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• W2068950689 abstract "In their article recently published in the Biophysical Journal, Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar) present a theoretical analysis of experimental data that we have previously published and analyzed (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar). Our work provided evidence for a random mechanism of inorganic phosphate (Pi) release subsequent to chemical cleavage of ATP on individual actin filaments. Burnett and Carlsson examine the alternative possibility of cooperativity during Pi release in actin filaments. We find that the presentation of our work by Burnett and Carlsson is misleading or incorrect in several instances, and wish to clarify the following points. In our article, depolymerization traces of individual filaments were measured, and each individual curve was fitted to investigate the possibility of different Pi release mechanisms. For the sake of comparison with Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar), we focus here on direct fits of depolymerization traces, which are detailed in the Supporting Material of our article, but the same conclusions are drawn when fitting the inverse of the depolymerization velocity, as we have done in the main text (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar). The best fits were obtained for a random Pi release model, and the release rates were found to be similar, but not identical (due to experimental noise) for each curve, with an average value of rd = 0.0074 s−1 (0.0068 s−1 with the inverse depolymerization velocity method). Our experimental data used by Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar) consists of the depolymerization trace of one single individual filament, which they have extracted from Fig. 2 B of Jégou et al. (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar). When comparing this individual depolymerization trace with traces computed for a random Pi release, Burnett and Carlsson use the average rate constant of rd = 0.0074 s−1 and the resulting curves do not agree well with the data (Fig. 6 D of Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar)). However, this is not a fit of this data. Our fit of this individual trace results in rd = 0.0045 s−1 (or rd = 0.0043 s−1, as stated in the caption of Fig. 2 of Jégou et al. (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar), using the inverse depolymerization velocity method), and the quality of this fit is very good, with Δ2 = 1.2 · 10−2 μm2, better in fact than the best fits with cooperativity shown in the inset of Fig. 6 (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar). Measuring the depolymerization traces of individual filaments, as we have done, allows one to look for details that would disappear when curves are averaged. As can be seen in Fig. 6 D of Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar), for a random Pi release there is little difference between individual curves, and it therefore makes sense to compare individual experimental traces to an average theoretical curve. In contrast, for the cooperative model, as shown in Fig. 6 C of Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar), each individual filament displays its own sharp transitions between ADP and ADP-Pi domains, which are smoothed out when averaging several traces. Comparing an individual experimental trace to an average theoretical curve, as done by Burnett and Carlsson—“the average trajectory (…) provides a good fit to the data, as shown in Fig. 6 C” (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar)—makes no sense in this case. To argue in favor of cooperativity, Burnett and Carlsson should have demonstrated that sample filament traces (blue curves in Fig. 6 C of Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar)), and not the mean filament time-course (red curve in Fig. 6 C), provide a good fit to our single filament data (black dots in Fig. 6 C). As suggested by Burnett and Carlsson, comparing the depolymerization traces of filaments elongated at different rates (i.e., using different actin concentrations) is a good way to test whether Pi release is a purely random mechanism or involves cooperativity (Fig. 7 of Burnett and Carlsson (1Burnett M.M. Carlsson A.E. Quantitative analysis of approaches to measure cooperative phosphate release in polymerized actin.Biophys. J. 2012; 103: 2369-2378Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar)). The authors write: “Thus, repeating the experiment of Jégou et al. with varying G should provide additional constraints on the cooperativity.” Our article, however, seems to have been overlooked here too, because this experiment has actually been performed and reported as follows in Jégou et al. (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar): “Filaments elongated at different actin concentrations, i.e. different velocities, or for different durations all displayed the same age-dependence of depolymerization rate (Figure 2 F), confirming that the ADP-Pi content depends only on the age of the F-actin, as expected for a random Pi release mechanism.” Further in the article (2Jégou A. Niedermayer T. Romet-Lemonne G. et al.Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin.PLoS Biol. 2011; 9: e1001161Crossref PubMed Scopus (103) Google Scholar), we show (see Fig. 4 E) examples of ADP-Pi profiles obtained with a 10-fold difference in actin concentrations. Experiments over a broader range of actin concentrations might reveal some cooperativity, but our data is in better agreement with a random Phosphate release mechanism than with a vectorial or highly cooperative mechanism. Response to “On Phosphate Release in Actin Filaments”Burnett et al.Biophysical JournalJune 18, 2013In BriefJégou et al. disagree with some of the findings of our article (1). They argue that 1), a different value of the release rate rd can improve the fit to depolymerization dynamics obtained by the random release model; 2), plotting depolymerization dynamics of single filaments would be more appropriate than comparing an average to a single filament; and 3), data in their article (2) for the dependence of the phosphate time courses on initial actin concentration (during growth) supports the random release model. Full-Text PDF Open ArchiveQuantitative Analysis of Approaches to Measure Cooperative Phosphate Release in Polymerized ActinBurnett et al.Biophysical JournalDecember 05, 2012In BriefWe use stochastic simulations that treat several experimental probes of actin dynamics to explore the extent to which phosphate dissociation in filamentous actin may be cooperative. Phosphate time-courses from polymerization and copolymerization experiments of ATP- and ADP-actin are studied, including the effects of variations in filament-number concentration as well as single-filament depolymerization time-courses. We find that highly cooperative models are consistent with the treated experimental data. Full-Text PDF Open Archive" @default.
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• W2068950689 title "On Phosphate Release in Actin Filaments" @default.
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