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Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis


Friedman, R; Caflisch, A (2008). Pepsinogen-like activation intermediate of plasmepsin II revealed by molecular dynamics analysis. Proteins, 73(4):814-827.

Abstract

Plasmepsins are pharmaceutically relevant aspartic proteases involved in haemoglobin degradation by the malaria causing parasites Plasmodium spp. They are translated as inactive proenzymes, with an elongated prosegment. On prosegment cleavage, plasmepsins undergo a series of hitherto unresolved conformational changes before becoming active. Here, the flexibility of plasmepsin and proplasmepsin and the activation process are investigated by multiple explicit water molecular dynamics simulations. The large N-terminal displacement and the interdomain shift from the proenzyme structure to active plasmepsin are promoted by essential dynamics sampling. An intermediate, stabilized by electrostatic interactions between the catalytic dyad and the N-terminus of mature plasmepsin, is observed along all activation trajectories. Notably, the stabilizing interactions in the activation intermediate of plasmepsin are similar to those in the X-ray structure of pepsinogen. In particular, the catalytic aspartates act as hydrogen bond acceptors for the N-terminal amino group and the Ser2 hydroxyl in plasmepsin, and the side chains of Lys36pro and Tyr9 in pepsinogen. The simulation results are used to suggest in vitro experiments to test the conformational transitions involved in the maturation of plasmepsin, and design small-molecule inhibitors.

Abstract

Plasmepsins are pharmaceutically relevant aspartic proteases involved in haemoglobin degradation by the malaria causing parasites Plasmodium spp. They are translated as inactive proenzymes, with an elongated prosegment. On prosegment cleavage, plasmepsins undergo a series of hitherto unresolved conformational changes before becoming active. Here, the flexibility of plasmepsin and proplasmepsin and the activation process are investigated by multiple explicit water molecular dynamics simulations. The large N-terminal displacement and the interdomain shift from the proenzyme structure to active plasmepsin are promoted by essential dynamics sampling. An intermediate, stabilized by electrostatic interactions between the catalytic dyad and the N-terminus of mature plasmepsin, is observed along all activation trajectories. Notably, the stabilizing interactions in the activation intermediate of plasmepsin are similar to those in the X-ray structure of pepsinogen. In particular, the catalytic aspartates act as hydrogen bond acceptors for the N-terminal amino group and the Ser2 hydroxyl in plasmepsin, and the side chains of Lys36pro and Tyr9 in pepsinogen. The simulation results are used to suggest in vitro experiments to test the conformational transitions involved in the maturation of plasmepsin, and design small-molecule inhibitors.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2008
Deposited On:04 Nov 2008 09:28
Last Modified:05 Apr 2016 12:31
Publisher:Wiley-Blackwell
ISSN:0887-3585
Publisher DOI:https://doi.org/10.1002/prot.22105
PubMed ID:18498105

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