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Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints.

Jayasundar JJ, Xing J, Robinson JM, Cheung HC, Dong WJ - PLoS ONE (2014)

Bottom Line: In the presence of saturating Ca(2+) the above said phenomenon were absent.We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin.Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

View Article: PubMed Central - PubMed

Affiliation: Voiland School of Chemical Engineering and Bioengineering and The Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington, United States of America.

ABSTRACT
Cardiac troponin (cTn) is the Ca(2+)-sensitive molecular switch that controls cardiac muscle activation and relaxation. However, the molecular detail of the switching mechanism and how the Ca(2+) signal received at cardiac troponin C (cTnC) is communicated to cardiac troponin I (cTnI) are still elusive. To unravel the structural details of troponin switching, we performed ensemble Förster resonance energy transfer (FRET) measurements and molecular dynamic (MD) simulations of the cardiac troponin core domain complex. The distance distributions of forty five inter-residue pairs were obtained under Ca(2+)-free and saturating Ca(2+) conditions from time-resolved FRET measurements. These distances were incorporated as restraints during the MD simulations of the cardiac troponin core domain. Compared to the Ca(2+)-saturated structure, the absence of regulatory Ca(2+) perturbed the cTnC N-domain hydrophobic pocket which assumed a closed conformation. This event partially unfolded the cTnI regulatory region/switch. The absence of Ca(2+), induced flexibility to the D/E linker and the cTnI inhibitory region, and rotated the cTnC N-domain with respect to rest of the troponin core domain. In the presence of saturating Ca(2+) the above said phenomenon were absent. We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin. Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

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Electrostatic surface analysis of the N-domain of cTnC.Depicts the N-domain of cTnC in the Ca2+-free state (figures a through c) and Ca2+-saturated states (figures d through f). The cTnC N-domain helices A through D are colored as red, green, cyan and blue respectively. (a) Transparent rendering of the electrostatic surface is shown with the protein in cartoon. (b) In the Ca2+-free state the loss of regulatory Ca2+ caused the rearrangement of helices B and C. These helices are no longer orthogonal to each other but nearly parallel. This resulted in a breach in the hydrophobic pocket that surrounded the cTnI-Rr (pointed out by the arrow). (c) The cTnC N-domain hydrophobic pocket when viewed from below the cTnC N-domain. This view shows the hydrophobic environment in which the cTnI-Rr is located. The arrows points to the gap in the hydrophobic pocket. (d) Transparent rendering of the electrostatic surface with the protein rendered as cartoon. (e) In the Ca2+-saturated state there is no breach in the hydrophobic pocket within which the cTnI-Rr is held. (f) The cTnC N-domain hydrophobic pocket in the Ca2+-saturated state when view from below.
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pone-0087135-g007: Electrostatic surface analysis of the N-domain of cTnC.Depicts the N-domain of cTnC in the Ca2+-free state (figures a through c) and Ca2+-saturated states (figures d through f). The cTnC N-domain helices A through D are colored as red, green, cyan and blue respectively. (a) Transparent rendering of the electrostatic surface is shown with the protein in cartoon. (b) In the Ca2+-free state the loss of regulatory Ca2+ caused the rearrangement of helices B and C. These helices are no longer orthogonal to each other but nearly parallel. This resulted in a breach in the hydrophobic pocket that surrounded the cTnI-Rr (pointed out by the arrow). (c) The cTnC N-domain hydrophobic pocket when viewed from below the cTnC N-domain. This view shows the hydrophobic environment in which the cTnI-Rr is located. The arrows points to the gap in the hydrophobic pocket. (d) Transparent rendering of the electrostatic surface with the protein rendered as cartoon. (e) In the Ca2+-saturated state there is no breach in the hydrophobic pocket within which the cTnI-Rr is held. (f) The cTnC N-domain hydrophobic pocket in the Ca2+-saturated state when view from below.

Mentions: Another interesting observation in our modeling study pertains to the cTnI-Rr held within the cTnC N-domain hydrophobic pocket. The cTnI-Rr was dilated in the Ca2+-free state but was still held within the cTnC N-domain hydrophobic pocket. It did not drop off the cTnC N-domain hydrophobic pocket as seen in the crystal structure of the sTn Ca2+-free state (1YVO.pdb) nor had it moved away from cTnC as suggested by the authors who solved the structure of cardiac troponin core domain [10]. Instead in the Ca2+-free state the cTnI-Rr was dilated and had rotated clockwise with the whole N-domain to 80 degrees to the normal (was positioned at 1 and 7 O'clock) and in the Ca2+-saturated state it retained it secondary structure and was oriented at 120 degrees to the normal (between 11 and 5 O'clock). It seemed like the cTnI-Rr undergoes a swivel like motion. To understand what could cause the dilation we ran an electrostatic surface analysis of the cTnC N-domain and observed that the reorientation of helix B caused a gap in the hydrophobic pocket within which the cTnI-Rr is held (Figures 7a through 7c). Whereas, in the Ca2+-saturated state the cTnC N-domain hydrophobic pocket was intact and the cTnI-Rr held within the hydrophobic pocket was well structured. The secondary structure timeline of the cTnI-Rr is presented in Figure 8. It is clearly seen that the cTnI-Rr does undergo loss of secondary structure in the Ca2+-free state with respect to the Ca2+-saturated state.


Molecular dynamics simulations of the cardiac troponin complex performed with FRET distances as restraints.

Jayasundar JJ, Xing J, Robinson JM, Cheung HC, Dong WJ - PLoS ONE (2014)

Electrostatic surface analysis of the N-domain of cTnC.Depicts the N-domain of cTnC in the Ca2+-free state (figures a through c) and Ca2+-saturated states (figures d through f). The cTnC N-domain helices A through D are colored as red, green, cyan and blue respectively. (a) Transparent rendering of the electrostatic surface is shown with the protein in cartoon. (b) In the Ca2+-free state the loss of regulatory Ca2+ caused the rearrangement of helices B and C. These helices are no longer orthogonal to each other but nearly parallel. This resulted in a breach in the hydrophobic pocket that surrounded the cTnI-Rr (pointed out by the arrow). (c) The cTnC N-domain hydrophobic pocket when viewed from below the cTnC N-domain. This view shows the hydrophobic environment in which the cTnI-Rr is located. The arrows points to the gap in the hydrophobic pocket. (d) Transparent rendering of the electrostatic surface with the protein rendered as cartoon. (e) In the Ca2+-saturated state there is no breach in the hydrophobic pocket within which the cTnI-Rr is held. (f) The cTnC N-domain hydrophobic pocket in the Ca2+-saturated state when view from below.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928104&req=5

pone-0087135-g007: Electrostatic surface analysis of the N-domain of cTnC.Depicts the N-domain of cTnC in the Ca2+-free state (figures a through c) and Ca2+-saturated states (figures d through f). The cTnC N-domain helices A through D are colored as red, green, cyan and blue respectively. (a) Transparent rendering of the electrostatic surface is shown with the protein in cartoon. (b) In the Ca2+-free state the loss of regulatory Ca2+ caused the rearrangement of helices B and C. These helices are no longer orthogonal to each other but nearly parallel. This resulted in a breach in the hydrophobic pocket that surrounded the cTnI-Rr (pointed out by the arrow). (c) The cTnC N-domain hydrophobic pocket when viewed from below the cTnC N-domain. This view shows the hydrophobic environment in which the cTnI-Rr is located. The arrows points to the gap in the hydrophobic pocket. (d) Transparent rendering of the electrostatic surface with the protein rendered as cartoon. (e) In the Ca2+-saturated state there is no breach in the hydrophobic pocket within which the cTnI-Rr is held. (f) The cTnC N-domain hydrophobic pocket in the Ca2+-saturated state when view from below.
Mentions: Another interesting observation in our modeling study pertains to the cTnI-Rr held within the cTnC N-domain hydrophobic pocket. The cTnI-Rr was dilated in the Ca2+-free state but was still held within the cTnC N-domain hydrophobic pocket. It did not drop off the cTnC N-domain hydrophobic pocket as seen in the crystal structure of the sTn Ca2+-free state (1YVO.pdb) nor had it moved away from cTnC as suggested by the authors who solved the structure of cardiac troponin core domain [10]. Instead in the Ca2+-free state the cTnI-Rr was dilated and had rotated clockwise with the whole N-domain to 80 degrees to the normal (was positioned at 1 and 7 O'clock) and in the Ca2+-saturated state it retained it secondary structure and was oriented at 120 degrees to the normal (between 11 and 5 O'clock). It seemed like the cTnI-Rr undergoes a swivel like motion. To understand what could cause the dilation we ran an electrostatic surface analysis of the cTnC N-domain and observed that the reorientation of helix B caused a gap in the hydrophobic pocket within which the cTnI-Rr is held (Figures 7a through 7c). Whereas, in the Ca2+-saturated state the cTnC N-domain hydrophobic pocket was intact and the cTnI-Rr held within the hydrophobic pocket was well structured. The secondary structure timeline of the cTnI-Rr is presented in Figure 8. It is clearly seen that the cTnI-Rr does undergo loss of secondary structure in the Ca2+-free state with respect to the Ca2+-saturated state.

Bottom Line: In the presence of saturating Ca(2+) the above said phenomenon were absent.We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin.Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

View Article: PubMed Central - PubMed

Affiliation: Voiland School of Chemical Engineering and Bioengineering and The Department of Integrated Physiology and Neuroscience, Washington State University, Pullman, Washington, United States of America.

ABSTRACT
Cardiac troponin (cTn) is the Ca(2+)-sensitive molecular switch that controls cardiac muscle activation and relaxation. However, the molecular detail of the switching mechanism and how the Ca(2+) signal received at cardiac troponin C (cTnC) is communicated to cardiac troponin I (cTnI) are still elusive. To unravel the structural details of troponin switching, we performed ensemble Förster resonance energy transfer (FRET) measurements and molecular dynamic (MD) simulations of the cardiac troponin core domain complex. The distance distributions of forty five inter-residue pairs were obtained under Ca(2+)-free and saturating Ca(2+) conditions from time-resolved FRET measurements. These distances were incorporated as restraints during the MD simulations of the cardiac troponin core domain. Compared to the Ca(2+)-saturated structure, the absence of regulatory Ca(2+) perturbed the cTnC N-domain hydrophobic pocket which assumed a closed conformation. This event partially unfolded the cTnI regulatory region/switch. The absence of Ca(2+), induced flexibility to the D/E linker and the cTnI inhibitory region, and rotated the cTnC N-domain with respect to rest of the troponin core domain. In the presence of saturating Ca(2+) the above said phenomenon were absent. We postulate that the secondary structure perturbations experienced by the cTnI regulatory region held within the cTnC N-domain hydrophobic pocket, coupled with the rotation of the cTnC N-domain would control the cTnI mobile domain interaction with actin. Concomitantly the rotation of the cTnC N-domain and perturbation of the D/E linker rigidity would control the cTnI inhibitory region interaction with actin to effect muscle relaxation.

Show MeSH
Related in: MedlinePlus