Journal of structural biology vol:113 issue:3 pages:239-245
A model of the reactive form of plasminogen activator inhibitor-1 (PAI-1) has been constructed using molecular graphics and starting from the known crystal structure of latent PAI-1. The residues P16 to P10', of which P16-P4 form strand 4 of the beta-sheet A (s4A) and P3-P10' form an extended loop in the latent form, have been removed and remodeled into this structure, based on the structures of ovalbumin and cleaved alpha(1)-proteinase inhibitor. Residues P4'-P10' were remodeled as a beta-strand s1C, located on the surface of the molecule and the N-terminal end (P16-P14) of the eliminated loop was rebuilt using appropriate backbone dihedrals. Subsequently, a secondary structure prediction program was applied and further optimization of the model was performed by several molecular dynamics runs. Apparently the beta-strand was stabilized by only two hydrogen bonds. Further analysis revealed that, although s4A was removed, s3A and s5A did not approach each other. In this current model it was also found that the large gap between the loop connecting s4C-s3C and the loop connecting s3B-hG remained 11 Angstrom in contrast to the small gap (4 Angstrom) at a similar position in other serpins. These observations may explain the ease of a conformational change of the reactive site loop of PAI-1 during transition to the latent and the preinserted form. In addition the current model can be used for the design of stable, functional, PAI-1 mutants. Detailed structural analysis of the latter may facilitate studies on the structure-function relationship in PAI-1 in particular and in other serpins in general. (C) 1994 Academic Press, Inc.