Thermodynamics of α- and β-Structure Formation in Proteins

Abstract

An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good approximation can be described by a simple two-state model, with parameters that are in reasonable quantitative agreement with experimental data. Despite the apparent two-state character of the melting curves, the energy distributions are found to lack a clear bimodal shape, which is discussed in some detail. We also perform a Monte Carlo-based kinetic study and find, in accord with experimental data, that the alpha-helix forms faster than the beta-hairpin.

Structural properties of small semiconductor-binding synthetic peptides

“…For sequences with more than 20 residues, studies of thermodynamics and kinetics employing realistic physical models are computationally extremely demanding. For such systems, reduced all-atom models [15] or models at a higher coarse-grained level [16,17] could be, depending on the particular question, much more promising. Coarse-grained lattice and off-lattice models allow for systematic thermodynamic studies and, at least partly, sequence analyses of heteropolymers with up to 100 monomers [18,19,20].…”

Secondary structure prediction of beta-hairpin peptide tryptophan zipper-I

“…Bolhuis did not find any α-helical structure in unfolded β-hairpin when using explicit solvent [34]. Irbäck et al have found two local minima in free energy surface, one of which corresponds to the non-native β-hairpin with ≈5Å RMSD while the other one corresponds to the α-helix [16]. These differences are mainly due to the potential energy functions used, rather than the simulation technique.…”

“…Peptides with 20 amino acids have been successfully studied with this potential energy function and program package [15,16]. There are also other folding and optimization packages based on Monte Carlo techniques with open codes like SMMP [17], GROMACS [18], and FANTOM [19].…”

Theory of Phase Transitions in Polypeptides and Proteins

“…The fitting function Eq. (5.7) was used for the description of the total energy of polypeptides in earlier papers [119,142]. The results of fitting are shown in Furthermore, MD simulations demonstrate that with an increase of the polypeptide length, the temperature of the phase transition shifts towards higher temperatures (see Fig.…”