Ensemble Interpretation of Domain Mobility in Modular Protein Pin1 by NMR and Molecular Dynamics

Doctoral Dissertation
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Abstract

The majority of proteins have multiple independently folding and functioning domains; this is known as protein modularity. Most of these molecular machines are tethered together by flexible linkers. Consequently, there is a lot of mobility between the domains of modular proteins. This mobility allows proteins to use interdomain motion to carry out their functions, often with different partners. Thus, if we want to understand how modular proteins function, we must characterize the range of conformations modular proteins sample. This thesis makes strides to describe the biophysical behavior of modular proteins and understand how their interdomain motions matter for function. The result is new developments in molecular biophysics on two levels; (i) methodological and (ii) biological.

A biophysical method to describe flexible systems needs to be dynamic, or at least, characterize the ensemble of conformations visited. This thesis demonstrates a new way to do this. We recognized the power of combining NMR parameters that can resolve long-range atomic information with molecular dynamics to view the atomic details of these large-scale motions. To this end, we developed the MapSGLD-NMR method for quantitatively describing interdomain orientations of modular proteins.

As a test system for this new method, this thesis focuses on human Pin1, a two-domain signaling protein of therapeutic relevance because it is implicated in Alzheimer?s disease, cancer, and many other human diseases. The ensemble description of Pin1 uncovers insights about its interaction modes with different binding partners. The results suggest we can control interdomain motions of Pin1. The biological impact of this work is that we may be able to account for interdomain motions to improve drug discovery tactics for modular proteins.

Attributes

Attribute NameValues
URN
  • etd-12082014-000142

Author Jill J Bouchard
Advisor Jeffrey W. Peng
Contributor Patricia L. Clark, Committee Member
Contributor Zachary Schultz, Committee Member
Contributor Jeffrey W. Peng, Committee Chair
Degree Level Doctoral Dissertation
Degree Discipline Chemistry and Biochemistry
Degree Name PhD
Defense Date
  • 2014-11-24

Submission Date 2014-12-08
Country
  • United States of America

Subject
  • binding

  • Pin1

  • SGLD

  • modularity

  • RDC

  • simulation

  • EMAP

  • NMR

Publisher
  • University of Notre Dame

Language
  • English

Record Visibility and Access Public
Content License
  • All rights reserved

Departments and Units

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