Modeling the uncleaved serpin antichymotrypsin and its chymotrypsin complex

Abstract

In order to provide a structural reference for protein engineering experiments involving the serpin alpha 1-antichymotrypsin (ACT) and its complexes with chymotrypsin and DNA, a homology model of ACT has been constructed based on the 3-D structure of the related protein ovalbumin [29% identical and 44% similar; see Stein, P., Leslie, A., Finch, J., Turnell, W., McLaughlin, P. and Carrell, R. (1990) Nature, 347, 99-102]. After mapping the amino acid sequence of ACT onto the peptide backbone of ovalbumin, the resulting model was subjected to simulated annealing and energy minimization. Overall, the final ACT model is structurally similar to ovalbumin, although the 2.4 A root mean square deviation of corresponding C alpha atoms reflects the presence of regions exhibiting notable structural differences. The hydrogen bond stereochemistry of the ACT model is consistent with patterns found in high resolution protein structures and 92% of its backbone atoms have acceptable conformations when evaluated in a Ramachandran analysis. Significantly, the homology model serves as a structural reference for protein engineering experiments aimed at redesigning the functional properties of ACT, particularly with regard to its protease-bound conformation. Additionally, the homology model may be useful as a probe for solving the crystal structures of certain ACT variants (e.g. Thr345-->Arg) by molecular replacement methods. Ultimately, the homology approach may be applied toward the construction of other serpin models starting with an experimentally determined structure of uncleaved ACT as a template.