Abstract

The idea of developing a Bio-molecular mechanical device has attracted the attention of many research groups due to its promising Nano and Bio- technological applications such as flow-control valves, switches and bio-sensors. T4 Lysozyme protein is an enzyme, which has been extensively studied. This protein provides a wealth of information regarding the structure/function relationship of proteins at atomic resolution. An engineered variant of T4 Lysozyme has been reported to trigger a large scale translocation of an engineered helix (∼ 2nm), upon the addition of an external ligand. The design was based on the duplication of a surface helix, followed by manipulating the stability of an adjacent loop, which caused the duplicated helix to switch between two conformations. The purpose of this study is to investigate the dynamics of the engineered motion for potential Nano and Biotechnological applications. Many wild type and mutant static crystal structures of T4 Lysozyme have been shown to display a range of about 50 degrees in hinge bending motion between the N- and C-terminal domains of the protein, indicating intrinsic flexibility. The present molecular dynamics simulations detect similar motion in the engineered protein, within 100 nanosecond time scale. A preliminary mathematical model (solvent free) describing the hinge bending motion and the impact force is constructed. However, in the nanosecond time scale, the engineered triggered motion (the helical trans location) was partially detected only when bond constraints were significantly relaxed.

Department

Physics Department

Degree Name

MS in Physics

Graduation Date

6-1-2016

Submission Date

May 2016

First Advisor

Elsheikh, Salah

Committee Member 1

Shawky, Ahmed

Committee Member 2

Yousef, Mohammad

Extent

82 p.

Document Type

Master's Thesis

Rights

The author retains all rights with regard to copyright. The author certifies that written permission from the owner(s) of third-party copyrighted matter included in the thesis, dissertation, paper, or record of study has been obtained. The author further certifies that IRB approval has been obtained for this thesis, or that IRB approval is not necessary for this thesis. Insofar as this thesis, dissertation, paper, or record of study is an educational record as defined in the Family Educational Rights and Privacy Act (FERPA) (20 USC 1232g), the author has granted consent to disclosure of it to anyone who requests a copy.

Institutional Review Board (IRB) Approval

Approval has been obtained for this item

Comments

This work was supported by the LinkSCEEM-2 project, funded by the European Commission under the 7th Framework Programme through Ca- pacities Research Infrastructure, INFRA-2010-1.2.3 Virtual Research Com- munities, Combination of Collaborative Project and Coordination and Sup- port Actions (CP-CSA) under grant agreement no RI-261600. Prepara- tory Projects IDs: lspre150, lspre176 and lspre228. Production Project ID: pro14b102s1.

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