Computational investigation of protein translocation and membrane insertion

"The protein-conducting channel, or translocon, is an evolutionarily conserved complex which allows nascent proteins to cross a cellular membrane or integrate into it, typically in concert with a bound partner (e.g ., the ribosome). The crystal structure of an archaeal translocon, the SecY complex, revealed a channel tightly closed by two elements: a small ""plug"" domain blocking the periplasmic region of the channel and a pore ring composed of six hydrophobic residues acting as a constriction point at the channel's center. However, how the channel's dynamic behavior leads to opening could only be inferred from the static structure. The work presented in this thesis uses molecular dynamics simulations to explore the dynamics of SecY in its native membrane/ water environment. In simulated translocation of a nascent protein across the membrane, it was found that both the pore ring and plug can adapt to the intrusion of the incoming polypeptide but are also resilient, returning to their closed positions after translocation. Forced opening of the lateral gate, the point of insertion for membrane protein helices, revealed that the accessory protein SecE, previously thought to form a clamp around SecY, likely plays no such role. The independent roles of pore ring and plug were also studied via simulations of two crystallized mutants in which half or all of the original plug was deleted. From these simulations, it was discovered that the pore ring is the primary barrier to permeation in the closed channel with the plug serving to restrain the pore ring. Finally, the behavior of both a Sec Y monomer and a constructed Sec Y dimer were explored in the context of a bound ribosome. The initial atomic model of the complex was built by using a recently developed method to flexibly fit individual structures to a low-resolution cryo-electron microscopy map. By analyzing the primary interactions between the ribosome and the channel, it was found that all occur in conserved regions of the channel, supporting the model of the complex."

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Year dc:date

2011

Author dc:creator

• Gumbart, James Conrad

Contributors dc:contributor

• Aksimentiev, Aleksei
• Schulten, Klaus J.
• Gruebele, Martin
• Flynn, C.P.

• protein
• membrane insertion

Statement dc:rights

• Copyright 2009 James Conrad Gumbart

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/27740

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/27740