Journal
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
Volume 36, Issue 15, Pages 4072-4084Publisher
TAYLOR & FRANCIS INC
DOI: 10.1080/07391102.2017.1407674
Keywords
chymotrypsin-like serine protease; specificity subsites; peptide recognition; in silico mutation; drug design
Categories
Funding
- Austrian Science Fund FWF [P23051, P26997, P25003-B21]
- Austrian Science Fund (FWF) [P26997, P25003] Funding Source: Austrian Science Fund (FWF)
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A ten microsecond molecular dynamics simulation of a kallikrein-related peptidase 7 peptide complex revealed an unexpected change in binding mode. After more than two microseconds unrestrained sampling we observe a spontaneous transition of the binding pose including a 180 degrees rotation around the P1 residue. Subsequently, the substrate peptide occupies the prime side region rather than the cognate non-prime side in a stable conformation. We characterize the unexpected binding mode in terms of contacts, solvent-accessible surface area, molecular interactions and energetic properties. We compare the new pose to inhibitor-bound structures of kallikreins with occupied prime side and find that a similar orientation is adopted. Finally, we apply in silico mutagenesis based on the alternative peptide binding position to explore the prime side specificity of kallikrein-related peptidase 7 and compare it to available experimental data. Our study provides the first microsecond time scale simulation data on a kallikrein protease and shows previously unexplored prime side interactions. Therefore, we expect our study to advance the rational design of inhibitors targeting kallikrein-related peptidase 7, an emerging drug target involved in several skin diseases as well as cancer.
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