Simplified lattice model for polypeptide fibrillar transitions.
Polypeptide fibrillar transitions are studied using a simplified lattice model, modified from the three-state 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 ɛh,ɛs,ɛf, structural entropies sh,ss,sf of helical, sheet, and fibrillar states, and number density ρ. The phase diagrams show the transition sequence is basically governed by ɛh, ɛs, and ɛf, while the transition temperature is determined by the competition among ɛh, ɛs, and ɛf, as well as sh, ss, sf, 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 nucleation-growth process. The finite-size effect in specific heat at transitions for the nonfibrillation case can be described by the scaling form of lattice model. With rich phase-transition properties, our model provides a useful reference for protein aggregation experiments and modeling.
Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
Xuhui
X
Xiao
Research Center for Adaptive Data Analysis, National Central University, Chungli 32001, Taiwan and Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan.
Ming-Chya
MC
Wu
D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D044367:Phase Transition; D044366:Transition Temperature
D010455:Peptides