4 and 5), an in depth analysis of CSN7 interactions (Goal 6), and the study of additional CSN subunits. Goal 7 was also abandoned as no data was found to support this interaction.

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Gui, Feng, and Sean Brossia. PR-186-073502-R01 Large-Scale Cathodic Disbondment Testing for Coal Tar Enamel(CTE). Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), September 2010. http://dx.doi.org/10.55274/r0010646.

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Corrosion protection of installed transmission pipelines is mainly achieved by isolating the pipeline from the environment through the use of applied coatings. In areas where coating damage (e.g., holidays) exist, cathodic protection (CP), often by impressed current, is used to protect any bare areas. The amount of current output required for CP tends to increase as the damaged area (e.g. holidays, cracks) progresses over time. Although CP is necessary to protect any bare areas, it can also enhance coating disbondment. Likewise, the extent of cathodic disbondment (CD) could increase as the current from the rectifier is augmented to compensate for the extended damage. In the United Stated approximately 50 % of the transmission pipelines are coated with coal tar enamel (CTE), many of which have been in service for more than 50 years. The extent of the coating damage (in the form of holidays, open disbondments, cracks and tears) requires incremental increases in CP levels to be applied over time. The objective of this work was to investigate the effect of CP levels on the growth of CD of CTE coated pipes. The CD extent at under protected CP levels was investigated as well. Additionally, the effect of surface contaminant (chloride) on CD of the CTE coated pipes was evaluated.

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Bradford, Kent, Haim Nerson, Gregory Wellbaum, and Menahem Edelstein. Environmental, Developmental and Physiological Determinants of Curcurbit Seed Quality. United States Department of Agriculture, October 1998. http://dx.doi.org/10.32747/1998.7695837.bard.

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Environmental, developmental, physiological and biochemical determinants of cucurbit seed quality were investigated in field and laboratory experiments. The major factor influencing seed quality is seed maturity at harvest, with both immature and overmature seeds exhibiting reduced quality. Planting density and fruit load per plant can be manipulated to maximize seed yield per unit area without adversely affecting seed quality. Seeds harvested at optimal maturity will have the greatest germination vigor and will maintain quality longer during storage. Seed priming can improve germination rates and uniformity, but can reduce storage life. Tissues enclosing the embryo (the endosperm envelope and seed coat) are involved in regulating germination. The seed coat (testa) may restrict oxygen diffusion to the embryo in some muskmelon genotypes. Weakening of the endosperm envelope is associated with radicle emergence. Callose deposition in the endosperm envelope results in semipermeability. Defense proteins such as chitinase are also present in the endosperm. Numerous genes were identified that are expressed specifically in association with germination, but their functions are yet to be elucidated. These studies have provided guidelines for producing and harvesting cucurbit seeds for maximum yield and quality and have identified physiological and biochemical processes contributing to seed germination vigor.

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Vavrin, John L., Ghassan K. Al-Chaar, Eric L. Kreiger, Michael P. Case, Brandy N. Diggs, Richard J. Liesen, Justine Yu, et al. Automated Construction of Expeditionary Structures (ACES) : Energy Modeling. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39641.

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The need to conduct complex operations over time results in U.S. forces remaining in deployed locations for long periods. In such cases, more sustainable facilities are required to better accommodate and protect forward deployed forces. Current efforts to develop safer, more sustainable operating facilities for contingency bases involve construction activities that redesign the types and characteris-tics of the structures constructed, reduce the resources required to build, and reduce resources needed to operate and maintain the com-pleted facilities. The Automated Construction of Expeditionary Structures (ACES) project was undertaken to develop the capability to “print” custom-designed expeditionary structures on demand, in the field, using locally available materials with the minimum number of personnel. This work investigated large-scale automated “additive construction” (i.e., 3D printing with concrete) for construction applications. This document, which documents ACES energy and modeling, is one of four technical reports, each of which details a major area of the ACES research project, its research processes, and associated results, including: System Requirements, Construction, and Performance; Energy and Modeling; Materials and Testing; Architectural and Structural Analysis.

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Diggs, Brandy N., Richard J. Liesen, Michael P. Case, Sameer Hamoush, and Ahmed C. Megri. Automated Construction of Expeditionary Structures (ACES) : Energy Modeling. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39759.

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Al-Chaar, Ghassan K., Peter B. Stynoski, Todd S. Rushing, Lynette A. Barna, Jedadiah F. Burroughs, John L. Vavrin, and Michael P. Case. Automated Construction of Expeditionary Structures (ACES) : Materials and Testing. Engineer Research and Development Center (U.S.), February 2021. http://dx.doi.org/10.21079/11681/39721.

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Complex military operations often result in U.S. forces remaining at deployed locations for long periods. In such cases, more sustaina-ble facilities are required to better accommodate and protect forward-deployed forces. Current efforts to develop safer, more sustaina-ble operating facilities for contingency bases involve construction activities that require a redesign of the types and characteristics of the structures constructed, that reduce the resources required to build, and that decrease the resources needed to operate and maintain the completed facilities. The Automated Construction of Expeditionary Structures (ACES) project was undertaken to develop the capa-bility to “print” custom-designed expeditionary structures on demand, in the field, using locally available materials with the minimum number of personnel. This work investigated large-scale automated “additive construction” (i.e., 3D printing with concrete) for con-struction applications. This report, which documents ACES materials and testing, is one of four technical reports, each of which details a major area of the ACES research project, its research processes, and its associated results. There major areas include System Require-ments, Construction, and Performance; Energy and Modeling; Materials and Testing; Architectural and Structural Analysis.

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