In contrast, a recent crystal structure of the isolated associ-ation domain of mouse CaMKIIa has revealed a tetradecameric assembly with two stacked 7-fold symmetric rings.. We also show
Trang 1holoenyzme of Ca2+⁄CaM kinase II
Oren S Rosenberg1,3, Sebastian Deindl1, Luis R Comolli2, Andre´ Hoelz5, Kenneth H Downing2, Angus C Nairn4and John Kuriyan1,2
1 Department of Molecular and Cell Biology and, Department of Chemistry and, Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
2 Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
3 Department of Cell Biology and 4 Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
5 The Rockefeller University, New York, NY, USA
Many cellular processes are modulated by fluctuations
in the cytosolic concentration of calcium ions (Ca2+)
[1] Ca2+⁄ calmodulin (Ca2+⁄ CaM) activated protein
kinases (CaMKs) are among the most important
intra-cellular transducers of Ca2+signals and the
multifunc-tional Ca2+⁄ calmodulin activated kinase II (CaMKII)
is one of the most abundant kinases of this class [2]
CaMKII is highly conserved throughout the animal
kingdom [3] and is found in virtually all mammalian
cell types, where it phosphorylates a large array of
different substrates, including itself [4] It has a
particularly important and well studied role in the response of neurons and myocytes to Ca2+ transients (reviewed in [5] and [6], respectively) In these cells, CaMKII has been shown to be important in complex physiological processes such as the generation of long-term potentiation and the regulation of the heartbeat There are four mammalian isoforms of CaMKII and many different splice variants, but all CaMKII proteins share the same basic architecture (Fig 1) All
of the isoforms assemble into multimeric holoenzymes Each polypeptide chain in the holoenzyme contains a
Keywords
association domain; Ca 2+ ⁄ calmodulin
dependent protein kinase II; holoenzyme;
kinase activation; oligomerization
Correspondence
J Kuriyan, University of California, Berkeley,
Barker Hall MC 3202, Berkeley, CA
94720-3202, USA
Fax ⁄ Tel: +1 510 643 0137
Fax: +1 510 643 2352
E-mail: kuriyan@berkeley.edu
Website: http://jkweb.berkeley.edu
(Received 6 September 2005, revised 27
November 2005, accepted 5 December
2005)
doi:10.1111/j.1742-4658.2005.05088.x
Ca2+⁄ calmodulin activated protein kinase II (CaMKII) is an oligomeric protein kinase with a unique holoenyzme architecture The subunits of CaMKII are bound together into the holoenzyme by the association domain, a C-terminal region of 140 residues in the CaMKII polypeptide Single particle analyses of electron micrographs have suggested previously that the holoenyzme forms a dodecamer that contains two stacked 6-fold symmetric rings In contrast, a recent crystal structure of the isolated associ-ation domain of mouse CaMKIIa has revealed a tetradecameric assembly with two stacked 7-fold symmetric rings In this study, we have determined the crystal structure of the Caenorhabditis elegans CaMKII association domain and it too forms a tetradecamer We also show by electron micro-scopy that in its fully assembled form the CaMKII holoenzyme is a dode-camer but without the kinase domains, either from expression of the isolated association domain in bacteria or following their removal by pro-teolysis, the association domains form a tetradecamer We speculate that the holoenzyme is held in its 6-fold symmetric state by the interactions of the N-terminal 1–335 residues and that the removal of this region allows the association domain to convert into a more stable 7-fold symmetric form
Abbreviations
Ca 2+ , calcium; CaMK, Ca 2+ ⁄ calmodulin dependent protein kinase; CaMKII, Ca 2+ ⁄ calmodulin dependent protein kinase II; PEG, polyethylene glycol; TCEP, tri(2-carboxyethyl)phosphine hydrochloride.
Trang 2kinase domain (residues 1–280 in the mouse CaMKIIa
numbering is used throughout this article) followed by
a regulatory segment (residues 281 to 316) that binds
to the kinase domain and inhibits its activity A linker
region follows the regulatory segment, the length of
which is variable and depends on the isoform or splice
variant The C-terminal segment of the polypeptide
contains the so-called association domain (residues
345–478) that is responsible for oligomerization
Previ-ous work has suggested that the association domains
form a ring at the center of the holoenzyme with the
kinase domains surrounding the central ring like
spokes on a wheel [7–10]
The number of subunits in the CaMKII
holo-enyzme has been assessed by many groups using a
number of different techniques, and has been
estima-ted to be from 4 to 14 [8,9,11–19] but with the
con-sensus being that the holoenzyme is a dodecamer
The crystal structure of the isolated association
domain (residues 335–478 of the mouse CaMKIIa)
has been solved, and found to be a tetradecamer
[10] This crystallization construct is also a
tetrade-camer in solution [10] In the structure, the 14
association domain protomers assemble into two
7-fold symmetric rings These rings face each other,
creating seven 2-fold axes of symmetry that are
per-pendicular to the 7-fold axis Single particle analysis
of electron micrographs suggest that CaMKII forms
dodecamers in its fully assembled state [9,11,13] and
the reason for, and significance of, this discrepancy
between the oligomerization state of the holoenzyme
and that of the crystal structure of the association
domain is unknown Although the association
domain is necessary and sufficient for formation of
oligomeric CaMKII [18,19], it is not known if other
parts of the protein play a role in determining the final functional form of the CaMKII holoenzyme
It has been hypothesized that a central function of the CaMKII holoenzyme is to respond, via an increase in persistent kinase activity, to the frequency of incoming
Ca2+spikes [20,21] This remarkable property relies on five features of CaMKII First, its oligomeric structure brings the kinase domains into a defined special rela-tionship with one another [10] Second, the event that triggers persistent activity of CaMKII is a trans-auto-phosphorylation, where one kinase subunit phosphory-lates another kinase subunit (on Thr286 in the auto-regulatory segment) [22–26] Third, this auto-phos-phorylation happens only between the subunits within a single holoenzyme, not between separate holoenzymes [27] Fourth, the trans-auto-phosphorylation event can only occur when both the phosphorylating subunit and the subunit that is the target of the phosphorylation are both bound to CaM [28] and, presumably, only if they can reach each other Finally, once the trans-auto-phos-phorylation has taken place, CaM becomes ‘trapped’
by the phosphorylated subunit due to an increase of
13 000-fold in the affinity for CaM [29]
The details of the physical distances between the different subunits in the assembled holoenzyme are
a crucial determinant of what defines a ‘neighboring’ subunit in the scheme described above In addition, interactions of the kinase domains with each other around the ring might affect the rate and dwell time of CaM binding Defining the predominant oligomeric state of the holoenzyme and thus better understanding the molecular dimensions and architecture of the holo-enyzme is a critical step towards a complete molecular characterization of this complex enzyme and its func-tional properties
In this paper we compare the oligomeric states of the isolated association domains of CaMKII from mouse and Caenorhabditis elegans with that of the holoenzyme using hydrodynamic techniques, electron microscopy, and X-ray crystallography We find that the assembled holoenyzmes are dodecameric, as noted previously by others [8,9,13] When the kinase domains are removed, either by deleting them from the expres-sion construct or by proteolysis of the holoenzyme, the association domains assemble into a tetradecameric form that we have now visualized for the C elegans protein by X-ray crystallography as well as for the mammalian enzyme We hypothesize that additional interactions of the N-termini of the subunits constrain the oligomerization state of the holoenzyme and that when these additional constraints are removed the isolated association domains transform into a 7-fold state
Fig 1 The domain structure of the CaMKII proteins All isoforms
have the same basic architecture although the different isoforms
have variable insertions of between 21 and 178 residues in the
lin-ker between the kinase and the association domain.
Trang 3Static light scattering
We expressed and purified full-length mouse CaMKIIa
and used static light scattering to estimate the number
of subunits in the assembly This estimate should be
independent of the shape of the protein complex [30]
The value of the molecular mass given by the analysis
of the scattering data is 689 000 kDa (error 1%)
(poly-dispersity Mw⁄ Mn¼ 1.002 where Mw is the
weight-averaged molar mass and Mn is the number-averaged
molar mass), suggesting 12.6 subunits per holoenzyme
(Fig 2) Values of the molecular mass obtained
previ-ously from a similar experiment with the isolated
association domain of mouse CaMKIIa indicated a
subunit stoichiometry of 14.8, which is consistent with
the tetradecameric crystal structure of the association domain [10]
The holoenzyme is 6-fold symmetric in negatively stained samples
We examined the full-length mouse CaMKIIa in uranyl acetate stained samples We picked 2673 particles, aligned them and classified them into 75 classes All of the particles appeared to be in the same orientation on the grid and thus all of the class averages are very sim-ilar in appearance (Fig 3Ai,Aii) These class averaged images show a strong inner ring of density with an outer radius of 6 nm and a much weaker outer ring with an outer radius of 12 nm The first four eigen images show a strong 6-fold modulation (Fig 3B) As previ-ously done in other electron microscopic analyses of CaMKIIa we interpret the 6 nm ring of density to be due to the association domains [7,9] The outer ring at
12 nm does not appear to be sufficiently dense to con-tain the kinase domains This apparent weakening of the density was noted previously by Kanaseki and coworkers, who saw that in uranyl acetate stained sam-ples the central ring of the presumed association domain
is easily visualized, but the presumed peripheral kinase domains, which they observed by other electron micros-copy techniques, are not seen [7]
The kinase domains form a second ring around the ring of the association domains
In order to attempt to more clearly define the position
of the kinase domains in relation to the association domain we examined the holoenzyme embedded in vi-trous ice We analyzed holoenzymes from two different species: mouse CaMKIIa discussed above and C ele-gansCaMKII (UNC-43, splice variant K11E8.d) These proteins are 69% identical in sequence, with no gaps lar-ger than four amino acids in the alignment We picked
3865 particles from images of the Mus musculus protein and 1859 particles from the C elegans set Initial classi-fications suggested that, as with the uranyl acetate stained samples, the ice embedded images also showed a preponderance of a single view along the 6-fold axis which we attribute to a nonrandom orientation of the holoenyzmes during electron microscopic grid prepar-ation We thus classified the images from each sample into five large classes Representative classes show a clear inner ring of density at radius 6 nm and an outer ring at radius 12 nm (Fig 4A,B) We interpret this outer ring of density to be the kinase domains In these images it is possible to see that the association domains and the kinase domains are made up of individual
A
B
Fig 2 Static light scattering analysis of M musculus CaMKII
holo-enyzme (A) Laser light scattered in a single direction from the
eluant of a gel filtration column Signal was measured at 0.5 s
inter-vals as a function of elution volume (red line, reported in the
pri-mary units of the signal, Volts) The relative concentration of
protein, as measured by the refractive index, is also shown (blue).
(B) A plot of the molar mass predicted from the analysis of the
con-centration and scattering data as a function of elution volume (red
dots) Superimposed for reference is the same concentration curve
shown above (blue line) The area highlighted in yellow is the
por-tion of the concentrapor-tion and scattering curves used in the analysis.
Trang 4subunits, but it is not possible to determine
unambigu-ously the symmetry of this particle in the C elegans
sample In the mouse CaMKIIa sample the first eigen
image appears to be 6-fold symmetric (Fig 4C) Thus
by examining the strong symmetry of the uranyl acetate
stained particles and the overall structure of the ice
embedded sample we conclude, in agreement with
Morris & Torok [9], that the association domain forms
a 6-fold symmetric ring of 6 nm outer radius with the
kinase domains surrounding this central ring in a second
ring of density with an outer radius of 12 nm
Bacterially expressed association domains form a
7-fold symmetric assembly in negatively stained
samples
In order to understand the discrepancy between the
results from light scattering and electron microscopic
analysis of the holoenzyme and the crystallographic results, we next examined the truncated association domain of mouse CaMKIIa (residues 336–478), puri-fied from bacteria, using electron microscopy We picked, aligned and classified 2317 association domain particles Again, all of the particles appeared to be in the same orientation on the grid (Fig 5A) The associ-ation domain particles revealed a strong 7-fold sym-metric modulation as seen in the first eigen image (Fig 5B)
Association domains prepared in diverse ways crystallize as 7-fold symmetric rings
Over the course of our experiments using full-length mouse CaMKIIa purified from baculovirus-infected insect cells we noticed that the protein would some-times degrade into two distinct fragments (as seen with
Fig 3 Uranyl acetate stained images of the
M musculus holoenyzme reveal a 6-fold
symmetry (A) Electron microscopic images
and class averages (i) Three representative
raw images of single particles (ii) Six
repre-sentative class averages, all of which look
very similar, suggesting a limited distribution
of orientations on the grid (B) The first four
eigen images of the association domain
classification The first eigen image shows a
strong 6-fold modulation, as seen in the
inset expanded view.
Trang 5SDS⁄ PAGE) In order to better define this degradation
process we treated the preparation with increasing
amounts of trypsin while incubating the samples on
ice At an intermediate concentration of trypsin
(0.01 mgÆmL)1 trypsin) and short time (30 min) the
protein was digested into two bands, as visualized by
SDS⁄ PAGE (Fig 6A) These two populations of
pro-teins were separated into two peaks on an HPLC
column and characterized by electrospray ion trap
mass spectrometry The first peak contained only a
35 198 kDa protein corresponding to residues 2–311 of
CaMKII (which encompasses the kinase domain and
the auto-inhibitory segment, and is acetylated on the
N-terminus) The other peak contained a mixture
of association domain fragments of masses 18 255,
17 811, 17 683, and 17 170 kDa, corresponding to
resi-dues 318–478, 323–478, 324–478, and 329–478,
respect-ively
We noticed that given sufficient time (overnight at
20C) the kinase domain fragment was digested
com-pletely by the trypsin; the association domain fragment
was resistant, however, to further degradation at this
concentration of protease After the extended
incuba-tion, all of the protein was degraded to a single band
on an SDS⁄ PAGE gel As the protein preparation
prior to the trypsin treatment was shown by electron microscopy to be 6-fold symmetric, we reasoned that that the association domain assemblies in the proteo-lyzed sample should also be 6-fold symmetric With the aim of obtaining the crystal structure of a 6-fold symmetric association domain assembly, the proteo-lysed protein solution was used in crystallization trials, resulting in large diamond-shaped crystals in mother liquor with a pH of 4.6 (Fig 6B) We analyzed the crystals by mass spectrometry, as above, and found them to contain a mixture of fragments 340–478 and 341–478 It is interesting to note that these are not the tryptic fragments that are present in the original mix-ture, indicating that additional cleavage took place during crystallization
These crystals diffract X-rays to 3.7 A˚ with a tetragonal lattice of a¼ b ¼ 166.4 A˚, c ¼ 192.4 A˚ (Table 1) that is distinct from the monoclinic lattice seen earlier for the bacterially expressed association domain [10] A single association domain dimer from the previously determined crystal structure was used as
a search model for molecular replacement We allowed the program phaser [31] to find a solution by placing monomers sequentially into the model, with each placement substantially increasing the significance of the solution (as measured by the Z-score) phaser placed seven dimers automatically into the unit cell, reproducing essentially the structure that has been determined earlier for the mouse CaMKIIa association domain We next used the original association domain structure as a model for molecular replacement and phaser found a highly significant solution (Z-score for the rotation function equal to 11 and for the transla-tion functransla-tion equal to 46), indicating that the contents
of the unit cell are very well described by the 7-fold symmetric model; the electron density maps (Fig 6C) produced from this model demonstrate unambiguously the presence of 7-fold symmetry in the crystals Because this structure has already been well described, further analysis of this crystal form was abandoned
We next investigated whether the tetradecameric oligomeric state of the association domain was an iso-form-specific feature of mouse CaMKIIa We repeated the proteolysis and crystallization protocol with the
C elegans CaMKII holoenzyme expressed in baculo-virus-infected insect cells We found that the C elegans association domain produced in this way also crystal-lized from a mother liquor with a pH of 6.4 and 5% polyethylene glycol (PEG) 400 in an orthorhombic, centered lattice The self-rotation function revealed the three 2-fold axes of the space group as well as six addi-tional 2-fold axes; that is, there are seven independent 2-fold axes arrayed in the b-c plane, indicating the
Fig 4 Cryo-electronmicroscopy reveals the position of the kinase
domains of CaMKII (A) A representative class average (1 of 5) from
the C elegans holoenyzme micrographs The central ring of density
of 10 nm radius is presumed to be the association domain The
outer ring of density of 22 nm radius is presumed to be the
kin-ase domains (B) As in (A) but from the mouse CaMKIIa isoform
micrographs (C) The first eigen image of the mouse CaMKIIa
iso-form dataset.
Trang 6presence of 7-fold symmetry in the asymmetric unit
(Fig 7A)
We carried out molecular replacement using X-ray
data to 2.7 A˚ with a single monomer of the
associ-ation domain in the search model using the program
phaser as described above The asymmetric unit
defined by molecular replacement solution consists of
seven protomers which are related by a
crystallo-graphic 2-fold axis along the a axis to another seven
protomers, forming a ring of dimeric association
domains The symmetry of the complex intersects
with the symmetry of the space group along one of
the 2-fold axes of the complex such that the
non-crystallographic 2-fold axis of the complex sits on
top of the crystallographic space group 2-fold This
explains the presence of six noncrystallographic
2-fold axes of symmetry in the self-rotation function
We have refined the model to R-values of
24.5%⁄ 29.6% (working and free, respectively)
The structure of the association domain of the
C elegansCaMKII is in general very similar to that of the mouse CaMKIIa association domain (PDB code: 1HKX) with a root mean square deviation in Ca atom positions of 1.8 A˚ (Fig 7B,C) over all 143 residues
in the monomer
The structure of CaMKII has been hypothesized to
be sensitive to pH [32,33] All of the crystallization conditions of the association domain found so far were at a pH < 7 We wondered whether perhaps pH could affect the oligomerization state of the complex seen in the crystal We screened for new crystallization conditions for the mouse CaMKIIa association domain construct (expressed in bacteria) at higher pH and found a new crystal form growing in 25% (w⁄ v) PEG 3350 at a pH of 8.0 The crystals diffract X-rays
to 3.7 A˚ resolution and are in the orthorhombic space group P212121 with unit cell dimensions of
a¼ 118.5 A˚, b ¼ 56.8 A˚ and c ¼ 374.9 A˚ Although
Fig 5 The CaMKIIa association domain
(residue 335–478) expressed in bacteria
forms 7-fold rings (A) Electron microscopic
images and class averages (i) Three
repre-sentative raw images from the micrographs
of the bacterially expressed CaMKIIa
associ-ation domain (ii) Six representative class
averages that look very similar, suggesting a
limited distribution of orientations on the
grid (B) The first four eigen images of the
association domain classification The first
eigen image shows a strong 7-fold
modula-tion.
Trang 7the crystals are grown at a pH that is 3.7 units higher
than the pH used to obtain the original crystal form
found by Hoelz and coworkers [10], molecular
replace-ment, carried out essentially as described above,
showed that these crystals also contain a
tetradeca-meric ring (not shown) We therefore conclude that
the tetradecameric assemby is a stable state of the
isolated association domain
Discussion and Conclusion
Determination of the crystal structure of the
associ-ation domain of mouse CaMKIIa [10] was an
import-ant step towards the ultimate goal of understanding
the organization of the kinase holoenzyme The
unex-pected oligomeric state of the crystal structures, which
contain 14 subunits in an assembly with 7-fold sym-metry, was surprising The consistent picture that emerged from previous electron microscopic analyses was that the CaMKII holoenzyme has 6-fold symmetry [9,13,34] In this work we have shown that the 7-fold symmetry of the association domain crystal structure is
a consequence of removing the residues N-terminal to the association domain Our analyses of the CaMKII holoenzyme by light scattering and by electron micros-copy show 6-fold symmetry in the assembly, consistent with the earlier work of others
An interesting result that emerges from our work
is that the 7-fold symmetry of the isolated associ-ation domain ring appears to be a conserved prop-erty of these domains across species The crystal structure of the association domain of C elegans
C
Fig 6 Proteolysis of the mouse CaMKIIa holoenzyme leads to a 7-fold symmetric association domain structure (A) Proteolysis
of the M musculus holoenyzme with tryp-sin leads to the production of two bands Subsequent mass spectrometric analysis showed these two bands to be the kinase domain and the association domain as indi-cated in the figure (B) Crystallization trials with the mixture shown in (A) produces large diamond like crystals (C) Molecular replacement with the dimer of association domains reveal a 7-fold ring structure in the electron density of the crystals produced from the proteolyzed material.
Trang 8CaMKII has been determined as part of this work
and it forms a tetradecamer with 7-fold symmetry
(Fig 7) Likewise, a high pH form of the mouse
CaMKIIa association domain, as well as new low
pH crystal forms of the same domain, all show
7-fold symmetry One important consequence of this
tendency of the isolated association domain to form
14-membered assemblies is the inability to obtain high-resolution crystal structures of the relevant 6-fold symmetric association domain assembly It appears that a direct view of this assembly at high resolution will have to await the determination of the crystal structure of an intact CaMKII holo-enyzme We have, in the meantime, found it useful
to model the 6-fold symmetric association domain assembly by removing a pair of subunits from the 7-fold symmetric crystal structure The resulting gap has been closed computationally by applying a con-straint that closes the ring while maintaining each interface to be as close as possible to those seen in the 7-fold structure (Fig 8C) This model is only an approximation to the true structure, and the details
of the interatomic contacts are incorrect at the inter-faces Nevertheless, the model is a useful guide to the overall geometry and architecture of the associ-ation domain To facilitate its use by others the model is made available as Supplementary material Previous analysis, using electron microscopy, of a somewhat longer construct of the isolated association domain (residues 317–478) of CaMKIIa expressed in baculovirus resulted in the conclusion that it is 6-fold symmetric [8] It is possible that the region between residues 317–335, which is not included as part of our bacterial expression constructs and is removed by pro-teolyic digestion of the baculovirus-expressed intact protein, makes a difference to the oligomerization state Nevertheless, we conclude from the results pre-sented in this study that some region of the holo-enzyme outside of the association domain affects the final assembled structure of the holoenzyme Whether this involves the whole auto-inhibited kinase domain
or a limited region of residues 1–335 is not clear at the present time
Our results raise the intriguing possibility that the kinase domains somehow prevent the association domains from relaxing from a 6-fold ring into a more stable 7-fold form Implicit in this idea is that the N-terminal kinase domains interact with each other around the ring of the association domains The binding of Ca2+⁄ CaM to the holoenzyme is highly cooperative [11,35] Both of these studies obtained a Hill coefficient for binding of around or above 2, suggesting that interactions between adjacent kinase domains impede the binding of Ca2+⁄ CaM These interactions may induce a strain in the ring that is released in the absence of the kinase domains allow-ing the association domains to relax into the 7-fold state (Fig 8)
Given the conservation of the 7-fold symmetry in the association domain ring, and the imposition of
Fig 7 Proteolysed C elegans CaMKII also crystallizes as 7-fold
association domain rings (A) The self rotation function reveals
seven 2-fold axes of rotation in the association domain crystals,
although one of the 2-fold axes coincides with a crystallographic
2-fold axis (B,C) The structure of the monomer (B) and the 7-fold
association domain ring (C) produced from the proteolysis of the
C elegans CaMKII holoenzyme.
Trang 96-fold symmetry in the holoenyzme, one can
specu-late whether this oligomerization state reflects some
important aspect of the function of CaMKII
CaMKII is thought to play a role in the storage of
long-term memories [5], based on its ability to
behave in a switch-like manner such that Ca2+
con-centrations above a certain threshold maintain the
holoenyzme in a phosphorylated ‘on’ state despite
the action of phosphatases and protein turnover
Recent studies have shown that the association
domain monomers do not exchange between different
rings when the association domain is expressed in
isolation [36] Our results suggest that there may be
a period of instability before the formation of the stable tetradecameric form observed in the crystal structure when exchange between rings is possible Perhaps some change in ring tension after activation could allow for swapping of damaged holoenzyme subunits, which would then be rapidly phosphorylated
by the active subunits in the holoenzyme, maintaining the activation state of the holoenzyme for long peri-ods of time The present study does not provide any information about the energetics of such instability, but understanding the mechanics of the transition from 6- to 7-fold symmetry is an important goal for future studies
Table 1 Data collection statistics for crystallography Highest resolution bins are indicated in parentheses alongside the resolution of each dataset.
Mouse CaMKIIa (trypsinized) C elegans CaMKII (trypsinized) CaMKIIa (bacterially expressed) (high pH)
Unit cell (A ˚ ) a ¼ b ¼ 166.4 c ¼ 192.5 a ¼ 70.9 b ¼ 186.9 c ¼ 182.8 a ¼ 56.9 b ¼ 115.4 c ¼ 371.2
Fig 8 Models of holoenzyme In the holo-enzyme the kinase domains may constrain the ring so as to maintain a dodecameric assembly (A) When the kinase domains are absent this constraint is released allowing the ring to relax into the 7-fold symmetric assembly (B) (C) A 6-fold symmetric associ-ation domain model in contrast with (D), the 7-fold association domain crystal structure from proteolyzed C elegans full-length CaMKII.
Trang 10Experimental procedures
Protein purification
The full-length C elegans CaMKII (UNC-43 splice variant
K11E8.d) was subcloned into pFastBac-1 (Gibco, Grand
Island, NY, USA) Aspartate 135 was mutated to
aspara-gine using the QuikChange mutagenesis kit (Stratagene, La
Jolla, CA, USA) to inactivate the kinase domain and
pre-vent autophosphorylation Recombinant bacmid DNA was
prepared according to the manufacturer’s instructions
(Bac-to-Bac expression system, Gibco) and transfected into Sf9
cells Baculovirus obtained from the transfection was used
to infect Sf9 cells grown in suspension to a density of
2.5· 106 per ml at a multiplicity of infection of
approxi-mately 10 Cells were grown for 48 h, centrifuged and
resuspended in 50 mm Hepes pH 7.4, 50 mm KCl, and
10% (v⁄ v) glycerol Cells (4 L) were lysed with a French
press and centrifuged in an ultracentrifuge at 100 000 g to
remove cellular debris The protein was purified with
HiTrap SP Sepharose Fast Flow (SP, Amersham
Bio-sciences, Piscataway, NJ, USA), HiTrap Q Sepharose Fast
Flow (Q, Amersham Biosciences) and size exclusion
chro-matography (Superose 6 Prep Grade, Amersham
Bio-sciences) The final buffer from the gel filtration was 20 mm
Tris pH 8.0, 150 mm KCl, 1 mm dithiothreitol The purified
protein was more than 95% pure and its identity was
confirmed with complete trypsin digestion and identification
of peptides by mass spectrometry
The full-length M musculus CaMKIIa was subcloned
into a pFastBac-1 plasmid (Gibco) modified to contain a
C-terminal, 6-histidine tag Aspartate 135 in the kinase
domain was mutated to asparagine as above The protein
was expressed and purified as described for the C elegans
full-length protein except that an additional nickel affinity
column was added after the initial SP column The final
buffer from the gel filtration was 20 mm Tris pH 8.3,
200 mm KCl, 5% (v⁄ v) glycerol The protein was 99%
pure and its identity was confirmed with complete trypsin
digest and identification of peptides by mass spectrometry
The association domain of mouse CaMKIIa (residues
336–478) was expressed and purified as described [10]
Static light scattering
Protein (20 lm) was injected onto a Superdex 200 H10⁄ 30
size exclusion chromatography column equilibrated in
20 mm Tris pH 7.4, 200 mm KCl, 10 mm MgCl2, and 1 mm
tri(2-carboxyethyl)phosphine hydrochloride (TCEP) The
column was coupled to an 18-angle light scattering detector
(DAWN EOS) and refractive index detector (Optilab DSP)
(Wyatt Technology, Santa Barbara, CA, USA) The
col-umn was run at 0.4 mLÆmin)1and data were collected every
0.5 s The data were analyzed using the program package
astra(Wyatt Technology)
Electron microscopy Sample preparation and data collection For negative stain microscopy, a 5 lL sample of protein (15–30 lgÆmL)1) in 20 mm Tris pH 8.0, 200 mm KCl and
1 mm TCEP was placed on the carbon side of a glow-dis-charged, Formvar⁄ carbon 300 mesh copper grid (Ted Pella, Redding, CA, USA), and the excess was removed by wick-ing with filter paper The bound particles were stained with
5 lL of 2% (w⁄ v) uranyl acetate for 30 s; the excess stain was removed by blotting with filter paper Images of stained full-length CaMKIIa were recorded on Kodak SO-163 film with a Philips CM200 transmission electron microscope (FEI, Hillsboro, OR, USA) at 200 kV using
a magnification of 66K Negatively stained association domain was examined using a JEOL-3100-SFF transmis-sion electron microscope (JEOL, Peabody, MA, USA) equipped with a field emission gun operating at 300 kV, at
a magnification of 70K (nominal value of 50K with post-column magnification of·1.4) Images were recorded on a
2048· 2048 slow-scan CCD camera (Gatan, Pleasanton,
CA, USA) with defocus values between 2 lm and 3 lm For cryo-electron microscopy, a 5 lL sample of CaMKIIa (150 lg mL)1) in 20 mm Tris pH 8.0, 200 mm KCl and 1 mm TCEP was deposited on the glow-dis-charged carbon side of a lacey Formvar⁄ carbon 300 mesh copper grid (Ted Pella), and the excess was removed by blotting with filter paper The grid was rapidly cooled by plunging into liquid ethane; specimens were stored in liquid nitrogen (77 K) and kept below )170 C Images were acquired in a JEOL-3100-SFF electron microscope, des-cribed before, also using an in-column Omega energy filter with a slit width of 32 ev Images were recorded on Kodak SO-163 film at a magnification of 60K and defocus values
2–5 lm All data were acquired under low dose condi-tions, allowing a maximum dose per image of 20e⁄ A2
Digitization and particle extraction Micrographs were digitized using a Nikon Super CoolScan
8000 scanner (Nikon USA, Melville, NY, USA) at a step size of 6.35 lm per pixel, and subsequently averaged to yield
a final pixel size corresponding to 2.12 A˚ (frozen hydrated specimen) and 1.93 A˚ (negatively stained particles) on the specimen scale CCD images of the association domain were recorded with a final pixel size of 4.45 A˚ on the specimen scale Micrographs showing significant frost, astigmatism,
or drift were rejected Particles were selected in 160· 160 (frozen hydrated full-length), 180· 180 (negative stained full-length) and 80· 80 (negative stained association domain)-pixel boxes using the boxer procedure of the eman software package [37,38] The particle data sets consisted of
3865 CaMKIIa (frozen hydrated), 2673 CaMKIIa (stain), and 2317 association domain (stain) particle images