Binding of amino acid side-chains to S1 cavities of serine proteinases

Wuyuan Lu, Izydor Apostol, M. A. Qasim, Nicholas Warne, Richard Wynn, Wen Lei Zhang, Stephen Anderson, Yi Wen Chiang, Eleanor Ogin, Irvin Rothberg, Kevin Ryan, Michael Laskowski

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153 Scopus citations


The P1 or primary specificity residue of standard mechanism canonical protein inhibitors of serine proteinases, inserts into the S1 primary specificity cavity of the cognate enzyme upon enzyme-inhibitor complex formation. Both natural evolution and protein engineering often change the P1 residue to greatly alter the specificity and the binding strength. To systematize such results we have obtained all 20 coded P1 variants of one such inhibitor, turkey ovomucoid third domain, by recombinant DNA technology. The variants were extensively characterized. The association equilibrium constants were measured at pH 8.30, 21 (±2)°C, for interaction of these variants with six well characterized serine proteinases with hydrophobic S1 cavities. The enzyme names are followed by the best, worst and most specific coded residue for each. Bovine chymotrypsin Aα (Tyr, Pro, Trp), porcine pancreatic elastase (Leu/Ala, Arg, Ala), subtilisin Carlsberg (Cys, Pro, Glu), Streptomyces griseus proteinase A (Cys, Pro, Leu) and B (Cys, Pro, Lys) and human leukocyte elastase (Ile, Asp, Ile). The data set was merged with K(a) values for five non-coded variants at P1 of turkey ovomucoid third domain obtained in our laboratory by enzymatic semisynthesis. The ratios of the highest to the lowest K(a) for each of the six enzymes range from 106 to 108. The dominant force for binding to these pockets is the hydrophobic interaction. Excess steric bulk (too large for the pocket), awkward shape (Pro, Val and Ile), polarity (Ser) oppose interaction. Ionic charges, especially negative charges on Glu- and Asp- are strongly unfavorable. The Pearson product moment correlations for all the 15 enzyme pairs were calculated. We suggest that these may serve as a quantitative description of the specificity of the enzymes at P1. The sets of Streptomyces griseus proteinases A and B and of the two elastases are strongly positively correlated. Strikingly, chymotrypsin and pancreatic elastase are negatively correlated (-0.10). Such correlations can be usefully extended to many other enzymes and to many other binding pockets to provide a general measure of pocket binding specificity.

Original languageEnglish (US)
Pages (from-to)441-461
Number of pages21
JournalJournal of molecular biology
Issue number2
StatePublished - Feb 21 1997

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology


  • Amino acid side-chains, binding of
  • Equilibrium constants for association
  • Protein-protein interaction
  • Proteinase inhibitors
  • Serine proteinases

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