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1 Life Science College, Peking University, Beijing 100871, People's Republic of China
2 Life Science College, Hunan Normal University, Changsha 410081, People's Republic of China
Reprint requests to: Song-Ping Liang, Life Science College, Hunan Normal University, Changsha 410081, People's Republic of China; e-mail: liangsp{at}public.cs.hu.cn; fax: 86731-8861304.
(RECEIVED July 24, 2001; FINAL REVISION October 12, 2001; ACCEPTED October 26, 2001)
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.30502
| Abstract |
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Keywords: Huwentoxin-II; spider toxin; three-dimensional structure; disulfide bond; inhibitor cystine knot motif; disulfide-directed ß-hairpin; two-dimensional NMR
Abbreviations: HWTX-II, huwentoxin-II 2D NMR, two dimensional nuclear magnetic resonance COSY, correlation spectroscopy DQF-COSY, double-quantum-filtered COSY NOESY, nuclear Overhauser effect spectroscopy TOCSY, total correlated spectroscopy NOE, nuclear Overhauser effect RMS, root mean square ICK, inhibitor cystine knot, DDH, disulfide-directed ß-hairpin
| Introduction |
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-agatoxin IVA (Reily et al. 1994; Kim et al. 1995),
-agatoxin IVB (Yu et al. 1993; Reily et al. 1995), µ-agatoxin I (Omecinsky et al. 1996),
-atracotoxin-HV1 (Fletcher et al. 1997a),
-atracotoxin-Hv1b (Fletcher et al. 1997b), robustoxin (Pallaghy et al. 1997), J-ACTX-Hv1c (Wang et al. 2000), huwentoxin-I (Qu et al. 1997), and S. huwena lectin-I (Lu et al. 1999) share the same structural scaffold known as the inhibitor cystine knot (ICK) motif (Pallaghy et al. 1994; Norton and Pallaghy 1998). The ICK motif is also adopted by a variety of toxic and inhibitory polypeptides from aquatic cone snails and other sources despite their dissimilar primary sequences and biological functions. The typical characteristic of these structures is the cystine knot formed by three disulfide bonds linked in the mode of I-IV, II-V, and III-VI, in which the III-VI disulfide passes through a ring consisting of a minimum of 10 residues formed by the I-IV and II-V disulfide bonds and the intervening polypeptide backbone. It is also found that only the II-V disulfide is conserved both in HWTX-II and the ICK folding molecules from the primary sequence comparison. Because of the importance of disulfide bridges in the structures of small, highly cross-linked peptides, the unique disulfide-bonding mode (I-III, II-V, and IV-VI) of HWTX-II implies that the three-dimensional structure of HWX-II might be unusual. To investigate the structural features and elucidate the structure-function relationship of HWTX-II, its solution structure is determined by 2D 1H-NMR.
The three-dimensional structure of HWTX-II demonstrates a fold different from the ICK motif found earlier in spider toxins and provides new insights into the evolution of structural motifs.
| Results |
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NH2 of Lys were identified in our previous paper (Shu et al. 2001b). The three-dimensional structure of HWTX-II was calculated using the program X-PLOR (Brünger 1992). A total of 592 non-redundant interproton distance constraints and 16 dihedral constraints were used by distance geometry algorithm to obtain 50 initial structures. The initial structures were refined by five rounds of simulated annealing with force constants 50 kcal/mole per Å2 and 200 kcal/mole per rad2 for NOE distance and dihedral angle constraints, respectively. The structures with lower energy and better Ramachandran plots were chosen for further refinement. A total of 47 structures agreeing with the experimental constraints were obtained, which converged to a common fold. A total of 10 structures with lower energy and better PROCHECK (Laskowski et al. 1993) results were chosen from the 47 to represent the solution structure of HWTX-II (Fig. 2A
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| Discussion |
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Both average distance between C
(i) and C
(i + 3) of loop 47 and 2427 are less than 7Å and form the type I ß-turn. For loop 47, the average
,
torsion angles for S5 and F6 are -93°, -24°, and -101°, -26°, respectively. The average
,
torsion angles for G25 and G26 in loop 2427 are -65°, -40° and -90°, 21°, respectively.
Some amide protons are involved in forming the secondary structures in HWTX-II. All hydrogen-bonded amide protons taking part in the secondary structures should be well solvent exposed, as no slow exchanging NH was recorded in the hydrogen-deuterium exchange experiments carried out under the same experimental condition used for the structure determination.
Description of the three-dimensional structure
The molecule of HWTX-II is composed of the N- and C-terminal parts and two connecting elements (the fragment 1922 and the disulfide C8-C29) between them (Fig. 2B
). The N part of the structure consists of the disulfide bond C4-C18 and the peptide backbone from N terminal to residue 18. It contains no regular secondary structure except for a ß-turn (loop 47). The C part is formed by the disulfide bond C23-C34 and the peptide fragment from the 23rd residue to the C terminus. It contains the double-stranded antiparallel ß-sheet (2729 and 3436) and a ß-turn 2427. The N and C parts are connected together to form a globular fold because of the extended fragment 1922 and the disulfide C8-C29. The fragment 1922 lying between two cysteine residues (C18 and C23) consists of four consecutive positively charged residues (K19, K20, K21, and K22). The disulfide bond C8-C29 should be the important covalent factor contributing to the globular folding of HWTX-II.
Charged residues
The insecticidal toxin HWTX-II contains many charged residues (15 among a total of 37 residues), including 10 alkaline residues (K12, K16, K19-K22, K24, K28, K30, and K36) and 5 acidic residues (E3, E9, E11, E13 and D15). Accordingly, HWTX-II is a positively charged molecule, in accordance with the experimental pI value of 9.2 from the two-dimensional electrophoresis results (Liang et al. 2000). All acidic residues with negatively charged side chains are distributed in the N part of the molecule (Fig. 2C
). Among the 10 positively charged residues, 4 are distributed in the connecting fragment residues 1922 as described formerly, 4 lie in the C part, and only 2 in the N part. This dipolar distribution of charged residues in structure is found not only in HWTX-II but also in other molecules such as the neutral or anionic µ-agatoxin I, which paralyzes insects by modifying the kinetics of neuronal voltage-activated sodium channels (Omecinsky et al. 1996). However, our whole-cell patch clamp recording results prove that HWTX-II shows little effect on the voltage-gated sodium, calcium, and potassium channel current in acutely isolated rat dorsal root ganglion neuron (Q. Shu and S.P. Liang).
Hydrophobic patches
The structure of HWTX-II is not so compact as huwentoxin-I purified from the venom of the same spider S. huwena (Fig. 3
, cf. A and B). Most residues of HWTX-II are solvent exposed and the molecule lacks a hydrophobic core, because of the loose main chain folding. However, the side chains of residues W27, M33, and V35 are distributed around the two disulfide bonds of C8-C29 and C23-C34 to form more hydrophobic patches on the surface of HWTX-II (Fig. 2C
). It is also shown that these residues mostly take part in forming the double-stranded antiparallel ß-sheet of the C-terminal part.
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-agatoxin IVA (Reily et al. 1994; Kim et al. 1995),
-agatoxin IVB (Yu et al. 1993; Reily et al. 1995), µ-agatoxin I (Omecinsky et al. 1996),
-atracotoxin-HV1 (Fletcher et al. 1997a),
-atracotoxin-Hv1b (Fletcher et al. 1997b; Szeto et al. 2000), robustoxin (Pallaghy et al. 1997), J-atracotoxin Hv1c (Wang et al. 2000), hanatoxin1 (Takahashi et al. 2000), heteropodatoxin 2 (Bernard et al. 2000), huwentoxin-I (Qu et al. 1997), and S. huwena lectin-I (Lu et al. 1999) and the predicted structure of µ-agatoxin IV (Omecinsky et al. 1996) have been reported. These polypeptides have different biological functions and come from different species of spiders, but their three-dimensional structures all adopt the ICK motif. It is shown that the numbers and linkage modes of disulfide bonds in these polypeptides are different and they can be divided into four categories. First, the normal ICK motif is where the three disulfide bridges are paired in I-IV, II-V, and III-VI mode.
-atracotoxin HV1(an inhibitor of insect voltage-gated calcium channel currents), hanatoxin1 (a gating modifier of voltage-dependent potassium channels), heteropodatoxin (a blocker of Kv4.2 potassium channel currents), neurotoxin huwentoxin-I, and lectin peptide SHL-I all belong to this category (see Fig. 1
-agatoxin IVA and
-agatoxin IVB (P-type calcium channel blocker), µ-agatoxin I, and µ-agatoxin IV (insecticidal toxin) all contain four disulfide bonds with I-IV, II-V, III-VIII, and VI-VII linkage (see Fig. 1
-atracotoxin-Hv1b (versutoxin) are sodium channel modulators, containing four disulfide bonds with I-IV, II-VI, III-VII, and V-VIII linkage (see Fig. 1
-atracotoxin-Hv1b (Fig. 3C
-agatoxin IVA (Fig. 3D
The three-dimensional structures of the four categories of ICK molecules all form the cystine knot although they contain different numbers and linkage modes of disulfide bonds. As shown in Figure 3C
E, the ICK molecules with four disulfide bridges linked in different modes always have three of the four playing similar roles of the three disulfide bonds paired as I-IV, II-V, and III-VI in the typical ICK fold molecule (Fig. 3B
) (shown in yellow). The fourth additional disulfide (shown in red) contributes to the stability of special regions such as C16-C42 in
-atracotoxin-Hv1b (Fig. 3C
) and C27-C34 in
-agatoxin IVA (Fig. 3D
) or is related to the biological activity as C13-C14 in J-atracotoxin Hv1c (Fig. 3E
). Therefore, the I-IV, II-V, and III-VI disulfide linkage dictated the structural scaffold of ICK motif is further compared with HWTX-II.
Although HWTX-II does not form the cystine knot because of the unique I-III, II-V, and IV-VI disulfide bond-pairing pattern (Fig. 3A
), it shows similarities in structure with the ICK motif molecules. The C-terminal parts in all the five structures (Fig. 3A
E), especially the double-stranded antiparallel ß-sheet and the correlative two disulfide bridges, are conserved. The disulfide bonds II-V and IV-VI in HWTX-II (shown in yellow in Fig. 3A
) are similar to the II-V and III-VI in the ICK motif molecules (Fig. 3B
E), respectively. The significant difference between HWTX-II and the ICK motif molecules is the N-terminal part, which is contributed from the I-III disulfide bond of HWTX-II (shown in red) (see Fig. 3
).
Novel structure motif
Because HWTX-II does not form a cystine knot, the structure of HWTX-II may be considered as the first representative of a novel structural scaffold found in spider toxins. Moreover, this fold may also be adopted by other molecules in addition to HWTX-II. The primary structure of HWTX-II (Shu and Liang 1999) is highly homologous with ESTX from the American tarantula spider Eurypelma californicum (Anette 1989) and venom protein 1 from the Mexican red knee tarantula spider Brachypelma smithii (Kaiser et al. 1994), as shown in Figure 4
(Shu et al. 2001a). The high homology of these three toxins in primary sequence may imply that the molecular folding of ESTX and venom protein 1 could be similar to HWTX-II. The three disulfide bonds of ESTX and venom protein 1 could also be linked in the HWTX-II mode of I-III, II-V, and IV-VI, although they are reported to be I-IV, II-V, and III-VI determined by similarity in the Swissprot Database (cf. ID number TX4K_EURCA and TXP1_BRASM, respectively). The structure of HWTX-II might serve as a new reference to modeling the three-dimensional structures of ESTX and venom protein 1.
|
-atracotoxin-HV1 and J-atracotoxin Hv1c (Fig. 5A
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It has been noted that the amino acid residue number of the loop 3 between CIII and CIV in the DDH fold is ranged 619, whereas it is 4 in the loop between C29-C34 in HWTX-II. The loop 3 is related to the lengths of the ß-hairpin and the loop inserting between two ß-strands. A lower limit of four amino acid residues in the loop 3 in the DDH fold should be reasonable to turn the peptide chain for forming the ß-hairpin. We also noted that the spaces between half-cystine residues have been summarized as CX37CX46CX05CX14CX410C in the ICK motif (Pallaghy et al. 1994; Norton and Pallaghy 1998). Because the C-terminal double-stranded ß-sheet directed by the II-V and III-VI disulfide bridges in the ICK motif refers to the DDH fold, the amino acid sequence of the ICK motif related to the DDH motif is CX46CX210CX410C. As it proposed that the ICK motif is an elaboration of the DDH motif, the upper limit of the amino acid residue number of loop 2 in the DDH fold can be 10 and the lower limit of loop 3 can be 4. It means that the loop 2 and 3 in the DDH fold should be more variable to the sequence CX519CX2(G or P)X2CX619C according to the ICK motif, and the loop 3 in HWTX-II also conforms to the DDH fold.
Comparison of the structures of HWTX-II (Fig. 5C
) and representatives of the DDH fold such as J-atracotoxin Hv1c (one of the ICK folding molecules) (Fig. 5A
) and the CBD-CBHI (Fig. 5B
) suggests that HWTX-II may have also evolved from the DDH fold. The structure of HWTX-II might be a molecular evidence for the proposition that the ICK motif was a minor elaboration of the DDH fold. The evolution relationship of HWTX-II, the ICK, the DDH fold, and other structural folds are under further study.
| Materials and methods |
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NMR spectroscopy
All NMR experiments were recorded on a 500 MHz Bruker DMX-500 spectrometer. All 2D spectra were recorded in phase-sensitive mode by the time-proportional phase incrementation (TPPI) method following standard pulse sequences and phase cycling. Solvent suppression was achieved by the presaturation method. Homonuclear 2D NMR spectra were recorded at temperature of 300 K, including COSY, DQF-COSY, TOCSY with mixing time of 44 and 85 msec, as well as NOESY with mixing time of 150 200, 250, and 400 msec. The recording data points of t1 x t2 were 512 x 2048 for COSY and TOCSY; 700 x 4096 for DQF-COSY; 512 x 2048 for all NOESY spectra except 768 x 4096 for the 150-msec spectrum. Spectra of NOESY with 400-msec mixing time and TOCSY with 85-msec mixing time were recorded at the temperature of 290 K, the data points of t1 x t2 were 512 x 2048.
Spectra were processed and viewed using software Felix 98.0 (Biosym Technologies) and Sybyl (Tripos) on the O2 workstation (Silicon Graphics). All data were zero-filled to produce a 2K x 4K real matrix to COSY, DQF-COSY and NOESY or 1K x 2K to TOCSY. Before Fourier transformation, sine bell or sine bell square window functions were used with phase shift of 3
/4 or
/2.
The hydrogen-deuterium exchange experiments were carried out by recording a set of 1D spectra after redissolving the lyophilized H2O experiment sample in D2O at time scalar of 10, 20, 30, 60, 90, and 120 min. As no slow exchanging amide proton was observed, no longer time scalar and no 2D experiments were performed.
Structure constraints
Distance constraints were derived primarily from the intensities of cross-peaks in NOESY spectra recorded in H2O and D2O with mixing times of 200 msec recorded at 300 K. Comparisons were made to the 150-, 250-, and 400-msec NOESY spectra to assess possible contributions from spin diffusion. All NOE data were classified as strong, medium, or weak, corresponding to upper bound inter-proton distance restraints of 2.7, 3.5, and 5.0 Å, respectively. Lower distance bounds were taken as 1.8 Å, the sum of the van der Waals radii of proton. Pseudo-atom corrections were applied to non-stereo specifically assigned methyl and methylene protons with the upper bound for 0.5 Å (Wüthrich et al. 1986).
Backbone dihedral constraints were inferred from 3JHNH
coupling constants measured from either 1D NMR spectra or the anti-phase cross-peak splitting in a high-digital-resolution DQF-COSY spectrum. 16
dihedral angles were restrained to -120 ± 40° for a 3J HNH
8 Hz and -65 ± 25° for 3J HNH
5.5 Hz.
Nine additional fake distance constraints were added to define the three disulfide bonds involved in HWTX-II. Three distance constraints for each disulfide bond are S(i)-S(j), S(i)-Cß(j), and S(j)-Cß(i), respectively, whose target values were set to 2.02 ± 0.02, 2.99 ± 0.5, and 2.99 ± 0.5 Å, respectively.
Structure calculation and evaluation
The three-dimensional structures were calculated by simulated annealing and energy minimization using the program of X-PLOR (Brünger 1992). A set of 50 structures was calculated as described by Qu et al. (1997). The programs of PROCHECK (Laskowski et al. 1993) were used to assess the overall quality of calculated structures. A family of 10 structures was chosen to represent the solution structure of HWTX-II. The software InsightII (Biosym Technologies) was used to view and plot the structures.
Convergence of the calculated structures was evaluated in terms of the structure parameters, including RMS deviations from experimental distance and dihedral constraints, values of energetic statistics, RMS deviations from idealized geometry, and atomic RMS differences of the family of 10 structures.
Structure comparison
The coordinates of structures used in structural comparison were obtained from the Brookhaven Protein Data Bank. Entry ID of 1OAV is for
-agatoxin IVA, 1VTX for
-atracotoxin Hv1b (versutoxin), 1DL0 for J-atracotoxin Hv1c, 1QK6 for huwentoxin-I, and 1AZ6 for CBD-CBHI, respectively.
| 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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