A Monte Carlo method with different treatments for short‐ and long‐range interactions in conformational statistics of polypeptide chains

Monte-Carlo calculations of the solvent effects on the conformation of angiotensin II

An efficient Metropolis Monte-Carlo (MMC) procedure is proposed in order to calculate averages of the energy of conformation and structural properties of a polypeptide chain in interaction with a solvent. The contribution of hydration to the free energy of conformation of the macromolecule is calculated using the accessible surface area method. This algorithm, performed with different sets of atomic solvation parameters (ASP), is applied to the peptidic hormone angiotensin II. Different situations of solvation of that molecule are described when the ASP of the polar atoms are fixed to 0, whereas those of the apolar atoms are given values varying from -1.0 to 1.0. From results thus obtained, transitions from extended to collapsed conformations of the polypeptide chain can be simulated. Such changes of conformation could be related to a possible mechanism of binding of this hormone on a membrane surface.

Monte Carlo simulation of the conformational behaviour of a polypeptide chain near a charged surface

The conformational behaviour of a short polypeptide chain in the neighbourhood of a charged plane is simulated using a Monte Carlo method. In this approach, the plane is taken as a model of an interface separating a hydrophobic region from a hydrophilic one. It is shown that in the neighbourhood of the plane, folded molecular conformations are prevailing whilst stretched conformations are preferred far from the interface. When the plane is not charged, the molecule adjusts itself parallel to the interface. For a given position of the molecule with respect to the plane, when the charge density of the plane is increased, the molecule tends to turn perpendicular to the plane. The surface may either attract or repulse the molecule depending on the value of the charge density (the plane is always negatively charged).

Influence of the solvent on the conformational-dependent properties of random-coil polypeptides. I. The mean-square of the end-to-end distance and of the dipole moment

Conformational energies for the N-acetyl-N'-methylamides of the 20 natural amino acids were calculated, including the solvent effects, as functions of the angles phi and psi for rotation of the main chain and for six positions chi 1 of the C alpha-C beta bond in the side chain (fixed values for chi 2, chi 3, ...). The computed energies were used to evaluate the mean-square end-to-end distance and mean-square dipole moment of homopolypeptides of the 20 natural amino acids. Ten proteins and three enzymes of current interest were also studied. Slight differences in both properties are found on taking the effects of solvent into consideration. Comparison with other computational and experimental results is made.