title: Serpin latency transition at atomic resolution.
abstract: Protease inhibition by serpins requires a large conformational transition from an active, metastable state to an inactive, stable state. Similar reactions can also occur in the absence of proteases, and these latency transitions take hours, making their time scales many orders of magnitude larger than are currently accessible using conventional molecular dynamics simulations. Using a variational path sampling algorithm, we simulated the entire serpin active-to-latent transition in all-atom detail with a physically realistic force field using a standard computing cluster. These simulations provide a unifying picture explaining existing experimental data for the latency transition of the serpin plasminogen activator inhibitor-1 (PAI-1). They predict a long-lived intermediate that resembles a previously proposed, partially loop-inserted, prelatent state; correctly predict the effects of PAI-1 mutations on the kinetics; and provide a potential means to identify ligands able to accelerate the latency transition. Interestingly, although all of the simulated PAI-1 variants readily access the prelatent intermediate, this conformation is not populated in the active-to-latent transition of another serpin, α1-antitrypsin, which does not readily go latent. Thus, these simulations also help elucidate why some inhibitory serpin families are more conformationally labile than others.
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Trento, 38100 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy;
authors.forename: Giorgia
authors.initials: G
authors.lastname: Cazzolli
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201;
authors.forename: Fang
authors.initials: F
authors.lastname: Wang
authors.affiliation: Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy; Interdisciplinary Laboratory for Computational Science, Fondazione Bruno Kessler, 38123 Povo (Trento), Italy; and.
authors.forename: Silvio
authors.initials: S
authors.lastname: a Beccara
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003.
authors.forename: Anne
authors.initials: A
authors.lastname: Gershenson
authors.affiliation: Dipartimento di Fisica, Università degli Studi di Trento, 38100 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy; pwintrod@rx.umaryland.edu faccioli@science.unitn.it.
authors.forename: Pietro
authors.initials: P
authors.lastname: Faccioli
authors.affiliation: Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201; pwintrod@rx.umaryland.edu faccioli@science.unitn.it.
authors.forename: Patrick L
authors.initials: PL
authors.lastname: Wintrode
mesh_terms: D000595:Amino Acid Sequence; D001384:Azetidines / Q000737:chemistry / Q000494:pharmacology; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017395:Plasminogen Activator Inhibitor 1 / Q000737:chemistry; D011485:Protein Binding / Q000187:drug effects; D017433:Protein Structure, Secondary; D011744:Pyrimidinones / Q000737:chemistry / Q000494:pharmacology; D015843:Serpins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: C579128:AZ3976; D001384:Azetidines; D017395:Plasminogen Activator Inhibitor 1; D011744:Pyrimidinones; D015843:Serpins
keywords: conformational change; molecular simulations; plasminogen activator inhibitor-1