A coarse-grained model and associated lattice Monte Carlo simulation of the coil–helix transition of a homopolypeptide

Abstract

A new coarse-grained lattice model neglecting atomic details is proposed for the coil-helix transition and a new physical parameter is suggested to characterize a helical structure. In our model, each residue is represented by eight lattice sites, and side groups are not considered explicitly. Chirality and hydrogen bonding are taken into consideration in addition to chain connectivity and the excluded volume effect. Through a dynamic Monte Carlo simulation, the physical properties of the coil-helix transition of a single homopolypeptide have been produced successfully within a short computing time on the PC. We also examined the effects of the variation of chain configurations including chain size and chain shape, etc. A spatial correlation function has been introduced in order to characterize periodicity of a helical chain in a simple way. A propagation parameter and a nucleation parameter have also been calculated, which compares favorably with the results of the Zimm-Bragg theory for the coil-helix transition.

The helix–coil transition revisited

“…α‐helix, first proposed by Pauling and coworkers in 1950,1, 2 is one of the basic structural elements in proteins 3. So far, it has been used as a model system for studying the formation of secondary structures in proteins by experimental,4–13 theoretical,14–25 and simulation methods 26–51. Theories of helix–coil transitions have been used for interpreting experimental and simulation results.…”

“…These experimental results revealed different tendencies of helical formations for different residues. The two parameters have also been determined by computer simulations 27–32, 38, 40, 46, 47, 49, 51. Recently, the importance of these parameters was reassessed by Baldwin 52…”

“…In this work, a dynamic Monte Carlo (MC) simulation has been performed to investigate the helix–coil transition of a self‐avoiding lattice chain in the three‐dimensional space. Statistical analysis of equilibrium constants for the dynamic processes of helical block formation and disruption allows us to directly calculate σ and s parameters in the simulation27, 51 in addition to evaluation of helicity θ and average helical block length L . The availability of σ, s, θ , and L from our simulations permits a detailed comparison between the simulated data and the predictions given by the Zimm–Bragg theory.…”

Lattice Monte Carlo simulation of coil-helix transition

“…4). In contrast, the period P slowly decreased to about 3.7 during annealing, which is much more close to 3.6, that of natural -helix, compared with 4, that via our previous lattice model [4].…”

“…So, a bond-fluctuation model originally to study polymers [3] has been extended to investigate coil-helix transition of polypeptide. This model, also called eight-site lattice model by us [4], contains much more permitted bond orientations and bond lengths than the conventional single-site lattice model, and can be considered a quasi-continuous or quasi-off-lattice model, while not evidently weaken the priority in efficiency for lattice model.…”