The elasticity of α-helices is examined using equilibrium molecular-dynamics simulations. From the statistics of curvatures and twists, we compute the elastic moduli of several representative α-helices, both in the presence and absence of aqueous solvent. We discover that the bending modulus (persistence length) of the helices is independent of the amino-acid sequence, although helices in water are slightly softer than in vacuum. The response of the helices under the action of an external force is also computed and compared with continuum mechanics predictions. Within the time scale of our simulation, we show that the properties of α-helices are well reproduced by an elastic and isotropic rod. The persistence length (bending modulus) of most α-helices in water or vacuum is 100nm, roughly twice that of DNA.

1.
H.
Wang
and
G.
Oster
,
Nature (London)
396
,
279
(
1998
).
2.
S. X.
Sun
,
H.
Wang
, and
G.
Oster
,
Biophys. J.
86
,
1373
(
2004
).
3.
G.
Lan
and
S. X.
Sun
,
Biophys. J.
88
,
999
(
2005
).
4.
O.
Kratky
and
G.
Porod
,
Recl. Trav. Chim. Pays-Bas
68
,
1106
(
1949
).
5.
M.
Fixman
and
J.
Kovac
,
J. Chem. Phys.
58
,
1564
(
1973
).
6.
J.
Kovac
and
C. C.
Crabb
,
Macromolecules
15
,
537
(
1982
).
7.
J.
Shimada
and
H.
Yamakawa
,
Macromolecules
17
,
689
(
1984
).
8.
C.
Bustamante
,
J. F.
Marko
,
E. D.
Siggia
, and
S.
Smith
,
Science
265
,
1599
(
1994
).
9.
G.
Kirchhoff
,
J. Reine Angew. Math.
56
,
285
(
1859
).
10.
S. X.
Sun
,
D.
Chandler
,
A. R.
Dinner
, and
G.
Oster
,
Eur. Biophys. J.
32
,
676
(
2003
).
11.
12.
F.
Tama
,
F. X.
Gadea
,
O.
Marques
, and
Y. H.
Sanejouand
,
Proteins: Struct., Funct., Genet.
41
,
1
(
2000
).
13.
M.
Delarue
and
Y. H.
Sanejouand
,
J. Mol. Biol.
320
,
1011
(
2002
).
14.
R. M.
Levy
,
M.
Karplus
,
J.
Kushick
, and
D.
Perahia
,
Macromolecules
17
,
1370
(
1984
).
15.
T.
Horiuchi
and
N.
Go
,
Proteins
10
,
106
(
1991
).
16.
T.
Ichiye
and
M.
Karplus
,
Proteins
11
,
205
(
1991
).
17.
B.
Space
,
H.
Rabitz
, and
A.
Askar
,
J. Chem. Phys.
99
,
9070
(
1993
).
18.
A.
Amadei
,
A. B. M.
Linssen
, and
H. J. C.
Berendsen
,
Proteins
17
,
412
(
1993
).
19.
K.
Mizuguchi
,
A.
Kidera
, and
N.
Go
,
Proteins
18
,
34
(
1994
).
20.
H. M.
Chun
,
C. E.
Padilla
,
D. N.
Chin
 et al,
J. Comput. Chem.
21
,
159
(
2000
).
21.
Y.
Suezaki
and
N.
Go
,
Biopolymers
15
,
2137
(
1976
).
22.
S.
Kumar
and
M.
Bansal
,
Biophys. J.
75
,
1935
(
1998
).
23.
J. N.
Bright
and
M. S. P.
Sansom
,
J. Phys. Chem. B
107
,
627
(
2003
).
24.
S.
Hvidt
,
H. M.
Nestler
,
M. L.
Greaser
, and
J. D.
Ferry
,
Biochemistry
21
,
4064
(
1982
).
25.
C.
Storm
and
P.
Nelson
,
Phys. Rev. E
67
,
051906
(
2003
);
C.
Storm
and
P.
Nelson
,
Phys. Rev. E
70
,
013902
(E) (
2004
).
26.
B.
Chakrabarti
and
A. J.
Levine
, e-print cond-mat/0405382;
e-print cond-mat/0411358 (
2004
).
27.
P. A.
Wiggins
,
R.
Phillips
, and
P. C.
Nelson
, e-print cond-mat/0409003 (
2004
).
28.
L. D.
Landau
and
E. M.
Lifschitz
,
Theory of Elasticity
, 4th ed. (
Pergamon
, New York,
1986
).
29.
S.
Padmanabhan
,
S.
Marqusee
,
T.
Ridgeway
,
T. M.
Laue
, and
R. L.
Baldwin
,
Nature (London)
344
,
268
(
1990
).
30.
D. J.
Tobias
and
C. L.
Brooks
 III
,
Biochemistry
30
,
6059
(
1991
).
31.
M.
Blaber
,
X.
Zhang
, and
B. W.
Matthews
,
Science
260
,
1637
(
1993
).
32.
B. R.
Brooks
,
R. E.
Bruccoleri
,
B. D.
Olafson
, and
D. J.
States
,
J. Comput. Phys.
4
,
187
(
1983
).
33.
A. D.
MacKerell
,
D.
Bashford
,
M.
Bellot
 et al,
J. Phys. Chem. B
102
,
3586
(
1998
).
34.
W.
Humphrey
,
A.
Dalke
, and
K.
Schulten
,
J. Mol. Graphics
14
(1),
33
(
1996
).
35.
S.
Arnott
and
S. D.
Dover
,
J. Mol. Biol.
30
,
209
(
1967
).
36.
IUPAC-IUB Commission on Biochemical Nomenclature
,
Biochemistry
9
,
3471
(
1970
).
37.
J. F.
Marko
and
E. D.
Siggia
,
Macromolecules
28
,
8759
(
1995
).
You do not currently have access to this content.