Scrambling of disulfide bond scaffolds in neurotoxin AuIB: A molecular dynamics simulation study

Abstract

AuIB, a neurotoxic conopeptide, is a "selective antagonist" of the α3-β4 subtype of the nicotinic acetylcholine receptors in human brain and is investigated extensively for its immense potency in the treatment of pain. It contains two disulfide linkages, which are decisive in maintaining its structure and functional selectivity. Here we report, a molecular dynamics simulation study of the role of disulfide bonds on the secondary structure of AuIB in water. The native form of AuIB (N) is found to be significantly stable in water with very robust 3 and α-helical domains, featuring ∼47% of the total structure. The partially reduced AuIB (P ), with the disulfide bond between cysteine 2, 8 broken, shows significantly perturbed secondary structural features with almost total loss in helicity. Breaking of the disulfide bond between cysteine 3, 15 (P ), on the other hand, has almost no effect on the helical region of the peptide, although the weightage of β-turn increased at the cost of random coil. Intriguingly, when both the disulfide bonds are broken (D), the helical region is affected, but the loss in helicity is less than that observed in the P case. To understand the disulfide scrambling process, the relative probabilities of forming three disulfide-bond isoforms of AuIB in water are estimated from the sulfur-sulfur (SS) distance distributions of the four cysteine residues present in AuIB (D). Simulations show that the native globular form dominates ∼73% of the isoform population, with the beads form being the second most populated one. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 196-209, 2016.

Temperature‐dependent molecular dynamics study reveals an ionic liquid induced 310‐ to α‐helical switch in a neurotoxin

“…In accordance with experimental observations, simulations predict that in water, at 305 K, native AuIB possesses a robust helical motif, comprising of ∼33% α ‐helix and ∼14% 3 10 ‐helix. In addition, AuIB also possesses ∼11% β‐ turn and ∼42% random coil (Table ) . At 400 K in water, AuIB loses ∼15% of the α‐ helix content, with a concomitant increase in the β‐ turn by ∼33% (Table , Figure ).…”

“…The AMBER all atom force field developed by Cornel et al, and modified in CHARMM format is used to describe the bonding and nonbonding potentials of AuIB . As mentioned in our previous work on AuIB, the choice of this particular force field is used to parameterize the terminal as well as the non‐terminal cysteine residues in AuIB, which may be either disulfide bonded or reduced. The water molecules are explicitly modeled by TIP3P force field as incorporated in CHARMM .…”

“…In addition, AuIB also possesses 11% b-turn and 42% random coil (Table 1). [49,65] At 400 K in water, AuIB loses 15% of the a-helix content, with a concomitant increase in the b-turn by 33% (Table 1, Figure 1). Previous experiments and simulations showed that the 3 10 -helix in AuIB runs from amino acids Gly-1 to Ser-4, while the robust a-helix runs from Pro-6 to Ala-10 in native globular AuIB.…”

Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect?

“…The AMBER all atom force field developed by Cornel et al, and modified in CHARMM format, has been used to describe the bonding and nonbonding potentials of AuIB (Cornell et al 1995). As mentioned in our previous works on AuIB (Roy and Lakshminarayanan 2016;Sajeevan 2017), this particular force field can parameterize the terminal as well as the non-terminal cysteine residues in AuIB, which may be either disulfidebonded or reduced. The water molecules are explicitly modeled by the TIP3P force field as incorporated in CHARMM (Jorgensen et al 1983;Jorgensen and Jenson 1998).…”

Simulation of differential structure and dynamics of disulfide bond isoforms of conopeptideAuIBin presence of humanα3β4nAChR

“…[29][30][31] While the isoforms differ only in the way the cysteine residues are linked to each other, each disulfide bond has the potential to alter the higher order structure of the peptides, which in turn gets reflected in the peptide thermal stability, receptor binding efficiency, surface hydrophobicity and other physical and chemical attributes like disparate behavior toward the drug conjugation site in cysteine-linked antibody-drug conjugates. [29,30,32,33] Grishin et al and Dutton et al in their pioneering works first reported the differential sensitivity toward stoichiometry and enhanced potency of the non-native ribbon isoform of AuIB in rat parasympathetic ganglion neurons as compared to the globular isoform, when bound to two stoichiometric variants of nAChRs, (α 3 ) 2 -(β 4 ) 3 and (α 3 ) 3 -(β 4 ) 2 , heterologously expressed in Xenopus oocytes. [34][35][36] In 2010, Grishin et al reported that the inhibitory mechanisms of the ribbon and globular disulfide bond isoforms of AuIB are different toward their selective receptor, α 3 -β 4 nAChR.…”