1
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Strand 1A variant in neuroserpin shows increased aggregation and no loss of inhibition: implication in ameliorating polymerization to retain activity. Biosci Rep 2022; 42:232125. [PMID: 36408789 PMCID: PMC9760604 DOI: 10.1042/bsr20221825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/31/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Neuroserpin (NS) is predominantly expressed in the brain and is the primary inhibitor of tissue plasminogen activator (tPA). NS variants are associated with the neurogenerative disease termed familial encephalopathy with neuroserpin inclusion bodies (FENIB). The disease is characterized by variable age of onset and severity. The reactive center loop (RCL) insertion-based inhibitory mechanism of NS requires a coordinated conformational change leading to a shift in the strands of the β-sheet A and movement of helix F. Strand 1A is connected to the helix F at its C terminal end and with the strand 2A at its N terminal, both these domain move for accommodating the inserting loop; therefore, a variant that influences their movement may alter the inhibition rates. A molecular dynamic simulation analysis of a H138C NS variant from strand 1A showed a large decrease in conformational fluctuations as compared with wild-type NS. H138 was mutated, expressed, purified and a native-PAGE and transmission electron microscopy (TEM) analysis showed that this variant forms large molecular weight aggregates on a slight increase in temperature. However, a circular dichroism analysis showed its secondary structure to be largely conserved. Surprisingly, its tPA inhibition activity and complex formation remain unhindered even after the site-specific labeling of H138C with Alexa fluor C5 maleimide. Further, a helix F-strand 1A (W154C-H138C) double variant still shows appreciable inhibitory activity. Increasingly, it appears that aggregation and not loss of inhibition is the more likely cause of shutter region-based variants phenotypes, indicating that hindering polymer formation using small molecules may retain inhibitory activity in pathological variants of NS.
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2
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Grønnemose AL, Østerlund EC, Otzen DE, Jørgensen TJD. EGCG has Dual and Opposing Effects on the N-terminal Region of Self-associating α-synuclein Oligomers. J Mol Biol 2022; 434:167855. [PMID: 36240861 DOI: 10.1016/j.jmb.2022.167855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/11/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Oligomers of the protein α-synuclein (α-syn) are thought to be a major toxic species in Parkinson's disease, particularly through their ability to permeabilize cell membranes. The green tea polyphenol epigallocatechin gallate (EGCG) has been found to reduce this ability. We have analyzed α-syn oligomer dynamics and interconversion by H/D exchange monitored by mass spectrometry (HDX-MS). Our results show that the two oligomers OI and OII co-exist in equilibrium; OI is a multimer of OII and its dissociation can be followed by HDX-MS by virtue of the correlated exchange of the N-terminal region. Urea destabilizes the α-syn oligomers, dissociating OI to OII and monomers. Oligomers exposed to EGCG undergo Met oxidation. Intriguingly, EGCG induces an oxidation-dependent effect on the structure of the N-terminal region. For the non-oxidized N-terminal region, EGCG increases the stability of the folded structure as measured by a higher level of protection against H/D exchange. In contrast, protection is clearly abrogated in the Met oxidized N-terminal region. Having a non-oxidized and disordered N-terminal region is known to be essential for efficient membrane binding. Therefore, our results suggest that the combined effect of a structural stabilization of the non-oxidized N-terminal region and the presence of a disordered oxidized N-terminal region renders the oligomers less cytotoxic by decreasing the ability of the N-terminal region to bind to cell membranes and facilitate their permeabilization.
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Affiliation(s)
- Anne Louise Grønnemose
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Eva Christina Østerlund
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology (BMB), University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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3
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Sillen M, Miyata T, Vaughan DE, Strelkov SV, Declerck PJ. Structural Insight into the Two-Step Mechanism of PAI-1 Inhibition by Small Molecule TM5484. Int J Mol Sci 2021; 22:ijms22031482. [PMID: 33540702 PMCID: PMC7867230 DOI: 10.3390/ijms22031482] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 01/19/2023] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1), a key regulator of the fibrinolytic system, is the main physiological inhibitor of plasminogen activators. By interacting with matrix components, including vitronectin (Vn), PAI-1 plays a regulatory role in tissue remodeling, cell migration, and intracellular signaling. Emerging evidence points to a role for PAI-1 in various pathological conditions, including cardiovascular diseases, cancer, and fibrosis. Targeting PAI-1 is therefore a promising therapeutic strategy in PAI-1-related pathologies. A class of small molecule inhibitors including TM5441 and TM5484, designed to bind the cleft in the central β-sheet A of PAI-1, showed to be potent PAI-1 inhibitors in vivo. However, their binding site has not yet been confirmed. Here, we report two X-ray crystallographic structures of PAI-1 in complex with TM5484. The structures revealed a binding site at the flexible joint region, which is distinct from the presumed binding site. Based on the structural analysis and biochemical data we propose a mechanism for the observed dose-dependent two-step mechanism of PAI-1 inhibition. By binding to the flexible joint region in PAI-1, TM5484 might restrict the structural flexibility of this region, thereby inducing a substrate form of PAI-1 followed by a conversion to an inert form.
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Affiliation(s)
- Machteld Sillen
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium;
| | - Toshio Miyata
- Department of Molecular Medicine and Therapy, United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8577, Japan;
| | - Douglas E. Vaughan
- Department of Medicine, Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium;
| | - Paul J. Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium;
- Correspondence:
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4
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Sillen M, Declerck PJ. Targeting PAI-1 in Cardiovascular Disease: Structural Insights Into PAI-1 Functionality and Inhibition. Front Cardiovasc Med 2020; 7:622473. [PMID: 33415130 PMCID: PMC7782431 DOI: 10.3389/fcvm.2020.622473] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/03/2020] [Indexed: 01/31/2023] Open
Abstract
Plasminogen activator inhibitor-1 (PAI-1), a member of the serine protease inhibitor (serpin) superfamily with antiprotease activity, is the main physiological inhibitor of tissue-type (tPA) and urokinase-type (uPA) plasminogen activators (PAs). Apart from being crucially involved in fibrinolysis and wound healing, PAI-1 plays a pivotal role in various acute and chronic pathophysiological processes, including cardiovascular disease, tissue fibrosis, cancer, and age-related diseases. In the prospect of treating the broad range of PAI-1-related pathologies, many efforts have been devoted to developing PAI-1 inhibitors. The use of these inhibitors, including low molecular weight molecules, peptides, antibodies, and antibody fragments, in various animal disease models has provided ample evidence of their beneficial effect in vivo and moved forward some of these inhibitors in clinical trials. However, none of these inhibitors is currently approved for therapeutic use in humans, mainly due to selectivity and toxicity issues. Furthermore, the conformational plasticity of PAI-1, which is unique among serpins, poses a real challenge in the identification and development of PAI-1 inhibitors. This review will provide an overview of the structural insights into PAI-1 functionality and modulation thereof and will highlight diverse approaches to inhibit PAI-1 activity.
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Affiliation(s)
| | - Paul J. Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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5
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Bastos VA, Gomes-Neto F, Rocha SLG, Teixeira-Ferreira A, Perales J, Neves-Ferreira AGC, Valente RH. The interaction between the natural metalloendopeptidase inhibitor BJ46a and its target toxin jararhagin analyzed by structural mass spectrometry and molecular modeling. J Proteomics 2020; 221:103761. [PMID: 32247172 DOI: 10.1016/j.jprot.2020.103761] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/08/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022]
Abstract
Snakebite envenoming affects millions of people worldwide, being officially considered a neglected tropical disease by the World Health Organization. The antivenom is effective in neutralizing the systemic effects of envenomation, but local effects are poorly neutralized, often leading to permanent disability. The natural resistance of the South American pit viper Bothrops jararaca to its venom is partly attributed to BJ46a, a natural snake venom metalloendopeptidase inhibitor. Upon complex formation, BJ46a binds non-covalently to the metalloendopeptidase, rendering it unable to exert its proteolytic activity. However, the structural features that govern this interaction are largely unknown. In this work, we applied structural mass spectrometry techniques (cross-linking-MS and hydrogen-deuterium exchange MS) and in silico analyses (molecular modeling, docking, and dynamics simulations) to understand the interaction between BJ46a and jararhagin, a metalloendopeptidase from B. jararaca venom. We explored the distance restraints generated from XL-MS experiments to guide the modeling of BJ46a and jararhagin, as well as the protein-protein docking simulations. HDX-MS data pinpointed regions of protection/deprotection at the interface of the BJ46a-jararhagin complex which, in addition to the molecular dynamics simulation data, reinforced our proposed interaction model. Ultimately, the structural understanding of snake venom metalloendopeptidases inhibition by BJ46a could lead to the rational design of drugs to improve anti-snake venom therapeutics, alleviating the high morbidity rates currently observed.
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Affiliation(s)
- Viviane A Bastos
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Francisco Gomes-Neto
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Surza Lucia G Rocha
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | | | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | | | - Richard H Valente
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.
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6
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Sillen M, Weeks SD, Zhou X, Komissarov AA, Florova G, Idell S, Strelkov SV, Declerck PJ. Molecular mechanism of two nanobodies that inhibit PAI-1 activity reveals a modulation at distinct stages of the PAI-1/plasminogen activator interaction. J Thromb Haemost 2020; 18:681-692. [PMID: 31858714 PMCID: PMC8855783 DOI: 10.1111/jth.14716] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND Plasminogen activator inhibitor-1 (PAI-1), a key inhibitor of plasminogen activators (PAs) tissue-type PA (tPA) and urokinase-type PA (uPA) plays a crucial role in many (patho)physiological processes (e.g., cardiovascular disease, tissue fibrosis) as well as in many age-related pathologies. Therefore, much effort has been put into the development of small molecule or antibody-based PAI-1 inhibitors. OBJECTIVE To elucidate the molecular mechanism of nanobody-induced PAI-1 inhibition. METHODS AND RESULTS Here we present the first crystal structures of PAI-1 in complex with two neutralizing nanobodies (Nbs). These structures, together with biochemical and biophysical characterization, reveal that Nb VHH-2g-42 (Nb42) interferes with the initial PAI-1/PA complex formation, whereas VHH-2w-64 (Nb64) redirects the PAI-1/PA interaction to PAI-1 deactivation and regeneration of active PA. Furthermore, whereas vitronectin does not have an impact on the inhibitory effect of Nb42, it strongly potentiates the inhibitory effect of Nb64, which may contribute to a strong inhibitory potential of Nb64 in vivo. CONCLUSIONS These findings illuminate the molecular mechanisms of PAI-1 inhibition. Nb42 and Nb64 can be used as starting points to engineer further improved antibody-based PAI-1 inhibitors or guide the rational design of small molecule inhibitors to treat a wide range of PAI-1-related pathophysiological conditions.
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Affiliation(s)
- Machteld Sillen
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Stephen D. Weeks
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Xiaohua Zhou
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Andrey A. Komissarov
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, TX, USA
| | - Galina Florova
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, TX, USA
| | - Steven Idell
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, TX, USA
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Paul J. Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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7
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Kielkopf CS, Ghosh M, Anand GS, Brown SHJ. HDX-MS reveals orthosteric and allosteric changes in apolipoprotein-D structural dynamics upon binding of progesterone. Protein Sci 2018; 28:365-374. [PMID: 30353968 DOI: 10.1002/pro.3534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/17/2022]
Abstract
Apolipoprotein-D is a glycosylated tetrameric lipocalin that binds and transports small hydrophobic molecules such as progesterone and arachidonic acid. Like other lipocalins, apolipoprotein-D adopts an eight-stranded β-barrel fold stabilized by two intramolecular disulphide bonds, with an adjacent α-helix. Crystallography studies of recombinant apolipoprotein-D demonstrated no major conformational changes upon progesterone binding. Amide hydrogen-deuterium exchange mass spectrometry (HDX-MS) reports structural changes of proteins in solution by monitoring exchange of amide hydrogens in the protein backbone with deuterium. HDX-MS detects changes in conformation and structural dynamics in response to protein function such as ligand binding that may go undetected in X-ray crystallography, making HDX-MS an invaluable orthogonal technique. Here, we report an HDX-MS protocol for apolipoprotein-D that solved challenges of high protein rigidity and low pepsin cleavage using rigorous quenching conditions and longer deuteration times, yielding 85% sequence coverage and 50% deuterium exchange. The relative fractional deuterium exchange of ligand-free apolipoprotein-D revealed apolipoprotein-D to be a highly structured protein. Progesterone binding was detected by significant reduction in deuterium exchange in eight peptides. Stabilization of apolipoprotein-D dynamics can be interpreted as a combined orthosteric effect in the ligand binding pocket and allosteric effect at the N-terminus and C-terminus. Together, our experiments provide insight into apolipoprotein-D structural dynamics and map the effects of progesterone binding that are relayed to distal parts of the protein. The observed stabilization of apolipoprotein-D dynamics upon progesterone binding demonstrates a common behaviour in the lipocalin family and may have implications for interactions of apolipoprotein-D with receptors or lipoprotein particles. Statement: We reveal for the first time how apolipoprotein-D, which is protective in Alzheimer's disease, becomes more ordered when bound to a molecule of steroid hormone. These results significantly extend the understanding of apolipoprotein-D structure from X-ray crystallography studies by incorporating information on how protein motion changes over time. To achieve these results an improved protocol was developed, suitable for proteins similar to apolipoprotein-D, to elucidate how proteins change flexibility when binding to small molecules.
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Affiliation(s)
- Claudia S Kielkopf
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.,Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia.,School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Madhubrata Ghosh
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Simon H J Brown
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.,Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia.,School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, Australia
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8
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Zhang F, Luo J, Zhu X. Ketamine ameliorates depressive-like behaviors by tPA-mediated conversion of proBDNF to mBDNF in the hippocampus of stressed rats. Psychiatry Res 2018; 269:646-651. [PMID: 30216916 DOI: 10.1016/j.psychres.2018.08.075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/26/2018] [Accepted: 08/17/2018] [Indexed: 12/29/2022]
Abstract
Some studies have indicated that ketamine has a rapid antidepressant effects, but the underlying molecular mechanism is still unclear. Researchers have found that mature brain-derived neurotrophic factor (mBDNF) and its precursor proBDNF are related to depression; they elicit opposite effects on cellular functions. It is clear that tissue plasminogen activator (tPA) is a key regulatory element in the conversion of proBDNF to mBDNF. The chronic unpredicted mild stress (CUMS) procedure is a classical and reliable method to establish the model of depression. This study found that sucrose preference and locomotor activity were both reduced in CUMS-treated rats while were increased in those who were injected with ketamine. The hippocampal proBDNF/mBDNF ratio was downregulated after ketamine treatment in those rats, together with an increased level of tPA in the hippocampus. However, tPA activity was unaltered after ketamine intraperitoneal injection. Intrahippocampal injection of active plasminogen activator inhibitor-1 (inhibitor of tPA) before ketamine treatment reversed the antidepressant effects and upregulated the proBDNF/mBDNF ratio. The results of this study suggest that the antidepressant action induced by ketamine may be related to tPA-mediated conversion of proBDNF to mBDNF in the hippocampus.
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Affiliation(s)
- Fan Zhang
- Department of Anesthesiology, The People's Hospital of Jianyang City, Chengdu 610000, China
| | - Jie Luo
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xianlin Zhu
- Department of Anesthesiology, The Central Hospital of Enshi Autonomous Prefecture, Enshi 445000, China.
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9
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Fast CS, Vahidi S, Konermann L. Changes in Enzyme Structural Dynamics Studied by Hydrogen Exchange-Mass Spectrometry: Ligand Binding Effects or Catalytically Relevant Motions? Anal Chem 2017; 89:13326-13333. [DOI: 10.1021/acs.analchem.7b03506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Courtney S. Fast
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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10
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Bucci JC, McClintock CS, Chu Y, Ware GL, McConnell KD, Emerson JP, Peterson CB. Resolving distinct molecular origins for copper effects on PAI-1. J Biol Inorg Chem 2017; 22:1123-1135. [PMID: 28913669 PMCID: PMC5613068 DOI: 10.1007/s00775-017-1489-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022]
Abstract
Components of the fibrinolytic system are subjected to stringent control to maintain proper hemostasis. Central to this regulation is the serpin plasminogen activator inhibitor-1 (PAI-1), which is responsible for specific and rapid inhibition of fibrinolytic proteases. Active PAI-1 is inherently unstable and readily converts to a latent, inactive form. The binding of vitronectin and other ligands influences stability of active PAI-1. Our laboratory recently observed reciprocal effects on the stability of active PAI-1 in the presence of transition metals, such as copper, depending on the whether vitronectin was also present (Thompson et al. Protein Sci 20:353–365, 2011). To better understand the molecular basis for these copper effects on PAI-1, we have developed a gel-based copper sensitivity assay that can be used to assess the copper concentrations that accelerate the conversion of active PAI-1 to a latent form. The copper sensitivity of wild-type PAI-1 was compared with variants lacking N-terminal histidine residues hypothesized to be involved in copper binding. In these PAI-1 variants, we observed significant differences in copper sensitivity, and these data were corroborated by latency conversion kinetics and thermodynamics of copper binding by isothermal titration calorimetry. These studies identified a copper-binding site involving histidines at positions 2 and 3 that confers a remarkable stabilization of PAI-1 beyond what is observed with vitronectin alone. A second site, independent from the two histidines, binds metal and increases the rate of the latency conversion.
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Affiliation(s)
- Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.,Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Carlee S McClintock
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
| | - Yuzhuo Chu
- Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Gregory L Ware
- Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Kayla D McConnell
- Department of Chemistry, Mississippi State University, Box 1115, Starkville, MS, 39762, USA
| | - Joseph P Emerson
- Department of Chemistry, Mississippi State University, Box 1115, Starkville, MS, 39762, USA
| | - Cynthia B Peterson
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA. .,Department of Biological Sciences, A221 Life Sciences Annex, Louisiana State University, Baton Rouge, LA, 70803, USA.
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11
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Petersen M, Madsen JB, Jørgensen TJD, Trelle MB. Conformational preludes to the latency transition in PAI-1 as determined by atomistic computer simulations and hydrogen/deuterium-exchange mass spectrometry. Sci Rep 2017; 7:6636. [PMID: 28747729 PMCID: PMC5529462 DOI: 10.1038/s41598-017-06290-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/12/2017] [Indexed: 11/25/2022] Open
Abstract
Both function and dysfunction of serine protease inhibitors (serpins) involve massive conformational change in their tertiary structure but the dynamics facilitating these events remain poorly understood. We have studied the dynamic preludes to conformational change in the serpin plasminogen activator inhibitor 1 (PAI-1). We report the first multi-microsecond atomistic molecular dynamics simulations of PAI-1 and compare the data with experimental hydrogen/deuterium-exchange data (HDXMS). The simulations reveal notable conformational flexibility of helices D, E and F and major fluctuations are observed in the W86-loop which occasionally leads to progressive detachment of β-strand 2 A from β-strand 3 A. An interesting correlation between Cα-RMSD values from simulations and experimental HDXMS data is observed. Helices D, E and F are known to be important for the overall stability of active PAI-1 as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment.
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Affiliation(s)
- Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Jeppe B Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark
| | - Morten B Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense, M, Denmark.
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12
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Trelle MB, Pedersen S, Østerlund EC, Madsen JB, Kristensen SR, Jørgensen TJD. An Asymmetric Runaway Domain Swap Antithrombin Dimer as a Key Intermediate for Polymerization Revealed by Hydrogen/Deuterium-Exchange Mass Spectrometry. Anal Chem 2016; 89:616-624. [PMID: 27783482 DOI: 10.1021/acs.analchem.6b02518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Antithrombin deficiency is associated with increased risk of venous thrombosis. In certain families, this condition is caused by pathogenic polymerization of mutated antithrombin in the blood. To facilitate future development of pharmaceuticals against antithrombin polymerization, an improved understanding of the polymerogenic intermediates is crucial. However, X-ray crystallography of these intermediates is severely hampered by the difficulty in obtaining well-diffracting crystals of transient and heterogeneous noncovalent protein assemblies. Furthermore, their large size prohibits structural analysis by NMR spectroscopy. Here, we show how hydrogen/deuterium-exchange mass spectrometry (HDX-MS) provides detailed insight into the structural dynamics of each subunit in a polymerization-competent antithrombin dimer. Upon deuteration, this dimer surprisingly yields bimodal isotope distributions for the majority of peptides, demonstrating an asymmetric configuration of the two subunits. The data reveal that one subunit is very dynamic, potentially intrinsically disordered, whereas the other is considerably less dynamic. The local subunit-specific deuterium uptake of this polymerization-competent dimer strongly supports a β4A-β5A β-hairpin runaway domain swap mechanism for antithrombin polymerization. HDX-MS thus holds exceptional promise as an enabling analytical technique in the efforts toward future pharmacological intervention with protein polymerization and associated diseases.
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Affiliation(s)
- Morten Beck Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Shona Pedersen
- Department of Clinical Biochemistry, Aalborg University Hospital , Hobrovej 18, 9000 Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University , Sdr. Skovvej 15, 9000 Aalborg, Denmark
| | - Eva Christina Østerlund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Jeppe Buur Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
| | - Søren Risom Kristensen
- Department of Clinical Biochemistry, Aalborg University Hospital , Hobrovej 18, 9000 Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University , Sdr. Skovvej 15, 9000 Aalborg, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense M, Denmark
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13
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Bucci JC, Trelle MB, McClintock CS, Qureshi T, Jørgensen TJD, Peterson CB. Copper(II) Ions Increase Plasminogen Activator Inhibitor Type 1 Dynamics in Key Structural Regions That Govern Stability. Biochemistry 2016; 55:4386-98. [DOI: 10.1021/acs.biochem.6b00256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joel C. Bucci
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
- Department
of Biological Sciences, Louisiana State University, A221 Life
Sciences Annex, Baton Rouge, Louisiana 70803, United States
| | - Morten Beck Trelle
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 55 Campusvej, 5000 Odense M, Denmark
| | - Carlee S. McClintock
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Tihami Qureshi
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 55 Campusvej, 5000 Odense M, Denmark
| | - Cynthia B. Peterson
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Walters Life Sciences Building, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
- Department
of Biological Sciences, Louisiana State University, A221 Life
Sciences Annex, Baton Rouge, Louisiana 70803, United States
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14
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Faure G, Bakouh N, Lourdel S, Odolczyk N, Premchandar A, Servel N, Hatton A, Ostrowski MK, Xu H, Saul FA, Moquereau C, Bitam S, Pranke I, Planelles G, Teulon J, Herrmann H, Roldan A, Zielenkiewicz P, Dadlez M, Lukacs GL, Sermet-Gaudelus I, Ollero M, Corringer PJ, Edelman A. Rattlesnake Phospholipase A2 Increases CFTR-Chloride Channel Current and Corrects ∆F508CFTR Dysfunction: Impact in Cystic Fibrosis. J Mol Biol 2016; 428:2898-915. [PMID: 27241308 DOI: 10.1016/j.jmb.2016.05.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 01/26/2023]
Abstract
Deletion of Phe508 in the nucleotide binding domain (∆F508-NBD1) of the cystic fibrosis transmembrane regulator (CFTR; a cyclic AMP-regulated chloride channel) is the most frequent mutation associated with cystic fibrosis. This mutation affects the maturation and gating of CFTR protein. The search for new high-affinity ligands of CFTR acting as dual modulators (correctors/activators) presents a major challenge in the pharmacology of cystic fibrosis. Snake venoms are a rich source of natural multifunctional proteins, potential binders of ion channels. In this study, we identified the CB subunit of crotoxin from Crotalus durissus terrificus as a new ligand and allosteric modulator of CFTR. We showed that CB interacts with NBD1 of both wild type and ∆F508CFTR and increases their chloride channel currents. The potentiating effect of CB on CFTR activity was demonstrated using electrophysiological techniques in Xenopus laevis oocytes, in CFTR-HeLa cells, and ex vivo in mouse colon tissue. The correcting effect of CB was shown by functional rescue of CFTR activity after 24-h ΔF508CFTR treatments with CB. Moreover, the presence of fully glycosylated CFTR was observed. Molecular docking allowed us to propose a model of the complex involving of the ABCβ and F1-like ATP-binding subdomains of ΔF508-NBD1. Hydrogen-deuterium exchange analysis confirmed stabilization in these regions, also showing allosteric stabilization in two other distal regions. Surface plasmon resonance competition studies showed that CB disrupts the ∆F508CFTR-cytokeratin 8 complex, allowing for the escape of ∆F508CFTR from degradation. Therefore CB, as a dual modulator of ΔF508CFTR, constitutes a template for the development of new anti-CF agents.
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Affiliation(s)
- Grazyna Faure
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France.
| | - Naziha Bakouh
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Stéphane Lourdel
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Norbert Odolczyk
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Aiswarya Premchandar
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Nathalie Servel
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Aurélie Hatton
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Maciej K Ostrowski
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Haijin Xu
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Frederick A Saul
- Institut Pasteur, Plate-forme de Cristallographie, CNRS-UMR 3528, Paris, France
| | - Christelle Moquereau
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Sara Bitam
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Iwona Pranke
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Gabrielle Planelles
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Jacques Teulon
- UPMC Université Paris 06, UMRS 872, Laboratoire de génomique, physiologie et physiopathologie rénales, Paris, France
| | - Harald Herrmann
- Department of Molecular Genetics, German Cancer Research Center, D-69120 Heidelberg, Germany; Institute of Neuropathology, University Hospital Erlangen, D-91054 Erlangen, Germany
| | - Ariel Roldan
- Department of Physiology, McGill University, Montreal, Canada
| | - Piotr Zielenkiewicz
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | - Michal Dadlez
- Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Warsaw, Poland
| | | | - Isabelle Sermet-Gaudelus
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Mario Ollero
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Unité Récepteurs-Canaux, CNRS,UMR 3571, 25, rue du Dr. Roux, F-75015, Paris, France
| | - Aleksander Edelman
- INSERM U1151, team Canalopathies épithéliales: la mucoviscidose et autres maladies, Université Paris Descartes, Paris, France
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15
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Qureshi T, Goswami S, McClintock CS, Ramsey MT, Peterson CB. Distinct encounter complexes of PAI-1 with plasminogen activators and vitronectin revealed by changes in the conformation and dynamics of the reactive center loop. Protein Sci 2015; 25:499-510. [PMID: 26548921 DOI: 10.1002/pro.2841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/05/2015] [Indexed: 11/07/2022]
Abstract
UNLABELLED Plasminogen activator inhibitor-1 (PAI-1) is a biologically important serine protease inhibitor (serpin) that, when overexpressed, is associated with a high risk for cardiovascular disease and cancer metastasis. Several of its ligands, including vitronectin, tissue-type and urokinase-type plasminogen activator (tPA, uPA), affect the fate of PAI-1. Here, we measured changes in the solvent accessibility and dynamics of an important unresolved functional region, the reactive center loop (RCL), upon binding of these ligands. Binding of the catalytically inactive S195A variant of tPA to the RCL causes an increase in fluorescence, indicating greater solvent protection, at its C-terminus, while mobility along the loop remains relatively unchanged. In contrast, a fluorescence increase and large decrease in mobility at the N-terminal RCL is observed upon binding of S195A-uPA to PAI-1. At a site distant from the RCL, binding of vitronectin results in a modest decrease in fluorescence at its proximal end without restricting overall loop dynamics. These results provide the new evidence for ligand effects on RCL conformation and dynamics and differences in the Michaelis complex with plasminogen activators that can be used for the development of more specific inhibitors to PAI-1. This study is also the first to use electron paramagnetic resonance (EPR) spectroscopy to investigate PAI-1 dynamics. SIGNIFICANCE Balanced blood homeostasis and controlled cell migration requires coordination between serine proteases, serpins, and cofactors. These ligands form noncovalent complexes, which influence the outcome of protease inhibition and associated physiological processes. This study reveals differences in binding via changes in solvent accessibility and dynamics within these complexes that can be exploited to develop more specific drugs in the treatment of diseases associated with unbalanced serpin activity.
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Affiliation(s)
- Tihami Qureshi
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Sumit Goswami
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Carlee S McClintock
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Matthew T Ramsey
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
| | - Cynthia B Peterson
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, 37996
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16
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Parker TJ, Broadbent JA, McGovern JA, Broszczak DA, Parker CN, Upton Z. Provisional Matrix Deposition in Hemostasis and Venous Insufficiency: Tissue Preconditioning for Nonhealing Venous Ulcers. Adv Wound Care (New Rochelle) 2015; 4:174-191. [PMID: 25785239 PMCID: PMC4352700 DOI: 10.1089/wound.2013.0462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Indexed: 01/07/2023] Open
Abstract
Significance: Chronic wounds represent a major burden on global healthcare systems and reduce the quality of life of those affected. Significant advances have been made in our understanding of the biochemistry of wound healing progression. However, knowledge regarding the specific molecular processes influencing chronic wound formation and persistence remains limited. Recent Advances: Generally, healing of acute wounds begins with hemostasis and the deposition of a plasma-derived provisional matrix into the wound. The deposition of plasma matrix proteins is known to occur around the microvasculature of the lower limb as a result of venous insufficiency. This appears to alter limb cutaneous tissue physiology and consequently drives the tissue into a 'preconditioned' state that negatively influences the response to wounding. Critical Issues: Processes, such as oxygen and nutrient suppression, edema, inflammatory cell trapping/extravasation, diffuse inflammation, and tissue necrosis are thought to contribute to the advent of a chronic wound. Healing of the wound then becomes difficult in the context of an internally injured limb. Thus, interventions and therapies for promoting healing of the limb is a growing area of interest. For venous ulcers, treatment using compression bandaging encourages venous return and improves healing processes within the limb, critically however, once treatment concludes ulcers often reoccur. Future Directions: Improved understanding of the composition and role of pericapillary matrix deposits in facilitating internal limb injury and subsequent development of chronic wounds will be critical for informing and enhancing current best practice therapies and preventative action in the wound care field.
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Affiliation(s)
- Tony J. Parker
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - James A. Broadbent
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jacqui A. McGovern
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Daniel A. Broszczak
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Christina N. Parker
- Institute of Health and Biomedical Innovation, School of Nursing, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Zee Upton
- Tissue Repair and Regeneration Program, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
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17
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Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
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18
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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.
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19
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Trelle MB, Madsen JB, Andreasen PA, Jørgensen TJD. Local Transient Unfolding of Native State PAI-1 Associated with Serpin Metastability. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Trelle MB, Madsen JB, Andreasen PA, Jørgensen TJD. Local Transient Unfolding of Native State PAI-1 Associated with Serpin Metastability. Angew Chem Int Ed Engl 2014; 53:9751-4. [DOI: 10.1002/anie.201402796] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/26/2014] [Indexed: 11/08/2022]
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21
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Mierzejewska K, Siwek W, Czapinska H, Kaus-Drobek M, Radlinska M, Skowronek K, Bujnicki JM, Dadlez M, Bochtler M. Structural basis of the methylation specificity of R.DpnI. Nucleic Acids Res 2014; 42:8745-54. [PMID: 24966351 PMCID: PMC4117772 DOI: 10.1093/nar/gku546] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
R.DpnI consists of N-terminal catalytic and C-terminal winged helix domains that are separately specific for the Gm6ATC sequences in Dam-methylated DNA. Here we present a crystal structure of R.DpnI with oligoduplexes bound to the catalytic and winged helix domains and identify the catalytic domain residues that are involved in interactions with the substrate methyl groups. We show that these methyl groups in the Gm6ATC target sequence are positioned very close to each other. We further show that the presence of the two methyl groups requires a deviation from B-DNA conformation to avoid steric conflict. The methylation compatible DNA conformation is complementary with binding sites of both R.DpnI domains. This indirect readout of methylation adds to the specificity mediated by direct favorable interactions with the methyl groups and solvation/desolvation effects. We also present hydrogen/deuterium exchange data that support ‘crosstalk’ between the two domains in the identification of methylated DNA, which should further enhance R.DpnI methylation specificity.
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Affiliation(s)
- Karolina Mierzejewska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Wojciech Siwek
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | | | - Monika Radlinska
- Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Krzysztof Skowronek
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland Institute of Biochemistry and Biophysics PAS, Pawinskiego 5a, 02-106 Warsaw, Poland
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22
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Sowole MA, Konermann L. Effects of Protein–Ligand Interactions on Hydrogen/Deuterium Exchange Kinetics: Canonical and Noncanonical Scenarios. Anal Chem 2014; 86:6715-22. [DOI: 10.1021/ac501849n] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Modupeola A. Sowole
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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23
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Trelle MB, Dupont DM, Madsen JB, Andreasen PA, Jørgensen TJD. Dissecting the effect of RNA aptamer binding on the dynamics of plasminogen activator inhibitor 1 using hydrogen/deuterium exchange mass spectrometry. ACS Chem Biol 2014; 9:174-82. [PMID: 24138169 DOI: 10.1021/cb400619v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
RNA aptamers, selected from large synthetic libraries, are attracting increasing interest as protein ligands, with potential uses as prototype pharmaceuticals, conformational probes, and reagents for specific quantification of protein levels in biological samples. Very little is known, however, about their effects on protein conformation and dynamics. We have employed hydrogen/deuterium exchange (HDX) mass spectrometry to study the effect of RNA aptamers on the structural flexibility of the serpin plasminogen activator inhibitor-1 (PAI-1). The aptamers have characteristic effects on the biochemical properties of PAI-1. In particular, they are potent inhibitors of the structural transition of PAI-1 from the active state to the inactive, so-called latent state. This transition is one of the largest conformational changes of a folded protein domain without covalent modification. Binding of the aptamers to PAI-1 is associated with substantial and widespread protection against deuterium uptake in PAI-1. The aptamers induce protection against exchange with the solvent both in the protein-aptamer interface as well as in other specific areas. Interestingly, the aptamers induce substantial protection against exchange in α-helices B, C and I. This observation substantiates the relevance of structural instability in this region for transition to the latent state and argues for involvement of flexibility in regions not commonly associated with regulation of latency transition in serpins.
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Affiliation(s)
- Morten B. Trelle
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Daniel M. Dupont
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Jeppe B. Madsen
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Peter A. Andreasen
- Department
of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10DK-8000 Århus C, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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24
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Konermann L, Rodriguez AD, Sowole MA. Type 1 and Type 2 scenarios in hydrogen exchange mass spectrometry studies on protein–ligand complexes. Analyst 2014; 139:6078-87. [DOI: 10.1039/c4an01307g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ligand binding to a protein can elicit a wide range of responses when studied by HDX mass spectrometry.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London, Canada
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25
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Mysling S, Salbo R, Ploug M, Jørgensen TJD. Electrochemical Reduction of Disulfide-Containing Proteins for Hydrogen/Deuterium Exchange Monitored by Mass Spectrometry. Anal Chem 2013; 86:340-5. [DOI: 10.1021/ac403269a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Simon Mysling
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
| | - Rune Salbo
- Protein
Technology, Novo Nordisk A/S, Novo Nordisk Park, Måløv DK-2760, Denmark
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet and Biotech Research
and Innovation Centre (BRIC), Copenhagen
Biocenter, Ole Maaløes Vej 5, Copenhagen N, DK-2200 Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark
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26
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Sowole MA, Alexopoulos JA, Cheng YQ, Ortega J, Konermann L. Activation of ClpP protease by ADEP antibiotics: insights from hydrogen exchange mass spectrometry. J Mol Biol 2013; 425:4508-19. [PMID: 23948506 DOI: 10.1016/j.jmb.2013.08.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 07/27/2013] [Accepted: 08/06/2013] [Indexed: 10/26/2022]
Abstract
The bacterial protease ClpP consists of 14 subunits that assemble into two stacked heptameric rings. The central degradation chamber can be accessed via axial pores. In free ClpP, these pores are obstructed by the N-terminal regions of the seven subunits at either end of the barrel. Acyldepsipeptides (ADEPs) are antibacterial compounds that bind in hydrophobic clefts surrounding the pore region, causing the pores to open up. The ensuing uncontrolled degradation of intracellular proteins is responsible for the antibiotic activity of ADEPs. Recently published X-ray structures yielded conflicting models regarding the conformation adopted by the N-terminal regions in the open state. Here, we use hydrogen/deuterium exchange (HDX) mass spectrometry to obtain complementary insights into the ClpP behavior with and without ADEP1. Ligand binding causes rigidification of the equatorial belt, accompanied by destabilization in the vicinity of the binding clefts. The N-terminal regions undergo rapid deuteration with only minor changes after ADEP1 binding, revealing a lack of stable H-bonding. Our data point to a mechanism where the pore opening mechanism is mediated primarily by changes in the packing of N-terminal nonpolar side chains. We propose that a "hydrophobic plug" causes pore blockage in ligand-free ClpP. ADEP1 binding provides new hydrophobic anchor points that nonpolar N-terminal residues can interact with. In this way, ADEP1 triggers the transition to an open conformation, where nonpolar moieties are clustered around the rim of the pore. This proposed mechanism helps reconcile the conflicting models that had been put forward earlier.
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Affiliation(s)
- Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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27
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Jensen PF, Jørgensen TJD, Koefoed K, Nygaard F, Sen JW. Affinity capture of biotinylated proteins at acidic conditions to facilitate hydrogen/deuterium exchange mass spectrometry analysis of multimeric protein complexes. Anal Chem 2013; 85:7052-9. [PMID: 23534402 DOI: 10.1021/ac303442y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of conformational and dynamic changes associated with protein interactions can be done by hydrogen/deuterium exchange mass spectrometry (HDX-MS) by comparing the deuterium uptake in the bound and unbound state of the proteins. Investigation of local hydrogen/deuterium exchange in heteromultimeric protein complexes poses a challenge for the method due to the increased complexity of the mixture of peptides originating from all interaction partners in the complex. Previously, interference of peptides from one interaction partner has been removed by immobilizing the intact protein on beads prior to the HDX-MS experiment. However, when studying protein complexes of more than two proteins, immobilization can possibly introduce steric limitations to the interactions. Here, we present a method based on the high affinity biotin-streptavidin interaction that allows selective capture of biotinylated proteins even under the extreme conditions for hydrogen/deuterium exchange quenching i.e. pH 2.5 and 0 °C. This biotin-streptavidin capture strategy allows hydrogen/deuterium exchange to occur in proteins in solution and enables characterization of specific proteins in heteromultimeric protein complexes without interference of peptides originating from other interaction partners in the complex. The biotin-streptavidin strategy has been successfully implemented in a model system with two recombinant monoclonal antibodies that target nonoverlapping epitopes on the human epidermal growth factor receptor (EGFR). We present a workflow for biotinylation and characterization of recombinant antibodies and demonstrate affinity capture of biotinylated antibodies under hydrogen/deuterium exchange quench conditions by the biotin-streptavidin strategy.
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28
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Florova G, Karandashova S, Declerck PJ, Idell S, Komissarov AA. Remarkable stabilization of plasminogen activator inhibitor 1 in a "molecular sandwich" complex. Biochemistry 2013; 52:4697-709. [PMID: 23734661 DOI: 10.1021/bi400470s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasminogen activator inhibitor 1 (PAI-1) levels are elevated in a number of life-threatening conditions and often correlate with unfavorable outcomes. Spontaneous inactivation due to active to latent transition limits PAI-1 activity in vivo. While endogenous vitronectin (Vn) stabilizes PAI-1 by 1.5-2.0-fold, further stabilization occurs in a "molecular sandwich" complex (MSC) in which a ligand that restricts the exposed reactive center loop is bound to PAI-1/Vn. The effects of S195A two-chain urokinase (tcuPA) and Vn on inactivation of wild-type (wt) glycosylated (Gl-PAI-1), nonglycosylated (rPAI-1), and nonglycosylated Q123K PAI-1 (lacks Vn binding) forms were studied. S195A tcuPA decreased the rate constant (kL) for spontaneous inactivation at 37 °C for rPAI-1, Q123K, and Gl-PAI-1 by 6.7-, 3.4-, and 7.8-fold, respectively, and both S195A tcuPA and Vn by 66.7-, 5.5-, and 103.3-fold, respectively. Analysis of the temperature dependences of kL revealed a synergistic increase in the Gibbs free activation energy for spontaneous inactivation of wt Gl-PAI-1 and rPAI-1 in MSC from 99.8 and 96.1 to 111.3 and 107.0 kJ/mol, respectively, due to an increase in the activation enthalpy and a decrease in the activation entropy. Anti-PAI-1 monoclonal antibodies (mAbs) competing with proteinase also stabilize PAI-1/Vn. The rate of inhibition of target proteinases by MSCs, with a stoichiometry close to unity, was limited by the dissociation (k = 10(-4) to 10(-3) s(-1)) of S195A tcuPA or mAb. The stabilization of PAI-1 in MSCs in vivo may potentiate uncontrolled thrombosis or extravascular fibrin deposition, suggesting a new paradigm for using PAI-1 inhibitors and novel potential targets for therapy.
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Affiliation(s)
- Galina Florova
- Texas Lung Injury Institute, University of Texas Health Science Center at Tyler , 11937 U.S. Highway 271, Tyler, Texas 75708-3154, United States
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Kaltashov IA, Bobst CE, Abzalimov RR. Mass spectrometry-based methods to study protein architecture and dynamics. Protein Sci 2013; 22:530-44. [PMID: 23436701 DOI: 10.1002/pro.2238] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 11/09/2022]
Abstract
Mass spectrometry is now an indispensable tool in the armamentarium of molecular biophysics, where it is used for tasks ranging from protein sequencing and mapping of post-translational modifications to studies of higher order structure, conformational dynamics, and interactions of proteins with small molecule ligands and other biopolymers. This mini-review highlights several popular mass spectrometry-based tools that are now commonly used for structural studies of proteins beyond their covalent structure with a particular emphasis on hydrogen exchange and direct electrospray ionization mass spectrometry.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.
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