Putative membrane lytic sites of P-type and S-type cardiotoxins from snake venoms as probed by all-atom molecular dynamics simulations

Abstract

Cardiotoxins (CTXs) belonging to the three-finger toxin superfamily of snake venoms are one of principal toxic components and the protein toxins exhibit membrane lytic activities when the venoms are injected into victims. In the present study, complex formations between CTX VI (a P-type CTX from Naja atra) and CTX1 (an S-type CTX from Naja naja) on zwitterionic POPC bilayers (a major lipid component of cell membranes) have been studied in near physiological conditions for a total dynamic time scale of 1.35 μs using all-atom molecular dynamics (MD) simulations. Comprehensive analyses of the MD data revealed that residues such as Leu1, Lys2, Tyr11, Lys31, Asp57 and Arg58 of CTX VI, and Ala16, Lys30 and Arg58 of CTX1 were crucial for establishing interactions with the POPC bilayer. Moreover, loop I, along with globular head and loop II of CTX VI, and loop II of CTX1 were found to be the structural regions chiefly governing complex formation of the respective proteins with POPC. Rationalizations for the differential binding modes of CTXs and implications of the findings for designing small molecular inhibitors to the toxins are also discussed. Graphical Abstract Binding modes of a P-type CTX and an S-type CTX towards the POPC bilayer.

Status of Asp29 and Asp40 in the Interaction of Naja atra Cardiotoxins with Lipid Bilayers

“…Structural and functional analyses have suggested that the interaction of CTXs with the membrane is mediated through the tips of loops I/II, and that the basic residues flanked by hydrophobic patch at loop I/II regions are involved in the membrane-permeabilizing activity of CTXs [2,4,6,8]. In agreement, previous studies have reported that modification of the conserved Met residues at loop II of CTXs causes a drastic drop in their membrane-damaging activity [16].…”

“…Loops I, II, and III are composed of nonpolar amino acids flanked with positively charged Lys and Arg residues [2]. It has been suggested that the positively charged amino acids of CTXs initiate the interaction with the negatively charged surface of the membrane, subsequently causing the hydrophobic amino acids to form complementary hydrophobic interactions, thus stabilizing the membrane insertion of toxins [5,6].…”

“…CTXs are subdivided into S-and P-type CTXs based on their interacted mode with phosphatidylcholine (PC). These CTXs have conserved Ser and Pro residues at positions 28 and 30, respectively [6,7]. P-Type CTXs bind to phospholipid membranes by anchoring two lipid-binding sites in loops I and II, whereas S-type CTXs bind to phospholipid membranes only by their binding site in loop I [7,8].…”

“…P-Type CTXs bind to phospholipid membranes by anchoring two lipid-binding sites in loops I and II, whereas S-type CTXs bind to phospholipid membranes only by their binding site in loop I [7,8]. Computer simulation analyses showed that the loop II region of S-type CTXs is also involved in the formation of the toxin-PC complexes, and that the phospholipid-binding residues of P-type CTXs are different from those of S-type CTXs [6]. Konshina et al [2] reported that P-type CTXs show higher membrane-damaging activity than that of S-type CTXs on liposomes composed of zwitterionic phospholipid or/and anionic phospholipid vesicles.…”

“…Previous studies have suggested that the salt bridge between Asp57 and Lys2 increases the structural stability of N. nigricollis toxin , thereby promoting its membrane-perturbing activity [9]. Because the positively charged residues have been implicated in CTX-membrane interactions [2,6], we wanted to explore whether the negatively charged Asp residues inversely modulate the membrane-targeting action of N. atra CTX1 and CTX3. To address this question, we investigated the biological and structural properties of Asp-modified CTX1 and CTX3.…”