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* School of Crystallography, Birkbeck College, University of London, London WC1E 7HX, UK; Bloomsbury Centre for Structural Biology, Birkbeck College and University College, University of London, London WC1E, UK; Department of Biochemistry and Molecular Biology, University College, University of London, London WC1E 6BT, UK; Ludwig Institute of Cancer Research, UCL School of Medicine Branch, London W1P 8BT, UK
Correspondence: Address reprint requests to B. A. Wallace. Tel: (+44) 20 7631 6857; Fax: (+44) 20 7631 6803; E-mail: b.wallace{at}mail.cryst.bbk.ac.uk.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONEXPERIMENTALRESULTSDISCUSSIONACKNOWLEDGEMENTSREFERENCES |
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INTRODUCTION |
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). Up to 16 microheterogeneous members of the family have been identified, termed antiamoebin I, II, etc., (Pandey et al., 1977; Pandey et al., 1978; Jaworski and Brukner, 2000). Antiamoebin I has the primary structure:
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-aminoisobutyric acid (-methylalanine), Iva is D-isovaline (-ethylalanine), Hyp is hydroxyproline, and Phl is phenylalaninol.
The peptaibols, including antiamoebin, are considered good models for studying ion channels, as they form stable, well characterized channels and are relatively abundant (Wallace, 2000). They also fall in the intermediate size range where both NMR spectroscopic and x-ray crystallographic techniques can be used to investigate three-dimensional structure.
High-resolution crystal structures of antiamoebin I published by Snook et al. (1998) and Karle et al. (1998) in different environments (methanol and octanol, respectively) and in different crystallographic space groups, show that the molecule has essentially the same backbone conformation in both environments. The polypeptide backbone atoms of the two crystal structures have a positional root mean square deviation (RMSD) of 0.24 Å (Wallace et al., 2000). The structures are mostly helical, with an N-terminal -helix (residues 1-9) followed by a small segment of 310-helix (residues 10-12) joined to an overlapping series of ß-turns at the C-terminus (residues 12-16), which is sometimes described as a ß-bend-ribbon (Di Blasio et al., 1992). The molecule has a deep bend centered on residue Hyp11, forming an angle of 56° between the two helix axes in the methanol crystal form (Snook et al., 1998).
The molecular conformations of other naturally occurring peptaibols determined by x-ray crystallography (Fox and Richards, 1982; Karle et al., 1991; Toniolo et al., 1994; Karle et al., 1998) or NMR spectroscopy (Esposito et al., 1987; Franklin et al., 1994; Anders et al., 2000; Balashova et al., 2000; Shenkarev et al., 2002) are predominantly helical, although they differ considerably in some parameters, such as bend-angle and helical type (310 versus -helical). A regularly updated database of peptaibol sequences, along with a collection of atomic coordinates, can be found at http://www.cryst.bbk.ac.uk/peptaibol (Chugh and Wallace, 2001). The peptaibols, which now number more than 200, have been grouped into nine different subfamilies (SFs) based on their structure and function (Chugh and Wallace, 2001). These have high sequence homology and are essentially groupings of naturally occurring "mutants." Comparative studies between the SFs demonstrate that quite subtle differences in sequence can lead to substantial variations in activity, and thus these molecules are a valuable resource for investigating structure/function properties. Antiamoebin is the only member of SF2 whose structure has been determined.
This study aimed to determine the detailed three-dimensional structure of antiamoebin I in methanol using NMR spectroscopy, thereby allowing direct comparison between solution and solid-state structures for this molecule. This study is unique in that it is the first time one of the peptaibol structures has been determined both in solution and in the solid state in the same solvent. Comparisons of the NMR and crystal structures thus provide information on environmental effects (i.e., isotropic versus anisotropic, solution versus crystal) and on peptide flexibility, that may be relevant to membrane insertion and function of this ion-channel forming polypeptide.
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EXPERIMENTAL |
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5 mg/ml (CD3OD) or 15 mg/ml (CD3OH).
Data collection
NMR experiments were performed on a 500-MHz Varian Unity+ spectrometer. All two-dimensional data (except the magnitude mode COSY) were recorded in phase sensitive mode using the States-TPPI method for quadrature detection (Marion et al., 1989), and data were apodized with shifted cosine-bell squared functions, followed by zero filling once in each dimension. Water suppression in all homonuclear experiments was achieved using WATERGATE (Sklenar et al., 1993). COSY, TOCSY, one-dimensional 1H, E.COSY, ROESY, NOESY and (1H-13C)-HSQC experiments were recorded on the methanol-d4 sample, at 298 K.
One-dimensional 1H, TOCSY, ROESY, NOESY, (1H-15N)-HSQC and (1H-13C)-HMBC experiments were recorded on the methanol-d3 sample. 3J(HN-H) values were obtained from the 1H spectrum, whereas 3J(H-Hß) coupling constants were measured from the E.COSY spectra. All methanol-d3 spectra were acquired at a temperature of 293 K, except the NOESY experiments, which were recorded at 278 K. A set of one-dimensional spectra were recorded at temperatures between 279.5 K and 313 K, in 5 K steps, to determine the temperature dependence of the chemical shifts of the amide protons.
Spectral assignment
Assignments of the resonances to specific protons of antiamoebin were carried out using information from the COSY, TOCSY, HMBC, and HSQC spectra, based on established techniques (Wüthrich, 1986). These assignments were then used to analyze the Overhauser effect data acquired in the ROESY and NOESY experiments.
Identification of the methyl resonances for the Aib and Iva residues was the most difficult part of the assignment process, because of the number of overlapping peaks involved. To carry out the assignment, we used amide resonance information from the (1H-15N)-HSQC, and linked them with carbon and proton resonances from the (1H-13C)-HMBC and TOCSY spectra. By a process of elimination and "walking" along the connectivities in the residues, we assigned all the methyl peaks to specific residues. Due to the primary structure, it was not possible to assign all of the resonance peaks to their atoms stereospecifically, leading to the need for pseudoatom terms in the structure modeling process.
Distance restraints
Initial distance restraints were derived from the ROESY spectra, by the r-6 method (Wüthrich, 1986; Hoogstraten and Markley, 1996; Gratias et al., 1998) using integrated resonance peak volumes. Ninety upper bound distance restraints were derived from crosspeaks in the 150-ms mixing time experiment, with only 69 of the corresponding crosspeaks seen in the 500-ms experiment. The distances were entered into a simulated annealing refinement protocol using the X-PLOR program (Brünger, 1992). During the course of the structural calculations, it became clear that the number and accuracy of these semiquantitative distance restraints alone was insufficient to produce a consistent structural ensemble.
The MARDIGRAS/CORMA package (Borgias and James, 1989; 1990) was then used to calculate proton-proton distances and error bounds from the crosspeak intensities in the NOESY and ROESY spectra. The MARDIGRAS output distances were averaged for all the Overhauser effect data (3 NOESY and 2 ROESY mixing times) and used as distance restraints for simulated annealing refinement using the X-PLOR program. Each experiment was scaled in proportion to the average crosspeak intensity of the ß-methylene protons, with a corresponding distance of 1.8 Å. Error bounds were added, using values of ± 1 standard deviation unit from the averaging process. Approximately 30 of the measured intensities were found in only one experiment, and therefore did not have a standard deviation from averaging. For these data we added ±20% of the calculated distance as error bounds. The total number of distance restraints derived from the MARDIGRAS program was 120.
Distance restraints that were impossible to assign stereospecifically (90 out of the total 120) were entered using pseudoatom terms during initial structure determination. They were resolved in an iterative manner by measuring the specified distances in the resultant model structures and assigning the pseudoatoms accordingly. Eventually a set of 87 restraints was obtained which combined the two sets of restraints (from the r-6 method and the MARDIGRAS output) and produced few or no restraint violations during simulated annealing. Of these 87 restraints, 60 specified pseudoatom terms resolved in the manner described above.
The primary structure of antiamoebin led to a lack of suitable coupling constant data from which to derive torsion angle restraints, and those which were measured were not of sufficient precision to be utilized. Therefore, no dihedral angle restraints were applied in the structure determination.
Simulated annealing refinement
One hundred random-configuration starting conformers were created and subjected to a simulated annealing run of the X-PLOR program. The 20 lowest energy conformers from each run were selected, and aligned to the lowest energy conformer using the LSQKAB program (CCP4 suite of programs: Bailey, 1994).
Analysis of preliminary structures
Hydrogen bonding in the preliminary ensembles was detected using two programs: SYBYL (Tripos Assoc., Inc., St. Louis, USA; Vanopdenbosch et al., 1985) and HBPLUS (McDonald and Thornton, 1994). Hydrogen bonding associations detected in at least 15 of the 20 lowest energy conformers by both programs were specified as distance restraints for subsequent runs of the simulated annealing protocol, similar to the method described by Balashova et al., (2000). Seven hydrogen bonds were assigned, with two standard distance restraints (O—N and O—HN) for each one. The resulting ensembles retained all the constrained hydrogen bonds after each simulated annealing run.
Temperature coefficient analysis of the relevant amide proton resonance peaks was carried out, following the change in chemical shift over a range of temperatures (from 279.5 to 313 K, in 5 K steps). The lower temperature dependence coefficients supported the involvement of the residues previously identified by SYBYL and HBPLUS in hydrogen bonding, as shown in Fig. 5, but were not used as criteria for assignment of the hydrogen bonds in the refinement procedure. It should be noted that the assignment of the acceptor groups for the suggested hydrogen bonds cannot be confirmed by experimental data without 13C, 15N-isotope labeling of the polypeptide. Therefore the assignments of the acceptor groups are based solely on the distance- and angle-based analyses of SYBYL and HBPLUS.
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), and only those which had no residues in the disallowed regions of the Ramachandran plot were used further. The SYBYL program was used to display the molecules shown in Figs. 3 and 4.
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RESULTS |
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positions of the lowest energy conformer. Structural statistics for this ensemble are shown in Table 1. The three different superpositions show how alike in structure the conformers of the ensemble are, when aligned about the N- or C-terminal regions separately, and aligned about the entire length of the polypeptide (Fig. 3). This comparison of superpositions suggests that a central, flexible "hinge" region, located around residues Gly7-Aib9, which may have functional importance, separates the well-defined terminal regions. The root mean square deviations (from the position of the lowest energy conformer) for these alignments are shown in Table 2, and suggest a tightly defined ensemble.
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). The structures are aligned about their most closely matched region, residues Aib9-Iva13. It can be seen that the backbone conformations of the C-termini are very similar, but that toward the N-termini, large differences exist. The crystal structure consists of right-handed helices throughout, whereas the NMR model forms a right-handed helix toward the C-terminal end, but a turn of left-handed helix from residue Leu8 toward the N-terminus. This is a significant difference in structure, enabled by the achiral amino acids Aib3,4,5 and Gly7, and the D-amino acid Iva6, which form a contiguous sequence five residues long near the N-terminal end of the polypeptide. This lack of L-form residues is likely to be important in allowing the polypeptide backbone to adopt a left-handed conformation. In none of the simulated annealing runs did we see the anticipated equal distribution of left-handed and right-handed helices, which would arise if the NMR data supported both possibilities. Also, swapping the stereospecific assignments of the resolved pseudoatom terms to specify their stereoisomer(s) still produced model structures with left-handed helices.
Hydrogen bonds in the final ensemble (Table 3) were detected as described in the Experimental section. The most frequently occurring backbone hydrogen bonds were of the (i, i+3) type, normally associated with 310-helices, and are commonly found in peptides containing Aib residues (Toniolo and Benedetti, 1991).
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Comparing the crystal structure with the NMR data resulted in 16 or 17 violations of the NOE distance restraints of greater than 0.5 Å. The most significant of these violations were those involving residues 4-8, including some resulting from the hydrogen bond restraints (Table 4). Thus it is clear that the NMR and crystal structures are distinct. The remainder of the violations are either between adjacent residues or within a residue, and are likely to be resolved by simple rotation of backbone and side-chain bonds.
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DISCUSSION |
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In a previous NMR study of antiamoebin I in dimethylsulphoxide, the results obtained were only sufficient to propose general models for the backbone conformation (Das et al., 1986). That study suggested that the polypeptide was highly ordered in solution, with ten of the backbone amide groups inaccessible to solvent (and therefore likely to be involved in intramolecular hydrogen bonding). The pattern of amide hydrogen bonding proposed by Das et al. was in agreement with that found in this study (Table 3). By analyzing possible hydrogen bonding patterns and specific interresidue NOEs, Das et al. calculated likely backbone angles and concluded that antiamoebin favors a left-handed 310-helix for residues Aib3-Gly7, with Type II ß-turns at the N-terminus and for residues Leu8-Aib9. The C-terminal segment was proposed to be a 310-helix, with a right-handed twist being considered more feasible. Our NMR data has led to a model ensemble that matches these predictions closely.
Detailed NMR and crystal structures exist for other peptaibols, most notably zervamicin (Karle, et al., 1991; Balashova et al., 2000; Shenkarev et al., 2002) and alamethicin (Fox and Richards, 1982; Esposito et al., 1987; Franklin et al., 1994), which form well characterized voltage-gated ion channels. The crystal structures of those peptaibols are broadly similar to that of antiamoebin: they are helical, with a bend near the center caused by an imino acid (Pro or Hyp).
Leu1-zervamicin is a bent helix, 29 Å long, and has the same number of residues as antiamoebin (16, with an acetylated N-terminus). The central bend is a little less marked than that of antiamoebin, varying between 30° and 45° in the different crystal forms. The crystal structure has an -helical N-terminal end (from residue 1 to 9), with the C-terminal part being made up of a ß-bend ribbon spiral similar to that of antiamoebin (Karle, et al., 1991). The primary structure differs from antiamoebin in that every third or fourth residue is polar, resulting in an amphipathic helix with the polar side chains arranged on one side of the helix. After association of a number of monomers, this allows a hydrophilic "face" of the polypeptide to provide solvation to water and ions passing through a central channel, while presenting the more hydrophobic side to the surrounding lipid bilayer. The crystal structures of zervamicin and antiamoebin are close enough for the zervamicin structure to have been used as a search model in the elucidation of the antiamoebin/octanol crystal structure (Karle et al., 1998) and the antiamoebin/methanol structure (Snook et al., 1998; Snook and Wallace, 1999).
Solution structures of zervamicin IIB have been determined by NMR spectroscopy in several isotropic solvents (Balashova et al., 2000). The structures obtained were broadly similar to the crystal structure, with the backbone RMSD between the lowest energy NMR monomer and the crystal structure being 1.3 Å. Much of this difference can be attributed to slightly different helix bend angles. A recent structure of zervamicin IIB bound to dodecylphosphocholine (DPC) micelles (Shenkarev et al., 2002) found that in the anisotropic environment of the lipid micelle gave rise to a smaller bend angle around Hyp10 (23° cf. 47° isotropic solvents), leading to slightly increased length of the peptide in DPC, but otherwise the two NMR structure ensembles were very similar.
Alamethicin has four more residues than zervamicin or antiamoebin, being a 20-mer, and is noticeably longer in dimension than antiamoebin or zervamicin at around 34 Å. They share common features such as a high proportion of Aib residues, a largely helical structure and the capped termini characteristic of peptaibols. The molecule in the crystal structure (Fox and Richards, 1982) has a less pronounced helix bend angle than antiamoebin or zervamicin, at around 33°, and is mostly -helical. In SDS micelles, NMR studies found that alamethicin is largely -helical, with a flexible central segment (Franklin et al., 1994). This flexibility was attributed to the central Pro14 residue, and the consequent absence of hydrogen bond partners for the residues in the preceding turn of the helix. However, amide exchange measurements suggest that any disruption in the -type hydrogen bond network around the Pro14 residue is offset by the formation of 310-type associations when alamethicin is reconstituted in lipid vesicles, (Dempsey and Handcock, 1996) or in methanol solution (Dempsey, 1995), resulting in a stable conformation.
The conformation of antiamoebin in methanol solution, as determined by NMR spectroscopy, differs significantly from the crystal structures previously determined (Snook et al., 1998; Karle et al., 1998).
Violations of the NMR-derived distance restraints and amide hydrogen bonds (Table 4) by the crystal structure show that the crystalline and methanol solution conformations cannot be identical. All the distance restraint violations of greater than 0.5 Å between nonadjacent residues involve those of the most dissimilar region between crystal and NMR structures, residues Aib4-Leu8. This is around the region where the NMR models adopt a left-handed helix. All of the violations are of the same type: the specified atoms are too far apart to satisfy the NMR data, due to the opposite-handed twist of the helix. This effect can be clearly seen (Fig. 4), where the backbone worms tracing the C backbone atoms are nearly mirror images of one another. The amide protons of residues Aib4 and Aib5 are likely to be involved in hydrogen bonding, as shown by the temperature dependence results (Fig. 5) and identification using the HBPLUS and SYBYL programs (Table 3). Because these amides were not found to be hydrogen bonded in the crystal structure, this represents a significant difference in structure between the two forms.
The NMR models have a fairly similar conformation to the crystal structure in the C-terminal half of the polypeptide, that of a right-handed 310-helix. However, a putative "hinge" region is observed in the center of the molecule (which may be functionally important), and the residues toward the N-terminus adopt a left-handed 310-helix conformation. One reason that antiamoebin in solution but not in the solid state could adopt this unusual conformation is the lack of crystal packing forces, which constrain the polypeptide in crystals. This is essentially the only major difference between the two systems, both having been studied in the same solvent and at similar temperatures.
The "hinge" region in the center of the NMR models may have functional importance for the insertion of the peptide into lipid membranes. The methods of insertion proposed for alamethicin (Boheim, 1974; Fox and Richards, 1982; Cascio and Wallace, 1988; He et al., 1996; Tieleman et al., 2001), suggest that the orientation of the peptide and its response to a transmembrane voltage is affected by the helix dipole of the polypeptide. In the absence of charged amino acids (as is the case in uncharged alamethicin variants, and in antiamoebin) this effect may be even more important, as the dipole is the only source of electrostatic interaction with the transmembrane potential (Dempsey and Handcock, 1996). It would seem plausible that flexibility in the center of the peptide would make this insertion more favorable, though the molecular dynamics studies for the recently proposed mechanism for alamethicin insertion (Tieleman et al., 2001) did not show significant change in the helix bend angle.
One question that arises for all of the studies of peptaibols in organic solvents is the relevance of the structures determined in these environments to their structures in membranes. Circular dichroism spectroscopy has been used to demonstrate the membrane-mimetic nature of these solvents for a number of these channel-forming molecules (Cascio and Wallace, 1988; Duclohier and Wroblewski, 2001). In the case of antiamoebin, the CD spectra in membranes and in methanol solution (Snook et al., 1998) are very similar but not identical, which suggests some conformational change may occur upon membrane insertion.
A mechanism for the membrane insertion of antiamoebin is proposed (Fig. 6), based on the findings in this study and consideration of other peptaibol insertion models discussed above. Before binding of the target membrane, antiamoebin is likely to exist as a monomer. The conformational freedom allowed by being in solution suggests that the NMR-derived structures (Fig. 3) may be relevant. Upon association with the membrane, the polypeptide may become more helical, as is observed with alamethicin. Channel formation of antiamoebin appears to be a less voltage-dependent, but more lipid-specific process (Duclohier et al., 1998) than found for alamethicin, and is likely to involve either a partial refolding or the reorientation of the molecular dipole with respect to the bilayer normal (Snook et al., 1998). The ordered nature of the bilayer, like that in the crystal, may induce conformational change during insertion of the peptide, and the anisotropy of the lipid could promote a straightening of the bend in antiamoebin. It is assumed that antiamoebin inserts as a monomer, and that monomers subsequently associate to form the conducting pore. Conductance studies by Duclohier et al. (1998) suggest that the antiamoebin channel will contain 4n monomers, and models for an octameric channel model which has an appropriate size to fit with these measurements have been proposed (Wallace et al., 2000). The insertion is likely to occur in a manner generally similar to the accepted "barrel-stave" model for alamethicin (reviewed by Sansom, 1993), which has also been suggested to be the mode of pore formation for zervamicin IIB (Shenkarev et al., 2002). However, the differences in channel-formation properties between antiamoebin and these other peptaibols (Snook et al., 1998; Duclohier et al., 1998) indicate there are subtle differences in the mechanisms, and are consistent with the more drastic structural rearrangement proposed for antiamoebin in this model.
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; Wallace et al., 2000). Although the NMR models may not represent the active structure of antiamoebin in membranes, they nonetheless provide insight into the flexibility and adaptability of channel-forming polypeptides, and may represent one of many intermediates in the process of membrane insertion. |
ACKNOWLEDGEMENTS |
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FOOTNOTES |
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Submitted on June 17, 2002; accepted for publication August 5, 2002.
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REFERENCES |
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