Abstract
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.
| Original language | English |
|---|---|
| Title of host publication | International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 |
| Publisher | American Institute of Physics Inc. |
| Volume | 1790 |
| ISBN (Electronic) | 9780735414549 |
| DOIs | |
| Publication status | Published - 2016 Dec 6 |
| Event | International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 - Athens, Greece Duration: 2016 Mar 17 → 2016 Mar 20 |
Other
| Other | International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 |
|---|---|
| Country | Greece |
| City | Athens |
| Period | 16/3/17 → 16/3/20 |
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Keywords
- Coarse-grained model
- Coulomb interaction
- Hydrophobic effect
- Molecular dynamics
- Protein fibers
ASJC Scopus subject areas
- Physics and Astronomy(all)
Cite this
Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. / Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, Satoshi; Yamagishi, A.; Takasu, M.
International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. Vol. 1790 American Institute of Physics Inc., 2016. 020023.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
}
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, Satoshi
AU - Yamagishi, A.
AU - Takasu, M.
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
UR - http://www.scopus.com/inward/record.url?scp=85008714409&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85008714409&partnerID=8YFLogxK
U2 - 10.1063/1.4968649
DO - 10.1063/1.4968649
M3 - Conference contribution
AN - SCOPUS:85008714409
VL - 1790
BT - International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
PB - American Institute of Physics Inc.
ER -