A refined model for the variable domains (Fv) of the J539 beta(1,6)-D-galactan-binding immunoglobulin

A refined protocol for building a hypothetical model of the J539 Fv is described. Computer programs for positioning amino acid side chains and structure energy minimization [CHARMM program of Brooks et al., J. comp. Chem. 4, 187-217 (1983)] were employed. Computer modeling was accomplished on an Evans and Sutherland picture system which permitted structure visualization in three dimensions. Peptide backbone breaksites were rejoined by monitoring for correct distances and torsion angles. A physical model was then constructed and used as a basis for further refinements such as aligning conformations around remodeled sites, adjusting proline substitutions and optimizing hydrogen-bond-forming potentials. This structure (J539-ADO) was energy minimized and the final coordinates were obtained from the energy-refined model. The resulting hypothetical J539 structure can be compared to the structure of J539 now being determined by X-ray crystallography. The procedures described can be used for other Fv fragments.