Classification of elapid snake neurotoxins and cytotoxins according to chain length: Evolutionary implications

Summary The amino acid sequences of the 139 homologous short neurotoxins, long neurotoxins and cytotoxins so far characterised from elapid snake venoms were compared on the basis of the amino acid deletion/insertion events that have occurred during evolution. Systematic grouping of the toxins according to similarity suggests that the short neurotoxins resemble the cytotoxins more closely than they do the long neurotoxins. The significance of this finding is discussed in relation to the methodology, the conformations of the toxins (as represented by circular dichroism spectra) and the outcome of the study that would have been obtained had more traditional methods been used. It appears probable that the cytotoxins evolved relatively recently from neurotoxic ancestors.     

Intermembrane exchange of lipids induced by cobra venom cytotoxins

Interaction between cytotoxin Vc5 from cobra venom and model membranes from phosphatidylcholine and phosphatidyl acid was investigated by means of 1H-NMR, ESR spin probes and microcalorimetric methods. Cytotoxic was shown to induce in the membrane formation of non-bilayer structures, to increase the membrane permeability and to produce the intermembrane exchange with lipids.     

The fusogenic properties of the cytotoxins of cobra venom in a model membrane system

By the methods of EPR spinal probes, energy migration of triplet excitation and NMR spectroscopy, the structural changes on hydrocarbon region of membranes, the changes in dynamic state of water of lipid hydrate jacket, the intermembrane lipid material exchange and fusion of membranes induced by cytotoxins of cobra venom have been studied. The sequence of events preceded the membrane fusion is suggested. The probability of membrane fusion has been shown not to be determined by fusogenic agent structure only, but much it depends on lipid composition of membranes.     

Effect of phospholipase A on actions of cobra venom cardiotoxins on erythrocytes and skeletal muscle

The actions of two phospholipase-free cardiotoxins from the venom of the cobra Naja naja siamensis were compared to phospholipase-contaminated cardiotoxins in terms of their ability to lyse human erythrocytes and to depolarize and contract skeletal muscle. The presence of 3–5% (w/w) phospholipase caused a 20–30-fold increase in the haemolytic activity of the two cardiotoxins, the pure cardiotoxins being virtually without haemolytic activity at 10^?7-10^?6 M. Phospholipase contamination did not enhance the ability of the cardiotoxins to cause contracture of chick biventer cervicis muscles and it caused less than a 2-fold increase in the depolarizing activity of the cardiotoxins on cultured skeletal muscle. Phospholipase-free cardiotoxins were about 10–20-times more active on cultured skeletal muscle fibres than on erythrocytes. These results support the hypothesis that some cardiotoxins have more affinity for the membranes of excitable cells than for those of other cells such as erythrocytes.     

The influence of cytotoxins from Central Asian cobra venom and melittin from bee venom on the thermodynamic properties of phospholipid bilayer

The interaction of cytotoxin Vc1 and Vc5 from Central Asian cobra and melittin from the bee venom with multilayer liposomes prepared from dimiristoylphosphatidylcholine with an addition of phosphatidic acid have been studied by the method of differential scanning calorimetry. Incorporation of Vc1, Vc5 and melittin into the lipid resulted in pronounced changes in the thermodynamic properties of the lipid. Polypeptides studied induced lateral phase separation in the lipid. Interaction between molecules of the toxins and the lipid resulted in the formation of a new lipid phase characterized by a higher melting temperature and lower phase transition enthalpy.     

血清白蛋白在多聚阳离子－壳聚糖共混材料表面的构象变化及其与细胞生长的关系

用L-多聚赖氨酸、聚乙烯亚胺及L-多聚鸟氨酸三种多聚阳离子对壳聚糖进行共混修饰,制备了三种共混材料.在这些材料表面吸附了血清白蛋白,并利用圆二色(CD)光谱研究了白蛋白吸附到材料表面后的构象变化.结果显示,与天然状态相比,白蛋白吸附到共混材料表面后,其α-螺旋、β-折叠及无规则卷曲的含量均发生了明显改变.通过研究MC3T3-E1细胞在这些材料表面的生长情况,发现细胞的增殖与血清白蛋白的构象变化有一定关系,在吸附的白蛋白构象与天然构象最接近的共混材料表面,MC3T3-E1细胞增殖水平最高.     

Interaction of central Asian cobra (Naja naja oxiana Eichwald) venom cytotoxins with phospholipase D

Effect of cytotoxins from the venom of Naja naja oxiana Eichwald on the hydrolytic function of phospholipase D has been further analysed. Cytotoxins in the absence of Ca2+ activated the enzyme, whereas in its presence they inhibited it. Inhibition is shown to be related to the interaction of cytotoxins with the enzyme which blocks the absorption of the enzyme at the surface of the substrate phase. Synergism in the action of cytotoxin and phospholipase D was not noticed.     

Separation and structure-function studies of Taiwan cobra cardiotoxins

Six cardiotoxins (CTXs) and one cardiotoxin-like basic protein (CLBP) from Naja naja atra (Taiwan cobra) venom were separated by a SP-Sephadex C-25 column. CTXn and CTXI were well separated by eluting with ammonium acetate buffer, and the separation of CLBP from CTXIV and CTXV mixtures was achieved using sodium phosphate buffer. These findings suggest a differential interaction of CTXs with the chromatographic matrix using different buffer systems. Chemical modification studies on cationic residues of CTXI suggested that there was no single lysine or arginine residue exclusively responsible for its biological activity. Moreover, it was found that the cytotoxicity and hemolytic sites of CTXI could be dissociated by chemical modifications. It suggests the potentiality for preparing toxin derivatives in which a specific activity is retained.     

The evolution of structural genomics

Structural genomics began as a global effort in the 1990s to determine the tertiary structures of all protein families as a response to large-scale genome sequencing projects. The immediate outcome was an influx of tens of thousands of protein structures, many of which had unknown functions. At the time, the value of structural genomics was controversial. However, the structures themselves were only the most obvious output. In addition, these newly solved structures motivated the emergence of huge data science and infrastructure efforts, which, together with advances in Deep Learning, have brought about a revolution in computational molecular biology. Here, we review some of the computational research carried out at the Protein Data Bank Japan (PDBj) during the Protein 3000 project under the leadership of Haruki Nakamura, much of which continues to flourish today.     

Compactness of protein molten globules: temperature-induced structural changes of the apomyoglobin folding intermediate

Apomyoglobin undergoes a two-step unfolding transition when the pH is lowered from 6 to 2. The partly folded intermediate (1) state at pH 4 and low ionic strength has properties of a molten globule. We have studied structural features of this state, its compactness, content of secondary structure, and specific packing of aromatic side chains, using dynamic light scattering, and small-angle X-ray scattering and far- and near-ultraviolet circular dichroism spectroscopy. Particular attention was paid to temperature-dependent structural changes. The results are discussed with reference to the native-like (N) state and the highly unfolded (U) state. It turned out that the I-state is most compact near 30°C, having a Stokes radius 20% larger and a radius of gyration 30% larger than those of the N-state. Both cooling and heating relative to 30°C led to an expansion of the molecule, but the structural changes at low and high temperatures were of a different kind. At temperatures above 40°C non co-operative melting of structural elements was observed, while the secondary structure was essentially retained on cooling. The results are discussed in context with theoretical predictions of the compactness and the stability of apomyoglobin by Alonso et al. [Alonso, D. O. V., Dill, K, A., and Stigler, D. (1991) Biopolymers 31:1631–1649]. Comparing the I-state of apomyoglobin with the molten globules of -lactalbumin and cytochrome c, we found that the compactness of the molten globule states of the three proteins decreases in the order -lactalbumin > apocytochrome c > apomyoglobin. While -lactalbumin and cytochrome c are rather homogeneously expanded, apomyoglobin exhibits a non uniform expansion, since two structural domains could clearly be detected by small-angle X-ray scattering.Abbreviations CD circular dichroism - DLS dynamic light scattering - SAXS small-angle X-ray scattering - N, 1, and U the native, intermediate, and unfolded forms of apomyoglobin Correspondence to: G. Damaschun     

The cytotoxins of cobra venoms. Isolation and partial characterization.

Eight basic proteins which lyse virus-transformed mouse fibroblasts in culture have been isolated from the venoms of six Asian Naja naja subspecies. These cytotoxins appear to represent an homologous series of proteins, all within the molecular weight range of 7000-8000. They have been divided into three arbitrary types on the basis of amino acid composition, electrophoretic mobilities and elution order upon ion-exchange chromatography. The rate at which the toxins effect cell lysis: (1) appears to be a function of the basicity of each toxin; (2) is dependent upon toxin concentration; (3) is temperature dependent; and (4) is inhibited by heparin sulfate. In view of the physical changes, which the cell undergoes during lysis and of the various factors which affect the action of these proteins, it is proposed that interaction of membrane receptors with the toxin, leading to alteration of cell membrane structure, is the principal event which ultimately leads to the disruption of the cell.     

The evolution of structural databases

Starting with the Protein Data Bank (PDB) as a common ancestor, the evolution of structural databases has been driven by the rapprochement of the structural world and the practical applications. The result is an impressive number of secondary structural databases that is welcomed by structural biologists and bioinformaticians but runs the risk of producing an embarrassment of riches among non-specialist users. Given that any profit depends on the number of customers, efficient interfaces between many structural data banks must be available to make their contents easily accessible. Increasing the information content of central structural repositories might be the best way to guide users through the many, sometimes overlapping databases.     

The SARS-CoV heptad repeat 2 exhibits pH-induced helix formation

The heptad repeats 1 and 2 of SARS-CoV spike, termed HR1 and HR2, play critical roles in viral entry. Moreover, HR1 and HR2 derived free peptides are inhibitors of SARS-CoV entry. In this work we used circular dichroism to show that HR2 helix formation is induced at pH 5, the pH of the endosome. In addition, we demonstrate that the HR2 helix is further stabilized at physiological ionic strengths. Together, these observations provide new insight into the mechanism of SARS-CoV entry and suggest that HR2 may be an attractive target for therapeutic intervention.     

The effect of non-enzymatic glycation on the unfolding of human serum albumin

We monitored the unfolding of human serum albumin (HSA) and glycated human serum albumin (gHSA) subjected to guanidine hydrochloride (GndHCl) by using fluorescence and circular dichroism (CD) spectroscopy. A two-state model with sloping baselines best described the Trp-214 fluorescence unfolding measurements, while a three-state model best described the far-UV CD unfolding data. Glycation of HSA increased the [D](50%) point by approximately 0.20M. This corresponded to an increase in the free energy of unfolding of gHSA relative to HSA of 2.6kJ/mol. The intrinsic fluorescence of Trp-214 in gHSA is 0.72 of that of HSA and the far-UV CD spectrum of gHSA is nearly identical to that of HSA. These results showed that glycation altered the local structure around Trp-214 while not significantly impacting the secondary structure, and this alteration translated into an overall change in the stability of gHSA compared to HSA.     

Amino-acid sequences of four cytotoxins (cytotoxins I, II, III and IV) purified from the venom of the Thailand cobra, Naja naja siamensis

Four cytotoxins, designated as cytotoxins I, II, III and IV, were isolated from the venom of the Thailand cobra (Naja naja siamensis) by gel filtration on Sephadex G-75 followed by CM-cellulose chromatography. The amino-acid sequences were determined by a combination of conventional methods. Cytotoxins I, II, III and IV were each composed of 60 amino-acid residues and their molecular weights were calculated to be 6693, 6646, 6709 and 6739, respectively. The amino-acid sequences were compared with those of cytotoxins from other cobra venoms already sequenced.     

Effects of neutral salts on the circular dichroism spectra of ribonuclease a and ribonuclease s

The circular dichroism (CD) spectra of ribonuclease A, ribonuclease S, and N-acetyltyrosineamide were recorded as a function of pH in the presence of various concentrations of inorganic salts. Above pH 9.0 salting-in of tyrosine residues increases their intramolecular associations. This association enhances the contribution from these residues to the CD spectrum leading to an apparent titration curve that is shifted toward lower pH. The data indicate that unfolding of ribonuclease A and S by inorganic salts does not begin with disrupting existing electrostatic interactions. But, as the unfolding process progresses, disruption of electrostatic interactions may take place. This is consistent with our previous calorimetric studies which suggest that unfolding of ribonuclease A by salts proceeds initially by energetically favorable solvation of the folded protein. An increase in ellipiticity at 275 nm of partially unfolded protein in salt was observed as the pH was changed from 7.0 to 4.0. This observation may suggest that the isothermal unfolding of the protein by salts at low pH proceeds through an intermediate step which involves histidine residues and causes a conformational change in the tyrosine's asymmetric environment.     

A host-specific factor is necessary for efficient folding of the autotransporter plasmid-encoded toxin

Autotransporters are the most common virulence factors secreted from Gram-negative pathogens. Until recently, autotransporter folding and outer membrane translocation were thought to be self-mediated events that did not require accessory factors. Here, we report that two variants of the autotransporter plasmid-encoded toxin are secreted by a lab strain of Escherichia coli. Biophysical analysis and cell-based toxicity assays demonstrated that only one of the two variants was in a folded, active conformation. The misfolded variant was not produced by a pathogenic strain of enteroaggregative E. coli and did not result from protein overproduction in the lab strain of E. coli. Our data suggest a host-specific factor is required for efficient folding of plasmid-encoded toxin.     

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c

The first structure for a member of the DUF3349 (PF11829) family of proteins, Rv0543c from Mycobacterium tuberculosis, has been determined using NMR-based methods and some of its biophysical properties characterized. Rv0543c is a 100 residue, 11.3 kDa protein that both size exclusion chromatography and NMR spectroscopy show to be a monomer in solution. The structure of the protein consists of a bundle of five α-helices, α1 (M1 – Y16), α2 (P21 – C33), α3 (S37 – G52), α4 (G58 – H65) and α5 (S72 – G87), held together by a largely conserved group of hydrophobic amino acid side chains. Heteronuclear steady-state {¹H}–¹⁵N NOE, T₁, and T₂ values are similar through-out the sequence indicating that the backbones of the five helices are in a single motional regime. The thermal stability of Rv0543c, characterized by circular dichroism spectroscopy, indicates that Rv0543c irreversibly unfolds upon heating with an estimated melting temperature of 62.5 °C. While the biological function of Rv0543c is still unknown, the presence of DUF3349 proteins predominately in Mycobacterium and Rhodococcus bacterial species suggests that Rv0543 may have a biological function unique to these bacteria, and consequently, may prove to be an attractive drug target to combat tuberculosis.     

Use of structural phylogenetic networks for classification of the ferritin-like superfamily

In the postgenomic era, bioinformatic analysis of sequence similarity is an immensely powerful tool to gain insight into evolution and protein function. Over long evolutionary distances, however, sequence-based methods fail as the similarities become too low for phylogenetic analysis. Macromolecular structure generally appears better conserved than sequence, but clear models for how structure evolves over time are lacking. The exponential growth of three-dimensional structural information may allow novel structure-based methods to drastically extend the evolutionary time scales amenable to phylogenetics and functional classification of proteins. To this end, we analyzed 80 structures from the functionally diverse ferritin-like superfamily. Using evolutionary networks, we demonstrate that structural comparisons can delineate and discover groups of proteins beyond the "twilight zone" where sequence similarity does not allow evolutionary analysis, suggesting that considerable and useful evolutionary signal is preserved in three-dimensional structures.