A joint project of the Graduate School, Peabody College, and the Jean & Alexander Heard Library

Title page for ETD etd-07102012-120901


Type of Document Dissertation
Author Leman, Julia Koehler
URN etd-07102012-120901
Title Membrane protein structure determination using NMR spectroscopy and computational techniques
Degree PhD
Department Chemical and Physical Biology
Advisory Committee
Advisor Name Title
Hassane Mchaourab Committee Chair
Brandt Eichman Committee Member
Charles Sanders Committee Member
Jens Meiler Committee Member
Keywords
  • paramagnetic NMR restraints
  • protein structure prediction
  • protein structure determination
  • membrane proteins
  • NMR spectroscopy
Date of Defense 2012-04-11
Availability unrestricted
Abstract
Membrane protein structures are very difficult to determine by solution NMR since severe line-broadening obstructs the measurement of restraints. To alleviate this problem we describe the measurement of paramagnetic restraints on membrane proteins, particularly Paramagnetic Relaxation Enhancements (PREs), Residual Dipolar Couplings (RDCs), and Pseudo-Contact-Shifts (PCSs). A paramagnetic center is introduced into the 12 kDa protein KCNE3. A single Cysteine residue binds an EDTA-derived chelating agent that coordinates a paramagnetic lanthanide ion.

Computationally, a knowledge-based hydrophobicity scale is derived for both α-helical and β-barrel membrane proteins, that is used to train an Artificial Neural Network to predict the membrane environment from a protein sequence. The approach is extended to develop a method that is able to simultaneously predict the secondary structure as well trans-membrane spans. The novelty of the approach is the application to both α-helical proteins as well as β-barrels. The prediction accuracies are comparable or higher to other available state-of-the-art prediction tools.

Files
  Filename       Size       Approximate Download Time (Hours:Minutes:Seconds) 
 
 28.8 Modem   56K Modem   ISDN (64 Kb)   ISDN (128 Kb)   Higher-speed Access 
  Thesis_JK_2012-07-07_final.pdf 8.67 Mb 00:40:07 00:20:38 00:18:03 00:09:01 00:00:46

Browse All Available ETDs by ( Author | Department )

If you have more questions or technical problems, please Contact LITS.