Calbindin D28k Exhibits Properties Characteristic of
a Ca2+ Sensor*
Tord
Berggård
§,
Simona
Miron
,
Patrik
Önnerfjord¶,
Eva
Thulin
,
Karin S.
Åkerfeldt
,
Jan J.
Enghild**,
Mikael
Akke
, and
Sara
Linse

From the
Department of Biophysical Chemistry, Lund
University, SE-221 00 Lund, Sweden, the
Department of
Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, the
** Department of Molecular and Structural Biology, University
of Aarhus, DK-8000 Aarhus C, Denmark, and ¶ Section for
Connective Tissue Biology, BMC, C12, Lund University,
SE-221 84 Lund, Sweden
Received for publication, January 15, 2002, and in revised form, February 27, 2002
 |
ABSTRACT |
Calbindin D28k is a member of
the calmodulin superfamily of Ca2+-binding proteins and
contains six EF-hands. The protein is generally believed to function as
a Ca2+ buffer, but the studies presented in this work
indicate that it may also act as a Ca2+ sensor. The results
show that Mg2+ binds to the same sites as Ca2+
with an association constant of ~1.4·103
M
1 in 0.15 M KCl. The four high
affinity sites in calbindin D28k bind Ca2+ in a
non-sequential, parallel manner. In the presence of physiological concentrations of Mg2+, the Ca2+ affinity is
reduced by a factor of 2, and the cooperativity, which otherwise is
modest, increases. Based on the binding constants determined in the
presence of physiological salt concentrations, we estimate that at the
Ca2+ concentration in a resting cell calbindin
D28k is saturated to 40-75% with Mg2+ but to
less than 9% with Ca2+. In contrast, the protein is
expected to be nearly fully saturated with Ca2+ at the
Ca2+ level of an activated cell. A substantial
conformational change is observed upon Ca2+ binding, but
only minor structural changes take place upon Mg2+ binding.
This suggests that calbindin D28k undergoes
Ca2+-induced structural changes upon Ca2+
activation of a cell. Thus, calbindin D28k displays several
properties that would be expected for a protein involved in
Ca2+-induced signal transmission and hence may function not
only as a Ca2+ buffer but also as a Ca2+
sensor. Digestion patterns resulting from limited proteolysis of the
protein suggest that the loop of EF-hand 2, a variant site that does
not bind Ca2+, becomes exposed upon Ca2+ binding.
 |
INTRODUCTION |
Calbindin D28k is a Ca2+-binding protein
expressed in brain as well as in kidney, bone, pancreas, and other
tissues (1). In some tissues it is exceptionally abundant. For example,
calbindin D28k constitutes between 0.1 and 1.5% of the
total soluble protein in brain, and protein levels in auditory neurons
are estimated to reach concentrations of up to 2 mM (2).
Calbindin D28k contains 261 amino acid residues forming six
EF-hands, which are organized in a single globular domain (Fig.
1) (3, 4). The protein is a member of the
calmodulin superfamily (5). Some members of this superfamily are
Ca2+ sensors that undergo Ca2+-induced
conformational changes resulting in the exposure of a hydrophobic
surface. The hydrophobic patch typically serves as a binding surface
for target molecules, which become activated or attenuated upon complex
formation (6). The targets include many membrane transport proteins and
enzymes (7). In this way, intracellular Ca2+ influx
triggers the regulation of cellular processes, such as muscle
contraction and the phosphoinositide cascade.

View larger version (19K):
[in this window]
[in a new window]
|
Fig. 1.
Amino acid sequence of human calbindin
D28k. The schematic on top outlines
secondary structure elements, including the helix-loop-helix motif.
Potential trypsin cleavage sites are shaded.
|
|
Another class of Ca2+-binding proteins are the
Ca2+ buffers or signal modulators. Parvalbumin and
calbindin D9k are examples of Ca2+-buffer
proteins. Unlike Ca2+ sensors, the Ca2+-buffer
proteins do not expose hydrophobic surfaces upon Ca2+
binding. In fact, the exposure of hydrophobic surfaces would be
unfavorable for these proteins because it may limit their stability and
Ca2+ affinity. Ca2+ buffer proteins are thought
to be involved in deactivation of signal transducers and/or quenching
of Ca2+ signals, thus protecting the cell against toxic
effects of Ca2+, such as the formation of insoluble calcium
phosphates (for a review see Ref. 8). The Ca2+ affinity is
generally higher for buffer proteins than for sensor proteins, and the
rates of Ca2+ binding and release are lower in the buffer
group. Calbindin D28k is thought to prevent sustained
elevations of Ca2+ by acting as an intracellular
Ca2+ buffer. There is evidence that calbindin
D28k has a Ca2+-buffering function in neurons.
For example, increased intracellular levels of calbindin
D28k causes blunted intracellular Ca2+
elevations (9), and Ca2+ transients are increased in
calbindin D28k null mutant mice (10). A number of examples
where Ca2+ buffering by calbindin D28k has an
effect on the electrophysiological behavior of cells have also been
reported (11-13). The notion that calbindin D28k acts as a
Ca2+-buffering system in the cytoplasm has led to the
hypothesis that calbindin D28k may protect neurons against
large fluctuations in free intracellular Ca2+ and, hence,
prevent cell death (14-17). However, experiments using calbindin
D28k-null mutant mice subjected to cerebral ischemia did
not support a cytoprotective effect of the protein (18). Although most
reports deal with the Ca2+-buffering function of calbindin
D28k, several lines of evidence suggest that the protein
also acts as a Ca2+ sensor. Spectroscopic investigations
(19) and in vitro studies using antibodies (20) have shown
that calbindin D28k undergoes a conformational shift upon
Ca2+ binding. Additionally, a number of putative
Ca2+-dependent interactions with target
proteins or brain membrane fractions have been reported (20-23), and
erythrocyte membrane Ca2+-ATPase and 3',5'-cyclic
nucleotide phosphodiesterase have been shown to be stimulated in a
dose-dependent, saturable manner with calbindin
D28k (24). Moreover, the finding that a fraction of calbindin D28k (9-55%) (20, 25-27) is specifically
associated with particulate structures in the cell indicates that the
protein plays other roles in addition to its function as a mobile
Ca2+ buffer.
In our previous study (28), we showed that although a conformational
change occurs upon Ca2+ binding, both the
Ca2+-free and Ca2+-loaded forms of calbindin
D28k have exposed hydrophobic surfaces. Thus, the protein
behaves neither like a classical Ca2+ sensor nor like a
Ca2+ buffer. The aim of the present study was to further
characterize the Ca2+-induced conformational change and to
determine whether calbindin D28k is likely to respond
structurally to changes in the intracellular concentration of
Ca2+ in the presence of physiological levels of
Mg2+ and salt.
 |
EXPERIMENTAL PROCEDURES |
Proteins--
Human recombinant calbindin D28k was
expressed in Escherichia coli and purified to homogeneity as
described (29). Bovine brain calbindin D28k was purified
from brain homogenate as described (28). F123 is a fragment containing
EF-hands 1-3 (residues 1-132) of human calbindin D28k,
whereas F456 contains EF-hands 4-6 (residues 133-261). F123 and F456
were produced by cloning techniques and expressed in E. coli
(4).
Chemicals--
CaCl2 and MgCl2 of Pro
Analysi quality were from Merck; quin 2 was from Fluka Buchs,
Switzerland, and
5,5'-Br2-BAPTA1
was from Molecular Probes, Eugene, OR. All chemicals were of highest
grade commercially available. Buffers were made Ca2+-free
by incubation with a dialysis tube filled with Chelex 100 (Bio-Rad) for
2 weeks.
Preparation of Apoprotein--
All apo solutions were made from
Ca2+-depleted protein, which was produced as follows.
Purified protein was dissolved in 1 ml of doubly distilled water,
containing an excess of EGTA (10-20 eq) at pH 8. It was then applied
to a 3.4 × 20-cm Sephadex G-25 superfine gel filtration column.
To abolish EGTA binding, the protein was applied to the column after 15 ml of saturated NaCl had been allowed to penetrate the top of the
column. The NaCl solution had been depleted from residual
Ca2+ by dialysis against Chelex 100 resin. During the gel
filtration, the protein was passed through the NaCl zone and eluted,
now free from EGTA, with doubly distilled Ca2+-free water.
The final product contained between 0.2 and 0.6 molar eq of
Ca2+, as determined from Ca2+ titrations in the
presence of the chelator quin 2 or by high resolution inductively
coupled plasma mass spectrometry (analysis performed by SGAB,
Luleå, Sweden). 1H NMR spectroscopy was used to
verify that the apo samples were free from EGTA.
Near UV CD Spectroscopy--
Near-UV CD spectra (250-300 nm)
were obtained using a Jasco J-720 spectropolarimeter at 25 °C
(thermostated) and quartz cuvettes with a path length of 10 mm. A
spectrum was first recorded for the apoprotein (25 µM
apocalbindin D28k in 0.15 M KCl, 2 mM Tris, 0.125 mM EGTA, pH 7.3). A second
spectrum was recorded after adding 10 mM MgCl2.
Finally, 0.5 mM CaCl2 was added, and a spectrum
for the Ca2+ form was recorded.
ANS Fluorescence--
Fluorescence spectra were obtained using a
PerkinElmer Life Sciences Luminescence Spectrometer LS 50 B connected
to a Julabo F25 water bath. All data were collected at 25.0 °C in a
quartz cuvette (10 mm path-length). For the
8-anilino-1-naphthalenesulfonic acid (ANS) fluorescence experiments,
ANS was added to a final concentration of 120 to 10 µM
protein in 10 mM DTT, 0.15 M KCl, 2 mM Tris, pH 7.3, with 0, 1, or 5 mM
MgCl2. Fluorescence spectra were recorded between 400 and
600 nm (bandwidth 5 nm) with excitation at 385 nm (bandwidth 3 nm) and
a scan rate of 50 nm per min. Two spectra were obtained for each sample
and averaged.
Determination of Macroscopic Ca2+ Binding
Constants--
The affinity and cooperativity of Ca2+
binding to F123, F456, or intact calbindin D28k were
determined by titration with CaCl2 in the presence of a
chromophoric chelator, quin 2, as described previously (30, 31). All
experiments were performed in 2 mM Tris/HCl buffer at pH
7.5, either with no added salt, with 0.15 M KCl, or with
0.15 M KCl in the presence of 2 mM
MgCl2. The macroscopic Ca2+ binding constants
were obtained by least squares fitting of the absorbance at 263 nm
versus total Ca2+ concentration by minimizing
the error square sum (e.s.s.) as shown in Equation 1,
|
(Eq. 1)
|
where the sum runs over the n + 1 data points in the
titration. The calculated absorbance at each titration point,
i, was obtained as shown in Equation 2,
|
(Eq. 2)
|
where Vi and V0 are
the total volumes at point i and before adding the first
CaCl2 aliquot, respectively. Amin
and Amax are the respective absorbances that the
Ca2+-chelator complex, and free chelator would have at no
dilution. KD is the dissociation constant of the
chelator-Ca2+ complex. The free Ca2+
concentration, Yi, was solved using the
Newton-Raphson method from Equation 3,
|
(Eq. 3)
|
where K1 through KN
are the N macroscopic binding constants and
CQi, CPi, and
CCai are the total chelator, protein, and
Ca2+ concentrations, respectively, at point i
corrected for the dilutions due to the CaCl2 additions. The
initial chelator concentration, CQ0, was
determined by withdrawing an aliquot of the solution and recording the
absorbance at 239.5 nm in the presence of excess Ca2+
(using
= 4.2 × 104 liter mol
1
cm
1). The initial Ca2+ concentration,
CCa0, was determined by high resolution
inductively coupled plasma mass spectrometry (at SGAB, Luleå,
Sweden). The initial protein concentration, CP0,
was determined by amino acid analysis after acid hydrolysis on a
withdrawn aliquot of the protein/chelator solution that had been
lyophilized in a hydrolysis tube (Biomedical Centre, Uppsala,
Sweden). The adjustable parameters in the fit were
Amin, Amax, and the
N macroscopic binding constants. The parameter F
was either fixed at 1.0 or could be used as an adjustable parameter to
analyze if the assumed stoichiometry (number of macroscopic binding
constants used) is correct (F will end up close to 1.0) or
not (F will deviate from 1.0). For presentation, the data
and fitted curves were normalized according to Equation 4,
|
(Eq. 4)
|
The apparent Ca2+-binding constants in the presence
of Mg2+ were derived using the same method as above but
with 5,5'-Br2-BAPTA instead of quin 2. The chelator
5,5'-Br2-BAPTA has a high level of selectivity against
Mg2+ (log KCa = 5.65; log
KMg <1, at 0.15 M KCl). Hence,
differences in titration curves obtained in the interval 0-10
mM Mg2+ are due to Mg2+ effects on
the protein. The resulting binding constants are apparent Ca2+ binding constants for the protein in the presence of
Mg2+. These constants result from the Ca2+
affinity, the Mg2+ affinity, and competition or coupling
between the two events.
Determination of Ca2+ and Mg2+ Binding
Constants by Fluorescence Spectroscopy--
Mg2+ or
Ca2+ binding constants were determined by monitoring the
intrinsic (tryptophan) fluorescence during Ca2+ or
Mg2+ titration in 0.15 M KCl, 2 mM
Tris, pH 7.3. Fluorescence spectra were obtained using a PerkinElmer
Life Sciences Luminescence Spectrometer LS 50 B connected to a Julabo
F25 water bath at 25.0 °C. Quartz cuvettes with a path length of 10 mm were used. The excitation wavelength was 280 nm, and the emission
scanned was between 300 and 450 nm. The protein concentration was 25 µM. Ca2+-free protein was titrated with
increasing amounts of metal ion (Ca2+ or Mg2+)
beyond saturation. The intensity at each point was corrected for
dilution. Ca2+ and Mg2+ titrations were also
performed in the presence of 120 µM ANS (excitation at
385 nm, emission scanned between 400 and 600 nm) with 10 µM calbindin D28k in 10 mM DTT,
0.15 M KCl, 2 mM Tris, pH 7.1. In some
experiments, MgCl2 was added to a final concentration of 1 or 5 mM. The excitation wavelength was 385 nm (bandwidth 3 nm), and the emission was scanned between 400 and 600 nm. The experimental data were fitted according to Equation 5,
|
(Eq. 5)
|
where Y is the free Ca2+ or
Mg2+ concentration; KA is the apparent
binding constant, and I0 and
Ip are the intensities for the free and bound state, respectively.
Limited Proteolysis of Calbindin D28k--
Calbindin
D28k was dissolved in 50 mM Tris, 150 mM KCl, containing either 1 mM
CaCl2, 1 mM EDTA, or 2.5 mM
MgCl2 + 0.5 mM EGTA (EGTA has a very high
selectivity for Ca2+ over Mg2+) at a protein
concentration of 0.5 mg/ml. The pH was adjusted to 7.5. Sequencing
grade modified trypsin (Promega) was dissolved in the supplied buffer,
yielding a stock solution with a concentration of 0.5 mg/ml.
Proteolysis was initiated by mixing 100 µl of calbindin D28k (0.5 mg/ml) with 1 µl of the trypsin stock at room
temperature. Aliquots of 5 µl were withdrawn at various time points,
and the digestion was blocked by the addition of 1 µl of soybean
trypsin inhibitor (1 mg/ml) (Roche Molecular Biochemicals). The
digested fragments were then separated by SDS-PAGE (15%). Following
electrophoresis, the protein bands were either stained by Coomassie
Blue and excised for mass spectrometry analysis (see below) or blotted
onto a poly(vinylidene difluoride) membrane (Immobilon, Millipore) and
subjected to N-terminal amino acid sequencing (automated Edman
degradation using an Applied Biosystems 477 A sequencer with on-line
detection of phenylthiohydantoin-derivatives with an Applied Biosystems
120A high pressure liquid chromatography).
Sample Preparation for Mass Spectrometry--
Coomassie-stained
protein fragments were excised from the gel and washed with water,
followed by 40% acetonitrile in 25 mM NH4HCO3, pH 7.8, until the gel piece was
transparent. The gel piece was dried in a SpeedVac vacuum centrifuge.
Reduction using 10 mM DTT at 48 °C for 30 min was
followed by alkylation in 55 mM iodoacetamide for 30 min in
darkness at room temperature. The gel piece was washed and dried again
before digestion with sequencing-grade trypsin (Promega) in 25 mM NH4HCO3 overnight at 37 °C.
The digestion was terminated, and the peptides were eluted by adding 10 µl of 2% trifluoroacetic acid. Peptides were purified from buffer
using C-18 reversed phase tips (Ziptips, Millipore).
Mass Spectrometry--
Mass spectrometric studies were performed
using a Bruker Scout 384 Reflex III matrix-assisted laser
desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer. The
instrument was operated in the positive ion mode with delayed
extraction and an acceleration voltage of 25 kV. Peptide samples were
analyzed using the reflector detector with 2,5-dihydroxybenzoic acid as matrix, whereas larger fragments and intact protein were measured in
the linear mode using ferulic acid as matrix. Improved signal-to-noise ratios were obtained by the accumulation of 50-150 single shot spectra. Autolysis fragments of trypsin were used for internal calibration, whereas an external calibration standard was used for the
analysis of intact protein fragments.
NMR Spectroscopy--
NMR spectra were acquired on a 600-MHz
Varian Inova spectrometer at 310 K. 15N HSQC
experiments utilizing pulsed field gradient and preservation of
equivalent path (32, 33) employing water flip-back (34) were performed
on calbindin D28K at different Mg2+ or
Ca2+ concentrations. The GARP-1 decoupling sequence (35)
was used for 15N decoupling during acquisition. All spectra
were acquired with spectral widths of 2000 and 8000 Hz in the
F1 and F2 dimensions, respectively, and
sampled using 128 and 1024 complex points in the t1 and
t2 dimensions, respectively, with 16 transients acquired for
each free induction decay. The data were processed and analyzed using
the Felix97 Software (Micron Separations, San Diego). The data were
multiplied by exponential (F2) and cosine-bell
(F1) functions prior to Fourier transformation, and
zero-filled to generate matrices of 2048 × 2048 real points.
Proton chemical shifts were referenced relative to the water signal,
which resonates at 4.64 ppm from the sodium 2,2-dimethyl-2-silapentane
sulfonate (DSS) at 310 K. Nitrogen chemical shifts were referenced
indirectly relative to DSS, using the nitrogen to proton frequency
ratio (36).
The NMR samples contained 0.73 mM apocalbindin
D28k (with less than 0.05 eq of Ca2+), 0.1 mM DSS, 10 mM deuterated DTT and were
prepared by dissolving the lyophilized protein and deuterated
DTT in 620 µl of 93% 1H2O, 7%
2H2O. The pH was adjusted to 6.8 with 0.1 M KOH or HCl. Aliquots from a 73 mM
CaCl2 stock solution was added to one sample directly in
the NMR tube using a Hamilton syringe (5 µl for each point of the
titration). The protein concentration was determined by amino acid
analysis following acid hydrolysis. The concentration of the
CaCl2 stock solution was determined by inductively coupled plasma mass spectrometry. HSQC spectra were also acquired for a 0.8 mM protein sample with 2 or 10 mM
MgCl2 as well as with 10 mM MgCl2
and 5 mM CaCl2.
 |
RESULTS |
Ca2+ Binding Determined from Competition with
Chromophoric Chelators--
Titration with Ca2+ in the
presence of a chromophoric chelator was used to determine the
macroscopic Ca2+ binding constants (30, 37). To minimize
experimental errors, care was taken to determine accurately the
Ca2+ concentrations before and after titration (by high
resolution inductively coupled plasma mass spectrometry), as well as
the protein concentration before titration (by amino acid analysis after acid hydrolysis). Reliable acid hydrolysis results were obtained
only when an aliquot of the sample was freeze-dried in the hydrolysis
tube (glass) before shipment to the analysis station. Samples sent as
liquid in Eppendorf tubes yielded unreasonably low and inconsistent
protein concentrations, probably due to protein adhesion to the plastic.
The stoichiometry of Ca2+ binding was analyzed by fitting
each titration in a simplified way using Equations 1-3 with
n = 2. CP0 was set to the value
obtained by acid hydrolysis, and the parameter F was used as
a variable parameter. After fitting, the stoichiometry was calculated
as 2F. By using this method, the number of high affinity
Ca2+-binding sites in the intact protein are 4.03 ± 0.11 (average and S.D. of 9 titrations). Thus the data convincingly
show that human calbindin D28k binds 4 Ca2+
ions with high affinity.
To obtain the values of the four macroscopic binding constants, each
titration was then fitted using Equations 1-3 with n = 4. CP0 was set to the value obtained by acid
hydrolysis, and F was fixed at 1.0. The intact protein
displayed macroscopic binding constants of 1.5·107
to 3.5·108 M
1 at low ionic
strength and 8.9·105 to 7.9·106
M
1 in 0.15 M KCl (Table
I).
The Ca2+ titration curves display a close to linear
decrease of the absorbance as a function of total Ca2+
concentration. The lack of sigmoidal shape may indicate a low degree of
cooperativity of Ca2+ binding. More quantitative
information on the cooperativity is derived from the relationships
between the macroscopic binding constants. For a protein with four
Ca2+-binding sites, values of lgK1
lgK2 < 0.426, lgK2
lgK3 < 0.352, lgK3
lgK4 < 0.426, and lgK1
lgK 4 < 1.204 imply positive cooperativity (38). The results obtained here for the intact protein in the absence
of Mg2+ yield the following: lgK1
lgK2 = 0.393; lgK2
lgK3 = 0.275; lgK3
lgK4 = 0.281; and lgK1
lgK4 = 0.948. Hence there is only a low degree
of cooperativity of Ca2+ binding. In the presence of 2 mM Mg2+, however, the values obtained are as
follows: lgK1
lgK2 = 0.18; lgK2
lgK3 = 0.55; lgK3
lgK4 = 0.03; and lgK1
lgK4 = 0.80. This indicates that the cooperativity of Ca2+ binding
is greater in the presence of Mg2+, which is the relevant
physiological condition. In summary, our results clearly show that
calbindin D28k has four high affinity Ca2+-binding sites, which act as a cooperative unit. Hence
the situation is very different from calmodulin, in which the four
sites are distributed into two groups with different affinity (30).
Ca2+ Binding Monitored by Trp
Fluorescence--
Calbindin D28k contains two Trp residues
located in the first helix of EF-hands 1 and 3, respectively. Analysis
of the Ca2+ titration curve monitored by Trp fluorescence
for calbindin D28k yields an apparent binding constant of
around 1·106 M
1 in 0.15 M KCl, which is similar to that obtained by
Ca2+ titrations with chromophoric chelators. Although the
titration monitored by Trp fluorescence does not provide the high
precision obtained using the competitive chromophoric chelator method,
it does confirm that the binding constants obtained by the chelator method are in the correct range.
Ca2+ Binding as Monitored by NMR
Spectroscopy--
Ca2+ binding to calbindin
D28k was monitored by heteronuclear two-dimensional
15N-1H HSQC NMR spectroscopy for samples
containing 0-6 eq of Ca2+. In the absence of
Ca2+, the signals are broad, and there are few well
resolved resonances (Fig. 2A).
Addition of Ca2+ to the protein sample causes significant
changes in the HSQC spectrum. The HSQC spectrum of the
Ca2+-saturated form shows predominantly sharp resonances
and improved spectral resolution (Fig. 2D). In the absence
of Ca2+, no aggregation or dimerization of the protein is
observed by size exclusion chromatography when 100 µl of a 1 mM protein sample is injected on a Superdex 75 column
(1.1 × 30 cm; Amersham Biosciences, data not shown). Therefore,
the NMR signals of the apo state are probably broadened due to exchange
between at least two conformational states with a fast-to-intermediate
rate on the NMR chemical shift time scale. During the titration, the
cross-peaks initially remain broadened (Fig. 2, B and
C) but start to become sharper after the addition of 3 eq of
Ca2+. Between 3 and 4 eq, very large changes in the
spectrum are seen, both in terms of line widths and chemical shift
dispersion. No further changes are observed beyond 4 eq of
Ca2+.

View larger version (40K):
[in this window]
[in a new window]
|
Fig. 2.
Two-dimensional
1H-15N HSQC spectra of uniformly
15N-labeled calbindin D28k recorded at 310 K
and at Ca2+/calbindin D28k ratios of 0 (A), 2.4 (B), 3.2 (C), and 4.0 (D).
|
|
The NMR signals of the apo form disappear, and new ones appear during
the Ca2+ titration. This shows that Ca2+
dissociation from calbindin D28k occurs in the slow
exchange regime of the NMR chemical shift time scale. The
Ca2+ binding process was therefore followed by measuring
the intensity of individual cross-peaks, well resolved in the HSQC
spectrum as a function of Ca2+ concentration. The signals
are grouped according to their behavior between 0 and 4 eq of
Ca2+ in Fig. 3,
A-C. A small number of resonances are affected already by
the addition of the 1st eq of Ca2+; others start to
increase during the addition of the 2nd or the 3rd eq of
Ca2+. However, the majority of the signals do not appear
until addition of the 3rd or 4th eq.

View larger version (19K):
[in this window]
[in a new window]
|
Fig. 3.
Signal intensities of cross-peaks in the
two-dimensional 1H-15N HSQC spectra of
calbindin D28k as a function of the
Ca2+/calbindin D28k ratio.
A-C, normalized experimental data grouped according to the
shape of the curve. D, fraction of the protein in the apo,
Ca1, Ca2, Ca3, and Ca4
forms during the titration calculated using the four macroscopic
binding constants.
|
|
Ca2+ binding to a four-site system may be a multibranched
process involving one apo state, four Ca1 states, six
Ca2 states, four Ca3 states, and one
Ca4 state. Using the macroscopic calcium binding constants,
determined by the chelator method, we have calculated for each point of
the HSQC Ca2+ titration the fraction of the protein in (i)
the apo, (ii) any of the Ca1 states, (iii) any
Ca2 state, (iv) any Ca3 state, and (v) the
Ca4 state (Fig. 3D). Comparisons of the
calculated curves with the NMR data reveal that a majority of the NMR
titration curves monitor the appearance of the Ca4 state.
This shows that most protons have a unique chemical shift in the
Ca4 form. A minority of titration curves follow the
disappearance of the apo state, whereas none of the monitored peaks
seems to correspond to curves expected for any of the Ca1,
Ca2 or Ca3 forms. This suggests that the
intermediate states are interconverting rapidly, leading to severe
broadening of the resonances. The small number of resonances appearing
before addition of the 3rd eq of Ca2+ may represent protons
having the same chemical shift in one or more intermediate states as in
the Ca4 species. The NMR data hence show that all four
sites have similar affinities and are filled in a parallel fashion and
that the Ca4 species has structural features distinct from
those of the intermediate states.
Mg2+ Binding as Monitored by Trp
Fluorescence--
Titration with MgCl2 to saturation
results in a 10% increase of the fluorescence intensity at 333 nm and
gives a small but reproducible blue shift of the intensity maximum from
333.5 to 332.5 nm (not shown). Addition of excess Ca2+ to
the Mg2+-saturated sample results in an additional 15%
increase in the fluorescence intensity (not shown). This shows that,
although Mg2+ binds to the protein, it does not invoke the
same structural response as Ca2+ binding. The
Mg2+ titration curve in the absence of Ca2+
yields an apparent Mg2+ binding constant of 1.4 × 103 M
1 in 0.15 M KCl
(average of four independent experiments). The stoichiometry of
Mg2+ binding cannot be deduced from the experiment, because
the Mg2+ concentration at half-saturation is almost 2 orders of magnitude higher than the protein concentration. However, the
obtained binding constant implies that under physiological
intracellular concentrations of Mg2+ (0.5-2
mM) and resting levels of Ca2+, the
Mg2+-binding sites in calbindin D28k are
40-75% occupied by Mg2+.
Mg2+ Binding as Monitored by NMR
Spectroscopy--
Mg2+ binding to calbindin
D28k was also monitored by heteronuclear two-dimensional
15N-1H HSQC NMR experiments. Fig.
4 shows spectra recorded using 0.8 mM Ca2+-free protein samples containing 2 and
10 mM Mg2+, corresponding to 2.5 and 12.5 eq of
Mg2+, respectively. Addition of Mg2+ to the
apoprotein causes an increase in the chemical shift dispersion with a
number of shifted peaks, although the effects are not as pronounced as
during addition of Ca2+. Even at 10 mM
Mg2+, most of the peaks are still broadened and clustered
between 8.5 and 7 ppm in the proton dimension and between 121 and 115 ppm in the nitrogen dimension. Addition of 3.2 mM
Ca2+ (4 eq) to the sample with 10 mM
Mg2+ yields an HSQC spectrum that is identical to the one
in Fig. 2D (data not shown). This shows that
Ca2+ efficiently displaces Mg2+, suggesting
that Mg2+ binds to the same sites as Ca2+.

View larger version (26K):
[in this window]
[in a new window]
|
Fig. 4.
Two-dimensional
1H-15N HSQC spectra of uniformly
15N-labeled calbindin D28k recorded at 310 K
with 0.8 mM Ca2+-free protein samples
containing 2 and 10 mM Mg2+ (corresponding to
2.5 and 12.5 eq of Mg2+, respectively).
|
|
Mg2+ Binding to Individual EF-hands as Monitored by CD
Spectroscopy--
The far-UV CD spectra were recorded for six
synthetic peptides, comprising EF-hands 1-6, at a concentration of 20 µM. The six peptides appear mostly unfolded in the apo
form as well as in the presence of 10 or 200 mM
MgCl2 (data not shown). This is in striking contrast to the
spectra obtained in the presence of Ca2+, which show a high
degree of helicity and are consistent with Ca2+ binding for
EF1, EF3, EF4, EF5, and EF6 (39). The results suggest that although
Mg2+ binds to the intact protein, the interaction between
Mg2+ and the individual EF-hands is not strong enough to
induce secondary structure in these peptides.
Ca2+ Binding in the Presence of Mg2+ and a
Chromophoric Chelator--
Ca2+ binding in the presence of
Mg2+ was determined using a chromophoric Ca2+
chelator (5,5'Br2-BAPTA), which has a high level of
discrimination against Mg2+. Fig.
5 shows the experimental data for
Ca2+ titrations of intact calbindin D28k in the
presence of 0 or 2 mM Mg2+, together with the
curves of best fit. Already from the appearance of the curves it is
evident that the presence of Mg2+ reduces the
Ca2+ affinity for calbindin D28k. The fitting
of the experimental data shows that the Ca2+ affinity of
calbindin D28k is reduced approximately 2-fold to yield
K = 3.5·106-5.6·105
M
1 in the presence of 2 mM
MgCl2 (Table I). Only very small ionic strength effects are
expected for the addition of 2 mM MgCl2 into 0.15 M KCl. Therefore, the data again suggest that
Mg2+ competes with Ca2+ for the same binding
sites.

View larger version (14K):
[in this window]
[in a new window]
|
Fig. 5.
Titration of 5,5'Br2-BAPTA with
Ca2+ in the presence of calbindin D28k with or
without Mg2+ in 0.15 M KCl, 2 mM
Tris, pH 7.3. The curves of optimal fit to the data points are
presented. , titration performed without MgCl2. ,
titration performed in the presence of 2 mM
MgCl2.
|
|
Changes in the Tertiary Structure as Monitored by Near
UV-CD--
Ca2+ binding induces changes in the near-UV CD
spectra of calbindin D28k, which indicates a rearrangement
of the tertiary structure (not shown, see also Ref. 28), in agreement
with the NMR data. In contrast, addition of 10 mM
MgCl2 to apocalbindin D28k does not alter the
near-UV CD spectrum to any significant degree (not shown).
Limited Proteolysis--
Limited tryptic digestion of human
recombinant calbindin D28k was performed in the presence of
EDTA, Ca2+, or Mg2+. The reaction was quenched
at different time points ranging from 1 min to 14 h and was
analyzed by SDS-gel electrophoresis (Fig. 6). Both the rate and pattern of tryptic
digestion are strongly Ca2+-dependent. The
Ca2+-loaded form of calbindin D28k is clearly
more resistant to proteolysis than the Ca2+-free form,
although many of the potential trypsin cleavage sites are protected in
both forms (Fig. 1). Significant digestion of the apo form is seen
already in the 1st min, whereas fragments of the
Ca2+-loaded form appear at a significantly lower rate. The
identities of the tryptic fragments were determined by mass
spectrometry and N-terminal amino acid sequencing. The deduced cleavage
sites are indicated by the arrows in Fig.
7, and the identity of the major
fragments are summarized in Table
II. Both apo- and Ca2+-bound
calbindin are cleaved at Lys-59 and Lys-235 in the N-terminal helices of EF-hands 2 and 6. The apoprotein is cleaved also at Arg-169
in the C-terminal helix of EF-hand 4. In contrast, the Ca2+-bound protein is not cleaved at this site but mainly
at Lys-72 in the loop of EF-hand 2 and at Lys-98 in the linker between
EF-hands 2 and 3. In addition, a minor cleavage site in the
Ca2+ form is found at Lys-245 in the loop of EF-hand 6.

View larger version (45K):
[in this window]
[in a new window]
|
Fig. 6.
Tryptic digestion of calbindin
D28k. Human recombinant calbindin D28k was
digested with trypsin as described under "Experimental Procedures."
Fragments were generated in the presence of 1 mM
CaCl2, in the presence of 1 mM EDTA, or in the
presence of or 2.5 mM MgCl2 + 0.5 mM EGTA and separated by SDS-PAGE (15%), transferred to an
Immobilon membrane, and stained with Coomassie Brilliant Blue.
|
|

View larger version (26K):
[in this window]
[in a new window]
|
Fig. 7.
Limited proteolysis of calbindin
D28k. Schematic of calbindin D28k
outlining secondary structure elements, including the helix-loop-helix
motifs and major tryptic fragments generated in 1 mM
CaCl2 (A) and 1 mM EDTA
(B). EF-hand motifs 1-6 are shown by arabic
numbers. EF hands 2 and 6, which contain sequence anomalies, are
shown by dashed lines. The major cleavage sites are
indicated by arrows. The regions that display a difference
in the cleavage patterns between the Ca2+ and apo forms are
shaded boxes.
|
|
View this table:
[in this window]
[in a new window]
|
Table II
Analysis of tryptic peptides of calbindin D28k by Edman
degradation and mass spectrometry
Human calbindin D28k was digested with trypsin; fragments were
separated by SDS-PAGE (15%), and gels were stained with Coomassie
Blue. Samples were collected after various time points. In some
experiments, the bands were blotted onto an Immobilon membrane.
|
|
At longer incubation times, a number of small fragments appear. These
are mainly due to further cleavage of larger fragments and may
therefore represent cleavage sites that are inaccessible in the intact
protein. It is noteworthy that in EDTA a small fragment containing
residues 181-261 (EF-hands 5 and 6) is fairly resistant to further
cleavage as its intensity increases all the way up to the last time
point (120 min, band A8 in Fig. 6).
Limited proteolysis of calbindin D28k in the presence of 2 mM Mg2+ results in nearly the same digestion
pattern as for the apoprotein (Fig. 6). Thus, all identified fragments
were equivalent in the EDTA and Mg2+ samples, except for a
very small amount of a peptide (residues 60-261),2 which was not
found in the EDTA samples. Mg2+ seems to offer some
protection to proteolytic digestion, although digestion is much faster
than in the presence of Ca2+.
Ca2+ Binding to F123 and F456 as Monitored by the
Chromophoric Chelator Quin 2--
Ca2+ binding to F123 and
F456, each comprising one-half of calbindin D28k, was
measured with the quin 2 method. The stoichiometry of Ca2+
binding to each half was analyzed as described for the intact protein,
yielding n = 2.01 ± 0.22 for F123 and 2.14 ± 0.24 for F456. Hence, there are two high affinity sites in each half
of calbindin D28k. One site in each half was found to
retain the Ca2+ affinity of the intact protein
(K1
1 × 108
M
1). The second site in each half binds
Ca2+ with ~50-fold lower affinity
(K2
2 × 106
M
1).
Ca2+-induced Conformational Changes as Monitored by ANS
Fluorescence--
The fluorescent probe ANS can be used as a sensitive
reporter of solvent-exposed hydrophobic patches in
proteins. In an attempt to investigate whether F123 and
F456 undergo Ca2+-induced conformational changes at the
tertiary level, we measured the Ca2+ dependence of ANS
binding for F123 and F456. In EDTA, both F123 (472 nm) and F456 (485 nm) yield a significant blue shift and intensity increase relative to
ANS in buffer (530 nm), indicating binding of ANS. When
Ca2+ is added, a further blue shift in the fluorescence
maximum from 485 to 475 nm is observed for F456 with a 30% increase in
intensity (Fig. 8B). In
contrast, addition of Ca2+ to F123 yields a 43% decrease
in intensity, with a shift from 472 to 483 nm. The results clearly
indicate that both halves undergo structural changes after binding of
Ca2+. The response is different in the two halves with the
local environment around the bound ANS becoming less polar in F456 but
more polar in F123.

View larger version (18K):
[in this window]
[in a new window]
|
Fig. 8.
ANS binding to F123 and F456.
F123 ( ) or F456 ( ) was dissolved to 6 µM
each in 2 ml of 60 µM ANS, 50 µM EDTA, 1 mM DTT, 0.15 M KCl, pH 7.1. The ANS
fluorescence emission spectra (excitation at 385 nm) were first
recorded at room temperature for the Ca2+-free form
(dotted line). CaCl2 (1 µl 1 M)
was then added to each solution (solid line), and the
measurements were repeated. The dash-dotted line shows the
spectrum for 60 µM ANS in buffer without protein.
|
|
ANS fluorescence spectra were also recorded for an equimolar mixture of
F123 and F456 and for the intact protein. These spectra were compared
with one another and to the sum of the ANS spectra recorded
individually for F123 and F456. No spectral differences were observed
between these three cases, neither in the absence nor in the presence
of Ca2+. The data suggest that ANS binds to the same
exposed hydrophobic patches in the intact protein as in the two halves.
Earlier work (4) has shown that each half-fragment has a tendency to
form homodimers, hence the contact surface between the two halves in the intact protein would be hidden in the separate fragments and not
accessible to ANS binding.
 |
DISCUSSION |
The results of the present work clearly demonstrate that the
tertiary structure of calbindin D28k is
Ca2+-dependent. The large
Ca2+-induced effects observed by two-dimensional
(1H-15N) HSQC NMR spectroscopy (Fig. 2)
indicate that the protein undergoes a conformational change. Whereas
the spectrum of the apo form shows limited chemical shift dispersion
and broad lines, the Ca2+-saturated protein displays shift
dispersion and narrow lines typical of a well folded helical protein.
Far-UV CD data (28) indicate a significant degree of helicity both for
the apo and Ca2+-loaded states, suggesting that the limited
chemical shift dispersion of the apo form represents a loosely
organized tertiary structure, similar to a molten globule. As seen in
Figs. 2 and 3, there is not a progressive change in the spectrum
throughout the Ca2+ titration. Rather, fairly small
spectral changes are observed until 4 eq of Ca2+ are added,
at which point there is a dramatic change with a large number of sharp
resonances appearing. For example, four signals appear in a region
where the glycine residue in position 6 of the Ca2+-bound
EF-hand loop is typically found (
1H = 10-10.5 ppm,
15N = 110-114 ppm). These signals most likely
represent the corresponding four glycine residues of the regular
EF-hands 1 and 3-5, because synthetic peptides corresponding to these
four sites also display 1H chemical shifts of these glycine
residues between 10 and 10.5 ppm in the Ca2+-bound form
(39). Whereas data on the rat protein have been interpreted as one site
having much higher affinity than two or three other sites (40), we do
not observe sites differing in affinity. Rather, we have strong
evidence from the quin 2 and NMR titrations that all four sites bind
Ca2+ in a parallel fashion with similar affinity and
positive cooperativity.
Limited tryptic proteolysis of the apo- and Ca2+ proteins
(Figs. 6 and 7 and Table II) provides further details on the
Ca2+-induced structural changes. In accordance with the
HSQC results, the protein appears more loosely folded in the apo state,
because it is considerably more sensitive to proteolysis than in the
Ca2+-loaded state. The cleavage patterns are also
distinctly different. Whereas the apoprotein is mainly cleaved at
Arg-169, the Ca2+ form is cleaved at Lys-72 and Lys-98.
Arg-169 is located in the middle of the second helix of EF-hand 4, whereas Lys-72 and Lys-98 are found in the loop of EF-hand 2 and in the
N-terminal helix of EF hand 3, respectively. This suggests that the
conformational changes upon Ca2+ binding involve burial or
rotation of the second helix in EF-hand 4 and exposure of the loop of
EF-hand 2 and of the N-terminal helix of EF hand 3. EF-hand 2 is a
variant site that does not appear to bind Ca2+ (39), and
its Ca2+-induced exposure to solvent is intriguing. One
could speculate that EF-hand 2 is part of a target-binding surface that
becomes exposed upon Ca2+ binding.
It is interesting to compare the limited proteolysis of calbindin
D28k to the digestion patterns of calretinin. Calretinin is
a hexa-EF-hand protein that is homologous to calbindin D28k (58% sequence identity), but in contrast to calbindin, it binds Ca2+ to EF-hand 2. In calretinin, regions in EF-hands 2 and
3 are not cleaved in the presence of Ca2+, which indicates
that this part of the protein is not exposed to solvent in a
Ca2+-dependent way (41, 42). Instead, cleavage
occurs in EF-hand 6 of calretinin, which corresponds to a minor
Ca2+-induced cleavage point in calbindin D28k.
EF-hand 6 represents a non-canonical sequence in both proteins. The
dissimilarities in digestion pattern may reflect functional and
evolutionary differences between the two proteins to adapt to different targets.
The heteronuclear two-dimensional 15N-1H HSQC
NMR experiments show that Ca2+ efficiently displaces
Mg2+, suggesting that Mg2+ binds to the same
sites as Ca2+. The results from limited proteolysis,
near-UV CD, and NMR spectroscopy show that the structural changes upon
Mg2+ binding are much smaller than upon Ca2+
binding. This indicates that although Mg2+ binds to
calbindin D28k, it coordinates in such a way that is does
not drive any substantial conformational change. This is consistent
with structural data on other EF-hand proteins, which show that the
coordination of Mg2+ and Ca2+ to the same site
generally differs (43). The bidendate Ca2+-ligating
glutamate at position 12 in the EF-hand loop is important for inducing
conformational changes in Ca2+ sensor proteins. In the
Mg2+-loaded form, the ion is often coordinated by none or
only by one of the side chain oxygens of this glutamate side chain.
Each of the two isolated halves, comprising EF-hands 1-3 and 4-6,
respectively, was found to contain two high affinity
Ca2+-binding sites. In each of the two halves, one site
retains the Ca2+ affinity as seen for intact calbindin
D28k, whereas the other site has lost affinity by a factor
of 50. Hence, truncation of the protein leads to loss of important
interactions between EF-hands at the interface between the two halves.
Thus, the Ca2+-binding sites of calbindin D28k
are clearly not grouped into two largely independent domains, as in
calmodulin. The two halves of calmodulin retain native-like
Ca2+ binding behavior even when separated (44). The present
Ca2+ binding data, obtained for F123 and F456, support
earlier findings that all six EF-hands in calbindin D28k
are part of one globular domain (3, 4).
Calbindin D28k appears to have evolved through triplication
of an ancestral gene coding for two EF-hands (5). EF-hands often
associate in pairs as they occur in the sequence, but in calbindin
D28k there are also extensive interactions beyond the pairwise contacts (3, 4). As isolated synthetic peptides, EF-hands 1 and 3-5 in calbindin D28k are the main
Ca2+-binding sites, whereas EF-hand 2 fails to bind
Ca2+ and EF-hand 6 does so only weakly (39). Hence, it
seems reasonable to assume that EF-hands 1 and 3 are active in the
Ca2+ titrations of the N-terminal half and EF-hands 4 and 5 of the C-terminal half. An attractive model for the intact protein is that EF hands 3 and 4 are paired with one another. A cut in this pair
would then have major influences on the Ca2+ affinity for
both EF-hands 3 and 4, which could explain the reduced Ca2+
affinity of one site in each half. In this model, the conformational properties and high Ca2+ affinities of EF-hands 1 and 5 depend mostly on interactions within the respective half.
The physiological role of calbindin D28k as a
neuroprotector in conditions related to Ca2+ overload, and
as a facilitator of neuronal Ca2+ signaling and renal
Ca2+ resorption, has been suggested to be linked to the
Ca2+-buffering capacity of the protein. However,
Ca2+-induced conformational changes, reported in an earlier
study (28) and further analyzed in the present work, suggest that some
of the physiological findings could be due to Ca2+ sensor
activity of calbindin D28k. All cells have transport
systems for the extrusion of Ca2+. The intracellular
Ca2+ concentration in a resting cell is therefore
relatively low, <0.1 µM. The cytosolic Ca2+
concentration can be abruptly raised to 1-10 µM when the
cell is activated by influx of Ca2+. In the activated cell,
Ca2+ is bound in a highly selective way to
Ca2+-signaling proteins (Ca2+ sensors) and
induce conformational changes, which lead to an altered activity of
target proteins. As discussed above, calbindin D28k clearly
undergoes a Ca2+-induced conformational change; however, to
be classified as a Ca2+ sensor, several other conditions
also need to be fulfilled. The intracellular concentration of
Mg2+, a potential competitor to Ca2+, is kept
at a relatively constant level around 0.5-2 mM.
Consequently, a Ca2+ sensor protein must have ~1000-fold
selectivity for Ca2+ over Mg2+. This condition
is met by calbindin D28k as the protein binds to
Mg2+ with an affinity constant around 1.4·103
M
1 in 0.15 M KCl, where the
average Ca2+ binding constant is 2.5·106
M
1. A Ca2+ sensor must further be
able to respond structurally within a biologically relevant range of
intracellular Ca2+ concentrations. This is also true for
calbindin as its average Ca2+ dissociation constant
(Kd,av = 7·10
7 M)
falls within the physiological range of intracellular free Ca2+ concentrations. In contrast, a Ca2+-buffer
protein would be expected to have higher affinity
(Kd <10
7 M), whereas
Ca2+-binding proteins with a lower affinity
(Kd >10
5 M) cannot act as
sensors because they are unable to detect the changes in intracellular
free Ca2+ concentrations that normally occur in cells. Fig.
9 shows the Ca2+ saturation
curves for calbindin D28k, calmodulin, and parvalbumin calculated from the Ca2+ binding constants in 0.15 M KCl and 1-2 mM MgCl2.
Parvalbumin is considered to be a Ca2+-buffering protein
and binds Ca2+ with ~20 times higher affinity than
calbindin D28k. It is clear from Fig. 9 that parvalbumin
cannot be a Ca2+ sensor because it is almost fully
saturated with Ca2+ at resting concentrations of
Ca2+. By contrast, calbindin D28k and
calmodulin are only
9 and
3% saturated with Ca2+,
respectively, at resting concentrations of Ca2+ (
0.1
µM). At Ca2+ concentrations similar to those
that follow Ca2+ activation of a cell, the saturation
levels of calbindin D28k and calmodulin are changed
dramatically, as would be expected for Ca2+ sensors.

View larger version (24K):
[in this window]
[in a new window]
|
Fig. 9.
Ca2+ saturation curves for
parvalbumin, calmodulin, and calbindin D28k. The
degree of saturation as a function of free Ca2+
concentration was calculated from the macroscopic binding constants in
1-2 mM Mg2+ and 0.15 M KCl, pH
7.3. The Ca2+ concentration intervals of a resting and
activated cell are shaded.
|
|