Journal of Surface Engineered Materials and Advanced Technology, 2013, 3, 13-19 Published Online October 2013 (
Copyright © 2013 SciRes. JSEMAT
AFM Investigation of the Organization of Actin Bundles
Formed by Actin-Binding Proteins
Jamie L. Gilmore, Masahiro Kumeta, Kunio Takeyasu
Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
Received June 21st, 2013; revised July 20th, 2013; accepted August 6th, 2013
Copyright © 2013 Jamie L. Gilmore et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
AFM is a powerful technique for revealing the morphological features of various biological systems at high resolution.
However, one of the complications of AFM is that samples must be attached to a flat surface in order to obtain images.
This often requires the development of specialized methods depending on the sample which is being used. In this study,
we developed a novel technique to image actin bundles on the mica surface. Using this technique, we were able to
image molecular assemblies of F-actin with two actin remodeling proteins: α-actinin and Caprice. High resolutio n AFM
images of F-actin fibers and bundle organization depicted two different types of molecular assemblies: F-actin bundles
forming an elongated “zipper” structure in the presence of α-actinin, and bundles forming a perpendicularly crossing th e
mesh structure in the presence of Caprice.
Keywords: F-Actin; Caprice; α-Actinin
1. Introduction
The biological applications of atomic force microscopy
(AFM) [1] were realized immediately after the instru-
ment was invented in 1986 [2]. Since AFM was useful
for examining the surface properties of relatively solid
specimens, it was initially used in the field of material
sciences. The physical properties of DNA, proteins, lip-
ids and carbohydrates have been extensively studied by
using AFM [3- 6] .
There have been a number of limitations associated
with AFM technology. However, the development of
new scanning methods [7] and cantilever production [8]
has facilitated the applications of AFM for studying bio-
logical macromolecules in physiological conditions. The
most fascinating technical endeavor has been the inven-
tion of high-speed AFM by Ando et al., which has en-
abled one to capture the motion of DNA [9-12] and pro-
teins [13-17] and to monitor enzymatic reactions [9,11,
18] in solution.
However, one of the inherent limitations associated
with AFM other than the instrument technology is the
specimen preparation procedure, which needs to be taken
into account the physicochemical properties of the speci-
men against substrates such as mica and glass surfaces.
Here we describe procedures to image the most abundant
protein in the cell: actin. We developed specimen pre-
paration procedures for imaging single filamentous actin
(F-actin) and actin-binding protein-promoted F-actin
bundles. AFM imaging of these samples provided high
resolution images of bundle nanostru ctures in addition to
the ultrastructure of actin networks. The data suggest that
F-actin bundles form an elongated “zipper” structure when
the α-actinin bundling protein is added and the bundles
form a perpendicularly crossing meshwork structure
when the Caprice protein is added. These structures pro-
vide insight into the molecular mechanisms of forming
distinct actin-based structures by different actin-binding
2. Materials and Methods
2.1. Chemicals and G-Actin
All chemicals used were first grade from Sigma and Na-
calai Tesque. The non-muscle human actin was obtained
from Cytoskeleton, Inc. (APHL99).
2.2. Actin-Binding Proteins
The α-actinin from rabbit skeletal muscle, which is a
mixture of the actinin-1, 2, 3, and 4 isoforms, was ob-
tained from Cytoskeleton, Inc. (AT01). Caprice (C19or f 2 1
AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins
Copyright © 2013 SciRes. JSEMAT
actin bundling protein in characteristic epithelial cells)
[19,20] (NM_173481) is a gene product of human
C19orf21, also called MISP (mitotic interactor and sub-
strate of Plk1) [21]. The full-length Caprice expressed in
Eschelichia coli cannot be purified due to its “scaffold”
nature and instability in the h ost cell. The actin-bundling
domain exists in the C-terminal region of Caprice. There-
fore, the 3’-region of the cDNA encoding the C-terminus
half of human Caprice, amino acid residues (352-680),
referred to as Caprice hereafter, was amplified by PCR
from a HeLa cDNA pool, which was reverse transcribed
by SuperScript II reverse transcriptase (Invitrogen) from
the total RNA extracted by RN-easy RNA extraction kit
(Qiagen). The cDNA was cloned into pGEX-6P vector
(Clontech) and expressed in BL21RIL E. coli. GST-fu-
sion proteins were purified with glutathione-conjugated
sepharose (GE) and the GST-tag was excised by PreScis-
sion protease (GE).
2.3. F-Actin Fiber and Bundle Preparation
The F-action was prepared from 20 µM (900 ng/µL)
G-action in polymerization buffer (5 mM Tris-HCl pH
8.0, 50 nN KCl, 0.2 mM CaCl2, 2 mM MgCl2, and 1 mM
ATP). To image the individual filaments, 10 µL 10 mM
spermidine was incubated for 3.5 min on a freshly cleav-
ed mica disc glued to a 15 mm metal specimen disc and
then washed three times with 1 mL of milli-Q water.
Without drying the mica, the 900 ng/µL solution of F-
actin was deposited onto the spermidine-modified mica,
incubated for 3.5 min, washed three times with 1 mL
milli-Q water, and then dried with a stream of nitrogen.
To get images of bundles, a centrifugation procedure was
Prior to forming the bundles, the F-actin, α-actinin,
and Caprice proteins were centrifuged for 15 min at
14,000 x g at room temperature in a TOMY MX-105
High speed Refrigerated Microcentrifuge (TOMY Tech
USA, Inc.) to remove any large aggregates. The bundles
were formed by adding 225 ng/µL F-action (5 µM G-
actin monomers) and 0.5 µM Caprice or α-actinin in a
final 20 µL solution of polymerization buffer and incu-
bated for 30 min at room temperature. For sample depo-
sition, 500 µL o f polyacrylamide gel was poly merized in
the bottom of a 1.5 mL microcentrifuge tube. Then a
mica disk cut with a hole punch was cleaved and placed
in the tube on top of the acrylamide. Then, either 10 µL
or 1 µL of the solution containing the actin bundle was
diluted in 200 µL of polymerization buffer and deposited
in the tube on top of the freshly cleaved mica. The tube
was then centrifuged for 15 min at 14,000 x g with a
swing-rotor. The samples were washed by gently dip-
ping the mica disc in milliQ water. The mica was then
either air-dried or vacuum-dried before affixing it to a
15 mm metal specimen disc with double stick tape for
2.4. AFM Imaging and Analysis
AFM images were acquired with the Multimode Atomic
Force Microscope, a Nanoscope III Controller, and a J-
scanner (Digital Instruments, Inc., USA). Rectangular
silicon cantilevers with sharpened tetrahedral tips were
used (OMCL AC160TS, Olympus Corp., Japan). These
probes had a tip radius of about 7 nm, a resonant fre-
quency of about 300 kH z, and a spring constant of about
26 N/m. The microscope was operated in the Tapping
Mode™ at a scanning rate of 0.5 - 1 Hz. The images
were flattened with the Nanoscope software (v.5.31 r1)
and exported as jpegs. The flattened images were ana-
lyzed using the Femtoscan software (Advanced Tech-
nologies Center, Russia). The heights were measured
using the curve tool to trace some of the image back-
ground, then along the fibers, and then along some of the
background again. This trace was then converted to a
cross section to generate a height profile. Profile data
was then copied into Microsoft Office Excel (Microsoft
Corp., USA) and the average height was calculated over
the region(s) of interest. The segmentation in the filament
was analyzed by taking the lateral peak-to-peak distance
from the height profile of the molecule. All reported er-
rors represent the standard deviation. All surface plots
displayed were also generated with the Femtoscan soft-
3. Results
3.1. F-Actin Assembly from G-Actin
In the initial experiments, the samples were prepared
using a typical deposition procedure in which either 10
µL 900 ng/µL F-actin or F-actin/Caprice was deposited
on freshly cleaved mica, washed with 3 mL of water, and
then dried by blowing with a stream of nitrogen gas.
However, with these methods, the imag es m ost ly sho w-
ed crystals and amorphous material decorating the surface.
Since actin has been reported to be negatively charged
at pH 7 [22], a spermidine-modified surface was tried
instead. In addition, we wanted to see if more rigorous
washing and drying procedures could be used in order to
remove the salt crystals observed in the previously de-
scribed experiments. This method enabled the visualiza-
tion of individual actin filaments (Figure 1(A)). How-
ever, the samples obtained with and without Caprice
were nearly identical except that the sample with the Ca-
price protein added had more background material, likely
due to the excess amount of protein in the sample. No
bundles could be observed, and there was no clear inter-
action of Caprice with the fibers, likely due to mechani-
cal disruption of the bundles and the Caprice-fiber inter-
actions or poor adsorption of the bundles to the mica
AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins
Copyright © 2013 SciRes. JSEMAT
surface. In addition, all filaments in the images were ori-
ented in a parallel fashion, suggesting that the actin still
does not adhere well to the mica surface even when
spermidine is used.
However, this method did provide a way to character-
ize the morphology of individual actin filaments. The
F-actin fibers in Figures 1(A) and (B) had the charac-
teristics segmentation pattern described by other AFM
studies of actin [23,24]. A peak-to-peak distance of 33 ±
11 nm was measured for the F-actin sample. This value
corresponds reasonably well to what has been reported in
other AFM actin studies [23,25]. A characteristic height
profile of an actin filament is displayed in Figure 1(C).
The profile depicts a 1.03 µm long actin filament with an
average height of 1.1 5 ± 0.19 nm.
3.2. From F-Actin Fiber to F-Actin Bundle
To get images of actin bundles, an alternative deposition
procedure was used. Solutions containing preformed actin
Figure 1. AFM imaging and analysis of individual actin
filaments. (A) A 5 × 5 µm2 AFM image of individual actin
filaments observed in the F-actin sample without the Ca-
price bundling protein. Scale bar = 200 nm; (B) A surface
plot showing the segmentation pattern of actin filaments
observed in the F-actin samples without the Caprice protein;
(C) A plot profile of an actin filament produced from the
dotted line drawn in (A).
bundles formed with either the Caprice or the α-actinin
protein were centrifuged onto a piece of freshly cleaved
mica placed at the bottom of a microcentrifuge tube. The
piece of mica was then removed from the tube, gently
dipped in water to wash the sample, then vacuum dried.
When a 200 µL so lution containing 0.28 ng/µL of F-actin
along with a bundling protein added at a 10:1 ac-
tin-protein ratio was centrifuged onto the mica, the im-
ages shown in Figures 2(A), 3(A) were obtained. Using
this method, we were able to get reasonable concentra-
tions of actin bundles on untreated mica with relatively
minimal amounts of crystals or other amorphous material,
suggesting that this centrifugation method aided in puri-
fication of the bu ndles.
Figure 2. AFM imaging and analysis of α-actinin actin bun-
dle nano-structures. (A) Two representative 5 × 5 µm2 im-
ages of the spread of bundle structure s on the mica surface;
(B) Three 1 × 1 µm2 images showing the “zipper” structures
formed with the α-actinin protein. All scale bars = 250 nm;
(C) Two characteristic plot profiles showing a clear distinc-
tion between the height of the “zipped” and “unzipped”
regions of the bundle. Parts of the dotted lines used to pro-
duce these profiles are shown in (B).
AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins
Copyright © 2013 SciRes. JSEMAT
For the α-actinin complexes, zipper-like structures
were often observed (Figure 2(B)). Two representative
height profiles are shown in Figure 2(C). The heights
were bipartite in nature. In these profiles, the area which
was “zipped up” had average heights of 7.3 ± 0.6 nm,
and 6.8 ± 0.4 for the respective top and bottom profiles,
whereas the “unzipped” areas had heights of 3.5 ± 0.3
and 3.2 ± 0.4 nm for the respective top and bottom pro-
files. These height values suggest that even the areas of
the fibers which appear “unzipped” are already bundled
since the height values exceed the height values of the
individual filaments measured earlier (Figure 1(C)).
In contrast to the α-actinin complexes, Caprice com-
plexes had a much more rigid and highly branched ap-
pearance (Figures 3(A) and (B)). In many places the
fibers crossed perpendicularly (Figure 3(B)), suggesting
that these filaments may have a propensity to form mesh-
work type structures. Looking at the height profiles of
these fibers, they do not have distinct height transitions
as observed for the α-actinin complexes. The three repr e-
sentative height profiles shown in Figure 3(C) have av-
erage heights of 7.0 ± 1.2 nm (top), 5.6 ± 2.2 nm (mid-
dle), and 5.9 ± 1.2 nm (bottom). In addition to lacking
clear height transitions, the height profiles also have a
higher noise level suggesting that the Caprice bundles
have some irregularities in the dimensions of the fibers in
comparison to the α-actinin complexes and individual
fibers. This trend is also reflected by the much larger
standard deviation values for the average height of the
When no bundling protein was added to the sample,
only an amorphous background with no noticeable actin
filaments could be imaged (data not shown). This sug-
gests that the 14,000 x g centrifugation speed which was
used is not enough to spin the single filaments out of
solution. Additionally, when comparing images of the
bundles formed with α-actinin and Caprice, the concen-
tration of fibers on the surface appears much larger for
the sample with the Caprice protein. This is likely a re-
flection of the increased bundling efficiency of the Ca-
price protein. This increased efficiency could be ob-
served with an F-actin bundling assay using an Actin
Binding Protein Spin-down Assay Biochem Kit (cosedi-
mentation) fr o m Cytoskeleton Inc. (data not shown ).
3.3. Nano-Meter Scale Analyses of F-Actin
When the concentration of protein used for deposition
was increased 10-fold with the same actin-protein ratio
maintained, the mica surface was densely coated with
networks of F-actin fibers (Figure 4). The F-actin bun-
dles formed with the Caprice protein had a noticeably
different morphology than the bundles formed with the
Figure 3. AFM imaging and analysis of Caprice-actin bun-
dle nanostructures. (A) Two representative 5 × 5 µm2 im-
ages of the spread of bundle structure s on the mica surface;
(B) Six 1 × 1 µm2 images showing areas where the fibers
crossed perpendicularly. All scale bars = 250 nm; (C) Three
characteristic plot profiles showing the height characteris-
tics of the fibers produced from the dotted lines drawn in
AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins
Copyright © 2013 SciRes. JSEMAT
α-Actinin Caprice
Figure 4. AFM imaging and analysis of actin bundles
formed with either the α-actinin (A), (C), (E) or the Caprice
(B), (D), (F) bundling proteins. (A) 10 × 10 µm2 image of the
α-actinin-actin bundle morphology; (B) 10 × 10 µm2 image
of the Caprice-actin bundle morphology; (C) 5 × 5 µm2 im-
age of a couple of α-actinin bundle foci which appear to be
at the center of fibers aligned in a parallel orientation; (D) 5 ×
5 µm2 image of compact Caprice-actin bundle structures;
(E) Another 5 × 5 µm2 image with an α-actinin-actin bundle
structure with fibers aligned in a parallel orientation with a
less distinct focal center; (F) Another 5 × 5 µm2 image with
a Caprice-actin bundle structure which appears to have
parallelly aligned fibers with additional fibers branching
out perpendicularly from it. All scales bars = 1 µm.
α-actinin protein. The actin network containing the Ca-
price protein had a compact morphology (Figures 4(B)
and (D)) whereas the actin network containing the α-
actinin protein had elongated structures which appeared
to be held together by globular foci (Figures 4(A), (C)
and (E)). In regi o ns of the Capri ce net work which did not
appear as dense, elongated structures could also be ob-
served. However, in contrast to the α-actinin structures,
these also appeared to have perpendicular branches radi-
ating outward from them (Figure 4(F), arrows). When
F-actin without a bundling protein was centrifuged onto
the mica, this resulted in a surface which appeared
amorphous with no observable actin filaments (data not
shown). This is unsurprising because in our preliminary
experiments, a cosedimentation spin-down assay at the
same centrifuge speed showed that actin did not readily
localize to the pellet.
4. Discussion
In this paper, we have developed a strategy to image ac-
tin bundles with AFM by centrifuging the preformed
bundles onto a mica surface. Previously, various strate-
gies have been applied to attempts to use AFM for imag-
ing of filamentous actin, including the use of glutaralde-
hyde fixation or phalloidin to stabilize the filaments [25 ],
the use of lipid monolayers with cationic lipids to attach
the actin [14,26], the use of photo-immobilization on
azopolymer surfaces [24], and even simple deposition on
unmodified mica [23]. The method employed here is
based on a F-actin co-sedimentation assay which is fre-
quently used to assess th e ability of variou s actin-binding
proteins to form actin bundles [27]. The use of this pro-
cedure is allowed for efficient deposition of the bundles
in solution onto the mica surface. In addition, the cen-
trifugation speeds used will limit the deposition of single
filaments, G-actin, or any non-actin binding proteins in
solution, which provide a way to essentially purify the
bundles. Moreover, it should be noted that this procedur e
does not require glutaraldehyde fixation nor chemical
modification of the mica surface.
Overall, our method was capable of revealing distinct
structures of actin bundles formed by two different actin
binding proteins. The α-actinin protein is well known to
cross-link actin and to bundle it into networks. It has
been reported to be involved in focal contacts, stress fi-
ber formations, and muscle cell contraction [28-31].
Structural studies of α-actinin-actin bundles have shown
that it parallelly cross-links actin filaments, and confocal
images have previously shown F-actin to have a bifur-
cated structure [32,33]. Thus, the zipper structures we
observed in this study correspond well to the previously
reported effects of α-actinin on F-actin bundle structures.
In contrast to α-actinin, Caprice is a protein which was
recently discovered through proteomic analyses of cell-
scaffold proteins [19,34]. It was shown to localize to the
actin cytoskeleton in HeLa cells. In our images, we ob-
served nanostructures which were perpendicularly cross-
linked along with higher order structures with the highly
condensed appearance. It is interesting to consider whe-
ther the protein is somehow bending the fibers so that
they interlink at an gles of about 90˚, or whether the fibers
are simply interwoven. Further examination of the bind-
ing mechanism of the Caprice protein to the actin fibers
can help to correlate the observed structures to the phy-
siological role of this protein in cells.
In conclusion, our method will be useful to further in-
vestigate the molecular mechanisms of F-actin fiber as-
sembly promoted by other actin-binding proteins without
the need for any special chemical modifications.
5. Acknowledgements
K.T. is supported by a Grant-in-Aid for Scientific Re-
search on Innovative Areas “Molecular basis of host cell
competency in virus inf ection” ( #24115 003 ) from MEXT
AFM Investigation of the Organization of Actin Bundles Formed by Actin-Binding Proteins
Copyright © 2013 SciRes. JSEMAT
Japan. M.K. is supported by a Grant-in-Aid for Scientific
Research on Innovative Areas “Spying minority in bio-
logical phenomen a” (#24115512 ) from MEXT Jap an and
a Cross-Disciplinary Research Promotion Project from
iCeMS, Kyoto University, Japan.
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