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

Content Provider	PubMed Central
Author	KuÄ era, TomÃ¡Å¡ Michal, Otyepka Anna, MatuÅ¡kovÃ¡ Samad, Abdul Eva, KutejovÃ¡ Janata, JiÅ Ã
Editor	Carloni, Paolo
Copyright Year	2013
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.
Related Links	http://dx.doi.org/10.1371/journal.pone.0074518
Starting Page	74518
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	9
Volume Number	8
Language	English
Publisher	Public Library of Science
Publisher Date	2013-09-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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

The Mitochondrial Peptidase Pitrilysin Degrades Islet Amyloid Polypeptide in Beta-Cells

Mitochondrial Ceramide-Rich Macrodomains Functionalize Bax upon Irradiation

Correction: Mitochondrial Ceramide-Rich Macrodomains Functionalize Bax upon Irradiation

A Computational Model of Neuro-Glio-Vascular Loop Interactions

Evolution of the Thermopsin Peptidase Family (A5)

A Cryptic Targeting Signal Creates a Mitochondrial FEN1 Isoform with Tailed R-Loop Binding Properties

A New TASK for Dipeptidyl Peptidase-like Protein 6

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

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

Similar Documents

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

The Mitochondrial Peptidase Pitrilysin Degrades Islet Amyloid Polypeptide in Beta-Cells

Mitochondrial Ceramide-Rich Macrodomains Functionalize Bax upon Irradiation

Correction: Mitochondrial Ceramide-Rich Macrodomains Functionalize Bax upon Irradiation

A Computational Model of Neuro-Glio-Vascular Loop Interactions

Evolution of the Thermopsin Peptidase Family (A5)

A Cryptic Targeting Signal Creates a Mitochondrial FEN1 Isoform with Tailed R-Loop Binding Properties

A New TASK for Dipeptidyl Peptidase-like Protein 6

Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation

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