Preparation and characterization of geodin
A bc-crystallin-type protein from a sponge
Concetta Giancola
1
, Elio Pizzo
2
, Antimo Di Maro
3
, Maria Vittoria Cubellis
2
and Giuseppe D’Alessio
2
1 Department of Chemistry, University ‘Federico II’ of Naples, Italy
2 Department of Biological Chemistry, University ‘Federico II’ of Naples, Italy
3 Department of Life Sciences, Second University of Naples, Italy
Vertebrate crystallins are proteins that last an entire life-
time, tightly packed in the eye lens which they provide
with the appropriate refractive index essential for vision.
There are three families of crystallins: the a-crystallins,
complex multimers made up of small proteins which
perform also chaperon-like functions; and the b- and
c-crystallins, which together constitute a superfamily of
homologous proteins including monomeric c-type and
oligomeric b-type proteins [1]. bc-Crystallins have been
extensively studied as models of molecular evolution
[2–5] and for their structural features [6,7]. The 3D
structures of many members of the superfamily have
been determined by X-ray crystallography [8–11], and
NMR [12,13]. They indicate that the smallest structural
unit in the bc-crystallin superfamily is a b-stranded
Greek key motif, with two such motifs making up a
2004)
doi:10.1111/j.1742-4658.2004.04536.x
Geodin is a protein encoded by a sponge gene homologous to genes from
the bc-crystallins superfamily. The interest for this crystallin-type protein
stems from the phylogenesis of porifera, commonly called sponges, the
earliest divergence event in the history of metazoans. Here we report the
preparation of geodin as a recombinant protein from Escherichia coli, its
characterization through physico-chemical analyses, and a model of its 3D
structure based on homology modelling. Geodin is a monomeric protein of
about 18 kDa, with an all-beta structure, as all other crystallins in the
superfamily, but more prone to unfold in the presence of chemical denatu-
rants, when compared with other homologues from the superfamily. Its
thermal unfolding, studied by far- and near-CD, and by calorimetry, is des-
cribed by a two-state model. Geodin appears to be structurally similar in
many respects to the bacterial protein S crystallin, with which it also shares
a significant, albeit more modest stabilizing effect exerted by calcium ions.
These results suggest that the crystallin-type structural scaffold, employed
in the evolution of bacteria and moulds, was successfully recruited very
early in the evolution of metazoa.
Abbreviations
DSC, differential scanning microcalorimetry; GuHCl, guanidine hydrochloride; TFA, trifluoroacetic acid.
FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS 1023
scaffold was used in the evolution of bacteria and
moulds, and then very early recruited in the metazo-
ans. Here we report the expression and purification of
recombinant geodin and its thermodynamic and spect-
roscopic characterization, and propose a putative
structure of the protein, as derived through homology
modelling.
Results and Discussion
Fig. 1. SDS ⁄ PAGE of protein preparations from the lysate of E. coli
cells transformed with geodin encoding cDNA. Lane 1, IB prepar-
ation from inclusion bodies; lane 2, S preparation from the lysate
soluble fraction; lane 3, geodin purified from the IB preparation;
lane 4, geodin purified from the S preparation.
A
B
C
D
Fig. 2. Gel filtration on Superdex G-75 of the proteins from the S
preparation (A) and the IB preparation (B) from the lysate of E. coli
cells transformed with geodin encoding cDNA. The inserts show
the results of SDS ⁄ PAGE separations of individual fractions from
each column as indicated by fraction numbers. Fractions 48
through 56 were pooled and dialysed. Each pool was then chroma-
tographed on a cation exchange column (Resource-S) as illustrated
in C (for the S preparation) and D (for the IB preparation).
Geodin, a sponge bc-crystallin-type protein C. Giancola et al.
1024 FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS
were subjected to RP-HPLC on a C4 column as des-
cribed in Methods. Also by this procedure, the pro-
tein, isolated from the S or IB preparation, was
found to be homogeneous and eluted in a single,
symmetrical peak from the HPLC column (data not
shown).
The two proteins eluted from the HPLC column,
analysed by MALDI-TOF MS, were found to have
the following molecular masses: 17 788, protein puri-
fied from S preparation; 17 785 protein purified from
IB preparation. These values compare very satisfactor-
trum of the protein exhibits a strong positive band at
217 nm, which indicates a well defined b-conformation
in solution. This suggests that geodin is an all-b pro-
tein. The different protonation state apparently does
not affect the secondary structure, as no drastic chan-
ges are observed in the far-UV signal (Fig. 3). In the
near-UV region the effects of protonation are signifi-
cant in the protein tertiary structure with a higher
exposure of chromophors at pH 5.0.
As for vertebrate crystallins ) such as mammalian
cB and bB2 crystallins ) geodin tends to aggregate,
especially at higher temperatures and concentrations.
However, because at relatively high concentrations
geodin was more soluble at pH 5.0 than at pH 7.0, a
pH value closer to geodin pI value of 7.9, as calculated
for from its amino acid sequence, we chose to study
the thermodynamic properties of the protein at pH 5.
Geodin stability against chemical denaturants was
investigated by measuring the molar ellipticity at
217 nm, and the shift in fluorescence maximum wave-
length, as a function of urea or guanidine (GuHCl)
concentration. As shown in Fig. 4, all denaturation
curves have monophasic, sigmoidal shapes with single
midpoints of denaturation determined at 3.5 m and
1.2 m for urea- and GuHCl-induced denaturation,
respectively. When the denatured protein solutions
were dialysed, their far-UV CD spectra were found to
be identical to that of the native protein. This indicates
that the unfolding of geodin as induced by chemical
denaturants is reversible.
also displays a single denaturation midpoint, detectable
at pH 5, but with no aggregation at any urea concen-
tration (Fig. 4, Table 1).
Fig. 4. (A, B) Urea and (C, D) GuHCl-induced
transitions of geodin at pH 5.0. The transi-
tions were monitored by the shift in the
wavelength corresponding to the maximum
of the fluorescence spectrum (A and C), and
by far-UV CD at 217 nm (B and D).
Geodin, a sponge bc-crystallin-type protein C. Giancola et al.
1026 FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS
Stability against temperature
When the thermal denaturation of geodin was investi-
gated by the dichroic absorption in far- and near-UV
(Fig. 5), at 217 nm and 280 nm, respectively, the
curves showed cooperative transitions in agreement
with a two-state model. For both, the midpoint tem-
perature was found to be 61 °C, which indicates a sim-
ultaneous collapse of secondary and tertiary structures.
The calorimetric profile obtained by differential scan-
ning microcalorimetry (Fig. 6), was not influenced by
protein concentration, although the endothermic peak
was followed by an exothermic process that coincides
with aggregation and precipitation, which lead to an
irreversible overall denaturation process.
A description of an irreversible protein denaturation
is in the model proposed by Lumry and Eyring [18]:
N $ U $ F
where N is the native protein, U is the reversibly
unfolded protein and F is the final, irreversibly dena-
0
ðTÞ
R
1
T
1
T
m
ð2Þ
At each temperature value, the enthalpy of this ther-
modynamic system can be described as:
Table 1. Physico-chemical data for geodin and other two-domain
crystallin-type proteins. Values of T
m
, DH
0
and DG
0
, determined by
DSC, are from reference [39] for protein S, and reference [26] for
spherulin 3a and human-cS. Data for denaturation with chemical
denaturants were obtained by CD spectroscopy for protein S [22],
spherulin 3a and human-cS [25].
c
1 ⁄ 2
GuCl
3.6
b
60.5
d
+Ca
2+
65.0
c,d
570 48
Human-cS 2.6 8.0 75 750 84
Protein S 1.7 3.7 52 ⁄ 64
e
399 ⁄ 263 29 ⁄ 16
+Ca
2+
1.9 4.8 64 ⁄ 65
e
454 ⁄ 332 39 ⁄ 25
Spherulin 3a 1.1 53.3 523 81
+Ca
2+
2.5 68.7 1020 137
a
Data from near-UV CD spectroscopy.
b
Data from fluorescence
spectroscopy.
c
Data from near- and far-UV CD spectroscopy.
d
ðT
m
Þð3Þ
where f
N
and f
D
are the fractions of molecules in the
native and denatured states, respectively. H
N
and H
D
are the corresponding enthalpies of native and dena-
tured states.
Choosing the native state as reference state, the fol-
lowing equation for the excess enthalpy is obtained:
< DH
0
ðTÞ > ¼ HðTÞH
N
¼ f
D
DH
0
ðT
m
Þ
¼½K=ð1 þ KÞ DH
0
ðT
firms that the equilibrium thermodynamic treatment
can be applied to this case, and the Gibbs’ energy
value can be calculated.
In Table 1 we compare the thermodynamic parame-
ters of geodin with those of two-domain crystallin-type
proteins for which values have been determined for
most physico-chemical parameters, such as monomeric
bacterial protein S and mammalian human-cS, and
spherulin, which is a two-domain noncovalent dimer.
The latter two proteins, as well as geodin, display a
single transition in the denaturation process. Protein S
instead undergoes a two-step denaturation, but the
main transition is centred at 64.4 °C, closer to that of
geodin (61 °C) when compared with the T
m
values of
75 °C and 53 ° C determined for human-cS and spheru-
lin, respectively. Furthermore, the values for DG°,asa
parameter of thermodynamic stability, are of about
80 kJÆmol
)1
for human-c S and spherulin 3a, and of 41
and 45 kJÆmol
)1
for geodin and protein S, respectively.
The value of 45 kJÆmol
)1
for protein S is the value cal-
culated for the overall unfolding process. Thus, the
conclusion can be proposed that, based on thermody-
sessment in the secondary structural order of the
protein upon calcium binding, are in contrast with the
results obtained in the case of homologous protein S,
for which calcium binding affects only the protein ter-
tiary structure [26].
The CD melting profile determined for geodin at
217 nm in the presence of Ca
2+
was found to be sig-
moidal as that obtained in the absence of calcium ions,
but the midpoint denaturation was increased to 65 °C
(Fig. 7C). A perfectly coincident value was obtained
by calorimetric measurements in the presence of cal-
cium ions (Table 1). The higher melting temperature
(increased by 4–5 °C) and higher denaturation
enthalpy (Table 1) indicate that calcium ions provide
an additional stabilization to geodin. In fact, the calcu-
lated DG
0
at 293 K was found to be 48 kJÆmol
)1
, com-
pared to 41 kJÆmol
)1
calculated from measurements in
the absence of Ca
2+
ions.
Fig. 6. Experimental (solid line) and simulated (dotted line) calori-
metric curves of geodin at pH 5.0.
N-terminal portion. The improvement produced was
tested by comparative model validation using anolea
[30,31] and prosaii [32].
Buried residues belonging to b-strands and facing
the intradomain hydrophobic core of each domain, as
well as other buried residues and positive-u glycine
residues were found to be mostly conserved in geodin,
which indicated the good quality of the alignment. It
should be noted that the sequence of protein S shows
the insertion of a valine at position 50, where the
sequences of the other homologues show a glycine.
The alternative to this insertion in the Homstrad align-
ment would have required both an insertion plus a
preceding gap. In the alignment by fugue of geodin a
glycine could align with the glycines of the other
homologues, and only a gap was required.
Recombinant geodin is monomeric, as are c-crystal-
lins and protein S. c-Crystallins have a symmetric
inter-domain interface made up by the second motifs
of both domains whereas protein S has a different
interface, made up by the second motif of the first
domain and the first motif of the second domain. The
inter-domain interface in c-crystallin (PDB code 4gcr)
is quite extended, made up of hydrophobic interactions
between the triad M43 ⁄ F56 ⁄ I81 in the N-terminal
domain and the other triad V132 ⁄ L145 ⁄ V170 in the
C-terminal domain, and Q54–F145 and F56–Q143
hydrogen bonds. These positions, marked by * in the
alignment (shown in Fig. 8), do not appear to be com-
pletely conserved in geodin, as some of the hydro-
prosaii [32] were run on the models and, as a control,
on the template structures. Even if the energy calcula-
ted for c-crystallins is much lower than that calculated
for protein S, anolea indicated that the energy of the
model based on 1 prs is comparable with the energy of
the model based on c-crystallins, while prosaii indica-
ted that the model based on 1 prs is much better than
that based on c-crystallins.
Figure 9 shows that in mod-prs, the model built
with protein S as a template, the inter-domain
Fig. 8. Alignment of geodin amino acid sequence with the sequences of homologous bc-crystallins. The sequences of bovine (PDB codes
1elp, 1a45, 4gcr, 2bb2) and murine (1a5d) crystallins, and of spore coat protein S from Myxococcus xanthus (1 prs) are decorated as follows:
blue for b-strands; red for a-helices, brown for 3–10 helices. Buried residues are in uppercase letters; residues with a positive u angle, in ital-
ics; hydrogen bonds to main-chain amides in bold; hydrogen bonds to main-chain carbonyls are underlined. Buried residues belonging to
b-strands and facing the intra-domain hydrophobic core of each domain, other buried residues, and positive-u glycine residues conserved in
geodin, are highlighted in green, blue and yellow, respectively. The inter-domain interface residues in 4gcr are marked by asterisks. The
inter-domain interface residues in 1 prs are marked by #.
Geodin, a sponge bc-crystallin-type protein C. Giancola et al.
1030 FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS
interface is hydrophobic, as made up of W57, I58,
L101, P102 and P106 (shown as yellow as ball-and-
stick residues). Furthermore, correctly intercalated resi-
dues were found, both positively charged (K59 and
R107; blue ball-and-stick residues), and negatively
charged residues (D61 and D100; red ball-and-stick
residues, Fig. 9). These charged residues, located at the
surface of the two domains, could also contribute with
hydrogen and ⁄ or ionic bonds to the stability of geodin
inter-domain interface. As these interactions were not
used as restraints with modeller, they further validate
(see above), the 3D model of geodin with protein
S as a template was analysed to verify whether it could
accommodate a Ca
2+
binding site. Protein S has two
binding sites for Ca
2+
, one per domain. They are
formed by residues in the folded hairpin of the first
Greek key motif and by residues in the loop connect-
ing the penultimate and ultimate strands in the second
Greek key motif of each domain. The site with the
highest affinity for Ca
2+
in protein S is in the N-ter-
minal domain and is defined by residues E10 and E71.
It can be proposed that T10, S11 and E62, located in
hydrophilic loops in the corresponding region of geo-
din, could play the same role. This tentative Ca
2+
binding site was thus modelled (green ball-and-stick
residues) in the geodin structure shown in Fig. 9.
Another presumable but weaker binding site could be
identified in the C-terminal domain of geodin, defined
by Asn93 and Asn145.
Spherulin 3A, a single-domain mould protein with
crystallin fold, has two distinct Ca
2+
binding sites per
domain, one site is located between the folded hairpin
in interface
38.09 43.61 32.79 64.11
% Non–polar
atoms in interface
61.90 56.30 67.20 35.80
Hydrogen bonds 3 3 1 1
Salt bridges 1 1 0 0
Gap volume 1644.62 1644.62 2927.67 2927.67
Gap volume index 1.19 1.19 3.57 3.57
C. Giancola et al. Geodin, a sponge bc-crystallin-type protein
FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS 1031
the first structural description of geodin, and validate
its identification as a homologue of the bc-crystallin
superfamily. Geodin is a monomeric, two-domain
protein, made up of b strands apparently folded in
Greek-key motifs, just as its mammalian, amphibian
and bacterial homologues. Of particular interest is that
its source is a sponge, G. cydonium, which makes geo-
din the most primitive metazoan bc-crystallin studied
so far.
By both fluorescence and CD spectroscopic analyses,
geodin is found to be, with respect to other bc-crystal-
lins, more readily but reversibly unfolded by chemical
denaturants, with a single midpoint of denaturation,
both in urea and GuHCl. These features are very sim-
ilar to those found for protein S [22]. Consistently, our
conclusion from homology modelling strongly suggests
that the closest structural homologue to geodin is bac-
terial protein S.
Geodin thermal denaturation, studied both by near-
0
contribu-
tion for protein S denaturation in the presence of
Ca
2+
, in turn apparently due to strengthened inter-
domain interactions.
As from the evolutionary point of view, it is of
interest that the crystallin-type structural organization,
already evolved in bacteria and moulds, was readily
recruited for porifera, the earliest metazoans. Further-
more, it is interesting that in the model as derived for
geodin the inter-domain interfaces appear to be stabil-
ized by hydrophobic interactions, but also by a
number of polar interactions, such as H-bonds and salt
linkages. These contacts can be interpreted, as it has
been proposed for vertebrate bc-crystallins [5], as remi-
niscent of the polar, solvent exposed surfaces in the
putative single-domain ancestor(s) that evolved to
associate into two-domain geodin.
Experimental procedures
Cloning and expression of geodin
Cloning into the pET22b
(+)
vector (Novagen, Madison,
WI, USA) of the DNA segment encoding geodin, a puta-
tive bc-crystallin-type protein from G. cydonium, was
carried out as described previously [17]. The plasmid was
used to transform E. coli strain BL21 (DE3) (from AMS
Biotechnology). For over-expression of geodin, the bacterial
ation of both S and IB preparations yielded three main UV
absorbing fractions. Only in the middle peak from either S
or IB preparations SDS ⁄ PAGE runs revealed the presence
of a protein band with the molecular size expected for geo-
din. The corresponding fractions (Fig. 2A,B, insets) were
pooled and dialysed against 50 mm ammonium acetate buf-
fer pH 5.
The Superdex G-75 fraction pools obtained from the S
and IB preparations were each loaded onto a cation
exchange Resource-S column (Amersham Biosciences)
equilibrated in 50 mm ammonium acetate pH 5, and eluted
with a 60-min linear gradient from 50 to 300 mm ammo-
nium acetate. As shown in Fig. 2C most of the protein
Geodin, a sponge bc-crystallin-type protein C. Giancola et al.
1032 FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS
material from the gel filtration step did not bind to the cat-
ion exchanger, and a single, symmetrical peak was eluted
from the column at about 100 mm ammonium acetate. This
contained a protein with the molecular size of geodin
(Fig. 1, lane 4). Figure 2D illustrates the same fractionation
by cation exchange chromatography of the IB fraction. In
the latter case, only a single peak was detected, eluted at
the same concentration of ammonium acetate as for the S
preparation, again containing a protein with the molecular
size of geodin (Fig. 1, lane 3).
Analytical methods
Sequence analyses were performed by automated Edman
degradation as previously reported [34]. Samples were
cleaned and concentrated prior to analysis through
absorption on a ProSorb cartridge (Applera Italia, Monza,
tein concentration ranged from 0.1 to 0.2 mgÆml
)1
. The
excitation wavelength was set at 280 nm, and the emission
measured between 300 and 450 nm. The spectra were recor-
ded at 20 °C with a 1-cm cell and a 5-nm emission slit
width, and corrected for background signal. The GuHCl-
or urea-induced transition curves at 20 °C were obtained
by recording the shift in fluorescence maximum wavelength
as function of denaturant concentration. The maximum
emission wavelength of geodin, recorded at 327 nm, was
shifted to 350 nm in the presence of denaturants. Measure-
ments were performed after an overnight incubation of
samples at 4 °C.
CD spectroscopy
CD spectra were obtained on a JASCO 715 CD spectro-
photometer equipped with a programmable, thermoelectri-
cally controlled cell holder (JASCO PTC-348). The
wavelength was varied from 200 to 340 nm. Near-UV and
far-UV spectra were recorded at 20 °C using a square
quartz cell with a 1 cm or 0.1 cm pathlength, respectively.
Protein concentration was 0.2 or 0.7 mgÆml
)1
for far- or
near-UV measurements. Molar ellipticity per mean residue
[h] in deg cm
2
Ædmol
)1
was calculated from the equation
P
> was
obtained after baseline subtraction, assuming that the base-
line is given by the linear temperature dependence of the
native state heat capacity [20]. A buffer vs. buffer scan was
subtracted from each peak. The denaturation enthalpies,
DH
0
(T
m
), were obtained by integrating the area under the
heat capacity vs. temperature curves. T
m
was the tempera-
ture corresponding to the maximum of each DSC peak.
DC
0
P
(T
m
), was the value of the excess heat capacity function
at T
m
. The entropy changes, DS
0
(T
m
), were determined by
integrating the curve obtained by dividing the heat capacity
curve by the absolute temperature. The denaturation
m
Þln
T
T
m
ð7Þ
DG
0
ðTÞ¼DH
0
ðTÞTDS
0
ðTÞð8Þ
Gibbs energies of denaturation, at the temperature of
293 K, were determined combining Eqns (6),(7),(8):
C. Giancola et al. Geodin, a sponge bc-crystallin-type protein
FEBS Journal 272 (2005) 1023–1035 ª 2005 FEBS 1033
DG
0
ð293Þ¼DH
0
ðT
m
Þ
T
m
293
T
m
413.
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