Solution structure of the variant‐3 neurotoxin from Centruroides sculpturatus Ewing

Abstract

The solution structure of the CsE-v3 neurotoxin from the venom of the North American scorpion Centruroides sculpturatus Ewing (CsE) has been determined by a hybrid refinement procedure that employed distance geometry and dynamical simulated annealing. Distance constraints deduced from the nuclear Overhauser effect spectroscopy data and torsion angle constraints deduced from the vicinal coupling constant data were used in the refinement procedure. A family of simulated annealing structures that showed no constraint violations was generated. The energy-minimized average structure exhibited root-mean-square deviations of 0.121 nm for the backbone and 0.182 nm for all atoms, with respect to this family. These studies confirm the previously qualitative NMR findings about the secondary structural features, viz. the presence of a short a-helix composed of residues 23-31 and an antiparallel P-sheet composed of the strands of residues 1-5, 45-50 and 36-42. A cluster of aromatic ring systems is located on one side of the protein. The solution and crystal structures have similar overall features, but show some minor differences.

Solution Structure of a Designed Amphipathic Antimicrobial Synthetic Peptide, PGAa

“…Three-dimensional structures were calculated using the hybrid distance geometry and dynamical simulated-annealing protocol, as previously described (20 -23), using the program X-PLOR 3.851 (Biosym/Molecular Simulations, Inc.). Fifty distance geometry substructures were generated using a subset of atoms in the peptide and followed an extensive refinement protocol described previously (21)(22)(23)(24). Finally, the 20 structures having the lowest energies out of fifty simulated-annealing were selected for structural analysis using PROCHECK (25), InsightII (Biosym/ Molecular Simulations, Inc.), and MOLMOL (26) programs.…”

Solution Structure, Backbone Dynamics, and Stability of a Double Mutant Single-chain Monellin

“…3. The angular order parameter for ⌽, ⌿, which indicates the degree of dihedral heterogeneity of structures, showed that the ⌽, ⌿ values of all residues except prolines and residues of Gly 30 -Thr 33 and Ile 8 in loop regions are close to 1, suggesting the well defined backbone angles of SCM DR (data not shown). The backbone torsion angles ⌽, ⌿ for the ͗SA͘ kr ensured that all of the ⌽, ⌿ values of final 20 structures were distributed in energetically favorable regions.…”

Automatic Assignment of NOESY Cross Peaks and Determination of the Protein Structure of a New World Scorpion Neurotoxin Using NOAH/DIAMOD

“…Two hydrophobic patches are observed in all structures, one hydrophobic patch is formed on one side of the protein by tyrosine 4, 36, and 41 and several other nonpolar residues nearby, and a second hydrophobic patch is observed on the other side of the protein by Cys15, Val16, Ala17, and Tyr20. Several scorpion toxins exhibit a "herringbone motif," consisting of orthogonally aligned aromatic side chains (32,36,37). This motif is also present in CsE-v5, as seen in Fig.…”

“…The backbone conformation of CsE-v5 contains an ␣-helix (residues 18 -26), an antiparallel ␤-sheet with three strands (residues 1-4, 32-36, and 39 -45), a ␤-bulge between residues 44 and 45, and several loops. The spatial orientation of the ␣-helix with respect to the ␤-sheet is stabilized by two disulfide bridges (Cys21-Cys40 and Cys25-Cys42) that connect the ␣-helix and the second ␤-strand to form a ␣␤DB motif (37). Note.…”