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Title page for ETD etd-04132012-150822

Type of Document Master's Thesis
Author Kim, Robert Jaewook
URN etd-04132012-150822
Title Structural Determination and Computational Prediction of Adenoviral Surface Epitopes Provide Insight into the Mechanisms of Adenoviral Inactivation by Human Defensin 5
Degree Master of Science
Department Chemical and Physical Biology
Advisory Committee
Advisor Name Title
Phoebe L. Stewart Committee Chair
Albert H. Beth Committee Member
Anne K. Kenworthy Committee Member
  • structural biology
  • molecular dynamics
  • cryo-electron microscopy
  • Human Defensin 5
  • HD5
  • CryoEM
  • Human Adenovirus
  • Adenovirus
  • Defensin
  • MDFF
Date of Defense 2012-04-06
Availability unrestricted
Adenovirus has been studied for many years for its potential as a gene delivery vector in gene therapy applications. One of the more challenging problems under research is the design of Adenoviral vectors that can be effectively targeted to tissues while evading detection and destruction by the immune system. Most serotypes of Human Adenovirus are readily defeated by the innate immune system through the action of small peptides known as defensins.

In this work, CryoEM single particle reconstruction and molecular dynamics techniques are employed to elucidate the mechanisms by which HD5 inactivates Adenovirus. Subnanometer structures of chimeric Adenoviral constructs exposed to HD5 were determined. One construct, Ad5.F35 is known to be sensitive to HD5, while another construct, Ad5.PB/GYAR, is known to be insensitive to HD5 inactivation. Structures of these constructs revealed key binding sites that mediate the inactivation of Adenovirus.

An atomic model of the vertex region of Ad5.F35 was constructed in order to simulate the interaction of HD5 with the Adenoviral capsid. Using the Ad5.F35 + HD5 electron density map as a restraint, molecular dynamics simulations were run in order to shed light on the nature of this interaction. These simulations suggest a role for flexible RGD loop regions of the Adenoviral penton base protein (protein III) in the stabilization of the Adenovirus-HD5 binding interaction. Further study and simulation may lead to the development of a testable working model of this interaction, opening up opportunities for exploitation of this mechanism for future endeavors in Adenoviral vector design.

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