Structure of agkistrodotoxin in an orthorhombic crystal form with six molecules per asymmetric unit

Abstract

The structure of agkistrodotoxin crystallized under basic conditions has been determined at 2.8 A resolution by the molecular-replacement technique and refined to a crystallographic R factor of 0.194 and a free R factor of 0.260 with good stereochemistry. The molecular packing in the crystal differs from other PLA(2)s. The six molecules in the asymmetric unit form three dimers linked by Ca(2+) ions in a near-perfect six-ligand octahedral coordinating system. Extensive intermolecular hydrophobic interactions occur at the interfacial recognition site of each neurotoxin molecule, which provides an insight into phospholipase A(2)-membrane interactions. This hydrophobic interaction-induced molecular association along the interfacial recognition site suggests a self-protection mechanism of agkistrodotoxin.

Modulation of the Pharmacological Activities of Secretory Phospholipase A2 from Crotalus durissus cascavella Induced by Naringin

“…To interpret such envelopes, different dimer configurations of several sPLA2 crystallographic models found in PDB were superimposed, including dimers formed by symmetric mates (results not shown). Using the program CRYSOL to compare the experimental scattering data and the scattering intensities computed from these models, the lowest discrepancy was found for the dimer made of chains A and E of agkistrodotoxin from Agkistrodon halys pallas venom (PDB ID 1BJJ) [ 27 ]. Analysis of protein assemblies and interfaces using the PISA web server suggested that assembly of chains A and E of agkistrodotoxin is stable in solution, showing one of the highest ΔdissG, equal to 6.7 kcal/mol.…”

Insights into the role of oligomeric state on the biological activities of crotoxin: Crystal structure of a tetrameric phospholipase A2formed by two isoforms of crotoxin B fromCrotalus durissus terrificusvenom

“…The CB1/CB2 tetrameric structure is formed by the association of the C/A and B/D dimers. However, this does not occur with the agkistrodoxin from Agkistrodon halys Pallas (PDB code 1BJJ),43 a hexameric neurotoxic Asp49‐PLA 2 which is only stable in solution as a dimer, according the program PISA 29. In contrast to CB1/CB2 model, the quaternary assembly of the agkistrodotoxin is apparently stabilized by Ca 2+ ions located in the contact interfaces of the hexameric structure.…”

Phospholipases A2 Protein Structure and Natural Products Interactions in Development of New Pharmaceuticals

“…Interpretation of native and naringin-tretated PLA2 SAXS models were performed by the superposition of crystallographic models of several PLA2 found in the Protein Data Bank (PDB) using the program SUPCOMB (Kozin, 2001). The smallest discrepancy (Chi) calculated by the program CRYSOL (Svergun et al, 1995) between experimental data and PLA2 PDB models was achieved to the dimer composed of chains A and E of agkistrodotoxin (PDB ID 1BJJ) (Tang, Zhou, Lin, 1999).…”

“…For this purpose, the structural optimization of the natural compounds are initially achieved using the quantum chemical AM1 method (Tang et al, 1999) implemented in the BioMedCache program with default values for the convergence criteria. Docking calculations are performed with the GOLD 4.0 program (Jones et al, 1997) to obtain the in silica affinity of natural compounds to the target proteins, herein, sPLA2 from snake venoms.…”