Skip to Main Content
 

Global Search Box

 
 
 
 

Files

File List


AustinCool_Dissertation.pdf (3.61 MB)

ETD Abstract Container

Abstract Header

Investigation of Cardiac Troponin Dynamics by Enhanced Sampling Methods

Cool, Austin
http://rave.ohiolink.edu/etdc/view?acc_num=osu1681730144044273

Abstract Details

2023, Doctor of Philosophy, Ohio State University, Biophysics.
This dissertation explores the use of applying molecular dynamics (MD) and enhanced sampling methods towards understanding dynamics of the cardiac troponin complex (cTn) and the thermodynamic and functional consequences introduced by cardiomyopathic mutations. Chapter 2 explores an idea from the Davis group at Ohio State that cardiomyopathic mutations in the cTnI inhibitory peptide region (cTnIIP) can cause a reduced effective concentration of the cTnI switch peptide (cTnISP) to the cTnC hydrophobic patch region (cTnCHP). We utilized the Ca2+-unbound cTn structure produced by Yamada and colleagues to simulate both a normal cTn complex (tethered) and a model of the cTn complex with the cTnIIP removed and a free cTnISP (untethered) using molecular dynamics. Our results showed that the tether was essential in producing an effective concentration of cTnISP necessary for physiological function. We also observed that cardiomyopathic mutations did not significantly affect the effective concentration of cTnISP to the cTnCHP but did cause alterations to the dynamics and flexibility of the cTnIIP region. We observed in our simulations from chapter 2 that the cTnCHP never opened for any significant amount of time. Therefore, in the third chapter we sought to produce a trajectory of the transition event between the Ca2+-unbound and Ca2+-bound cTn forms by again using structures produced by Yamada. We successfully performed this using Targeted MD (TMD) and were able to observe a transition from a Ca2+-unbound, cTnCHP closed, cTnISP unbound form of cTn to a Ca2+-bound, cTnCHP open, cTnISP bound cTn. We then selected windows from the trajectory that correlated strongly with the cTnCHP opening and cTnISP binding transition events and performed umbrella sampling (US) simulations. Our results show near perfect replication of NMR studies on the cTnISP binding event and strong correlation with previous computational studies on the cTnCHP opening event. We then introduced mutations to the cTn complex that cause cardiomyopathy or alter its Ca2+-sensitivity and observed a general decrease in the free energy of opening the cTnCHP. For the fourth chapter, we sought to employ the previously successful TMD and US combinatorial approach, but with the cTn within the context of the thin filament. This increase in system complexity would allow us to characterize the effect actin and tropomyosin have on the thermodynamics of the cTnCHP opening and cTnISP binding events. We were again able to successfully produce a trajectory and the transition event and the resulting US simulations elucidated that the thin filament causes and increase in the cTnCHP opening event and facilitate more favorable binding between the cTnISP and cTnCHP. We again observed a general decrease in the free energy of opening the cTnCHP upon the introduction of cardiomyopathic mutations to R145 of the cTnIIP. These mutations were also observed to cause a decrease in interactions between cTnI-R145 and actin residues E334, so we introduced a small molecule to the intersubunit space to intentionally mimic a cardiomyopathic mutation by disrupting contacts between these two residues. US simulations of the small molecule models produced the same thermodynamic consequences as the cardiomyopathic mutations, indicating this intersubunit region could be a potential site for drug discovery to correct disease states of the heart.
Steffen Lindert (Advisor)
Mark Ziolo (Committee Member)
Marcos Sotomayor (Committee Member)
Xiaolin Cheng (Committee Member)
127 p.
Biophysics
Molecular Dynamics; Enhanced Sampling Methods; Cardiac Troponin; Umbrella Sampling; Targeted Molecular Dynamics; Computational Biophysics

Recommended Citations

Citations

  • Cool, A. (2023). Investigation of Cardiac Troponin Dynamics by Enhanced Sampling Methods [Doctoral dissertation, Ohio State University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=osu1681730144044273

    APA Style (7th edition)

  • Cool, Austin. Investigation of Cardiac Troponin Dynamics by Enhanced Sampling Methods. 2023. Ohio State University, Doctoral dissertation. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=osu1681730144044273.

    MLA Style (8th edition)

  • Cool, Austin. "Investigation of Cardiac Troponin Dynamics by Enhanced Sampling Methods." Doctoral dissertation, Ohio State University, 2023. http://rave.ohiolink.edu/etdc/view?acc_num=osu1681730144044273

    Chicago Manual of Style (17th edition)

osu1681730144044273
0
© 2023, all rights reserved.
This open access ETD is published by The Ohio State University and OhioLINK.