Abstract
In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid- Β peptides AΒ40 and AΒ42 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 DT of 1.61× 10-6 cm2 /s and 1.43× 10-6 cm2 /s for AΒ40 and AΒ42, 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 DR for AΒ40 and AΒ42 at 300 K are 0.085 and 0.071 ns -1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of AΒ40 and AΒ42 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 (Ctot(t)) of AΒ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both AΒ40 and AΒ42. In addition, an effective rotational correlation time of AΒ40 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 S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of AΒ40 and AΒ42 are in accord with the previous studies.
| Original language | English |
|---|---|
| Article number | 155103 |
| Journal | Journal of Chemical Physics |
| Volume | 131 |
| Issue number | 15 |
| DOIs | |
| State | Published - Nov 17 2009 |
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ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry
- Medicine(all)
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Translational, rotational and internal dynamics of amyloid Β -peptides (AΒ40 and AΒ42) from molecular dynamics simulations. / Bora, Ram Prasad; Prabhakar, Rajeev.
In: Journal of Chemical Physics, Vol. 131, No. 15, 155103, 17.11.2009.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Translational, rotational and internal dynamics of amyloid Β -peptides (AΒ40 and AΒ42) from molecular dynamics simulations
AU - Bora, Ram Prasad
AU - Prabhakar, Rajeev
PY - 2009/11/17
Y1 - 2009/11/17
N2 - In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid- Β peptides AΒ40 and AΒ42 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 DT of 1.61× 10-6 cm2 /s and 1.43× 10-6 cm2 /s for AΒ40 and AΒ42, 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 DR for AΒ40 and AΒ42 at 300 K are 0.085 and 0.071 ns -1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of AΒ40 and AΒ42 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 (Ctot(t)) of AΒ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both AΒ40 and AΒ42. In addition, an effective rotational correlation time of AΒ40 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 S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of AΒ40 and AΒ42 are in accord with the previous studies.
AB - In this study, diffusion constants [translational (DT) and rotational (DR)], correlation times [rotational (τrot) and internal (τint)], and the intramolecular order parameters (S2) of the Alzheimer amyloid- Β peptides AΒ40 and AΒ42 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 DT of 1.61× 10-6 cm2 /s and 1.43× 10-6 cm2 /s for AΒ40 and AΒ42, 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 DR for AΒ40 and AΒ42 at 300 K are 0.085 and 0.071 ns -1, respectively. The rotational (Crot(t)) and internal (Cint(t)) correlation functions of AΒ40 and AΒ42 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 (Ctot(t)) of AΒ peptides into Crot(t) and Cint(t). At both short and long time scales, the Clore-Szabo model that was used as Cint(t) provided the best behavior of Ctot(t) for both AΒ40 and AΒ42. In addition, an effective rotational correlation time of AΒ40 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 S2 parameters for the central hydrophobic core, the loop region, and C-terminal domains of AΒ40 and AΒ42 are in accord with the previous studies.
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U2 - 10.1063/1.3249609
DO - 10.1063/1.3249609
M3 - Article
C2 - 20568886
AN - SCOPUS:70449411752
VL - 131
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
SN - 0021-9606
IS - 15
M1 - 155103
ER -