Relaxation to Native Conformation of a Bond-Fluctuating Protein Chain With Hydrophobic and Polar Nodes

Authors

Johan Bjursell, George Mason University
Ras B. Pandey, University of Southern MississippiFollow

Document Type

Article

Publication Date

11-1-2004

Department

Physics and Astronomy

School

Mathematics and Natural Sciences

Abstract

The conformation and dynamics of a protein chain with hydrophobic and polar nodes are examined by the bond-fluctuation model using Monte Carlo simulations on a cubic lattice. The minimal (nearest neighbor) interaction leads to standard (self-avoiding walk) conformation, i.e., the scaling of the radius of gyration R_g with the molecular weight N R_g ∝ N^γ with γ ≃ 3/5/ Specific interactions with longer range and higher strength are needed to approach the native globular conformations with γ < 3/5. Relaxation into the globular ground state shows a weak power-law decay, i.e., R_g ∝ t^-α, α ~ 0.06-0.12.

Comments

©Physical Review E

Publisher Version

Publication Title

Physical Review E

Volume

70

Issue

5

Recommended Citation

Bjursell, J., Pandey, R. B. (2004). Relaxation to Native Conformation of a Bond-Fluctuating Protein Chain With Hydrophobic and Polar Nodes. Physical Review E, 70(5).
Available at: https://aquila.usm.edu/fac_pubs/2988