The helix-coil transition revisited.
In this article, we perform a dynamic Monte Carlo simulation study of the helix-coil transition by using a bond-fluctuation lattice model. The results of the simulations are compared with those predicted by the Zimm-Bragg statistical thermodynamic theory with propagation and nucleation parameters determined from simulation data. The Zimm-Bragg theory provides a satisfactory description of the helix-coil transition of a homopolypeptide chain of 32 residues (N = 32). For such a medium-length chain, however, the analytical equation based on a widely-used large-N approximation to the Zimm-Bragg theory is not suitable to predict the average length of helical blocks at low temperatures when helicity is high. We propose an analytical large-eigenvalue (lambda) approximation. The new equation yields a significantly improved agreement on the average helix-block length with the original Zimm-Bragg theory for both medium and long chain lengths in the entire temperature range. Nevertheless, even the original Zimm-Bragg theory does not provide an accurate description of helix-coil transition for longer chains. We assume that the single-residue nucleation of helix formation as suggested in the original Zimm-Bragg model might be responsible for this deviation. A mechanism of nucleation by a short helical block is proposed by us and provides a significantly improved agreement with our simulation data.
Chen
Yantao
Y
Department of Macromolecular Science, Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China.
Zhou
Yaoqi
Y
Ding
Jiandong
J
D003198:Computer Simulation; D008433:Mathematics; D008958:Models, Molecular; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins