Molecular dynamics simulations of chymotrypsin inhibitor 2 in different polyols (glycerol, xylitol, sorbitol, trehalose, and sucrose) at 363 K were performed to probe the molecular basis of the stabilizing effect, and the data in water, ethanol, and glycol were compared. It is found that protein protection by polyols is positively correlated with both the molecular volume and the fractional polar surface area, and the former contributes more significantly to the protein’s stability. Polyol molecules have only a few direct hydrogen bonds with the protein, and the number of hydrogen bonds between a polyol and the protein is similar for different polyols. Thus, it is concluded that the direct interactions contribute little to the stabilizing effect. It is clarified that the preferential exclusion of the polyols is the origin of their protective effects, and it increases with increasing polyol size. Namely, there is preferential hydration on the protein surface (2 Å), and polyol molecules cluster around the protein at a distance of about 4 Å. The preferential exclusion of polyols leads to indirect interactions that prevent the protein from thermal unfolding. The water structure becomes more ordered with increasing the polyol size. So, the entropy of water in the first hydration shell decreases, and a larger extent of decrease is observed with increasing polyol size, leading to larger transfer free energy. The findings suggest that polyols protect the protein from thermal unfolding via indirect interactions. The work has thus elucidated the molecular mechanism of structural stability of the protein in polyol solutions.

1.
P. R.
Davis-Searles
,
A. J.
Saunders
,
D. A.
Erie
,
D. J.
Winzor
, and
G. J.
Pielak
,
Annu. Rev. Biophys. Biomol. Struct.
30
,
271
(
2001
).
2.
R.
Usha
and
T.
Ramasami
,
Colloids Surf., B
61
,
39
(
2008
).
3.
D.
Roccatano
,
Curr. Protein Pept. Sci.
9
,
407
(
2008
).
4.
S. J.
Prestrelski
,
N.
Tedeschi
,
T.
Arakawa
, and
J. F.
Carpenter
,
Biophys. J.
65
,
661
(
1993
).
5.
G. B.
Strambini
,
E.
Balestreri
,
A.
Galli
, and
M.
Gonnelli
,
J. Phys. Chem. B
112
,
4372
(
2008
).
6.
T.
Kamiyama
,
Y.
Sadahide
,
Y.
Nogusa
, and
K.
Gekko
,
Biochim. Biophys. Acta
1434
,
44
(
1999
).
7.
Gangadhara
,
P. R.
Kumar
, and
V.
Prakash
,
Protein
27
,
440
(
2008
).
8.
X.
Liu
,
P.
Zhou
,
A.
Tran
, and
T. P.
Labuza
,
J. Agric. Food Chem.
57
,
2339
(
2009
).
9.
M.
Carlevaro
,
E. R.
Caffarena
, and
J. R.
Grigera
,
Int. J. Biol. Macromol.
23
,
149
(
1998
).
10.
R.
Politi
,
L.
Sapir
, and
D.
Harries
,
J. Phys. Chem. A
113
,
7548
(
2009
).
11.
Y.
Liu
and
D. W.
Bolen
,
Biochemistry
34
,
12884
(
1995
).
12.
M.
Auton
and
D. W.
Bolen
,
Proc. Natl. Acad. Sci. U.S.A.
102
,
15065
(
2005
).
13.
T. O.
Street
,
D. W.
Bolen
, and
G. D.
Rose
,
Proc. Natl. Acad. Sci. U.S.A.
103
,
13997
(
2006
).
14.
S. D.
Allison
,
B.
Chang
,
T. W.
Randolph
, and
J. F.
Carpenter
,
Arch. Biochem. Biophys.
365
,
289
(
1999
).
15.
Y. H.
Liao
,
M. B.
Brown
,
T.
Nazir
,
A.
Quader
, and
G. P.
Martin
,
Pharm. Res.
19
,
1847
(
2002
).
16.
J. F.
Carpenter
and
J. H.
Crowe
,
Biochemistry
28
,
3916
(
1989
).
17.
J. F.
Back
,
D.
Oakenfull
, and
M. B.
Smith
,
Biochemistry
18
,
5191
(
1979
).
18.
A.
Hédoux
,
J. F.
Willart
,
L.
Paccou
,
Y.
Guinet
,
F.
Affouard
,
A.
Lerbret
, and
M.
Descamps
,
J. Phys. Chem. B
113
,
6119
(
2009
).
19.
A.
Tiwari
and
R.
Bhat
,
Biophys. Chem.
124
,
90
(
2006
).
20.
S. L.
Lee
,
P. G.
Debenedetti
, and
J. R.
Errington
,
J. Chem. Phys.
122
,
204511
(
2005
).
21.
J. K.
Kaushik
and
R.
Bhat
,
J. Phys. Chem. B
102
,
7058
(
1998
).
22.
S. E.
Jackson
and
A. R.
Fersht
,
Biochemistry
30
,
10428
(
1991
).
23.
A. G.
Ladurner
,
L. S.
Itzhaki
,
V.
Daggett
, and
A. R.
Fersht
,
Proc. Natl. Acad. Sci. U.S.A.
95
,
8473
(
1998
).
24.
R.
Day
,
B. J.
Bennion
,
S.
Ham
, and
V.
Daggett
,
J. Mol. Biol.
322
,
189
(
2002
).
25.
R.
Day
and
V.
Daggett
,
Protein Sci.
14
,
1242
(
2005
).
26.
Y.
Harpaz
,
N.
Elmasry
,
A. R.
Fersht
, and
K.
Henrick
,
Proc. Natl. Acad. Sci. U.S.A.
91
,
311
(
1994
).
27.
A. W.
Schüttelkopf
and
D. M.
van Aalten
,
Acta Crystallogr., Sect. D: Biol. Crystallogr.
60
,
1355
(
2004
).
28.
C.
Oostenbrink
,
A.
Villa
,
A. E.
Mark
, and
W. F.
van Gunsteren
,
J. Comput. Chem.
25
,
1656
(
2004
).
29.
R. D.
Lins
and
P. H.
Hunenberger
,
J. Comput. Chem.
26
,
1400
(
2005
).
30.
See supplementary material at http://dx.doi.org/10.1063/1.3453713 for the GROMACS topology files for each of the cosolvents.
31.
S.
Cabani
,
P.
Gianni
,
V.
Mollica
, and
L.
Lepori
,
J. Solution Chem.
10
,
563
(
1981
).
32.
D. R.
Lide
,
CRC Handbook of Chemistry and Physics, Internet Version
, 87th ed. (
Cleveland
,
Ohio
,
2007
).
33.
G.
Xie
and
S. N.
Timasheff
,
Biophys. Chem.
64
,
25
(
1997
).
34.
M. B.
Blodgett
,
S. P.
Ziemer
,
B. R.
Brown
,
T. L.
Niederhauser
, and
E. M.
Woolley
,
J. Chem. Thermodyn.
39
,
627
(
2007
).
35.
D.
Van Der Spoel
,
E.
Lindahl
,
B.
Hess
,
G.
Groenhof
,
A. E.
Mark
, and
H. J.
Berendsen
,
J. Comput. Chem.
26
,
1701
(
2005
).
36.
H. J.
Berendsen
,
J. P.
Postma
,
W. F.
van Gunsteren
, and
J.
Hernans
,
Intermolecular Forces
(
Reidel
,
Dordrecht
,
1981
).
37.
L.
Verlet
,
Phys. Rev.
159
,
98
(
1967
).
38.
T.
Darden
,
D.
York
, and
L.
Pedersen
,
J. Chem. Phys.
98
,
10089
(
1993
).
39.
B.
Hess
,
H. J. C.
Berendsen
, and
J. G. E. M.
Fraaije
,
J. Comput. Chem.
18
,
1463
(
1997
).
40.
H. J. C.
Berendsen
,
J. P. M.
Postma
,
W. F.
van Gunsteren
,
A.
Di Nola
, and
J. R.
Haak
,
J. Chem. Phys.
81
,
3684
(
1984
).
41.
W.
Humphrey
,
A.
Dalke
, and
K.
Schulten
,
J. Mol. Graphics
14
,
33
(
1996
).
42.
E.
Espinosa
,
E.
Molins
, and
C.
Lecomte
,
Chem. Phys. Lett.
285
,
170
(
1998
).
43.
D. A.
Beck
and
V.
Daggett
,
Biophys. J.
93
,
3382
(
2007
).
44.
A.
Lerbret
,
P.
Bordat
,
F.
Affouard
,
A.
Hedoux
,
Y.
Guinet
, and
M.
Descamps
,
J. Phys. Chem. B
111
,
9410
(
2007
).
45.
S.
Shimizu
,
J. Chem. Phys.
120
,
4989
(
2004
).
46.
I.
Baskakov
and
D. W.
Bolen
,
J. Biol. Chem.
273
,
4831
(
1998
).
47.
D. W.
Bolen
and
G. D.
Rose
,
Annu. Rev. Biochem.
77
,
339
(
2008
).
48.
49.
K.
Gekko
and
S. N.
Timasheff
,
Biochemistry
20
,
4667
(
1981
).
50.
T.
Arakawa
and
S. N.
Timasheff
,
Biochemistry
21
,
6536
(
1982
).
51.
M.
Civera
,
A.
Fornili
,
M.
Sironi
, and
S. L.
Fornili
,
Chem. Phys. Lett.
367
,
238
(
2003
).
52.
S.
Pieraccini
,
L.
Burgi
,
A.
Genoni
,
A.
Benedusi
, and
M.
Sironi
,
Chem. Phys. Lett.
438
,
298
(
2007
).
53.
M.
Sola-Penna
,
A.
Ferreira-Pereira
,
A. P.
Lemos
, and
J. R.
Meyer-Fernandes
,
Eur. J. Biochem.
248
,
24
(
1997
).
54.
J.
Faber-Barata
and
M.
Sola-Penna
,
Mol. Cell. Biochem.
269
,
203
(
2005
).
55.
T. F.
O’Connor
,
P. G.
Debenedetti
, and
J. D.
Carbeck
,
J. Am. Chem. Soc.
126
,
11794
(
2004
).

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