Abstract
In this study, diffusion constants [translational
(
D
T
)
and rotational
(
D
R
)
], correlation times [rotational
(
τ
rot
)
and internal
(
τ
int
)
], and the intramolecular order parameters
(
S
2
)
of the Alzheimer amyloid-
β
peptides
A
β
40
and
A
β
42
have been calculated from 150 ns molecular dynamics simulations in aqueous solution. The computed parameters have been compared with the experimentally measured values. The calculated
D
T
of
1.61
×
10
−
6
cm
2
/
s
and
1.43
×
10
−
6
cm
2
/
s
for
A
β
40
and
A
β
42
, respectively, at 300 K was found to follow the correct trend defined by the Debye-Stokes-Einstein relation that its value should decrease with the increase in the molecular weight. The estimated
D
R
for
A
β
40
and
A
β
42
at 300 K are 0.085 and
0.071
ns
−
1
, respectively. The rotational
(
C
rot
(
t
)
)
and internal
(
C
int
(
t
)
)
correlation functions of
A
β
40
and
A
β
42
were observed to decay at nano- and picosecond time scales, respectively. The significantly different time decays of these functions validate the factorization of the total correlation function
(
C
tot
(
t
)
)
of
A
β
peptides into
C
rot
(
t
)
and
C
int
(
t
)
. At both short and long time scales, the Clore-Szabo model that was used as
C
int
(
t
)
provided the best behavior of
C
tot
(
t
)
for both
A
β
40
and
A
β
42
. In addition, an effective rotational correlation time of
A
β
40
is also computed at
18
°
C
and the computed value (2.30 ns) is in close agreement with the experimental value of 2.45 ns. The computed
S
2
parameters for the central hydrophobic core, the loop region, and C-terminal domains of
A
β
40
and
A
β
42
are in accord with the previous studies.
