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

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.

Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood

“…In the PMPCA individuals, the severity of disease seemed to depend on the mutation's vicinity to the glycine-rich loop of PMPCA, which has been implicated in substrate recognition and binding. 13 The more severe phenotype seen in the PMPCB individuals may be due to a stronger impact on MPP activity by mutations in the catalytic PMPCB subunit, suggesting a correlation of the variability of the phenotype and the degree of MPP dysfunction. First, while the Mas1 yeast cells bearing the homologous mutations of individuals A:II-1, B:II-2, and C:II-1 were viable at lower temperature, introduction of the PMPCB c.1265T>C (p.Ile422Thr) mutation of individuals D:II-1 and D:II-2 into yeast resulted in a lethal phenotype even at low temperature.…”

“…While PMPCB/Mas1 is a metalloprotease with a zinc-binding motif, PMPCA/Mas2 has been implicated in substrate recognition and binding. [11][12][13][14][15] Here, we report on four families with five affected individuals carrying biallelic variants in PMPCB (MIM: 603131). All children presented with episodic neurological regression, basal ganglia lesions, and cerebellar atrophy and were suspected of having a mitochondrial disorder.…”

Mutations in the substrate binding glycine-rich loop of the mitochondrial processing peptidase-α protein (PMPCA) cause a severe mitochondrial disease

“…Once imported into the mitochondria, the TP is cleaved off and the protein can fold and fully mature, allowing for optimal protein function. The majority of these essential cleavage reactions are catalyzed by MPP (mitochondrial processing peptidase), a matrix-localized, soluble heterodimer of α-MPP and β-MPP subunits, encoded by PMPCA and PMPCB , respectively ( Kucera et al 2013 ). In budding yeast, when either MPP subunit is eliminated, the cells continue to import proteins into the mitochondria, but they fail to cleave TPs, the precursor proteins accumulate, and the cells fail to grow ( Geli and Glick 1990 ).…”

Global Proteomics of the Extremophile Black Fungus <i>Cryomyces antarcticus</i> Using 2D-Electrophoresis

“…Indeed, no inherited disorders have been linked with any mutants of MMP, indicating that its biological function is so vital that even relatively moderate disruption to its activity are also likely to produce non-viable organisms. This may be linked to its essential role in mitochondrial biogenesis [55].…”

“…The ability of the pre-sequence to adopt context-dependent conformations during different steps of MPP's action is a basic requirement for substrate recognition processing [55]. The mitochondrial precursors are translocated across the outer and the inner mitochondrial membrane via the translocase of the outer membrane (TOM) and the translocase of the inner membrane (TIM) machineries, respectively.…”