TY - JOUR
T1 - Theoretical analysis of the domain-swapped dimerization of cytochrome c
T2 - An MD and 3D-RISM approach
AU - Yoshida, Norio
AU - Higashi, Masahiro
AU - Motoki, Hideyoshi
AU - Hirota, Shun
N1 - Funding Information:
Numerical calculations were conducted in part at the Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences. This work was supported by grants-in-aid (Nos. JP25410021, JP26104526, JP16H00842, JP16K05519, JP16H00778, JP16KT0165, JP17K05757, JP16H00839, and JP26288080) from MEXT/JSPS Japan.
Funding Information:
Numerical calculations were conducted in part at the Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences. This work was supported by grants-in-aid (Nos. JP25410021, JP26104526, JP16H00842, JP16K05519, JP16H00778, JP16KT0165, JP17K05757, JP16H00839, and JP26288080) from MEXT/JSPS, Japan.
Publisher Copyright:
© 2018 Author(s).
PY - 2018/1/14
Y1 - 2018/1/14
N2 - The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.
AB - The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.
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U2 - 10.1063/1.5009785
DO - 10.1063/1.5009785
M3 - Article
C2 - 29331115
AN - SCOPUS:85040458690
VL - 148
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 2
M1 - 025102
ER -