This chapter discusses the simple force field for use in the study of peptide and protein conformation. Both backbone and side chains have been examined and are shown to be in generally good agreement with properties derived from high-resolution protein structures. CRASS, a simple force field for use in the study of conformational properties of peptides and proteins is derived. CRASS explores the conformational properties of small peptides. To keep CRASS simple, the united atoms approximation is adopted: nonpolar hydrogens are not included explicitly; instead, the radii of the atoms to which they are attached are enlarged accordingly. A set of vander Waals radii, Ri, is determined from a survey of small molecule crystal structures. CRASS vander Waals radii and atom (and group) types are listed. The residue is simulated in the center of flexible blocked tripeptides using the CRASS force field at a temperature of 298 K. The simulated serine and threonine distributions do not agree with those observed in proteins, presumably because electrostatic interactions are ignored in CRASS. In particular, within CRASS it is possible for two atoms of like charge (for example, two oxygen) to interact favorably at short distances.
ASJC Scopus subject areas
- Molecular Biology