Enzymatic cyclization of a potent bowman-birk protease inhibitor, sunflower trypsin inhibitor-1, and solution structure of an acyclic precursor peptide

The most potent known naturally occurring Bowman-Birk inhibitor, sunflower trypsin inhibitor-1 (SFTI-1), is a bicyclic 14-amino acid peptide from sunflower seeds comprising one disulfide bond and a cyclic backbone. At present, little is known about the cyclization mechanism of SFTI-1. We show here that an acyclic permutant of SFTI-1 open at its scissile bond, SFTI-1[6,5], also functions as an inhibitor of trypsin and that it can be enzymatically backbone-cyclized by incubation with bovine beta-trypsin. The resulting ratio of cyclic SFTI-1 to SFTI-1[6,5] is approximately 9:1 regardless of whether trypsin is incubated with SFTI-1[6,5] or SFTI-1. Enzymatic resynthesis of the scissile bond to form cyclic SFTI-1 is a novel mechanism of cyclization of SFTI-1[6,5]. Such a reaction could potentially occur on a trypsin affinity column as used in the original isolation procedure of SFTI-1. We therefore extracted SFTI-1 from sunflower seeds without a trypsin purification step and confirmed that the backbone of SFTI-1 is indeed naturally cyclic. Structural studies on SFTI-1[6,5] revealed high heterogeneity, and multiple species of SFTI-1[6,5] were identified. The main species closely resembles the structure of cyclic SFTI-1 with the broken binding loop able to rotate between a cis/trans geometry of the I7-P8 bond with the cis conformer being similar to the canonical binding loop conformation. The non-reactive loop adopts a beta-hairpin structure as in cyclic wild-type SFTI-1. Another species exhibits an iso-aspartate residue at position 14 and provides implications for possible in vivo cyclization mechanisms.

Peptide mimics of the Bowman-Birk inhibitor reactive site loop

Bowman-Birk Inhibitors (BBIs) are small highly cross-linked proteins that typically display an almost symmetrical "double-headed" structure. Each "head" contains an independent proteinase binding domain. The realization that one BBI molecule could form a 1:1:1 complex with two enzymes led early workers to dissect this activity. Now, after three decades of research, it has been possible to isolate the antiproteinase activity as small ( approximately 11 residues), cyclic, synthetic peptides, which display most of the functional aspects of the protein. More recently, it has been found that these peptide fragments are not just a synthetic curiosity-a natural 14-residue cyclic peptide (SFTI-1), which too encapsulates the BBI inhibitory motif, is found to occur in sunflowers. This article reviews the properties of BBI-based peptides (including SFTI-1) and discusses the features that are important for inhibitory activity.

The (1)H-NMR solution structure of the antitryptic core peptide of Bowman-Birk inhibitor proteins: a minimal canonical loop

Bowman-Birk inhibitor (BBI) proteins contain an inhibitory motif comprising a disulfide-bonded sequence that interacts with serine proteinases. Recently, a small 14-residue peptide from sunflowers (SFTI-1), which has potent anti-trypsin activity, has been found to have the same motif. However, this peptide also has an unusual head-to-tail cyclisation. To address the role of the core inhibitory sequence itself, we have solved the (1)H-NMR solution structure of an antitryptic 11-residue cyclic peptide that corresponds to the core reactive site loops of both SFTI-1 and Bowman-Birk inhibitor proteins. A comparison is made between the secondary chemical shifts found in this family and the canonical regions of several other inhibitors, giving some insight into relative flexibility and hydrogen bonding patterns in these inhibitors. The solution structure of the core peptide in isolation is found to retain essentially the same three-dimensional arrangement of both backbone and side chains as observed in larger antitryptic BBI and SFTI-1 fragments as well as in the complete proteins. The retention of the canonical conformation in the core peptide explains the peptids inhibitory potency. It therefore represents a minimization of both the BBI and SFTI-1 sequences. We conclude that the core peptide is a conformationally defined, canonical scaffold, which can serve as a minimal platform for the engineering of biological activity.

Chemical synthesis and kinetic study of the smallest naturally occurring trypsin inhibitor SFTI-1 isolated from sunflower seeds and its analogues

The smallest known naturally occurring trypsin inhibitor SFTI-1 (14 amino acid residues head-to-tail cyclic peptide containing one disulfide bridge) and its two analogues with one cycle each were synthesized by the solid phase method. Their trypsin inhibitory activity was determined as association equilibrium constants (K(a)). Additionally, hydrolysis rates with bovine beta-trypsin were measured. Among all three peptides, the wild SFTI-1 and the analogue with the disulfide bridge only had, within the experimental error, the same activity (the K(a) values 1.1 x 10(10) and 9.9 x 10(9) M(-1), respectively). Both peptides displayed unchanged inhibitory activity up to 6 h. The trypsin inhibitory activity of the analogue with the head-to-tail cycle only was 2.4-fold lower. It was also remarkably faster hydrolyzed (k = 1.1 x 10(-4) mol(peptide) x mol(enzyme)(-1) x s(-1)) upon the incubation with the enzyme than the other two peptides. This indicates that the head-to-tail cyclization is significantly less important than the disulfide bridge for maintaining trypsin inhibitory activity.

The Bowman-Birk inhibitor reactive site loop sequence represents an independent structural beta-hairpin motif

We have determined the NMR structure in aqueous solution of a disulphide-cyclised 11-residue peptide that forms a stable beta-hairpin, incorporating a type VIb beta-turn. The structure is found to be extremely well ordered for a short peptide, with the 30 lowest energy simulated annealing structures having an average pairwise r.m.s. deviation of only 0.36 A over the backbone. All but three side-chains adopt distinct conformations, allowing a detailed analysis of their involvement in cross-strand interactions. The peptide sequence analysed originates from a previously reported study, which identified potent inhibitors of human leukocyte elastase from screening a combinatorial peptide library based on the short protein beta-sheet segment that forms the reactive site loop of Bowman-Birk inhibitors. A detailed comparison of the peptide's solution structure with the corresponding region in the whole protein structure reveals a very good correspondence not only for the backbone (r.m.s. deviation approximately 0.7 A) but also for the side-chains. This isolated beta-hairpin retains the biologically active "canonical conformation" typical of small serine proteinase inhibitor proteins, which explains why it retains inhibitory activity. Since the structural integrity is sequence-inherent and does not depend upon the presence of the remaining protein, this beta-hairpin represents an independent structural motif and so provides a useful model of this type of protein architecture and its relation to biological function. The relationship between the conformation of this beta-hairpin and its biological activity is discussed.

The role of the P2' position of Bowman-Birk proteinase inhibitor in the inhibition of trypsin. Studies on P2' variation in cyclic peptides encompassing the reactive site loop

The role of the P2' residue in proteinase inhibitors of the Bowman-Birk family was investigated using synthetic cyclic peptides based on the reactive site loop of the inhibitor. A series of 21 variants having different P2' residues was tested for inhibition of trypsin, and the rate at which they were hydrolysed by this enzyme was also measured. Variation at P2' was found to result in marked differences in inhibitory potency, with the best sequence (Ile) having a Ki value of 9 nM. Peptides with P2' Gly, Pro or Glu failed to demonstrate any measurable inhibition (Ki>1 mM). The peptides also displayed significant differences in the rates at which they were hydrolysed, which varied by over three orders of magnitude between the difference sequences. There was found to be overall correlation between the Ki value and the rate of hydrolysis, with peptides that inhibited best also being hydrolysed more slowly. The results are discussed in light of the sequence information for Bowman-Birk inhibitor proteins.

The role of threonine in the P2 position of Bowman-Birk proteinase inhibitors: studies on P2 variation in cyclic peptides encompassing the reactive site loop

Previously, we have described a template-assisted combinatorial peptide library based on the anti-tryptic reactive site loop of a Bowman-Birk inhibitor (BBI). Sequences that displayed inhibitory activity re-directed towards chymotrypsin were found to have a consensus binding motif, with their most striking feature being that exclusively threonine was found at the P2 position. The present study investigates the reason for this surprising specificity by maintaining the binding motif but systematically varying the P2 residue. From analysis of 26 variants, it is found that the requirements for inhibitory activity at P2 are finely tuned, and in agreement with the library work, threonine at P2 provides optimal inhibition. In addition, peptides with threonine at P2 are significantly less susceptible to hydrolysis. Examination of all available BBI sequences shows that threonine is very highly conserved at P2, which implies that the functional requirement extends to the full-length BBI protein. Our results are consistent with a dual requirement for hydrophobic recognition within the S2 pocket and maintenance of an inhibitory conformation via hydrogen bonding within the reactive-site loop. As the isolated peptide loop reproduces the active region of full-length BBI, these results explain why threonine is well conserved at P2 in this class of inhibitor. Furthermore, they illustrate that proteinase inhibitor specificity can have characteristics that are not easily predicted from information on the substrate preferences of a proteinase.

Stability of protease inhibitors based on the Bowman-Birk reactive site loop to hydrolysis by proteases

Bowman-Birk proteinase inhibitor proteins contain two inhibitory regions, each of which is encapsulated within nine-residue disulfide-linked loops. It is known that short cyclic peptides that retain the nine-residue disulfide-bridged motif have inhibitory activity, and can be used as models of the natural inhibitor protein. Two factors are important in determining the effectiveness of such inhibitor peptides: the value of the inhibition constant, and rate at which the inhibitor peptide is hydrolyzed by the proteinase. In this paper we report a study of the inhibitory properties and stability towards proteolytic hydrolysis of a family of synthetic peptides derived from the trypsin reactive site loop of the Bowman-Birk inhibitors. The addition of a single amino acid residue to each end of the nine-residue disulfide-linked loop is found to reduce the rate at which the peptide is hydrolyzed. In addition, changing the P2' residue from Asn-->Ile gives inhibitors with considerably enhanced stability to proteolysis, as well as reduced values of Ki. The implications of these factors for the design of inhibitors based on this loop motif is discussed.

Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution. Structural peculiarities in a folded protein conformation

The Bowman-Birk inhibitor from soybean is a small protein that contains a binary arrangement of trypsin-reactive and chymotrypsin-reactive subdomains. In this report, the crystal structure of this anticarcinogenic protein has been determined to 0.28-nm resolution by molecular replacement from crystals grown at neutral pH. The crystal structure differs from a previously determined NMR structure [Werner, M. H. & Wemmer, D. E. (1992) Biochemistry 31, 999-1010] in the relative orientation of the two enzyme-insertion loops, in some details of the main chain trace, in the presence of favourable contacts in the trypsin-insertion loop, and in the orientation of several amino acid side chains. The proximity of Met27 and Gln48 in the X-ray structure contradicts the solution structure, in which these two side chains point away from each other. The significant effect of a Met27-->Ile replacement on the inhibitory activity of the chymotrypsin-reactive subdomain agrees with the X-ray structure. Exposed hydrophobic patches, the presence of charged amino acid residues, and the presence of water molecules in the protein interior are in contrast to standard proteins that comprise a hydrophobic core and exposed polar amino acids.

Synthesis of a mixture of cyclic peptides based on the Bowman-Birk reactive site loop to screen for serine protease inhibitors

A peptide mixture containing 21 peptide sequences has been constructed to test the Bowman-Birk inhibitor reactive-site loop motif as the basis of inhibition for a range of serine proteases. The 21 peptides are all based on an 11 amino acid sequence designed from a Bowman-Birk like inhibitor reactive-site loop. Variation has been introduced at the P1 site of the loop, which has been randomised to include all the natural L-amino acids (except for cysteine), plus the non-natural L-amino acids ornithine and norleucine, The mixture of peptides was screened for specific binding to immobilised porcine pancreatic elastase, subtilisin BPN', alpha-chymotrypsin, trypsin, anhydro-alpha-chymotrypsin and anhydrotrypsin. Five peptides from the mixture bind to alpha-chymotrypsin, two of which also bind to anhydro-alpha-chymotrypsin, and two peptides bind trypsin, neither of which binds to anhydro-trypsin. The competitive inhibition constants (K(i)) and the rates of proteolytic hydrolysis of the individual peptides with their respective enzymes were determined. The rates of hydrolysis were found to vary widely and show little correlation with the K(i) values. In the case of the alpha-chymotrypsin inhibitors, the peptides with the lowest K(i) (0.1-0.05 mM) were the only peptides that bound to anhydro-alpha-chymotrypsin. However, no peptides bound to anhydrotrypsin, suggesting a fundamental difference in the way that alpha-chymotrypsin and trypsin are inhibited by these cyclic peptides.