Structure of scorpion toxin variant-3 at 1·2 Å resolution

doi:10.1016/0022-2836(92)90694-F

Journal of Molecular Biology

Volume 227, Issue 1, 5 September 1992, Pages 239-252

https://doi.org/10.1016/0022-2836(92)90694-F Get rights and content

Abstract

The crystal structure of the variant-3 protein neurotoxin from the scorpion Centruroides sculpturatus Ewing has been refined at 1·2 Å resolution using restrained least-squares. The final model includes 492 non-hydrogen protein atoms, 453 protein hydrogen atoms, eight 2-methyl-2,4-pentanediol (MPD) solvent atoms, and 125 water oxygen atoms. The variant-3 protein model geometry deviates from ideal bond lengths by 0·024 Å and from ideal angles by 3·6 °. The crystallographic R-factor for structure factors calculated from the final model is 0·192 for 17,706 unique reflections between 10·0 to 1·2 Å.

A comparison between the models of the initial 1·8 Å and the 1·2 Å refinement shows a new arrangement of the previously poorly defined residues 31 to 34. Multiple conformations are observed for four cysteine residues and an MPD oxygen atom. The electron density indicates that disulfide bonds between Cys12 and Cys65 and between Cys29 and Cys48 have two distinct side-chain conformations. A molecule of MPD bridges neighboring protein molecules in the crystal lattice, and both MPD enantiomers are present in the crystal. A total of 125 water molecules per molecule of protein are included in the final model with B-values ranging from 11 to 52 Å² and occupancies from unity down to 0·4. Comparisons between the 1·2 Å and 1·8 Å models, including the bound water structure and crystal packing contacts, are emphasized.

References (44)

R.J. Almassy et al.
Structure of variant-3 scorpion neurotoxin from Centruroides sculpturatus Ewing, refined at 1.8 Å resolution
J. Mol. Biol
(1983)
D.R. Babin et al.
Amino acid sequence of neurotoxin I from Centruroides sculpturatus Ewing
Arch. Biochem. Biophys
(1975)
F.C. Bernstein et al.
The Protein Data Bank: a computer-based archival file for macromolecular structures
J. Mol. Biol
(1977)
C.C.F. Blake et al.
X-ray studies of water in crystals of lysozyme
J. Mol. Biol
(1983)
W.A. Catterall
Membrane potential-dependent binding of scorpion toxin to the action potential Na⁺ ionophore
J. Biol. Chem
(1977)
F. Couraud et al.
Two types of scorpion toxin receptor sites, one related to the activation, the other to the inactivation of the action potential sodium channel
Toxicon
(1982)
H. Darbon et al.
Structural mapping of the voltage-dependent sodium channel
J. Biol. Chem
(1984)
H. Darbon et al.
Photoaffinity labelling of alpha and beta scorpion toxin receptors asssociated with rat brain sodium channels
Biochem. Biophys. Res. Commun
(1983)
J.C. Fontecilla-Camps et al.
Crystals of a toxic protein from the venom of the scorpion Centruroides sculpturatus Ewing: preparation and preliminary X-ray investigation
J. Mol. Biol
(1978)
J.C. Fontecilla-Camps et al.
Architecture of scorpion neurotoxins: a class of membrane-binding proteins
Trends Biochem. Sci
(1981)

C. Granier et al.

Review: the antigenic structure of a scorpion toxin

Mol. Immunol

(1989)

W.A. Hendrickson

Stereochemically restrained refinement of macromolecular structures

E. Jover et al.

Two types of scorpion neurotoxins characterized by their binding to two separate receptor sites on rat brain synaptosomes

Biochem. Biophys. Res. Commun

(1980)

G.N. Ramachandran et al.

Stereochemistry of polypeptide chain configurations

J. Mol. Biol

(1963)

G. Romey et al.

Scorpion neurotoxin: a presynaptic toxin which affects both Na⁺ and K⁺ channels in axons

Biochem. Biophys. Res. Commun

(1975)

K. Suguna et al.

Structure and refinement at 1·8 Å resolution of the aspartic proteinase from Rhizopus chinensis

J. Mol. Biol

(1987)

K.D. Watenpaugh et al.

Water structure in a protein crystal: rubredoxin at 1·2 Å resolution

J. Mol. Biol

(1978)

E. Zlotkin et al.

Proteins in scorpion venoms toxic to mammals and insects

Toxicon

(1972)

A.T. Brünger et al.

Crystallographic R factor refinement by molecular dynamics

Science

(1987)

M. Carson et al.

W.A. Catterall

Binding of scorpion toxin to receptor sites associated with sodium channels in frog muscle, correlation of voltage-dependent binding with activation

J. Gen. Physiol

(1979)

F. Couraud et al.

Binding of scorpion neurotoxins to chick embryonic heart cells in culture and relationship to calcium uptake and membrane potential

Biochemistry

(1980)

Cited by (80)

Analysis of binding residues between scorpion neurotoxins and D2 dopamine receptor: A computational docking study
2008, Computers in Biology and Medicine
We report the results on the computation of binding affinity, electrostatic free energies, contact free energies, secondary structures, stabilization centers and stabilizing residues of binding residues during the molecular docking of selected scorpion neurotoxins with D2 dopamine receptor. All the scorpion neurotoxins showed a good and satisfactory docking with the D2 receptor molecule except one neurotoxin 2SN3. We computed multiple alignment studies, solvent accessibility calculations, secondary structure analysis, stabilization centers and stabilizing residues before and after the docking process. Overall, we emphasize that the results obtained in this work will be very helpful in further enhancement of understanding the research on modeling and drug design with respect to the D2 dopamine receptor.
Investigations on the interactions of scorpion neurotoxins with the predicted structure of D1 dopamine receptor by protein-protein docking method. A bioinformatics approach
2008, Comptes Rendus - Biologies
Dopamine receptors play a critical role in the cell signalling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for disorders like Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors. Scorpion neurotoxins are unique source of structural templates from which new therapeutic agents might be developed. We report here the 3D structure of the human D1 dopamine receptor, predicted from primary sequence using computational techniques. The predicted structure of the human D1 dopamine receptor is used to understand the mechanism of interactions between scorpion neurotoxins through the protein–protein docking method. CHARMM force field was used for the energy minimization step before applying the docking method. To cite this article: C. Sudandiradoss et al., C. R. Biologies 331 (2008).
Density-based score for selecting near-native atomic models of unknown structures
2007, Journal of Structural Biology
We present a low-resolution density-based scoring scheme for selecting high-quality models from a large pool of lesser quality models. We use pre-configured decoy data sets that contain large numbers of models with different degrees of correctness to evaluate the performance of the strategy. We find that the scoring scheme consistently identifies one of the highest quality models for a wide variety of target structures, resolution ranges, and noise models. Tests with experimental data yield similar results.
X-ray Structure and Mutagenesis of the Scorpion Depressant Toxin LqhIT2 Reveals Key Determinants Crucial for Activity and Anti-Insect Selectivity
2007, Journal of Molecular Biology
Scorpion depressant β-toxins show high preference for insect voltage-gated sodium channels (Na_vs) and modulate their activation. Although their pharmacological and physiological effects were described, their three-dimensional structure and bioactive surface have never been determined. We utilized an efficient system for expression of the depressant toxin LqhIT2 (from Leiurus quinquestriatus hebraeus), mutagenized its entire exterior, and determined its X-ray structure at 1.2 Å resolution. The toxin molecule is composed of a conserved cysteine-stabilized α/β-core (core-globule), and perpendicular to it an entity constituted from the N and C-terminal regions (NC-globule). The surface topology and overall hydrophobicity of the groove between the core and NC-globules (N-groove) is important for toxin activity and plays a role in selectivity to insect Na_vs. The N-groove is flanked by Glu24 and Tyr28, which belong to the “pharmacophore” of scorpion β-toxins, and by the side-chains of Trp53 and Asn58 that are important for receptor site recognition. Substitution of Ala13 by Trp in the N-groove uncoupled activity from binding, suggesting that this region of the molecule is also involved in “voltage-sensor trapping”, the mode of action that typifies scorpion β-toxins. The involvement of the N-groove in recognition of the receptor site, which seems to require a defined topology, as well as in sensor trapping, which involves interaction with a moving channel region, is puzzling. On the basis of the mutagenesis studies we hypothesize that following binding to the receptor site, the toxin undergoes a conformational change at the N-groove region that facilitates the trapping of the voltage-sensor in its activated position.
Crystal structure of a highly acidic neurotoxin from scorpion Buthus tamulus at 2.2 Ǻ resolution reveals novel structural features
2006, Journal of Structural Biology
The crystal structure of a highly acidic neurotoxin from the scorpion Buthus tamulus has been determined at 2.2 Ǻ resolution. The amino acid sequence determination shows that the polypeptide chain has 64 amino acid residues. The pI measurement gave a value of 4.3 which is one of the lowest pI values reported so far for a scorpion toxin. As observed in other α-toxins, it contains four disulphide bridges, Cys12–Cys63, Cys16–Cys36, Cys22–Cys46, and Cys26–Cys48. The crystal structure reveals the presence of two crystallographically independent molecules in the asymmetric unit. The conformations of two molecules are identical with an r.m.s. value of 0.3 Å for their C^α tracings. The overall fold of the toxin is very similar to other scorpion α-toxins. It is a βαββ protein. The β-sheet involves residues Glu2–Ile6 (strand β1), Asp32–Trp39 (strand β3) and Val45–Val55 (strand β4). The single α-helix formed is by residues Asn19–Asp28 (α2). The structure shows a trans peptide bond between residues 9 and 10 in the five-membered reverse turn Asp8–Cys12. This suggests that this toxin belongs to classical α-toxin subfamily. The surface features of the present toxin are highly characteristic, the first (A-site) has residues, Phe18, Trp38 and Trp39 that protrude outwardly presumably to interact with its receptor. There is another novel face (N-site) of this neurotoxin that contains several negatively charged residues such as, Glu2, Asp3, Asp32, Glu49 and Asp50 which are clustered in a small region of the toxin structure. On yet another face (P-site) in a triangular arrangement, with respect to the above two faces there are several positively charged residues, Arg58, Lys62 and Arg64 that also protrude outwardly for a potentially potent interaction with other molecules. This toxin with three strong features appears to be one of the most toxic molecules reported so far. In this sense, it may be a new subclass of neurotoxins with the largest number of hot spots.
Three structurally related, highly potent, peptides from the venom of Parabuthus transvaalicus possess divergent biological activity
2005, Toxicon
The venom of South African scorpion Parabuthus transvaalicus contains a novel group of peptide toxins. These peptides resemble the long chain neurotoxins (LCN) of 60–70 residues with four disulfide bridges; however they are 58 residues long and have only three disulfide bridges constituting a new family of peptide toxins. Here we report the isolation and characterization of three new members of this mammal specific group of toxins. Dortoxin is a lethal peptide, bestoxin causes writhing in mice and altitoxin is a highly depressant peptide. Binding ability of these peptides to rat brain synaptosomes is tested. While the crude venom of P. transvaalicus enhances the binding of [³H] BTX to rat brain synaptosomes none of these individual toxins had a positive effect on binding. Although the primary structures of these toxins are very similar to birtoxin, their 3D models indicate significant differences. Dortoxin, bestoxin and altitoxin cumulatively constitute at least 20% of the peptide contained in the venom of P. transvaalicus and contribute very significantly to the toxicity of the venom of this medically important scorpion species. Therefore the amino acid sequences presented here can be used to make more specific and effective antivenins. Possible approaches to a systematic nomenclature of toxins are suggested.

View all citing articles on Scopus

^☆: This work was made possible by grants from the NIH (ES-02467) the UAB Comprehensive Cancer Center (CA-13148), NASA (NAGW-813) and the Alabama Research Institute.

^†: Present address: Department of Biochemistry, Cornell University, Ithaca, NY 14853, U.S.A.

View full text

Journal of Molecular Biology

ArticleStructure of scorpion toxin variant-3 at 1·2 Å resolution☆

Abstract

J. Mol. Biol

Arch. Biochem. Biophys

J. Mol. Biol

J. Mol. Biol

J. Biol. Chem

Toxicon

J. Biol. Chem

Biochem. Biophys. Res. Commun

J. Mol. Biol

Trends Biochem. Sci

Mol. Immunol

Biochem. Biophys. Res. Commun

J. Mol. Biol

Biochem. Biophys. Res. Commun

J. Mol. Biol

J. Mol. Biol

Toxicon

Crystallographic R factor refinement by molecular dynamics

Science

Binding of scorpion toxin to receptor sites associated with sodium channels in frog muscle, correlation of voltage-dependent binding with activation

J. Gen. Physiol

Binding of scorpion neurotoxins to chick embryonic heart cells in culture and relationship to calcium uptake and membrane potential

Biochemistry

Article
Structure of scorpion toxin variant-3 at 1·2 Å resolution☆