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Modeling insertion of transmembrane beta-barrels for designing outer membrane proteins
Descriptive
TitleInfo
Title
Modeling insertion of transmembrane beta-barrels for designing outer membrane proteins
Name
(type = personal)
NamePart
(type = family)
Hsieh
NamePart
(type = given)
Daniel
NamePart
(type = date)
1984-
DisplayForm
Daniel Hsieh
Role
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(authority = RULIB)
author
Name
(type = personal)
NamePart
(type = family)
Nanda
NamePart
(type = given)
Vikas
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Vikas Nanda
Affiliation
Advisory Committee
Role
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(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Stock
NamePart
(type = given)
Ann M
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Ann M Stock
Affiliation
Advisory Committee
Role
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(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Morozov
NamePart
(type = given)
Alexandre V
DisplayForm
Alexandre V Morozov
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Levy
NamePart
(type = given)
Ronald M
DisplayForm
Ronald M Levy
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Caputo
NamePart
(type = given)
Greg
DisplayForm
Greg Caputo
Affiliation
Advisory Committee
Role
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(authority = RULIB)
outside member
Name
(type = corporate)
NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
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NamePart
Graduate School - New Brunswick
Role
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(authority = RULIB)
school
TypeOfResource
Text
Genre
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theses
OriginInfo
DateCreated
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2012
DateOther
(qualifier = exact);
(type = degree)
2012-10
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
(authority = ISO639-2b);
(type = code)
eng
Abstract
(type = abstract)
Outer membrane proteins (OMPs) perform a range of important functions in the cell biology of Gram-negative bacteria, mitochondria and chloroplasts. These functions include biogenesis, virulence, signal transduction, nutrient transport and apoptosis. In contrast to their inner membrane counterparts, OMPs have been more difficult to study due to the relative paucity of crystal structures. Although outer membrane proteins have been characterized and studied extensively by various structural and biophysical methods, our understanding of their folding, insertion and oligomerization is far behind that of inner membrane proteins. The goal of this study is to elucidate the folding and insertion mechanism of these transmembrane β-barrel proteins (TMBs) and ultimately to provide guidelines for computationally designing OMP sequences that fold and insert efficiently. Using a subset of amino acids from thirty-five outer membrane proteins from Gram-negative bacteria and mitochondria, a propensity vs depth in membrane profile for each residue was derived. Although results indicate similar trends between amino acids of inner and outer membrane proteins, there are also differences that can be explained by differences in factors such as environment, secondary structural preferences, and folding/insertion pathway. The propensity profiles were converted into energies of insertion as a function of depth from the center of the membrane. This thesis explores the many ways of using the statistical potential to answer questions about OMP folding, insertion and oligomerization that could not have been framed due to the experimental limitations. We conclude with a discussion of ways to improve our potential, including the assumption of asymmetry of the lipid bilayer as well as incorporating homology model building.
Subject
(authority = RUETD)
Topic
Computational Biology and Molecular Biophysics
Subject
(authority = ETD-LCSH)
Topic
Bacterial proteins
Subject
(authority = ETD-LCSH)
Topic
Mitochondria--Formation
RelatedItem
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
(type = local)
rucore19991600001
Identifier
ETD_4210
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000066761
PhysicalDescription
Form
(authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xii, 172 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = vita)
Includes vita
Note
(type = statement of responsibility)
by Daniel Hsieh
Location
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3HX1BGV
Genre
(authority = ExL-Esploro)
ETD doctoral
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Rights
RightsDeclaration
(ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder
(type = personal)
Name
FamilyName
Hsieh
GivenName
Daniel
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = start)
2012-08-28 15:19:13
AssociatedEntity
Name
Daniel Hsieh
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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