TY - GEN
T1 - Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation
AU - Ishioka, T.
AU - Yamada, H.
AU - Miyakawa, T.
AU - Morikawa, R.
AU - Akanuma, S.
AU - Yamagishi, A.
AU - Takasu, M.
N1 - Publisher Copyright:
© 2016 Author(s).
PY - 2016/12/6
Y1 - 2016/12/6
N2 - Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.
AB - Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.
KW - Coarse-grained model
KW - Coulomb interaction
KW - Hydrophobic effect
KW - Molecular dynamics
KW - Protein fibers
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U2 - 10.1063/1.4968649
DO - 10.1063/1.4968649
M3 - Conference contribution
AN - SCOPUS:85008714409
T3 - AIP Conference Proceedings
BT - International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
A2 - Kalogiratou, Zacharoula
A2 - Simos, Theodore E.
A2 - Monovasilis, Theodore
A2 - Simos, Theodore E.
A2 - Simos, Theodore E.
PB - American Institute of Physics Inc.
T2 - International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
Y2 - 17 March 2016 through 20 March 2016
ER -