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Results

NEIMO calculations were carried out on a wide variety of peptide and protein systems, ranging from the five-residue peptide Met-enkephalin to the tomato bushy stunt virus (TBSV) protomer, which contains three proteins totaling 893 residues. Table contains a list of the ten systems studied. The two peptides were built using the Peptide Builder of BIOGRAF[37], which uses standard amino acid geometries. They were initially configured as alpha helices, but were minimized to a local potential energy minimum using conjugate gradients minimization. As in all calculations reported here, the DREIDING forcefield was used for these minimizations. No solvent or counterions were used, but the dielectric constant for each pair of atoms and was set proportional to , the distance between them. This crudely represents the electrostatic shielding of aqueous solvent. For these peptides, no nonbond cutoff was used; i.e., all possible pairs were included in the van der Waals and electrostatic calculations. The initial conformations of the proteins were derived from the X-ray crystal structures listed in Table . All metal ions, solvent molecules, and disulfide bridges were removed, leaving only protein chains which conformed to a tree topology. (As mentioned above, sidechain aromatic rings and proline rings are treated as single clusters). Hydrogen atoms were then added to non-carbon atoms. As was done for the peptides, the DREIDING forcefield was used to energy-minimize these conformations. Nonbonds, however, were treated differently. The large size of the proteins precluded the inclusion of all possible nonbond pairs, a number close to for an -atom protein. Therefore, the cell-multipole method (CMM) of Ding et al.[25] was used to calculate the van der Waals and electrostatic interactions. This method is roughly proportional to , but provides far greater accuracy than the standard approach of excluding all nonbond interactions greater than 9 Å.




Next: Timing Up: Chapter 2 Previous: Methodology


ktl@sgi1.wag.caltech.edu
Sat Jun 18 14:06:11 PDT 1994