Structure of the cytoplasmic domain of p23 in solution. Implications for the formation of COPI vesicles Marcus Weidler†, Constanze Reinhard*, Felix Wieland*, and Paul Rösch†) * Biochemie-Zentrum Heidelberg (BZH), Ruprecht-Karls-Universität Heidelberg † Institut für Struktur und Chemie der Biopolymere, Universität Bayreuth § ) Corresponding author: Prof. Dr. Paul Rösch Institut für Struktur und Chemie der Biopolymere Universität Bayreuth Universitätsstr. 30 D-95440 Bayreuth Tel.: +49-921-553540 Fax.: +49-921-553544 E-mail: paul.roesch@uni-bayreuth.de 1 ABSTRACT Coatomer, the coat protein complex of COPI vesicles, is involved in the budding of these vesicles, but the underlying mechanism is unknown. Here, we present the structure of peptides analogous to the cytoplasmic domain of p23 as determined by two-dimensional nuclear magnetic resonance spectroscopy. These peptides are able to interact with coatomer and to induce a conformational change of it, leading to the polymerization of the complex. An improved strategy for structure calculation revealed that the peptides form -helices and adopt a tetrameric state. Based on these results we propose the first model for the binding of coatomer by p23 and the thereby induced conformational change of coatomer which results in its polymerization, and thus drives formation of the bud on the Golgi membrane during biogenesis of a COPI vesicle. 2 COPI-coated vesicles mediate protein transport in the early secretory pathway[Rothman, 1994 #1; Rothman, 1996 #2; Schekman, 1996 #4]. The COPI coat consists of a small G protein, ADP-ribosylation factor 1 (ARF1) [Serafini, 1991 #6; Taylor, 1992 #7] and coatomer, a hetero-oligomeric protein complex of seven subunits (- COPs, for coat proteins) [Waters, 1991 #8; Stenbeck, 1993 #9; Harter, 1995 #10]. COPI bud formation is initiated by membrane recruitment of ARF1, which in its GTP-bound form [Donaldson, 1992 #11; Palmer, 1993 #12], together with members of the p24 family, provides membrane binding sites for coatomer [Stamnes, 1995 #13; Nickel, 1997 #14]. Subsequent coat assembly leads to membrane deformation and the morphological appearance of a bud [Orci, 1993 #15]. Recently, it was shown that upon interaction with peptides analogous to the cytoplasmic domain of p23, a member of the p24 family [Sohn, 1996 #16], coatomer undergoes a conformational change, which induces the polymerization of the complex [XXX Paper von Constanze XXX]. p23, a type I transmembrane protein, is highly enriched in COPI vesicles and is present in a ratio to coatomer of approximately 4:1 [Sohn, 1996 #16]. The cytoplasmic domain of p23 (YLRRFFKAKKLIE) is structurally similar to a classical dilysine motif (KKXX) for retrieval to the endoplasmic reticulum (ER) [Nilsson, 1989 #17; Jackson, 1993 #19; Jackson, 1990 #18; Cosson, 1994 #20], and binds coatomer with the same efficiency as the KKXX motif [Sohn, 1996 #16]. p23 binding, however, depends on its phenylalanine residues as well as its lysine residues. Interestingly, a dimeric form of the above mentioned peptide which is disulfid-bridged via additional cysteines at the N-terminus is far more efficient in inducing the conformational change of coatomer leading to the formation of a bud [XXX Paper von Constanze XXX]: 3 _1 5 9 13 p23w t-m _YLRRFFKAKKLIE CYLRRFFKAKKLIE S S CYLRRFFKAKKLIE XXX (Eventuell entfallen lassen) The essential components needed for the biogenesis of p23w t-d additional coated vesicles are defined as well. Clathrin coated [Takei, 1998 #21] and COPIIcoated vesicles [Matsuoka, 1998 #22] have been generated in vitro from defined constituents. Most recently, a conformational change was shown upon binding of GTP to Dynamin [Sweitzer, 1998 #23], and this structural change was correlated to the process of pinching off a coated vesicular intermediate. However, two questions remain: (i) how are coat proteins normally bound and (ii) how does this association lead to a mechanical deformation of a membrane. XXX In view of the central role played by the cytoplasmic domain of p23 in the formation of COPIcoated vesicles, the determination of the three-dimensional structure of peptides analogous to this domain is a problem of considerable biochemical interest. We decided to determine the structure of these peptides in the presence of the crowding reagent, 2,2,2-trifluoroethanol, in order to approximate the conditions on the surface of a membrane. Our studies show that the small cytoplasmic tail domains of p23 adopt a tetrameric state, and offer a model as to how the amino acid residues essential for binding coatomer are positioned within the tetramer on the surface of the membrane The strikingly higher efficiency of p23wt-d to aggregate coatomer might imply that the dimeric peptide adopts a distinct and defined structure in solution. Therefore, a complete structural analysis of p23wt-m and p23wt-d by NMR techniques was performed in aqueous buffer solution with addition of various amounts of trifluoroethanol (TFE) [Luo, 1997 #45]. 4 MATERIALS AND METHODS Synthetic Peptides. p23wt-m and p23wt-d (sequences are shown above) were obtained as a commercial product (Deutsches Krebsforschungszentrum, Heidelberg). Dimers were formed by disulfide bridges linking the peptides via N-terminally introduced cysteine residues. For this purpose, newly synthesized monomeric peptides were oxidized in 20 % dimethyl sulfoxide in water for 48 h. Subsequently the dimers were isolated by high pressure liquid chromatography. Nuclear Magnetic Resonance Spectroscopy of p23wt-m and p23wt-d. The solution structures of p23wt-m and p23wt-d were obtained from 2D 1H NMR data (4.0 mM peptide, pH 3.6 in 9:1 H2O:D2O, 8:2 H2O:d2-TFE, 7:3 H2O:d2-TFE, or 6:4 H2O:d2-TFE, 100 mM potassium phosphate buffer, 50 mM NaCl, 280 K. Complete sequence-specific assignments of backbone and side-chain protons were obtained by total correlation spectroscopy (TOCSY) with 80 ms mixing time [Braunschweiler, 1983 #27; Griesinger, 1988 #28], correlation spectroscopy (COSY) [Jeener, 1979 #29], and NOE spectroscopy (NOESY) (mixing times 150 ms and 300 ms) [States, 1982 #30]. All spectra were acquired on a Bruker DRX600 spectrometer using standard pulse sequences [Wüthrich, 1986 #31]. Saturation of the water signal was accomplished by continuous coherent irradiation prior to the first excitation pulse and during the mixing time of the NOESY experiments. 4096 512 data points were collected with a spectral width of 6024 Hz in both dimensions. Base-line correction up to 6th order was performed for all two-dimensional spectra along the F2 as well as the F1 dimension. A sinebell-squared filter with a phase shift of /2, /4 or /8 prior to Fourier transformation was used. Zero-filling resulted in a data size of 4096 1024 data points in the frequency domain. In addition to the standard Bruker spectrometer control software, the NDEE 2.0 5 software package (Software Symbiose, Inc., Bayreuth, Germany) was used for data processing. Chemical shift values are reported relative to 2,2-dimethyl-2-silapentane sulfonate. For structure calculations, only NOEs visible in the spectra recorded in the presence of 40 % TFE with 150 ms mixing time were taken into account. Identical calculations combining information obtained in the presence of 20 % TFE resulted in virtually identical structures for p23wt-d. The structure of p23wt-m, however, could not be determined at TFE concentrations lower than 40 %. An estimate of secondary structure element can be obtained from the proton chemical shifts [Wishart, 1995 #52; Wishart, 1995 #53; Wishart, 1992 #54; Wishart, 1991 #55]. CH resonances shifted to high field relative to the corresponding random coil values [Wishart, 1995 #52] indicate local -helical structure, whereas downfield shifted resonances are typical for local -sheet conformation. Elements of regular secondary structure are assumed to be present if a deviation from the random coil value of more than 0.1 ppm is observed. To get a more reliable picture it is suggested that only resonances with the same sense chemical shift deviation for a stretch of more than 3 sequential residues be taken into account [Wishart, 1995 #52]. Restrained And Unrestrained Molecular Dynamics calculations. Simulated annealing calculations [Nilges, 1988 #36] were performed on DEC Alpha workstations with X-PLOR V3.840 [Brünger, 1993 #37]. The 3JN coupling constants were obtained from cross-peak measurements in a COSY spectrum. The NOE intensities were classified as strong, medium, and weak and assumed to correspond to proton-proton distances of 1.8 - 2.7 Å, 1.8 - 4.0 Å, and 1.8 - 5.5 Å, respectively. Stereospecific assignments for the methyl, methylene, and aromatic protons have not been performed, and appropriate corrections were added for constraints including pseudoatoms[Clore, 1987 #32; Wagner, 1987 6 #33; Qi, 1994 #34]. Torsion angles were derived from 3JN coupling constants [Pardi, 1984 #35]. An interval of 30° around the experimental value was allowed. Frequency degenerated cross-peaks were incorporated into the structure calculations as ‘ambiguous’ in order to extract as much structural information as possible from the NOESY spectrum [Brünger, 1993 #37]. Subsequently, the proton-proton distances in the calculated structures were determined using the program ‘BackCalc_db 2.0’ (Software Symbiose, Inc., Bayreuth, Germany) and compared with the combinations of distances possible for each frequency degenerated NOESY cross-peak. If only one of the possible distance combinations was fulfilled in more than 50% of the calculated structures, the distance information was used in further structure calculations. This procedure was repeated several times. Elements of regular secondary structure were deduced by chemical shift analysis (cf. above) and the inspection of the NOE pattern. In addition, the structures were checked for the existence of secondary structural elements by MOLMOL 2.5.1 [Koradi, 1996 #56]. For the unrestrained molecular dynamics simulation (MD) a water/TFE box consisting of 3392 water and 768 TFE molecules with a spatial extension of 6.2 x 6.2 x 6.2 nm was generated [Jorgensen, 1983 #39; Sticht, 1994 #38]. The structure with the lowest energy was chosen as the starting structure for the MD calculations. The further calculation strategy was described earlier [Jorgensen, 1983 #39; Sticht, 1994 #38; Powell, 1977 #40; Verlet, 1967 #41; van Gunsteren, 1977 #42]. Size Exclusion Chromatography of Monomeric and Dimeric p23wt. Size exclusion chromatography was performed on a SMART System (Pharmacia Biotech) using the Superdex Peptide PC 3.2/30. The column was equilibrated with buffer 1 at a flow rate of 40 µl/min at 8°C. Peptides were dissolved in buffer 1 at a concentration of 1 mg/ml (Fig. 7A, B) or 0.1 mg/ml (Fig. 7D) and injected as indicated in the figure. Chromatography of the peptides was performed at a flow rate of 20 µl/min at 8°C and fractions of 40 µl were collected. 7 8 RESULTS Sequence-specific assignments of the spin systems identified in the COSY and TOCSY spectra could be performed with standard techniques [Wüthrich, 1986 #31] as the spectra were well resolved (Tab. 5-2, Tab. 5-5, Dipl. Arbeit). Chemical shift data of the CH resonances was analyzed according to the chemical shift index strategy [Wishart, 1995 #53; Wishart, 1992 #54], yielding an estimate of elements of regular secondary structure (Fig. Wishart-Plot). This preliminary estimate was confirmed and refined by analysis of NOESY crosspeak patterns: According to sequential short-range dNN(i,i+1) NOEs, medium-range d(i,i+3), d(i,i+3), and d(i,i+4) NOEs (Fig. 5A, B), both, p23wt-m and p23wt-d form helices from L2 to I12, fringing at Y1 and E13. For p23wt-m, 180 intraresidual, 179 interresidual NOE connectivities and 10 dihedral angle constraints derived from coupling constants (Tab. 2) were used in an SA protocol with subsequent refinement to generate 100 structures from an elongated starting conformation. The 30 structures with lowest total energies were superimposed, and the local root mean square deviation (rmsd) of the backbone atoms were calculated. The four residues involved in coatomer binding, F5, F6, and K9, K10 [Sohn, 1996 #16], are located at the same side of the helix (Fig. 6B, C). Remarkably, this helix clearly shows amphipathic character, its hydrophobic face composed of residues Y1, F5, A8, and I12. Amphipathicity is increased by a salt bridge between K9 and E13, stable in molecular dynamics simulations (Fig. 5-26, Dipl. Arbeit). The root-mean-square deviation (RMSD) for the backbone heavy atoms of the 10 structures with lowest internal energies of p23wt-m is 0.17 Å (Fig. 6A). A break down of the NOEs of both p23wt-m and p23wt-d into short, medium and long range is listed in table 1, as are average violations of the distance and dihedral restraints in the final ensemble of 9 conformers, deviations of the structures from ideal geometries and rms deviations from the average coordinates. The structure of p23wt-d, calculated under the assumption of a monomeric state of the dimerized peptide (data not shown), could not satisfactorily explain 15 long-range NOEs between I12 and Y1 and I12 and F5 (at lower TFE concentrations, 20 and 15 % (v/v), additional NOEs between F6 and E13 could be observed). This implies oligomerization of p23wt-d at least to a p23wt-d dimer, analogous to a tetrameric form of the p23 cytoplasmic domain. In order to analyze this dimerization of p23wt-d biochemically, size exclusion chromatography was performed at pH 7.4 without the addition of TFE and under the conditions used for NMR spectroscopy. p23wt-m and p23wt-d reduced by dithiothreitol elute in a single peak (Fig. 7A). p23wt-d, however, gives rise to two peaks (Fig. 7B): Peak 2 elutes with the same retention time as p23wt-m (Fig. 7A), indicating very similar Stokes’ radii of the two species, whereas peak 1, judged from its retention time, represents a p23wt-d dimer. Accordingly, rechromatography of the fraction corresponding to peak 1 in Fig. 7B results in an elution profile similar to the p23wt-d sample applied in Fig. 7B. However, a different ratio of peak sizes is observed with peak 2 enlarged at the expense of peak 1 (Fig. 7C), indicating an equilibrium of the two states of the peptide. This equilibrium depends on the concentration of the peptide (Fig. 7D), revealing its bimolecular nature. Thus, peak 1 is caused by the dimeric, and peak 2 by the monomeric state of p23wt-d. Size exclusion chromatography clearly confirms a dimeric state of p23wt-d even in the absence of TFE (Experiments carried out under the conditions used for NMR spectroscopy yielded identical results). These results clearly show that p23wt-d is dimerized in solution. Possible arrangements of the two peptides of a dimer are sketched in fig. XXX. Comparing the experimental NMR spectra with the spectra expected for the four possible structures of a dimer, only one structure is plausible (fig. XXXD). In detail: Structure A can not explain the 15 observed NOEs between 10 I12 (near COOH-terminus) and Y1 or F5 (near NH2-terminus). The same is true for model B. While model C fulfills the above mentioned distance restraints, it does not reflect the symmetry detected by NMR spectroscopy. In the NMR spectra the four amino acids with the same sequence position give rise only to one spin system, i.e. the magnetic environment of the four residues must be identical (Fig. Ausschnitt aus TOCSY-Spectrum). Only an arrangement of the two p23wt-d with a XXX symmetry depicted in Fig. XXD meets all experimental constraints: (i) dimeric; (ii) helical conformation; (iii) proximity of NH2- and COOHterminus; (iv) an identical magnetic environment for the four helices of a p23wt-d dimer. In the Clean-TOCSY spectrum of p23wt-d dimer three different spin systems, corresponding to three different conformations, for each of the COOH-terminal residues I12 and E13 are discernible. In both cases, however, only one of the spin systems shows interresidual NOEs (data not shown), which were then used in the structure determination. No indication for an oligomerization state of the dimerized peptide higher than a dimer corresponding to four -helices could be observed. The overall structure of the p23wt-d dimer is bipartite (Fig. 6C). The -helices are well defined, and a hydrophobic core is formed through interactions of the side chains of residues F5, A8, L11, and I12 of the two dimers. A halfcircle is formed by residues K9 and K10 of two antiparallel helices (Fig. 6C). The corresponding diphenylalanine motifs of the two antiparallel -helices are separated by this "K-halfcircle" (Fig. 6C). This quaternary structure "FKF motif" is present twice in the tetrameric arrangement. Thus, p23wt-d dimer comprises a tetramer of the cytoplasmic domain of p23. Likewise, the stoichiometry found for both p23 and coatomer in isolated COPI vesicles and in coatomer precipitated by p23 wt-d was approximately 4:1 XXX Paper von Constanze XXX. Taken together, from this data we propose that this tetramer is the species active in coatomer binding in vivo (Fig. 8). 11 The stability of the calculated structure was probed by and MD simulation over 200 ps and in Fig. XXX (Abb. 5-35 Dipl. Arbeit) the radius of gyration, a measure for the compactness of a molecule, as a function of the simulation time is shown. After an rapid increase which is caused by the equilibration of the system, the radius of gyration decreases slightly from 12.0 to 11.8 Å. 12 DISCUSSION The structure of p23 that triggers the recently observed conformational change of coatomer [XXX Paper von Constanze XXX] is a tetramer of four equivalent -helical domains, as judged from nuclear magnetic resonance spectroscopy and molecular dynamics simulations. A tetrameric form of this domain is confirmed by size exclusion chromatography and determination of its stoichiometry in the precipitated coatomer complex [XXX Paper von ConstanzeXXX]. The structure arising from tetramerization of the p23-tail domain represents a symmetrical molecule of two equivalent half's, two "FKF"-motifs (Fig. 6 C). We figure that one such motif is directed towards the surface of the Golgi membrane and may well be stabilized by interactions with membrane lipid headgroups, and the other motif protrudes from the membrane and serves as a "plug" for coatomer. In vitro precipitation of coatomer was recently observed in the presence of some bivalent aminoglycoside antibiotics [Hudson, 1997 #46], and interpreted in terms of aggregation of coatomer by crosslinking. In light of the data described here these aminoglycosides may well fit into the binding site for the cytoplasmic domain of p23 that resides in the -subunit of the complex [Harter, in press #44] and induce its conformational change. It is of note that a Wbp1p-peptide with a characteristic ER-retrieval motif does bind coatomer but, in contrast to the cytoplasmic domain of p23, does not trigger a conformational change of the complex. Thus, the two classes of domains have distinct and different functions: interaction of the Wbp1p-type of peptide might serve the sorting of cargo to be retrieved to the ER into retrograde COPI vesicles. p23, however, may represent part of the machinery of a 13 COPI vesicle. Not only does it bind to coatomer during the budding reaction, but it also triggers a conformational change that leads to polymerization of the complex (Fig. 8). The stoichiometry described here in the precipitate between p23 peptide and coatomer and the solution structure of the dimeric peptide strongly favour a tertramerized state of p23 when it binds to coatomer in vivo. Similarly, other members of the p24 family known to bind coatomer and bearing a diphenylalanine and dilysine motif might interact in a tetrameric state with coatomer. Thus receptor induced polymerization of coatomer might represent a general mechanism for COPI vesicle formation. However, at present it is not known in which stoichiometries the various p24 family members interact with each other [Dominguez, 1998 #47] or whether they are able also to form homooligomers. In any case, various oligomers would allow different classes of COPI vesicle to exist, specified by the different p24 members they contain. According to this model, oligomerization of p23 and its relatives must be regulated in vivo. Such regulation might occur via interaction of p24 members with cargo, if p24 members serve as cargo receptors [Schimmoller, 1995 #48; Fiedler, 1996 #49; Kuehn, 1998 #50]. Another candidate to regulate oligomerization of p24 members is ARF 1, the recruitment of which to Golgi membranes precedes binding of coatomer. However, such a role of ARF 1 in oligomerization of p24 members waits to be elucidated. As coatomer is used in many cycles, an important question concerns a reversibility of the conformational change of complex. Since ARF 1 is a component of COPI vesicle and known to be involved in the uncoating process by hydrolysis of its bound GTP [Tanigawa, 1993 #51], this energy providing step might well help to reverse the conformational change of coatomer and thus dissociate the coat. 14 In general, receptor induced polymerization of coat proteins during their recruitment would strongly increase the efficiency of the coating process, and with the resulting geometry ruled by the nature of the conformationally changed proteins, may well be the driving force to shape a membrane. 15 FIGURE LEGENDS Fig. 1. Precipitation of coatomer with synthetic peptides corresponding to the COOH-termini of p23wt, p23AS and Wbp1p. (A) Peptides used in this study. p23wt represents the cytoplasmic domain of p23 which binds coatomer depending on its dilysine and diphenylalanine motifs, whereas p23AS lacks these residues and therefore does not bind coatomer. Wbp1p represents the cytoplasmic domain of a subunit of the yeast Noligosaccharyl transferase complex bearing a characteristic KKXX ER-retrieval motif known to bind coatomer. (B, C) Precipitation of coatomer (0.09 µM) with monomeric peptides (B) and dimeric peptides (C). Only p23wt (filled squares) precipitates the complex, whereas mutated p23 peptide (p23AS, filled circles) and Wbp1p (filled triangles) have no effect. The error bars indicate standard errors (n=3). Fig. 2. Limited proteolysis of coatomer. Proteolysis of coatomer (0.09 µM) with thermolysin (0.008 µM) in the presence of dimerized peptides (50 µM), p23wt-d (A), p23AS-d (B) and Wbp1p-d (C). Western blot analysis of proteolytic fragments of the -COP subunit reveals a better susceptibility of this subunit to the protease in the presence of p23wt-d (A, lanes 2, 3) as compared to p23AS-d (B, lanes 2, 3) and Wbp1p-d (C, lanes 2, 3). Fig. 3. Limited proteolysis of COPI vesicles. (A) Suspension of purified COPI vesicles containing 0.009 µM coatomer treated with thermolysin (0.009 µM) in the presence of p23AS-d (50 µM) as a substrate for the protease. Western blot analysis of proteolytic fragments of -COP reveals a prominent fragment of about 59 kD (lane 2) which is highly susceptible to the protease (lane 3). (B) Coatomer (0.009 µM) incubated with p23wt-d (50 16 µM) and treated with thermolysin under the same conditions as used for the COPI vesicles yields a result comparable to that of COPI vesicles (lanes 2, 3). In contrast, partial digestion in the presence of p23AS-d (50 µM) yields a different result: the 59 kD fragment is more stable (C, lanes 2, 3). Fig. 4. Stoichiometry between coatomer and p23wt-d. 125I-labelled p23wt-d (filled squares) or p23AS-d (filled circle) were incubated with increasing concentrations of coatomer . The amounts of peptide in the precipitates were determined by counting the 125 I radioactivity. The error bars indicate standard errors (n=4). Fig. 5. NOEs indicative of secondary structures. The width of the lines represents the relative strength of the NOEs; a gray line indicates that the NOE could not be identified because of spectral overlap. (A) p23wt-m, (B) p23wt-d. Fig. 6. (A) Superimposition of the 10 structures with lowest internal energies of p23wt-m obtained from simulated-annealing molecular dynamics using NOE-derived an dihedral restraints. The heavy atoms of all structures are shown. (B) Ribbons depiction of p23wt-m showing the secondary structure, diphenylalanine (green) and the dilysine (blue) motif. Top: view perpendicular to the helix axis; bottom: parallel view. A similar representation from the structure of p23wt-d dimer, representing the tetramer of the cytoplasmic domain of p23, is shown in (C). Fig. 7. Dimer formation of p23wt-d confirmed by size exclusion chromatography. (A) Monomeric p23wt (p23wt-m: 1 mg/ml, inject 20 µl). (B) Dimeric p23wt (p23wt-d: 1 mg/ml, inject 20 µl). Peak 1 represents the dimerized form of p23wt-d, peak 2 the monomeric form of 17 p23wt-d. (C) Rechromatography of peak 1 of (B) (40 µl). The appearance of both peak 1 and 2 demonstrates an equilibrium between monomeric and dimeric states of p23wt-d. (D) Dimeric p23wt (p23wt-d: 0.1 mg/ml, inject 40 µl). The concentration dependence of the equilibrium of peak 1 and 2 indicates a bimolecular event. Thus, peak 1 is caused by the dimeric and peak 2 by the monomeric state of the peptide. Fig. 8. Hypothetical model for bud formation. According to this model, interaction of coatomer with a tetramer of p23 induces a conformational change of the complex. This leads to its polymerization on the surface of a membrane resulting in the formation 18 REFERENCES Acknowledgements We thank Dr. Suzanne Pfeffer, Dr. Kai Simons, and Dr. Graham Warren, for critically reading the manuscript. This work was supported by grants of the Deutsche Forschungsgemeinschaft (SFB 352, to C. H., J.B. H., F. W.), the Human Frontier Science Program (to F. W.) and the Fonds der Chemischen Industrie (to F. W., P. R.). 19