Simplified lattice model for polypeptide fibrillar transitions
Abstract
Polypeptide fibrillar transitions are studied using a simplified lattice model, modified from the threestate Potts model, where uniform residues as spins, placed on a cubic lattice, can interact with neighbors to form coil, helical, sheet, or fibrillar structure. Using the transfer matrix method and numerical calculations, we analyzed the partition function and construct phase diagrams. The model manifests phase transitions among coil, helix, sheet, and fibril through parameterizing bond coupling energy ∊_{h},∊_{s},∊_{f}, structural entropies s_{h},s_{s},s_{f} of helical, sheet, and fibrillar states, and number density ρ. The phase diagrams show the transition sequence is basically governed by ∊_{h}, ∊_{s}, and ∊_{f}, while the transition temperature is determined by the competition among ∊_{h}, ∊_{s}, and ∊_{f}, as well as s_{h}, s_{s}, s_{f}, and ρ. Furthermore, the fibrillation is accompanied with an abrupt phase transition from coil, helix, or sheet to fibril even for short polypeptide length, resembling the feature of nucleationgrowth process. The finitesize effect in specific heat at transitions for the nonfibrillation case can be described by the scaling form of lattice model. With rich phasetransition properties, our model provides a useful reference for protein aggregation experiments and modeling.
 Publication:

Physical Review E
 Pub Date:
 October 2014
 DOI:
 10.1103/PhysRevE.90.042701
 Bibcode:
 2014PhRvE..90d2701X
 Keywords:

 87.15.Cc;
 87.15.A;
 64.60.De;
 Folding and sequence analysis;
 Theory modeling and computer simulation;
 Statistical mechanics of model systems