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gorzata Palczewska1
nicki1,4
1 Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
2 Research Group for Antibiotics, Department of Chemistry, University of Debrecen, H-4010 Debrecen, Hungary
3 Centre for Design and Structure in Biology (CDSB), Institute for Molecular Biotechnology, D-07745 Jena, Germany
4 Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
Reprint requests to: Ma
gorzata Palczewska, Dept. of Molecular and Cellular Neurobiology, Nencki Inst. of Experimental Biology, 3 Pasteur St., 02-093 Warsaw, Poland; e-mail: bromba{at}nencki.gov.pl; fax: 48 (22) 822-5342.
(RECEIVED May 14, 2002; FINAL REVISION October 17, 2002; ACCEPTED October 17, 2002)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.0215303.
5 The proteins and fragments used in this study include: CR (full-length, residues 1271); CR I (160); CR 1II (1100); CRIIII (1142); CR IIVI (61271); CR IIIVI (100271); CR IVVI (145271) and, for affinity chromatography, their GST fusions. All protein sequences (except CR IIVI) are preceded by a GlySer dipeptide as a result of the thrombin cleavage site engineered into the GST fusions. ![]()
| Abstract |
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Keywords: Calretinin; calbindin D28k; hexa EF-hand; calcium; domain organization
| Introduction |
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In the past, the general rule was that EF-hand proteins contain an even number of EF-hand motifs that are organized into paired domains separated by linkers allowing a high degree of relative domain orientation. Structures of calmodulin (two paired domains; Ikura et al. 1992), troponin C (two paired domains; Slupsky and Sykes 1995), and calbindin D9k (one paired domain; Kördel et al. 1989) provided model examples. The structure of parvalbumin (a three-EF-hand domain, from which the term EF-hand was derived; Kretsinger and Nockolds 1973) is a notable exception to this rule. Since the mid-1990s, exceptions to the paired EF-hand domain rule have come to predominate: sorcin, with five EF-hands, forms dimers that do not appear to contain any truly independent paired EF-hand domains (Xie et al. 2001); the majority of S100 proteins (with two EF-hands) form integrated homodimers (Drohat et al. 1998, 1999) or heterodimers (Hessian and Fisher 2001); recoverin consists of a single, rigid four EF-hand domain, although two EF-hand pairs are discerned within this structure (Tanaka et al. 1995); and a number of bacterial proteins contain a single EF-hand motif integrated into a larger domain structure (e.g., van Asselt et al. 1999). A mutant of calbindin D9k, a protein with two EF-hands that is normally found in a monomeric state, was found to produce stable, intertwined dimers (Hakansson et al. 2001), thus further breaking down the original structural rule. Linse and coworkers made no assumptions when studying the domain organization of Calb as a prelude towards more detailed structural and functional analyses of the protein. They concluded that Calb consists of a single domain of six EF-hands (Linse et al. 1997; Berggard et al. 2000). This rigid domain structure might confer a high degree of target specificity to the protein or better adapt Calb to a multiple-target scaffolding role.
We decided to define the domain organization of CR in order to support our high-resolution nuclear magnetic resonance (NMR) structural studies of CR. To achieve this, we applied NMR, size exclusion, and affinity chromatography methods to study the interactions between CR fragments.
The heteronuclear single-quantum correlation (HSQC) spectrum of a C-terminal fragment of CR (EF-hands IIIVI, CR IIIVI) does not change in the presence of its complementary, unlabeled N-terminal fragment consisting of the first two EF-hands (CR III; Fig. 1A
5). If CR IIIVI interacted with CR III, then a shift in some of the CR IIIVI resonances should be detected. For example, the interaction of a 12-amino acid polypeptide derived from actin capping protein CapZ with S100B (a homodimeric S100 protein with two EF-hand motifs) resulted in the visible shift of almost all of the
100 S100B resonances in a similar HSQC-based experiment (Kilby et al. 1997). Figure 1B
indicates that the overlaid spectra of 15N-labeled CR III and CR IIIVI resemble that of CR (Fig. 1C
). This suggests the CR III and CR IIIVI regions do not interact within intact CR. The conclusion from the NMR data presented in Figure 1
is that CR III forms a domain that is independent of the CR IIIVI fragment of CR.
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The conditions under which our experiments were performed represent physiologically relevant conditions that overlap those used for Calb (Linse et al. 1997; Berggard et al. 2000). No interaction between CR III and CR IIIVI was observed using three different experimental techniques at protein concentrations up to 50 µM. In contrast, SEC and affinity chromatography provided positive data for the CR I/CR IIVI and CR IIII/CR IVVI interactions at
10 µM fragment concentrations (Figs. 2
,3
). Linse et al. (1997) reconstituted a native-like Calb from six polypeptides, constituting individual EF-hand sequences, at micromolar concentrations. This reconstitution required the presence of all six Calb EF-hand polypeptides. In a follow-up study using larger fragments, Calb was confirmed to reconstitute into a single domain (Berggard et al. 2000). The latter study removes any doubt that the reconstitution of Calb was facilitated by the
30% excised residues in the earlier study. We have already commented on the monomeric state of CR III (Palczewska et al. 2001) compared to the homodimeric Calb III domain (Klaus et al. 1999). We think that the homodimeric interface of Calb III may represent a heterodimeric interface between the highly identical Calb III and Calb IIIIV segments. Clearly, considering fragment concentrations and the degree of reconstitution in the two sets of studies, our results distinguish the domain organizations of CR and Calb.
CR and Calb have different domain organizations, perhaps pointing to different structures and potential functions. This is supported by the results of Bellido et al. (2000) showing that caspase-3 is a specific binding partner for Calb. Secretagogin is the newest member of the hexa-EF-hand family (Wagner et al. 2000) with
40% identity to CR and Calb. Clues to the structure of secretagogin would be difficult to accurately predict on the basis of the different domain organizations of Calb and CR.
Our results might also have wider implications for studies involving homologous modeling. For example, DREAM has unique (for an EF-hand protein) DNA-binding properties (Carrion et al. 1999), and the structure of recoverin (Tanaka et al. 1995) would be expected to provide a suitable structural model (both proteins belong to the neuronal calcium sensor subgroup of four EF-hand proteins). DREAM and recoverin share only 35% identity. On the basis of our results on more identical proteins, how accurate is a threaded homologous model of DREAM based on the recoverin structure? Could a theoretical DREAM structure provide clues to the interactions between DREAM and DNA? Our work indicates that the links between structure and function within the EF-hand protein family are still unclear and diverse. In addition, our observations highlight the potential dangers of homologous modeling, although it can be successful in many applications.
| Materials and methods |
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nicki et al. 1995a; Palczewska et al. 2001) with one modification: overnight cultures of bacteria were transferred from Luria Broth to 15N-labeled Martek-9 media (Martek) for large-scale culture and expression of 15N-labeled protein. Cell extracts containing the glutathione-S-transferase (GST) fusion proteins were applied to glutathione-Sepharose columns and cleaved with thrombin. Protein solutions, after ion exchange chromatography, were dialyzed against Milli-Q grade water and lyophilized.
Limited proteolysis
A mixture of CR I (residues 160) and CR IIVI (61271) was obtained by limited trypsinolysis of CR in 50 mM Tris, 150 mM NaCl, pH 8.0 buffer for 10 min (Ku
nicki et al. 1995b), using immobilized trypsin (trypsin-agarose, Sigma). The reaction was terminated by centrifugation on a 0.45 µm filter microspin column.
NMR spectroscopy
HSQC spectra of 0.25 mM 15N-labeled CR III and 50 µM CR IIIVI (Bruker DRX 500), and 1 mM CR (Varian UNITYINOVA 750) in 50 mM Tris, 10 mM CaCl2, 20 mM NaCl, pH 7.7 buffer were acquired using standard pulse sequences. The CR IIIVI spectrum was acquired once more after the addition of an equivalent of unlabeled CR III. The integrated volumes of peaks in the 611 ppm region of 1D 1H NMR spectra were used to confirm the 1:1 stoichiometry of 15N-labeled CR IIIVI and unlabeled CR III in the sample. Processing was performed using standard Spectrometer software, and spectra were manipulated in SPARKY 3 (Goddard and Kneller 2001).
Size exclusion chromatography
Pharmacia FPLC equipment fitted with an HR1030 SEC column was used to obtain SEC data at room temperature in 50 mM Tris, 1 mM CaCl2, 20 mM NaCl, pH 8.0 buffer. Approximately 50 µg protein was injected into a 25 µL loop, and the elution times were noted.
Affinity chromatography
Ten µL of glutathione-Sepharose was applied to a microspin column and equilibrated in PBS containing 1% triton. Aliquots of cell extract containing fusion proteins of CR fragments, stored at -70°C, were then applied to the gel. The gel was washed with PBS-T (4 x 100 µL) and then with binding buffer (50 mM Tris, 20 mM NaCl, 1 mM CaCl2, 2 x 200 µL). An aliquot of complementary CR fragment (or mixture of CR I and CR IIVI obtained by limited trypsinolysis) was applied to the column and the flowthrough collected, as were 2 x 100 and 1 x 20 µL washes with binding buffer. The bound proteins were eluted with 1% SDS, which also removed the attached GST fusion proteins. All fractions, together with total applied complementary protein and GST-tagged protein washed and eluted with SDS as controls, were subjected to 10% Tris-tricine PAGE (Schagger and von Jagow 1987) and stained with Coomassie Blue.
| Acknowledgments |
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The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
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