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Improving the quality of protein NMR structures by Rosetta refinement and its application in molecular replacement
Descriptive
TitleInfo
Title
Improving the quality of protein NMR structures by Rosetta refinement and its application in molecular replacement
Name
(type = personal)
NamePart
(type = family)
Mao
NamePart
(type = given)
Binchen
NamePart
(type = date)
1981-
DisplayForm
Binchen Mao
Role
RoleTerm
(authority = RULIB)
author
Name
(type = personal)
NamePart
(type = family)
Montelione
NamePart
(type = given)
Gaetano T.
DisplayForm
Gaetano T. Montelione
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Berman
NamePart
(type = given)
Helen
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Helen Berman
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Anderson
NamePart
(type = given)
Steve
DisplayForm
Steve Anderson
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Nanda
NamePart
(type = given)
Vikas
DisplayForm
Vikas Nanda
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
outside member
Name
(type = corporate)
NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
(type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm
(authority = RULIB)
school
TypeOfResource
Text
Genre
(authority = marcgt)
theses
OriginInfo
DateCreated
(qualifier = exact)
2012
DateOther
(qualifier = exact);
(type = degree)
2012-10
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
(authority = ISO639-2b);
(type = code)
eng
Abstract
(type = abstract)
This dissertation demonstrates restrained Rosetta refinement can improve the quality of protein NMR structures and describes a protocol to improve their phasing power. Recent studies manifest unrestrained Rosetta refinement can improve the stereochemical quality and geometry of protein NMR structures, to move NMR structures closer to their X-ray counterparts and consequently to improve their phasing power in a few cases. In this study, we intend to explore whether those observations stand corrected in general and the impact of incorporating NMR experimental restraints into Rosetta refinement. We developed a newer version of PdbStat software to convert Cyana/Xplor formatted restraints into Rosetta formatted restraints. Based on a dataset of 41 NESG NMR/X-ray structure pairs, we have done unrestrained and restrained Rosetta refinement for all the NMR structures. The knowledge based structural quality Z-scores are significantly improved by Rosetta refinement with or without restraints. Compared with unrestrained Rosetta refined structures, restrained Rosetta refined structures fit the experimental data better, are in better agreement with their X-ray counterparts and are generally of better phasing power, while unrestrained Rosetta refinement often drives the NMR structures further from their X-ray counterparts especially when the structural similarity between NMR structures and X-ray structures is high. To summarize, a majority of the experimental NMR restraints still apply for X-ray crystal structures determined at crystalline environment, and they can be utilized to guide Rosetta refinement to improve the quality of NMR structures. Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR structures as MR search models, using a dataset of 25 NESG NMR/X-ray structure pairs. Starting from NMR ensembles prepared by an improved protocol, FindCore, correct MR solutions were obtained for 22 targets. Rosetta refinement of NMR structures provided MR solutions for another two proteins. We also demonstrate that such properly prepared NMR ensembles and X-ray crystal structures have similar performance when used as MR search models for homologous structures, particularly for targets with sequence identity >40%.
Subject
(authority = RUETD)
Topic
Biochemistry
RelatedItem
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TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
Identifier
ETD_4200
PhysicalDescription
Form
(authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xiii, 130 p. : ill.
Note
(type = degree)
Ph.D.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = vita)
Includes vita
Note
(type = statement of responsibility)
by Binchen Mao
Subject
(authority = ETD-LCSH)
Topic
Nuclear magnetic resonance
Subject
(authority = ETD-LCSH)
Topic
Proteins--Spectra
Identifier
(type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000066907
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
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rucore19991600001
Location
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T31J98JT
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
Mao
GivenName
Binchen
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
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(qualifier = exact);
(point = start)
2012-08-24 11:57:56
AssociatedEntity
Name
Binchen Mao
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.
RightsEvent
DateTime
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(qualifier = exact);
(point = start)
2012-10-31
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = end)
2014-10-31
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after October 31st, 2014.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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4152832
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