TY - JOUR

T1 - Simplified lattice model for polypeptide fibrillar transitions

AU - Xiao, Xuhui

AU - Wu, Ming Chya

N1 - Publisher Copyright:
© 2014 American Physical Society.

PY - 2014/10/2

Y1 - 2014/10/2

N2 - 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 h,s,f, 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 h, s, and f, while the transition temperature is determined by the competition among h, s, and f, 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.

AB - 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 h,s,f, 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 h, s, and f, while the transition temperature is determined by the competition among h, s, and f, 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.

UR - http://www.scopus.com/inward/record.url?scp=84907835185&partnerID=8YFLogxK

U2 - 10.1103/PhysRevE.90.042701

DO - 10.1103/PhysRevE.90.042701

M3 - 期刊論文

C2 - 25375517

AN - SCOPUS:84907835185

SN - 1539-3755

VL - 90

JO - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

JF - Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

IS - 4

M1 - 042701

ER -