リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models

Mori, Toshifumi 森, 俊文 モリ, トシフミ Yoshida, Norio 吉田, 紀生 ヨシダ, ノリオ 九州大学

2023.07.17

概要

The adenosine triphosphate (ATP)–protein interactions have been of great interest since the recent experimental finding of ATP’s role as a hydrotrope. The interaction between ATP and disordered protei

この論文で使われている画像

参考文献

W. Merlevede, J. R. Vandenheede, J. Goris,

and S. Yang, “Regulation of atp–mg-

dependent protein phosphatase,” Current Topics in Cellular Regulation 23, 177–215

(1984).

T. W. Traut, “Physiological concentrations of purines and pyrimidines,” Molecular and

Cellular Biochemistry 140, 1–22 (1994).

N. Sakaki, R. Shimo-Kon, K. Adachi, H. Ito, S. Furuike, E. Muneyuki, M. Yoshida, and

K. Kinosita, “One rotary mechanism for f1-atpase over atp concentrations from millimolar

down to nanomolar,” Biophysical Journal 88, 2047–2056 (2005).

J. V. Greiner and T. Glonek, “Hydrotropic function of atp in the crystalline lens,” Experimental Eye Research 190, 107862 (2020).

A. Patel, L. Malinovska, S. Saha, J. Wang, S. Alberti, Y. Krishnan, and A. A. Hyman,

“Atp as a biological hydrotrope,” Science 356, 753–756 (2017).

S. Sridharan, N. Kurzawa, T. Werner, I. Gnthner, D. Helm, W. Huber, M. Bantscheff, and

M. M. Savitski, “Proteome-wide solubility and thermal stability profiling reveals distinct

regulatory roles for atp,” Nature Communications 10, 1155 (2019).

J. Kang, L. Lim, and J. Song, “Atp binds and inhibits the neurodegeneration-associated

fibrillization of the fus rrm domain,” Communications Biology 2, 223 (2019).

F. Paoletti, F. Merzel, A. Cassetta, I. Ogris, S. Covaceuszach, J. Grdadolnik, D. Lamba,

and S. G. Grdadolnik, “Endogenous modulators of neurotrophin signaling: Landscape of

the transient atp-ngf interactions,” Computational and Structural Biotechnology Journal

19, 2938–2949 (2021).

Z. Tian and F. Qian, “Adenosine triphosphate-induced rapid liquid-liquid phase separation

of a model igg1 mab,” Molecular Pharmaceutics 18, 267–274 (2021).

10

J. Kang, L. Lim, and J. Song, “Atp enhances at low concentrations but dissolves at high

concentrations liquid-liquid phase separation (llps) of als/ftd-causing fus,” Biochemical

21

Accepted to J. Chem. Phys. 10.1063/5.0158046

and Biophysical Research Communications 504, 545–551 (2018).

11

J. Kang, L. Lim, Y. Lu, and J. Song, “A unified mechanism for llps of als/ftld-causing

This is the author’s peer reviewed, accepted manuscript. However, the online version of record will be different from this version once it has been copyedited and typeset.

PLEASE CITE THIS ARTICLE AS DOI: 10.1063/5.0158046

fus as well as its modulation by atp and oligonucleic acids,” PLoS Biology 17, e3000327

(2019).

12

L. Wang, L. Lim, M. Dang, and J. Song, “A novel mechanism for atp to enhance the

functional oligomerization of tdp-43 by specific binding,” Biochemical and Biophysical

Research Communications 514, 809–814 (2019).

13

C. Neuberg, “Hydrotropic phenomena. i,” Biochem. Z. 76, 107–176 (1916).

14

J. Mehringer and W. Kunz, “Carl neuberg’s hydrotropic appearances (1916),” Advances

in Colloid and Interface Science 294, 102476 (2021).

15

M. Nishizawa, E. Walinda, D. Morimoto, B. Kohn, U. Scheler, M. Shirakawa, and K. Sugase, “Effects of weak nonspecific interactions with atp on proteins,” Journal of the American Chemical Society 143, 11982–11993 (2021).

16

X. Ou, Y. Lao, J. Xu, Y. Wutthinitikornkit, R. Shi, X. Chen, and J. Li, “Atp can efficiently

stabilize protein through a unique mechanism,” JACS Au 1, 1766–1777 (2021).

17

G. Hu, X. Ou, and J. Li, “Mechanistic insight on general protein-binding ability of atp

and the impacts of arginine residues,” Journal of Physical Chemistry B 126, 4647–4658

(2022).

18

S. Sarkar and J. Mondal, “Mechanistic insights on atp’s role as a hydrotrope,” Journal of

Physical Chemistry B 125, 7717–7731 (2021).

19

M. P. Pandey, S. Sasidharan, V. A. Raghunathan, and H. Khandelia, “Molecular mechanism of hydrotropic properties of gtp and atp,” Journal of Physical Chemistry B 126,

8486–8494 (2022).

20

J. Mehringer, T. M. Do, D. Touraud, M. Hohenschutz, A. Khoshsima, D. Horinek, and

W. Kunz, “Hofmeister versus neuberg: is atp really a biological hydrotrope?” Cell Reports

Physical Science 2, 100343 (2021).

21

R. Roy and S. Paul, “Potential of atp toward prevention of hiapp oligomerization and

destabilization of hiapp protofibrils: An in silico perspective,” Journal of Physical Chemistry B 125, 3510–3526 (2021).

22

S. Pal and S. Paul, “Atp controls the aggregation of a16-22 peptides,” Journal of Physical

Chemistry B 124, 210–223 (2020).

22

Accepted to J. Chem. Phys. 10.1063/5.0158046

23

I. Kurisaki and S. Tanaka, “Atp converts a42 oligomer into off-pathway species by making contact with its backbone atoms using hydrophobic adenosine,” Journal of Physical

This is the author’s peer reviewed, accepted manuscript. However, the online version of record will be different from this version once it has been copyedited and typeset.

PLEASE CITE THIS ARTICLE AS DOI: 10.1063/5.0158046

Chemistry B 123, 9922–9933 (2019).

24

H. Aida, Y. Shigeta, and R. Harada, “The role of atp in solubilizing rna-binding protein

fused in sarcoma,” Proteins: Structure, Function and Bioinformatics 90, 1606–1612 (2022).

25

T. R. Sosnick and D. Barrick, “The folding of single domain proteinshave we reached a

consensus?” Current Opinion in Structural Biology 21, 12–24 (2011).

26

S. Piana, J. L. Klepeis, and D. E. Shaw, “Assessing the accuracy of physical models

used in protein-folding simulations: Quantitative evidence from long molecular dynamics

simulations,” Current Opinion in Structural Biology 24, 98–105 (2014).

27

P. S. Nerenberg, B. Jo, C. So, A. Tripathy, and T. Head-Gordon, “Optimizing SoluteWater

van der Waals Interactions To Reproduce Solvation Free Energies,” J. Phys. Chem. B 116,

4524–4534 (2012).

28

R. B. Best, W. Zheng,

and J. Mittal, “Balanced ProteinWater Interactions Improve

Properties of Disordered Proteins and Non-Specific Protein Association,” J. Chem. Theory

Comput. 10, 5113–5124 (2014).

29

D. Song, R. Luo, and H.-F. Chen, “The IDP-Specific Force Field ff14IDPSFF Improves

the Conformer Sampling of Intrinsically Disordered Proteins,” J. Chem. Inf. Model. 57,

1166–1178 (2017).

30

S. Piana, A. G. Donchev, P. Robustelli, and D. E. Shaw, “Water dispersion interactions

strongly influence simulated structural properties of disordered protein states,” Journal of

Physical Chemistry B 119, 5113–5123 (2015).

31

P. S. Shabane, S. Izadi, and A. V. Onufriev, “General purpose water model can improve

atomistic simulations of intrinsically disordered proteins,” Journal of Chemical Theory and

Computation 15, 2620–2634 (2019).

32

L. Martinez, R. Andrade, E. G. Birgin, and J. M. Martnez, “Packmol: A package for building initial configurations for molecular dynamics simulations,” Journal of Computational

Chemistry 30, 2157–2164 (2009).

33

K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J. L. Klepeis, R. O. Dror, and

D. E. Shaw, “Improved side-chain torsion potentials for the amber ff99sb protein force

field,” Proteins: Structure, Function and Bioinformatics 78, 1950–1958 (2010), amber

FF99SB-ILDN parameter.

23

Accepted to J. Chem. Phys. 10.1063/5.0158046

34

K. L. Meagher, L. T. Redman, and H. A. Carlson, “Development of polyphosphate parameters for use with the amber force field,” Journal of Computational Chemistry 24,

This is the author’s peer reviewed, accepted manuscript. However, the online version of record will be different from this version once it has been copyedited and typeset.

PLEASE CITE THIS ARTICLE AS DOI: 10.1063/5.0158046

1016–1025 (2003), aMBER phosphate parameters.

35

I. S. Joung and T. E. Cheatham, “Determination of alkali and halide monovalent ion

parameters for use in explicitly solvated biomolecular simulations,” Journal of Physical

Chemistry B 112, 9020–9041 (2008).

36

Z. Li, L. F. Song, P. Li, and K. M. Merz, “Systematic parametrization of divalent metal

ions for the opc3, opc, tip3p-fb, and tip4p-fb water models,” Journal of Chemical Theory

and Computation 16, 4429–4442 (2020).

37

D. A. Case, K. Belfon, I. Y. Ben-Shalom, S. R. Brozell, D. S. Cerutti, V. W. D. Cruzeiro,

T. A. Darden, R. E. Duke, and G. Giambasu, “Amber 20,”.

38

R. Salomn-Ferrer, A. W. Goetz, D. Poole, S. L. Grand, and R. C. Walker, “Routine microsecond molecular dynamics simulations with amber on gpus. 2. explicit solvent particle

mesh ewald,” Journal of Chemical Theory and Computation 9, 3878–3888, reference for

the GPU version of Amber 12.

39

K. H. Scheller, F. Hofstetter, P. R. Mitchell, B. Prijs, and H. Sigel, “Macrochelate formation in monomeric metal ion complexes of nucleoside 5’-triphosphates and the promotion

of stacking by metal ions. comparison of the self-association of purine and pyrimidine 5’triphosphates using proton nuclear magnetic resonance,” Journal of the American Chemical Society 103, 247–260 (1981).

40

J. E. Wilson and A. Chin, “Chelation of divalent cations by atp, studied by titration

calorimetry,” Analytical Biochemistry 193, 16–19 (1991).

41

A. C. Storer and A. Cornish-Bowden, “Concentration of mgatp2- and other ions in solution.

calculation of the true concentrations of species present in mixtures of associating ions,”

Biochemical Journal 159, 1–5 (1976).

42

J. Huang, S. Rauscher, G. Nawrocki, T. Ran, M. Feig, B. L. de Groot, H. Grubmller,

and A. D. MacKerell, “Charmm36m: an improved force field for folded and intrinsically

disordered proteins,” Nature Methods 14, 71–73 (2017).

43

P. Robustelli, S. Piana, and D. E. Shaw, “Developing a molecular dynamics force field for

both folded and disordered protein states,” Proc. Natl. Acad. Sci. U. S. A. 115, E4758–

E4766 (2018).

24

...

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る