Calculation of the minimum energy conformation of biomolecules using a global optimization technique II. Conformation of N-acetylglycine N-methyl amide, a model dipeptide unit

Electrostatic interactions in globular proteins. Different dielectric models applied to the packing of alpha-helices

The alpha-helix has an electric dipole arising from the alignment of peptide dipoles parallel to the helix axis. The effect of this alpha-helix dipole in the stabilization of the tertiary structure of globular proteins is examined using three of the commonly used dielectric models. These models are; (1) the uniform dielectric model, (2) the distance dependent dielectric model and (3) the cavity dielectric model. Of these the cavity model is the most reasonable since it attempts to describe the markedly different dielectric responses of the solvent and the protein. The protein is set at a low continuous dielectric value and the solvent is set at a high continuous dielectric value. It is found that for the cavity model of the dielectric the calculated interaction energy between two helices is strongly dependent upon how exposed the helix termini are to solvent. For helices with exposed termini the calculations using the cavity model yield electrostatic interaction energies which are lower by an order of magnitude than those obtained using the uniform dielectric model.

The combinatorial distance geometry method for the calculation of molecular conformation. II. Sample problems and computational statistics

The performance of a branch and bound algorithm for molecular energy minimization is evaluated on a variety of test problems. Although not at present efficient enough for use in most practical situations, we show that it has distinct advantages over more conventional methods of global minimization. In addition, this study illustrates the technique on which the present algorithm is based, and the problems which must be overcome in developing an efficient algorithm based on similar principles.