Computational investigation of the conformational dynamics in Tom20‐mitochondrial presequence tethered complexes

Abstract

The translocase of the outer membrane (TOM) mediates the membrane permeation of mitochondrial matrix proteins. Tom20 is a subunit of the TOM complex and binds to the N‐terminal region (ie, presequence) in mitochondrial matrix precursor proteins. Previous experimental studies indicated that the presequence recognition by Tom20 was achieved in a dynamic‐equilibrium among multiple bound states of the α‐helical presequence. Accordingly, the co‐crystallization of Tom20 and a presequence peptide required a disulfide‐bond cross‐linking. A 3‐residue spacer sequence (XAG) was inserted between the presequence and the anchoring Cys residue at the C‐terminus to not disturb the movement of the presequence peptide in the binding site of Tom20. Two crystalline forms were obtained according to Ala or Tyr at the X position of the spacer sequence, which may reflect the dynamic‐equilibrium of the presequence. Here, we have performed replica‐exchange molecular dynamics (REMD) simulations to study the effect of disulfide‐bond linker and single amino acid difference in the spacer region of the linker on the conformational dynamics of Tom20‐presequence complex. Free energy and network analyses of the REMD simulations were compared against previous simulations of non‐tethered system. We concluded that the disulfide‐bond tethering did not strongly affect the conformational ensemble of the presequence peptide in the complex. Further investigation showed that the choice of Ala or Tyr at the X position did not affect the most distributions of the conformational ensemble of the presequence. The present study provides a rational basis for the disulfide‐bond tethering to study the dynamics of weakly binding complexes.

Synthetic Mitochondria-Targeting Peptides Incorporating α-Aminoisobutyric Acid with a Stable Amphiphilic Helix Conformation in Plant Cells

“…The Tom20 structure was taken from the structure of rat Tom20 bound to the rat ALDH presequence LSRLL motif (PDB ID: 2v1t). , The selenium methionine present in Tom20 was mutated to a methionine. The rat ALDH presequence motif was used to align the folded peptide structures ((LARL) 3 , (LURL) 3 , (LURR) 3 , and (LURS) 3 ) obtained from the previous simulations, and then the rat ALDH presequence motif was removed.…”

Advances in enhanced sampling molecular dynamics simulations for biomolecules

“…Since REMD and its adaptations allow unconstrained enhanced sampling without setting specific CVs to use them, many applications of these methods exist, in-DOI:10.1063/1674-0068/cjcp1905091 c ⃝2019 Chinese Physical Society cluding the studies of protein folding [3,76], protein structural ensemble generation [77,78], protein-protein recognition mechanism [79], peptide-nanomaterials interaction [80,81], binding/unbinding kinetics [82], RNA structural dynamics [83], and polymers assembly [84].…”