Troponin structure: its modulation by Ca²⁺and phosphorylation studied by molecular dynamics simulations

Abstract

The only available crystal structure of the human cardiac troponin molecule (cTn) in the Ca(2+) activated state does not include crucial segments, including the N-terminus of the cTn inhibitory subunit (cTnI). We have applied all-atom molecular dynamics (MD) simulations to study the structure and dynamics of cTn, both in the unphosphorylated and bis-phosphorylated states at Ser23/Ser24 of cTnI. We performed multiple microsecond MD simulations of wild type (WT) cTn (6, 5 μs) and bisphosphorylated (SP23/SP24) cTn (9 μs) on a 419 amino acid cTn model containing human sequence cTnC (1-161), cTnI (1-171) and cTnT (212-298), including residues not present in the crystal structure. We have compared our results to previous computational studies, and proven that longer simulations and a water box of at least 25 Å are needed to sample the interesting conformational shifts both in the native and bis-phosphorylated states. As a consequence of the introduction into the model of the C-terminus of cTnT that was missing in previous studies, cTnC-cTnI interactions that are responsible for the cTn dynamics are altered. We have also shown that phosphorylation does not increase cTn fluctuations, and its effects on the protein-protein interaction profiles cannot be assessed in a significant way. Finally, we propose that phosphorylation could provoke a loss of Ca(2+) by stabilizing out-of-coordination distances of the cTnC's EF hand II residues, and in particular Ser 69.

Restrictive Cardiomyopathy Troponin I R145W Mutation Does Not Perturb Myofilament Length-dependent Activation in Human Cardiac Sarcomeres

“…However, we did not see such intramolecular interactions in preliminary MD simulation runs. This preliminary result is consistent with a recent MD study by Gould and co-workers (42) who reported that this intramolecular interaction is both rare and not affected by PKA-mediated phosphorylation. Accordingly, we focused instead on the impact of R145W and T43E on dynamic interactions between cTnI residue 145 and helix C of cTnC (residues Glu-56, Glu-59, and Glu-63).…”

Interaction of N-3-oxododecanoyl homoserine lactone with transcriptional regulator LasR ofPseudomonas aeruginosa: Insights from molecular docking and dynamics simulations

“…The analysis protocol approach was similar to the works of Wolf et al (48) and Zamora et al (49) and the following techniques were used for the analysis:…”

“…The process of applying PCA to a protein trajectory is called Essential Dynamics (ED) (49)(50)(51). PC analysis, performed on Cartesian coordinates has become an important tool for the examination of conformational changes.…”

The Importance of Intrinsically Disordered Segments of Cardiac Troponin in Modulating Function by Phosphorylation and Disease-Causing Mutations

“…Blue represents TnC (1–161), red represents TnI (1–171) and green represents TnT (212–298). The image was adapted from Zamora et al (2016a) with permission from the PCCP Owner Societies.…”

“…The more recent MD simulation study by Zamora et al provides an even more complete model of human cardiac troponin sequence (Figure 1B), including the C-terminal peptide of TnT not present in previous studies. Multiple 750 ns simulations, totaling over 10 μs, were performed and the size of the box simulated has been increased to 25Å to avoid virtual self-association (Zamora et al, 2016a). …”