Journal articles: 'Processivité'

1

Taylor, Edwin W., and Gary G. Borisy. "Kinesin Processivity." Journal of Cell Biology 151, no. 5 (November 27, 2000): F27—F30. http://dx.doi.org/10.1083/jcb.151.5.f27.

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2

O'Donnell, Mike. "Processivity factors." Current Biology 9, no. 15 (August 1999): R545. http://dx.doi.org/10.1016/s0960-9822(99)80348-0.

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3

Moriarty, Tara J., Delphine T. Marie-Egyptienne, and Chantal Autexier. "Functional Organization of Repeat Addition Processivity and DNA Synthesis Determinants in the Human Telomerase Multimer." Molecular and Cellular Biology 24, no. 9 (May 1, 2004): 3720–33. http://dx.doi.org/10.1128/mcb.24.9.3720-3733.2004.

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ABSTRACT Human telomerase is a multimer containing two human telomerase RNAs (hTRs) and most likely two human telomerase reverse transcriptases (hTERTs). Telomerase synthesizes multiple telomeric repeats using a unique repeat addition form of processivity. We investigated hTR and hTERT sequences that were essential for DNA synthesis and processivity using a direct primer extension telomerase assay. We found that hTERT consists of two physically separable functional domains, a polymerase domain containing RNA interaction domain 2 (RID2), reverse transcriptase (RT), and C-terminal sequences, and a major accessory domain, RNA interaction domain 1 (RID1). RID2 mutants defective in high-affinity hTR interactions and an RT catalytic mutant exhibited comparable DNA synthesis defects. The RID2-interacting hTR P6.1 helix was also essential for DNA synthesis. RID1 interacted with the hTR pseudoknot-template domain and hTERT's RT motifs and putative thumb and was essential for processivity, but not DNA synthesis. The hTR pseudoknot was essential for processivity, but not DNA synthesis, and processivity was reduced or abolished in dimerization-defective pseudoknot mutants. trans-acting hTERTs and hTRs complemented the processivity defects of RID1 and pseudoknot mutants, respectively. These data provide novel insight into the catalytic organization of the human telomerase complex and suggest that repeat addition processivity is one of the major catalytic properties conferred by telomerase multimerization.

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Vuong, Thu V., and David B. Wilson. "Processivity, Synergism, and Substrate Specificity of Thermobifida fusca Cel6B." Applied and Environmental Microbiology 75, no. 21 (September 4, 2009): 6655–61. http://dx.doi.org/10.1128/aem.01260-09.

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ABSTRACT A relationship between processivity and synergism has not been reported for cellulases, although both characteristics are very important for hydrolysis of insoluble substrates. Mutation of two residues located in the active site tunnel of Thermobifida fusca exocellulase Cel6B increased processivity on filter paper. Surprisingly, mixtures of the Cel6B mutant enzymes and T. fusca endocellulase Cel5A did not show increased synergism or processivity, and the mutant enzyme which had the highest processivity gave the poorest synergism. This study suggests that improving exocellulase processivity might be not an effective strategy for producing improved cellulase mixtures for biomass conversion. The inverse relationship between the activities of many of the mutant enzymes with bacterial microcrystalline cellulose and their activities with carboxymethyl cellulose indicated that there are differences in the mechanisms of hydrolysis for these substrates, supporting the possibility of engineering Cel6B to target selected substrates.

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5

LeBrasseur, Nicole. "Profilin for processivity." Journal of Cell Biology 167, no. 4 (November 15, 2004): 581. http://dx.doi.org/10.1083/jcb1674rr5.

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Varrot, A., S. J. Charnock, M. Schülein, H. Driguez, and G. J. Davies. "Cellobiohydrolases and processivity." Acta Crystallographica Section A Foundations of Crystallography 56, s1 (August 25, 2000): s254. http://dx.doi.org/10.1107/s0108767300025460.

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7

Brenner, Sibylle, Florian Berger, Lu Rao, Matthew P. Nicholas, and Arne Gennerich. "Force production of human cytoplasmic dynein is limited by its processivity." Science Advances 6, no. 15 (April 2020): eaaz4295. http://dx.doi.org/10.1126/sciadv.aaz4295.

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Cytoplasmic dynein is a highly complex motor protein that generates forces toward the minus end of microtubules. Using optical tweezers, we demonstrate that the low processivity (ability to take multiple steps before dissociating) of human dynein limits its force generation due to premature microtubule dissociation. Using a high trap stiffness whereby the motor achieves greater force per step, we reveal that the motor’s true maximal force (“stall force”) is ~2 pN. Furthermore, an average force versus trap stiffness plot yields a hyperbolic curve that plateaus at the stall force. We derive an analytical equation that accurately describes this curve, predicting both stall force and zero-load processivity. This theoretical model describes the behavior of a kinesin motor under low-processivity conditions. Our work clarifies the true stall force and processivity of human dynein and provides a new paradigm for understanding and analyzing molecular motor force generation for weakly processive motors.

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8

Li, Yongchao, Diana C. Irwin, and David B. Wilson. "Processivity, Substrate Binding, and Mechanism of Cellulose Hydrolysis by Thermobifida fusca Cel9A." Applied and Environmental Microbiology 73, no. 10 (March 16, 2007): 3165–72. http://dx.doi.org/10.1128/aem.02960-06.

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ABSTRACT Thermobifida fusca Cel9A-90 is a processive endoglucanase consisting of a family 9 catalytic domain (CD), a family 3c cellulose binding module (CBM3c), a fibronectin III-like domain, and a family 2 CBM. This enzyme has the highest activity of any individual T. fusca enzyme on crystalline substrates, particularly bacterial cellulose (BC). Mutations were introduced into the CD or the CBM3c of Cel9A-68 using site-directed mutagenesis. The mutant enzymes were expressed in Escherichia coli; purified; and tested for activity on four substrates, ligand binding, and processivity. The results show that H125 and Y206 play an important role in activity by forming a hydrogen bonding network with the catalytic base, D58; another important supporting residue, D55; and Glc(−1) O1. R378, a residue interacting with Glc(+1), plays an important role in processivity. Several enzymes with mutations in the subsites Glc(−2) to Glc(−4) had less than 15% activity on BC and markedly reduced processivity. Mutant enzymes with severalfold-higher activity on carboxymethyl cellulose (CMC) were found in the subsites from Glc(−2) to Glc(−4). The CBM3c mutant enzymes, Y520A, R557A/E559A, and R563A, had decreased activity on BC but had wild-type or improved processivity. Mutation of D513, a conserved residue at the end of the CBM, increased activity on crystalline cellulose. Previous work showed that deletion of the CBM3c abolished crystalline activity and processivity. This study shows that it is residues in the catalytic cleft that control processivity while the CBM3c is important for loose binding of the enzyme to the crystalline cellulose substrate.

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9

Sharma, Prem L., and Clyde S. Crumpacker. "Decreased Processivity of Human Immunodeficiency Virus Type 1 Reverse Transcriptase (RT) Containing Didanosine-Selected Mutation Leu74Val: a Comparative Analysis of RT Variants Leu74Val and Lamivudine-Selected Met184Val." Journal of Virology 73, no. 10 (October 1, 1999): 8448–56. http://dx.doi.org/10.1128/jvi.73.10.8448-8456.1999.

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ABSTRACT We previously showed that a didanosine-selected mutation in pNL4-3 background conferred a replication disadvantage on human immunodeficiency virus type 1, resulting in a loss of replication fitness. This work has been extended by showing that a recombinant virus with the HXBc2 backbone and reverse transcriptase (RT) fragments from pNL4-3 containing the Leu74Val mutation produce decreasing amounts of p24 antigen over a 3-week period. The HXBc2 recombinant containing the wild-type RT from pNL4-3 replicated efficiently. When the virion-associated RT containing the Leu74Val mutation was used in an RT processivity assay with homopolymer RNA template-primer, poly(A), and oligo(dT), the RT with altered Leu74Val mutation was less processive, generating fewer cDNA products in comparison to wild-type pNL4-3 RT. The replication kinetics and RT processivity of the mutant with the Leu74Val mutation were compared to those of a lamivudine-selected mutant Met184Val. In replication kinetics assays, mutant Leu74Val replicated slower than the mutant Met184Val. In a processivity assay, the mutant RTs from both viruses show comparable decreases in processivity. These observations provide biochemical evidence of decreased processivity to support the decrease in replication fitness observed with the Leu74Val or Met184Val mutations.

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10

Diatlova, Evgeniia A., Grigory V. Mechetin, Anna V. Yudkina, Vasily D. Zharkov, Natalia A. Torgasheva, Anton V. Endutkin, Olga V. Shulenina, et al. "Correlated Target Search by Vaccinia Virus Uracil–DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery." International Journal of Molecular Sciences 24, no. 11 (May 23, 2023): 9113. http://dx.doi.org/10.3390/ijms24119113.

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The protein encoded by the vaccinia virus D4R gene has base excision repair uracil–DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.

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11

Peng, Yun, I. Saira Mian, and Neal F. Lue. "Analysis of Telomerase Processivity." Molecular Cell 7, no. 6 (June 2001): 1201–11. http://dx.doi.org/10.1016/s1097-2765(01)00268-4.

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12

Yakovlieva, Liubov, and Marthe T. C. Walvoort. "Processivity in Bacterial Glycosyltransferases." ACS Chemical Biology 15, no. 1 (November 21, 2019): 3–16. http://dx.doi.org/10.1021/acschembio.9b00619.

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13

Santamaria-Holek, Ivan, and Jared López Alamilla. "Determining Molecular Motors Processivity." Biophysical Journal 102, no. 3 (January 2012): 367a. http://dx.doi.org/10.1016/j.bpj.2011.11.2004.

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14

Adio, Sarah, Johann Jaud, Bettina Ebbing, Matthias Rief, and Günther Woehlke. "Dissection of Kinesin's Processivity." PLoS ONE 4, no. 2 (February 26, 2009): e4612. http://dx.doi.org/10.1371/journal.pone.0004612.

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15

Bagshaw, Clive R., Jendrik Hentschel, and Michael D. Stone. "The Processivity of Telomerase: Insights from Kinetic Simulations and Analyses." Molecules 26, no. 24 (December 13, 2021): 7532. http://dx.doi.org/10.3390/molecules26247532.

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Telomerases are moderately processive reverse transcriptases that use an integral RNA template to extend the 3′ end of linear chromosomes. Processivity values, defined as the probability of extension rather than dissociation, range from about 0.7 to 0.99 at each step. Consequently, an average of tens to hundreds of nucleotides are incorporated before the single-stranded sDNA product dissociates. The RNA template includes a six nucleotide repeat, which must be reset in the active site via a series of translocation steps. Nucleotide addition associated with a translocation event shows a lower processivity (repeat addition processivity, RAP) than that at other positions (nucleotide addition processivity, NAP), giving rise to a characteristic strong band every 6th position when the product DNA is analyzed by gel electrophoresis. Here, we simulate basic reaction mechanisms and analyze the product concentrations using several standard procedures to show how the latter can give rise to systematic errors in the processivity estimate. Complete kinetic analysis of the time course of DNA product concentrations following a chase with excess unlabeled DNA primer (i.e., a pulse-chase experiment) provides the most rigorous approach. This analysis reveals that the higher product concentrations associated with RAP arise from a stalling of nucleotide incorporation reaction during translocation rather than an increased rate constant for the dissociation of DNA from the telomerase.

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16

Sandhu, Ranjodh, Madhav Sharma, Derek Wei, and Lifeng Xu. "The structurally conserved TELR region on shelterin protein TPP1 is essential for telomerase processivity but not recruitment." Proceedings of the National Academy of Sciences 118, no. 30 (July 19, 2021): e2024889118. http://dx.doi.org/10.1073/pnas.2024889118.

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The shelterin protein TPP1 is involved in both recruiting telomerase and stimulating telomerase processivity in human cells. Assessing the in vivo significance of the latter role of TPP1 has been difficult, because TPP1 mutations that perturb telomerase function tend to abolish both telomerase recruitment and processivity. The Saccharomyces cerevisiae telomerase-associated Est3 protein adopts a protein fold similar to the N-terminal region of TPP1. Interestingly, a previous structure-guided mutagenesis study of Est3 revealed a TELR surface region that regulates telomerase function via an unknown mechanism without affecting the interaction between Est3 and telomerase [T. Rao et al., Proc. Natl. Acad. Sci. U.S.A. 111, 214–218 (2014)]. Here, we show that mutations within the structurally conserved TELR region on human TPP1 impaired telomerase processivity while leaving telomerase recruitment unperturbed, hence uncoupling the two roles of TPP1 in regulating telomerase. Telomeres in cell lines containing homozygous TELR mutations progressively shortened to a critical length that caused cellular senescence, despite the presence of abundant telomerase in these cells. Our findings not only demonstrate that telomerase processivity can be regulated by TPP1 in a process separable from its role in recruiting telomerase, but also establish that the in vivo stimulation of telomerase processivity by TPP1 is critical for telomere length homeostasis and long-term viability of human cells.

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17

Druck Shudofsky, Abigail M., Janice Elaine Y. Silverman, Debasish Chattopadhyay, and Robert P. Ricciardi. "Vaccinia Virus D4 Mutants Defective in Processive DNA Synthesis Retain Binding to A20 and DNA." Journal of Virology 84, no. 23 (September 22, 2010): 12325–35. http://dx.doi.org/10.1128/jvi.01435-10.

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ABSTRACT Genome replication is inefficient without processivity factors, which tether DNA polymerases to their templates. The vaccinia virus DNA polymerase E9 requires two viral proteins, A20 and D4, for processive DNA synthesis, yet the mechanism of how this tricomplex functions is unknown. This study confirms that these three proteins are necessary and sufficient for processivity, and it focuses on the role of D4, which also functions as a uracil DNA glycosylase (UDG) repair enzyme. A series of D4 mutants was generated to discover which sites are important for processivity. Three point mutants (K126V, K160V, and R187V) which did not function in processive DNA synthesis, though they retained UDG catalytic activity, were identified. The mutants were able to compete with wild-type D4 in processivity assays and retained binding to both A20 and DNA. The crystal structure of R187V was resolved and revealed that the local charge distribution around the substituted residue is altered. However, the mutant protein was shown to have no major structural distortions. This suggests that the positive charges of residues 126, 160, and 187 are required for D4 to function in processive DNA synthesis. Consistent with this is the ability of the conserved mutant K126R to function in processivity. These mutants may help unlock the mechanism by which D4 contributes to processive DNA synthesis.

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18

Biragyn, A., and S. A. Nedospasov. "Lipopolysaccharide-induced expression of TNF-alpha gene in the macrophage cell line ANA-1 is regulated at the level of transcription processivity." Journal of Immunology 155, no. 2 (July 15, 1995): 674–83. http://dx.doi.org/10.4049/jimmunol.155.2.674.

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Abstract Increasing evidence suggests that regulation of transcription at the level of elongation or processivity may be an important mechanism governing expression of eukaryotic genes. In this study we compared LPS- and IFN-gamma-induced transcription of the TNF-alpha gene in two murine macrophage cell lines, ANA1 and Pu5-1.8. Our data from nuclear run-on analysis indicate that in ANA-1 cells TNF-alpha expression is regulated at the transcriptional level, as previously found in primary macrophages. In contrast, in Pu5-1.8 cells the TNF gene is constitutively transcribed. Using several short probes spanning the TNF gene we find that in ANA-1 cells transcription can be initiated before activation, but such transcripts have low processivity and are prematurely terminated or arrested within the gene. Induction with LPS alone or with LPS plus IFN-gamma results both in increased transcription initiation, and in the increased processivity of these transcripts. In Pu 5-1.8 cells neither type of transcriptional regulation of the TNF gene is observed. Our results indicate that the TNF gene is preactivated in ANA-1 cells, and RNA polymerase is allowed to initiate transcription, but due to the low processivity of the transcripts very little mRNA is formed. After LPS stimulation the TNF gene is maximally activated both by increased initiation and by higher processivity of the transcript, and each of these components of activation do not require a new protein synthesis. Our findings are consistent with a recently proposed model that the same transcriptional activators contribute to both initiation and processivity of transcription. In the case of LPS and LPS+IFN-gamma stimulation of macrophages, inducible members of NF-kappa B/Rel family are likely candidate transcriptional activators.

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19

Etson, Candice M., Samir M. Hamdan, Charles C. Richardson, and Antoine M. van Oijen. "Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA." Proceedings of the National Academy of Sciences 107, no. 5 (January 11, 2010): 1900–1905. http://dx.doi.org/10.1073/pnas.0912664107.

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The DNA polymerases involved in DNA replication achieve high processivity of nucleotide incorporation by forming a complex with processivity factors. A model system for replicative DNA polymerases, the bacteriophage T7 DNA polymerase (gp5), encoded by gene 5, forms a tight, 1∶1 complex with Escherichia coli thioredoxin. By a mechanism that is not fully understood, thioredoxin acts as a processivity factor and converts gp5 from a distributive polymerase into a highly processive one. We use a single-molecule imaging approach to visualize the interaction of fluorescently labeled T7 DNA polymerase with double-stranded DNA. We have observed T7 gp5, both with and without thioredoxin, binding nonspecifically to double-stranded DNA and diffusing along the duplex. The gp5/thioredoxin complex remains tightly bound to the DNA while diffusing, whereas gp5 without thioredoxin undergoes frequent dissociation from and rebinding to the DNA. These observations suggest that thioredoxin increases the processivity of T7 DNA polymerase by suppressing microscopic hopping on and off the DNA and keeping the complex tightly bound to the duplex.

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20

Zheng, Fei, and Shaojun Ding. "Processivity and Enzymatic Mode of a Glycoside Hydrolase Family 5 Endoglucanase from Volvariella volvacea." Applied and Environmental Microbiology 79, no. 3 (November 30, 2012): 989–96. http://dx.doi.org/10.1128/aem.02725-12.

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ABSTRACTEG1 is a modular glycoside hydrolase family 5 endoglucanase fromVolvariella volvaceaconsisting of an N-terminal carbohydrate-binding module (CBM1) and a catalytic domain (CD). The ratios of soluble to insoluble reducing sugar produced from filter paper after 8 and 24 h of exposure to EG1 were 6.66 and 8.56, respectively, suggesting that it is a processive endoglucanase. Three derivatives of EG1 containing a core domain only or additional CBMs were constructed in order to evaluate the contribution of the CBM to the processivity and enzymatic mode of EG1 under stationary and agitated conditions. All four enzymatic forms exhibited the same mode of action on both soluble and insoluble cellulosic substrates with cellobiose as a main end product. An additional CBM fused at either the N or C terminus reduced specific activity toward soluble and insoluble celluloses under stationary reaction conditions. Deletion of the CBM significantly decreased enzyme processivity. Insertion of an additional CBM also resulted in a dramatic decrease in processivity in enzyme-substrate reaction mixtures incubated for 0.5 h, but this effect was reversed when reactions were allowed to proceed for longer periods (24 h). Further significant differences were observed in the substrate adsorption/desorption patterns of EG1 and enzyme derivatives equipped with an additional CBM under agitated reaction conditions. An additional family 1 CBM improved EG1 processivity on insoluble cellulose under highly agitated conditions. Our data indicate a strong link between high adsorption levels and low desorption levels in the processivity of EG1 and possibly other processive endoglucanses.

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21

Romberg, Laura, Daniel W. Pierce, and Ronald D. Vale. "Role of the Kinesin Neck Region in Processive Microtubule-based Motility." Journal of Cell Biology 140, no. 6 (March 23, 1998): 1407–16. http://dx.doi.org/10.1083/jcb.140.6.1407.

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Kinesin is a dimeric motor protein that can move along a microtubule for several microns without releasing (termed processive movement). The two motor domains of the dimer are thought to move in a coordinated, hand-over-hand manner. A region adjacent to kinesin's motor catalytic domain (the neck) contains a coiled coil that is sufficient for motor dimerization and has been proposed to play an essential role in processive movement. Recent models have suggested that the neck enables head-to-head communication by creating a stiff connection between the two motor domains, but also may unwind during the mechanochemical cycle to allow movement to new tubulin binding sites. To test these ideas, we mutated the neck coiled coil in a 560-amino acid (aa) dimeric kinesin construct fused to green fluorescent protein (GFP), and then assayed processivity using a fluorescence microscope that can visualize single kinesin–GFP molecules moving along a microtubule. Our results show that replacing the kinesin neck coiled coil with a 28-aa residue peptide sequence that forms a highly stable coiled coil does not greatly reduce the processivity of the motor. This result argues against models in which extensive unwinding of the coiled coil is essential for movement. Furthermore, we show that deleting the neck coiled coil decreases processivity 10-fold, but surprisingly does not abolish it. We also demonstrate that processivity is increased by threefold when the neck helix is elongated by seven residues. These results indicate that structural features of the neck coiled coil, although not essential for processivity, can tune the efficiency of single molecule motility.

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22

Chan, Szeman Ruby, and Bala Chandran. "Characterization of Human Herpesvirus 8 ORF59 Protein (PF-8) and Mapping of the Processivity and Viral DNA Polymerase-Interacting Domains." Journal of Virology 74, no. 23 (December 1, 2000): 10920–29. http://dx.doi.org/10.1128/jvi.74.23.10920-10929.2000.

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ABSTRACT Human herpesvirus 8 (HHV-8) or Kaposi's sarcoma-associated herpesvirus (KSHV) ORF59 protein (PF-8) is a processivity factor for HHV-8 DNA polymerase (Pol-8) and is homologous to processivity factors expressed by other herpesviruses, such as herpes simplex virus type 1 UL42 and Epstein-Barr virus BMRF1. The interaction of UL42 and BMRF1 with their corresponding DNA polymerases is essential for viral DNA replication and the subsequent production of infectious virus. Using HHV-8-specific monoclonal antibody 11D1, we have previously identified the cDNA encoding PF-8 and showed that it is an early-late gene product localized to HHV-8-infected cell nuclei (S. R. Chan, C. Bloomer, and B. Chandran, Virology 240:118–126, 1998). Here, we have further characterized PF-8. This viral protein was phosphorylated both in vitro and in vivo. PF-8 bound double-stranded DNA (dsDNA) and single-stranded DNA independent of DNA sequence; however, the affinity for dsDNA was approximately fivefold higher. In coimmunoprecipitation reactions, PF-8 also interacted with Pol-8. In in vitro processivity assays with excess poly(dA):oligo(dT) as a template, PF-8 stimulated the production of elongated DNA products by Pol-8 in a dose-dependent manner. Functional domains of PF-8 were determined using PF-8 truncation mutants. The carboxyl-terminal 95 amino acids (aa) of PF-8 were dispensable for all three functions of PF-8: enhancing processivity of Pol-8, binding dsDNA, and binding Pol-8. Residues 10 to 27 and 279 to 301 were identified as regions critical for the processivity function of PF-8. Interestingly, aa 10 to 27 were also essential for binding Pol-8, whereas aa 1 to 62 and aa 279 to 301 were involved in binding dsDNA, suggesting that the processivity function of PF-8 is correlated with both the Pol-8-binding and the dsDNA-binding activities of PF-8.

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23

Lan, Ganhui, and Sean X. Sun. "Dynamics of Myosin-V Processivity." Biophysical Journal 88, no. 2 (February 2005): 999–1008. http://dx.doi.org/10.1529/biophysj.104.047662.

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24

Nara, I., S. Uemura, I. Fujiwara, and S. Ishiwata. "Temperature dependence of kinesin processivity." Seibutsu Butsuri 41, supplement (2001): S194. http://dx.doi.org/10.2142/biophys.41.s194_4.

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Yajima, J., Maria C. Alonso, Robert A. Cross, and Y. Y. Toyoshima. "Kinesin processivity at low load." Seibutsu Butsuri 41, supplement (2001): S195. http://dx.doi.org/10.2142/biophys.41.s195_2.

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Srere, Paul A., and Balazs Sumegi. "Processivity and fatty acid oxidation." Biochemical Society Transactions 22, no. 2 (May 1, 1994): 446–50. http://dx.doi.org/10.1042/bst0220446.

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Breyer, Wendy A., and Brian W. Matthews. "A structural basis for processivity." Protein Science 10, no. 9 (September 2001): 1699–711. http://dx.doi.org/10.1110/ps.10301.

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Zhang, Jun-Ping, Yi Liu, Wei Sun, Xiao-Yang Zhao, La Ta, and Wei-Sheng Guo. "Characteristics of Myosin V Processivity." IEEE/ACM Transactions on Computational Biology and Bioinformatics 16, no. 4 (July 1, 2019): 1302–8. http://dx.doi.org/10.1109/tcbb.2017.2669311.

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delCardayre, Stephen B., and Ronald T. Raines. "Structural Determinants of Enzymic Processivity." Biochemistry 33, no. 20 (May 1994): 6031–37. http://dx.doi.org/10.1021/bi00186a001.

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Higley, Michelle, and R. Stephen Lloyd. "Processivity of uracil DNA glycosylase." Mutation Research/DNA Repair 294, no. 2 (August 1993): 109–16. http://dx.doi.org/10.1016/0921-8777(93)90019-d.

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31

Behrens, Vincent, Tim Scholz, Bernhard Brenner, Michael A. Geeves, and Walter Steffen. "Regulating Native Cytoplasmic Dynein's Processivity." Biophysical Journal 112, no. 3 (February 2017): 261a. http://dx.doi.org/10.1016/j.bpj.2016.11.1418.

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Schindler, Tony D., and Zev Bryant. "Processivity Determinants of Engineered Myosins." Biophysical Journal 102, no. 3 (January 2012): 568a. http://dx.doi.org/10.1016/j.bpj.2011.11.3095.

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HIPPEL, PETER H. VON, FREDERIC R. FAIRFIELD, and MARY KAY DOLEJSI. "On the Processivity of Polymerases." Annals of the New York Academy of Sciences 726, no. 1 DNA Damage (July 1994): 118–31. http://dx.doi.org/10.1111/j.1749-6632.1994.tb52803.x.

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34

Cao, LuYan, Mikaël Kerleau, Antoine Jégou, and Guillaume Romet-Lemonne. "Formin's Processivity under Applied Force." Biophysical Journal 114, no. 3 (February 2018): 144a. http://dx.doi.org/10.1016/j.bpj.2017.11.807.

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Lee, Jaeyoon, Meiling Wu, Gundeep Singh, James Inman, Seong ha Park, Joyce H. Lee, Robert M. Fullbright, et al. "Chromatinization modulates topoisomerase II processivity." Biophysical Journal 123, no. 3 (February 2024): 499a. http://dx.doi.org/10.1016/j.bpj.2023.11.3019.

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Lee, Seung-Joo, Kajal Chowdhury, Stanley Tabor, and Charles C. Richardson. "Rescue of Bacteriophage T7 DNA Polymerase of Low Processivity by Suppressor Mutations Affecting Gene 3 Endonuclease." Journal of Virology 83, no. 17 (June 17, 2009): 8418–27. http://dx.doi.org/10.1128/jvi.00855-09.

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ABSTRACT The DNA polymerase encoded by gene 5 (gp5) of bacteriophage T7 has low processivity, dissociating after the incorporation of a few nucleotides. Upon binding to its processivity factor, Escherichia coli thioredoxin (Trx), the processivity is increased to approximately 800 nucleotides per binding event. Several interactions between gp5/Trx and DNA are required for processive DNA synthesis. A basic region in T7 DNA polymerase (residues K587, K589, R590, and R591) is located in proximity to the 5′ overhang of the template strand. Replacement of these residues with asparagines results in a threefold reduction of the polymerization activity on primed M13 single-stranded DNA. The altered gp5/Trx exhibits a 10-fold reduction in its ability to support growth of T7 phage lacking gene 5. However, T7 phages that grow at a similar rate provided with either wild-type or altered polymerase emerge. Most of the suppressor phages contain genetic changes in or around the coding region for gene 3, an endonuclease. Altered gene 3 proteins derived from suppressor strains show reduced catalytic activity and are inefficient in complementing growth of T7 phage lacking gene 3. Results from this study reveal that defects in processivity of DNA polymerase can be suppressed by reducing endonuclease activity.

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Harker, Alyssa J., Harshwardhan H. Katkar, Tamara C. Bidone, Fikret Aydin, Gregory A. Voth, Derek A. Applewhite, and David R. Kovar. "Ena/VASP processive elongation is modulated by avidity on actin filaments bundled by the filopodia cross-linker fascin." Molecular Biology of the Cell 30, no. 7 (March 21, 2019): 851–62. http://dx.doi.org/10.1091/mbc.e18-08-0500.

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Ena/VASP tetramers are processive actin elongation factors that localize to diverse F-actin networks composed of filaments bundled by different cross-linking proteins, such as filopodia (fascin), lamellipodia (fimbrin), and stress fibers (α-actinin). Previously, we found that Ena takes approximately threefold longer processive runs on trailing barbed ends of fascin-bundled F-actin. Here, we used single-molecule TIRFM (total internal reflection fluorescence microscopy) and developed a kinetic model to further dissect Ena/VASP’s processive mechanism on bundled filaments. We discovered that Ena’s enhanced processivity on trailing barbed ends is specific to fascin bundles, with no enhancement on fimbrin or α-actinin bundles. Notably, Ena/VASP’s processive run length increases with the number of both fascin-bundled filaments and Ena “arms,” revealing avidity facilitates enhanced processivity. Consistently, Ena tetramers form more filopodia than mutant dimer and trimers in Drosophila culture cells. Moreover, enhanced processivity on trailing barbed ends of fascin-bundled filaments is an evolutionarily conserved property of Ena/VASP homologues, including human VASP and Caenorhabditis elegans UNC-34. These results demonstrate that Ena tetramers are tailored for enhanced processivity on fascin bundles and that avidity of multiple arms associating with multiple filaments is critical for this process. Furthermore, we discovered a novel regulatory process whereby bundle size and bundling protein specificity control activities of a processive assembly factor.

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Fan, Zheng, Jennifer R. Devlin, Simon J. Hogg, Maria A. Doyle, Paul F. Harrison, Izabela Todorovski, Leonie A. Cluse, et al. "CDK13 cooperates with CDK12 to control global RNA polymerase II processivity." Science Advances 6, no. 18 (April 29, 2020): eaaz5041. http://dx.doi.org/10.1126/sciadv.aaz5041.

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The RNA polymerase II (POLII)–driven transcription cycle is tightly regulated at distinct checkpoints by cyclin-dependent kinases (CDKs) and their cognate cyclins. The molecular events underpinning transcriptional elongation, processivity, and the CDK-cyclin pair(s) involved remain poorly understood. Using CRISPR-Cas9 homology-directed repair, we generated analog-sensitive kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with cellular growth signaling pathways and/or DNA damage, with minimal effects on cell viability. In contrast, dual kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including widespread use of alternative 3′ polyadenylation sites. At the molecular level, dual kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define substantial redundancy between CDK12 and CDK13 and identify both as fundamental regulators of global POLII processivity and transcription elongation.

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Szabo, Horvath, Schad, Murvai, Tantos, Kalmar, Chemes, Han, and Tompa. "Intrinsically Disordered Linkers Impart Processivity on Enzymes by Spatial Confinement of Binding Domains." International Journal of Molecular Sciences 20, no. 9 (April 29, 2019): 2119. http://dx.doi.org/10.3390/ijms20092119.

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(1) Background: Processivity is common among enzymes and mechanochemical motors that synthesize, degrade, modify or move along polymeric substrates, such as DNA, RNA, polysaccharides or proteins. Processive enzymes can make multiple rounds of modification without releasing the substrate/partner, making their operation extremely effective and economical. The molecular mechanism of processivity is rather well understood in cases when the enzyme structurally confines the substrate, such as the DNA replication factor PCNA, and also when ATP energy is used to confine the succession of molecular events, such as with mechanochemical motors. Processivity may also result from the kinetic bias of binding imposed by spatial confinement of two binding elements connected by an intrinsically disordered (ID) linker. (2) Method: By statistical physical modeling, we show that this arrangement results in processive systems, in which the linker ensures an optimized effective concentration around novel binding site(s), favoring rebinding over full release of the polymeric partner. (3) Results: By analyzing 12 such proteins, such as cellulase, and RNAse-H, we illustrate that in these proteins linker length and flexibility, and the kinetic parameters of binding elements, are fine-tuned for optimizing processivity. We also report a conservation of structural disorder, special amino acid composition of linkers, and the correlation of their length with step size. (4) Conclusion: These observations suggest a unique type of entropic chain function of ID proteins, that may impart functional advantages on diverse enzymes in a variety of biological contexts.

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Nara, I., and S. Ishiwata. "1O1500 Temperature dependence of kinesin processivity." Seibutsu Butsuri 42, supplement2 (2002): S91. http://dx.doi.org/10.2142/biophys.42.s91_2.

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Rosenfeld, Steven S., and H. Lee Sweeney. "A Model of Myosin V Processivity." Journal of Biological Chemistry 279, no. 38 (July 14, 2004): 40100–40111. http://dx.doi.org/10.1074/jbc.m402583200.

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Barel, Itay, Norbert O. Reich, and Frank L. H. Brown. "Extracting enzyme processivity from kinetic assays." Journal of Chemical Physics 143, no. 22 (December 14, 2015): 224115. http://dx.doi.org/10.1063/1.4937155.

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Bonderoff, J. M., and R. E. Lloyd. "Time-dependent increase in ribosome processivity." Nucleic Acids Research 38, no. 20 (June 22, 2010): 7054–67. http://dx.doi.org/10.1093/nar/gkq566.

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Krementsova, Elena B., Alex R. Hodges, Hailong Lu, and Kathleen M. Trybus. "Processivity of Chimeric Class V Myosins." Journal of Biological Chemistry 281, no. 9 (December 23, 2005): 6079–86. http://dx.doi.org/10.1074/jbc.m510041200.

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Higuchi, Hideo, and Sharyn A. Endow. "Directionality and processivity of molecular motors." Current Opinion in Cell Biology 14, no. 1 (February 2002): 50–57. http://dx.doi.org/10.1016/s0955-0674(01)00293-9.

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Lawrence, Michael S., and David P. Bartel. "Processivity of Ribozyme-Catalyzed RNA Polymerization†." Biochemistry 42, no. 29 (July 2003): 8748–55. http://dx.doi.org/10.1021/bi034228l.

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Yildiz, Ahmet. "The Mechanism of Cytoplasmic Dynein Processivity." Biophysical Journal 102, no. 3 (January 2012): 371a. http://dx.doi.org/10.1016/j.bpj.2011.11.2029.

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Xie, Ping, Shuo-Xing Dou, and Peng-Ye Wang. "Processivity of single-headed kinesin motors." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1767, no. 12 (December 2007): 1418–27. http://dx.doi.org/10.1016/j.bbabio.2007.09.006.

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Barel, Itay, and Frank L. H. Brown. "Extracting Enzyme Processivity from Kinetic Assays." Biophysical Journal 110, no. 3 (February 2016): 241a. http://dx.doi.org/10.1016/j.bpj.2015.11.1326.

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Bhattacharyya, Sanjib, Kyongwan Kim, and Winfried Teizer. "Restoring the Processivity of Kinesin Nanomotors." Advanced Biosystems 1, no. 3 (February 2, 2017): 1600034. http://dx.doi.org/10.1002/adbi.201600034.

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Journal articles on the topic 'Processivité'

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