Relaxation to Native Conformation of a Bond-Fluctuating Protein Chain With Hydrophobic and Polar Nodes
Physics and Astronomy
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) proportional to N(gamma) with gamma similar or equal to 3/5. Specific interactions with longer range and higher strength are needed to approach the native globular conformations with gamma< 3/5. Relaxation into the globular ground state shows a weak power-law decay, i.e., R(g) proportional to t(-alpha), alpha similar to 0.06-0.12.
Physical Review E
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: http://aquila.usm.edu/fac_pubs/2988