Статті в журналах: "Loop unwinding"

1

Nicolau, Alexandru. "Loop quantization: A generalized loop unwinding technique." Journal of Parallel and Distributed Computing 5, no. 5 (October 1988): 568–86. http://dx.doi.org/10.1016/0743-7315(88)90013-5.

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2

Blagosklonny, MV. "Unwinding the loop of Bcl-2 phosphorylation." Leukemia 15, no. 6 (June 2001): 869–74. http://dx.doi.org/10.1038/sj.leu.2402134.

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3

Yang, Tao, Lin Yin Liu, and Wei Rong Dai. "Dynamic Characteristics and Double Closed Loop Control Method of Warping Machine." Advanced Materials Research 627 (December 2012): 428–34. http://dx.doi.org/10.4028/www.scientific.net/amr.627.428.

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The warp tension is caused by the speed difference between rewinding shaft and unwinding shaft. The mathematical dynamic models of the system are established based on rewinding shaft and unwinding shaft．Double closed loop are included in the control system. One is winding speed closed loop which could control warping speed according to the requirements; the other is tension closed loop which ensure the yarn tension to be kept constant. The experimental results show the curve of tension enters a stable state after two or three times’ oscillation. The accuracy of the yarn tension has reached ±3%.

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4

Howard, Jamieson A. L., Stephane Delmas, Ivana Ivančić-Baće, and Edward L. Bolt. "Helicase dissociation and annealing of RNA-DNA hybrids by Escherichia coli Cas3 protein." Biochemical Journal 439, no. 1 (September 14, 2011): 85–95. http://dx.doi.org/10.1042/bj20110901.

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CRISPR (clustered regularly interspaced short palindromic repeat)/Cas (CRISPR-associated) is a nucleic acid processing system in bacteria and archaea that interacts with mobile genetic elements. CRISPR DNA and RNA sequences are processed by Cas proteins: in Escherichia coli K-12, one CRISPR locus links to eight cas genes (cas1, 2, 3 and casABCDE), whose protein products promote protection against phage. In the present paper, we report that purified E. coli Cas3 catalyses ATP-independent annealing of RNA with DNA forming R-loops, hybrids of RNA base-paired into duplex DNA. ATP abolishes Cas3 R-loop formation and instead powers Cas3 helicase unwinding of the invading RNA strand of a model R-loop substrate. R-loop formation by Cas3 requires magnesium as a co-factor and is inactivated by mutagenesis of a conserved amino acid motif. Cells expressing the mutant Cas3 protein are more sensitive to plaque formation by the phage λvir. A complex of CasABCDE (‘Cascade’) also promotes R-loop formation and we discuss possible overlapping roles of Cas3 and Cascade in E. coli, and the apparently antagonistic roles of Cas3 catalysing RNA–DNA annealing and ATP-dependent helicase unwinding.

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5

Ivanov, Ivan E., Addison V. Wright, Joshua C. Cofsky, Kevin D. Palacio Aris, Jennifer A. Doudna, and Zev Bryant. "Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling." Proceedings of the National Academy of Sciences 117, no. 11 (March 2, 2020): 5853–60. http://dx.doi.org/10.1073/pnas.1913445117.

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The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

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6

Dudas, Kathleen C., and Kenneth N. Kreuzer. "UvsW Protein Regulates Bacteriophage T4 Origin-Dependent Replication by Unwinding R-Loops." Molecular and Cellular Biology 21, no. 8 (April 15, 2001): 2706–15. http://dx.doi.org/10.1128/mcb.21.8.2706-2715.2001.

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ABSTRACT The UvsW protein of bacteriophage T4 is involved in many aspects of phage DNA metabolism, including repair, recombination, and recombination-dependent replication. UvsW has also been implicated in the repression of origin-dependent replication at late times of infection, when UvsW is normally synthesized. Two well-characterized T4 origins, ori(uvsY) andori(34), are believed to initiate replication through an R-loop mechanism. Here we provide both in vivo and in vitro evidence that UvsW is an RNA-DNA helicase that catalyzes the dissociation of RNA from origin R-loops. Two-dimensional gel analyses show that the replicative intermediates formed atori(uvsY) persist longer in a uvsWmutant infection than in a wild-type infection. In addition, the inappropriate early expression of UvsW protein results in the loss of these replicative intermediates. Using a synthetic origin R-loop, we also demonstrate that purified UvsW functions as a helicase that efficiently dissociates RNA from R-loops. These and previous results from a number of studies provide strong evidence that UvsW is a molecular switch that allows T4 replication to progress from a mode that initiates from R-loops at origins to a mode that initiates from D-loops formed by recombination proteins.

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7

Wei, Ze Ding, Han Chao Xu, and Hui Su. "A Constant Tension Control Device of Mechanical Feedback." Applied Mechanics and Materials 397-400 (September 2013): 409–12. http://dx.doi.org/10.4028/www.scientific.net/amm.397-400.409.

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A constant tension control device of mechanical feedback is designed for the tension adjustment between the unwinding and rewinding of the flexible material, and the structure and size of the device are given. According to torque balance principle and based on purely mechanical structure, this device can control tension by adjusting the frictional force between the brake block and the unwinding wheel. The tension of controlling the unwinding and rewinding of the flexible material is analyzed, and then the control method of the tension is illustrated. Compared with the common closed loop control devices with tension feedback, the structure of the proposed device is simpler, and it has a stronger capacity of resisting disturbance in complicated electromagnetic environment.

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8

Guo, Yong, Shen-Min Song, and Xue-Hui Li. "Backstepping sliding mode control for formation flying spacecraft." Aircraft Engineering and Aerospace Technology 90, no. 1 (January 2, 2018): 56–64. http://dx.doi.org/10.1108/aeat-08-2014-0129.

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Purpose This paper aims to investigate the problem of finite-time consensus tracking control without unwinding for formation flying spacecraft in the presence of external disturbances. Design/methodology/approach Two distributed finite-time controllers are developed using the backstepping sliding mode. The first robust controller can compensate for external disturbances with known bounds, and the second one can compensate for external disturbances with unknown bounds. Findings Because the controllers are designed on the basis of rotation matrix, which represents the set of attitudes both globally and uniquely, the system can overcome the drawback of unwinding, which results in extra fuel consumption. Through introducing a novel virtual angular velocity, exchange of control signals between neighboring spacecraft becomes unnecessary, and it is able to reduce the communication burden. Practical implications The two robust controllers can deal with unwinding that may result in fuel consumption by traveling a long distance before returning to a desired attitude when the closed-loop system is close to the desired attitude equilibrium. Originality/value Two finite-time controllers without unwinding are proposed for formation flying spacecraft by using backstepping sliding mode. Furthermore, exchange of control signals between neighboring spacecraft is unnecessary.

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9

Baggs, Eric, and Lisa Warner. "Larp6 Regulates Collagen mRNA by Targeted Unwinding of a Conserved Stem‐Loop." FASEB Journal 34, S1 (April 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.09740.

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10

Manthei, Kelly A., Morgan C. Hill, Jordan E. Burke, Samuel E. Butcher, and James L. Keck. "Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases." Proceedings of the National Academy of Sciences 112, no. 14 (March 23, 2015): 4292–97. http://dx.doi.org/10.1073/pnas.1416746112.

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RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3′ single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.

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11

George, Biju, Rajrani Ruhel, Mohit Mazumder, Veerendra Kumar Sharma, Swatantra Kumar Jain, Samudrala Gourinath та Supriya Chakraborty. "Mutational analysis of the helicase domain of a replication initiator protein reveals critical roles of Lys 272 of the B′ motif and Lys 289 of the β-hairpin loop in geminivirus replication". Journal of General Virology 95, № 7 (1 липня 2014): 1591–602. http://dx.doi.org/10.1099/vir.0.064923-0.

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Replication initiator protein (Rep) is indispensable for rolling-circle replication of geminiviruses, a group of plant-infecting circular ssDNA viruses. However, the mechanism of DNA unwinding by circular ssDNA virus-encoded helicases is unknown. To understand geminivirus Rep function, we compared the sequence and secondary structure of Rep with those of bovine papillomavirus E1 and employed charged residue-to-alanine scanning mutagenesis to generate a set of single-substitution mutants in Walker A (K227), in Walker B (D261, 262), and within or adjacent to the B′ motif (K272, K286 and K289). All mutants were asymptomatic and viral accumulation could not be detected by Southern blotting in both tomato and N. benthamiana plants. Furthermore, the K272 and K289 mutants were deficient in DNA binding and unwinding. Biochemical studies and modelling data based on comparisons with the known structures of SF3 helicases suggest that the conserved lysine (K289) located in a predicted β-hairpin loop may interact with ssDNA, while lysine 272 in the B′ motif (K272) located on the outer surface of the protein is presumably involved in coupling ATP-induced conformational changes to DNA binding. To the best of our knowledge, this is the first time that the roles of the B′ motif and the adjacent β-hairpin loop in geminivirus replication have been elucidated.

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12

Sarek, Grzegorz, Jean-Baptiste Vannier, Stephanie Panier, John H. J. Petrini, and Simon J. Boulton. "TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding." Molecular Cell 57, no. 4 (February 2015): 622–35. http://dx.doi.org/10.1016/j.molcel.2014.12.024.

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13

Sarek, Grzegorz, Jean-Baptiste Vannier, Stephanie Panier, John H. J. Petrini, and Simon J. Boulton. "TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding." Molecular Cell 61, no. 5 (March 2016): 788–89. http://dx.doi.org/10.1016/j.molcel.2016.02.016.

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14

Nečasová, Ivona, Eliška Janoušková, Tomáš Klumpler, and Ctirad Hofr. "Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it." Nucleic Acids Research 45, no. 21 (September 13, 2017): 12170–80. http://dx.doi.org/10.1093/nar/gkx812.

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15

Nečasová, Ivona, Eliška Janoušková, Tomáš Klumpler, and Ctirad Hofr. "Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it." Nucleic Acids Research 45, no. 21 (October 11, 2017): 12599. http://dx.doi.org/10.1093/nar/gkx968.

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16

Harami, Gábor M., Yeonee Seol, Junghoon In, Veronika Ferencziová, Máté Martina, Máté Gyimesi, Kata Sarlós, et al. "Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination." Proceedings of the National Academy of Sciences 114, no. 4 (January 9, 2017): E466—E475. http://dx.doi.org/10.1073/pnas.1615439114.

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Cells must continuously repair inevitable DNA damage while avoiding the deleterious consequences of imprecise repair. Distinction between legitimate and illegitimate repair processes is thought to be achieved in part through differential recognition and processing of specific noncanonical DNA structures, although the mechanistic basis of discrimination remains poorly defined. Here, we show thatEscherichia coliRecQ, a central DNA recombination and repair enzyme, exhibits differential processing of DNA substrates based on their geometry and structure. Through single-molecule and ensemble biophysical experiments, we elucidate how the conserved domain architecture of RecQ supports geometry-dependent shuttling and directed processing of recombination-intermediate [displacement loop (D-loop)] substrates. Our study shows that these activities together suppress illegitimate recombination in vivo, whereas unregulated duplex unwinding is detrimental for recombination precision. Based on these results, we propose a mechanism through which RecQ helicases achieve recombination precision and efficiency.

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17

Lin, Min-Guan, Yi-Ching Li, and Chwan-Deng Hsiao. "Characterization of Streptococcus pneumoniae PriA helicase and its ATPase and unwinding activities in DNA replication restart." Biochemical Journal 477, no. 19 (October 16, 2020): 3911–22. http://dx.doi.org/10.1042/bcj20200269.

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DNA replication forks often encounter template DNA lesions that can stall their progression. The PriA-dependent pathway is the major replication restart mechanism in Gram-positive bacteria, and it requires several primosome proteins. Among them, PriA protein — a 3′ to 5′ superfamily-2 DNA helicase — is the key factor in recognizing DNA lesions and it also recruits other proteins. Here, we investigated the ATPase and helicase activities of Streptococcus pneumoniae PriA (SpPriA) through biochemical and kinetic analyses. By comparing various DNA substrates, we observed that SpPriA is unable to unwind duplex DNA with high GC content. We constructed a deletion mutant protein (SpPriAdeloop) from which the loop area of the DNA-binding domain of PriA had been removed. Functional assays on SpPriAdeloop revealed that the loop area is important in endowing DNA-binding properties on the helicase. We also show that the presence of DnaD loader protein is important for enhancing SpPriA ATPase and DNA unwinding activities.

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18

Jia, Zhihui, Liming Yan, Zhilin Ren, Lijie Wu, Jin Wang, Jing Guo, Litao Zheng, et al. "Delicate structural coordination of the Severe Acute Respiratory Syndrome coronavirus Nsp13 upon ATP hydrolysis." Nucleic Acids Research 47, no. 12 (May 27, 2019): 6538–50. http://dx.doi.org/10.1093/nar/gkz409.

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Abstract To date, an effective therapeutic treatment that confers strong attenuation toward coronaviruses (CoVs) remains elusive. Of all the potential drug targets, the helicase of CoVs is considered to be one of the most important. Here, we first present the structure of the full-length Nsp13 helicase of SARS-CoV (SARS-Nsp13) and investigate the structural coordination of its five domains and how these contribute to its translocation and unwinding activity. A translocation model is proposed for the Upf1-like helicase members according to three different structural conditions in solution characterized through H/D exchange assay, including substrate state (SARS-Nsp13-dsDNA bound with AMPPNP), transition state (bound with ADP-AlF4−) and product state (bound with ADP). We observed that the β19–β20 loop on the 1A domain is involved in unwinding process directly. Furthermore, we have shown that the RNA dependent RNA polymerase (RdRp), SARS-Nsp12, can enhance the helicase activity of SARS-Nsp13 through interacting with it directly. The interacting regions were identified and can be considered common across CoVs, which provides new insights into the Replication and Transcription Complex (RTC) of CoVs.

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19

Tan, Chao, Guodong Xu, Limin Dong, Han Zhao, Jun Li, and Sai Zhang. "Neural Network-Based Finite-Time Fault-Tolerant Control for Spacecraft without Unwinding." International Journal of Aerospace Engineering 2021 (February 23, 2021): 1–10. http://dx.doi.org/10.1155/2021/9269438.

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In this paper, we focus on solving the problems of inertia-free attitude tracking control for spacecraft subject to external disturbance, unknown inertial parameters, and actuator faults. The robust control architecture is designed by using the rotation matrix and neural networks. In the presence of external disturbance and parametric uncertainties, a fault-tolerant control (FTC) scheme synthesized with the minimum-learning-parameter (MLP) algorithm is proposed to improve the reliability of the system when unknown actuator faults occur. These methods are developed based on backstepping to ensure that finite-time convergence is achievable for the entire closed-loop system states with low computational complexity. The validity and advantage of the designed controllers are highlighted by using Lyapunov-based analysis. Finally, the simulation results demonstrate the satisfactory performance of the developed controllers.

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20

Register, J. C., and J. Griffith. "Direct visualization of RecA protein binding to and unwinding duplex DNA following the D-loop cycle." Journal of Biological Chemistry 263, no. 23 (August 1988): 11029–32. http://dx.doi.org/10.1016/s0021-9258(18)37911-0.

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21

Hamann, Florian, Lars C. Zimmerningkat, Robert A. Becker, Tim B. Garbers, Piotr Neumann, Jochen S. Hub, and Ralf Ficner. "The structure of Prp2 bound to RNA and ADP-BeF3−reveals structural features important for RNA unwinding by DEAH-box ATPases." Acta Crystallographica Section D Structural Biology 77, no. 4 (March 30, 2021): 496–509. http://dx.doi.org/10.1107/s2059798321001194.

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Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excisedviathe spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct ofChaetomium thermophilumPrp2 was crystallized in the presence of ADP-BeF3−and a poly-U12RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF3−- and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures.

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22

Paolini, Chantal, Raffaele De Francesco, and Paola Gallinari. "Enzymatic properties of hepatitis C virus NS3-associated helicase." Microbiology 81, no. 5 (May 1, 2000): 1335–45. http://dx.doi.org/10.1099/0022-1317-81-5-1335.

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The hepatitis C virus non-structural protein 3 (NS3) possesses a serine protease activity in the N-terminal one-third, whereas RNA-stimulated NTPase and helicase activities reside in the C-terminal portion. In this study, an N-terminal hexahistidine-tagged full-length NS3 polypeptide was expressed in Escherichia coli and purified to homogeneity by conventional chromatography. Detailed characterization of the helicase activity of NS3 is presented with regard to its binding and strand release activities on different RNA substrates. On RNA double-hybrid substrates, the enzyme was shown to perform unwinding activity starting from an internal ssRNA region of at least 3 nt and moving along the duplex in a 3′ to 5′ direction. In addition, data are presented suggesting that binding to ATP reduces the affinity of NS3 for ssRNA and increases its affinity for duplex RNA. Furthermore, we have ascertained the capacity of NS3 to specifically interact with and resolve the stem–loop RNA structure (SL I) within the 3′-terminal 46 bases of the viral genome. Finally, our analysis of NS3 processive unwinding under single cycle conditions by addition of heparin in both helicase and RNA-stimulated ATPase assays led to two conclusions: (i) NS3-associated helicase acts processively; (ii) most of the NS3 RNA-stimulated ATPase activity may not be directly coupled to translocation of the enzyme along the substrate RNA molecule.

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23

Felisberto-Rodrigues, Catarina, Jemima C. Thomas, Craig McAndrew, Yann-Vaï Le Bihan, Rosemary Burke, Paul Workman, and Rob L. M. van Montfort. "Structural and functional characterisation of human RNA helicase DHX8 provides insights into the mechanism of RNA-stimulated ADP release." Biochemical Journal 476, no. 18 (September 14, 2019): 2521–43. http://dx.doi.org/10.1042/bcj20190383.

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Abstract DHX8 is a crucial DEAH-box RNA helicase involved in splicing and required for the release of mature mRNA from the spliceosome. Here, we report the biochemical characterisation of full-length human DHX8 and the catalytically active helicase core DHX8Δ547, alongside crystal structures of DHX8Δ547 bound to ADP and a structure of DHX8Δ547 bound to poly(A)6 single-strand RNA. Our results reveal that DHX8 has an in vitro binding preference for adenine-rich RNA and that RNA binding triggers the release of ADP through significant conformational flexibility in the conserved DEAH-, P-loop and hook-turn motifs. We demonstrate the importance of R620 and both the hook-turn and hook-loop regions for DHX8 helicase activity and propose that the hook-turn acts as a gatekeeper to regulate the directional movement of the 3′ end of RNA through the RNA-binding channel. This study provides an in-depth understanding of the activity of DHX8 and contributes insights into the RNA-unwinding mechanisms of the DEAH-box helicase family.

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24

Sun, Yingjie, Evrim Atas, Lisa Lindqvist, Nahum Sonenberg, Jerry Pelletier, and Amit Meller. "The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase." Nucleic Acids Research 40, no. 13 (March 28, 2012): 6199–207. http://dx.doi.org/10.1093/nar/gks278.

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25

Lo, Chen-Yu, and Yang Gao. "DNA Polymerase-Parental DNA Interaction Is Essential for Helicase-Polymerase Coupling during Bacteriophage T7 DNA Replication." International Journal of Molecular Sciences 23, no. 3 (January 25, 2022): 1342. http://dx.doi.org/10.3390/ijms23031342.

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DNA helicase and polymerase work cooperatively at the replication fork to perform leading-strand DNA synthesis. It was believed that the helicase migrates to the forefront of the replication fork where it unwinds the duplex to provide templates for DNA polymerases. However, the molecular basis of the helicase-polymerase coupling is not fully understood. The recently elucidated T7 replisome structure suggests that the helicase and polymerase sandwich parental DNA and each enzyme pulls a daughter strand in opposite directions. Interestingly, the T7 polymerase, but not the helicase, carries the parental DNA with a positively charged cleft and stacks at the fork opening using a β-hairpin loop. Here, we created and characterized T7 polymerases each with a perturbed β-hairpin loop and positively charged cleft. Mutations on both structural elements significantly reduced the strand-displacement synthesis by T7 polymerase but had only a minor effect on DNA synthesis performed against a linear DNA substrate. Moreover, the aforementioned mutations eliminated synergistic helicase-polymerase binding and unwinding at the DNA fork and processive fork progressions. Thus, our data suggested that T7 polymerase plays a dominant role in helicase-polymerase coupling and replisome progression.

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26

Huang, Cheng, Yan Wang, and Xing-lin Chen. "Finite-time attitude tracking control of air bearing table for spacecraft rendezvous and docking." Proceedings of the Institution of Mechanical Engineers, Part G: Journal of Aerospace Engineering 232, no. 1 (September 30, 2016): 96–110. http://dx.doi.org/10.1177/0954410016671539.

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This paper studies the problem of attitude tracking control for spacecraft rendezvous and docking based on a physical ground simulation system. Two finite-time controllers based on quaternion are proposed by using a novel fast nonsingular terminal sliding mode surface associated with the adaptive control, the novel fast nonsingular terminal sliding mode surface not only contains the advantages of the fast nonsingular terminal sliding mode surface, but also can eliminate unwinding caused by the quaternion. The first controller, which is continuous and chattering-free, can compensate unknown constant external disturbances, while the second controller can both compensate parametric uncertainties and varying external disturbances with unknown bounds without chattering. Lyapunov theoretical analysis and simulation results show that the two controllers can make the closed-loop system errors converge to zero in finite time and guarantee the finite-time stability of the system.

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27

Wang, Zhiqiang, Haibao Nan, Tingna Shi, Qiang Geng, and Changliang Xia. "No-Tension Sensor Closed-Loop Control Method with Adaptive PI Parameters for Two-Motor Winding System." Mathematical Problems in Engineering 2018 (2018): 1–14. http://dx.doi.org/10.1155/2018/1851845.

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In a winding system, it is very important to control the tension precisely. Based on the process of rewinding and unwinding, a sensorless tension control method with PI parameters of adaptive speed controllers is proposed in this paper. According to the principle of torque balance, a tension observer is designed to replace the tension sensor, and the observed value instead of the measured value of tension is used as feedback. Then the measurement delay caused by tension sensor is reduced. For the time-variable inertia, Landau discrete-time recursive algorithm is used to estimate the inertias of the rewind and unwind motors. Moreover, the estimated inertias are used to adjust the PI parameters of the speed controllers. As the tension control system has the ability to adapt to the change of inertia, its dynamic performance is improved to some extent. In addition, the proposed sensorless tension control method is simple and easy to implement, which only uses the current and speed signals of the motors without any additional hardware needed. At last, the feasibility and effectiveness of the proposed method are verified by the experimental results.

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28

Watanabe, Satoshi, Manami Harayama, Shingo Kanemura, Roberto Sitia, and Kenji Inaba. "Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER–Golgi interface." Proceedings of the National Academy of Sciences 114, no. 16 (April 3, 2017): E3224—E3232. http://dx.doi.org/10.1073/pnas.1621426114.

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ERp44 retrieves some endoplasmic reticulum (ER)-resident enzymes and immature oligomers of secretory proteins from the Golgi. Association of ERp44 with its clients is regulated by pH-dependent mechanisms, but the molecular details are not fully understood. Here we report high-resolution crystal structures of human ERp44 at neutral and weakly acidic pH. These structures reveal key regions in the C-terminal tail (C tail) missing in the original crystal structure, including a regulatory histidine-rich region and a subsequent extended loop. The former region forms a short α-helix (α16), generating a histidine-clustered site (His cluster). At low pH, the three Trx-like domains of ERp44 (“a,” “b,” and “b′”) undergo significant rearrangements, likely induced by protonation of His157 located at the interface between the a and b domains. The α16-helix is partially unwound and the extended loop is disordered in weakly acidic conditions, probably due to electrostatic repulsion between the protonated histidines in the His cluster. Molecular dynamics simulations indicated that helix unwinding enhances the flexibility of the C tail, disrupting its normal hydrogen-bonding pattern. The observed pH-dependent conformational changes significantly enlarge the positively charged regions around the client-binding site of ERp44 at low pH. Mutational analyses showed that ERp44 forms mixed disulfides with specific cysteines residing on negatively charged loop regions of Ero1α. We propose that the protonation states of the essential histidines regulate the ERp44–client interaction by altering the C-tail dynamics and surface electrostatic potential of ERp44.

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29

Wu, Xianqing, and Minming Gu. "Adaptive control of the TORA system with partial state constraint." Transactions of the Institute of Measurement and Control 41, no. 4 (September 18, 2018): 1172–77. http://dx.doi.org/10.1177/0142331218794813.

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In this paper, we consider the problem of stabilization of a translational oscillator with a rotational actuator (TORA) system. In practical applications, TORA systems usually suffer from parametric uncertainties. Moreover, existing control methods for TORA systems cannot guarantee the rotational scope of the actuator and often lead to unwanted unwinding behaviour. To handle these issues, we present an adaptive control strategy for TORA systems with uncertain or unknown parameters, which is robust to parameter uncertainties and can guarantee that the rotational actuator rotates in a preset range. Specifically, a Lyapunov function is elegantly constructed on the basis of the nonlinear interaction between the translational oscillator and the eccentric rotational proof mass. Then an adaptive control method, along with an online estimation mechanism, is proposed straightforwardly and the stability of the closed-loop system is proven, invoking Lyapunov techniques and LaSalle’s invariance principle. Simulation results are provided to demonstrate the performance of the presented method.

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30

Xu, Kexin, Xianqing Wu, Miao Ma, and Yibo Zhang. "Energy-based output feedback control of the underactuated 2DTORA system with saturated inputs." Transactions of the Institute of Measurement and Control 42, no. 14 (July 2, 2020): 2822–29. http://dx.doi.org/10.1177/0142331220933475.

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In this paper, we consider the control issues of the two-dimensional translational oscillator with rotational actuator (2DTORA) system, which has two translational carts and one rotational rotor. An output feedback controller for the 2DTORA system is proposed, which can prevent the unwinding behaviour. In addition, the velocity signal unavailability and actuator saturation are taken into account, simultaneously. In particular, the dynamics of the 2DTORA system are given first. On the basis of the passivity and control objectives of the 2DTORA system, an elaborate Lyapunov function is constructed. Then, based on the introduced Lyapunov function, a novel output feedback control method is proposed straightforwardly for the 2DTORA system. Lyapunov theory and LaSalle’s invariance principle are utilized to analyse the stability of the closed-loop system and the convergence of the states. Finally, simulation results are provided to illustrate the excellent control performance of the proposed controller in comparison with the existing method.

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31

Makhov, A. M., P. E. Boehmer, I. R. Lehman, and J. D. Griffith. "The herpes simplex virus type 1 origin-binding protein carries out origin specific DNA unwinding and forms stem-loop structures." EMBO Journal 15, no. 7 (April 1996): 1742–50. http://dx.doi.org/10.1002/j.1460-2075.1996.tb00520.x.

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32

Wang, Lei, Qing-Man Wang, Yi-Ran Wang, Xu-Guang Xi, and Xi-Miao Hou. "DNA-unwinding activity of Saccharomyces cerevisiae Pif1 is modulated by thermal stability, folding conformation, and loop lengths of G-quadruplex DNA." Journal of Biological Chemistry 293, no. 48 (October 10, 2018): 18504–13. http://dx.doi.org/10.1074/jbc.ra118.005071.

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33

Urban, Sinisa. "Taking the plunge: integrating structural, enzymatic and computational insights into a unified model for membrane-immersed rhomboid proteolysis." Biochemical Journal 425, no. 3 (January 15, 2010): 501–12. http://dx.doi.org/10.1042/bj20090861.

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Rhomboid proteases are a fascinating class of enzymes that combine a serine protease active site within the core of an integral membrane protein. Despite having key roles in animal cell signalling and microbial pathogenesis, the membrane-immersed nature of these enzymes had long imposed obstacles to elucidating their biochemical mechanisms. But recent multidisciplinary approaches, including eight crystal structures, four computer simulations and nearly 100 engineered mutants interrogated in vivo and in vitro, are coalescing into an integrated model for one rhomboid orthologue in particular, bacterial GlpG. The protein creates a central hydrated microenvironment immersed below the membrane surface to support hydrolysis by its serine protease-like catalytic apparatus. Four conserved architectural elements in particular act as ‘keystones’ to stabilize this structure, and the lateral membrane-embedded L1 loop functions as a ‘flotation device’ to position the protease tilted in the membrane. Complex interplay between lateral substrate gating by rhomboid, substrate unwinding and local membrane thinning leads to intramembrane proteolysis of selected target proteins. Although far from complete, studies with GlpG currently offer the best prospect for achieving a thorough and sophisticated understanding of a simplified intramembrane protease.

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34

Dekker, Job, Panagiotis N. Kanellopoulos, Joost A. W. M. van Oosterhout, Gunter Stier, Paul A. Tucker, and Peter C. van der Vliet. "ATP-independent DNA unwinding by the adenovirus single-stranded DNA binding protein requires a flexible DNA binding loop 1 1Edited by M. Yaniv." Journal of Molecular Biology 277, no. 4 (April 1998): 825–38. http://dx.doi.org/10.1006/jmbi.1998.1652.

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35

Kontos, Harry, Sawsan Napthine, and Ian Brierley. "Ribosomal Pausing at a Frameshifter RNA Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency." Molecular and Cellular Biology 21, no. 24 (December 15, 2001): 8657–70. http://dx.doi.org/10.1128/mcb.21.24.8657-8670.2001.

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ABSTRACT Here we investigated ribosomal pausing at sites of programmed −1 ribosomal frameshifting, using translational elongation and ribosome heelprint assays. The site of pausing at the frameshift signal of infectious bronchitis virus (IBV) was determined and was consistent with an RNA pseudoknot-induced pause that placed the ribosomal P- and A-sites over the slippery sequence. Similarly, pausing at the simian retrovirus 1 gag/pol signal, which contains a different kind of frameshifter pseudoknot, also placed the ribosome over the slippery sequence, supporting a role for pausing in frameshifting. However, a simple correlation between pausing and frameshifting was lacking. Firstly, a stem-loop structure closely related to the IBV pseudoknot, although unable to stimulate efficient frameshifting, paused ribosomes to a similar extent and at the same place on the mRNA as a parental pseudoknot. Secondly, an identical pausing pattern was induced by two pseudoknots differing only by a single loop 2 nucleotide yet with different functionalities in frameshifting. The final observation arose from an assessment of the impact of reading phase on pausing. Given that ribosomes advance in triplet fashion, we tested whether the reading frame in which ribosomes encounter an RNA structure (the reading phase) would influence pausing. We found that the reading phase did influence pausing but unexpectedly, the mRNA with the pseudoknot in the phase which gave the least pausing was found to promote frameshifting more efficiently than the other variants. Overall, these experiments support the view that pausing alone is insufficient to mediate frameshifting and additional events are required. The phase dependence of pausing may be indicative of an activity in the ribosome that requires an optimal contact with mRNA secondary structures for efficient unwinding.

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36

Brister, J. Rodney, and Nicholas Muzyczka. "Mechanism of Rep-Mediated Adeno-Associated Virus Origin Nicking." Journal of Virology 74, no. 17 (September 1, 2000): 7762–71. http://dx.doi.org/10.1128/jvi.74.17.7762-7771.2000.

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ABSTRACT The single-stranded adeno-associated virus type 2 (AAV) genome is flanked by terminal repeats (TRs) that fold back on themselves to form hairpinned structures. During AAV DNA replication, the TRs are nicked by the virus-encoded Rep proteins at the terminal resolution site (trs). This origin function apparently requires three sequence elements, the Rep binding element (RBE), a small palindrome that comprises a single tip of an internal hairpin within the TR (RBE′), and the trs. Previously, we determined the sequences at the trs required for Rep-mediated cleavage and demonstrated that the trs endonuclease reaction occurs in two discrete steps. In the first step, the Rep DNA helicase activity unwinds the TR, thereby extruding a stem-loop structure at thetrs. In the second step, Rep transesterification activity cleaves the trs. Here we investigate the contribution of the RBE and RBE′ during this process. Our data indicate that Rep is tethered to the RBE in a specific orientation duringtrs nicking. This orientation appears to align Rep on the AAV TR, allowing specific nucleotide contacts with the RBE′ and directing nicking to the trs. Accordingly, alterations in the polarity or position of the RBE relative to the trsgreatly inhibit Rep nicking. Substitutions within the RBE′ also reduce Rep specific activity, but to a lesser extent. Interestingly, Rep interactions with the RBE and RBE′ during nicking seem to be functionally distinct. Rep contacts with the RBE appear necessary for both the DNA helicase and trs cleavage steps of the endonuclease reaction. On the other hand, RBE′ contacts seem to be required primarily for TR unwinding and formation of thetrs stem-loop structure, not cleavage. Together, these results suggest a model of Rep interaction with the AAV TR during origin nicking through a tripartite cleavage signal comprised of the RBE, the RBE′, and the trs.

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37

DeStefano, Jeffrey J., and Oduyebo Titilope. "Poliovirus Protein 3AB Displays Nucleic Acid Chaperone and Helix-Destabilizing Activities." Journal of Virology 80, no. 4 (February 15, 2006): 1662–71. http://dx.doi.org/10.1128/jvi.80.4.1662-1671.2006.

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ABSTRACT Poliovirus protein 3AB displayed nucleic acid chaperone activity in promoting the hybridization of complementary nucleic acids and destabilizing secondary structure. Hybridization reactions at 30°C between 20- and 40-nucleotide RNA oligonucleotides and 179- or 765-nucleotide RNAs that contained a complementary region were greatly enhanced in the presence of 3AB. The effect was nonspecific as reactions between DNA oligonucleotides and RNA or DNA templates were also enhanced. Reactions were optimal with 1 mM MgCl2 and 20 mM KCl. Analysis of the reactions with various 3AB and template concentrations indicated that enhancement required a critical amount of 3AB that increased as the concentration of nucleic acid increased. This was consistent with a requirement for 3AB to “coat” the nucleic acids for enhancement. The helix-destabilizing activity of 3AB was tested in an assay with two 42-nucleotide completely complementary DNAs. Each complement formed a strong stem-loop (ΔG = −7.2 kcal/mol) that required unwinding for hybridization to occur. DNAs were modified at the 3′ or 5′ end with fluorescent probes such that hybridization resulted in quenching of the fluorescent signal. Under optimal conditions at 30°C, 3AB stimulated hybridization in a concentration-dependent manner, as did human immunodeficiency virus nucleocapsid protein, an established chaperone. The results are discussed with respect to the role of 3AB in viral replication and recombination.

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38

Fitzmaurice, Tim J., David F. Burke, Lee Hopkins, Sujeong Yang, Shuiliang Yu, Man-Sun Sy, Alana M. Thackray, and Raymond Bujdoso. "The stability and aggregation of ovine prion protein associated with classical and atypical scrapie correlates with the ease of unwinding of helix-2." Biochemical Journal 409, no. 2 (December 21, 2007): 367–75. http://dx.doi.org/10.1042/bj20071122.

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Susceptibility to scrapie disease in sheep, the archetypal prion disease, correlates with polymorphisms within the ovine PrP (prion-related protein) gene. The VRQ (Val136Arg154Gln171) and AL141RQ (Ala136Leu141Arg154Gln171) allelic variants are associated with classical scrapie, whereas the ARR (Ala136Arg154Arg171), AF141RQ (Ala136Phe141Arg154Gln171) and AHQ (Ala136His154Gln171) allelic variants are associated with atypical scrapie. Recent studies have suggested that there are differences in the stability of PrPSc (abnormal disease-specific conformation of PrP) associated with these different forms of scrapie. To address which structural features of ovine PrP may contribute to this difference, in the present study we have investigated the conformational stability and susceptibility to aggregation of allelic variants of ovine PrP associated with classical or atypical scrapie. We find that the melting temperature of ovine recombinant VRQ and AL141RQ PrP is higher than that of AF141RQ, AHQ and ARR. In addition, monoclonal-antibody studies show that the region around helix-1 of VRQ and AL141RQ is less accessible compared with other ovine PrP allelic variants. Furthermore, the extent of both the structural change to copper-ion-treatment and denaturant-induced aggregation was reduced in PrP associated with atypical scrapie compared with PrP associated with classical scrapie. Through the use of molecular dynamics simulations we have found that these biochemical and biophysical properties of ovine PrP correlate with the ease of unwinding of helix-2 and a concurrent conformational change of the helix-2–helix-3 loop. These results reveal significant differences in the overall stability and potential for aggregation of different allelic variants of ovine PrP and consequently have implications for the differences in stability of PrPSc associated with classical and atypical scrapie.

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39

Montemayor, Eric J., Allison L. Didychuk, Honghong Liao, Panzhou Hu, David A. Brow, and Samuel E. Butcher. "Structure and conformational plasticity of the U6 small nuclear ribonucleoprotein core." Acta Crystallographica Section D Structural Biology 73, no. 1 (January 1, 2017): 1–8. http://dx.doi.org/10.1107/s2059798316018222.

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U6 small nuclear RNA (snRNA) is a key component of the active site of the spliceosome, a large ribonucleoprotein complex that catalyzes the splicing of precursor messenger RNA. Prior to its incorporation into the spliceosome, U6 is bound by the protein Prp24, which facilitates unwinding of the U6 internal stem-loop (ISL) so that it can pair with U4 snRNA. A previously reported crystal structure of the `core' of the U6 small nuclear ribonucleoprotein (snRNP) contained an ISL-stabilized A62G mutant of U6 bound to all four RNA-recognition motif (RRM) domains of Prp24 [Montemayoret al.(2014),Nature Struct. Mol. Biol.21, 544–551]. The structure revealed a novel topology containing interlocked rings of protein and RNA that was not predicted by prior biochemical and genetic data. Here, the crystal structure of the U6 snRNP core with a wild-type ISL is reported. This complex crystallized in a new space group, apparently owing in part to the presence of an intramolecular cross-link in RRM1 that was not observed in the previously reported U6-A62G structure. The structure exhibits the same protein–RNA interface and maintains the unique interlocked topology. However, the orientation of the wild-type ISL is altered relative to the A62G mutant structure, suggesting inherent structural dynamics that may facilitate its pairing with U4. Consistent with their similar architectures in the crystalline state, the wild-type and A62G variants of U6 exhibit similar Prp24-binding affinities and electrophoretic mobilities when analyzed by gel-shift assay.

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40

Baranova, Svetlana V., Polina V. Zhdanova, Alexander A. Lomzov, Vladimir V. Koval, and Alexander A. Chernonosov. "Structure- and Content-Dependent Efficiency of Cas9-Assisted DNA Cleavage in Genome-Editing Systems." International Journal of Molecular Sciences 23, no. 22 (November 11, 2022): 13889. http://dx.doi.org/10.3390/ijms232213889.

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Genome-editing systems, being some of the key tools of molecular biologists, represent a reasonable hope for progress in the field of personalized medicine. A major problem with such systems is their nonideal accuracy and insufficient selectivity. The selectivity of CRISPR-Cas9 systems can be improved in several ways. One efficient way is the proper selection of the consensus sequence of the DNA to be cleaved. In the present work, we attempted to evaluate the effect of formed non-Watson–Crick pairs in a DNA duplex on the efficiency of DNA cleavage in terms of the influence of the structure of the formed partially complementary pairs. We also studied the effect of the location of such pairs in DNA relative to the PAM (protospacer-adjacent motif) on the cleavage efficiency. We believe that the stabilization of the Cas9-sgRNA complex with a DNA substrate containing noncomplementary pairs is due to loop reorganization in the RuvC domain of the enzyme. In addition, PAM-proximal mismatches in the DNA substrate lower enzyme efficiency because the “seed” region is involved in binding and cleavage, whereas PAM-distal mismatches have no significant impact on target DNA cleavage. Our data suggest that in the case of short duplexes with mismatches, the stages of recognition and binding of dsDNA substrates by the enzyme determine the reaction rate and time rather than the thermodynamic parameters affected by the “unwinding” of DNA. The results will provide a theoretical basis for predicting the efficiency and accuracy of CRISPR-Cas9 systems at cleaving target DNA.

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41

Hanke, Andreas, Riccardo Ziraldo, and Stephen D. Levene. "DNA-Topology Simplification by Topoisomerases." Molecules 26, no. 11 (June 3, 2021): 3375. http://dx.doi.org/10.3390/molecules26113375.

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The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.

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42

Shen, Miaoqing, Qixin Wang, Yan Yang, Harsh B. Pathak, Jamie J. Arnold, Christian Castro, Stanley M. Lemon, and Craig E. Cameron. "Human Rhinovirus Type 14 Gain-of-Function Mutants for oriI Utilization Define Residues of 3C(D) and 3Dpol That Contribute to Assembly and Stability of the Picornavirus VPg Uridylylation Complex." Journal of Virology 81, no. 22 (September 12, 2007): 12485–95. http://dx.doi.org/10.1128/jvi.00972-07.

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ABSTRACT VPg linkage to the 5′ ends of picornavirus RNAs requires production of VPg-pUpU. VPg-pUpU is templated by an RNA stem-loop (the cre or oriI) found at different locations in picornavirus genomes. At least one adaptive mutation is required for human rhinovirus type 14 (HRV-14) to use poliovirus type 3 (PV-3) or PV-1 oriI efficiently. One mutation changes Leu-94 of 3C to Pro; the other changes Asp-406 of 3Dpol to Asn. By using an in vitro VPg uridylylation system for HRV-14 that recapitulates biological phenotypes, we show that the 3C adaptive mutation functions at the level of 3C(D) and the 3D adaptive mutation functions at the level of 3Dpol. Pro-94 3C(D) has an expanded specificity and enhanced stability relative to wild-type 3C(D) that leads to production of more processive uridylylation complexes. PV-1/HRV-14 oriI chimeras reveal sequence specificity in 3C(D) recognition of oriI that resides in the upper stem. Asn-406 3Dpol is as active as wild-type 3Dpol in RNA-primed reactions but exhibits greater VPg uridylylation activity due to more efficient recruitment to and retention in the VPg uridylylation complex. Asn-406 3Dpol from PV-1 exhibits identical behavior. These studies suggest a two-step binding mechanism in the assembly of the 3C(D)-oriI complex that leads to unwinding of at least the upper stem of oriI and provide additional support for a direct interaction between the back of the thumb of 3Dpol and 3C that is required for 3Dpol recruitment to and retention in the uridylylation complex.

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43

Zhang, Mingjie, and Tao Yuan. "Molecular mechanisms of calmodulin's functional versatility." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 313–23. http://dx.doi.org/10.1139/o98-027.

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Calmodulin (CaM) is a primary Ca2+-binding protein found in all eukaryotic cells. It couples the intracellular Ca2+ signal to many essential cellular events by binding and regulating the activities of more than 40 different proteins and enzymes in a Ca2+-dependent manner. CaM contains two structurally similar domains connected by a flexible central linker. Each domain of the protein binds two Ca2+ ions with positive cooperativity. The binding of Ca2+ transforms the protein into its active form through a reorientation of the existing helices of the protein. The two helices in each helix-loop-helix Ca2+-binding motif are almost antiparallel in Ca2+-free CaM. The binding of Ca2+ induces concerted helical pair movements and changes the two helices in each Ca2+ binding motif to a nearly perpendicular orientation. These concerted helix pair movements are accompanied by dramatic changes on the molecular surface of the protein. Rather than exhibiting a flat, hydrophilic molecular surface as seen in Ca2+-free CaM, the Ca2+-saturated form of the protein contains a Met-rich, cavity-containing hydrophobic surface in each domain. These hydrophobic surfaces are largely responsible for the binding of CaM to its targets. The unique flexibility and high polarizability of the Met residues located at the entrance of each hydrophobic pocket together with other hydrophobic amino acid residues create adjustable, sticky interaction surface areas that can accommodate CaM's targets, which have various sizes and shapes. Therefore, CaM is able to bind to a large array of targets without obvious sequence homology. Upon binding to its target peptides, the unwinding of the central linker allows the two domains of the protein to engulf the hydrophobic face of target peptides of differing lengths. The binding of Ca2+ reduces the backbone flexibility of CaM. Formation of complexes with its target peptides further decreases the backbone motion of CaM.Key words: calmodulin, NMR, structure and dynamics, peptide targets, ligand specificity.

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44

Lin, Biing Yuan, Alexander M. Makhov, Jack D. Griffith, Thomas R. Broker, and Louise T. Chow. "Chaperone Proteins Abrogate Inhibition of the Human Papillomavirus (HPV) E1 Replicative Helicase by the HPV E2 Protein." Molecular and Cellular Biology 22, no. 18 (September 15, 2002): 6592–604. http://dx.doi.org/10.1128/mcb.22.18.6592-6604.2002.

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ABSTRACT Human papillomavirus (HPV) DNA replication requires the viral origin recognition protein E2 and the presumptive viral replicative helicase E1. We now report for the first time efficient DNA unwinding by a purified HPV E1 protein. Unwinding depends on a supercoiled DNA substrate, topoisomerase I, single-stranded-DNA-binding protein, and ATP, but not an origin. Electron microscopy revealed completely unwound molecules. Intermediates contained two single-stranded loops emanating from a single protein complex, suggesting a bidirectional E1 helicase which translocated the flanking DNA in an inward direction. We showed that E2 protein partially inhibited DNA unwinding and that Hsp70 or Hsp40, which we reported previously to stimulate HPV-11 E1 binding to the origin and promote dihexameric E1 formation, apparently displaced E2 and abolished inhibition. Neither E2 nor chaperone proteins were detected in unwinding complexes. These results suggest that chaperones play important roles in the assembly and activation of a replicative helicase in higher eukaryotes. An E1 mutation in the ATP binding site caused deficient binding and unwinding of origin DNA, indicating the importance of ATP binding in efficient helicase assembly on the origin.

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45

Wanka, F. "Functional aspects of the nuclear matrix." Acta Biochimica Polonica 42, no. 2 (June 30, 1995): 127–31. http://dx.doi.org/10.18388/abp.1995_4599.

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A model is proposed of the way in which the unwinding of the chromosomal DNA loops is controlled during DNA replication. It is based on the observation of a permanent binding of replication origins to the nuclear matrix and of a transient attachment of replicating DNA regions to sites in the immediate neighbourhood. DNA unwinding is controlled while the replicating loops are reeled through the replication binding sites. Also a mechanism is proposed to explain how the once-per-cycle replication of individual replicons can be controlled. DNA synthesis is initiated at single-stranded loops exposed by tandemly repeated DNA sequences at the replication origins. The single-stranded loops turn into fully double-stranded DNA during replication, becoming inaccessible for a second initiation during the same cell cycle. The configuration competent for initiation is restored by specific protein-DNA rearrangements coupled to mitotic condensation of the matrix into chromosomal scaffolds and its reversal.

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46

Dascal, Michael. "Unwinding the universe: a brief look at String Theory." McGill Science Undergraduate Research Journal 2, no. 1 (March 31, 2007): 22–23. http://dx.doi.org/10.26443/msurj.v2i1.136.

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“String Theory” has been a buzz-word in contemporary physics for years. It is at the very edge of theoretical ontology, predicting bizarre qualities of the universe – even claiming we exist in 11-dimensional space-time. These predictions may be strange, but the Theory can account for many of the laws of the universe if we put aside our preconceptions and accept the strange possibilities the Theory suggests.

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47

Lee, Seung-Jae, Salman Syed, Eric J. Enemark, Stephen Schuck, Arne Stenlund, Taekjip Ha, and Leemor Joshua-Tor. "Dynamic look at DNA unwinding by a replicative helicase." Proceedings of the National Academy of Sciences 111, no. 9 (February 18, 2014): E827—E835. http://dx.doi.org/10.1073/pnas.1322254111.

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48

Wang, Hua Qing, Jian Cheng Yang, Kai Yang, Jian Feng Qin, Yu Bai, Shuang Hu Hu, and Xiu Ming Jiang. "Carbon Fiber Multilayer Loom Let off the Mathematical Model of Control System." Advanced Materials Research 846-847 (November 2013): 157–60. http://dx.doi.org/10.4028/www.scientific.net/amr.846-847.157.

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Let-off system application of computer and electronic technology, may at any time adjust the loom is likely to change in the process of weaving yarn tension and density, thus improve the quality of the fabric. In this paper, based on the study of the function of the let-off motion, let-off servo control system is established the mathematical model of the warp beam unwinding; According to the carbon fiber Angle of multilayer union loom warp tension requirement, design a set of tension compensation device,and established the mathematical model of back rest. Easy and convenient, the whole control system has better reliability and real-time performance.

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49

Delagoutte, Emmanuelle, and Peter H. von Hippel. "Helicase mechanisms and the coupling of helicases within macromolecular machines Part I: Structures and properties of isolated helicases." Quarterly Reviews of Biophysics 35, no. 4 (November 2002): 431–78. http://dx.doi.org/10.1017/s0033583502003852.

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1. Mechanisms of nucleic acid (NA) unwinding by helicases 4322. Helicases may take advantage of ‘breathing’ fluctuations in dsNAs 4342.1 Stability and dynamics of dsNAs 4342.2 dsNAs ‘breathe’ in isolation 4352.3 Thermodynamics of terminal base pairs of dsNA 4382.4 Thermal fluctuations may be responsible for sequential base-pair opening at replication forks 4392.5 Helicases may capture single base-pair opening events sequentially 4403. Biochemical properties of helicases 4433.1 Binding of NAs 4433.2 Binding and hydrolysis of NTP 4453.3 Coordination between NA binding and NTP binding and hydrolysis activities 4464. Helicase structures and mechanistic consequences 4474.1 Amino-acid sequence analysis reveals conserved motifs that constitute the NTP-binding pocket and a portion of the NA-binding site 4474.2 Organization of hepatitis virus C NS3 RNA helicase 4494.2.1 Biochemical properties of HCV NS3 4494.2.2 Crystal structures of HCV NS3 helicase 4504.2.2.1 The apoprotein 4504.2.2.2 The protein–dU8 complex 4504.2.3 A possible unwinding mechanism 4524.2.4 What is the functional oligomeric state of HCV NS3? 4524.3 Organization of the PcrA helicase 4534.3.1 The apoenzyme and ADP–PcrA complex 4544.3.2 The protein–DNA–sulfate complex 4564.3.3 The PcrA–DNA–ADPNP complex 4564.3.4 A closer look at the NTP-binding site in the crystal structure of PcrA–ADPNP–DNA 4574.3.5 Communication between domains A and B 4574.3.6 How might ssDNA stimulate the ATPase activity of PcrA? 4574.3.7 A possible helicase translocation mechanism 4584.3.8 A possible unwinding mechanism 4584.4 Organization of the Rep helicase 4594.4.1 Biochemical properties 4594.4.2 Crystal structure of Rep bound to ssDNA 4624.5 Organization of the RecG helicase 4624.6 Hexameric helicases 4664.6.1 Insights from crystal structures of hexameric helicases 4674.6.2 Possible translocation and unwinding mechanisms 4685. Conclusions 4696. Acknowledgments 4727. References 472Helicases are proteins that harness the chemical free energy of ATP hydrolysis to catalyze the unwinding of double-stranded nucleic acids. These enzymes have been much studied in isolation, and here we review what is known about the mechanisms of the unwinding process. We begin by considering the thermally driven ‘breathing’ of double-stranded nucleic acids by themselves, in order to ask whether helicases might take advantage of some of these breathing modes. We next provide a brief summary of helicase mechanisms that have been elucidated by biochemical, thermodynamic, and kinetic studies, and then review in detail recent structural studies of helicases in isolation, in order to correlate structural findings with biophysical and biochemical results. We conclude that there are certainly common mechanistic themes for helicase function, but that different helicases have devised solutions to the nucleic acid unwinding problem that differ in structural detail. In Part II of this review (to be published in the next issue of this journal) we consider how these mechanisms are further modified to reflect the functional coupling of these proteins into macromolecular machines, and discuss the role of helicases in several central biological processes to illustrate how this coupling actually works in the various processes of gene expression.

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Gutierrez-Rodrigues, Fernanda, Sachiko Kajigaya, Xingmin Feng, Maria del Pilar Fernandez Ibanez, Marie J. Desierto, Keyvan Keyvanfar, Zejuan Li, et al. "Heterozygous RTEL1 variants in Patients with Bone Marrow Failure Associate with Telomere Dysfunction in the Absence of Telomere Shortening." Blood 128, no. 22 (December 2, 2016): 1044. http://dx.doi.org/10.1182/blood.v128.22.1044.1044.

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Abstract The pathophysiology of bone marrow failure (BMF) can be immune, as in acquired aplastic anemia (AA), or constitutional, due to germline mutations in genes critical for DNA repair and telomere maintenance. Variability in penetrance and phenotype can complicate diagnosis, as patients with underlying genetic defects may present in adulthood and without characteristic physical anomalies. RTEL1 encodes a helicase crucial for telomere maintenance and DNA repair. The gene has two main transcripts in human cells: the 1300 amino acid isoform 3 and the 1219 amino acid isoform 1. RTEL1 isoform 3 contains a conserved C4C4-RING domain responsible for resolving the t-loop required for telomere replication. Using next-generation sequencing (NGS), RTEL1 germline variants with unknown clinical significance have been found in AA patients. Functional tests may elucidate RTEL1 variants' pathogenic role in telomere biology. Here, we describe RTEL1 heterozygous germline mutations in patients with BMF and investigate their impact in telomere maintenance. We screened 63 patients with a suggestive familial phenotype for germline mutations in peripheral blood cells using a targeted, 49 gene NGS panel. To investigate variants' impact in telomere functions, telomere length (TL) was measured by Southern blot (SB), t-circles were quantified by telomere circle assay, and single-stranded overhang was measured by non-denaturing SB. Eight patients carried novel heterozygous non-synonymous RTEL1 variants: four nucleotide changes were located in the RAD3 domain, six in the harmonin-like domain, and one in the RING domain. Clinical features and TL were heterogeneous (Table 1). The only RTEL1 variant predicted as pathogenic in silico was F1262L (c.3786 C>G) in patient 2; this mutation affects a highly conserved amino acid residue located in the RING domain, which is responsible for RTEL1 interaction with TRF2 at telomeres and t-loop unwinding. Patient 2 had very short telomeres, abnormal accumulation of t-circles, and eroded single-stranded telomeric overhangs in leukocytes, indicating a disrupted RTEL1 RING domain. To confirm observations made in clinical samples, 293T cells transfected with a plasmid carrying wild-type RTEL1-FLAG isoform 3 or its F1262L mutated version were assessed for TRF2 and FLAG co-localization in the nucleus. By confocal microscopy, wild-type RTEL1, but not mutant RTEL1 co-localized with TRF2. These findings strongly implicate RTEL1-F1262L as pathogenic, and thus the first autosomal dominant mutation in the RING domain in an AA patient. In patient 1, D743N variant in silico prediction was indeterminate, but telomeres were very short and there was a family history of typical telomeropathy (AA, liver cirrhosis, and pulmonary fibrosis) without any other suspicious germline mutations. The D743N variant is located close to the V745M variant that has been reported in a patient with dyskeratosis congenita. Increased amounts of t-circles and telomeric overhang attrition were observed in three other patients (#4, 5, and 7). While not specific for RTEL1 function, these results suggest telomere dysfunction, despite TLs in the normal range for patient 4 and 5. The RTEL1 P82L variant also appeared related to clonal evolution and leukemic progression observed in patient 5. For patients 3, 4, 6, 7, and 8, several mutations were observed in other genes concomitant to RTEL1, and a more complex genomic architecture may be the cause of patients' phenotype. A previously reported TERC variant, and a TERT variant of undetermined in silico prediction, could be pathogenic in patients 7 and 6, respectively. In these cases, RTEL1 variants may modulate disease, or represent only coincidental abnormalities. To our knowledge, this is the first report of heterozygous RTEL1 mutations in AA. We also describe a TL-independent association between RTEL1 haploinsufficiency and telomere dysfunction in humans. Haploinsufficiency of RTEL1 may disrupt DNA repair, destabilize the genome, and promote leukemogenesis by a mechanism different than typical accelerated telomere attrition associated with very short telomeres. T-circle quantification and overhang measurement may be better measures of telomere dysfunction in patients with RTEL1 variants than simple TL assessment. The combination of different functional tests was useful to the assessment of novel variants impact in telomere maintenance and DNA repair. Disclosures Fernandez Ibanez: GSK/Novartis: Research Funding. Desierto:GSK/Novartis: Research Funding. Townsley:GSK/Novartis: Research Funding. Young:GSK/Novartis: Research Funding.

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