Cavities of alpha(1)-antitrypsin that play structural and functional roles

Protein Sci. 2001 Jul;10(7):1446-53. doi: 10.1110/ps.840101.


The native form of inhibitory serine protease inhibitors (serpins) is strained, which is critical for their inhibitory activity. Previous studies on stabilizing mutations of alpha(1)-antitrypsin, a prototype of serpins, indicated that cavities provide a structural basis for the native strain of the molecule. We have systematically mapped the cavities of alpha(1)-antitrypsin that play such structural and functional roles by designing cavity-filling mutations at residues that line the walls of the cavities. Results show that energetically unfavorable cavities are distributed throughout the alpha(1)-antitrypsin molecule, and the cavity-filling mutations stabilized the native conformation at 8 out of 10 target sites. The stabilization effect of the individual cavity-filling mutations of alpha(1)-antitrypsin varied (0.2-1.9 kcal/mol for each additional methylene group) and appeared to depend largely on the structural flexibility of the cavity environment. Cavity-filling mutations that decreased inhibitory activity of alpha(1)-antitrypsin were localized in the loop regions that interact with beta-sheet A distal from the reactive center loop. The results are consistent with the notion that beta-sheet A and the structure around it mobilize when alpha(1)-antitrypsin forms a complex with a target protease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution
  • Animals
  • Drug Stability
  • Guanidine / pharmacology
  • Mutagenesis, Site-Directed
  • Pancreatic Elastase / antagonists & inhibitors
  • Pancreatic Elastase / metabolism
  • Protein Denaturation / drug effects
  • Protein Structure, Tertiary
  • Swine
  • alpha 1-Antitrypsin / chemistry*
  • alpha 1-Antitrypsin / genetics
  • alpha 1-Antitrypsin / pharmacology*


  • alpha 1-Antitrypsin
  • Pancreatic Elastase
  • Guanidine