A Computational Study of the Glycine-Rich Loop of Mitochondrial Processing Peptidase

Tomáš Kučera,Anna Matušková,Eva Kutejová,Michal Otyepka,Jiří Janata,Abdul Samad,Paolo Carloni

doi:10.1371/journal.pone.0074518

Abstract

An all atomic, non-restrained molecular dynamics (MD) simulation in explicit water was used to study in detail the structural features of the highly conserved glycine-rich loop (GRL) of the α-subunit of the yeast mitochondrial processing peptidase (MPP) and its importance for the tertiary and quaternary conformation of MPP. Wild-type and GRL-deleted MPP structures were studied using non-restrained MD simulations, both in the presence and the absence of a substrate in the peptidase active site. Targeted MD simulations were employed to study the mechanism of substrate translocation from the GRL to the active site. We demonstrate that the natural conformational flexibility of the GRL is crucial for the substrate translocation process from outside the enzyme towards the MPP active site. We show that the α-helical conformation of the substrate is important not only during its initial interaction with MPP (i.e. substrate recognition), but also later, at least during the first third of the substrate translocation trajectory. Further, we show that the substrate remains in contact with the GRL during the whole first half of the translocation trajectory and that hydrophobic interactions play a major role. Finally, we conclude that the GRL acts as a precisely balanced structural element, holding the MPP subunits in a partially closed conformation regardless the presence or absence of a substrate in the active site.

Highlights

The majority of mitochondrial proteins are synthesized as precursor proteins on cytosolic ribosomes and posttranslationally transported into the mitochondria
Targeted molecular dynamics (TMD) simulation was carried out to examine the translocation of the substrate from the glycine-rich loop (GRL) to the mitochondrial processing peptidase (MPP) active site
A peptide derived from the malate dehydrogenase (MDH: residues L2SRVAKRAFSST13; the R-2 motif is underlined) signal presequence was chosen as a model substrate

Summary

Introduction

The majority of mitochondrial proteins are synthesized as precursor proteins on cytosolic ribosomes and posttranslationally transported into the mitochondria This process is facilitated by specific matrix-targeting signal presequences which are normally part of the N-termini of these proteins prior to their transportation. These preproteins are unfolded and imported into the mitochondrial matrix across a double membrane through protein translocation machinery comprising translocases of the outer [1] and inner mitochondrial membrane [2]. No inherited disorders have been linked with any mutants of MPP, indicating that its biological function is so vital that even relatively moderate disruptions to its activity are likely to produce non-viable organisms This may be linked to its essential role in mitochondrial biogenesis

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Conclusion