Using experimentally determined structures of ubiquitin at 1 and 3000 bar, we generate sufficiently large ensembles of model structures in the native and pressure-induced (denatured) states by means of molecular dynamics simulations with explicit water. We calculate the values of a free-energy function (FEF), which comprises the hydration free energy (HFE) and the intramolecular (conformational) energy and entropy, for the two states at 1 and 3000 bar. The HFE and the conformational entropy, respectively, are calculated using our statistical-mechanical method, which has recently been shown to be accurate, and the Boltzmann-quasi-harmonic method. The HFE is decomposed into a variety of physically insightful components. We show that the FEF of the native state is lower than that of the denatured state at 1 bar, whereas the opposite is true at 3000 bar, thus being successful in reproducing the pressure denaturation. We argue that the following two quantities of hydration play essential roles in the denaturation: the WASA-dependent term in the water-entropy loss upon cavity creation for accommodating the protein (WASA is the water-accessible surface area of the cavity) and the protein–water Lennard-Jones interaction energy. At a high pressure, the mitigation of the serious water crowding in the system is the most important, and the WASA needs to be sufficiently enlarged with the increase in the excluded-volume being kept as small as possible. The denatured structure thus induced is characterized by the water penetration into the protein interior. The pressure denaturation is accompanied by a significantly large gain of water entropy.

1.
G. S.
Chryssomallis
,
P. M.
Torgerson
,
H. G.
Drickamer
, and
G.
Weber
,
Biochemistry
20
,
3955
(
1981
).
2.
C.
Clery
,
F.
Renault
, and
P.
Masson
,
FEBS Lett.
370
,
212
(
1995
).
3.
G.
Panick
,
R.
Malessa
,
R.
Winter
,
G.
Rapp
,
K. J.
Frye
, and
C. A.
Royer
,
J. Mol. Biol.
275
,
389
(
1998
).
4.
G.
Panick
,
G. J. A.
Vidugiris
,
R.
Malessa
,
G.
Rapp
,
R.
Winter
, and
C. A.
Royer
,
Biochemistry
38
,
4157
(
1999
).
5.
C. A.
Royer
,
Biochim. Biophys. Acta
1595
,
201
(
2002
).
6.
R.
Kitahara
,
S.
Yokoyama
, and
K.
Akasaka
,
J. Mol. Biol.
347
,
277
(
2005
).
7.
F.
Meersman
,
C. M.
Dobson
, and
K.
Heremans
,
Chem. Soc. Rev.
35
,
908
(
2006
).
8.
D. J.
Wilton
,
R. B.
Tunnicliffe
,
Y. O.
Kamatari
,
K.
Akasaka
, and
M. P.
Williamson
,
Proteins
71
,
1432
(
2008
).
9.
H.
Yamada
,
T.
Nagae
, and
N.
Watanabe
,
Acta Crystallogr., Sect. D: Biol. Crystallogr.
71
,
742
(
2015
).
10.
T.
Ikkai
and
T.
Ooi
,
Biochemistry
5
,
1551
(
1966
).
11.
P. S.
Niranjan
,
P. B.
Yim
,
J. G.
Forbes
,
S. C.
Greer
,
J.
Dudowicz
,
K. F.
Freed
, and
J. F.
Douglas
,
J. Chem. Phys.
119
,
4070
(
2003
).
12.
D.
Foguel
,
M. C.
Suarez
,
A. D.
Ferrao-Gonzales
,
T. C. R.
Porto
,
L.
Palmieri
,
C. M.
Einsiedler
,
L. R.
Andrade
,
H. A.
Lashuel
,
P. T.
Lansbury
,
J. W.
Kelly
, and
J. L.
Silva
,
Proc. Natl. Acad. Sci. U. S. A.
100
,
9831
(
2003
).
13.
C. F. S.
Bonafe
,
C. M. R.
Vital
,
R. C. B.
Telles
,
M. C.
Goncalves
,
M. S. A.
Matsuura
,
F. B. T.
Pessine
,
D. R. C.
Freitas
, and
J.
Vega
,
Biochemistry
37
,
11097
(
1998
).
14.
T.
Imai
and
Y.
Sugita
,
J. Phys. Chem. B
114
,
2281
(
2010
).
15.
G.
Hummer
,
S.
Garde
,
A. E.
García
,
M. E.
Paulaitis
, and
L. R.
Pratt
,
Proc. Natl. Acad. Sci. U. S. A.
95
,
1552
(
1998
).
16.
A.
Paliwal
,
D.
Asthagiri
,
D. P.
Bossev
, and
M. E.
Paulaitis
,
Biophys. J.
87
,
3479
(
2004
).
17.
D.
Pascheck
and
A. E.
García
,
Phys. Rev. Lett.
93
,
238105
(
2004
).
18.
J. R.
Grigera
and
A. N.
McCarthy
,
Biophys. J.
98
,
1626
(
2010
).
19.
Y.
Harano
and
M.
Kinoshita
,
J. Phys.: Condens. Matter
18
,
L107
(
2006
).
20.
Y.
Harano
and
M.
Kinoshita
,
J. Chem. Phys.
125
,
024910
(
2006
).
21.
Y.
Harano
,
T.
Yoshidome
, and
M.
Kinoshita
,
J. Chem. Phys.
129
,
145103
(
2008
).
22.
T.
Yoshidome
,
Y.
Harano
, and
M.
Kinoshita
,
Phys. Rev. E
79
,
011912
(
2009
).
23.
M.
Kinoshita
,
Biophys. Rev.
5
,
283
(
2013
).
24.
H.
Oshima
and
M.
Kinoshita
,
J. Chem. Phys.
142
,
145103
(
2015
).
25.
S.
Hikiri
,
T.
Hayashi
,
M.
Inoue
,
T.
Ekimoto
,
M.
Ikeguchi
, and
M.
Kinoshita
,
J. Chem. Phys.
150
,
175101
(
2019
).
26.
E. W.
Lemmon
,
M. O.
McLinden
, and
D. G.
Friend
, “
Thermophysical properties of fluid systems
,” in
NIST Chemistry WebBook: NIST Standard Reference Database Number 69
, edited by
P. J.
Linstrom
and
W. G.
Mallard
(
National Institute of Standards and Technology
,
Gaithersburg, MD
,
2005
); retrieved March 7, 2019.
27.
S.
Hikiri
,
T.
Yoshidome
, and
M.
Ikeguchi
,
J. Chem. Theory Comput.
12
,
5990
(
2016
).
28.
P. G.
Kusalik
and
G. N.
Patey
,
J. Chem. Phys.
88
,
7715
(
1988
).
29.
P. G.
Kusalik
and
G. N.
Patey
,
Mol. Phys.
65
,
1105
(
1988
).
30.
N. M.
Cann
and
G. N.
Patey
,
J. Chem. Phys.
106
,
8165
(
1997
).
31.
M.
Kinoshita
,
J. Chem. Phys.
128
,
024507
(
2008
).
32.
T.
Hayashi
,
H.
Oshima
,
Y.
Harano
, and
M.
Kinoshita
,
J. Phys.: Condens. Matter
28
,
344003
(
2016
).
33.
R.
Roth
,
Y.
Harano
, and
M.
Kinoshita
,
Phys. Rev. Lett.
97
,
078101
(
2006
).
34.
D.
Beglov
and
B.
Roux
,
J. Chem. Phys.
103
,
360
(
1995
).
35.
D.
Beglov
and
B.
Roux
,
J. Chem. Phys.
104
,
8678
(
1996
).
36.
A.
Kovalenko
and
F.
Hirata
,
J. Chem. Phys.
110
,
10095
(
1999
).
37.
J.-P.
Hansen
and
L. R.
McDonald
,
Theory of Simple Liquids
, 3rd ed. (
Academic Press
,
London
,
2006
).
38.
T.
Luchko
,
S.
Gusarov
,
D. R.
Roe
,
C.
Simmerling
,
D. A.
Case
,
J.
Tuszynski
, and
A.
Kovalenko
,
J. Chem. Theory Comput.
6
,
607
(
2010
).
39.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
113
,
6070
(
2000
).
40.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
117
,
3605
(
2002
);
Erratum,
118
,
2446
(
2003
).
41.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
119
,
9686
(
2003
).
42.
J. P. M.
Postma
,
H. J. C.
Berendsen
, and
J. R.
Haak
,
Faraday Symp. Chem. Soc.
17
,
55
(
1982
).
43.
B. L.
Tembe
and
J. A.
McCammon
,
Comput. Chem.
8
,
281
(
1984
).
44.
W. L.
Jorgensen
and
C.
Ravimohan
,
J. Chem. Phys.
83
,
3050
(
1985
).
45.
J. G.
Kirkwood
,
J. Chem. Phys.
3
,
300
(
1935
).
46.
Y.
Karino
,
M. V.
Fedorov
, and
N.
Matubayasi
,
Chem. Phys. Lett.
496
,
351
(
2010
).
47.
Y.
Karino
and
N.
Matubayasi
,
Phys. Chem. Chem. Phys.
15
,
4377
(
2013
).
48.
T.
Yamada
,
T.
Hayashi
,
S.
Hikiri
,
N.
Kobayashi
,
H.
Yanagawa
,
M.
Ikeguchi
,
M.
Katahira
,
T.
Nagata
, and
M.
Kinoshita
,
J. Chem. Inf. Model.
59
,
3533
(
2019
).
49.
S.
Vijay-Kumar
,
C. E.
Bugg
, and
W. J.
Cook
,
J. Mol. Biol.
194
,
531
(
1987
).
50.
D. A.
Case
,
I. Y.
Ben-Shalom
,
S. R.
Brozell
,
D. S.
Cerutti
,
T. E.
Cheatham
 III
,
V. W. D.
Cruzeiro
,
T. A.
Darden
,
R. E.
Duke
,
D.
Ghoreishi
,
M. K.
Gilson
,
H.
Gohlke
,
A. W.
Goetz
,
D.
Greene
,
R.
Harris
,
N.
Homeyer
,
Y.
Huang
,
S.
Izadi
,
A.
Kovalenko
,
T.
Kurtzman
,
T. S.
Lee
,
S.
LeGrand
,
P.
Li
,
C.
Lin
,
J.
Liu
,
T.
Luchko
,
R.
Luo
,
D. J.
Mermelstein
,
K. M.
Merz
,
Y.
Miao
,
G.
Monard
,
C.
Nguyen
,
H.
Nguyen
,
I.
Omelyan
,
A.
Onufriev
,
F.
Pan
,
R.
Qi
,
D. R.
Roe
,
A.
Roitberg
,
C.
Sagui
,
S.
Schott-Verdugo
,
J.
Shen
,
C. L.
Simmerling
,
J.
Smith
,
R.
Salomon-Ferrer
,
J.
Swails
,
R. C.
Walker
,
J.
Wang
,
H.
Wei
,
R. M.
Wolf
,
X.
Wu
,
L.
Xiao
,
D. M.
York
, and
P. A.
Kollman
, AMBER 2018,
University of California
,
San Francisco
,
2018
.
51.
V.
Hornak
,
R.
Abel
,
A.
Okur
,
B.
Strockbine
,
A.
Roitberg
, and
C.
Simmerling
,
Proteins
65
,
712
(
2006
).
52.
H. J. C.
Berendsen
,
J. R.
Grigera
, and
T. P.
Straatsma
,
J. Phys. Chem.
91
,
6269
(
1987
).
53.
S.
Asakura
and
F.
Oosawa
,
J. Chem. Phys.
22
,
1255
(
1954
).
54.
S.
Asakura
and
F.
Oosawa
,
J. Polym. Sci.
33
,
183
(
1958
).
55.
N.
Matubayasi
and
M.
Nakahara
,
J. Chem. Phys.
112
,
8089
(
2000
).
56.
T.
Lazaridis
,
J. Phys. Chem. B
104
,
4964
(
2000
).
57.
J. G.
Kirkwood
and
F. P.
Buff
,
J. Chem. Phys.
19
,
774
(
1951
).
58.
J.
Woenckhaus
,
R.
Kohling
,
P.
Thiyagarajan
,
K. C.
Litterell
,
S.
Seifert
,
C. A.
Royer
, and
R.
Winter
,
Biophys. J.
80
,
1518
(
2001
).
59.
K. J.
Frye
and
C. A.
Royer
,
Protein Sci.
7
,
2217
(
1998
).
60.
J. B.
Rouget
,
T.
Aksel
,
J.
Roche
,
J. L.
Saldana
,
A. E.
García
,
D.
Barrick
, and
C. A.
Royer
,
J. Am. Chem. Soc.
133
,
6020
(
2011
).
61.
J.
Roche
,
J. A.
Caro
,
D. R.
Norberto
,
P.
Barthe
,
C.
Roumestand
,
J. L.
Schlessman
,
A. E.
García
,
B.
García-Moreno
, and
C. A.
Royer
,
Proc. Natl. Acad. Sci. U. S. A.
109
,
6945
(
2012
).
62.
G.
Graziano
,
Biopolymers
103
,
711
(
2015
).
63.
M.
Kinoshita
and
Y.
Sugai
,
J. Comput. Chem.
23
,
1445
(
2002
).
64.
C. Y.
Lee
,
J. A.
McCammon
, and
P. J.
Rossky
,
J. Chem. Phys.
80
,
4448
(
1984
).
65.
M.
Kinoshita
,
J. Mol. Liq.
119
,
47
(
2005
).
66.
M.
Kinoshita
,
N.
Matubayasi
,
Y.
Harano
, and
M.
Nakahara
,
J. Chem. Phys.
124
,
024512
(
2006
).
67.
M.
Kinoshita
and
H.
Oshima
,
Chem. Phys. Lett.
610-611
,
1
(
2014
).
You do not currently have access to this content.