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Treadmilling of actin filaments via Brownian dynamics simulations
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10.1063/1.3497001
/content/aip/journal/jcp/133/15/10.1063/1.3497001
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/15/10.1063/1.3497001

Figures

Image of FIG. 1.
FIG. 1.

Schematic view of the different processes that determine the time evolution of actin polymerization and ATP hydrolysis. Actin monomers and protomers with a bound ATP, , and ADP molecule are denoted by , and , respectively. The two conical regions at the barbed (right) and pointed (left) end of the filament have linear dimensions and . These regions represent capture zones for the diffusing monomers and determine the attachment rates and for these monomers at the two ends. The protomers of the filament are transformed into protomers with the ATP cleavage rate , the protomers are changed into protomers with the release rate . The two terminal protomers at the two filament ends can also detach from the filament as illustrated for a protomer at the barbed end and for a protomer at the pointed end. Since both terminal protomers can attain three different nucleotide states, one has to distinguish six detachment rates, see text.

Image of FIG. 2.
FIG. 2.

The overall growth rate as a function of free actin concentration . The two different sets of data have been obtained by measuring the average filament length (black squares) and the average waiting times between successive attachment and detachment events (red stars) as explained in the text. The transition rates are the same as in Table I.

Image of FIG. 3.
FIG. 3.

Filament length and positions of barbed and pointed end as functions of simulation time . The length is measured in units of protomer number (left -axis), the end positions are measured in units of the basic length scale (right -axis). The filament grows parallel to the long side of the simulation box, which has an extension of , the longitudinal extension of one protomer is . The transition rates are the same as in Table I, the free actin concentration is close to the critical concentration .

Image of FIG. 4.
FIG. 4.

Normalized histograms for time intervals between two successive monomer attachments and two successive protomer detachments at the (a) barbed and (b) pointed end. The parameters are the same as in Fig. 3.

Image of FIG. 5.
FIG. 5.

The three probabilities with , and for the terminal protomer at the (a) barbed and (b) pointed end as a function of free actin concentration . The transition rates are the same as in Table I.

Image of FIG. 6.
FIG. 6.

Overall growth rate as a function of free actin concentration for three different values of the rate , which governs the detachment of protomers from the barbed end. The other transition rates have the same values as in Table I.

Image of FIG. 7.
FIG. 7.

Overall growth rate as a function of free actin concentration for three different choices of the release rates and , which govern the internal and terminal protomers, respectively. The values of all other transition rates are in Table I.

Image of FIG. 8.
FIG. 8.

The density profiles (left) and (right) for , and protomers as a function of the spatial coordinate where is measured in units of the projected protomer size. The barbed end is located at , the pointed end at or . The values of the transition rates are given in Table I; the free actin concentration is .

Tables

Generic image for table
Table I.

Numerical values for the different transition rates as used in the simulations: Attachment rate constants for monomers; detachment rates for , , and protomers; ATP cleavage rate ; and release rate . All rates are given in units of 1/s, all rate constants in units of . The superscripts ba and po refer to the barbed and pointed end, respectively. Except for the detachment rate , all rates have the same numerical values as those in Table I of Ref. 23. The rate is determined by detailed balance in the absence of ATP hydrolysis.

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/content/aip/journal/jcp/133/15/10.1063/1.3497001
2010-10-19
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Treadmilling of actin filaments via Brownian dynamics simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/15/10.1063/1.3497001
10.1063/1.3497001
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