Dissertation
THE EFFECT OF MUTATIONS ON INDUCED PROTEIN FOLDING STUDIED BY MOLECULAR DYNAMICS SIMULATIONS
Washington State University
Doctor of Philosophy (PhD), Washington State University
07/2024
DOI:
https://doi.org/10.7273/000007084
Abstract
The purpose of this dissertation is to advance the understanding of molecular dynamics simulations (MDS) as a tool to screen the effects of mutations on protein folding. In the first chapter, two systems to test by MDS are described. The second chapter delves into utilizing MDS to forecast the binding affinity between leiomodin (Lmod) and tropomyosin (Tpm), proteins pivotal in cardiac muscle proper formation. We used circular dichroism (CD) to measure the stability of the complex between Lmod2 and Tpm fragments that contained Tpm- and Lmod2-binding sites, respectively. We examined effects of mutations in Lmod2 fragment on the complex stability both by CD and MDS. From MDS data we calculated standard free energies, and a correlation between CD-determined complex stabilities and MDS-derived free energies was determined, highlighting MDS's utility in studying point mutations for the complex formation. In the third chapter, we used MDS to understand the folding of Pro-rich proteins using as an example granulin modules. The secreted glycoprotein progranulin has 7.5 modules (p,G,F,B,A,C,D and E), each full-size module contains 12 Cys. Mutations in granulin have been linked to frontotemporal lobar degeneration (FTLD), which is an early-onset dementia syndrome. So far the residue specific interactions on the structural characteristics and cysteine-cysteine pairing pattern of granulin are not well understood. Using MDS we studied the effect of W541 mutation on granulin E stability and disulfide bond pattern. The folding behavior of granulin was validated by comparing the computational models to the experimental data obtained using gel electrophoresis and circular dichroism (CD).
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Details
- Title
- THE EFFECT OF MUTATIONS ON INDUCED PROTEIN FOLDING STUDIED BY MOLECULAR DYNAMICS SIMULATIONS
- Creators
- Eduardo J. Sánchez Díaz
- Contributors
- Alla Kostyukova (Co-Chair)Dmitri Tolkatchev (Co-Chair)Wenji Dong (Committee Member)Steven Saunders (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- School of Chemical Engineering and Bioengineering
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 111
- Identifiers
- 99901152337901842
- Language
- English
- Resource Type
- Dissertation