An NMR Study of the Interaction of Cardiotoxin gamma from Naja nigricollis with Perdeuterated Dodecylphosphocholine Micelles

Development of a high-throughput in vitro screening method for the assessment of cell-damaging activities of snake venoms

Snakebite envenoming is a globally important public health issue that has devastating consequences on human health and well-being, with annual mortality rates between 81,000 and 138,000. Snake venoms may cause different pathological effects by altering normal physiological processes such as nervous transfer and blood coagulation. In addition, snake venoms can cause severe (local) tissue damage that may result in life-long morbidities, with current estimates pointing towards an additional 450,000 individuals that suffer from permanent disabilities such as amputations, contractions and blindness. Despite such high morbidity rates, research to date has been mainly focusing on neurotoxic and haemotoxic effects of snake venoms and considerably less on venom-induced tissue damage. The molecular mechanisms underlaying this pathology include membrane disruption and extracellular matrix degradation. This research describes methods used to study the (molecular) mechanisms underlaying venom-induced cell- and tissue damage. A selection of cellular bioassays and fluorescent microscopy were used to study cell-damaging activities of snake venoms in multi-well plates, using both crude and fractionated venoms. A panel of 10 representative medically relevant snake species was used, which cover a large part of the geographical regions most heavily affected by snakebite. The study comprises both morphological data as well as quantitative data on cell metabolism and viability, which were measured over time. Based on this data, a distinction could be made in the ways by which viper and elapid venoms exert their effects on cells. We further made an effort to characterise the bioactive compounds causing these effects, using a combination of liquid chromatography methods followed by bioassaying and protein identification using proteomics. The outcomes of this study might prove valuable for better understanding venom-induced cell- and tissue-damaging pathologies and could be used in the process of developing and improving snakebite treatments.

Membrane-Disrupting Activity of Cobra Cytotoxins Is Determined by Configuration of the N-Terminal Loop

In aqueous solutions, cobra cytotoxins (CTX), three-finger folded proteins, exhibit conformational equilibrium between conformers with either cis or trans peptide bonds in the N-terminal loop (loop-I). The equilibrium is shifted to the cis form in toxins with a pair of adjacent Pro residues in this loop. It is known that CTX with a single Pro residue in loop-I and a cis peptide bond do not interact with lipid membranes. Thus, if a cis peptide bond is present in loop-I, as in a Pro-Pro containing CTX, this should weaken its lipid interactions and likely cytotoxic activities. To test this, we have isolated seven CTX from Naja naja and N. haje cobra venoms. Antibacterial and cytotoxic activities of these CTX, as well as their capability to induce calcein leakage from phospholipid liposomes, were evaluated. We have found that CTX with a Pro-Pro peptide bond indeed exhibit attenuated membrane-perturbing activity in model membranes and lower cytotoxic/antibacterial activity compared to their counterparts with a single Pro residue in loop-I.

Variability in the Spatial Structure of the Central Loop in Cobra Cytotoxins Revealed by X-ray Analysis and Molecular Modeling

Cobra cytotoxins (CTs) belong to the three-fingered protein family and possess membrane activity. Here, we studied cytotoxin 13 from Naja naja cobra venom (CT13Nn). For the first time, a spatial model of CT13Nn with both “water” and “membrane” conformations of the central loop (loop-2) were determined by X-ray crystallography. The “water” conformation of the loop was frequently observed. It was similar to the structure of loop-2 of numerous CTs, determined by either NMR spectroscopy in aqueous solution, or the X-ray method. The “membrane” conformation is rare one and, to date has only been observed by NMR for a single cytotoxin 1 from N. oxiana (CT1No) in detergent micelle. Both CT13Nn and CT1No are S-type CTs. Membrane-binding of these CTs probably involves an additional step—the conformational transformation of the loop-2. To confirm this suggestion, we conducted molecular dynamics simulations of both CT1No and CT13Nn in the Highly Mimetic Membrane Model of palmitoiloleoylphosphatidylglycerol, starting with their “water” NMR models. We found that the both toxins transform their “water” conformation of loop-2 into the “membrane” one during the insertion process. This supports the hypothesis that the S-type CTs, unlike their P-type counterparts, require conformational adaptation of loop-2 during interaction with lipid membranes.

Bactericidal effect of Naja nigricollis toxin γ is related to its membrane-damaging activity

The aim of the present study is to investigate the causal relationship between membrane-damaging activity and bactericidal activity of Naja nigricollis toxin γ. Toxin γ showed a similar inhibitory activity on the growth of Staphylococcus aureus (Gram-positive bacteria) and Escherichia coli (Gram-negative bacteria). Antibacterial activity of toxin γ correlated positively with increase in membrane permeability of bacterial cells. Morphological examination showed that toxin γ disrupted the integrity of bacterial membrane. Toxin γ showed similar binding capability with lipopolysaccharide (LPS) and lipoteichoic acid (LTA), and destabilization of LPS layer and inhibition of LTA biosynthesis on cell wall increased bactericidal effect of toxin γ on E. coli and S. aureus, respectively. Although the potency of toxin γ on permeabilizing model membrane of E. coli and S. aureus was similar, the mode of interaction between toxin γ and model membrane of E. coli and S. aureus differed. Membrane-damaging activity of toxin γ was inhibited by either LPS or LTA. Nevertheless, LPS and LTA altered differently membrane-bound conformation of toxin γ. Taken together, our data suggest that bactericidal activity of toxin γ depends on its ability to induce membrane permeability, and that LPS and LTA structurally suppresses bactericidal effect of toxin γ.

Snake cytotoxins bind to membranes via interactions with phosphatidylserine head groups of lipids

The major representatives of Elapidae snake venom, cytotoxins (CTs), share similar three-fingered fold and exert diverse range of biological activities against various cell types. CT-induced cell death starts from the membrane recognition process, whose molecular details remain unclear. It is known, however, that the presence of anionic lipids in cell membranes is one of the important factors determining CT-membrane binding. In this work, we therefore investigated specific interactions between one of the most abundant of such lipids, phosphatidylserine (PS), and CT 4 of Naja kaouthia using a combined, experimental and modeling, approach. It was shown that incorporation of PS into zwitterionic liposomes greatly increased the membrane-damaging activity of CT 4 measured by the release of the liposome-entrapped calcein fluorescent dye. The CT-induced leakage rate depends on the PS concentration with a maximum at approximately 20% PS. Interestingly, the effects observed for PS were much more pronounced than those measured for another anionic lipid, sulfatide. To delineate the potential PS binding sites on CT 4 and estimate their relative affinities, a series of computer simulations was performed for the systems containing the head group of PS and different spatial models of CT 4 in aqueous solution and in an implicit membrane. This was done using an original hybrid computational protocol implementing docking, Monte Carlo and molecular dynamics simulations. As a result, at least three putative PS-binding sites with different affinities to PS molecule were delineated. Being located in different parts of the CT molecule, these anion-binding sites can potentially facilitate and modulate the multi-step process of the toxin insertion into lipid bilayers. This feature together with the diverse binding affinities of the sites to a wide variety of anionic targets on the membrane surface appears to be functionally meaningful and may adjust CT action against different types of cells.

Mixed-SAM surfaces monitoring CTX-protein part I: Using atomic force microscope measurements

Fast and efficient detection of Cobra cardiotoxin (CTX) protein molecules on biochip surfaces is an example of application in biotechnology. One potential application of mixed self assembled monolayers (SAMs) as chip surfaces yield different binding affinities of the CTX proteins, a series of studies on the interaction force between CTX proteins and the mixed SAMs surfaces formed from mixtures of two thiols with the same/different chain lengths and/or with the same/different terminal groups will be investigated. In these dual papers, the mixed SAMs of n-alkinethiol SAMs of different chain lengths are chosen as the first examples of this series due to the simple functions of the mixed SAMs surface structure. Thus, the adhesion force measurements of CTX protein molecules on mixed SAMs of n-alkinethiol SAMs of different chain lengths: 1-decanethiol (C9) and 1-hexanethiol (C5) with different mixing ratios are developed and conducted using atomic force microscope (AFM). There are two major tasks in Part I of the dual papers: the development of the AFM measurements providing reliable information, and selection of the surface with highest binding affinity among this mixed SAMs group. Results indicate that the adhesion forces for CTX protein molecules on mixed SAMs with mixing ratio (χ(C9)) of 0.25, 0.5, 0.75 and 1, are 1.26, 1.8, 1.38, and 1.25 folds respectively, compared with the adhesion force of CTX protein molecules on the C5 surface only. Therefore, the SAM surfaces of χ(C9) = 0.5 is the best choice as a biomaterial sensor of this group of mixed SAMs because the strongest binding force and highest efficiency. Effects of the loading force of the AFM operation, the radius of curvature of the AFM tip, and the AFM tip endurance as well as control experiments were examined to ensure the quantitative determination of adhesion force for AFM measurement. The physical mechanism of protein adsorption on SAM surfaces will be studied and analyzed by molecular dynamics (MD) simulations and will be reported in Part II of the dual papers to compensate the limited information on the interaction taking place at atomic level that experiments cannot provide.

Structure, function and evolution of three-finger toxins: mini proteins with multiple targets

Snake venoms are complex mixtures of pharmacologically active peptides and proteins. These protein toxins belong to a small number of superfamilies of proteins. Three-finger toxins belong to a superfamily of non-enzymatic proteins found in all families of snakes. They have a common structure of three beta-stranded loops extending from a central core containing all four conserved disulphide bonds. Despite the common scaffold, they bind to different receptors/acceptors and exhibit a wide variety of biological effects. Thus, the structure-function relationships of this group of toxins are complicated and challenging. Studies have shown that the functional sites in these 'sibling' toxins are located on various segments of the molecular surface. Targeting to a wide variety of receptors and ion channels and hence distinct functions in this group of mini proteins is achieved through a combination of accelerated rate of exchange of segments as well as point mutations in exons. In this review, we describe the structural and functional diversity, structure-function relationships and evolution of this group of snake venom toxins.

Roles of lysine residues and N-terminal alpha-amino group in membrane-damaging activity of Taiwan cobra cardiotoxin 3 toward anionic and zwitterionic phospholipid vesicles

In contrast to a slight increase in activity toward phosphatidylcholine (EYPC)/dimyristoyl phosphatidic acid (DMPA) vesicles, guanidination of Naja naja atra cardiotoxin 3 (CTX3) and selective trinitrophenylation of N-terminal alpha-amino group enhanced notably membrane-damaging activity on EYPC/egg yolk sphingomyelin (EYSM) vesicles. Chemically modified CTX3 showed a reduction in its hemolytic activity and cytotoxicity. These reflected that membrane-damaging activity of CTX3 was affected by phospholipid compositions. Phospholipid-binding capability and oligomeric assembly upon binding with lipid vesicles did not closely correlate with membrane-damaging potency of native and modified CTX3. Moreover, different topographical contacts and distinctive modes for the binding of CTX3 and its modified derivatives with anionic phospholipid vesicles (EYPC/DMPA) and zwitterionic phospholipid vesicles (EYPC/EYSM) were observed. Compared with in the case of EYPC/DMPA, the interaction between CTX molecules and EYPC/EYSM was drastically reduced by increasing salt concentration and heparin. Taken together, our data indicate that guanidination of Lys residues and trinitrophenylation of alpha-amino group alter differently the interacted modes upon absorption on anionic phospholipid vesicles and zwitterionic phospholipid vesicles. The findings also suggest that positively charged residues of CTX3 play a distinctive role in damaging anionic and zwitterionic phospholipid vesicles.

Membrane-bound conformation of Naja nigricollis toxin gamma affects its membrane-damaging activity

To address whether the conformational events associated with the absorption of Naja nigricollis toxin gamma on water-lipid interface plays a vital role in its membrane-damaging activity, the present study is carried out. Membrane-damaging activity of toxin gamma on 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC)/1, 2-dimyristoyl-phosphatidic acid (DMPA) vesicles was approximately 13-fold of that on 1, 2-dipalmitoyl-phosphatidylcholine (DPPC)/DMPA vesicles, while the binding affinity of toxin gamma for POPC/DMPA was twofold of that for DPPC/DMPA. Time-resolved fluorescence, acrylamide quenching and Fourier transform infrared spectra showed that POPC/DMPA-bound toxin gamma and DPPC/DMPA-bound toxin gamma did not adopt the same conformation. Moreover, geometrical arrangement of toxin gamma in contact with POPC/DMPA vesicles was different from that with DPPC/DMPA vesicles as evidenced by N-(fluorescein-5-thiocarbamoyl)-1,2-dihexadecanoyl-phosphatidylcholine fluorescence enhancement and cross-linking of membrane-bound toxin gamma. Taken together, our data show that different membrane packing densities arising from phospholipid acyl chain affect membrane-bound conformation of toxin gamma, thus changing its membrane-damaging activity.

Structural analysis of cassiicolin, a host-selective protein toxin from Corynespora cassiicola

Cassiicolin is a host-selective toxin (HST) produced by the fungus Corynespora cassiicola (strain CCP). It is responsible for the Corynespora leaf fall (CLF) disease, which is among the main pathologies affecting rubber tree (Hevea brasiliensis). Working on purified cassiicolin and using electron microscopy, we have demonstrated that this 27-residue O-glycosylated protein is able to induce cellular damages identical to those induced by the fungus on rubber tree leaves and displays the same host selectivity. The solution structure and disulfide pairing of cassiicolin have been determined using NMR spectroscopy and simulated annealing calculations. Cassiicolin appears to have an original structure with a prolate ellipsoid shape. It adopts an over-all fold consisting of three strands arranged in a right-handed twisted, antiparallel beta-sheet knitted by three disulfide bonds. Its conformation resembles that found in small trypsine-like inhibitors isolated from the brain, the fat body and the hemolymph of locust grasshoppers. But cassiicolin has no sequence homology with these protease inhibitors, and lacks their characteristic substrate-binding loop. Probably, this motif represents one of the few highly stabilized "minimal" scaffolds, with a high sequence permissiveness, that nature has selected to evolve over different phyla and to support different functions. The knowledge of the 3D structure opens the way to the delineation of the mechanism of action of the toxin using site-directed mutagenesis.

Molecular dynamics simulation of the enhancement of cobra cardiotoxin and E6 protein binding on mixed self-assembled monolayer molecules

Molecular dynamics simulations are performed on n-alkinethiol self-assembled monolayers (SAMs) and their mixture on a gold surface so that the orientations of the binding of cobra cardiotoxin and E6 protein molecules can be selected using the mixing ratio of CH3-terminated SAMs with different chain lengths. The simulations suggest that a SAM surface with different mixing ratios may provide a possible platform for aligning protein molecules with a desired orientation and for enhancing the binding energy of the protein on the designed surface.

Peripheral binding mode and penetration depth of cobra cardiotoxin on phospholipid membranes as studied by a combined FTIR and computer simulation approach

Cobra cardiotoxin, a cytotoxic beta-sheet basic polypeptide, is known to cause membrane leakage in many cells including human erythrocytes. Herein, we demonstrate that the major cobra cardiotoxin from Naja atra, CTX A3, can cause leakage of vesicle contents in phosphatidylglycerol (PG) and phosphatidylserine containing, but not in pure phosphatidylcholine (PC), membrane bilayers. By the combined polarized attenuated total reflection infrared spectroscopy and computer simulation studies, CTX A3 is shown to peripherally bind to both zwitterionic and anionic monolayers in a similar edgewise manner with a tilted angle of approximately 48 +/- 20 degrees between the beta-sheet plane of the CTX molecule and the normal of the membrane surface. The average surface area expansion induced by CTX A3 binding to the PG monolayer, however, is two times larger than that of the PC monolayer as determined by the Langmuir minitrough method. Interaction energy considerations of CTX A3 on neutral and negatively charged membrane surfaces suggests that the electrostatic interaction between anionic lipid and cationic CTXs plays a role in modulating the penetration depth of CTX molecules on the initial peripheral binding mode and reveals a pathway leading to the formation of an inserted mode in negatively charged membrane bilayers.

Membrane protein dynamics versus environment: simulations of OmpA in a micelle and in a bilayer

The bacterial outer membrane protein OmpA is one of the few membrane proteins whose structure has been solved both by X-ray crystallography and by NMR. Crystals were obtained in the presence of detergent, and the NMR structure is of the protein in a detergent micelle. We have used 10 ns duration molecular dynamics simulations to compare the behaviour of OmpA in a detergent micelle and in a phospholipid bilayer. The dynamic fluctuations of the protein structure seem to be ca 1.5 times greater in the micelle environment than in the lipid bilayer. There are subtle differences between the nature of OmpA-detergent and OmpA-lipid interactions. As a consequence of the enhanced flexibility of the OmpA protein in the micellar environment, side-chain torsion angle changes are such as to lead to formation of a continuous pore through the centre of the OmpA molecule. This may explain the experimentally observed channel formation by OmpA.

Structural basis of membrane-induced cardiotoxin A3 oligomerization

Cobra cardiotoxins (CTXs) have previously been shown to induce membrane fusion of vesicles formed by phospholipids such as cardiolipin or sphingomyelin. CTX can also form a pore in membrane bilayers containing a anionic lipid such as phosphatidylserine or phosphatidylglycerol. Herein, we show that the interaction of CTX with negatively charged lipids causes CTX dimerization, an important intermediate for the eventual oligomerization of CTX during the CTX-induced fusion and pore formation process. The structural basis of the lipid-induced oligomerization of CTX A3, a major CTX from Naja atra, is then illustrated by the crystal structure of CTX A3 in complex with SDS; SDS likely mimics anionic lipids of the membrane under micelle conditions at 1.9-A resolution. The crystal packing reveals distinct SDS-free and SDS-rich regions; in the latter two types of interconnecting CTX A3 dimers, D1 and D2, and several SDS molecules can be identified to stabilize D1 and D2 by simultaneously interacting with residues at each dimer interface. When the three CTXSDS complexes in the asymmetric unit are overlaid, the orientation of CTX A3 monomers relative to the SDS molecules in the crystal is strikingly similar to that of the toxin with respect to model membranes as determined by NMR and Fourier transform infrared methods. These results not only illustrate how lipid-induced CTX dimer formation may be transformed into oligomers either as inverted micelles of fusion intermediates or as membrane pore of anionic lipid bilayers but also underscore a potential role for SDS in x-ray diffraction study of protein-membrane interactions in the future.

Interaction of the P-type cardiotoxin with phospholipid membranes

The cardiotoxin (cytotoxin II, or CTII) isolated from cobra snake (Naja oxiana) venom is a 60-residue basic membrane-active protein featuring three-finger beta sheet fold. To assess possible modes of CTII/membrane interaction 31P- and 1H-NMR spectroscopy was used to study binding of the toxin and its effect onto multilamellar vesicles (MLV) composed of either zwitterionic or anionic phospholipid, dipalmitoylglycerophosphocholine (Pam2Gro-PCho) or dipalmitoylglycerophosphoglycerol (Pam2Gro-PGro), respectively. The analysis of 1H-NMR linewidths of the toxin and 31P-NMR spectral lineshapes of the phospholipid as a function of temperature, lipid-to-protein ratios, and pH values showed that at least three distinct modes of CTII interaction with membranes exist: (a) nonpenetrating mode; in the gel state of the negatively charged MLV the toxin is bound to the surface electrostatically; the binding to Pam2Gro-PCho membranes was not observed; (b) penetrating mode; hydrophobic interactions develop due to penetration of the toxin into Pam2Gro-PGro membranes in the liquid-crystalline state; it is presumed that in this mode CTII is located at the membrane/water interface deepening the side-chains of hydrophobic residues at the tips of the loops 1-3 down to the boundary between the glycerol and acyl regions of the bilayer; (c) the penetrating mode gives way to isotropic phase, stoichiometrically well-defined CTII/phospholipid complexes at CTII/lipid ratio exceeding a threshold value which was found to depend at physiological pH values upon ionization of the imidazole ring of His31. Biological implications of the observed modes of the toxin-membrane interactions are discussed.

Molecular moulds with multiple missions: functional sites in three-finger toxins

1. Snake venoms are complex mixtures of pharmacologically active peptides and proteins. 2. These protein toxins belong to a small number of superfamilies of proteins. The present review describes structure-function relationships of three-finger toxins. 3. All toxins share a common structure of three beta-stranded loops extending from a central core. However, they bind to different receptors/acceptors and exhibit a wide variety of biological effects. 4. Thus, the structure-function relationships of this group of toxins are complicated and challenging. 5. Studies have shown that the functional sites in these "sibling" toxins are located on various segments of the molecular surface.

Interaction of cardiotoxins with membranes: a molecular modeling study

Incorporation of beta-sheet proteins into membrane is studied theoretically for the first time, and the results are validated by the direct experimental data. Using Monte Carlo simulations with implicit membrane, we explore spatial structure, energetics, polarity, and mode of insertion of two cardiotoxins with different membrane-destabilizing activity. Both proteins, classified as P- and S-type cardiotoxins, are found to retain the overall "three-finger" fold interacting with membrane core and lipid/water interface by the tips of the "fingers" (loops). The insertion critically depends upon the structure, hydrophobicity, and electrostatics of certain regions. The simulations reveal apparently distinct binding modes for S- and P-type cardiotoxins via the first loop or through all three loops, respectively. This rationalizes an earlier empirical classification of cardiotoxins into S- and P-type, and provides a basis for the analysis of experimental data on their membrane affinities. Accomplished with our previous simulations of membrane alpha-helices, the computational method may be used to study partitioning of proteins with diverse folds into lipid bilayers.

Heparin binding stabilizes the membrane-bound form of cobra cardiotoxin

It has been shown previously that the long chain fragments of heparin bind to the beta-strand cationic belt of the three-finger cobra cardiotoxin (or cytotoxin, CTX) and hence enhance its penetration into phospholipid monolayer under physiological ionic conditions. By taking lysophosphatidylcholine (LPC) micelles as a membrane model, we have shown by (1)H NMR study that the binding of heparin-derived hexasaccharide (Hep-6) to CTX at the beta-strand region can induce conformational changes of CTX near its membrane binding loops and promote the binding activity of CTX toward LPC. The Fourier-transform infrared spectra and NMR nuclear Overhauser effect of Hep-6.CTX and CTX.LPC complex in aqueous buffer also supplemented the aforementioned observation. Thus, the detected conformational change may presumably be the result of structural coupling between the connecting loops and its beta-strands. This is the first documentation of results showing how the association of hydrophilic carbohydrate molecules with amphiphilic proteins can promote hydrophobic protein-lipid interaction via the stabilization of its membrane-bound form. A similar mechanism involving tripartite interactions of heparin, protein, and lipid molecules may be operative near the extracellular matrix of cell membranes.

Dynamic characterization of the water binding loop in the P-type cardiotoxin: implication for the role of the bound water molecule

Recent studies of cobra P-type cardiotoxins (CTXs) have shown that the water-binding loop (loop II) plays a crucial role in toxin binding to biological membranes and in their cytotoxicity. To understand the role of bound water in the loop, the structure and dynamics of the major P-type CTX from Taiwan cobra, CTX A3, were determined by a comprehensive NMR analysis involving (1)H NOESY/ROESY, (13)C[1)H]NOE/T(1) relaxation, and (17)O triple-quantum filtered NMR. A single water molecule was found to be tightly hydrogen bonded to the NH of Met26 with a correlation time (5-7 ns) approaching the isotropic tumbling time (3.8-4.5 ns) of the CTX A3 molecule. Surprisingly, despite the relatively long residence time (ca. 5 ns to 100 micros), the bound water molecule of CTX A3 is located within a dynamic (order parameter S(2) approximately 0.7) and solvent accessible loop. Comparison among several P-type CTXs suggests that proline residues in the consensus sequence of MxAxPxVPV should play an important role in the formation of the water binding loop. It is proposed that the exchange rate of the bound water may play a role in regulating the lipid binding mode of amphiphilic CTX molecules near membrane surfaces.

Membrane binding motif of the P-type cardiotoxin

Carditoxins (CTXs) from cobra snake venoms, the basic 60-62 residue all-beta sheet polypeptides, are known to bind to and impair the function of cell membranes. To assess the membrane induced conformation and orientation of CTXs, the interaction of the P-type cardiotoxin II from Naja oxiana snake venom (CTII) with perdeuterated dodecylphosphocholine (DPC) was studied using ( 1 )H-NMR spectroscopy and diffusion measurements. Under conditions where the toxin formed a well-defined complex with DPC, the spatial structure of CTII with respect to the presence of tightly bound water molecules in loop II, was calculated using the torsion angle dynamics program DYANA. The structure was found to be similar, except for subtle changes in the tips of all three loops, to the previously described "major" form of CTII in aqueous solution illustrated by the "trans" configuration of the Val7-Pro8 peptide bond. No "minor" form with the "cis" configuration of the above bond was found in the micelle-bound state. The broadening of the CTII backbone proton signals by 5, 16-doxylstearate relaxation probes, together with modeling based on the spatial structure of CTII, indicated a periphery mode of binding of the toxin molecule to the micelle and revealed its micelle interacting domain. The latter includes a hydrophobic region of CTII within the extremities of loops I and III (residues 5-11, 46-50), the basement of loop II (residues 24-29,31-37) and the belt of polar residues encircling these loops (lysines 4,5,12,23,50, serines 11,46, histidine 31, arginine 36). It is suggested that this structural motif and the mode of binding can be realized during interaction of CTXs with lipid and biological membranes.

Two forms of cytotoxin II (cardiotoxin) from Naja naja oxiana in aqueous solution: spatial structures with tightly bound water molecules

1H-NMR spectroscopy data, such as NOE intraprotein and (bound water)/protein contacts, 3J coupling constants and deuterium exchange rates were used to determine the in-solution spatial structure of cytotoxin II from Naja naja oxiana snake venom (CTII). Exploiting information from two 1H-NMR spectral components, shown to be due to cis/trans isomerization of the Val7-Pro8 peptide bond, spatial structures of CTII minor and major forms (1 : 6) were calculated using the torsion angle dynamics algorithm of the DYANA program and then energy refined using the FANTOM program. Each form, major and minor, is represented by 20 resulting conformers, demonstrating mean backbone rmsd values of 0.51 and 0.71 A, respectively. Two forms of CTII preserve the structural skeleton as three large loops, including two beta-sheets with bend regions, and demonstrate structural differences at loop I, where cis/trans isomerization occurs. The CTII side-chain distribution constitutes hydrophilic and hydrophobic belts around the protein, alternating in the trend of the three main loops. Because of the Omega-shaped backbone, formed in participation with two bound water molecules, the tip of loop II bridges the tips of loops I and III. This ensures the continuity of the largest hydrophobic belt, formed with the residues of these tips. Comparison revealed pronounced differences in the spatial organization of the tips of the three main loops between CTII and previous structures of homologous cytotoxins (cardiotoxins) in solution.

Characterization of low-molecular-mass trypsin isoinhibitors from oil-rape (Brassica napus var. oleifera) seed

A new low-molecular-mass (6767.8 Da) serine proteinase isoinhibitor has been isolated from oil-rape (Brassica napus var. oleifera) seed, designated 5-oxoPro1-Gly62-RTI-III. The 5-oxoPro1-Gly62-RTI-III isoinhibitor is longer than the Asp2-Pro61-RTI-III and the Ser3-Pro61-RTI-III forms, all the other amino acid residues being identical. In RTI-III isoinhibitors, the P1-P1' reactive site bond (where residues forming the reactive site have been identified as PnellipsisP1 and P1'ellipsisPn', where P1-P1' is the inhibitor scissile bond) has been identified at position Arg21-Ile22. The inhibitor disulphide bridges pattern has been determined as Cys5-Cys27, Cys18-Cys31, Cys42-Cys52 and Cys54-Cys57. The disulphide bridge arrangement observed in the RTI-III isoinhibitors is reminiscent of that found in a number of toxins (e.g. erabutoxin b). Moreover, the organization of the three disulphide bridges subset Cys5-Cys27, Cys18-Cys31 and Cys42-Cys52 is reminiscent of that found in epidermal growth factor domains. Preliminary 1H-NMR data indicates the presence of alphaalphaNOEs and 3JalphaNH coupling constants, typical of the beta-structure(s). These data suggest that the three-dimensional structure of the RTI-III isoinhibitors may be reminiscent of that of toxins and epidermal growth factor domains, consisting of three-finger shaped loops extending from the crossover region. Values of the apparent association equilibrium constant for RTI-III isoinhibitors binding to bovine beta-trypsin and bovine alpha-chymotrypsin are 3.3 x 109 m-1 and 2.4 x 106 m-1, respectively, at pH 8.0 and 21.0 degrees C. The serine proteinase : inhibitor complex formation is a pH-dependent entropy-driven process. RTI-III isoinhibitors do not show any similarity to other serine proteinase inhibitors except the low molecular mass white mustard trypsin isoinhibitor, isolated from Sinapis alba L. seed (MTI-2). Therefore, RTI-III and MTI-2 isoinhibitors could be members of a new class of plant serine proteinase inhibitors.

Elapid venom toxins: multiple recruitments of ancient scaffolds

Nigroxins A and B, two myotoxic phospholipases A2 (PLA2s) from the venom of the American elapid Micrurus nigrocinctus, belong to a new PLA2 subclass. Their primary structures were established and compared with those of PLA2s that have already been studied with respect to myotoxic activity. The combination of amino acid residues Arg15, Ala100, Asn108 and a hydrophobic residue at position 109 is present exclusively in class I PLA2s that display myotoxic activity. These residues cluster within a surface region rich in positive charges and are suggested to play a role in the interaction with the target membrane of the muscle fibers. It is concluded that the myotoxic PLA2s resulted from recruitment of an ancient scaffold. Dendrotoxins and alpha-neurotoxins are similarly derived from other old structures, which are, however, now also present in nontoxic proteins that are widely distributed throughout the animal kingdom. The evolutionary pathways by which elapid PLA2s acquired myotoxicity and dendrotoxins acquired K+-channel blocker activity are traced. They demonstrate how existing scaffolds were adapted stepwise to serve toxic functions by exchange of a few surface-exposed residues.

Interaction of the wheat endosperm lipid-binding protein puroindoline-a with phospholipids

Puroindoline-a is the main component of a new family of proteins that has been suggested to exert an antimicrobial activity in plant seeds through an interaction with lipid membranes. Here the interaction of puroindoline-a with model phospholipid membranes and micelles has been studied using intrinsic tryptophan fluorescence, fluorescence polarization of diphenyl hexatriene, and proteolysis experiments. The protein appears to interact with both zwitterionic and negative phospholipids. The interaction with phosphatidylcholine is characterized by low-affinity surface binding with very limited penetration into the hydrophobic membrane interior. On the other hand, the interaction with phosphatidylglycerol displays a high affinity and involves a partial penetration of the protein into the bilayer interior that disrupts acyl chain packing. The specificity appears to be due to the presence of a stretch of positively charged residues in the protein sequence. In all, the lipid-binding properties of puroindoline-a resemble those of cardiotoxins, another family of proteins for which a disruptive effect on the membrane structure has been involved to explain their biological function.

Action of Taiwan cobra cardiotoxin on membranes: binding modes of a beta-sheet polypeptide with phosphatidylcholine bilayers

The interaction of Taiwan cobra cardiotoxin (CTX A3), a basic polypeptide consisting of three-fingered loops and five-strand beta-sheet structure, with zwitterionic dipalmitoylphosphatidylcholine (DPPC) has been studied by 31P and 2H NMR to understand the binding modes of CTX in membrane bilayers. The results, in conjunction with DPH fluorescence anisotropy and differential scanning calorimetry studies, show that CTX may penetrate and lyse the bilayers into small aggregates at a lipid/protein molar ratio of about 20 in the ripple Pbeta' phase. Elevating the temperature to that of the liquid crystalline Lalpha phase leads to the fusion of the small aggregates into larger ones as evidenced by the change of the isotropic signal into a magnetically aligned 31P signal with a marked reduction in the chemical shift anisotropy. 2H NMR study on deuterium-labeled DPPC in the head group and fatty acyl region as a function of temperature and CTX concentration reveals a molecular model that CTX undergoes a redistribution between penetrating and peripheral binding states depending on the temperature studied. In addition, both the conformational and dynamic states of the phosphocholine head group of DPPC bilayers are significantly perturbed in the presence of CTX. Structural consideration of the CTX molecule indicates that the penetration binding mode of CTX with the DPPC bilayer may involve a novel membrane-binding motif identified recently in the three-fingered loops of P-type CTX. CTX can only bind to DPPC membrane peripherally in the Lalpha phase due to the mismatch of their hydrophobic lengths.

Crystal structure of cardiotoxin V from Taiwan cobra venom: pH-dependent conformational change and a novel membrane-binding motif identified in the three-finger loops of P-type cardiotoxin

The crystal structure of cardiotoxin V from Taiwan cobra venom (CTX A5) has been solved at pH 8.5 and refined to an R-factor of 20.7% for 7013 reflections [>2sigma(F)] between 8- and 2.19-A resolution. The refined model shows that CTX A5 exists as a dimer. The assembly consists of 974 non-hydrogen atoms from 124 residues and 73 water molecules. The global monomeric structure is similar to that determined by NMR at pH 3.7, characterized by a core formed by two beta-sheets connected with three-finger loops. However, local conformational differences are detected in two functionally important regions, loops I and II. A disparity between the NMR and X-ray structure of CTX A5 is detected near the tip of loop I and can be attributed to the difference in the protonation state of His4 at different pH, resulting in a reorientation of the His4 imidazole ring. A concerted motion of amino acid side chains located near His4 is detected and possibly contributes to the pH-dependent binding ability of CTX A5 to phospholipid model membranes. The second difference, detected at the tip of loop II, is due to the hydrophobic contact between CTX dimers in the crystal packing and the interaction of water molecules with amino acid residues in the loop II region of the CTX containing Pro31 (P-type CTX). This interaction forces loop II into a more rigid omega shape bridging the main chain at positions 27 and 34, contradictory to the flexible, tapering shape detected by NMR. Thus, a novel continuous hydrophobic column capable of binding to and possibly penetrating the membrane lipid bilayer is formed by the tips of the three-finger loops. In this respect, the X-ray crystal structure of CTX A5 may represent the CTX structure in the membrane-binding mode.

Folding properties of an annexin I domain: a 1H-15N NMR and CD study

The annexin fold consists of four 70-residue domains with markedly homologous sequences and nearly identical structures. Each domain contains five helices designated A to E. Domain 2 of annexin I was obtained by chemical synthesis including ten specifically labeled residues and studied by 1H-15N NMR and circular dichroism (CD). In pure aqueous solution this annexin domain presents, at most, 25% of residual helix secondary structure compared to 75%-85% for the native helix content and thus does not constitute an autonomous folding unit. Dodecylphosphocholine (DPC) micelles were used to provide the annexin domain with non-specific hydrophobic interactions. The structuring effect of micelles was thoroughly investigated by CD and 1H-15N NMR. Most, but not all, of the native helix secondary structure was recovered at DPC saturation. NMR data made it possible to determine the intrinsic helix propensity hierarchy of the different helix segments of the domain: A approximately B approximately E > C, D. This hierarchy is remarkably well correlated with the location of the helices in the native protein since A, B, and E helices are those in contact with the remaining parts of the protein. This result tends to support the view that, for large proteins like annexins (35 kDa), high intrinsic secondary structure propensities, at least helix propensity, in selected protein segments is necessary for a correct folding process. As a consequence this also indicates that important information concerning the folding pathway is encoded in the protein sequence.

The role of acidic amino acid residues in the structural stability of snake cardiotoxins

We have recently shown that membrane-related activities of cardiotoxin V from Naja naja atra (CTX A5) are diminished at acidic pH although the overall beta-sheet structure of the molecule is maintained. In order to understand more about the mechanism of inactivation of CTX at acidic pH, we studied the effect of pH and denaturing reagents on the structural stability of CTX. We found, first, pH-induced structural transitions occurred in CTX A5 at two pH values as judged by the CD ellipticity around 195 nm: an increase in the beta-sheet content occurred around pH 4 and followed by a decrease, therein, around pH 2. The pKa of three acidic amino acid residues in CTX A5, i.e., Glu-17, Asp-42, and Asp-59, were determined to be 4.0, 3.2, and below 2.3, respectively, by NMR spectroscopy. The low pKa value of Asp-59 implies salt bridge formation between Lys-2 and Asp-59. Thus, electrostatic interaction may stabilize the three loop structure in addition to the hydrogen bonds between N- and C-termini of CTX molecule. Second, 2,2,2-trifluoroethanol (TFE) and guanidinium chloride (GdmHCI) were found to induce alpha-helical and random coil formation, respectively, in CTX A5 and eight other beta-sheet CTXs. Comparison of the relative potencies of TFE and GdmHCI to induce structural changes suggests that the amino acid residue located at position 17 plays a role in the structural stability. Specifically, CTXs containing negatively charged Glu-17 are least stable. It is suggested that Glu-17 may perturb the interaction between Lys-2 and Asp-59, and thus the overall stability of beta-sheet, in the presence of denaturing reagent. In conclusion, the perturbed structural stability of CTXs may partially explain the lower activity CTX exhibits at acidic pH. A structural model to account for the unfolding and refolding of CTX molecules without the breaking of disulfide bonds is also proposed.

Conformational change and inactivation of membrane phospholipid-related activity of cardiotoxin V from Taiwan cobra venom at acidic pH

The phospholipid binding activity of cardiotoxin V from Naja naja atra (CTX A5) was studied by use of Langmuir monolayers and found to exhibit pH-dependence in binding to phosphatidylcholine membrane with an apparent pKa around 6.0. Proton NMR investigation of the CTX A5 molecule in the presence of phosphatidylcholine micelles reveals a decrease in association of CTX A5 with membranes at low pH as a result of the protonation of His-4 near the membrane binding site of loop I region of CTX. The pH-dependent binding can be attributed mainly, but not solely, to the change in charge content of the CTX molecule upon His-4 protonation at the membrane/water interface. This is shown by analyzing the pH- and ionic strength dependence of binding of CTXs to phospholipid monolayers according to Gouy-Chapman theory. The protonation of the His-4 residue also results in a local conformational change in the loop I region since the chemical shifts of amide protons for the amino acid residues from Cys-3 to Thr-14 are all found to vary as a function of pH with an apparent pKa similar to that of His-4. Interestingly, the effect is relayed to other amino acid residues in the structural core of the protein such as those in C-terminal (Lys-60, Cys-61, and Asn-62) and triple-stranded antiparallel beta-sheet (Cys-22, Lys-24, Ala-25, Arg-38, and Ala-41) regions. An additional local conformational change in the molecule results around pH 5 as evidenced by circular dichroism spectroscopic studies, although this change does not affect the characteristic beta-sheet and three-finger loop structure of CTX molecule as revealed by two-dimensional NOESY 1H NMR study. The latter conformational change at acidic pH, however, completely inactivates CTX-induced aggregation/fusion activity of sphingomyelin vesicles. The results suggest that deciphering the functional sites of CTXs on the basis of structure and dynamics determined at low pH should be done with caution. Since 19 out of 44 CTX homologues with known amino acid sequence contain His-4, the effect of His-4 on the structure and function of CTX molecules is important and is discussed in terms of the diverse membrane targets of CTX subtypes. Also discussed is the pH-induced activation of snake venom proteins in the victim.

Cardiotoxin II segregates phosphatidylglycerol from mixtures with phosphatidylcholine: (31)P and (2)H NMR spectroscopic evidence

The interaction of the cationic protein cardiotoxin II (CTX II) with mixtures of zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) was investigated using phosphorus ((31)P) and deuterium ((2)H) nuclear magnetic resonance (NMR) spectroscopy. Adding CTX II to 1:1 POPC/POPG mixtures produced a two-component (31)P NMR spectrum, in which the second component had a decreased chemical shift anisotropy. Simultaneously, the (2)H NMR quadrupolar splitting measured from both POPC-alpha-d(2) and POPC-beta-d(2) decreased. Thus, CTX II produces an altered macroscopic phase state of the lipid bilayers, and this obscures any effects on bilayer surface electrostatics observed by (2)H NMR. Using magic angle spinning (MAS) (31)P NMR spectroscopy, two isotropic resonances were resolved in the absence of CTX II and were assigned to POPG (0.47 ppm) and POPC (-.58 ppm). Adding CTX II produced two new isotropic resonances shifted approximately 0.5 ppm downfield. Quantifying the intensities of the various resonance lines revealed that the binding isotherms for different POPC/POPG mixtures shifted onto a universal curve when expressed as a function of the CTX II/POPG ratio. The results indicate that CTX II binds preferentially to POPG and is able to laterally segregate POPG from POPC. Fitting of the binding isotherms was achieved using a two-site model derived from statistical-thermodynamic considerations. One class of binding site is specific for POPG and the other is nonspecific, capable of binding both POPC and POPG.

Amino acid residue: is it structural or functional?

A new approach is suggested for delineating the structural and functional amino acid residues in proteins with known three-dimensional structure, basing on the involvement of residues in intramolecular hydrophobic and hydrophilic interactions and additional information about the conservativity of the residues. The approach is applied to the families of homologous neurotoxins and cardiotoxins. The results obtained concerning the role of amino acid residues in both families of toxins accord well with the similarity of their fold, but different mechanisms of action. Current approach can be used for detailed characterization of protein spatial structures, as well as for rational protein engineering.