FACTORS INFLUENCING ACCURACY OF COMPUTER-BUILT MODELS - A STUDY BASEDON LEUCINE-ZIPPER GCN4 STRUCTURE

A three-dimensional model of the leucine zipper GCN4 built from its am ino acid sequence had been reported previously by us. When the two alt ernative x-ray structures of the GCN4 dimer became available, the root mean square (r.m.s.) shifts between our model and the structures were determined as similar to 2.7 Angstrom on all atoms. These values are similar to the r.m.s. shift of 2.8 Angstrom between the two GCN4 struc tures in the different crystal forms (C-2 and P2(1)2(1)2(1)). CONGEN c onformational searches were run to better understand the conditions th at may determine the preference of different conformers in different e nvironments and to test the sensitivity of our current modeling techni ques. With a judicious choice of CONGEN search parameters, the backbon e r.m.s, deviation improved to 0.8 Angstrom and 2.5 Angstrom on all at oms. The side-chain conformations of Val and Leu at the helical interf ace were well reproduced (1.2 Angstrom r.m.s.), and the large side-cha in misplacements occurred with only a small number of charged amino ac ids and a tyrosine. Inclusion of the crystal environment (C-2 symmetry ), as a passive background, into the side-chain conformational search further improved the accuracy of the model to an r.m.s. deviation of 2 .1 Angstrom. Conformational searches carried out in the two different crystal environments and employing the AMBER protein/DNA forcefield, a s implemented in CONGEN, gave the r.m.s. values of 2.2 Angstrom (for t he C-2 symmetry) and 2.5 Angstrom (for the P2(1)2(1)2(1) symmetry). In the C-2 symmetry crystal, as much as 40% of the surface of each dimer was involved in crystal contacts with other dimers, and the charged r esidues on the surface often interacted with immobilized water molecul es. Thus, occasional large r.m.s. deviations between the model acid th e x-ray side chains were due to specific conditions that did not occur in solution.