Computational Investigation of Protein-Membrane Systems Involved in Cellular Trafficking
Yin, Ying
This item is only available for download by members of the University of Illinois community. Students, faculty, and staff at the U of I may log in with your NetID and password to view the item. If you are trying to access an Illinois-restricted dissertation or thesis, you can request a copy through your library's Inter-Library Loan office or purchase a copy directly from ProQuest.
Permalink
https://hdl.handle.net/2142/80626
Description
Title
Computational Investigation of Protein-Membrane Systems Involved in Cellular Trafficking
Author(s)
Yin, Ying
Issue Date
2009
Doctoral Committee Chair(s)
Martin Gruebele
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biophysics, General
Language
eng
Abstract
"Living cells are enclosed by lipid membranes, and the inside of a cell is also subdivided into different functionally distinct membrane-bound compartments. To overcome the barrier the membranes pose for cellular trafficking between the outside and the inside, or between different compartments of the cell, nature has evolved elaborate ways of transporting targets across the membranes, utilizing specially designed protein machines. In this thesis, two protein-membrane systems involved in cellular trafficking are investigated. The first system consists of a family of membrane-sculpting proteins, BAR-domains, which can reshape lipid membranes. BAR domains possess a positively charged concave surface, which bends negatively charged membrane into high-curvature tubes and vesicles. Experiments have suggested that BAR domains bend membrane in teams by arranging themselves in lattice-like scaffolds. We have developed models describing membrane sculpting by BAR domains at four levels of resolutions. Multiscale simulations elucidated how different types of BAR domain lattices determine the membrane curvature generated. Formation of entire membrane tubes by BAR domain lattices over time scales of 200 microseconds was observed in molecular dynamics simulations using a simplified, or ""coarse-grained"" description. An all-atom simulation of a 2.3-million-atom system covering 0.3 microsecond probed the dynamics of one specific BAR domain lattice in atomic detail. The second system studied in this thesis is a protein called lactose permease (LacY), which transports lactose across the cell membrane. We have identified a crucial salt-bridge that might play role in controlling the access of the sugar to the protein, and probed the molecular and energetic details of lactose translocation across LacY using steered molecular dynamics simulations."
Use this login method if you
don't
have an
@illinois.edu
email address.
(Oops, I do have one)
IDEALS migrated to a new platform on June 23, 2022. If you created
your account prior to this date, you will have to reset your password
using the forgot-password link below.
