Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins

Authors

Jeevan GC, Florida International UniversityFollow

Document Type

Dissertation

Degree

Doctor of Philosophy (PhD)

Major/Program

Physics

First Advisor's Name

Prem Chapagain

First Advisor's Committee Title

Co-major Professor

Second Advisor's Name

Bernard Gerstman

Second Advisor's Committee Title

Co-major Professor

Third Advisor's Name

Jessica Liberles

Third Advisor's Committee Title

Committee member

Fourth Advisor's Name

Jin He

Fourth Advisor's Committee Title

committee member

Keywords

Transformer Proteins, Ebola Virus Protein VP40, Molecular Dynamics simulation, RfaH, Jarzynski Equality, Transfer Entropy

Date of Defense

3-22-2017

Abstract

Multifunctional proteins that undergo major structural changes to perform different functions are known as “Transformer Proteins”, which is a recently identified class of proteins. One such protein that shows a remarkable structural plasticity and has two distinct functions is the transcription antiterminator, RfaH. Depending on the interactions between its N-terminal domain and its C-terminal domain, the RfaH CTD exists as either an all-α-helix bundle or all-β-barrel structure. Another example of a transformer protein is the Ebola virus protein VP40 (eVP40), which exists in different conformations and oligomeric states (dimer, hexamer, and octamer), depending on the required function.I performed Molecular Dynamics (MD) computations to investigate the structural conversion of RfaH-CTD from its all-a to all-b form. I used various structural and statistical mechanics tools to identify important residues involved in controlling the conformational changes. In the full-length RfaH, the interdomain interactions were found to present the major barrier in the structural conversion of RfaH-CTD from all-a to all-b form. I mapped the energy landscape for the conformational changes by calculating the potential of mean force using the Adaptive Biasing Force and Jarzynski Equality methods. Similarly, the interdomain salt-bridges in the eVP40 protomer were found to play a critical role in domain association and plasma membrane (PM) assembly. This molecular dynamic simulation study is supported by virus like particle budding assays investigated by using live cell imaging that highlighted the important role of these saltbridges. I also investigated the plasma membrane association of the eVP40 dimer in various PM compositions and found that the eVP40 dimer readily associates with the PM containing POPS and PIP₂ lipids. Also, the CTD helices were observed to be important in stabilizing the dimer-membrane complex. Coarse-grained MD simulations of the eVP40 hexamer and PM system revealed that the hexamer enhances the PIP₂ lipid clustering at the lower leaflet of the PM. These results provide insight on the critical steps in the Ebola virus life cycle.

Identifier

FIDC001746

ORCID

orcid.org/0000-0002-3589-0408

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

Recommended Citation

GC, Jeevan, "Molecular Dynamics Investigations of Structural Conversions in Transformer Proteins" (2017). FIU Electronic Theses and Dissertations. 3225.
https://digitalcommons.fiu.edu/etd/3225