Monitoring Polymorphism-Induced Conformational and Dynamics Changes in Hiv-1 Protease via Pulsed Electron Paramagnetic R...

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Material Information

Title:
Monitoring Polymorphism-Induced Conformational and Dynamics Changes in Hiv-1 Protease via Pulsed Electron Paramagnetic Resonance and Nuclear Magnetic Resonance Spectroscopy
Physical Description:
1 online resource (261 p.)
Language:
english
Creator:
Huang, Xi
Publisher:
University of Florida
Place of Publication:
Gainesville, Fla.
Publication Date:

Thesis/Dissertation Information

Degree:
Doctorate ( Ph.D.)
Degree Grantor:
University of Florida
Degree Disciplines:
Chemistry
Committee Chair:
FANUCCI,GAIL E
Committee Co-Chair:
BOWERS,CLIFFORD RUSSELL
Committee Members:
DUNN,BEN M
ROITBERG,ADRIAN E
MCKENNA,ROBERT

Subjects

Subjects / Keywords:
deer -- hiv
Chemistry -- Dissertations, Academic -- UF
Genre:
Chemistry thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract:
HIV-1 Protease (HIV-1 PR) is an essential enzyme for generating infectious HIV virus particles, and thus serves as a target in the fight against HIV infection. Current therapeutic inhibitors were designed against HIV-1 PR subtype B, which is prevalent in North America and Europe, and thus are less potent against other subtypes. Thus, if we can understand how the polymorphisms alter protein structure, flexibility and interaction with protease inhibitors, it may provide insights for optimizing drug candidate against highly variable targets. The access of substrates and inhibitors to the HIV-1PR active site is controlled by two-ß hairpins (terms as flap). Site-directed spinlabeling with double electron-electron resonance has been used to conclude that the average flap conformations are altered by natural polymorphisms. In this dissertation, we first used 1H-15N heteronuclear single quantum coherence (HSQC) titration to validate that DEERis a robust method to characterize HIV-1 PR conformation ensembles, even with its cryogenic measurement condition and glassing additives to HIV-1 PR system. The ligand binding affinity, which influences the binding conformational change monitoredby DEER, correlates with the exchange rate that alters HSQC peak pattern. Secondly, we focused on studying the mechanism for the appearance of the additional curled-open conformation peak in CRF01_A/E. We elucidated a possible structural explanation for the existence of this additional curled-open conformation and the increased backbone dynamics. We concluded that altered salt-bridge pattern caused by mutation is the key for the variation in HIV-1 PR subtypes’ properties. Finally, we extended the backbone dynamics study to subtype C, and three drug-resistant related single site mutants E35D, A71V and I63P. We found that constructs showing more closed flap conformation have decreased backbone dynamics. Structural explanations were proposed for the altered backbone dynamics and conformations. Subtype C has increased backbone dynamics and wide-open conformation, which probably resulted from the different salt bridge pattern caused by the H69K mutation. A71V and I63P could change the conformation and flexibility through a ß-sheets shifting mechanism.
General Note:
In the series University of Florida Digital Collections.
General Note:
Includes vita.
Bibliography:
Includes bibliographical references.
Source of Description:
Description based on online resource; title from PDF title page.
Source of Description:
This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Statement of Responsibility:
by Xi Huang.
Thesis:
Thesis (Ph.D.)--University of Florida, 2013.
Local:
Adviser: FANUCCI,GAIL E.
Local:
Co-adviser: BOWERS,CLIFFORD RUSSELL.
Electronic Access:
RESTRICTED TO UF STUDENTS, STAFF, FACULTY, AND ON-CAMPUS USE UNTIL 2014-12-31

Record Information

Source Institution:
UFRGP
Rights Management:
Applicable rights reserved.
Classification:
lcc - LD1780 2013
System ID:
UFE0046105:00001