N-terminal extension of the yeast IA3 aspartic proteinase inhibitor relaxes the strict intrinsic selectivity.
Yeast IA(3) aspartic proteinase inhibitor operates through an unprecedented mechanism and exhibits a remarkable specificity for one target enzyme, saccharopepsin. Even aspartic proteinases that are very closely similar to saccharopepsin (e.g. the vacuolar enzyme from Pichia pastoris) are not susceptible to significant inhibition. The Pichia proteinase was selected as the target for initial attempts to engineer IA(3) to re-design the specificity. The IA(3) polypeptides from Saccharomyces cerevisiae and Saccharomyces castellii differ considerably in sequence. Alterations made by deletion or exchange of the residues in the C-terminal segment of these polypeptides had only minor effects. By contrast, extension of each of these wild-type and chimaeric polypeptides at its N-terminus by an MK(H)(7)MQ sequence generated inhibitors that displayed subnanomolar potency towards the Pichia enzyme. This gain-in-function was completely reversed upon removal of the extension sequence by exopeptidase trimming. Capture of the potentially positively charged aromatic histidine residues of the extension by remote, negatively charged side-chains, which were identified in the Pichia enzyme by modelling, may increase the local IA(3) concentration and create an anchor that enables the N-terminal segment residues to be harboured in closer proximity to the enzyme active site, thus promoting their interaction. In saccharopepsin, some of the counterpart residues are different and, consistent with this, the N-terminal extension of each IA(3) polypeptide was without major effect on the potency of interaction with saccharopepsin. In this way, it is possible to convert IA(3) polypeptides that display little affinity for the Pichia enzyme into potent inhibitors of this proteinase and thus broaden the target selectivity of this remarkable small protein.
Winterburn
Tim J
TJ
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
Phylip
Lowri H
LH
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
Bur
Daniel
D
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
Wyatt
David M
DM
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
Berry
Colin
C
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
Kay
John
J
 School of Biosciences, Cardiff University, UK Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.
D017398:Alternative Splicing / Q000235:genetics; D000595:Amino Acid Sequence; D000953:Antigens, Protozoan; D016282:Aspartic Acid Endopeptidases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D008565:Membrane Proteins; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012680:Sensitivity and Specificity; D017386:Sequence Homology, Amino Acid; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D000953:Antigens, Protozoan; C085964:EMA-1 protein, Babesia equi; D008565:Membrane Proteins; C018134:PAI3 protein, S cerevisiae; D015800:Protozoan Proteins; D011994:Recombinant Proteins; D029701:Saccharomyces cerevisiae Proteins; D016282:Aspartic Acid Endopeptidases