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TheproximitybetweenC-terminiofdimeric vacuolar
H
+
-pyrophosphatase determinedusingatomic force
microscopy andagoldnanoparticle technique
Tseng-Huang Liu
1
, Shen-Hsing Hsu
1
, Yun-Tzu Huang
1
, Shih-Ming Lin
1
, Tsu-Wei Huang
2
,
Tzu-Han Chuang
3
, Shih-Kang Fan
4
, Chien-Chung Fu
3
, Fan-Gang Tseng
2,
* and Rong-Long Pan
1,
*
1 Department of Life Sciences and Institute of Bioinformatics and Structural Biology, College of Life Sciences, National Tsing Hua Univer-
sity, Hsin Chu, Taiwan, ROC
2 Department of Engineering and System Science, National Tsing Hua University, Hsin Chu, Taiwan, ROC
3 Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsin Chu, Taiwan, ROC
4 Institute of Nanotechnology, National Chiao Tung University, Hsin Chu, Taiwan, ROC
Introduction
Vacuolar H
+
-pyrophosphatase (V-PPase; EC 3.6.1.1)
is a homodimeric protein with a monomeric molecular
mass of 71–80 kDa [1]. V-PPase catalyzes electrogenic
proton translocation from the cytosol to the vacuolar
lumen to generate an inside-acidic and inside-positive
membrane potential for the secondary transport of
ions, metabolites, and toxic substances [1–3]. The
cDNAs of V-PPase have been cloned from several
higher plants, some protozoa, and several species of
eubacteria and archeubacteria, and are highly similar
(86–91% deduced amino acid identity) [1,3,4]. V-PPase
requires Mg
2+
as a cofactor, andthe binding of Mg
2+
Keywords
atomic force microscopy; proton
translocation; tonoplast; vacuolar
H
+
-pyrophosphatase; vacuole
Correspondence
R L. Pan, Department of Life Sciences and
Institute of Bioinformatics and Structural
Biology, College of Life Sciences, National
Tsing Hua University, Hsin Chu 30013,
Taiwan, ROC
Fax: +886 3 5742688
Tel: +886 3 5742685
E-mail: rlpan@life.nthu.edu.tw
*These authors contributed equally to this
work
(Received 1 March 2009, revised 17 May
2009, accepted 10 June 2009)
doi:10.1111/j.1742-4658.2009.07146.x
Vacuolar H
+
-translocating inorganic pyrophosphatase [vacuolar H
+
-pyro-
phosphatase (V-PPase); EC 3.6.1.1] is a homodimeric proton translocase; it
plays a pivotal role in electrogenic translocation of protons from the cyto-
sol to thevacuolar lumen, at the expense of PP
i
hydrolysis, for the storage
of ions, sugars, and other metabolites. Dimerization of V-PPase is neces-
sary for full proton translocation function, although the structural details
of V-PPase within thevacuolar membrane remain uncertain. The C-termi-
nus presumably plays a crucial role in sustaining enzymatic and proton-
translocating reactions. We used atomicforcemicroscopy to visualize
V-PPases embedded in an artificial lipid bilayer under physiological condi-
tions. V-PPases were randomly distributed in reconstituted lipid bilayers;
approximately 43.3% ofthe V-PPase protrusions faced the cytosol, and
56.7% faced thevacuolar lumen. The mean height and width ofthe cyto-
solic V-PPase protrusions were 2.8 ± 0.3 nm and 26.3 ± 4.7 nm, whereas
those ofthe luminal protrusions were 1.2 ± 0.1 nm and 21.7 ± 3.6 nm,
respectively. Moreover, both C-terminiofdimeric subunits of V-PPase are
on the same side ofthe membrane, and they are close to each other, as
visualized with antibody andgold nanoparticles against 6·His tags on
C-terminal ends ofthe enzyme. The distance betweenthe V-PPase C-termi-
nal ends was determined to be approximately 2.2 ± 1.4 nm. Thus, our
study is the first to provide structural details ofa membrane-bound
V-PPase dimer, revealing its adjacent C-termini.
Abbreviations
AFM, atomicforce microscopy; DDM, n-dodecyl-b-
D-maltoside; GNP, gold nanoparticle; SD, standard deviation; V-PPase, vacuolar
H
+
-pyrophosphatase; TEM, transmission electron microscopy.
FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS 4381
can stabilize and activate the enzyme [1,5]. Relatively
high concentrations of K
+
stimulate the proton-trans-
locating function of V-PPase, whereas excess amounts
of PP
i
,Ca
2+
,Na
+
and F
)
inhibit its enzymatic activ-
ity [6–8]. It is conceivable that the V-PPase provides
specific binding domains for the substrate and the
above-mentioned ions, as well as proton translocation.
Truncation ofthe C-terminus induces a dramatic
decline in V-PPase enzymatic activity, proton translo-
cation, and coupling efficiency [9]. In addition, deletion
of the C-terminus of V-PPase increases its susceptibil-
ity to heat stress and substantially increases the appar-
ent K
+
binding constant. It is thus likely that the
C-terminus plays an essential role in sustaining the
physiological functions of V-PPase.
Interactions betweenthe subunits ofthe V-PPase
dimer have been studied [1,2,10–12]. Radiation inac-
tivation analysis demonstrated that the proper
dimeric structure of V-PPase on tonoplastic mem-
branes is a prerequisite for both enzymatic activity
and PP
i
-supported proton translocation [2,11,12].
Further target size measurements revealed that only
one subunit ofthe purified dimeric complex was suf-
ficient for the enzymatic reaction of V-PPase,
although proton translocation requires the presence
of both subunits [2]. Moreover, high hydrostatic
pressure was employed to inhibit V-PPase through
subunit dissociation ofthe enzyme, resulting in inac-
tive forms [10]. The physiological substrate and sub-
strate analogs enhance the high-pressure inhibition of
V-PPase, indicating the vulnerability ofthe subunit–
subunit interaction [10]. The above lines of evidence
illustrate explicitly the importance of dimer forma-
tion for V-PPase function, and suggest nonrandom
and sequestered association of V-PPase subunits
within thevacuolar membrane. Furthermore, the
structures of purified V-PPases from pumpkin (Cu-
curbita sp. Kurokawa Amagur) and Thermotoga mar-
itime have been examined by electron microscopy
[13,14]. Notwithstanding this, structure–function rela-
tionships within this proton-translocating complex
require further study.
Atomic forcemicroscopy (AFM) is a powerful
tool used for nanoscale structural analysis of protein
complexes [15,16], andof supported lipid bilayers in
particular [17–20]. For instance, AFM has provided
marvelously high-resolution images of purified
dimeric membrane proteins in 2D crystals and of
densely packed proteins in native membranes [21–23].
In the present study, we used AFM to directly
observe purified V-PPases reconstituted into planar
lipid bilayers under physiological conditions. Our
images unambiguously reveal adimeric complex for
this proton-transporting V-PPase. Furthermore, the
molecular volume of V-PPase calculated from AFM
images suggests the presence of two identical subun-
its, verifying the notion ofthe homodimeric V-PPase
enzyme. Agoldnanoparticle (GNP) technique com-
bined with transmission electron microscopy (TEM)
analysis was utilized to determine the distance
between C-termini within a membrane-bound
V-PPase dimer, and indicated that theC-termini are
located at the interface of subunits.
Results and discussion
AFM analysis of purified V-PPase adsorbed onto
mica
Recombinant DNAs for overexpression of V-PPases
containing a 6·His tag at either the C-terminus or
N-terminus were prepared and transformed into a
yeast host. Recombinant V-PPase containing a 6·His
tag at the C-terminus (Fig. 1C) was overexpressed in
yeast and successfully purified from microsomes.
Unfortunately, V-PPase containing a 6·His tag at
the N-terminus was poorly expressed in yeast and
was therefore excluded from the study (data not
shown). SDS/PAGE analysis ofthe purified C-termi-
nal 6·His-tagged V-PPase followed by Coomassie
Blue staining or western blotting showed that it was
highly purified, comprising a single major band with
a molecular mass of 73 kDa (Fig. 1A), as expected
from the known structure ofthe V-PPase monomer
[1,2,10]. During size exclusion chromatography,
V-PPase was eluted with an apparent molecular mass
of 145 kDa, similar to its native form and in
agreement with previous studies suggesting a dimeric
conformation [2,10–12].
The purified V-PPase was then reconstituted into
liposomes by a detergent removal method using Bio-
Rad SM-2 beads combined with freeze–thaw sonica-
tion [13]. On addition of PP
i
to the proteoliposome
solution containing Mg
2+
, a dramatic decrease in pH
was generated in the interior ofthe liposomes (Fig. 1B,
lower trace). The acidic pH was eliminated by the
addition ofthe ionophore gramicidine D (5 lgÆmL
)1
),
indicating the integrity ofthe membrane (data not
shown). The liposomes alone (without V-PPase) did
not exhibit proton-translocating activity (Fig. 1B,
upper trace).
Individual V-PPase molecules were adsorbed
randomly on the mica surface and exhibited a proto-
typical globular structure under physiological condi-
tions (Fig. 2A). Figure 2B shows the heights of the
adsorbed particles along the cross-section in Fig. 2A.
Adjacent C-terminiofdimeric H
+
-pyrophosphatase T H. Liu et al.
4382 FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS
The width of individual protein molecules was
measured at half the vertical height. The mean width
and height [± standard deviation (SD), n = 21] of
purified V-PPase were 22.5 ± 3.2 nm and 1.6 ±
0.4 nm, respectively. Furthermore, major peaks on
height and width histograms for the AFM images
also concurred with those parameters obtained above
for V-PPase molecules (Fig. 2C,D). The flattening of
particles was presumably caused by the interaction
between the polar surface ofthe protein molecules
and the charged surface ofthe mica [24]. These
images represent the first direct nanoscale observation
of V-PPase.
Determination of molecular volume provides the
stoichiometry of subunit components for functional
enzymes [24]. In this study, the volume of V-PPase
was calculated using Eqn (1) anddetermined to be
302.4 ± 40.6 nm
3
(V
s
)(n = 21), which was slightly
larger than the theoretical value (V
prot
; 274.5 nm
3
)of
the protein (Table 1). This slight overestimation in
volume probably arose from the broadening effect of
the AFM tip [24]. It is also likely that variations in
volume measurements might arise from distinct inter-
actions ofthe tip with the individual purified
V-PPase particles [25]. Nonetheless, these results
unambiguously demonstrate the feasibility of this
technique for nanoscale investigation of purified
V-PPase molecules.
AFM analysis of V-PPase reconstituted into
liposomes
The homodimeric structure of V-PPase in a planar
lipid bilayer was imaged directly by AFM (Fig. 3).
Purified V-PPase was first reconstituted into a sup-
ported lipid bilayer, as confirmed by immunofluores-
cence imaging (Fig. 3A). Figure 3A1 shows a planar
lipid bilayer reconstituted with V-PPases and ana-
lyzed by immunofluorescence usinga primary anti-
body against His followed by a Cy3-conjugated
secondary antibody; no fluorescence was detected in
bilayers without immunofluorescence labeling of the
protein (Fig. 3A2). In addition, no immunofluores-
cence was observed when the reconstituted sample
was incubated directly with the Cy3-conjugated sec-
ondary antibody in the absence of primary antibody
against His (Fig. 3A3). Lipid bilayers lacking
V-PPases also did not exhibit detectable fluorescence
(Fig. 3A4). These results indicated successful incorpo-
ration of V-PPase into a lipid bilayer, allowing for
subsequent AFM analysis.
To obtain high-resolution AFM images of individ-
ual V-PPases within reconstituted membranes, the
proteoliposomes prepared above were fused into a
large planar lipid bilayer for direct observation. The
thickness ofthe lipid bilayer without any protein was
approximately 4.6 ± 0.5 nm (n = 12), determined
Fig. 1. Purification and proton transport
activity of V-PPase. (A) Analysis of purified
V-PPase by western blotting (top) and SDS/
PAGE and Coomassie Blue staining (bot-
tom). Lane 1: V-PPase-enriched microsome.
Lane 2: purified V-PPase. Lane 3: reconsti-
tuted V-PPase. Molecular mass (kDa) mark-
ers are indicated on the left. (B) PP
i
-
associated proton translocation of reconsti-
tuted V-PPase. Proton transport was initi-
ated by adding 1.0 m
M PP
i
. At the end of
each reaction, 5 lgÆmL
)1
gramicidin D was
added to stop the fluorescence quenching
of acridine orange. (C) Topological model of
V-PPase. Cylinders 1–16 indicate mem-
brane-spanning domains.
T H. Liu et al. Adjacent C-terminiofdimeric H
+
-pyrophosphatase
FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS 4383
from a cross-section ofthe lipid bilayer. The bilayer
thickness was consistent with previous AFM mea-
surements ofa lipid bilayer composed ofa phospha-
tidylcholine/cholesterol mixture and prepared in a
similar aqueous environment [26]. V-PPases reconsti-
tuted into the lipid bilayer protruded from the
bilayer surface in a diffuse pattern with a random
distribution. The V-PPase images fell within two cat-
egories according to the extramembranous protrusion
height. These height differences reflect two distinct
populations of individual V-PPases facing the recon-
stituted membrane surface (Fig. 3D,E). Three-dimen-
sional analysis of individual V-PPases randomly
distributed on the membrane surface indicated that
56.7% ofthe protrusions were small, with a mean
height of 1.2 ± 0.1 nm (n = 20) (Fig. 3B, solid cir-
cles), andthe remainder ofthe protrusions (43.3%)
were large, with a mean height of 2.8 ± 0.3 nm
(n = 17) (Fig. 3B, dotted circle). The uneven distri-
bution and/or orientation of V-PPases on the mem-
brane suggests that targeting ofthe V-PPase into the
vacuolar membrane of plant cells may follow a spe-
cific pattern, as previously suggested [10]. Figure 3C
shows a cross-section along the line in Fig. 3B. The
widths and heights ofthe reconstituted V-PPase pro-
trusions in Fig. 3B are listed in Table 1. The AFM
image of reconstituted V-PPase shows a ratio of
approximately 2.40 : 1 for the height values of the
cytosolic and luminal sides. In addition, the theoreti-
cal ratio ofthe total amount of amino acids on the
cytosolic and luminal sides was calculated as 2.31 : 1
(data not shown), verifying the efficacy of this tech-
nique.
The high protein density in 2D crystals or in native
membranes allows high-resolution AFM topographs
and the elucidation of protein subunit organization
[21–23]. However, it is presently difficult to obtain
V-PPase reconstituted in 2D crystals or packed at high
density into a membrane (data not shown). Notwith-
standing this, current AFM techniques suffice to
provide unambiguous images ofthedimeric structure
of V-PPase. Four representative examples exhibiting
minor variations are shown in Fig. 4A. The small
differences in topography ofthe individual V-PPases in
A
B
D
C
Fig. 2. AFM analysis of purified V-PPase. (A) Three-dimensional
AFM image of purified V-PPase adsorbed onto mica. (B) Profile of
peak heights along the cross-section shown in (A). Purified V-PPase
protrudes 1.6 ± 0.4 nm (n = 21) from the mica surface. (C) Histo-
gram of V-PPase height determinedusingthe AFM image in (A).
(D) Histogram of V-PPase width determinedusingthe AFM image
in (A).
Adjacent C-terminiofdimeric H
+
-pyrophosphatase T H. Liu et al.
4384 FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS
the reconstituted lipid bilayer have probably resulted
from contact with the AFM tip during scanning.
Nevertheless, these AFM images are adequate for
nanoscale resolution ofthe structural details of
V-PPase [27,28]. Moreover, the resolution of the
images from V-PPases in reconstituted membranes was
Table 1. Dimensions of free and membrane-bound recombinant V-PPase determined by AFM. Values represent means ± SD. n = number
of observations. Observed and predicted volumes were determined from AFM analysis using Eqn (1) and from theoretical analysis using
Eqn (2).
Protein (145 kDa) Height (nm) Width (nm)
Volume (nm
3
)
Observed Predicted
Purified V-PPase (n = 21) 1.6 ± 0.4 22.5 ± 3.2 302.4 ± 40.6 274.5
Reconstituted V-PPase 332.9 ± 46.9 274.5
Lumen side (n = 20) 1.2 ± 0.1 21.7 ± 3.6
Cytosolic side (n = 17) 2.8 ± 0.3 26.3 ± 4.7
Lipid bilayer (n = 12) 4.6 ± 0.5
Fig. 3. Reconstitution of V-PPase into proteoliposomes. (A) Immunofluorescence imaging of V-PPases reconstituted into lipid bilayers. (1)
Sample treated with primary and secondary antibodies. (2) Sample not treated with either antibody. (3) Sample treated with only secondary
antibody. (4) Lipid bilayer lacking V-PPases but treated with primary and secondary antibodies. (B) AFM image of V-PPase extramembranous
protrusions on the luminal and cytosolic sides ofthe membrane. Solid circle, luminal side; dotted circle, cytosolic side. Inset: section of a
lipid bilayer with thickness of 4.6 ± 0.5 nm (n = 12). (C) Profile of protrusion heights along the cross-section shown in (B). Two populations
of V-PPase protrusions were observed: one with a mean height of 1.2 ± 0.1 nm (n = 20), and one with a mean height of 2.8 ± 0.3 nm
(n = 17). (D) Histogram of V-PPase protrusion heights determinedusingthe AFM image in (B). (E) Histogram of V-PPase peak widths deter-
mined usingthe AFM image in (B).
T H. Liu et al. Adjacent C-terminiofdimeric H
+
-pyrophosphatase
FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS 4385
typically higher than that of those directly adsorbed
onto a mica surface.
The volume ofthe V-PPase homodimers (V
m
) in the
reconstituted membrane was estimated usingthe height
of the protein protrusion andthe thickness ofthe lipid
bilayer as the parameters for the volume ofa sphere
(Fig. 4B). The volume of reconstituted V-PPase was
measured as 332.9 ± 46.9 nm
3
(n = 17). The V
prot
of
a V-PPase homodimer with a molecular mass of
145 kDa, calculated on the basis ofthe amino acid
composition, was determined to be 274.5 nm
3
[29].
This theoretical volume correlates very well with that
measured from the AFM images. Note that these
images were obtained by AFM scanning in a fluid,
and therefore probably provide an authentic illustra-
tion of V-PPase structure under physiological condi-
tions. The AFM images indicate thedimeric structure
of V-PPase reconstituted in a lipid bilayer. This study
provides the first 3D representation of individual
V-PPases protruding from the cytosolic and luminal
sides ofa membrane in aqueous solution.
Proximity of V-PPase C-termini in reconstituted
membranes
Topology studies examining heterologous V-PPase
expression in yeast suggested that both the C-termini
and the N-termini of each subunit are located on the
lumen side and are opposite the catalytic domain on
the cytosolic side ofthe vesicular membrane [1].
Because V-PPase is homodimeric, there are two possi-
ble configurations for association ofthe two subunits;
the C-terminiof both subunits may protrude from the
same side or from opposite sides ofthe membrane
Fig. 4. High-resolution AFM image of
V-PPase dimers in a reconstituted
membrane. (A) AFM analysis of
extramembranous protrusions on the
cytosolic side of proteoliposomes containing
V-PPase (top panels) and those on the
luminal side (bottom panels). (B) Topological
model ofthe homodimeric structure of
V-PPase.
Adjacent C-terminiofdimeric H
+
-pyrophosphatase T H. Liu et al.
4386 FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS
[30]. The present study demonstrated two distinct types
of protrusions randomly distributed in reconstituted
lipid bilayers. If theC-terminiof each V-PPase subunit
within a dimer protruded from opposite sides of the
membrane, the measured heights of these two types of
protrusion should presumably be the same. The nega-
tive results above thus indicate that theC-termini of
the individual subunits ofthe enzyme are facing the
same side ofthe membrane.
The relative positions andproximityofthe V-PPase
C-termini on the surface ofthe reconstituted mem-
branes were examined using an IgG antibody against
the C-terminal His tag ofthe enzyme (Fig. 5). The
AFM image ofthe immunolabeled V-PPase showed
that protrusions of different heights and widths were
randomly distributed on the lipid bilayer (Fig. 5A). The
antibody could bind to V-PPase on either one or two
molecules (Fig. 5B). Clearly, Fig. 5B2 depicts that two
antibodies bind respectively to a single V-PPase mole-
cule in close vicinity. AFM image analysis using spip
software was used to generate histograms delineating
the distribution of protrusion heights and widths
(Fig. 5C,D), and this revealed three major groups of
protrusions: (a) lower peaks (peak 1; 1.4 ± 0.2 nm
mean height, n = 10) for structures of V-PPase on the
lumen side ofthe membrane lacking bound antibody;
(b) intermediate peaks (peak 2; 2.9 ± 0.2 nm mean
height, n = 20) for those on the cytosolic side of the
membrane; and (c) higher peaks (peak 3; 4.2 ± 0.3 nm
mean height, n = 10) for antibodies bound presumably
to the lumen side. The ratio ofthe sum of integrals for
peak 1 and peak 3 (free lumen side and antibodies bind-
ing to the lumen side) to peak 2 (cytosolic side) is con-
sistent with our prior results (approximately 5.6 : 4.4).
Fig. 5. AFM analysis of V-PPase in a reconstituted lipid bilayer immunolabeled with an antibody against His to detect the C-terminal 6·His
tag of V-PPase. (A) Image ofa large section of immunolabeled lipid bilayer reconstituted in the presence of V-PPase. (B) High-resolution
images of immunolabeled protrusions in (A). (1) Protrusion showing a single antibody bound to V-PPase. (2) Protrusion showing two
antibodies bound to V-PPase. (C) Histogram of protrusion height determinedusingthe AFM image in (A). (D) Histogram of protrusion width
determined usingthe AFM image in (A).
T H. Liu et al. Adjacent C-terminiofdimeric H
+
-pyrophosphatase
FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS 4387
Previous AFM imaging studies have demonstrated
that the height ofa single IgG molecule is
2.4 ± 0.1 nm [24]. Taking this value into account, the
height of peak 3 protrusions (4.2 ± 0.3 nm, n = 10)
would be that of IgG molecules (2.4 ± 0.1 nm) sitting
on V-PPase at the lumen side (1.2 ± 0.1 nm, n = 20).
There were also two major groups in the histogram
representing the distribution of protrusion widths,
probably for those ofthe single IgG molecule (mean
width = 41.5 ± 1.8 nm, n = 12; 38.5% of protru-
sions) and those of two IgG molecules (mean width =
51.3 ± 0.8 nm, n = 20; 62.5% of protrusions) bound
to a V-PPase in the lipid bilayer, respectively
(Fig. 5D). It is well established that the hinge region of
IgG links the two Fab arms to the Fc portion, provid-
ing global flexibility to the IgG. The flexibility of the
IgG molecule results in Fab ‘elbow bending’, Fab ‘arm
waving’ and rotation, and Fc ‘wagging’ [31]. The
observed variations in the number of IgG molecules
bound to the 6·His-tagged C-terminiof V-PPase
subunits have presumably arisen from such antibody
flexibility. Therefore, the space betweenthe two anti-
body molecules could not be precisely determined
using current techniques. As a result, we were also
unable to accurately determine theproximityof the
V-PPase C-terminiusingthe antibody-binding
technique.
We hence employed Ni
2+
–nitrilotriacetic acid GNP
labeling as an alternative technique to evaluate the
proximity ofC-termini within V-PPase homodimers.
Extremely small Ni
2+
–nitrilotriacetic acid GNPs were
bound to the 6·His tags of V-PPase C-termini recon-
stituted in lipid bilayers in aqueous solution, resulting
in two major types of protrusion as observed with
AFM: the cytosolic side of V-PPase, andthe particles
bound to the lumen side of V-PPase, respectively
(Fig. 6). The solid circle in Fig. 6B indicates GNP
bound to V-PPase C-terminus protruding from the
surface ofthe lipid bilayer, whereas the dotted circle,
V-PPase protrusion at the lumen side lacking bound
GNP (Fig. 6B). More than 70% of V-PPases were
covered by GNPs on the luminal side (data not
shown). The height distribution histogram indicated
that the heights ofthe lower V-PPase protrusions
(peak 1) were consistent with those of its cytosolic por-
tions, whereas the heights ofthe higher ones (peak 2)
represented those ofthe GNPs bound to the C-termini
of the enzyme (Fig. 6C). The height ofthe latter
protrusions (4.9 ± 0.1 nm) reflects the sum of Ni
2+
–
nitrilotriacetic acid GNP heights (mean height =
2.0 ± 0.1 nm, n = 16) and V-PPase heights on the
luminal side (mean height = 1.2 ± 0.1 nm, n = 20).
In contrast, the lower V-PPase protrusions represent
those of its cytosolic sides alone. Moreover, in the
width distribution histogram, the higher peaks (peak
1) represent either cytosolic protrusions of V-PPase
lacking GNPs (mean width = 26.3 ± 4.7 nm, n = 17)
or the luminal side containing GNP-bound C-termini
(mean width = 28.2 ± 1.4 nm, n = 48). Other peaks
(peaks 2 and 3) in the width distribution histogram
(> 50 nm) probably reflect GNP clusters, because
20% of GNPs in solution are visualized as collec-
tions after sonication (data not shown).
The number of GNPs bound to V-PPase C-termini
was then predicted usinga Microscope Simulator (Com-
puter Integrated Systems for Microscopyand Manipula-
tion, University of North Carolina, Chapel Hill, NC,
USA) (Fig. 6E). The width ofthe image for a single
GNP on mica was empirically determined as
21.2 ± 1.1 nm (n = 27, data not shown); the theoreti-
cal width ofa single GNP on the surface of V-PPase was
24 nm (Fig. 6E, solid rhombus). The mean width of
GNPs on the surface of V-PPase was empirically mea-
sured as 28.2 ± 1.4 nm (n = 48), suggesting that more
than one GNP was present on the surface of V-PPase.
Because V-PPase is a homodimeric enzyme, it is conceiv-
able that one GNP was bound to each C-terminus.
Moreover, the distance between two GNPs (reflecting
that between two V-PPase C-termini) was extrapolated
from a simulation plot (Fig. 6E, solid circles). The solid
triangle in Fig. 6E reflects the mean width of GNPs on
the surface of V-PPase, corresponding to a GNP dis-
tance of 2.2 ± 1.4 nm. Our results suggest explicitly that
the two C-terminiof V-PPase are in close proximity.
To validate the prediction that the V-PPase C-termini
are adjacent, a TEM analysis was used to directly mea-
sure the distance between two GNPs bound to the C-ter-
mini of purified V-PPase. The TEM image displays the
bound GNPs as solid spheres with a diameter of
2.0 ± 0.2 nm (n = 18) (Fig. 7A). In addition, GNPs
bound to V-PPase C-termini occurred in pairs (Fig. 7B),
indicating thedimeric structure ofthe enzyme. The his-
togram showing the distribution of distances between
GNP pairs observed from the TEM image yields a mean
distance of 1.9 ± 0.8 nm (Fig. 7C), concurring with the
result generated by AFM analysis of GNP-labeled
V-PPase (Fig. 6E; distance = 2.2 ± 1.4 nm). The slight
fluctuation in distances between GNP pairs most likely
arose from the flexibility ofthe V-PPase C-termini. For
instance, the shorter distance observed indicates two
closed GNPs on theC-terminiofthe enzyme. In con-
trast, the longer distance indicates a probable extension
of theC-terminiof V-PPase. Verification of these possi-
bilities requires further investigation.
The C-terminus of V-PPase has been determined to
be relatively conserved among various plant V-PPases,
Adjacent C-terminiofdimeric H
+
-pyrophosphatase T H. Liu et al.
4388 FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS
and is presumed to be proximal to the catalytic site
[32]. In addition, the importance ofthe V-PPase C-
terminus in sustaining enzymatic and proton-translo-
cating function and for indirect regulation of K
+
binding has been demonstrated [9]. Moreover, inter-
subunit interactions of V-PPase are critical for proper
enzyme function [10], suggesting that the interface
between the two subunits may participate in enzy-
matic and proton-pumping reactions. In the present
study, AFM measurements and single nanoparticle
analysis using TEM further demonstrated that the
two C-terminiof V-PPase homodimers are approxi-
mately 1.9–2.2 nm apart. In conclusion, our study
provides high-resolution images of single V-PPase
molecules within a membrane, allowing analysis of
the architecture, size and structure of V-PPase in a
physiologically relevant environment. We propose a
working model in which the proton channel lies at
the interface betweentheC-terminiofthe V-PPase
homodimer (Fig. 8).
Fig. 6. AFM analysis of Ni
2+
–nitrilotriacetic
acid GNPs bound to the C-terminal 6·His
tag of V-PPase. (A) Lipid bilayer reconsti-
tuted in the presence of Ni
2+
–nitrilotriacetic
acid GNP-bound V-PPase. (B) High-resolu-
tion image of individual dimeric structures of
V-PPase labeled with GNPs in reconstituted
membrane. Solid circle, GNP-bound V-PPase
protrusion on the luminal side ofthe recon-
stituted membrane; dotted circle, V-PPase
protrusion lacking a GNP label on the lumi-
nal side ofthe membrane. (C) Histogram of
the protrusion heights determinedusing the
AFM image in (A). (D) Histogram ofthe pro-
trusion widths determinedusingthe AFM
image in (A). (E) Simulation of potential
V-PPase protrusion widths based on dis-
tances between GNP pairs bound to the
V-PPase C-termini. Solid rhombus, predicted
protrusion width based on a single GNP
molecule bound to the C-terminus of
V-PPase; solid circle, predicted protrusion
widths based on the distance between two
GNP molecules bound to V-PPase C-termini;
solid triangle, actual protrusion width of
GNP-bound V-PPase determined by AFM.
Data represent the mean ± SD.
T H. Liu et al. Adjacent C-terminiofdimeric H
+
-pyrophosphatase
FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS 4389
Experimental procedures
Cloning, expression, and purification
The mung bean (Vigna radiata L.) V-PPase cDNA (VPP;
accession number P21616) [33] was cloned into the yeast
expression vector pYES2 (Invitrogen, Carlsbad, CA, USA),
and the two synthesized oligonucleotides P
his
(5¢-CCTCG
AGCCATCATCATCATCATCATTAGGGCCGCATCAT
GTAATTAGTTATGT-3¢) and P
MluI
(5¢-GTACACGCG
TCTGATCAG-3¢) were inserted into the 3¢-end of the
pYES2–VPP plasmid to generate the V-PPase–(His)
6
tail.
The pYES2–VPP–(His)
6
cDNA was transferred into the
Saccharomyces cerevisiae strain BJ2168 (MATa, prc-407,
prb1-1122, pep4-3, leu2, trp1, ura3, GAL) according to the
method described previously [34]. The yeast microsomal
membranes enriched in 6 · His-tagged V-PPase were pre-
pared as described by Kim et al. [35], with minor modifica-
tions. Finally, V-PPase-enriched membrane fractions were
resuspended in the storage buffer [10 mm Tris/HCl (pH
7.6) and 10% (w/v) glycerol] and stored at )70 °C for fur-
ther use. The V-PPase (1 mgÆmL
)1
)-enriched microsomal
membrane fraction was solubilized in an extraction buffer
[10 mm Tris/HCl (pH 8.0), 400 mm KCl, 15% (w/v) glyc-
erol, 1 mm phenylmethanesulfonyl fluoride, 0.1% (w/v)
n-dodecyl-b-d-maltoside (DDM)] by adding the detergent
DDM dropwise, to a final concentration of 6 mgÆmL
)1
,
and gently stirred for 30 min on ice. The solution was
diluted with the extraction buffer described above three-
fold to five-fold, and unsolubilized materials were removed
by ultracentrifugation at 75 000 g at 4 °C for 1 h. The
supernatant was incubated with Ni
2+
–nitrilotriacetic acid
beads prewashed with the extraction buffer for 1 h. The
Ni
2+
–nitrilotriacetic acid beads were injected into the
empty column and eluted at a flow rate of 0.5 mLÆmin
)1
with the elution medium [10 mm Tris/HCl (pH 8.0), 15%
(w/v) glycerol, 10 mm b-mercaptoethanol, 1 mm phen-
ylmethanesulfonyl fluoride, 0.1% (w/v) DDM] with a step
gradient of 20, 40, 60 and 250 mm imidazole, respectively.
The fractions with highest PP
i
hydrolysis activity at
250 mm imidazole were pooled and dialyzed against med-
ium containing 10 mm Tris/HCl (pH 8.0), 15% (w/v) glyc-
erol, and 0.1% (w/v) Triton X-100, and then stored at
)70 °C for further studies.
Fig. 7. TEM analysis of Ni
2+
–nitrilotriacetic acid GNP-labeled
V-PPase. (A) TEM image of Ni
2+
–nitrilotriacetic acid GNP-labeled
purified V-PPase. (B) A gallery of zoomed images for the GNP pairs
labelled on purified V-PPases. (C) Histogram ofthe distances
between GNP pairs determinedusingthe TEM image in (A).
Fig. 8. A working model of V-PPase. The distance between
C-termini of V-PPase is approximately 2.2 nm.
Adjacent C-terminiofdimeric H
+
-pyrophosphatase T H. Liu et al.
4390 FEBS Journal 276 (2009) 4381–4394 ª 2009 The Authors Journal compilation ª 2009 FEBS
[...]... 32 Takasu A, Nakanishi Y, Yamauchi T & Maeshima M (1997) Analysis ofthe substrate binding site and carboxyl terminal region ofvacuolarH+-pyrophosphataseof mung bean with peptide antibodies J Biochem 122, 883–889 33 Hung SH, Chiu SJ, Lin LY & Pan RL (1995) A cDNA clone encoding theA subunit ofthevacuolar H+-ATPase from etiolated mung bean seedlings Plant Physiol 109, 1125–1127 34 Hsiao YY, Van... H+-translocating inorganic pyrophosphatase of plant vacuoles Biochem Biophys Res Commun 168, 1157–1162 12 Sarafian V, Potier M & Poole RJ (1992) Radiationinactivation analysis ofvacuolar H+-ATPase and H+pyrophosphatase from Beta vulgaris L Functional sizes for substrate hydrolysis and for H+ transport Biochem J 283, 493–497 13 Sato MH, Kasahara M, Ishii N, Homareda H, Matsui H & Yoshida M (1994) Purified vacuolar. .. lm acridine orange, and 100 lgÆmL)1 microsomes The reaction was initiated by adding 1 mm sodium pyrophosphate (pH 7.6) The initial rate of fluorescence quenching was calculated as the proton transport activity [34,39–41] The ionophore, gramicidin D (5 lgÆmL)1), was then included at the end of each assay to confirm the integrity ofthe membrane SDS/PAGE and western analysis SDS/PAGE was performed according... Kim Y, Sarafian V, Poole RJ, Davies JM & Sanders D (1992) Vacuolar H+-translocating pyrophosphatases: a new category of ion translocase Trends Biochem Sci 17, 348–353 5 Gordon-Weeks R, Steele SH & Leigh RA (1996) The role of magnesium, pyrophosphate, and their complexes as substrates and activators ofthevacuolar H+-pumping inorganic pyrophosphatase (studies using ligand protection from covalent inhibitors)... 4391 Adjacent C-terminiofdimericH+-pyrophosphatase T.-H Liu et al Nanogold solution (Nanoprobes, NY, USA), washed twice with NaCl/Pi, and then subjected to AFM imaging V2 is the specific volume of water (1 cm3Æg)1), and d is a factor describing the extent of hydration for air-dried proteins (0.4 mol H2O/mol protein) [44] AFM AFM was performed in the contact mode usinga Nanoscope IIIa Multimode atomic. .. V-PPase was performed in the imaging buffer at room temperature (22–23 °C) All images were captured at 512 · 512 pixel resolution and processed using nanoscope III software (Digital Instruments, Santa Barbara, CA, USA) and spip software (Scanning Probe Image Processor; Image Metrology, Lyngby, Denmark) In general, AFM images were low-pass filtered, and single protein images were further passed through an... the volume ofa single soluble or purified protein was calculated by regarding the molecule as a segment ofa sphere, using Eqn (1) [29]: Vs ¼ ðph=6Þð3r2 þ h2 Þ ð1Þ where Vs is the molecular volume, and h and r are the height andthe radius (half ofthe measured width) ofthe protein, respectively In addition, molecular volume based on molecular mass was calculated usingthe Eqn (2): Mo ¼ ðNA Vprot Þ=ðV1... H+-pyrophosphatase Biochim Biophys Acta 1465, 37–51 2 Tzeng CM, Yang CY, Yang SJ, Jiang SS, Kuo SY, Hung SS, Ma JT & Pan RL (1996) Subunit structure ofvacuolar proton pyrophosphatase as determined by radiation inactivation Biochem J 316, 143–147 3 Drozdowicz YM & Rea PA (2001) Vacuolar protonpyrophosphatases: from the evolutionary backwaters into the mainstream Trends Plant Sci 6, 206–211 4 Rea PA, Kim Y, Sarafian... polyclonal antibody raised against the MAP (Mitogen-activated protein kinase)-conjugated synthetic peptide ofthe sequence KVERNIPEDDPRNPA, which corresponds to positions 261–275 ofthe substrate-binding domain of mung bean V-PPase Bands of immunoblots were visualized usinga chemiluminescence kit (New England Nuclear, Boston, MA, USA), according to the manufacturer’s recommendations Reconstitution of V-PPase... to Laemmli [42] Denatured proteins were subjected to SDS/PAGE on a Phast System (Pharmacia, Uppsala, Sweden) with a 12.5% (w/v) polyacrylamide PhastGel The gels were stained with Coomassie Blue or electrotransferred to a poly(vinylidene difluoride) membrane by using semidry electrotransblotting apparatus (Nova Blot, Amersham Pharmacia Biotech, Piscataway, NJ, USA) The blots were incubated with the rabbit . Carlsbad, CA, USA),
and the two synthesized oligonucleotides P
his
(5¢-CCTCG
AGCCATCATCATCATCATCATTAGGGCCGCATCAT
GTAATTAGTTATGT-3¢) and P
MluI
(5¢-GTACACGCG
TCTGATCAG-3¢). The proximity between C-termini of dimeric vacuolar
H
+
-pyrophosphatase determined using atomic force
microscopy and a gold nanoparticle technique
Tseng-Huang