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Relevant bibliographies by topics / SF2 helicase

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Academic literature on the topic 'SF2 helicase'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "SF2 helicase"

1

Gilman, Benjamin, Pilar Tijerina, and Rick Russell. "Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs." Biochemical Society Transactions 45, no. 6 (November 17, 2017): 1313–21. http://dx.doi.org/10.1042/bst20170095.

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Structured RNAs and RNA–protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how their distinct mechanisms enable DEAD-box proteins to disrupt RNA base pairs on the surfaces of structured RNAs and RNPs, while some DEAH-box proteins are adept at disrupting base pairs in the interior of RNPs. Proteins from these families use these mechanisms to chaperone folding and promote rearrangements of structured RNAs and RNPs, including the spliceosome, and may use related mechanisms to maintain cellular messenger RNAs in unfolded or partially unfolded conformations.

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Seybert, Anja, Leonie C. van Dinten, Eric J. Snijder, and John Ziebuhr. "Biochemical Characterization of the Equine Arteritis Virus Helicase Suggests a Close Functional Relationship between Arterivirus and Coronavirus Helicases." Journal of Virology 74, no. 20 (October 15, 2000): 9586–93. http://dx.doi.org/10.1128/jvi.74.20.9586-9593.2000.

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ABSTRACT The arterivirus equine arteritis virus nonstructural protein 10 (nsp10) has previously been predicted to contain a Zn finger structure linked to a superfamily 1 (SF1) helicase domain. A recombinant form of nsp10, MBP-nsp10, was produced in Escherichia coli as a fusion protein with the maltose-binding protein. The protein was partially purified by affinity chromatography and shown to have ATPase activity that was strongly stimulated by poly(dT), poly(U), and poly(dA) but not by poly(G). The protein also had both RNA and DNA duplex-unwinding activities that required the presence of 5′ single-stranded regions on the partial-duplex substrates, indicating a 5′-to-3′ polarity in the unwinding reaction. Results of this study suggest a close functional relationship between the arterivirus nsp10 and the coronavirus helicase, for which NTPase and duplex-unwinding activities were recently demonstrated. In a number of biochemical properties, both arterivirus and coronavirus SF1 helicases differ significantly from the previously characterized RNA virus SF1 and SF2 enzymes. Thus, the combined data strongly support the idea that nidovirus helicases may represent a separate group of RNA virus-encoded helicases with distinct properties.

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Fan, Li, and Kevin T. DuPrez. "XPB: An unconventional SF2 DNA helicase." Progress in Biophysics and Molecular Biology 117, no. 2-3 (March 2015): 174–81. http://dx.doi.org/10.1016/j.pbiomolbio.2014.12.005.

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4

Woodman, Isabel L., and Edward L. Bolt. "Molecular biology of Hel308 helicase in archaea." Biochemical Society Transactions 37, no. 1 (January 20, 2009): 74–78. http://dx.doi.org/10.1042/bst0370074.

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Hel308 is an SF2 (superfamily 2) helicase with clear homologues in metazoans and archaea, but not in fungi or bacteria. Evidence from biochemistry and genetics implicates Hel308 in remodelling compromised replication forks. In the last 4 years, significant advances have been made in understanding the biochemistry of archaeal Hel308, most recently through atomic structures from cren- and eury-archaea. These are good templates for SF2 helicase function more generally, highlighting co-ordinated actions of accessory domains around RecA folds. We review the emerging molecular biology of Hel308, drawing together ideas of how it may contribute to genome stability through the control of recombination, with reference to paradigms developed in bacteria.

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Du Pont, Kelly E., Russell B. Davidson, Martin McCullagh, and Brian J. Geiss. "Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft." Journal of Biological Chemistry 295, no. 6 (December 30, 2019): 1551–64. http://dx.doi.org/10.1074/jbc.ra119.011922.

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The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential “communication hub” for this energy transduction pathway. To investigate the role of Motif V in this process, here we combined molecular dynamics, biochemistry, and virology approaches. We tested Motif V mutations in both the replicon and recombinant protein systems to investigate viral genome replication, RNA-binding affinity, ATP hydrolysis activity, and helicase-mediated unwinding activity. We found that the T407A and S411A substitutions in NS3 reduce viral replication and increase the helicase-unwinding turnover rates by 1.7- and 3.5-fold, respectively, suggesting that flaviviruses may use suboptimal NS3 helicase activity for optimal genome replication. Additionally, we used simulations of each mutant to probe structural changes within NS3 caused by each mutation. These simulations indicate that Motif V controls communication between the ATP-binding pocket and the helical gate. These results help define the linkage between ATP hydrolysis and helicase activities within NS3 and provide insight into the biophysical mechanisms for ATPase-driven NS3 helicase function.

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Moukhtar, Mirna, Wafi Chaar, Ziad Abdel-Razzak, Mohamad Khalil, Samir Taha, and Hala Chamieh. "ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea." Computers in Biology and Medicine 80 (January 2017): 185–89. http://dx.doi.org/10.1016/j.compbiomed.2016.12.004.

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7

Kawaoka, Jane, Eckhard Jankowsky, and Anna Marie Pyle. "Backbone tracking by the SF2 helicase NPH-II." Nature Structural & Molecular Biology 11, no. 6 (May 16, 2004): 526–30. http://dx.doi.org/10.1038/nsmb771.

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Halgasova, Nora, Radka Matuskova, Daniel Kraus, Adela Tkacova, Lenka Balusikova, and Gabriela Bukovska. "Gp41, a superfamily SF2 helicase from bacteriophage BFK20." Virus Research 245 (February 2018): 7–16. http://dx.doi.org/10.1016/j.virusres.2017.12.005.

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Romero, Zachary J., Stefanie H. Chen, Thomas Armstrong, Elizabeth A. Wood, Antoine van Oijen, Andrew Robinson, and Michael M. Cox. "Resolving Toxic DNA repair intermediates in every E. coli replication cycle: critical roles for RecG, Uup and RadD." Nucleic Acids Research 48, no. 15 (July 9, 2020): 8445–60. http://dx.doi.org/10.1093/nar/gkaa579.

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Abstract DNA lesions or other barriers frequently compromise replisome progress. The SF2 helicase RecG is a key enzyme in the processing of postreplication gaps or regressed forks in Escherichia coli. A deletion of the recG gene renders cells highly sensitive to a range of DNA damaging agents. Here, we demonstrate that RecG function is at least partially complemented by another SF2 helicase, RadD. A ΔrecGΔradD double mutant exhibits an almost complete growth defect, even in the absence of stress. Suppressors appear quickly, primarily mutations that compromise priA helicase function or recA promoter mutations that reduce recA expression. Deletions of uup (encoding the UvrA-like ABC system Uup), recO, or recF also suppress the ΔrecGΔradD growth phenotype. RadD and RecG appear to avoid toxic situations in DNA metabolism, either resolving or preventing the appearance of DNA repair intermediates produced by RecA or RecA-independent template switching at stalled forks or postreplication gaps. Barriers to replisome progress that require intervention by RadD or RecG occur in virtually every replication cycle. The results highlight the importance of the RadD protein for general chromosome maintenance and repair. They also implicate Uup as a new modulator of RecG function.

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10

Hajj, Mirna, Petra Langendijk-Genevaux, Manon Batista, Yves Quentin, Sébastien Laurent, Régine Capeyrou, Ziad Abdel-Razzak, et al. "Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase." Biomolecules 11, no. 7 (June 26, 2021): 950. http://dx.doi.org/10.3390/biom11070950.

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Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA metabolism. To investigate this, we performed in-depth phylogenomic analyses to report the classification and taxonomic distribution of Lhr-type proteins in Archaea, and to better understand their relationship with bacterial Lhr. Furthermore, with the goal of envisioning the role(s) of aLhr2 in Thermococcales cells, we deciphered the enzymatic activities of aLhr2 from Thermococcus barophilus (Tbar). We showed that Tbar-aLhr2 is a DNA/RNA helicase with a significant annealing activity that is involved in processes dependent on DNA and RNA transactions.

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Book chapters on the topic "SF2 helicase"

1

Beyer, David C., Mohamed Karem Ghoneim, and Maria Spies. "Structure and Mechanisms of SF2 DNA Helicases." In Advances in Experimental Medicine and Biology, 47–73. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-5037-5_3.

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Raney, Kevin D., Alicia K. Byrd, and Suja Aarattuthodiyil. "Structure and Mechanisms of SF1 DNA Helicases." In Advances in Experimental Medicine and Biology, 17–46. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-5037-5_2.

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Raney, Kevin D., Alicia K. Byrd, and Suja Aarattuthodiyil. "Erratum to: Structure and Mechanisms of SF1 DNA Helicases." In Advances in Experimental Medicine and Biology, E1. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-5037-5_14.

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Hajj, Mirna, Samar El-Hamaoui, Manon Batista, Marie Bouvier, Ziad Abdel-Razzak, Béatrice Clouet d'Orval, and Hala Chamieh. "Archaeal SF1 and SF2 Helicases." In Helicases from All Domains of Life, 1–18. Elsevier, 2019. http://dx.doi.org/10.1016/b978-0-12-814685-9.00001-4.

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Antony, E., and T. M. Lohman. "Nonhexameric SF1 DNA Helicases/Translocases." In Encyclopedia of Biological Chemistry, 261–65. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-378630-2.00393-5.

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Antony, Edwin, and Timothy M. Lohman. "Nonhexameric SF1 DNA Helicases/Translocases." In Reference Module in Life Sciences. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-819460-7.00039-6.

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7

Lohman, Timothy M., John Hsieh, Nasib K. Maluf, Wei Cheng, Aaron L. Lucius, Christopher J. Fischer, Katherine M. Brendza, Sergey Korolev, and Gabriel Waksman. "DNA helicases, motors that move along nucleic acids: Lessons from the SF1 helicase superfamily." In Energy Coupling and Molecular Motors, 303—VII. Elsevier, 2003. http://dx.doi.org/10.1016/s1874-6047(04)80008-8.

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8

Guo, Rong, and Anna Marie Pyle. "Monitoring functional RNA binding of RNA-dependent ATPase enzymes such as SF2 helicases using RNA dependent ATPase assays: A RIG-I case study." In Methods in Enzymology. Elsevier, 2022. http://dx.doi.org/10.1016/bs.mie.2022.03.064.

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Conference papers on the topic "SF2 helicase"

1

Li, Siyuan, Aimin Zhang, Songtao Ji, and Yanlin Li. "Numerical Simulation of Thermo-Hydraulic Characteristics of 7-Pin SFR Test Fuel Bundle With Variable-Pitch Helical Wire." In 2021 28th International Conference on Nuclear Engineering. American Society of Mechanical Engineers, 2021. http://dx.doi.org/10.1115/icone28-64755.

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Abstract This paper is focused on the applicability of variable-pitch helical wire in a 7-pin SFR test fuel bundle by using CFD method. The differences between the variable-pitch helical wire scheme and the even-pitch helical wire scheme in the pressure loss, velocity, temperature field of the test fuel bundle are compared and analyzed. The simulation results show that it is reliable to carry out the thermo-hydraulic analysis of SFR test fuel bundle by using CFD numerical simulation method. The helical wire mixing ability to the coolant and the pressure drop is influenced by the helical wire pitch. Compared with the even-pitch helical wire scheme on fuel rod surface, the variable-pitch helical wire doesn’t drastically change the flow field structure while the pitch changes, but gradually increases its mixing ability to the coolant along the axial direction, which is more conducive to accelerating balance the thermal inhomogeneity and inhomogeneity ratio of the coolant, solve the problem of temperature rise caused by the coolant congestion on the contact structure between the helical wire and fuel rod surface. The stronger the mixing ability of the helical wire to the coolant, the more effective it is to lower the maximum temperature of the coolant. The application of the variable-pitch helical wire can well match the demand of the coolant for thermal and hydraulic needs, and the safety and economy of the assembly can be correspondingly improved.

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2

Kim, Dehee, Jaehyuk Eoh, and Tae-Ho Lee. "An Optimal Design Approach for the Decay Heat Removal System in PGSFR." In ASME 2014 4th Joint US-European Fluids Engineering Division Summer Meeting collocated with the ASME 2014 12th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2014. http://dx.doi.org/10.1115/fedsm2014-21971.

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Sodium-cooled Fast Reactor (SFR) is one of the generation IV (Gen-IV) nuclear reactors. Prototype Gen-IV SFR (PGSFR) is a SFR being developed in Korea Atomic Energy Research Institute (KAERI). Decay Heat Removal System (DHRS) in the PGSFR has a safety function to make shutdown the reactor under abnormal plant conditions. Single DHRS loop consists of sodium-to-sodium decay heat exchanger (DHX), helical-tube sodium-to-air heat exchanger (AHX) or finned-tube sodium-to-air heat exchanger (FHX), loop piping, and expansion vessel. The DHXs are located in the cold pool and the AHXs and FHXs are installed in the upper region of the reactor building. The DHRS loop is a closed loop and liquid sodium coolant circulates inside the loop by natural circulation head for passive system and by forced circulation head for active system. There are three independent heat transport paths in the DHRS, i.e., the DHX shell-side sodium flow path, the DHRS sodium loop path through the piping, the AHX shell-side air flow path. To design the components of the DHRS and to determine its configuration, key design parameters such as mass flow rates in each path, inlet/outlet temperatures of primary and secondary flow sides of each heat exchanger should be determined reflecting on the coupled heat transfer mechanism over the heat transfer paths. The number of design parameters is larger than that of the governing equations and optimization approach is required for compact design of the DHRS. Therefore, a genetic algorithm has been implemented to decide the optimal design point. The one-dimensional system design code which can predict heat transfer rates and pressure losses through the heat exchangers and piping calculates the objective function and the genetic algorithm code searches a global optimal point. In this paper, we present a design methodology of the DHRS, for which we have developed a system code coupling a one-dimensional system code with a genetic algorithm code. As a design result, the DHRS layouts and the sizing of the heat exchangers have been shown.

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3

Ohno, Jun, Takero Mori, Masutake Sotsu, and Hiroaki Ohira. "Multidimensional Thermal-Hydraulic Analysis on Natural Circulation Behavior in Ex-Vessel Fuel Storage Tank of MONJU." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-64037.

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Since the accident of the Fukushima Dai-ichi Nuclear Power Station, analysis evaluations for stress tests have been conducted on the prototype fast breed reactor MONJU. In these evaluations, it has been necessary to evaluate the plant characteristics including the Ex-Vessel fuel Storage Tank (EVST) under the severe accident conditions such as station blackout. The EVST is a coaxial cylindrical tank to store spent fuels (SFs) stored in fuel transfer pots (FTPs) until the radioactivity enough decays. It is able to store 252 fuel transfer pots in the rotating rack and cool them by internal natural circulation of sodium coolant under both the severe accident and normal operation. The heat produced by SFs removed by the helical cooling coils installed in the annular space. Evaluations of natural circulation in the EVST have been performed with a one-dimensional flow-network code. However, it would be difficult to predict its behavior exactly, because it would include multidimensional flow such as local natural convection. Then, in order to clarify the natural circulation behavior and multidimensional effects and evaluate appropriateness of this flow network model, we have performed a thermal-hydraulic analysis using a three-dimensional model which has high resolution meshes and the almost same geometry as the actual equipment. This model makes it possible to take into account the following multidimensional phenomena, the heat distribution of the FTPs, the mixing in plenums, the bypass flow through the flow holes and the other geometry effects. In this study, we have used a commercial computational thermal-hydraulics code, “FrontFlow/red”. As a result of steady analyses, we have confirmed the following: The coolant temperature in the plenums is almost uniform and its difference is in a few degrees. The influence of the flow holes is also limited because its flow rate is relatively low to main flow rate. On the other hand, pressure loss at supporting plates of the rotating rack, which are main causes of flow resistance in the EVST, is larger than the case without multidimensional effects because of the natural convection concentrated in the high temperature region near heated FTPs. The result leads to our presumption that the flow network model of the EVST is almost appropriate. It should be noted that flow resistance coefficient of the supporting plates or the heat transfer center of the cooling coils should be set to conservative for the safety analysis on the EVST.

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