RESEARCH ARTICLE

elifesciences.org

Cofilin-induced unidirectional cooperative
conformational changes in actin filaments
revealed by high-speed atomic force
microscopy
Kien Xuan Ngo1†, Noriyuki Kodera2,3*†, Eisaku Katayama4, Toshio Ando2,5,Taro QP Uyeda1,6,7*
Biomedical Research Institute, National Institute of Advanced Industrial Science andTechnology, Tsukuba, Japan; 2Department of Physics and Bio-AFM Frontier ResearchCenter, Kanazawa University, Kanazawa, Japan; 3Precursory Research for Embryonic
Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan;
4
Department of Biology, Graduate School of Science, Osaka City University, Osaka,
Japan; 5Core Research for Evolutionary Science and Technology, Japan Science andTechnology Agency, Kawaguchi, Japan; 6Graduate School of Life and Environmental
Sciences, University of Tsukuba, Tsukuba, Japan; 7Graduate School of Medical Life
Science, Yokohama City University, Yokohama, Japan
1

Abstract High-speed atomic force microscopy was employed to observe structural changes in*For correspondence: nkodera@
staff.kanazawa-u.ac.jp (NK);t-uyeda@aist.go.jp (TQU)
These authors contributed
equally to this work†

Competing interests: The
authors declare that nocompeting interests exist.

actin filaments induced by cofilin binding. Consistent with previous electron and fluorescencemicroscopic studies, cofilin formed clusters along actin filaments, where the filaments were 2-nm
thicker and the helical pitch was ∼25% shorter, compared to control filaments. Interestingly, theshortened helical pitch was propagated to the neighboring bare zone on the pointed-end side of
the cluster, while the pitch on the barbed-end side was similar to the control. Thus, cofilin clusters
induce distinctively asymmetric conformational changes in filaments. Consistent with the idea that
cofilin favors actin structures with a shorter helical pitch, cofilin clusters grew unidirectionally toward
the pointed-end of the filament. Severing was often observed near the boundaries between barezones and clusters, but not necessarily at the boundaries.
DOI: 10.7554/eLife.04806.001

Funding: See page 19
Received: 17 September 2014
Accepted: 02 January 2015
Published: 02 February 2015
Reviewing editor: Brad J Nolen,
Institute of Molecular Biology,
University of Oregon,
United States
Copyright Ngo et al. This
article is distributed under theterms of the Creative Commons
Attribution License, which
permits unrestricted use andredistribution provided that theoriginal author and source arecredited.

Introduction
Actin filaments are involved in a variety of important functions in eukaryotic cells, including muscle
contraction, amoeboid movement, cytokinesis, intracellular transport, and transcriptional regulation
within the nucleus. These diverse functions depend on the interaction between actin and specific actin
binding proteins (ABPs), and it is generally assumed that specific biochemical signaling is involvedin the spatial and temporal regulation of each actin–ABP interaction. During migration of amoeboid
cells, for instance, cofilin plays essential roles in continuous extension of lamellipodia by severing actin
filaments to promote filament depolymerization or to initiate polymerization from new barbed ends
(reviewed by Bravo-Cordero et al., 2013). Three independent biochemical mechanisms are known to
inhibit cofilin activity; phosphorylation of Ser3, sequestration to phosphatidylinositol 4,5-bisphosphate(PIP2) in plasma membrane, and lower pH (Bernstein and Bamburg, 2010; Bravo-Cordero et al., 2013).
These inhibitory mechanisms are implicated in the regulation of cofilin activity during cell migration, since experimental unleashing of inactive cofilin has been shown to initiate cofilin-dependent
processes (Bernstein and Bamburg, 2010; Bravo-Cordero et al., 2013). Critically speaking, however,

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eLife digest Actin is one of the most abundant proteins found inside all eukaryotic cells
including plant, animal, and fungal cells. This protein is involved in a wide range of biologicalprocesses that are essential for an organism's survival. Actin proteins form long filaments that help
cells to maintain their shape and also provide the force required for cells to divide and/or move.
Actin filaments are helical in shape and are made up of many actin subunits joined together.
Actin filaments are changeable structures that continuously grow and shrink as new actin subunits
are added to or removed from the ends of the filaments. One end of an actin filament grows fasterthan the other; the fast-growing end is known as the barbed-end, while the slow-growing end isreferred to as the pointed-end.
Over 100 other proteins are known to bind to and work with actin to regulate its roles in cells
and how it forms into filaments. Cofilin is one such protein that binds to and forms clusters on actin
filaments and it can also sever actin filaments. Severing an actin filament can encourage the filament
to disassemble, or it can help produce new barbed ends that can then grow into new filaments.
Previous work had suggested that cofilin severs actin filaments at the junction between regions on
the filament that are coated with cofilin and those that are not. It was also known that cofilinbinding to a filament causes the filament to change shape, and that the shape change is propagatedto neighboring sections of the filaments not coated with cofilin. However, the details of where
cofilin binds and how changes in shape are propagated along an actin filament were not known.
Furthermore, the findings of these previous studies were largely based on examining still images ofactin filaments, which are unlike the constantly changing filaments of living cells.
Ngo, Kodera et al. have now analyzed what happens when cofilin binds to and forms clusters
along actin filaments using a recently developed imaging technique called high-speed atomic force
microscopy. This technique can be used to directly visualize individual proteins in action. Consistent
with previous findings, Ngo, Kodera et al. observed that filaments coated with cofilin are thicker
than those filaments without cofilin; and that cofilin binding also substantially reduces the helicaltwist of the filament. Ngo, Kodera et al. also found that these changes in shape are propagatedalong the filament but in only one direction—towards the pointed-end. Moreover, cofilin clusters
also only grew towards the pointed-end of the actin filament—and the filaments were often
severed near, but not exactly at, the junctions between cofilin-coated and uncoated regions. Such
one-directional changes in shape of the actin filaments presumably help to regulate how other actin
binding proteins can interact with the filament and consequently regulate the roles of the filaments
themselves.
DOI: 10.7554/eLife.04806.002

these data do demonstrate that active cofilin is required, but there is little experimental evidence that
localized activation of cofilin is necessary for proper cofilin functions in cell migration. Indeed, overexpression of constitutively active S3A cofilin did not inhibit motility (Endo et al., 2003; Popow-Wozniak
et al., 2012). Thus, biochemical signaling is not sufficient to explain how cofilin activities are properly
regulated spatially and temporally in cells.
On the other hand, many ABPs alter the atomic structure of actin subunits within filaments, andin certain cases these conformational changes are cooperative. For instance, the pioneering work of
Oosawa and his colleagues demonstrated that the increase in fluorescence intensity of a fluorophoreon actin saturates when only one molecule of the myosin motor domain is added for each 10 actin
subunits within filaments (Oosawa et al., 1973). Similar myosin-induced cooperative conformationalchanges have been detected in various other assays (Tawada, 1969; Fujime and Ishiwata, 1971;
Loscalzo et al., 1975; Miki et al., 1982; Prochniewicz et al., 2010). In addition, dense binding of
cofilin shortens the helical pitch of actin filaments by 25% (McGough et al., 1997; Galkin et al., 2001;
Sharma et al., 2011), and time-resolved phosphorescence anisotropy (Prochniewicz et al., 2005) anddifferential scanning calorimetry (Dedova et al., 2004; Bobkov et al., 2006) showed that one molecule of bound cofilin changes the structure of ∼100 actin subunits within a filament. Moreover, bindingof cofilin to actin filaments is cooperative (Hawkins et al., 1993; Hayden et al., 1993; McGoughet al., 1997; De La Cruz, 2005; Hayakawa et al., 2014). This implies that cooperative conformationalchanges induced by an ABP are propagated to neighboring actin subunits, increasing their affinity for

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that, or another, ABP. This could provide a novel mechanism by which actin filaments change theirfunction by regulating their affinities for various ABPs (Tokuraku et al., 2009; Michelot and Drubin,
2011; Schoenenberger et al., 2011; Uyeda et al., 2011; Galkin et al., 2012; Romet-Lemonne andJegou, 2013).
However, the currently available information on structural changes to actin filaments is limited tohigh-resolution static images (electron microscopy), low-resolution dynamic changes (fluorescencemicroscopy), and bulk biochemical analyses. There is little information available in the molecular mechanism that mediates the propagation of structural changes to neighboring actin subunits. Atomic
force microscope (AFM) is unique in that it enables detailed structural analysis of wet protein samples(Müller and Dufrêne, 2008), and recent dramatic improvements in scanning speed now enables realtime imaging of conformational changes in protein samples with high-spatial resolution (Ando et al.,2013). This high-speed AFM (HS-AFM) has been used to visualize molecular movements such as the
stepping motion of myosin V along actin filaments (Kodera et al., 2010), rotary catalysis of F1 ATPase
without a rotor (Uchihashi et al., 2011), and light-induced conformational changes in bacteriorhodopsin (Shibata et al., 2010). Here, we used HS-AFM to directly visualize conformational changes in
actin filaments induced by cofilin binding. We found that conformational changes within cofilin clusters
unidirectionally propagate to the neighboring bare actin zone in a cooperative manner and that thegrowth of the cofilin cluster follows this unidirectional cooperative conformational change.

Results
Observation of actin filaments on a supported lipid bilayer
For AFM, actin filaments must be immobilized on the stage, yet they must have the freedom of movement to bind cofilin and exhibit the resultant changes in the helical twist that accompany cofilinbinding. We therefore formed a bilayer of positively charged lipid on the surface of freshly peeled mica
(Yamamoto et al., 2010) fixed to the observation stage. A solution of actin filaments was then placedon the supported lipid bilayer and HS-AFM was performed. Right-handed double helical filaments
were clearly visualized (Figure 1), as in earlier reports (Weisenhorn et al., 1990; Schmitz et al., 2010).
We approximated the positions of the crossover points, where the two strands of actin filament arealigned vertically, using the position of the highest point (peak) in each half helix identified in the AFM
images. Quantitative analysis indicated that the height of those peaks, or the thickness of the filaments, was 8.6 ± 0.8 nm (average ± SD), and the spacing between the peaks, or half helical pitch, was36.8 ± 4.3 nm (Figure 1D,E). These values, which are consistent with previously reported structural
data (Hanson and Lowy, 1963; Hanson, 1973; Egelman et al., 1982), will hereafter be referred to as
normal height and normal half helical pitch, respectively. The distribution of half helical pitches ranged
from ∼26 nm to ∼45 nm and was well fit by a normal distribution with a standard deviation of 4.3 nm.
This distribution should reflect natural variation in half helical pitch, as was proposed on the basis ofa similar distribution of half helical pitches in electron micrographs of negatively stained specimens(Hanson, 1967; Egelman et al., 1982) and also measurement errors. To assess the overall magnitudeof the measurement errors, we prepared paracrystals of actin filaments in the presence of 30 mM
MgCl2 (Figure 1C) (Hanson, 1973). The distribution of the half helical pitches of the paracrystals measured under the same conditions was narrower than that of free filaments, with a mean of 36.5 nm andstandard deviation of 3.0 nm (Figure 1F). In a hypothetical case where the paracrystals do not undergo
spontaneous conformational changes, this distribution is the upper limit of the measurement errors inour system. Furthermore, assuming normal distributions of the true half helical pitches and measurement errors, the true standard deviation of the half helical pitches of control filaments was calculated
to be 3.1 nm or larger, by subtracting the variance of the actin paracrystals from that of control filaments.
This indicated that the structure of the actin filaments does indeed vary with changes in helical twist.

Observation of actin filaments fully bound with cofilin
When 75 nM cofilin was added to actin filaments immobilized on the lipid surface, cofilin graduallybound to the actin filaments, and sections of filaments bound with cofilin molecules were easily identified, as the bound filaments appeared thicker and the peaks were taller (Figure 1B). Peak heights
within long cofilin clusters (longer than eight consecutive half helices) showed a single distribution of
10.6 nm ± 1.0 nm, approximately 2 nm taller than the control filaments (Figure 1D). This is consistent
with electron microscopic analysis (Galkin et al., 2011), which showed that filaments fully decorated

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Figure 1. HS-AFM observation of control and cofilin-bound actin filaments. (A) Control actin filaments without
cofilin. (B) Actin filaments fully bound with cofilin over an extended distance. (C) Paracrystals of actin filaments.
Bars: 25 nm, Z-scale: 0–12 nm. (D and E) Histograms of peak heights (D) and lengths of half helical pitches (E) incontrol actin filaments and cofilin-decorated actin segments. N was between 1722 and 2536. (F) Half helical pitchesof actin paracrystals (N = 1009). Solid lines show Gaussian fittings with confidence intervals of 99.73%. For comparison, the dark line in (F) shows the Gaussian fitting of control actin filaments. Measurements were made in F buffer
containing 1 mM ATP (A), 1 mM ATP, and 75 nM cofilin (B) or 1 mM ATP and 30 mM MgCl2 (C). Student's t-test
comparing control and cofilin-decorated actin segments showed that the differences in peak heights and half
helical pitches are statistically significant at p ≤ 0.00001. The mean of the half helical pitches of control actin
filaments and paracrystals did not differ significantly. Models of control actin filaments and cofilin-decorated actin
filaments with two different orientations on substrates are shown in Figure 1—figure supplement 1.
DOI: 10.7554/eLife.04806.003
The following figure supplement is available for figure 1:
Figure supplement 1. Models of control actin filaments and cofilin-decorated filaments on a flat substrate.
DOI: 10.7554/eLife.04806.004

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with cofilin are ∼2.3-nm thicker than control filaments due to the presence of cofilin molecules(Figure 1—figure supplement 1). Moreover, the height distribution was fit well by a single normal
distribution, which suggests that within those long cofilin clusters, both actin strands are homogeneously bound with cofilin molecules.
Cofilin binding shortened the half helical pitch by 27% to 26.9 nm (Figure 1E), which is again consistent with earlier electron microscopic (McGough et al., 1997; Galkin et al., 2001) and AFM analyses(Sharma et al., 2011). The standard deviation of the distribution of half helical pitches of the fully cofilindecorated filaments was 3.8 nm, and subtracting the maximum possible measurement error yielded astandard deviation of 2.3 nm or larger. This value is smaller than that of the control filaments (3.1 nm)
and suggests that cofilin binding restricts torsional movements of the filaments within cofilin clusters.

Half helical pitch on either side of the cofilin cluster
We next analyzed shorter cofilin clusters along otherwise apparently bare filaments (Figure 2) so thatboth ends of the cluster were visible within the imaged area. Intriguingly, we noticed that the half
helical pitch in the apparently bare section on one side of the cofilin cluster was short, while the pitchon the other side of the cluster was nearly normal.
The observation buffer was then changed to F buffer containing 0.1 mM ATP, 1 mM ADP, hexokinase, glucose, 20 nM subfragment-1 (S1) of skeletal myosin II, and 75–100 nM cofilin, so that thepolarity of the actin filaments could be identified from the characteristic tilted binding angle seen
when S1 transiently binds the filament (Huxley, 1963). This analysis revealed that the half helical pitchof the bare zone on the pointed-end side of the cofilin cluster was short, while that on the barbed-end
side was slightly longer than the normal pitch (Figure 2 and Table 1). Student's t-test indicated thatthe differences in the mean half helical pitches between the first neighbor bare zone on either side of
the cluster and the control filaments are statistically significant (p < 0.00001 and p < 0.001 for pointedend and barbed-end side, respectively). Pitches of the neighboring half helices second from the cofilinclusters were nearly normal (Table 1).

Half helical pitch around sparsely bound cofilin
The results summarized above demonstrate that cofilin clusters induce distinctively asymmetric conformational changes in bare zones immediately neighboring the clusters, but it is still uncertain whether
a stretch of many bound cofilin molecules, as in clusters, is necessary to induce such conformationalchanges. To answer that question, we needed to visualize individual cofilin molecules bound to actin
filaments, and measure the half helical pitch of the filament around those bound molecules. This has
not been possible because cofilin molecules are too small to image individually using electron microscopy or AFM. We therefore engineered a fusion protein in which the N-terminal half of the rod domainof α-actinin was attached to the C-terminus of cofilin. In electron micrographs of negatively stained
specimens (Figure 3A), as well as in HS-AFM images (Video 1 and Figure 3—figure supplement 4),
we were able to see clusters of cofilin-rod with a half helical pitch ∼25% shorter than the bare zones,
which is similar to control cofilin molecules bound to actin filaments (Figure 3C).
Rod-like structures were often observed to stick out from apparently bare sections of the filaments(Figure 3B). These are most likely the rod portions of the cofilin-rod molecules bound sparsely along
seemingly bare sections of the filaments, because their length was ∼10 nm, which is expected for half
an α-actinin rod (Yan et al., 1993; Anson et al., 1996), and because similar rod-like structures wererarely observed in control images of cofilin added to actin filaments (Figure 3C). We therefore estimated the helical pitches on both sides of single rod-like structures sticking out from the filaments bymeasuring the filament length that encompassed three actin subunits along one strand on either sideof the bound molecule. In addition, because we did not know the polarity of each filament, we compared the helical pitches on both sides by dividing the longer helical pitch by the shorter one. This
yielded a value of 1.02 ± 0.02 (average ± SD, n = 9), which was much smaller than the 1.30 ± 0.18
(n = 4) measured for cofilin clusters in electron micrographs or 1.37 calculated from the AFM data
(Figure 1E) and was comparable to the value of randomly selected regions along control actin filaments (1.04 ± 0.05, n = 18). Furthermore, the helical pitches around the apparently singly boundcofilin-rod molecules (36.0 ± 1.0 nm, n = 5) did not significantly differ from the control helical pitch(36.3 ± 1.0 nm, n = 8) measured in electron micrographs.
In HS-AFM observations, we were able to observe four cases of an apparently single cofilin-rod
molecule binding transiently to an actin filament (Figure 3D and Video 2). Consistent with the electron

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Figure 2. Asymmetric structure of bare actin zones neighboring a cofilin cluster. (A and B) HS-AFM image of a short
cofilin cluster transiently associating with two S1 molecules (yellow arrowheads), which persisted for ∼1 s, enabling
identification of the filament polarity (B). Measurements were made in F buffer containing 20 nM S1, 75 nM cofilin,
1 mM ADP, and 0.1 mM ATP. Bar: 25 nm; Z-scale: 0–12 nm. (C and D) Time-dependent changes in the heights of theindicated peaks (white arrowheads) and half helical pitches between the indicated peaks. (E and F) Histograms of
the lengths of the half helical pitches of bare actin segments immediately neighboring cofilin clusters. Filaments
were incubated in F buffer containing 1 mM ADP and 0.1 mM ATP for 5 min before observation (E) as in (A and B)
or were incubated in F buffer containing 1 mM ADP for 30 min before observation (F). Pitches of the half helices ofthe first immediate neighbor on each side of cofilin clusters were measured. These values, together with those forthe second neighbors, are summarized in Table 1.
DOI: 10.7554/eLife.04806.005

microscopic observation described above, we were unable to detect significant changes in peak heights
and half helical pitches, such as those observed around cofilin clusters, around those singly boundcofilin-rod molecules (Figure 3E,F).
These results suggest that a single cofilin molecule cannot induce conformational changes, either
symmetric or asymmetric, that involve detectable changes in helical pitch when it binds to bare sections of the filament.

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Table 1. Peak heights and lengths of half helical pitches in bare actin segments neighboring cofilinclusters
1 mM ADP + 0.1 mM ATP

1 mM ADP

Peak height (nm) Half helix (nm) Peak height (nm) Half helix (nm)First neighbor on the P-end side 9.2 ± 1.0

28.8 ± 4.5

8.9 ± 1.0

28.7 ± 4.7

Second neighbor on the
P-end side

9.1 ± 1.0

36.5 ± 4.1

8.8 ± 1.1

36.9 ± 4.9First neighbor on the B-end side 9.0 ± 0.9

37.3 ± 4.6

8.7 ± 0.9

38.4 ± 4.3

Second neighbor on the
B-end side

35.4 ± 3.9

8.7 ± 0.8

36.7 ± 4.2

9.2 ± 0.6

Actin filaments were incubated in F buffer containing 1 mM ADP and 0.1 mM ATP for 5 min or in F buffer containing
1 mM ADP for 30 min prior to the addition of cofilin. Filaments under the latter condition were shorter than thoseunder the former condition and were apparently in the process of spontaneous depolymerization.
Each mean and SD were calculated from 423 to 446 data.
DOI: 10.7554/eLife.04806.006

Growth of the cofilin clusters
Real time AFM imaging taken at 1.5 or 2 frames/s enabled us to follow the growth of individual cofilinclusters along actin filaments. In the case illustrated in Figure 4A and Video 3, observed in F buffer
containing 1 mM ADP and 0.1 mM ATP, P4 was already tall when imaging started (∼10.5 nm, averageof t = 0–5 s), while P3 had an intermediate height (∼9.5 nm), and P1 and P2 were normal (∼8.5 nm)(Figure 4A, middle). We interpreted this to mean that the initial cofilin cluster extended beyond P4 but
ended near P3. P3 gradually became taller and plateaued beyond ∼25 s. Thereafter, P2 started to riseat ∼15 s and plateaued at ∼63 s, whereas P1 started to rise at ∼60 s. The distance between P2 and P3
rapidly shortened to ∼27 nm between 0 and 15 s, before P2 started to rise, while the distance between
P1 and P2 shortened between 30 and 40 s, before P1 started to rise (Figure 4A, bottom). This sequenceof events implies gradual growth of this cofilin cluster into the neighboring bare zone on the pointedend side where the helical pitch was shortened.
Cofilin binds preferentially to actin subunits carrying ADP, compared to those carrying ATP or ADP
and Pi (Carlier et al., 1997; Blanchoin and Pollard, 1999). Since actin filaments in F buffer containing
ATP should have ATP–actin caps near the barbed ends, and since subunits on the pointed-end side
tend to carry ADP only due to ATP hydrolysis and Pi release (Carlier, 1990), the directional growthof cofilin clusters toward the pointed-end might reflect the asymmetric distribution of actin subunits
with different nucleotides. To test this possibility, we prepared two different types of actin filamentswith homogenous nucleotide states along the lengths. In the first case, filaments polymerized in buffer
containing 1 mM ATP were incubated for 30 min in buffer containing 1 mM ADP, which is much longer
than the 350 s required to hydrolyze ATP and release the resultant Pi from half of the polymerizing
ATP–actin molecules (Melki et al., 1996), so that most of the actin subunits should carry ADP only. In
the second case, filaments polymerized in buffer containing 1 mM ATP were incubated for 10 min in
buffer containing 1 mM ADP and 10 mM Pi. Under this condition, most of the actin subunits should
carry ADP and Pi, considering a Kd of 1.5 mM for Pi (Carlier and Pantaloni, 1988). HS-AFM observations after the addition of 20 nM S1 and 75 nM cofilin or 150 nM S1 and 900 nM cofilin demonstrated
that, in both cases, the growth of cofilin clusters was primarily to the pointed-end direction (Figure 4B
and Video 4, and Figure 4C and Video 5). Results of a large number of observations are compiled in
Figure 5.
The rate of formation and growth of cofilin clusters depended on the nucleotide state of actin subunits as well as the concentration of cofilin. In most experiments we used 75 nM cofilin since we wereable to observe de novo formation of clusters and tractable growth, after mixing and settling of thesystem. When 1 µM cofilin was added and mixed, we were unable to find bare zones of actin filaments.
When actin filaments were incubated with 1 mM ADP and 10 mM Pi, much higher concentrations ofcofilin (e.g., 900 nM) was needed to induce cofilin clusters. The growth rates of cofilin clusters were
within tractable range even in the presence of 1 µM cofilin, when 10 mM Pi was present (Figure 4C).
These results are consistent with the weaker affinity of cofilin for actin subunits carrying ADP and Pi(Carlier et al., 1997; Blanchoin and Pollard, 1999).

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Figure 3. Actin filaments with bound cofilin or cofilin-rod fusion protein. (A–C) are electron micrographs ofnegatively stained samples, and (D) is a HS-AFM image of a sample similar to that shown in (B). (A) Actin filamentsbound with cofilin-rod. Arrowheads show crossover points in clusters of cofilin-rod. The rod portions of the fusion
proteins are not readily visible, which may be due to alignment of the rods along the cofilin clusters. Severing
activity and stoichiometric binding of cofilin-rod to actin filaments were confirmed by HS-AFM (Video 1) andco-sedimentation assays (Figure 3—figure supplement 3), respectively. (B) Cofilin-rod molecules sparsely boundto actin filaments, identified by the rod-like structures (black arrowheads). (C) Actin filaments with bound cofilinmolecules (without rod fusion). Arrowheads show crossover points in clusters. Actin filaments and cofilin or
cofilin-rod were mixed at a 2:1 (A and C) or 1:1 (B) molar ratio in F buffer containing 1 mM ATP. Bars: 25 nm.
(D) HS-AFM image of an actin filament and an apparently singly bound cofilin-rod molecule (blue arrowhead in theupper image) near P2 (white arrowhead). Conditions: F buffer containing 1 mM ATP and 75 nM cofilin-rod (without
His-tag). Bar: 25 nm. See Video 2. (E) shows heights of the three peaks and (F) shows spacing between them.
DOI: 10.7554/eLife.04806.007
The following figure supplements are available for figure 3:
Figure supplement 1. Co-sedimentation of cofilin (with or without His-tag) with actin filaments.
DOI: 10.7554/eLife.04806.008
Figure supplement 2. Actin binding curves of cofilin and cofilin without His tag.
DOI: 10.7554/eLife.04806.009
Figure supplement 3. Co-sedimentation of cofilin-rod with (+) and without (−) His-tag.
DOI: 10.7554/eLife.04806.010
Figure supplement 4. Representative still images from Video 1, demonstrating cluster formation and severingfunction of cofilin-rod without His-tag.
DOI: 10.7554/eLife.04806.011

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Severing of filaments by cofilin
Cofilin is an actin filament severing protein(reviewed by Pollard (2000)), and although ourexperiments were performed at pH 6.8, whichshould suppress severing activity (Yonezawa
et al., 1985; Hawkins et al., 1993; Pavlov et al.,2006), we observed frequent severing of thefilaments near or within short cofilin clusters
Video 1. Cluster formation and severing functions of(Figure 6A–C, Videos 6–10 and Figure 6—
cofilin-rod. Conditions: F buffer containing 1 mM ATP,and 300 nM cofilin-rod without His-tag, imaging rate:
figure supplements 1 and 2). Because a previous
2 frames/s, and playing rate: 5 frames/s. White
study by Adrianantoandro and Pollard (2006)
arrowheads indicate clusters of cofilin-rod, and red andfound that severing activity is highest at 10 nM
blue arrowheads show severing points inside a clusterof human cofilin and that this activity sharply
and in a bare half helix immediately neighboring adeclines above and below 10 nM, we observed
cluster, respectively. Z-scale was 0–12 nm. Related tosevering events at several different cofilin conFigure 3—figure supplement 4.
centrations, including 10 nM. In the presence of
DOI: 10.7554/eLife.04806.012
10 or 20 nM cofilin, severing was very infrequent(Video 11 and Figure 6—figure supplement 3).
Severing was often observed between 40(Video 12 and Figure 6—figure supplement 4)
and 200 nM cofilin. In the presence of 650 nM
cofilin, many of the filaments were fully decorated
with cofilin when observations started, and severing was observed exclusively near the ends of thelong clusters (Video 12 and Figure 6—figure
supplement 4). When the cofilin concentration
was increased to 1 µM, all the filaments were
fully decorated with cofilin, and severing wasVideo 2. Sparse binding of individual cofilin-rod
infrequent along those fully decorated filaments
molecules to actin filaments. Conditions: F buffer(Video 12). Thus, we also observed that cofilin's
containing 1 mM ATP and 75 nM cofilin-rod without
severing activity was highest in the medium conHis-tag, imaging rate: 4 frames/s, and playing rate:
centration range (i.e., 40–200 nM), but this con5 frames/s. Transient binding of cofilin-rod to andcentration is at least several-fold higher thandissociation from an actin filament was followed forthat reported by Adrianantoandro and Pollard
approximately 90.5 s, shown by the presence and(2006). These two studies used the same pair ofabsence of a blue arrowhead. No severing wasproteins (i.e., skeletal muscle actin and humanobserved in all four similar cases of successful imagingof sparse binding of cofilin-rod to actin filaments.
cofilin), and we can only speculate that this disZ-scale was 0–12 nm. Related to Figure 3D.
crepancy is due to differences in experimental
DOI: 10.7554/eLife.04806.013
conditions.
We next quantitatively analyzed the severing
positions of the filaments relative to the short
cofilin clusters in the presence of 40–200 nM cofilin (Figure 6D). Approximately 60% of severing
events occurred inside the cofilin clusters, mostly within half helices neighboring bare zones. Severing
also occurred in half helices in bare zones neighboring a cofilin cluster, which accounted for approximately 40% of severing events. Overall, ∼80% of the severing events occurred within one-half of ahelix on either side of the boundary between a bare zone and a cofilin cluster. Severing in bare zones
far from cofilin clusters was very rare.
In the presence of 40 nM cofilin, the lowest concentration we used for quantitative severing assay,
we observed a total of 22 cases of severing events in 31 actin filaments. Among those, 18 cases
occurred in half helices immediately neighboring the boundary between a bare zone and a cofilincluster, even though cluster formation was relatively rare at this concentration of cofilin. Three cases
occurred in ‘far’ bare zones more than half a helix away from the boundary, and one occurred in an‘inner’ cofilin cluster more than half a helix away from the boundary (Video 11).
Based on these observations, we conclude that severing under the present experimental condition
preferentially occurs near the boundary between a bare zone and a cofilin cluster, but not necessarily
at the boundary. Considering the difference in spatial resolution, this conclusion is also consistent with
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Figure 4. Growth of cofilin clusters along actin filaments. Growth of cofilin clusters along actin filaments in F buffer containing 1 mM ADP and 0.1 mM
ATP (A), along actin filaments carrying ADP, prepared by incubating filaments in F buffer containing 1 mM ADP, hexokinase, and glucose at room
temperature for 30 min (B), and along actin filaments carrying ADP and Pi, prepared by incubating filaments in 1 mM ADP and 10 mM Pi for 10 min atroom temperature (C). The concentrations of cofilin were 75 nM (A and B) or 900 nM (C) and those of S1 were 20 nM (A and B) or 150 nM (C). Each panel
consists of four sequential snapshots (top), a figure showing the heights of the indicated peaks (middle), and the half helical pitches between theindicated peaks (bottom). Yellow arrowheads show the transient association of S1. Note that P1 in (A) and P3 in (B) rose in two substeps. Bars: 25 nm;
Z-scale: 0–12 nm.
DOI: 10.7554/eLife.04806.014

that made by Suarez et al. (2011), who used fluorescence microscopy and concluded that severing
occurs at the boundary between cofilin clusters and bare zones.

Discussion
Using HS-AFM to visualize wet samples with high-spatial and -temporal resolution, we were able tocreate an image of conformational changes in actin filaments induced by cofilin binding, including
asymmetric changes in the helical twist on either side of a bound cofilin cluster, growth of the clusters
toward the pointed-end, and the severing of filaments near the ends of cofilin clusters.

Unidirectional propagation of the cofilin-induced supertwisted
conformation
The short helical pitch in the cofilin clusters was propagated to the immediately neighboring bare zone
on the pointed-end side of the cluster. Since our current analysis method only measures heights andNgo et al. eLife 2015;4:e04806. DOI: 10.7554/eLife.04806

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Video 3. Growth of a cofilin cluster toward the pointedend of a filament in F buffer containing 1 mM ADP,
0.1 mM ATP, 20 nM S1, and 75 nM cofilin. Imaged at
2 frames/s and played at 5 frames/s. White arrowheads
show growth of the cofilin cluster, and yellow andmagenta arrowheads show binding of S1. Magenta
arrowheads indicate S1 molecules whose binding angle
could not be determined, either for geometric reasons(i.e., binding on the upper face of the filament) or
because the binding was too short-lived. Z-scale was
0–12 nm. For magnifications and polarity of the analyzed
filaments, refer to Figure 4 in the main text. Related to
Figure 4A.
DOI: 10.7554/eLife.04806.015

Video 4. Growth of a cofilin cluster toward the pointedend of a filament in F buffer containing 1 mM ADP,
20 nM S1, and 75 nM cofilin. Imaged at 2 frames/s andplayed at 5 frames/s. For color codes of arrowheads,
see the legend to Video 3. Z-scale was 0–12 nm. For
magnifications and polarity of the analyzed filaments,
refer to Figure 4 in the main text. Related to Figure 4B.
DOI: 10.7554/eLife.04806.016

distances between peaks, we were unable toexamine if the supertwisted structure returns to anormal state abruptly or gradually. Also, we wereunable to determine the positions of the ends ofcofilin clusters precisely above the spatial resolution of half helices, making it difficult to estimate
accurately how far the supertwisting conformational changes propagate into neighboring barezones. Nonetheless, the fact that the pitches of
the neighboring half helices second from the cofilin clusters were nearly normal suggests that theeffect does not propagate longer than one-half ofa helix.
The neighboring bare zone on the barbedend side of the cluster had slightly longer helicalpitch than the control. Although a t-test indicatedthat the untwisting was statistically significant,we are not certain if it was an active process. If
interactions between actin filaments and the lipid
surface produced resistive force against local
rotation of the filament, supertwisting in the cluster would induce passive, compensating untwisting of the nearby helix. If that is the case, thefact that actin filaments are not necessarily free
to rotate in vivo suggests similar passive untwisting may occur in vivo as well. In any case, it isnoteworthy that cofilin clusters induced distinctly
asymmetric cooperative conformational changes
in neighboring bare zones. Propagation of thesupertwisted conformation from cofilin clusters
to neighbor bare zones had been suggested byimage analysis of electron micrographs of cofilin–
actin complexes (Galkin et al., 2001).

Growth of cofilin clusters is also
unidirectional and independent on
actin-bound nucleotides

Our observation that the cofilin clusters grew inthe pointed-end direction supports the conclusion of Galkin et al. (2001) that cofilin preferentially binds to the supertwisted segments of actin
subunits. This tendency of cofilin clusters to growunidirectionally was unaffected when most of thefilament subunits carried ADP or ADP+Pi, demonstrating that the directional growth of cofilin clusters does not depend on a gradient of different
nucleotide states on actin subunits within each filament. Instead, it presumably depends on asymmetric cofilin-induced conformational changes in the actin filaments, which is an intrinsic property ofthe polar structure of the actin filaments.
The rise of peaks and shortening of half helical pitches that accompanied the growth of cofilin clusters were sometimes rapid, but at other times slow and gradual (Figure 4). If we assume that the rise
was due to simple addition of cofilin molecules at the two binding sites closest to the crossover point,
and if the cofilin clusters grow in perfect synchrony along two strands of the double helix, then the
crossover points should rise abruptly in one step. If, on the other hand, there is a time-lag between
cofilin bindings at the two critical binding sites, due to delayed growth along one strand, for example,
the rise would occur in two smaller discrete substeps. Indeed, in many cases, the rise of peaks appeared

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to occur in two discrete substeps (Figure 4), supporting this possibility. In other cases, however,the peaks rose gradually over the course of 40 s(e.g., P2 in Figure 4A), although we have no
mechanistic explanation for those events.
In certain cases the next peak (P1 in the caseshown in Figure 4A) only rose when the previous
peak (P2) had reached a plateau, whereas in othercases the new peak (P2) started to rise while theprevious one (P3) was still rising. This latter caseis more consistent with the possibility that cofilin
Video 5. Growth of a cofilin cluster toward the pointed
clusters do not necessarily grow in concert along
end of a filament in F buffer containing 1 mM ADP,
the two strands, and the delay may sometimes
10 mM Pi, 150 nM S1, and 900 nM cofilin (without
exceed one-half of a helix.
His-tag). For color codes of arrowheads, see the legend
Another uncertainty is whether the new cofito Video 3. For magnifications and polarity of thelinmolecule always binds to the vacant binding
analyzed filaments, refer to Figure 4 in the main text.
site immediately neighboring the cluster. If theUnder this condition, binding of S1 was so short-lived
unidirectional cluster growth to the pointed-end
that the tilted binding was not obvious in some cases
is driven by the shortened helical pitch on the(magenta). The S1 molecule indicated by a double
magenta arrowhead appears to tilt in the direction
pointed-end side of the cluster, the new molecule
opposite to other S1 molecules indicated by yellow
is likely to bind any of the vacant binding sites inarrowhead, and we speculate that this is because thisthe supertwisted, apparently, bare zone on the
S1 molecule was not stably bound to the filament whenpointed-end side of the cluster. This view is conimaged. Imaged at 2 frames/s and played at 3 frames/s.
sistent with the result of recent high-resolution
Z-scale was 0–12 nm. Related to Figure 4C.
single molecule fluorescence microscopic assays
DOI: 10.7554/eLife.04806.017
that showed that free cofilin molecules preferto bind within 65 nm of an already bound cofilinmolecule, but not necessarily to the site immediately neighboring the already bound molecule(Hayakawa et al., 2014). We thus speculate that there are vacant binding sites behind the advancing
front of cofilin clusters, which are eventually filled by other cofilin molecules to form tight clusters, andthat the advances are not necessarily in concert between the two strands of the double helix.

Severing
In the presence of cofilin, actin filaments are frequently severed at or near the boundary between
cofilin clusters and bare zones, at least when examined at the spatial resolution of fluorescencemicroscopy (Suarez et al., 2011). That observation is consistent with the idea that severing preferentially occurs at sites of structural discontinuity, such as the boundary between supertwisted
and normal helical pitches (Michelot et al., 2007; De La Cruz, 2009). An alternative view is that
cofilin binding weakens longitudinal contacts between actin subunits within cofilin clusters andalso in neighboring bare zones, but because bound cofilin bridges two actin subunits, strengthening interactions between them, severing occurs in nearby supertwisted bare zones (Galkin et al.,
2001; Bobkov et al., 2002). Roughly 40% of the severing events in our AFM observations occurredat the boundary between a cluster and a bare zone or within the neighboring bare zone, which
may be explained by these hypotheses. However, more than half of the severing events occurred
within the cofilin clusters, albeit close to the cluster ends. One plausible explanation is that the
scattered unoccupied cofilin binding sites near the ends of the cluster, discussed above, may
be easy to break due to the lack of bridging cofilin molecules. Alternatively, if growth of cofilinclusters on one of the two filament strands lags the growth on the other, conformational stress
may develop between the two strands, leading to breaks in the filament near the ends of cofilinclusters.

How many bound cofilin molecules are required for severing andcluster growth?
Previous biochemical (Andrianantoandro and Pollard, 2006) and simulation studies (De La Cruz,
2005; De La Cruz, 2009) suggested that one or a few bound cofilin molecules are sufficient to severactin filaments. However, our AFM observations are more consistent with the view that efficient

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severing requires a cofilin cluster longer than onehalf of a helix, since most of the severing eventswere observed within or very near cofilin clusters
that were recognizable in our AFM images. The
need of contiguously bound cofilin molecules for
efficient severing is consistent with our earlier
mutant analysis. Within filaments in solution, D11Q
mutant actin subunits rapidly exchange bound
ADP for ATP in solution. Consequently, mostsubunits within D11Q actin filaments have ATPbound, reducing their affinity for cofilin and protecting them from severing. Interestingly, cofilin
was able to bind to copolymers of D11Q andwild-type actins, but severing was inefficient(Umeki et al., 2012), suggesting that contigFigure 5. Directional preference of the growth of cofilin
uous clusters of cofilin-bound actin subunits are
clusters. The growth of cofilin clusters was observed
under three buffer conditions: in the presence of 1 mM
necessary for efficient severing activity.
ADP and 0.1 mM ATP (+ADP +ATP); 1 mM ADP (+ADP)
A related question is how many bound cofiand 1 mM ADP and 10 mM Pi (+ADP +Pi), as in Figure 4.
lin molecules are required to induce cooperative
Growth of a cluster by one-half helix was counted assupertwisting conformational changes in actin filone growth event. The total number of observed
aments? Answering this question is technically
growth events was 37, 46, and 188 for each condition.
difficult when the imaging power is not sufficient
We speculate that at least some of the cluster growth
to see individual bound cofilin molecules, but
events in the barbed-end direction were actually growth
our observations using a cofilin-rod fusion proteinin the preferred direction from invisibly small clusters on
showed that one is not enough. Consistent withthe barbed side of a visible cluster.
this view, previous simulation studies suggested
DOI: 10.7554/eLife.04806.018
that two cofilin molecules bound close to one
another along an actin filament serve as a nucleus
to initiate cooperative binding of cofilin to form a cluster (Ressad et al., 1998; Blanchoin and Pollard,1999). Future high-resolution HS-AFM studies using cofilin fused with a rod or some other structural
marker to make it visible with AFM will directly test those hypotheses.
Even if a singly bound cofilin molecule cannot induce supertwisting of the helix or initiate cluster growth,
it does not exclude the possibility that single bound cofilin molecules induce subtler, perhaps longer range,
cooperative conformational changes, such as those indirectly detected through biophysical measurements (Dedova et al., 2004; Prochniewicz et al., 2005; Bobkov et al., 2006). Apparently cofilin isable to induce at least two distinct types of cooperative conformational changes: one that requires cluster
formation, involves ∼25% supertwisting of the helix, and propagates over half a helix toward the pointedend of the filament; and a second type that singly bound cofilin molecules can induce which involves
relatively subtle conformational changes, and propagates much longer. Simulation studies by De La
Cruz and Sept (2010) suggest that there are two distinct states of cofilin–actin complexes, which may
be correlated with the two types of cooperative conformational changes we propose here.

Physiological implications of cofilin-induced unidirectional cooperative
conformational changes in actin filaments
Cooperativity in the binding of cofilin to actin filaments could have multiple physiological implications. Generally speaking, cooperativity would amplify small changes in the input (concentration ofactive cofilin) to a larger difference in output (cluster formation and severing). In addition, the cellularconcentration of cofilin is lower than that of polymerized actin, and cooperativity would be a usefulmeans of disrupting selected filaments under those conditions (Pollard et al., 2000).
Second, we propose that the propagation of cofilin-induced conformational changes into neighboring cofilin-unbound zones of actin filaments would give cofilin an advantage in competition withother ABPs, once a small cofilin cluster is established as a foothold. For example, cofilin is implicatedin severing and depolymerization of aged actin filaments in lamellipodia. However, those actin filaments are often bound with tropomyosin (Gunning et al., 2008), which inhibits binding of cofilin andprotects the filaments from cofilin's severing and depolymerizing activities (Bernstein and Bamburg,
1982; Ono and Ono, 2002). If cofilin forms a small cluster at a vacant site on an actin filament that is

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Figure 6. Severing of actin filaments near cofilin clusters. (A–C) Typical cases of filament severing (red arrowheads)
within or near cofilin clusters (white arrowheads). The observation buffers were F-buffer containing 1 mM ADP(A and C) and 1 mM ATP (B). Concentration of cofilin was 40 nM (A and C) and 75 nM. The first break in (A) was inside
a cluster, while the second was at or near the junction between a bare zone and a cluster. Red, blue, and green
arrowheads show severing points within cofilin clusters, in bare zone close to cofilin clusters, and in bare zones
more than half a helix away from a cofilin cluster, while white arrowheads show cofilin clusters. Bars: 25 nm; Z-scale:
0–12 nm. See Videos 6–8. (D) Classification of severing sites into four categories: (1) in ‘far’ bare zone (between atall and a short black arrow or between two short black arrows, indicated by green bars in (E)); (2) in bare zone half
helices immediately neighboring a cofilin cluster (between a tall black and a tall orange arrow, indicated by blue barsin (E)); (3) in ‘end’ cofilin cluster half helices immediately neighboring bare zones (between a tall and a short orange
arrow, indicated by red bars in (E)); and (4) in ‘inner’ cofilin cluster half helices (between two short orange arrows,
indicated by a red bar in (E)). Comparison of the last two categories demonstrates that severing within cofilin clusters
occurs preferentially near the ends. Note, however, that this comparison does not necessarily show a quantitative
difference in the susceptibility to severing between end and inner half helices, since the number of end and innerhelices examined are not the same. (E) A schematic summary of the proposed distributions of bound cofilin molecules(red spheres), segments of normal (yellow) and shortened (orange) helical pitch, and normal (black arrows) and tall(orange arrows) crossover points. Free cofilin molecules tend to bind to the supertwisted bare zone on the pointedend side of the cluster (gray arrows), driving the growth of the cluster in the pointed-end direction. This is mostcertainly an oversimplification, ignoring a number of complex issues, some of which are discussed in the main text.
DOI: 10.7554/eLife.04806.019
Figure 6. Continued on next page

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Figure 6. Continued
The following figure supplements are available for figure 6:
Figure supplement 1. Representative still images from Video 9, demonstrating severing of actin filaments bycofilin with His-tag.
DOI: 10.7554/eLife.04806.020
Figure supplement 2. Representative still images from Video 10, showing severing of actin filaments by cofilin
without His-tag.
DOI: 10.7554/eLife.04806.021
Figure supplement 3. Representative still images from Video 11, showing severing of actin filaments in thepresence and absence of low concentration of cofilin.
DOI: 10.7554/eLife.04806.022
Figure supplement 4. Representative still images from Video 12, showing severing in actin filaments decorated
with high concentrations of cofilin.
DOI: 10.7554/eLife.04806.023

otherwise decorated and protected by tropomyosin, the cluster would induce, or apply conformational stress to induce, supertwisting on
the neighboring tropomyosin-bound segmenton the pointed-end side. This would acceleratedissociation of tropomyosin, resulting in faster
growth of the cofilin cluster than when cluster
growth needed to wait for spontaneous dissoVideo 6. Severing of actin filaments in a cofilin cluster.
ciation of neighboring tropomyosin molecules.
Conditions: F buffer containing 1 mM ADP and 40 nM
Furthermore, that cluster growth is directed only
cofilin. Severing of actin filaments occurred within ato the pointed-end may be beneficial in selective
cofilin cluster (at 53 s) and then at or near the boundary
disassembly of aged actin filaments.
between a bare zone and another cofilin cluster (atWithin cells, formin remains bound to the64.5 s). Imaged at 2 frames/s and played at 5 frames/s.
Red, blue, and green arrowheads indicate severingbarbed-end when it catalyzes filament elongain half helices in cofilin clusters, in a bare half helix
tion. This causes relative rotation between theimmediately neighboring a cofilin cluster, and in bareformin molecule and the filament (Mizuno et al.,zones more than half a helix away from cofilin clusters,2011). Thus, if the formin molecule and the filarespectively. White arrowheads: cofilin clusters. Z-scale
ment are not free to rotate, the filament will be
was 0–12 nm. Related to Figure 6A.
untwisted, and if cofilin has a lower affinity for
DOI: 10.7554/eLife.04806.024
untwisted actin filaments, rapidly polymerizing
actin filaments in a formin-dependent manner will
be protected from severing by cofilin (Mizuno
and Watanabe, 2012). It should be noted, however, that formin bound to the barbed-end of an actin
filament also allosterically changes the structure of the filament (Bugyi et al., 2006), which may interfere with the interactions of the filament with cofilin, independent of mechanically forced untwisting of
the filament helix.
Sharma et al. (2012) discovered that the untwisted conformation of actin filaments induced by adrebrin N-terminal fragment propagates to neighboring bare zones; however, their findings seem toindicate that this propagation is in both directions from the drebrin clusters, though the authors did
not address that point. It thus appears that there are multiple forms of ABP-induced cooperative conformational changes to actin filaments that propagate into bare zones, which implies there are also
multiple physiological functions for such cooperative conformational changes to actin filaments.

Materials and methods
Proteins
cDNA encoding human cofilin 1 was amplified from a human cDNA library using PCR with primers
5′-ggtaccatggcctccggtgt and 5′-tctagacaaaggcttgccctcca. After confirmation of its sequence, theamplified DNA fragment was subcloned into pColdI expression vector (Takara Bio, Otsu, Japan) at
the XbaI and KpnI sites. The pColdI vector had been modified to contain a TEV cleavage site between
the His tag and the multi-cloning sites, so that the amino acid sequence near the N-terminus was

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M N H K V H H H H H H I E G R H M E N LY F Q G T M
ASGVAVS… (italics indicate the TEV cleavage site).
The cofilin-rod fusion gene was constructedby cloning the cDNA encoding the first half of
the Dictyostelium α-actinin rod downstream of
the cofilin gene in pColdITEV. The amino acidsequence at the junction of the two proteins
was …SAVISLEGKPLEQTKSDYLKRA…, and the
C terminal sequence was …QKIEDSLVSR (italics
show extra amino acid residues derived from recognition sites for restriction enzymes). The firstVideo 7. Severing of actin filaments at or near ahalf of the Dictyostelium α-actinin rod, correboundary between a bare zone and a cofilin cluster.
sponding to amino acid residues 265–505 of theConditions: F buffer containing 1 mM ATP and 75 nM
parent molecule, forms a monomeric12-nm long
cofilin. Severing occurred at 42 s. Imaged at 2 frames/s
rod-like structure (Yan et al., 1993) and has beenand played at 5 frames/s. For color codes of theused as an artificial lever arm of myosin motors
arrowheads, see the legend to Video 6. Z-scale was(Anson et al., 1996).
0–12 nm. Related to Figure 6B.
The proteins were expressed in Escherichia
DOI: 10.7554/eLife.04806.025
coli, purified using Ni-NTA affinity chromatography, and dialyzed against a buffer containing
10 mM HEPES, pH 7.4, 50 mM KCl, 0.1 mM DTT,
and 0.01% NaN3 overnight at 4°C. After concentrating with a centrifugal concentrator (Amicon
Ultra 4), aliquots were snap-frozen in liquid nitrogen and stored at −80°C. Unless otherwise stated,the experiments used those His-tagged cofilin
or cofilin-rod proteins. However, we repeatedsome key experiments after removing the His-tag
by treatments with TEV protease and obtained
qualitatively similar results. These experiments
included asymmetric conformational changes ofVideo 8. Severing of actin filaments in a bare zone
actin filaments on either side of a cofilin cluster,
more than one half helix away from a cofilin cluster.
unidirectional growth of cofilin clusters in theConditions: F buffer containing 1 mM ADP and 40 nM
pointed-end direction, and frequent severing
cofilin. Severing occurred at 28 s. Imaged at 2 frames/sof filaments near the boundary between a bareand played at 5 frames/s. For color codes of thezone and a cofilin cluster. Cofilin with and without
arrowheads, see the legend to Video 6. Z-scale was
His-tag bound to actin filaments at a 1:1 molar
0–12 nm. Related to Figure 6C.
ratio with a similar affinity (Figure 3—figure supDOI: 10.7554/eLife.04806.026
plements 1 and 2). Cofilin-rod with and without His-tag also did not sediment on its own,
then bound to actin filaments with affinities similar to cofilin without the rod fusion (Figure 3—figure
supplement 3).
Rabbit skeletal muscle actin and chymotryptic subfragment-1, S1, were purified as described previously (Spudich and Watt, 1971; Margossian and Lowey, 1982) and stored in liquid nitrogen. Someexperiments used G-actin that was further purified by gel filtration column chromatography, yielding
identical results.
Before use, an aliquot of frozen stock was thawed for 1 hr on ice and clarified by ultracentrifugation
at 80,000 rpm for 5 min at 5°C. Protein concentration was then measured using an Advanced Protein
Assay (Cytoskeleton, Denver, CO), using calibrated skeletal actin as the standard.

High-speed atomic force microscopy
We used a laboratory built high-speed atomic force microscope (HS-AFM) as described previously(Ando et al., 2013). HS-AFM imaging was carried out in the tapping mode with small cantilevers(BL-AC10DS-A2, Olympus, Tokyo, Japan) whose spring constant, resonant frequency in water, andquality factor in water were ∼0.10 N/m, ∼400 kHz, and ∼2, respectively. The probe tip was grown on
the original tip end of a cantilever through electron beam deposition and was further sharpened using

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a radio frequency plasma etcher (PE-2000, SouthBay Technology, Redondo Beach, CA) under anargon gas atmosphere (typically at 180 mTorr and
15 W for 3 min). During HS-AFM imaging, thefree-oscillation peak-to-peak amplitude of thecantilever (A0) was set to ∼2 nm, and the feedback amplitude set point was set at more than
0.9A0. Details of the method for HS-AFM imaging
are described elsewhere (Uchihashi et al., 2012).

Video 9. Severing of actin filaments by cofilin. To show
more general view of severing events, in addition to
the small number of representative cases shown inVideos 6–8, 10 different image sequences fromdifferent experiments were merged. Sequence numbers
are shown in the first 10 frames of each sequence. For
color codes of the arrowheads, see the legend toVideo 6. Conditions: F buffer containing 1 mM ATP(sequences 1–6), 1 mM ADP (sequence 7–8) or 1 mM
ATP + 10 mM Pi (sequence 9–10). The concentrationof cofilin shown in this video was 75 nM, except insequences 9 and 10, in which it was 300 and 150 nM,
respectively. Z-scale was 0–12 nm. Related to
Figure 6—figure supplement 1.
DOI: 10.7554/eLife.04806.027

Mica-supported lipid bilayer
We prepared small unilamellar vesicles (SUVs)
and mica-supported lipid bilayer as described
previously (Yamamoto et al., 2010; Uchihashi
et al., 2012). The typical lipid composition was
1,2-dipamitoyl-sn-glycero-3-phosphocholine(DPPC) and 1,2-dipalmitoyl-3-trimethylammoniumpropane (DPTAP) at a weight ratio of 9:1. The
lipids were purchased from Avanti Polar Lipids(Alabaster, AL). SUVs were dispersed in Milli-Q
water at 2 mg/ml and stocked at −20°C. Before
use, the SUVs were diluted in 5 mM MgCl2 to
0.5 mg/ml and sonicated with a bath sonicator(AUC-06L, AS ONE, Osaka, Japan) for 1 min. An
aliquot of the sonicated SUVs was deposited on
the surface of freshly cleaved mica, which had been
glued onto a sample stage beforehand, and incubated for more than 3 hr at room temperature(24–26°C) in a humid sealed container to avoid surface drying. Up to 10 sample stages were prepared
simultaneously and stored in the sealed container.

HS-AFM imaging
Before deposition of actin filaments, the surface of the sample stage was rinsed with a large
amount of Milli-Q water (∼20 µl × five times) toremove excess SUVs and lipid bilayers. Actin filaVideo 10. Severing of actin filaments by cofilin withoutments were then deposited onto the lipid bilayer
His-tag. In this video, seven different image sequencesusing one of the following methods.
from different filaments and experiments were merged.
G-actin (5–10 µM) was polymerized in F buffer
Conditions: F buffer containing 1 mM ATP and 75 nM(40 mM KCl, 20 mM PIPES–KOH, pH 6.8, 1 mM
cofilin, except in sequence 3 in which cofilin
MgCl2, 0.5 mM EGTA, 0.5 mM DTT) containing
concentration was 150 nM. For color codes of the
1 mM ATP for 30 min on ice. The resultant actin
arrowheads, see the legend to Video 6. Z-scale was
0–12 nm. Related to Figure 6—figure supplement 2.
filaments were diluted to 0.5–1.0 μM in F buffer
DOI: 10.7554/eLife.04806.028
containing 1 mM ATP. Water on the lipid bilayer
on a sample stage was replaced with 1–2 µl of
F buffer containing 1 mM ATP, to which 2 µl of thediluted actin solution was added. After 5–10 min of incubation at room temperature, unattached actin
filaments were removed by exchanging the solution with 50 µl of one of the four different F bufferbased observation buffers each containing (i) 1 mM ATP, (ii) 0.1 mM ATP and 1 mM ADP, (iii) 1 mM ADP,
5 U/ml hexokinase, and 10 mM glucose, and (iv) 1 mM ADP and 10 mM Pi. In the case (iii), incubation
was continued for 30 min to ensure that all actin subunits within the filaments carried ADP.
Alternatively, G-actin (20 µM) was polymerized in F buffer containing 1 mM ATP and 30 mM
MgCl2 for 1 hr at room temperature. After introduction of this solution to the sample stage and 10 minof incubation at room temperature, unattached actin filaments were removed by gently exchanging
the solution with F buffer containing 1 mM ATP and 30 mM MgCl2.

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Video 11. Severing of actin filaments in the absenceor presence of low concentrations of cofilin. Four
independent image sequences are merged.
Conditions: F buffer containing 1 mM ATP and 0, 10
or 40 nM cofilin without His-tag. In this video, three
data sets which represent three cases of the absenceor presence of cofilin are sequentially shown andindicated before each sequence begins as (i) Control:
Without Cofilin, (ii) 10 nM Cofilin (two different image
sequences), and (iii) 40 nM Cofilin. Note that severingof actin filaments was not observed not only in theabsence but also in the presence of 10 nM cofilin. In
the presence of 40 nM cofilin, severing was infrequently
observed. For color codes of the arrowheads, see thelegend to Video 6. Images were taken at 0.5 frames/s,
except in the presence of 40 nM cofilin they wererecorded at 0.25 frames/s, and the video is played at
5 frames/s. Z-scale was 0–12 nm. Related to Figure 6—
figure supplement 3.
DOI: 10.7554/eLife.04806.029

Video 12. Actin filaments decorated with highconcentrations of cofilin. The first three quarter of thisvideo were taken in F buffer containing 1 mM ATP and1 µM cofilin, and the last one quarter was taken in thepresence of 650 nM cofilin. In the presence of 1 µM
cofilin, filaments were fully decorated along the length,
and no severing was observed. In the presence of
650 nM cofilin, there were some bare zones, andsevering occurred near the boundary of the bare zone
and the cofilin clusters, regardless of the size of cofilinclusters. For color codes of the arrowheads, see thelegend to Video 6. Images were taken at 2 frames/s
and played at 5 frames/s. Z-scale was 0–12 nm. Related
to Figure 6—figure supplement 4.
DOI: 10.7554/eLife.04806.030

Finally, the sample stage was mounted to thez-scanner of a HS-AFM apparatus and immersed
in a liquid cell containing the same observationbuffer used in the last step, and HS-AFM imaging
was performed.
To follow binding of cofilin to actin filaments,
6 µl of cofilin diluted in the observation buffer
was injected into the observation cell during AFM
imaging. In some experiments, S1 was added in
the observation buffer in the concentration of
20 nM (in cases [i], [ii], and [iii]) or 150 nM (in case[iv]) to identify the polarity of actin filaments.

Data analyses of HS-AFM image
HS-AFM images were viewed and analyzed using
the laboratory built software, Kodec4.4.7.39. In
brief, a low-pass filter to remove spike noise anda flattening filter to make the xy-plane flat wereapplied to individual images. The position andheight of the peak within each half helix were
determined semi-automatically using the following
steps. First, the most probable highest point neara crossover point was selected manually. Second,
the actual highest point was automatically determined by searching a 5 × 5 pixel area (typically
7.5 × 7.5 nm2) around the selected point. Third,
the peak position was refined based on a centerof mass calculation using information on theheights and positions within the 5 × 5 pixel areaaround the selected point, after which the refinedpeak position and height were used to represent
the peak of the half helix.
The Kodec4.4.7.39 for HS-AFM image viewing
and analysis software is coded in Visual C# (Visual
Studio 2010, Microsoft, USA) and is available as
Source code 1. All filters and subroutines forimage analysis used in the present study areincluded in the software. We confirmed the compatibility between the software and computers
operated with Windows 7 or 8. Installer of thesoftware, Kodec4_Setup.msi, is available in the
subfolder of ‘Kodec 4.4.7.39\Setup\Release’.
This software should be cited as: Sakashita M, M
Imai, N Kodera, D Maruyama, H Watanabe, Y
Moriguchi, and T Ando. 2013. Kodec4.4.7.39.

Electron microscopy

Actin filaments were prepared by polymerizationof G-actin (20 µM) in F buffer containing 40 mM
KCl, 20 mM PIPES, pH 6.8, 1 mM MgCl2, 0.5 mM
EGTA, 0.5 mM DTT, and 1 mM ATP for 30 min on
ice. Cofilin or cofilin-rod was added to 1 µM actin
filaments in 50 µl of F buffer at a molar ratio of
1:2 or 1:1, and the solutions were mixed by gentle pipetting, after which the mixture was incubated for 3–5 min at room temperature. This mixture
was then added to F buffer containing sodium phosphate (pH 6.8) so that the concentration of actin

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was 0.5–1 µM and that of Pi was 5 mM, and a drop of this solution was immediately placed on a copper
grid. The samples were fixed and negatively stained using a solution containing 1% uranyl acetate and20 µg/ml bacitracin (Katayama, 1989). The fixed samples were dried under an incandescent lamp toform films over the holes of the grid. Electron microscopic data were then acquired using a Hitachi
H-7650 transmission electron microscope.

Acknowledgements
We thank Dr Akira Nagasaki for cooperation in preliminary characterization of actin–cofilin interactions
using TIRF microscopy, Dr Shin-ichiro Kojima for help in statistical analysis, and Dr Masafumi Yamada
for providing actin. We are also indebted to Drs Keiko Hirose, Makoto Miyata and Taro Noguchi forcomments on the manuscript. This work was supported in part by Grants-in-aid from the Ministry of
Education, Culture, Sports, Science and Technology for TU, a PRESTO grant from the Japan Scienceand Technology Agency (JST) to NK, and a CREST grant from JST to TA.

Additional information
Funding
FunderAuthor

Ministry of Education, Culture, Sports,
Science, and Technology

Taro QP Uyeda

Japan Science and Technology
AgencyNoriyuki Kodera,
Toshio Ando

The funders had no role in study design, data collection and interpretation, or thedecision to submit the work for publication.

Author contributions
KXN, Acquisition of data, Analysis and interpretation of data, Drafting or revising the article; NK,
Conception and design, Acquisition of data, Analysis and interpretation of data, Drafting or revising
the article; EK, Acquisition of data, Analysis and interpretation of data; TA, TQPU, Conception anddesign, Drafting or revising the article

Additional files
Supplementary file
• Source code 1. The Kodec4.4.7.39 for HS-AFM image viewing and analysis software is coded in
Visual C# (Visual Studio 2010, Microsoft, USA).
DOI: 10.7554/eLife.04806.031

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