Dissecting the steps of substrate processing by the energy-dependent protease ClpXP

Intracellular proteolysis is carried out by self-compartmentalized, energy dependent proteases which contain a regulatory and a proteolytic component. The regulatory component, which contains ATPases, has crucial activities necessary for the mechanism of degradation. To degrade a substrate the regulatory component recognizes and binds the substrate, then processes it further for degradation by actively unfolding and translocating it into a sequestered proteolytic compartment. The substrate is degraded into small fragments, approximately 9-11 amino acids long, that are then released. Both the regulatory and proteolytic components have pores which align to form a channel through which substrates are proposed to travel. In the bacterial energy-dependent protease ClpXP, ClpX is the regulatory component and ClpP is the proteolytic component. To better understand the proteolytic activity of ClpXP we investigated the steps involved in processing of substrates by ClpXP. The aim of this thesis is to present studies that have provided information about the roles of the important features of the ClpXP complex, namely the central pore of ClpX, the N-domain of ClpX and the channel of the ClpXP protease, during processing of substrates. Using mutational analysis I have found that the central pore of ClpX is involved in processing of C-motif 1 signals, one of the five classes of recognition signals, suggesting that ClpX processes its substrates with different recognition signals in at least two distinct manners. The central pore is also involved in engagement of C-motif 1 substrates, a step following binding but prior to further processing of substrates.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2004

Author dc:creator

• Siddiqui, Samia M. (Siddiqui Mohammed), 1977-

Advisor dc:contributor.advisor

• Tania A. Baker.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/32253

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/32253