Computational investigation of protein translocation and membrane insertion
Gumbart, James Conrad
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https://hdl.handle.net/2142/27740
Description
Title
Computational investigation of protein translocation and membrane insertion
Author(s)
Gumbart, James Conrad
Issue Date
2009
Doctoral Committee Chair(s)
Aksimentiev, Aleksei
Committee Member(s)
Schulten, Klaus J.
Gruebele, Martin
Flynn, C.P.
Department of Study
Physics
Discipline
Physics
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
protein
membrane insertion
Language
en
Abstract
"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."
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