Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

T. Ishioka; H. Yamada; T. Miyakawa; R. Morikawa; S. Akanuma; A. Yamagishi; M. Takasu

doi:10.1063/1.4968649

Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

T. Ishioka, H. Yamada^*, T. Miyakawa, R. Morikawa, S. Akanuma, A. Yamagishi, M. Takasu

^*Corresponding author for this work

School of Human Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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
Editors	Zacharoula Kalogiratou, Theodore E. Simos, Theodore Monovasilis, Theodore E. Simos, Theodore E. Simos
Publisher	American Institute of Physics Inc.
ISBN (Electronic)	9780735414549
DOIs	https://doi.org/10.1063/1.4968649
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

Publication series

Name	AIP Conference Proceedings
Volume	1790
ISSN (Print)	0094-243X
ISSN (Electronic)	1551-7616

Other

Other	International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016
Country/Territory	Greece
City	Athens
Period	16/3/17 → 16/3/20

Keywords

Coarse-grained model
Coulomb interaction
Hydrophobic effect
Molecular dynamics
Protein fibers

ASJC Scopus subject areas

Physics and Astronomy(all)

Access to Document

10.1063/1.4968649

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Ishioka, T., Yamada, H., Miyakawa, T., Morikawa, R., Akanuma, S., Yamagishi, A., & Takasu, M. (2016). Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. In Z. Kalogiratou, T. E. Simos, T. Monovasilis, T. E. Simos, & T. E. Simos (Eds.), International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 [020023] (AIP Conference Proceedings; Vol. 1790). American Institute of Physics Inc.. https://doi.org/10.1063/1.4968649

Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. / Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.

International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. ed. / Zacharoula Kalogiratou; Theodore E. Simos; Theodore Monovasilis; Theodore E. Simos; Theodore E. Simos. American Institute of Physics Inc., 2016. 020023 (AIP Conference Proceedings; Vol. 1790).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Ishioka, T, Yamada, H, Miyakawa, T, Morikawa, R, Akanuma, S, Yamagishi, A & Takasu, M 2016, Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. in Z Kalogiratou, TE Simos, T Monovasilis, TE Simos & TE Simos (eds), International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016., 020023, AIP Conference Proceedings, vol. 1790, American Institute of Physics Inc., International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016, Athens, Greece, 16/3/17. https://doi.org/10.1063/1.4968649

Ishioka T, Yamada H, Miyakawa T, Morikawa R, Akanuma S, Yamagishi A et al. Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. In Kalogiratou Z, Simos TE, Monovasilis T, Simos TE, Simos TE, editors, International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. American Institute of Physics Inc. 2016. 020023. (AIP Conference Proceedings). https://doi.org/10.1063/1.4968649

Ishioka, T. ; Yamada, H. ; Miyakawa, T. ; Morikawa, R. ; Akanuma, S. ; Yamagishi, A. ; Takasu, M. / Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation. International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016. editor / Zacharoula Kalogiratou ; Theodore E. Simos ; Theodore Monovasilis ; Theodore E. Simos ; Theodore E. Simos. American Institute of Physics Inc., 2016. (AIP Conference Proceedings).

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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.",

keywords = "Coarse-grained model, Coulomb interaction, Hydrophobic effect, Molecular dynamics, Protein fibers",

author = "T. Ishioka and H. Yamada and T. Miyakawa and R. Morikawa and S. Akanuma and A. Yamagishi and M. Takasu",

note = "Publisher Copyright: {\textcopyright} 2016 Author(s).; International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016 ; Conference date: 17-03-2016 Through 20-03-2016",

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AU - Ishioka, T.

AU - Yamada, H.

AU - Miyakawa, T.

AU - Morikawa, R.

AU - Akanuma, S.

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

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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.

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T2 - International Conference of Computational Methods in Sciences and Engineering 2016, ICCMSE 2016

Y2 - 17 March 2016 through 20 March 2016

ER -

Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation

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