6 Appendix 2: Morphometric Approach
79
this causes no problems at all. The structural fluctuation of the solute in water can
readily be taken into account in accordance with the following two steps [13]: (I)
An ensemble consisting of sufficiently many solute structures is generated by a short
MD simulation in explicit aqueous solution; and (II) a thermodynamic quantity of
hydration is calculated for all the structures generated, and it is determined as the
average value. In the MD simulation, the generation of the ensemble is much less
time consuming than the calculation of the thermodynamic quantity of hydration. It
was shown, for instance, that the relative values of the binding free energy calculated
for an oncoprotein MDM2 and two different peptides (the reference peptide is the
extreme N-terminal peptide region of a tumor suppressor protein p53 (p53NTD)) by
employing the two steps explained above are in quantitatively good agreement with
those obtained by experiments [10].
References
1. Roth R, Harano Y, Kinoshita M (2006) Phys Rev Lett 97:078101
2. Oshima H, Kinoshita M (2015) J Chem Phys 142:145103
3. Hayashi T, Inoue M, Yasuda S, Petretto E, Škrbi´ c T, Giacometti A, Kinoshita M (2018) J Chem
Phys 149:045105
4. Kusalik PG, Patey GN (1988) J Chem Phys 88:7715
5. Kusalik PG, Patey GN (1988) Mol Phys 65:1105
6. Cann NM, Patey GN (1997) J Chem Phys 106:8165
7. Kinoshita M (2008) J Chem Phys 128:024507
8. Hayashi T, Oshima H, Harano Y, Kinoshita M (2016) J Phys: Condens Matter 28:344003
9. Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M (2019) J Chem Phys
150:175101
10. Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata
T, Kinoshita M (2019) J Chem Inf Model 59:3533
11. Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M (2020) J Chem Phys 152:065103
12. Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M (2020) J Mol Liq 317:114129
13. Kinoshita M, Hayashi T (2020) Biophys Rev 12:469
14. Postma JPM, Berendsen HJC, Haak JR (1982) Faraday Symp Chem Soc 17:55
15. Tembe BL, McCammon JA (1984) Comput Chem 8:281
16. Jorgensen WL, Ravimohan C (1985) J Chem Phys 83:3050
17. Kirkwood JG (1935) J. Chem. Phys. 3:300
18. Kollman P (1993) Chem Rev 93:2395
19. Shirts MR, Pitera JW, Swope WC, Pande VS (2003) J Chem Phys 119:5740
20. Matubayasi N, Nakahara M (2000) J Chem Phys 113:6070
21. Matubayasi N, Nakahara M (2003) J Chem Phys 117:3605 (2002); 118:2446 (2003)
22. Matubayasi N, Nakahara M (2003) J Chem Phys 119:9686
79
this causes no problems at all. The structural fluctuation of the solute in water can
readily be taken into account in accordance with the following two steps [13]: (I)
An ensemble consisting of sufficiently many solute structures is generated by a short
MD simulation in explicit aqueous solution; and (II) a thermodynamic quantity of
hydration is calculated for all the structures generated, and it is determined as the
average value. In the MD simulation, the generation of the ensemble is much less
time consuming than the calculation of the thermodynamic quantity of hydration. It
was shown, for instance, that the relative values of the binding free energy calculated
for an oncoprotein MDM2 and two different peptides (the reference peptide is the
extreme N-terminal peptide region of a tumor suppressor protein p53 (p53NTD)) by
employing the two steps explained above are in quantitatively good agreement with
those obtained by experiments [10].
References
1. Roth R, Harano Y, Kinoshita M (2006) Phys Rev Lett 97:078101
2. Oshima H, Kinoshita M (2015) J Chem Phys 142:145103
3. Hayashi T, Inoue M, Yasuda S, Petretto E, Škrbi´ c T, Giacometti A, Kinoshita M (2018) J Chem
Phys 149:045105
4. Kusalik PG, Patey GN (1988) J Chem Phys 88:7715
5. Kusalik PG, Patey GN (1988) Mol Phys 65:1105
6. Cann NM, Patey GN (1997) J Chem Phys 106:8165
7. Kinoshita M (2008) J Chem Phys 128:024507
8. Hayashi T, Oshima H, Harano Y, Kinoshita M (2016) J Phys: Condens Matter 28:344003
9. Hikiri S, Hayashi T, Inoue M, Ekimoto T, Ikeguchi M, Kinoshita M (2019) J Chem Phys
150:175101
10. Yamada T, Hayashi T, Hikiri S, Kobayashi N, Yanagawa H, Ikeguchi M, Katahira M, Nagata
T, Kinoshita M (2019) J Chem Inf Model 59:3533
11. Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M (2020) J Chem Phys 152:065103
12. Inoue M, Hayashi T, Hikiri S, Ikeguchi M, Kinoshita M (2020) J Mol Liq 317:114129
13. Kinoshita M, Hayashi T (2020) Biophys Rev 12:469
14. Postma JPM, Berendsen HJC, Haak JR (1982) Faraday Symp Chem Soc 17:55
15. Tembe BL, McCammon JA (1984) Comput Chem 8:281
16. Jorgensen WL, Ravimohan C (1985) J Chem Phys 83:3050
17. Kirkwood JG (1935) J. Chem. Phys. 3:300
18. Kollman P (1993) Chem Rev 93:2395
19. Shirts MR, Pitera JW, Swope WC, Pande VS (2003) J Chem Phys 119:5740
20. Matubayasi N, Nakahara M (2000) J Chem Phys 113:6070
21. Matubayasi N, Nakahara M (2003) J Chem Phys 117:3605 (2002); 118:2446 (2003)
22. Matubayasi N, Nakahara M (2003) J Chem Phys 119:9686
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