Ionizable P1 Residues in Serine Proteinase Inhibitors Undergo Large pK Shifts on Complex Formation

Abstract

The burial of charged residues in proteins is rare as it is thermodynamically strongly disfavored. However, in "standard mechanism" protein inhibitors of serine proteinases, the P 1 residue, which is highly exposed, becomes buried in the S 1 specificity pocket of the enzyme. In many enzymes, such as Streptomyces griseus proteinase B (SGPB) the S 1 pocket is hydrophobic. We measured the pH dependence of the association equilibrium constant for the interaction of SGPB with turkey ovomucoid third domain P 1 mutants,

Calculations of the binding affinities of protein-protein complexes with the fast multipole method

“…15͒ since this program is known to be the most accurate one to predict the pK a values of amino acids based on extensive comparisons with a large set of experimentally determined pK a . 44 For our calculations it gives pK a values 8.7 and 8.8 for P 1 Asp and P 1 Glu mutants in BPTI-trypsin complexes and also gives pK a value 8.8 for P 1 Glu mutant in OMTKY3-SGPB complex which is essentially the same as the experimental one 8.74 from Qasim et al 42 With this shifted pK a due to local environments, the calculated binding free energies are much improved as compared with the experimental one shown in Fig. 4͑a͒.…”

“…The pK a shift of P 1 Glu mutant in OMTKY3-SGPB complex from 4.46 ͑unbound͒ to 8.74 ͑bound͒ was measured by Qasim et al 42 Brandsdal et al 43 calculated the pK a of P 1 Glu mutant in OMTKY3-SGPB complex to be 13.1. They also calculated the pK a shift of P 1 Glu mutant of BPTItrypsin complex upon binding from 4.3 to 14.3.…”

“…The experimental pK a shift of OMTKY3 P 1 Glu bound to SGPB is 8.7 ͑see Qasim et al͒, 42 using the PROPKA 2.0 ͑Ref. 15͒ pK a values 8.7 and 8.8 for OMTKY3 P 1 Asp and P 1 Glu are obtained.…”

Binding of amino acid side-chains to S 1 cavities of serine proteinases 1 1Edited by R. Huber

“…These data are rather compactly organized and discussed by Lee (1993) (Molina et al, 1994 (Matthews, 1993 Huang, 1995) Bigler et al (1993) (Huang, 1995) (Qasim et al 1995) (Qasim et al, 1995). (Qasim et al, 1995 and unpublished; (Read & James, 1986;Bode & Huber, 1992).…”

Dissecting the energetics of a protein-protein interaction: the binding of ovomucoid third domain to elastase 1 1Edited by P. E. Wright

“…However, if desolvation were the only mechanism responsible for the pK a change, one might expect the pK a shift to be much larger (e.g. see Stites et al, 1991;Langsetmo et al, 1991;Qasim et al, 1995). Inhibitor binding to serine proteases causes a small reorientation of the side-chain of Ser195, placing its hydroxyl oxygen atom within hydrogen-bonding distance of NE2 of His57 (Read & James, 1986;Bolognesi et al, 1982).…”