The binding mechanism of a peptidic cyclic serine protease inhibitor

TY - JOUR

T1 - The binding mechanism of a peptidic cyclic serine protease inhibitor

AU - Jiang, Longguang

AU - Svane, Anna Sigrid P.

AU - Sørensen, Hans Peter

AU - Jensen, Jan K

AU - Hosseini, Masood

AU - Chen, Zhuo

AU - Weydert, Caroline

AU - Nielsen, Jakob Toudahl

AU - Christensen, Anni

AU - Yuan, Cai

AU - Jensen, Knud Jørgen

AU - Nielsen, Niels Chr

AU - Malmendal, Anders

AU - Huang, Mingdong

AU - Andreasen, Peter

N1 - Copyright © 2011 Elsevier Ltd. All rights reserved.

PY - 2011/9/16

Y1 - 2011/9/16

N2 - 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.

AB - 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.

KW - Amino Acid Sequence

KW - Humans

KW - Molecular Sequence Data

KW - Peptides, Cyclic

KW - Protein Binding

KW - Serine Proteinase Inhibitors

KW - Surface Plasmon Resonance

U2 - 10.1016/j.jmb.2011.07.028

DO - 10.1016/j.jmb.2011.07.028

M3 - Journal article

C2 - 21802428

SN - 0022-2836

VL - 412

SP - 235

EP - 250

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

IS - 2

ER -