Input files for targeted MD and umbrella sampling of cardiac thin filament

The cardiac thin filament is comprised of F-actin, tropomyosin, and
troponin (cTn). cTn is composed of three subunits: troponin C (cTnC),
troponin I (cTnI), and troponin T (cTnT). To computationally study the
effect of the thin filament on cTn activation events, we employed targeted
molecular dynamics followed by umbrella sampling using a model of the thin
filament to measure the thermodynamics of cTn transition events. Our
simulations revealed that the thin filament causes an increase in the free
energy required to open the cTnC hydrophobic patch and causes a more
favorable interaction between this region and the cTnI switch peptide.
Mutations to the cTn complex can lead to cardiomyopathy, a collection of
diseases that present clinically with symptoms of hypertrophy or dilation
of the cardiac muscle, leading to impairment of the heart’s ability to
function normally, and ultimately myocardial infarction or heart failure.
Upon introduction of cardiomyopathic mutations to R145 of cTnI, we
observed a general decrease in the free energy of opening the cTnC
hydrophobic patch, which is on par with previous experimental results.
These mutations also exhibited a decrease in electrostatic interactions
between cTnI-R145 and actin-E334. After introduction of a small molecule
to the wild-type cTnI-actin interface to intentionally disrupt
intersubunit contacts, we successfully observed similar thermodynamic
consequences and disruptions to the same protein-protein contacts as
observed with the cardiomyopathic mutations. Computational studies
utilizing the cTn complex in isolation would have been unable to observe
these effects, highlighting the importance of using a more physiologically
relevant thin filament model to investigate the global consequences of
cardiomyopathic mutations to the cTn complex.