Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution.

Atomic coordinates determined from a 2.5 Å electron density map are given for erabutoxin b, a sea snake venom postsynaptic neurotoxin. The principal structural features, anti-parallel β pleated sheet, β bulge and β bends are described. The erabutoxin b structure is discussed as structural prototype of this class of homologous curare-mimetic neurotoxins from both land and sea snakes.     

Erabutoxin b. Initial protein refinement and sequence analysis at 0.140-nm resolution

The crystal structure of the protein postsynaptic neurotoxin, erabutoxin b, has been refined at 0.140-nm resolution (R = 0.22) by restrained least-squares and interactive computer graphics. The study has established complete structural identity of the two sea-snake venom toxins, erabutoxin b and neurotoxin b, isolated from Laticauda semifasciata snakes taken in different Pacific Ocean waters. Two chemical-sequence inversion errors in erabutoxin b have been discovered during refinement, corrected and subsequently confirmed in both erabutoxin b and erabutoxin a by chemical analysis. The correct sequences are His6-Gln7, hitherto unsuspected, and Ser18-Pro19. The sequence correction His6-Gln7 explains the anomalous results of 1H NMR solution studies and those of early chemical modification experiments, which were in conflict with the previously published three-dimensional structure of erabutoxin b. On refinement, the five-stranded beta sheet described earlier is now shown to be discontinuous, split into a two-stranded beta loop and a three-stranded beta sheet. Unique features of the Pro44-Gly49 peripheral segment have now been identified. 51 water molecule positions have been located.     

Three-dimensional solution structure of a curaremimetic toxin from Naja nigricollis venom: a proton NMR and molecular modeling study.

The solution conformation of toxin alpha from Naja nigricollis (61 amino acids and four disulfides), a snake toxin which specifically blocks the activity of the nicotinic acetylcholine receptor (AcChoR), has been determined using nuclear magnetic resonance spectroscopy and molecular modeling. The solution structures were calculated using 409 distance and 73 dihedral angle restraints. The average atomic rms deviation between the eight refined structures and the mean structure is approximately 0.5 A for the backbone atoms. The overall folding of toxin alpha consists of three major loops which are stabilized by three disulfide bridges and one short C terminal loop stabilized by a fourth disulfide bridge. All the disulfides are grouped in the same region of the molecule, forming a highly constrained structure from which the loops protrude. As predicted, this structure appears to be very similar to the 1.4-A resolution crystal structure of another snake neurotoxin, namely, erabutoxin b from Laticauda semifasciata. The atomic rms deviation for the backbone atoms between the solution and crystal structures is approximately 1.7 A. The minor differences which are observed between the two structures are partly related to the deletion of one residue from the chain of toxin alpha. It is notable that, although the two toxins differ from each other by 16 amino acid substitutions, their side chains have an essentially similar spatial organization. However, most of the side chains which constitute the presumed AcChoR binding site for the curaremimetic toxins are poorly resolved in toxin alpha.(ABSTRACT TRUNCATED AT 250 WORDS)     

Erabutoxin b. Structure/function relationships following initial protein refinement at 0.140-nm resolution

A study has been made, following high-resolution refinement at 0.14 nm, of the structure of erabutoxin b, prototype postsynaptic neurotoxin from snake venom. The detailed patterns of intramolecular van der Waal's interactions have been determined. From information, hitherto unavailable, about atomic temperature parameters, the relative mobilities in different regions of the molecule have been estimated. A detailed model of structure/function relationships in these neurotoxins, which bind to the acetylcholine receptor, has thus been established: the probable dynamic mode of toxin-receptor binding is described. The model identifies, and the binding mode depends on a unique structural feature of these protein toxins: the hydrophobic 'Trp' cleft. Charge-charge interactions are implicated in initial toxin orientation on the receptor surface. Possible reactive-site extension in short-chain toxins is described. Modifications in binding mode of long-chain toxins are considered. The relative mobilities of antigenic site residues are discussed.     

The crystal structure of alpha-bungarotoxin at 2.5 A resolution: relation to solution structure and binding to acetylcholine receptor

We report collection of 2.5 A resolution X-ray diffraction data from newly grown crystals of the rare 'small unit cell' form of the long snake neurotoxin, alpha-bungarotoxin. The previous model of the molecule has been rebuilt, and refined using least-square methods to a crystallographic residual of 0.24 at 2.5 A resolution. alpha-Bungarotoxin's crystal structure is compared with the crystal structures of two other snake neurotoxins (cobratoxin and erabutoxin), and with its solution structure inferred from spectroscopic studies. Significant differences include less beta-sheet in bungarotoxin's crystal structure than in solution, or in the crystal structures of other neurotoxins, and an unusual orientation in the crystal of the invariant tryptophan. The functional, binding surface of bungarotoxin is described; it consists primarily of hydrophobic and hydrogen-bonding groups and only a few charged side-chains. The structure is compared with experimental binding parameters for neurotoxins.     

Modeling the third loop of short-chain snake venom neurotoxins: roles of the short-range and long-range interactions

The influence of long-range interactions on local structures is an important issue in understanding protein folding process and protein structure stability. Using short-chain snake venom neurotoxin as a model system, we have studied the conformational properties of eight different loop III sequences either in the environment of one of the short-chain neurotoxin, erabutoxin b (PDB ID 1nxb), or in free state by Monte Carlo simulated annealing method. The surrounding protein structure was found to be crucial in stabilizing the loop conformation. Although all the eight peptides prefer type V beta turn in solution, three of them (KPGI, KPGV, KSGI) turn to type II beta turn and the other five (KKGI, KKGV, KNGI, KQGI, and KRGV) are confined to more rigid type V beta turn conformation in the protein structure. Using flexible tetra-glycine-peptide to screen the backbone conformational space in the protein environment also validates the results. This study shows that long-range interactions do contribute to the stability and the types of conformation for a surface loop in protein, while short-range interactions may only provide candidate conformations, which then have to be filtered by the long-range interactions further.     

The 1H nuclear-magnetic-resonance spectra of Neurotoxin I and cardiotoxin Vii4 from Naja mossambica mossambica.

Two toxins from the venom of Naja mossambica mossambica, neurotoxin I and cardiotoxin VII4, were investigated in aqueous solution by high-resolution 1H nuclear magnetic resonance (NMR) techniques at 360 MHz. The spectral characterization of the proteins included determination of the number of slowly exchanging amide protons which can be observed in 2H2O solution, measurement of the amide proton chemical shifts and exchange rates, characterization of the aromatic spin systems and the internal mobilities of aromatic rings, and studies of the pH dependence of the NMR spectra. For numerous resonances of labile and non-labile protons quite outstanding pH titration shifts were observed. It is suggested that these NMR parameters provide a useful basis for comparative structural studies of different proteins in the large group of homologous snake toxins. As a first application the NMR data presently available in the literature on neurotoxin II from Naja naja oxiana, toxin alpha from Naja nigricollis and erabutoxin a and b from Laticauda semifasciata have been used to compare these three proteins with neurotoxin I from Naja mossambica mossambica. This preliminary comparative study provides evidence that the same type of spatial structure prevails for these four homologous neurotoxins and that the folding of the backbone corresponds quite closely to that observed in the crystal structure of erabutoxin b. A second application is the comparison of cardiotoxin VII4 from Naja mossambica mossambica with the neurotoxins. The experimental data indicate that the folding of the polypeptide backbone is closely similar, but that the cardiotoxin molecule is markedly more flexible than the neurotoxins.     

The isolation, properties and amino acid sequence of erabutoxin c, a minor neurotoxic component of the venom of a sea snake Laticauda semifasciata

Erabutoxin c, a minor neurotoxic component of the venom of a sea snake Laticauda semifasciata, was isolated in pure form by repeated column chromatography on CM-cellulose columns. The toxin was crystallizable and monodisperse in rechromatography, disc electrophoresis and isoelectric focusing (isoelectric point, pH9.23-9.25). The molecular weight of the toxin, as estimated by gel filtration, was 7000. The toxin showed the same lethal activity to mice (0.13mug/g body wt., intramuscular injection) and the same effect on isolated frog muscle as erabutoxins a and b, the main toxic components of the venom. The toxin inhibited the acetylcholine contracture but not the potassium chloride contracture of muscle. Erabutoxin c consisted of 62 amino acid residues, containing one fewer lysine and one more histidine than erabutoxin a and one fewer lysine and one more aspartic acid (or asparagine) than erabutoxin b. Erabutoxin c was reduced, S-carboxymethylated and hydrolysed with trypsin. The only fragment different from the corresponding fragments from erabutoxin b was hydrolysed further with pepsin. One of the peptic fragments, which was assumed to have the aspartic acid (or asparagine) residue in question at the C-terminal end, was treated with carboxypeptidase A. The C-terminal residue was found to be an asparagine. It was therefore concluded that erabutoxin c was [51-asparagine]-erabutoxin b.     

1.9-A resolution structure of fasciculin 1, an anti-acetylcholinesterase toxin from green mamba snake venom.

The crystal structure of fasciculin 1, a potent acetylcholinesterase inhibitor from green mamba snake venom, has been solved by the multiple isomorphous replacement method complemented with anomalous scattering and subsequently refined at 1.9-A resolution. The overall structure of fasciculin is similar to those of the short alpha-neurotoxins and cardiotoxins, with a dense core rich in disulfide bridges and three long loops disposed as the central fingers of a hand. A comparison of these three prototypic toxin types shows that fasciculin 1 has structural features that are intermediate between those of the other two molecules. Its core region, which can be defined as a continuous stretch of conserved residues, is very similar to that of erabutoxin b, whereas the orientation of its long loops resembles that of cardiotoxin VII4. This result introduces a new element in the study of phylogenetic relationships of snake toxins and suggests that, after divergency from an ancestral gene, convergent evolution may have played an important factor in the evolution of these proteins. In fasciculin 1, several arginine and lysine residues are well ordered and relatively exposed to the solvent medium and may play a role in the binding to the peripheral site of acetylcholinesterases.     

Separation of intermediates in the refolding of reduced erabutoxin b by analytical isoelectric focusing in layers of polyacrylamide gel

Isoelectric focusing in a thin layer of polyacrylamide gel is shown to be a suitable method for the resolution of intermediates trapped during the refolding process of reduced cystine-containing proteins. The method has been applied to the well-characterized snake neurotoxin erabutoxin b. An explanation is offered for the relatively low rate of refolding of this polypeptide.     

Identification of a novel family of proteins in snake venoms. Purification and structural characterization of nawaprin from Naja nigricollis snake venom

The three-dimensional structure of nawaprin has been determined by nuclear magnetic resonance spectroscopy. This 51-amino acid residue peptide was isolated from the venom of the spitting cobra, Naja nigricollis, and is the first member of a new family of snake venom proteins referred to as waprins. Nawaprin is relatively flat and disc-like in shape, characterized by a spiral backbone configuration that forms outer and inner circular segments. The two circular segments are held together by four disulfide bonds, three of which are clustered at the base of the molecule. The inner segment contains a short antiparallel beta-sheet, whereas the outer segment is devoid of secondary structures except for a small turn or 310 helix. The structure of nawaprin is very similar to elafin, a human leukocyte elastase-specific inhibitor. Although substantial parts of the nawaprin molecule are well defined, the tips of the outer and inner circular segments, which are hypothesized to be critical for binding interactions, are apparently disordered, similar to that found in elafin. The amino acid residues in these important regions in nawaprin are different from those in elafin, suggesting that nawaprin is not an elastase-specific inhibitor and therefore has a different function in the snake venom.     

Sequence characterization of venom toxins from Thailand cobra

Several toxins with distinct pharmacological properties were isolated from the venom of Thailand cobra (Naja naja siamensis) by cation-exchange chromatography. Two neurotoxins and one basic toxin with cardiotoxic activity were further purified and sequenced. The neurotoxins characterized were closely similar to the previously reported long- and short-chain neutrotoxins. The complete sequences of one minor neurotoxin and one cardiotoxin analogue were determined with the automatic protein sequencer in non-stop single runs of Edman degradation coupled with C-terminal sequence determination with carboxypeptidase digestion. The minor neurotoxin consists of 62 amino-acid residues with 8 cysteine residues and is found to be almost identical to cobrotoxin, a major toxic component of Formosa cobra (Naja naja atra). The sequence comparison of the 60-residue cardiotoxin with other reported cytotoxins of snake venoms indicates that 8 cysteine residues at the positions 3, 14, 21, 38, 42, 53, 54, and 59 are invariant among all sequences, with only two conservative changes at other positions along the sequence. The upshot of this report exemplified the facile sequence analysis of venom toxins by the application of pulsed-liquid phase protein sequencer and also revealed new analogues of a minor neurotoxin and one major cardiotoxin reported previously on the same species of Thailand cobra.     

Crystal structure determination of alkaline haemorrhagin AaH III from snake venom ofAgkistrodon acutus

The haemorrhagin AaH III isolated from the snake venom ofAgkistrodon acutus is one of the few alkaline ones in snake venoms. Its crystals belong to space group P2₁2₁2₁ witha = 9. 573 4 nm,b = 4. 996 7 nm andc = 4.728 8 nm. Its crystal structure was determined by the molecular replacement method according to the model of metalloproteinase Adamalysin II from eastern rattlesnake venom. The AaH III structure has been refined by PROLSQ. The finalR factor was 0.254 and the RMS deviations of bond lengths and angles were 0.001 8 nm and 1.5°. The structure comparison suggested that AaH III has a similar structure to other snake venom zinc-metalloproteinases. They all belong to matrix metalloproteinases super-family.     

Cloning and sequence analysis of the cDNA encoding a snake neurotoxin precursor

A recombinant plasmid has been constructed containing a sequence of 186 nucleotides encoding a potent neurotoxin found in the venom of the sea-snake Laticauda semifasciata and designated as erabutoxin a. This sequence is flanked, in the upstream region, by a sequence of 60 nucleotides encoding a hydrophobic peptide fragment presumably involved in the secretion process of the neurotoxin. The sequence coding for the toxin ends with a termination codon which is followed by a 3'-untranslated sequence of approximately 240 nucleotides (excluding the poly(A) tract).     

Conformational and functional variability supported by the BPTI fold: solution structure of the Ca2+ channel blocker calcicludine

Calcicludine, a 60-amino acid protein isolated from the green mamba venom, has been recently identified as blocking a large set (i.e., L-, N- and P-type) of Ca2+ channels. The three-dimensional structure of calcicludine has been determined by NMR and molecular modeling using a data set of 723 unambiguous and 265 ambiguous distance restraints, as 33 phi and 13 chi1 dihedral angle restraints. Analysis of the 15 final structures (backbone root-mean-square deviation = 0.6 A) shows that calcicludine adopts the Kunitz-type protease inhibitor fold. Its three-dimensional structure is similar to that of snake K+ channel blockers dendrotoxins. Conformational differences with protease inhibitors and dendrotoxins are localized in the 3(10) helix and loop 1 (segments 1-7 and 10-19), the extremity of the beta-hairpin (segment 27-30), and loop 2 (segment 39-44). These regions correspond to the functional sites of bovine pancreatic trypsin inhibitor (BPTI) and dendrotoxins. The positioning of the N-terminal segment 1-7 relative to the rest of the protein is characteristic of calcicludine. The involvement of this segment and the positively charged K31 at the tip of the beta-hairpin in the biological activity of calcicludine is discussed.     

Studies on the subunit structure of textilotoxin, a potent neurotoxin from the venom of the Australian common brown snake (Pseudonaja textilis)

Textilotoxin is a presynaptic neurotoxin from the venom of the Australian common brown snake, Pseudonaja textilis. It has the highest lethality and is structurally the most complex of any known snake venom neurotoxin. It was resolved into its five non-covalently linked subunits in a single step by reverse-phase HPLC. Two of the subunits were identical. The N-terminal amino-acid sequence and amino-acid composition of each subunit were determined. Subunit A was the only one found to possess phospholipase A activity. Separation of textilotoxin into its subunits was reversible and reformed textilotoxin had the same Mr and lethality in mice as the native toxin. Experiments with various unnatural combinations of subunits have led to interesting variations in lethality and Mr of the resulting complexes.     

Snake toxin secondary structure predictions. Structure activity relationships

Modified Chou &; Fasman (1974a,b) secondary structure prediction rules have been successfully applied to the 57 snake venom toxins described as being neurotoxic or cytotoxic. Despite the different toxicities involved, a common distribution of secondary structure was detected throughout these toxins. The results also highlight the contrasts between short and long neurotoxins, and neurotoxins and cytotoxins. From comparisons of the typical structure of each toxin group with the known X-ray data an erabutoxin b and Philippines sea-snake toxin b, regions that dictate neurotoxicity or cytotoxicity can be tentatively identified. These deductions are discussed with regard to known chemical properties of these molecules. Similarly, the relevance of the differences between short and long neurotoxins to the superior binding of the latter to the cholinergic receptor is considered.It appears that the cytotoxins and neurotoxins are variations on a central toxic theme, but have differing specificities, whose origin can be traced to certain regions of the toxin in question.     

Crystal structure determination of alkaline haemorrhagin AaHⅢ from snake venom of Agkistrodon acutus

The haemorrhagin AaH III isolated from the snake venom ofAgkistrodon acutus is one of the few alkaline ones in snake venoms. Its crystals belong to space group P2₁2₁2₁ witha = 9. 573 4 nm,b = 4. 996 7 nm andc = 4.728 8 nm. Its crystal structure was determined by the molecular replacement method according to the model of metalloproteinase Adamalysin II from eastern rattlesnake venom. The AaH III structure has been refined by PROLSQ. The finalR factor was 0.254 and the RMS deviations of bond lengths and angles were 0.001 8 nm and 1.5°. The structure comparison suggested that AaH III has a similar structure to other snake venom zinc-metalloproteinases. They all belong to matrix metalloproteinases super-family. Project supported by the Chinese Academy of Sciences, State Key Laboratory of Biomacromolecules and State Education Commission of China.     

Lipid-protein interactions. A comparative study of the binding of cardiotoxins and neurotoxins to phospholipid vesicles

It has recently been shown that cardiotoxin II from Naja mossambica mossambica specifically interacts with negatively charged phospholipids (Dufourcq, J. and Faucon, J.F. (1978) Biochemistry 17, 1170–1176). In order to investigate whether or not short neurotoxins give rise to similar interactions, four techniques have been used, namely intrinsic fluorescence, fluorescence polarization of 1,6-diphenylhexatriene, turbidity measurements and release of 6-carboxyfluorescein trapped inside single shelled vesicles.Neurotoxin III from Naja mossambica mossambica and neurotoxin I from the venom of the scorpion Androctonus australis Hector, specifically interact with negatively charged phospholipids leading to changes in tryptophan fluorescence and to a decrease of the fluidity of the bilayer. Cardiotoxin II from the same snake venom gives similar results. On the other hand, it seems that either a very weak or no interaction at all occurs in the case of neurotoxin I from the same Naja venom.There are important differences in the behaviour of cardiotoxin and neurotoxins: (i) neurotoxins lead to only weak release of 6-carboxyfluorescein from lipid vesicles, whereas cardiotoxin II induces fast and quantitative escape of the dye and then a general breakdown of the vesicular structure; (ii) binding of neurotoxins can be easily reversed by 100–200 mM NaCl or less than 1 mM Ca²⁺ and so it is essentially electrostatic, whereas binding of cardiotoxin II seems to involve some hydrophobic contribution.The short neurotoxins and cardiotoxins from snake venom having a great homology in sequence, their differences on binding properties are discussed in terms of changes in a particular area of the sequence.