title: Quantitative Correlation of Conformational Binding Enthalpy with Substrate Specificity of Serine Proteases.
abstract: Members of the same protease family show different substrate specificity, even if they share identical folds, depending on the physiological processes they are part of. Here, we investigate the key factors for subpocket and global specificity of factor Xa, elastase, and granzyme B which despite all being serine proteases and sharing the chymotrypsin-fold show distinct substrate specificity profiles. We determined subpocket interaction potentials with GRID for static X-ray structures and an in silico generated ensemble of conformations. Subpocket interaction potentials determined for static X-ray structures turned out to be insufficient to explain serine protease specificity for all subpockets. Therefore, we generated conformational ensembles using molecular dynamics simulations. We identified representative binding site conformations using distance-based hierarchical agglomerative clustering and determined subpocket interaction potentials for each representative conformation of the binding site. Considering the differences in subpocket interaction potentials for these representative conformations as well as their abundance allowed us to quantitatively explain subpocket specificity for the nonprime side for all three example proteases on a molecular level. The methods to identify key regions determining subpocket specificity introduced in this study are directly applicable to other serine proteases, and the results provide starting points for new strategies in rational drug design.
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Birgit J
authors.initials: BJ
authors.lastname: Waldner
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.|Centre for Molecular Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.
authors.forename: Julian E
authors.initials: JE
authors.lastname: Fuchs
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.|Bioinformatics Institute (BII), Agency of Science, Technology and Research (A* STAR) , 30 Biopolis Street, Matrix#07-01, 138671 Singapore.
authors.forename: Roland G
authors.initials: RG
authors.lastname: Huber
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Susanne
authors.initials: S
authors.lastname: von Grafenstein
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Schauperl
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Kramer
authors.affiliation: Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck , Innrain 82, 6020 Innsbruck, Austria.
authors.forename: Klaus R
authors.initials: KR
authors.lastname: Liedl
mesh_terms: D011487:Protein Conformation; D057057:Serine Proteases / Q000737:chemistry / Q000378:metabolism*; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D057057:Serine Proteases