RCSB PDB - 3OY6: The crystal structure of uPA complex with peptide inhibitor MH036 at pH4.6 (original) (raw)
The binding mechanism of a peptidic cyclic serine protease inhibitor
[Jiang, L.G.](/search?q=citation.rcsb%5Fauthors:Jiang, L.G.), [Svane, A.S.P.](/search?q=citation.rcsb%5Fauthors:Svane, A.S.P.), [Sorensen, H.P.](/search?q=citation.rcsb%5Fauthors:Sorensen, H.P.), [Jensen, J.K.](/search?q=citation.rcsb%5Fauthors:Jensen, J.K.), [Hosseini, M.](/search?q=citation.rcsb%5Fauthors:Hosseini, M.), [Chen, Z.](/search?q=citation.rcsb%5Fauthors:Chen, Z.), [Weydert, C.](/search?q=citation.rcsb%5Fauthors:Weydert, C.), [Nielsen, J.T.](/search?q=citation.rcsb%5Fauthors:Nielsen, J.T.), [Christensen, A.](/search?q=citation.rcsb%5Fauthors:Christensen, A.), [Yuan, C.](/search?q=citation.rcsb%5Fauthors:Yuan, C.), [Jensen, K.J.](/search?q=citation.rcsb%5Fauthors:Jensen, K.J.), [Nielsen, N.C.](/search?q=citation.rcsb%5Fauthors:Nielsen, N.C.), [Malmendal, A.](/search?q=citation.rcsb%5Fauthors:Malmendal, A.), [Huang, M.D.](/search?q=citation.rcsb%5Fauthors:Huang, M.D.), [Andreasen, P.A.](/search?q=citation.rcsb%5Fauthors:Andreasen, P.A.)
(2011) J Mol Biology 412: 235-250
PubMed: 21802428 Search on PubMed
PubMed Abstract:
Serine proteases are classical objects for studies of catalytic and inhibitory mechanisms as well as interesting as therapeutic targets. Since small-molecule serine protease inhibitors generally suffer from specificity problems, peptidic inhibitors, isolated from phage-displayed peptide libraries, have attracted considerable attention. Here, we have investigated the mechanism of binding of peptidic inhibitors to serine protease targets. Our model is upain-1 (CSWRGLENHRMC), a disulfide-bond-constrained competitive inhibitor of human urokinase-type plasminogen activator with a noncanonical inhibitory mechanism and an unusually high specificity. Using a number of modified variants of upain-1, we characterised the upain-1-urokinase-type plasminogen activator complex using X-ray crystal structure analysis, determined a model of the peptide in solution by NMR spectroscopy, and analysed binding kinetics and thermodynamics by surface plasmon resonance and isothermal titration calorimetry. We found that upain-1 changes both main-chain conformation and side-chain orientations as it binds to the protease, in particular its Trp3 residue and the surrounding backbone. The properties of upain-1 are strongly influenced by the addition of three to four amino acids long N-terminal and C-terminal extensions to the core, disulfide-bond-constrained sequence: The C-terminal extension stabilises the solution structure compared to the core peptide alone, and the protease-bound structure of the peptide is stabilised by intrapeptide contacts between the N-terminal extension and the core peptide around Trp3. These results provide a uniquely detailed description of the binding of a peptidic protease inhibitor to its target and are of general importance in the development of peptidic inhibitors with high specificity and new inhibitory mechanisms.
Organizational Affiliation:
Danish-Chinese Centre for Proteases and Cancer, Aarhus University, DK-8000 Aarhus C, Denmark.