Computational Modeling of Conformer Stability in Benenodin-1, A Thermally-Actuated Lasso Peptide Switch

Abstract

Benenodin-1 is a thermally-actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically-favored and the other is entropically-favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamics (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically-favored conformer having more intra-peptide hydrogen bonds between Gln15 sidechain and nearby residues. Evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically-favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.

LassoHTP: a High-throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

“…Benenodin-1 conformer 2 involves a cis-isopeptide bond, 15 which was not considered in the current version of LassoHTP. For streptomonomicin, the NMR structure was determined in methanol.…”

“…Computational studies have elucidated the physical basis of folding, threading, and thermally-actuated switching for specific lasso peptides. 6,11,15,16 Ferguson et al showed that uncyclized microcin J25 can spontaneously adopt a left-handed coil configuration using replicaexchange molecular dynamics (MD). 6 Allen et al applied classical classical MD simulations with umbrella sampling to study the energetic preference of different pulling mechanisms for astexin-3 unthreading.…”

“…13 The [1]rotaxane slipknot conformation enables lasso peptides to be resilient towards thermal degradation (via the presence of bulky stopper residues) and proteolysis (via burial of the amide backbone). [14][15][16][17] The slipknot conformation can be formally represented by the C-terminus peptide tail threading into the macrolactam ring. The ring is connected by an isopeptide bond between the nitrogen of the N-terminus and a glutamate or aspartate carboxylate carbon located at the 7 th , 8 th , or 9 th amino acid position.…”

“…Yang et al performed multiscale simulations on benenodin-1, a thermally-actuated molecular swtich between two conformers that differ by the position of the steric plug Q15. 15 By combining classical MD and large-scale quantum mechanics calculations, they quantified the entropy and enthalpy that accompany the conformational switching and elucidated the roles of steric plugs in mediating entropy-enthalpy compensation.…”

LassoHTP: A High-Throughput Computational Tool for Lasso Peptide Structure Construction and Modeling

“…Computational studies have elucidated the physical basis of folding, threading, and thermally actuated switching for specific lasso peptides. 6,11,15,16 Ferguson et al showed that uncyclized microcin J25 can spontaneously adopt a left-handed coil configuration using replica-exchange molecular dynamics (MD). 6 Allen et al applied classical MD simulations with umbrella sampling to study the energetic preference of different pulling mechanisms for astexin-3 unthreading.…”