Abstract
The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis, a cluster analysis of the time dependence of PA assembly and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semifiber structure. We also find that head group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated, and the pillar-like intermediate structure was also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of nanoseconds, the PA self-assembly process can be recognized as involving two steps, (a) transition from the disordered state to the noncylindrical pillar-like intermediate and (b) pillar-like to final semifiber transition. These results are important to the further design of PAs as functional nanostructures.
| Original language | English |
|---|---|
| Pages (from-to) | 14059-14064 |
| Number of pages | 6 |
| Journal | Journal of Physical Chemistry B |
| Volume | 117 |
| Issue number | 45 |
| DOIs | |
| Publication status | Published - Nov 14 2013 |
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ASJC Scopus subject areas
- Physical and Theoretical Chemistry
- Materials Chemistry
- Surfaces, Coatings and Films
Cite this
Free-energy landscape for peptide amphiphile self-assembly : Stepwise versus continuous assembly mechanisms. / Yu, Tao; Schatz, George C.
In: Journal of Physical Chemistry B, Vol. 117, No. 45, 14.11.2013, p. 14059-14064.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Free-energy landscape for peptide amphiphile self-assembly
T2 - Stepwise versus continuous assembly mechanisms
AU - Yu, Tao
AU - Schatz, George C
PY - 2013/11/14
Y1 - 2013/11/14
N2 - The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis, a cluster analysis of the time dependence of PA assembly and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semifiber structure. We also find that head group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated, and the pillar-like intermediate structure was also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of nanoseconds, the PA self-assembly process can be recognized as involving two steps, (a) transition from the disordered state to the noncylindrical pillar-like intermediate and (b) pillar-like to final semifiber transition. These results are important to the further design of PAs as functional nanostructures.
AB - The mechanism of self-assembly of 140 peptide amphiphiles (PAs) to give nanofiber structures was investigated using a coarse-grained method to quantitatively determine whether the assembly process involves discrete intermediates or is a continuous process. Two novel concepts are introduced for this analysis, a cluster analysis of the time dependence of PA assembly and use of the fraction of native contacts as reaction coordinates for characterizing thermodynamic functions during assembly. The cluster analysis of the assembly kinetics demonstrates that a pillar-like intermediate state is formed before the final cylindrical semifiber structure. We also find that head group assembly occurs on a much shorter time scale than tail group assembly. A 2D free-energy landscape with respect to the fraction of native contacts was calculated, and the pillar-like intermediate structure was also found, with free energies about 1.2 kcal/mol higher than the final state. Although this intermediate state exists for only hundreds of nanoseconds, the PA self-assembly process can be recognized as involving two steps, (a) transition from the disordered state to the noncylindrical pillar-like intermediate and (b) pillar-like to final semifiber transition. These results are important to the further design of PAs as functional nanostructures.
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U2 - 10.1021/jp409305e
DO - 10.1021/jp409305e
M3 - Article
VL - 117
SP - 14059
EP - 14064
JO - Journal of Physical Chemistry B Materials
JF - Journal of Physical Chemistry B Materials
SN - 1520-6106
IS - 45
ER -