| Literature DB >> 23342149 |
Nikolaus M Loening1, Zachary N Wilson, Pamela A Zobel-Thropp, Greta J Binford.
Abstract
We present solution-state NMR structures for two putative venom peptides from Sicarius dolichocephalus. These peptides were identified from cDNA libraries created from venom gland mRNA and then recombinantly expressed. They are the first structures from any species of Sicarius spiders, and the first peptide structures for any haplogyne spiders. These peptides are homologous to one another, and while they have at most only 20% sequence identity with known venom peptides their structures follow the inhibitor cystine knot motif that has been found in a broad range of venom peptides.Entities:
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Year: 2013 PMID: 23342149 PMCID: PMC3544742 DOI: 10.1371/journal.pone.0054401
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Figure 1Sequence alignment for the translated sequences of S64 and S67.
This sequence alignment for S64 and S67 illustrates the signal sequence, linker, and mature toxin. Small arrows show the predicted cleavage sites for the mature toxins. The experimentally determined disulfide bond connectivity shown applies to both peptides. Sequences were aligned using ClustalX 2.1 and visualized using JalView 2.7 [36]. The coloring makes use of the default ClustalX color scheme, which is a function of sequence identity and amino acid type.
Figure 2HPLC chromatograms for the cleavage reaction products from S64
(top) and S67 (bottom). The solid line corresponds to the left axis and represents the absorbance at 280 nm; the dashed line corresponds to the right axis and represents the solvent composition. In both chromatograms, the cleaved peptide is well-resolved from other peaks. The large peak that appears at high acetonitrile concentrations corresponds to a combination of the maltose binding domain (MBP) tag, uncleaved fusion protein (MBP:S64/MBP:S67) and TEV protease. Peak identities were confirmed by performing gel electrophoresis and mass spectrometry for select fractions. The flow rate was 4 mL/min (top) and 2 mL/min (bottom).
Figure 3MALDI-TOF mass spectra for unlabeled S64
(left) and S67 (right). The predicted monoisotopic masses for fully oxidized S64 are 3558.3 Da for the [M+H]+ ion and 1779.69 Da for the [M+2H]2+ ion. Likewise, the predicted mass for fully oxidized S67 is 2121.41 Da for the [M+2H]2+ ion. The appearance of peaks at these masses indicates that the cysteines are oxidized for both S64 and S67. The additional peaks seen to the left of the [M+2H]2+ peak in the S67 mass spectrum correspond to ions that have dehydrated. These peaks are also present in the S64 spectrum but are difficult to discern due to the much wider scale used for this spectrum.
Figure 415N-HMQC spectra for S64
(top) and S67 (bottom). The S64 spectrum includes some minor peaks that are not assigned. These peaks do not have discernable cross-peaks in the NOESY spectra and only very weak cross-peaks in the 3D assignment spectra, which suggest that they are due to unfolded peptide rather than a minor conformation with a different disulfide-bonding pattern.
Structural statistics for the S64 and S67 ensembles.
| S64 | S67 | |||
| Physical Parameters (including nonnative N-terminal residue) | ||||
| Number of residues | 32 | 36 | ||
| Average molecular weight (reduced, unlabeled, Da) | 3565.98 | 4249.82 | ||
| Monoisotopic molecular weight (reduced, unlabeled, Da) | 3563.40 | 4246.85 | ||
| Structural Restraints | ||||
| NOE-derived distance restrains (ARIA cycle 8) | ||||
| Intraresidue (| | 209 | 319 | ||
| Sequential (| | 66 | 94 | ||
| Short (2≤| | 9 | 20 | ||
| Medium (4≤| | 11 | 23 | ||
| Long (| | 34 | 83 | ||
| Ambiguous | 84 | 137 | ||
| Total | 413 | 676 | ||
| Dihedral constraints | ||||
| Phi | 24 | 25 | ||
| Psi | 24 | 25 | ||
| Sγ-Sγ distance restraints | 3 | 3 | ||
| Hydrogen bond restraints | 0 | 7 | ||
| Statistics for accepted structures | ||||
| Accepted structures | 20 | 20 | ||
| Mean CNS energy terms | ||||
|
| −786 (±41) | −714 (±47) | ||
|
| −100 (±49) | −126 (±10) | ||
|
| 183 (±15) | 294 (±21) | ||
| Restraint violations >0.3 Å (average # per structure) | 5.6 (±1.7) | 5.7 (±2.5) | ||
| RMS deviations from the ideal geometry used within CNS | ||||
| Bond lengths (Å) | 0.0040 | 0.0043 | ||
| Bond angles (°) | 0.55 | 0.64 | ||
| Improper angles (°) | 1.86 | 3.00 | ||
| Ramachandran Statistics (PROCHECK 3.5.4 | ||||
| Most favored (%) | 88.5 | 68.6 | ||
| Additionally allowed (%) | 10.8 | 25.9 | ||
| Generously allowed (%) | 0.42 | 1.07 | ||
| Disallowed (%) | 0.21 | 4.47 | ||
| Average atomic RMS deviations from average structure (±SD) | ||||
| N, Cα, C, and O atoms (all residues, Å) | 0.86 (±0.22) | 0.87 (±0.33) | ||
| All heavy atoms (all residues, Å) | 1.43 (±0.21) | 1.33 (±0.16) | ||
| N, Cα, C, and O atoms (for residues with cop ≥0.9, Å) | 0.57 (±0.17) | 0.33 (±0.08) | ||
| All heavy atoms (for residues with cop ≥0.9, Å) | 1.30 (±0.17) | 1.04 (±0.14) | ||
| MolProbity analyses (v3.19 | ||||
| Clashscore | 12 (±4) | 18.7 (±5.4) | ||
| Clashscore percentile (%) | 63 (±18) | 39 (±19) | ||
| Clashscore Z-score | 0.42 (±0.62) | −0.25 (±0.48) | ||
Two sets of atomic RMS deviations are provided. The first set is for the full peptide (residues 1–32 for S64, 1–36 for S67) whereas the second set is calculated only including residues for which the circular order parameters (cop) for both φ and ψ are ≥0.9 (residues 2 and 4–30 for S64, and residues 5–35 for S67).
Figure 5Sequence alignment for mature toxin sequences.
This figure displays the mature toxin sequences for S64 and S67 aligned with representative toxins found using a BLASTp search using the Arachnoserver toxin peptide database. Sequences were aligned using ClustalX 2.1 and visualized using JalView 2.7. The coloring makes use of the default ClustalX color scheme, which is a function of sequence identity and amino acid type.
Figure 6Ensemble
(top) and cartoon (bottom) representations of S64 (left) and S67 (right). The N and C termini are labeled in both the ensemble (top) and cartoon (bottom) representations of the structures of S64 (left) and S67 (right). The three disulfide bonds in the cartoon representations are also labeled. The ensembles represents the 20 structures with the lowest total energy out of 100 calculated structures. The cartoon representations show the lowest energy structure from each ensemble. Note that in the cartoon representation for S64 the third disulfide bond connects to the β sheet (red), not the strand (teal) in front of it.