1
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Crha R, Kozeleková A, Hofrová A, Iľkovičová L, Gašparik N, Kadeřávek P, Hritz J. Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3ζ protein variants. Int J Biol Macromol 2024; 266:130802. [PMID: 38492709 DOI: 10.1016/j.ijbiomac.2024.130802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Tau protein is an intrinsically disordered protein that plays a key role in Alzheimer's disease (AD). In brains of AD patients, Tau occurs abnormally phosphorylated and aggregated in neurofibrillary tangles (NFTs). Together with Tau, 14-3-3 proteins - abundant cytosolic dimeric proteins - were found colocalized in the NFTs. However, so far, the molecular mechanism of the process leading to pathological changes in Tau structure as well as the direct involvement of 14-3-3 proteins are not well understood. Here, we aimed to reveal the effects of phosphorylation by protein kinase A (PKA) on Tau structural preferences and provide better insight into the interaction between Tau and 14-3-3 proteins. We also addressed the impact of monomerization-inducing phosphorylation of 14-3-3 at S58 on the binding to Tau protein. Using multidimensional nuclear magnetic resonance spectroscopy (NMR), chemical cross-linking analyzed by mass spectrometry (MS) and PAGE, we unveiled differences in their binding affinity, stoichiometry, and interfaces with single-residue resolution. We revealed that the interaction between 14-3-3 and Tau proteins is mediated not only via the 14-3-3 amphipathic binding grooves, but also via less specific interactions with 14-3-3 protein surface and, in the case of monomeric 14-3-3, also partially via the exposed dimeric interface. In addition, the hyperphosphorylation of Tau changes its affinity to 14-3-3 proteins. In conclusion, we propose quite complex interaction mode between the Tau and 14-3-3 proteins.
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Affiliation(s)
- Radek Crha
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Alena Hofrová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lucia Iľkovičová
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Norbert Gašparik
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Kadeřávek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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2
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Basheer N, Buee L, Brion JP, Smolek T, Muhammadi MK, Hritz J, Hromadka T, Dewachter I, Wegmann S, Landrieu I, Novak P, Mudher A, Zilka N. Shaping the future of preclinical development of successful disease-modifying drugs against Alzheimer's disease: a systematic review of tau propagation models. Acta Neuropathol Commun 2024; 12:52. [PMID: 38576010 PMCID: PMC10993623 DOI: 10.1186/s40478-024-01748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/21/2024] [Indexed: 04/06/2024] Open
Abstract
The transcellular propagation of the aberrantly modified protein tau along the functional brain network is a key hallmark of Alzheimer's disease and related tauopathies. Inoculation-based tau propagation models can recapitulate the stereotypical spread of tau and reproduce various types of tau inclusions linked to specific tauopathy, albeit with varying degrees of fidelity. With this systematic review, we underscore the significance of judicious selection and meticulous functional, biochemical, and biophysical characterization of various tau inocula. Furthermore, we highlight the necessity of choosing suitable animal models and inoculation sites, along with the critical need for validation of fibrillary pathology using confirmatory staining, to accurately recapitulate disease-specific inclusions. As a practical guide, we put forth a framework for establishing a benchmark of inoculation-based tau propagation models that holds promise for use in preclinical testing of disease-modifying drugs.
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Affiliation(s)
- Neha Basheer
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia
| | - Luc Buee
- Inserm, CHU Lille, CNRS, LilNCog - Lille Neuroscience & Cognition, University of Lille, 59000, Lille, France.
| | - Jean-Pierre Brion
- Faculty of Medicine, Laboratory of Histology, Alzheimer and Other Tauopathies Research Group (CP 620), ULB Neuroscience Institute (UNI), Université Libre de Bruxelles, 808, Route de Lennik, 1070, Brussels, Belgium
| | - Tomas Smolek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia
| | - Muhammad Khalid Muhammadi
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia
| | - Jozef Hritz
- CEITEC Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 62500, Brno, Czech Republic
| | - Tomas Hromadka
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia
| | - Ilse Dewachter
- Biomedical Research Institute, BIOMED, Hasselt University, 3500, Hasselt, Belgium
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases, Charitéplatz 1, 10117, Berlin, Germany
- Einstein Center for Neurosciences Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Isabelle Landrieu
- CNRS EMR9002 - BSI - Integrative Structural Biology, 59000, Lille, France
- Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille, 59000, Lille, France
| | - Petr Novak
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia
| | - Amritpal Mudher
- School of Biological Sciences, Faculty of Environment and Life Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Norbert Zilka
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska Cesta 9, 845 10, Bratislava, Slovakia.
- AXON Neuroscience R&D Services SE, Dubravska Cesta 9, 845 10, Bratislava, Slovakia.
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Lasorsa A, Bera K, Malki I, Dupré E, Cantrelle FX, Merzougui H, Sinnaeve D, Hanoulle X, Hritz J, Landrieu I. Conformation and Affinity Modulations by Multiple Phosphorylation Occurring in the BIN1 SH3 Domain Binding Site of the Tau Protein Proline-Rich Region. Biochemistry 2023. [PMID: 37167199 DOI: 10.1021/acs.biochem.2c00717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
An increase in phosphorylation of the Tau protein is associated with Alzheimer's disease (AD) progression through unclear molecular mechanisms. In general, phosphorylation modifies the interaction of intrinsically disordered proteins, such as Tau, with other proteins; however, elucidating the structural basis of this regulation mechanism remains challenging. The bridging integrator-1 gene is an AD genetic determinant whose gene product, BIN1, directly interacts with Tau. The proline-rich motif recognized within a Tau(210-240) peptide by the SH3 domain of BIN1 (BIN1 SH3) is defined as 216PTPP219, and this interaction is modulated by phosphorylation. Phosphorylation of T217 within the Tau(210-240) peptide led to a 6-fold reduction in the affinity, while single phosphorylation at either T212, T231, or S235 had no effect on the interaction. Nonetheless, combined phosphorylation of T231 and S235 led to a 3-fold reduction in the affinity, although these phosphorylations are not within the BIN1 SH3-bound region of the Tau peptide. Using nuclear magnetic resonance (NMR) spectroscopy, these phosphorylations were shown to affect the local secondary structure and dynamics of the Tau(210-240) peptide. Models of the (un)phosphorylated peptides were obtained from molecular dynamics (MD) simulation validated by experimental data and showed compaction of the phosphorylated peptide due to increased salt bridge formation. This dynamic folding might indirectly impact the BIN1 SH3 binding by a decreased accessibility of the binding site. Regulation of the binding might thus not only be due to local electrostatic or steric effects from phosphorylation but also to the modification of the conformational properties of Tau.
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Affiliation(s)
- Alessia Lasorsa
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Idir Malki
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Elian Dupré
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - François-Xavier Cantrelle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Hamida Merzougui
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
| | - Davy Sinnaeve
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Xavier Hanoulle
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Isabelle Landrieu
- CNRS EMR9002 Integrative Structural Biology, Lille F-59000, France
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille F-59000, France
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4
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Simončič M, Hritz J, Lukšič M. Biomolecular Complexation on the "Wrong Side": A Case Study of the Influence of Salts and Sugars on the Interactions between Bovine Serum Albumin and Sodium Polystyrene Sulfonate. Biomacromolecules 2022; 23:4412-4426. [PMID: 36134887 PMCID: PMC9554918 DOI: 10.1021/acs.biomac.2c00933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the protein purification, drug delivery, food industry, and biotechnological applications involving protein-polyelectrolyte complexation, proper selection of co-solutes and solution conditions plays a crucial role. The onset of (bio)macromolecular complexation occurs even on the so-called "wrong side" of the protein isoionic point where both the protein and the polyelectrolyte are net like-charged. To gain mechanistic insights into the modulatory role of salts (NaCl, NaBr, and NaI) and sugars (sucrose and sucralose) in protein-polyelectrolyte complexation under such conditions, interaction between bovine serum albumin (BSA) and sodium polystyrene sulfonate (NaPSS) at pH = 8.0 was studied by a combination of isothermal titration calorimetry, fluorescence spectroscopy, circular dichroism, and thermodynamic modeling. The BSA-NaPSS complexation proceeds by two binding processes (first, formation of intrapolymer complexes and then formation of interpolymer complexes), both driven by favorable electrostatic interactions between the negatively charged sulfonic groups (-SO3-) of NaPSS and positively charged patches on the BSA surface. Two such positive patches were identified, each responsible for one of the two binding processes. The presence of salts screened both short-range attractive and long-range repulsive electrostatic interactions between both macromolecules, resulting in a nonmonotonic dependence of the binding affinity on the total ionic strength for both binding processes. In addition, distinct anion-specific effects were observed (NaCl < NaBr < NaI). The effect of sugars was less pronounced: sucrose had no effect on the complexation, but its chlorinated analogue, sucralose, promoted it slightly due to the screening of long-range repulsive electrostatic interactions between BSA and NaPSS. Although short-range non-electrostatic interactions are frequently mentioned in the literature in relation to BSA or NaPSS, we found that the main driving force of complexation on the "wrong side" are electrostatic interactions.
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Affiliation(s)
- Matjaž Simončič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia.,Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czechia
| | - Miha Lukšič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna Pot 113, SI-1000 Ljubljana, Slovenia
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5
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Jaklin M, Hritz J, Hribar-Lee B. A new fibrillization mechanism of β-lactoglobulin in glycine solutions. Int J Biol Macromol 2022; 216:414-425. [PMID: 35803407 PMCID: PMC10039397 DOI: 10.1016/j.ijbiomac.2022.06.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/15/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2. By combining atomic force microscopy (AFM), transmission emission microscopy (TEM), dynamic light scattering (DLS) and circular dichroism (CD) we predict that the basic building blocks of fibrils made in glycine are not peptides, but rather spheroid oligomers of different height that form by stacking of ring-like structures. Spheroid oligomers linearly align to form fibrils by opening up and combining. We suspect that glycine acts as an hydrolysation inhibitor which consequently promotes a different fibrillization path. By combining the known data on fibrillization in water with our experimental conclusions we come up with a new fibrillization scheme for BLG. We show that by changing the fibrillization conditions just by small changes in buffer composition can dramatically change the aggregation pathway and the effect of buffer shouldn't be neglected. Fibrils seen in our study are also gaining more and more attention because of their pore-like structure and a possible cytotoxic mechanism by forming pernicious ion-channels. By preparing them in a simple model system as BLG we opened a new way to study their formation.
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Affiliation(s)
- Matej Jaklin
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Jozef Hritz
- CEITEC Masaryk University Kamenice 5, Brno 625 00, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University Kamenice 5, Brno 625 00, Czech Republic
| | - Barbara Hribar-Lee
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia.
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6
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Kozeleková A, Náplavová A, Brom T, Gašparik N, Šimek J, Houser J, Hritz J. Phosphorylated and Phosphomimicking Variants May Differ—A Case Study of 14-3-3 Protein. Front Chem 2022; 10:835733. [PMID: 35321476 PMCID: PMC8935074 DOI: 10.3389/fchem.2022.835733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Protein phosphorylation is a critical mechanism that biology uses to govern cellular processes. To study the impact of phosphorylation on protein properties, a fully and specifically phosphorylated sample is required although not always achievable. Commonly, this issue is overcome by installing phosphomimicking mutations at the desired site of phosphorylation. 14-3-3 proteins are regulatory protein hubs that interact with hundreds of phosphorylated proteins and modulate their structure and activity. 14-3-3 protein function relies on its dimeric nature, which is controlled by Ser58 phosphorylation. However, incomplete Ser58 phosphorylation has obstructed the detailed study of its effect so far. In the present study, we describe the full and specific phosphorylation of 14-3-3ζ protein at Ser58 and we compare its characteristics with phosphomimicking mutants that have been used in the past (S58E/D). Our results show that in case of the 14-3-3 proteins, phosphomimicking mutations are not a sufficient replacement for phosphorylation. At physiological concentrations of 14-3-3ζ protein, the dimer-monomer equilibrium of phosphorylated protein is much more shifted towards monomers than that of the phosphomimicking mutants. The oligomeric state also influences protein properties such as thermodynamic stability and hydrophobicity. Moreover, phosphorylation changes the localization of 14-3-3ζ in HeLa and U251 human cancer cells. In summary, our study highlights that phosphomimicking mutations may not faithfully represent the effects of phosphorylation on the protein structure and function and that their use should be justified by comparing to the genuinely phosphorylated counterpart.
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Affiliation(s)
- Aneta Kozeleková
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | | | - Tomáš Brom
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Norbert Gašparik
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jan Šimek
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Josef Houser
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czechia
- *Correspondence: Jozef Hritz,
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Trošanová Z, Louša P, Kozeleková A, Brom T, Gašparik N, Tungli J, Weisová V, Župa E, Žoldák G, Hritz J. Quantitation of human 14-3-3ζ dimerization and the effect of phosphorylation on dimer-monomer equilibria. J Mol Biol 2022; 434:167479. [DOI: 10.1016/j.jmb.2022.167479] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
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Kitoka K, Skrabana R, Gasparik N, Hritz J, Jaudzems K. NMR Studies of Tau Protein in Tauopathies. Front Mol Biosci 2021; 8:761227. [PMID: 34859051 PMCID: PMC8632555 DOI: 10.3389/fmolb.2021.761227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
Tauopathies, including Alzheimer's disease (AD), are the most troublesome of all age-related chronic conditions, as there are no well-established disease-modifying therapies for their prevention and treatment. Spatio-temporal distribution of tau protein pathology correlates with cognitive decline and severity of the disease, therefore, tau protein has become an appealing target for therapy. Current knowledge of the pathological effects and significance of specific species in the tau aggregation pathway is incomplete although more and more structural and mechanistic insights are being gained using biophysical techniques. Here, we review the application of NMR to structural studies of various tau forms that appear in its aggregation process, focusing on results obtained from solid-state NMR. Furthermore, we discuss implications from these studies and their prospective contribution to the development of new tauopathy therapies.
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Affiliation(s)
- Kristine Kitoka
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Rostislav Skrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- AXON Neuroscience R&D Services SE, Bratislava, Slovakia
| | - Norbert Gasparik
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristaps Jaudzems
- Laboratory of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
- Faculty of Chemistry, University of Latvia, Riga, Latvia
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Bera K, Reeda VSJ, Babila PR, Dinesh DC, Hritz J, Karthick T. An in silico molecular dynamics simulation study on the inhibitors of SARS-CoV-2 proteases (3CL pro and PL pro) to combat COVID-19. Molecular Simulation 2021. [DOI: 10.1080/08927022.2021.1957884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Krishnendu Bera
- CEITEC MU, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - V. S. Jeba Reeda
- Department of Physics and Research Center, Women's Christian College, Nagercoil, India (Affiliated to Manonmaniam Sundaranar University, Tirunelveli, India)
| | - P. R. Babila
- Department of Physics and Research Centre, Muslim Arts College, Thiruvithancode, India (Affiliated to Manonmaniam Sundaranar University, Tirunelveli, India)
| | | | - Jozef Hritz
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - T. Karthick
- Department of Physics, School of Electrical and Electronics Engineering, SASTRA Deemed University, Thanjavur, India
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Hofrova A, Lousa P, Kubickova M, Hritz J, Otasevic T, Repko M, Knight A, Piskacek M. Universal two-point interaction of mediator KIX with 9aaTAD activation domains. J Cell Biochem 2021; 122:1544-1555. [PMID: 34224597 DOI: 10.1002/jcb.30075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023]
Abstract
The nine-amino-acid activation domain (9aaTAD) is defined by a short amino acid pattern including two hydrophobic regions (positions p3-4 and p6-7). The KIX domain of mediator transcription CBP interacts with the 9aaTAD domains of transcription factors MLL, E2A, NF-kB, and p53. In this study, we analyzed the 9aaTADs-KIX interactions by nuclear magnetic resonance. The positions of three KIX helixes α1-α2-α3 are influenced by sterically-associated hydrophobic I611, L628, and I660 residues that are exposed to solvent. The positions of two rigid KIX helixes α1 and α2 generate conditions for structural folding in the flexible KIX-L12-G2 regions localized between them. The three KIX I611, L628, and I660 residues interact with two 9aaTAD hydrophobic residues in positions p3 and p4 and together build a hydrophobic core of five residues (5R). Numerous residues in 9aaTAD position p3 and p4 could provide this interaction. Following binding of the 9aaTAD to KIX, the hydrophobic I611, L628, and I660 residues are no longer exposed to solvent and their position changes inside the hydrophobic core together with position of KIX α1-α2-α3 helixes. The new positions of the KIX helixes α1 and α2 allow the KIX-L12-G2 enhanced formation. The second hydrophobic region of the 9aaTAD (positions p6 and p7) provides strong binding with the KIX-L12-G2 region. Similarly, multiple residues in 9aaTAD position p6 and p7 could provide this interaction. In conclusion, both 9aaTAD regions p3, p4 and p6, p7 provide co-operative and highly universal binding to mediator KIX. The hydrophobic core 5R formation allows new positions of the rigid KIX α-helixes and enables the enhanced formation of the KIX-L12-G2 region. This contributes to free energy and is the key for the KIX-9aaTAD binding. Therefore, the 9aaTAD-KIX interactions do not operate under the rigid key-and-lock mechanism what explains the 9aaTAD natural variability.
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Affiliation(s)
- Alena Hofrova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Lousa
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Monika Kubickova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Core Facility Biomolecular Interactions and Crystallization (CF BIC), Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Otasevic
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Martin Repko
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Waløen K, Jung-Kc K, Vecchia ED, Pandey S, Gasparik N, Døskeland A, Patil S, Kleppe R, Hritz J, Norton WHJ, Martinez A, Haavik J. Cysteine Modification by Ebselen Reduces the Stability and Cellular Levels of 14-3-3 Proteins. Mol Pharmacol 2021; 100:155-169. [PMID: 34031189 DOI: 10.1124/molpharm.120.000184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/11/2021] [Indexed: 11/22/2022] Open
Abstract
The 14-3-3 proteins constitute a family of adaptor proteins with many binding partners and biological functions, and they are considered promising drug targets in cancer and neuropsychiatry. By screening 1280 small-molecule drugs using differential scanning fluorimetry (DSF), we found 15 compounds that decreased the thermal stability of 14-3-3ζ Among these compounds, ebselen was identified as a covalent, destabilizing ligand of 14-3-3 isoforms ζ, ε, γ, and η Ebselen bonding decreased 14-3-3ζ binding to its partner Ser19-phosphorylated tyrosine hydroxylase. Characterization of site-directed mutants at cysteine residues in 14-3-3ζ (C25, C94, and C189) by DSF and mass spectroscopy revealed covalent modification by ebselen of all cysteines through a selenylsulfide bond. C25 appeared to be the preferential site of ebselen interaction in vitro, whereas modification of C94 was the main determinant for protein destabilization. At therapeutically relevant concentrations, ebselen and ebselen oxide caused decreased 14-3-3 levels in SH-SY5Y cells, accompanied with an increased degradation, most probably by the ubiquitin-dependent proteasome pathway. Moreover, ebselen-treated zebrafish displayed decreased brain 14-3-3 content, a freezing phenotype, and reduced mobility, resembling the effects of lithium, consistent with its proposed action as a safer lithium-mimetic drug. Ebselen has recently emerged as a promising drug candidate in several medical areas, such as cancer, neuropsychiatric disorders, and infectious diseases, including coronavirus disease 2019. Its pleiotropic actions are attributed to antioxidant effects and formation of selenosulfides with critical cysteine residues in proteins. Our work indicates that a destabilization of 14-3-3 may affect the protein interaction networks of this protein family, contributing to the therapeutic potential of ebselen. SIGNIFICANCE STATEMENT: There is currently great interest in the repurposing of established drugs for new indications and therapeutic targets. This study shows that ebselen, which is a promising drug candidate against cancer, bipolar disorder, and the viral infection coronavirus disease 2019, covalently bonds to cysteine residues in 14-3-3 adaptor proteins, triggering destabilization and increased degradation in cells and intact brain tissue when used in therapeutic concentrations, potentially explaining the behavioral, anti-inflammatory, and antineoplastic effects of this drug.
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Affiliation(s)
- Kai Waløen
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Kunwar Jung-Kc
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Elisa D Vecchia
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Sunil Pandey
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Norbert Gasparik
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Anne Døskeland
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Sudarshan Patil
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Rune Kleppe
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Jozef Hritz
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - William H J Norton
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Aurora Martinez
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
| | - Jan Haavik
- Department of Biomedicine (K.W., K.J.K.C., S.Pan., A.D., S.Pat., A.M., J.Ha.), Proteomics Unit (PROBE), (A.D.), University of Bergen, Bergen, Norway; Department of Neuroscience, Psychology and Behaviour, College of Medicine, Biological Sciences and Psychology, University of Leicester, Leicester, UK (E.D.V., W.H.J.N.); CEITEC-MU, Masaryk University, Brno, Czech Republic (N.G., J.Hr.); Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic and Norwegian Centre for Maritime and Diving Medicine, Department of Occupational Medicine (R.K.), Division of Psychiatry (J.Ha.), Haukeland University Hospital, Bergen, Norway
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12
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Subadini S, Bera K, Hritz J, Sahoo H. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach. Colloids Surf B Biointerfaces 2021; 202:111696. [PMID: 33770701 DOI: 10.1016/j.colsurfb.2021.111696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
The importance of macromolecules paves the way towards a detailed molecular level investigation as all most all cellular processes occurring at the interior of cells in the form of proteins, enzymes, and other biological molecules are significantly affected because of their crowding. Thus, exploring the role of crowding environment on the denaturation and renaturation kinetics of protein molecules is of great importance. Here, CRABP I (cellular retinoic acid binding protein I) is employed as a model protein along with different molecular weights of Polyethylene glycol (PEG) as molecular crowders. The experimental evaluations are done by accessing the protein secondary structure analysis using circular dichroism (CD) spectroscopy and unfolding kinetics using intrinsic fluorescence of CRABP I at 37 °C to mimic the in vivo crowding environment. The unfolding kinetics results indicated that both PEG 2000 and PEG 4000 act as stabilizers by retarding the unfolding kinetic rates. Both kinetic and stability outcomes presented the importance of crowding environment on stability and kinetics of CRABP I. The molecular dynamics (MD) studies revealed that thirteen PEG 2000 molecules assembled during the 500 ns simulation, which increases the stability and percentage of β-sheet. The experimental findings are well supported by the molecular dynamics simulation results.
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Affiliation(s)
- Suchismita Subadini
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India
| | - Krishnendu Bera
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Harekrushna Sahoo
- Biophysical and Protein Chemistry Lab, Department of Chemistry, NIT Rourkela, Rourkela, 769008, India; Center of Nanomaterials, NIT Rourkela, Rourkela, 769008, India.
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13
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Zapletal V, Mládek A, Melková K, Louša P, Nomilner E, Jaseňáková Z, Kubáň V, Makovická M, Laníková A, Žídek L, Hritz J. Choice of Force Field for Proteins Containing Structured and Intrinsically Disordered Regions. Biophys J 2020; 118:1621-1633. [PMID: 32367806 DOI: 10.1016/j.bpj.2020.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 01/06/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
Biomolecular force fields optimized for globular proteins fail to properly reproduce properties of intrinsically disordered proteins. In particular, parameters of the water model need to be modified to improve applicability of the force fields to both ordered and disordered proteins. Here, we compared performance of force fields recommended for intrinsically disordered proteins in molecular dynamics simulations of three proteins differing in the content of ordered and disordered regions (two proteins consisting of a well-structured domain and of a disordered region with and without a transient helical motif and one disordered protein containing a region of increased helical propensity). The obtained molecular dynamics trajectories were used to predict measurable parameters, including radii of gyration of the proteins and chemical shifts, residual dipolar couplings, paramagnetic relaxation enhancement, and NMR relaxation data of their individual residues. The predicted quantities were compared with experimental data obtained within this study or published previously. The results showed that the NMR relaxation parameters, rarely used for benchmarking, are particularly sensitive to the choice of force-field parameters, especially those defining the water model. Interestingly, the TIP3P water model, leading to an artificial structural collapse, also resulted in unrealistic relaxation properties. The TIP4P-D water model, combined with three biomolecular force-field parameters for the protein part, significantly improved reliability of the simulations. Additional analysis revealed only one particular force field capable of retaining the transient helical motif observed in NMR experiments. The benchmarking protocol used in our study, being more sensitive to imperfections than the commonly used tests, is well suited to evaluate the performance of newly developed force fields.
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Affiliation(s)
- Vojtěch Zapletal
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnošt Mládek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kateřina Melková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Petr Louša
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Erik Nomilner
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zuzana Jaseňáková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vojtěch Kubáň
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Markéta Makovická
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Alice Laníková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lukáš Žídek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic; Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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Pavlíková Přecechtělová J, Mládek A, Zapletal V, Hritz J. Quantum Chemical Calculations of NMR Chemical Shifts in Phosphorylated Intrinsically Disordered Proteins. J Chem Theory Comput 2019; 15:5642-5658. [DOI: 10.1021/acs.jctc.8b00257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jana Pavlíková Přecechtělová
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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15
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Melková K, Zapletal V, Narasimhan S, Jansen S, Hritz J, Škrabana R, Zweckstetter M, Ringkjøbing Jensen M, Blackledge M, Žídek L. Structure and Functions of Microtubule Associated Proteins Tau and MAP2c: Similarities and Differences. Biomolecules 2019; 9:biom9030105. [PMID: 30884818 PMCID: PMC6468450 DOI: 10.3390/biom9030105] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/09/2019] [Accepted: 03/13/2019] [Indexed: 12/16/2022] Open
Abstract
The stability and dynamics of cytoskeleton in brain nerve cells are regulated by microtubule associated proteins (MAPs), tau and MAP2. Both proteins are intrinsically disordered and involved in multiple molecular interactions important for normal physiology and pathology of chronic neurodegenerative diseases. Nuclear magnetic resonance and cryo-electron microscopy recently revealed propensities of MAPs to form transient local structures and long-range contacts in the free state, and conformations adopted in complexes with microtubules and filamentous actin, as well as in pathological aggregates. In this paper, we compare the longest, 441-residue brain isoform of tau (tau40), and a 467-residue isoform of MAP2, known as MAP2c. For both molecules, we present transient structural motifs revealed by conformational analysis of experimental data obtained for free soluble forms of the proteins. We show that many of the short sequence motifs that exhibit transient structural features are linked to functional properties, manifested by specific interactions. The transient structural motifs can be therefore classified as molecular recognition elements of tau40 and MAP2c. Their interactions are further regulated by post-translational modifications, in particular phosphorylation. The structure-function analysis also explains differences between biological activities of tau40 and MAP2c.
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Affiliation(s)
- Kateřina Melková
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Vojtěch Zapletal
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Subhash Narasimhan
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Séverine Jansen
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Jozef Hritz
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
| | - Rostislav Škrabana
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10 Bratislava, Slovakia.
- Axon Neuroscience R&D Services SE, Dvořákovo nábrežie 10, 811 02 Bratislava, Slovakia.
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany.
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | | | | | - Lukáš Žídek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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16
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Melková K, Zapletal V, Jansen S, Nomilner E, Zachrdla M, Hritz J, Nováček J, Zweckstetter M, Jensen MR, Blackledge M, Žídek L. Functionally specific binding regions of microtubule-associated protein 2c exhibit distinct conformations and dynamics. J Biol Chem 2018; 293:13297-13309. [PMID: 29925592 DOI: 10.1074/jbc.ra118.001769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is a 49-kDa intrinsically disordered protein regulating the dynamics of microtubules in developing neurons. MAP2c differs from its sequence homologue Tau in the pattern and kinetics of phosphorylation by cAMP-dependent protein kinase (PKA). Moreover, the mechanisms through which MAP2c interacts with its binding partners and the conformational changes and dynamics associated with these interactions remain unclear. Here, we used NMR relaxation and paramagnetic relaxation enhancement techniques to determine the dynamics and long-range interactions within MAP2c. The relaxation rates revealed large differences in flexibility of individual regions of MAP2c, with the lowest flexibility observed in the known and proposed binding sites. Quantitative conformational analyses of chemical shifts, small-angle X-ray scattering (SAXS), and paramagnetic relaxation enhancement measurements disclosed that MAP2c regions interacting with important protein partners, including Fyn tyrosine kinase, plectin, and PKA, adopt specific conformations. High populations of polyproline II and α-helices were found in Fyn- and plectin-binding sites of MAP2c, respectively. The region binding the regulatory subunit of PKA consists of two helical motifs bridged by a more extended conformation. Of note, although MAP2c and Tau did not differ substantially in their conformations in regions of high sequence identity, we found that they differ significantly in long-range interactions, dynamics, and local conformation motifs in their N-terminal domains. These results highlight that the N-terminal regions of MAP2c provide important specificity to its regulatory roles and indicate a close relationship between MAP2c's biological functions and conformational behavior.
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Affiliation(s)
- Kateřina Melková
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Zapletal
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Séverine Jansen
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Erik Nomilner
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Milan Zachrdla
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Nováček
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic
| | - Markus Zweckstetter
- the Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,the German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany, and
| | | | | | - Lukáš Žídek
- From Masaryk University, Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic, .,Masaryk University, Faculty of Science, National Centre for Biomolecular Research, Kamenice 5, 625 00 Brno, Czech Republic
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17
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Jandova Z, Trosanova Z, Weisova V, Oostenbrink C, Hritz J. Free energy calculations on the stability of the 14-3-3ζ protein. Biochim Biophys Acta Proteins Proteom 2017; 1866:442-450. [PMID: 29203375 DOI: 10.1016/j.bbapap.2017.11.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/31/2017] [Accepted: 11/25/2017] [Indexed: 01/08/2023]
Abstract
Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
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Affiliation(s)
- Zuzana Jandova
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Zuzana Trosanova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Veronika Weisova
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Jozef Hritz
- CEITEC-MU, Masaryk University, Kamenice 753/5, Bohunice, Brno, Czech Republic.
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Otrusinová O, Demo G, Padrta P, Jaseňáková Z, Pekárová B, Gelová Z, Szmitkowska A, Kadeřávek P, Jansen S, Zachrdla M, Klumpler T, Marek J, Hritz J, Janda L, Iwaï H, Wimmerová M, Hejátko J, Žídek L. Conformational dynamics are a key factor in signaling mediated by the receiver domain of a sensor histidine kinase from Arabidopsis thaliana. J Biol Chem 2017; 292:17525-17540. [PMID: 28860196 DOI: 10.1074/jbc.m117.790212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP-mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1RD) from Arabidopsis thaliana We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1RD (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1RD variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the β3-α3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the β3-α3 loop while keeping the active-site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the β3-α3 loop directly interacts with the ATP-binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the β3-α3 loop of CKI1RD was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic β3-α3 loop of CKI1RD, the corresponding loop of the ETR1 receiver domain (ETR1RD) exhibited little conformational exchange and adopted a different orientation in crystals. Biochemical data indicated that ETR1RD is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.
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Affiliation(s)
- Olga Otrusinová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Gabriel Demo
- From the Central European Institute of Technology and
| | - Petr Padrta
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Jaseňáková
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Blanka Pekárová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Zuzana Gelová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Agnieszka Szmitkowska
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Pavel Kadeřávek
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Séverine Jansen
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Milan Zachrdla
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | | | - Jaromír Marek
- From the Central European Institute of Technology and
| | - Jozef Hritz
- From the Central European Institute of Technology and
| | - Lubomír Janda
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Hideo Iwaï
- the Institute of Biotechnology, University of Helsinki, Viikinkaari 1 (P. O. Box 65), 00014 Helsinki, Finland
| | - Michaela Wimmerová
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Jan Hejátko
- From the Central European Institute of Technology and.,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
| | - Lukáš Žídek
- From the Central European Institute of Technology and .,Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic and
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Nagy G, Oostenbrink C, Hritz J. Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints. PLoS One 2017; 12:e0180633. [PMID: 28727767 PMCID: PMC5519036 DOI: 10.1371/journal.pone.0180633] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 06/19/2017] [Indexed: 11/19/2022] Open
Abstract
The 14-3-3 protein family performs regulatory functions in eukaryotic organisms by binding to a large number of phosphorylated protein partners. Whilst the binding mode of the phosphopeptides within the primary 14-3-3 binding site is well established based on the crystal structures of their complexes, little is known about the binding process itself. We present a computational study of the process by which phosphopeptides bind to the 14-3-3ζ protein. Applying a novel scheme combining Hamiltonian replica exchange molecular dynamics and distancefield restraints allowed us to map and compare the most likely phosphopeptide-binding pathways to the 14-3-3ζ protein. The most important structural changes to the protein and peptides involved in the binding process were identified. In order to bind phosphopeptides to the primary interaction site, the 14-3-3ζ adopted a newly found wide-opened conformation. Based on our findings we additionally propose a secondary interaction site on the inner surface of the 14-3-3ζ dimer, and a direct interference on the binding process by the flexible C-terminal tail. A minimalistic model was designed to allow for the efficient calculation of absolute binding affinities. Binding affinities calculated from the potential of mean force along the binding pathway are in line with the available experimental estimates for two of the studied systems.
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Affiliation(s)
- Gabor Nagy
- CEITEC-MU, Masaryk University, Brno, Czech Republic
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Jozef Hritz
- CEITEC-MU, Masaryk University, Brno, Czech Republic
- * E-mail:
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Jansen S, Melková K, Trošanová Z, Hanáková K, Zachrdla M, Nováček J, Župa E, Zdráhal Z, Hritz J, Žídek L. Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau. J Biol Chem 2017. [PMID: 28623194 DOI: 10.1074/jbc.a116.771097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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21
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Jansen S, Melková K, Trošanová Z, Hanáková K, Zachrdla M, Nováček J, Župa E, Zdráhal Z, Hritz J, Žídek L. Quantitative mapping of microtubule-associated protein 2c (MAP2c) phosphorylation and regulatory protein 14-3-3ζ-binding sites reveals key differences between MAP2c and its homolog Tau. J Biol Chem 2017; 292:6715-6727. [PMID: 28258221 DOI: 10.1074/jbc.m116.771097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Indexed: 11/06/2022] Open
Abstract
Microtubule-associated protein 2c (MAP2c) is involved in neuronal development and is less characterized than its homolog Tau, which has various roles in neurodegeneration. Using NMR methods providing single-residue resolution and quantitative comparison, we investigated molecular interactions important for the regulatory roles of MAP2c in microtubule dynamics. We found that MAP2c and Tau significantly differ in the position and kinetics of sites that are phosphorylated by cAMP-dependent protein kinase (PKA), even in highly homologous regions. We determined the binding sites of unphosphorylated and phosphorylated MAP2c responsible for interactions with the regulatory protein 14-3-3ζ. Differences in phosphorylation and in charge distribution between MAP2c and Tau suggested that both MAP2c and Tau respond to the same signal (phosphorylation by PKA) but have different downstream effects, indicating a signaling branch point for controlling microtubule stability. Although the interactions of phosphorylated Tau with 14-3-3ζ are supposed to be a major factor in microtubule destabilization, the binding of 14-3-3ζ to MAP2c enhanced by PKA-mediated phosphorylation is likely to influence microtubule-MAP2c binding much less, in agreement with the results of our tubulin co-sedimentation measurements. The specific location of the major MAP2c phosphorylation site in a region homologous to the muscarinic receptor-binding site of Tau suggests that MAP2c also may regulate processes other than microtubule dynamics.
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Affiliation(s)
- Séverine Jansen
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Melková
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zuzana Trošanová
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Kateřina Hanáková
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Milan Zachrdla
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jiří Nováček
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Erik Župa
- From the National Centre for Biomolecular Research, Faculty of Science, and.,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jozef Hritz
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Lukáš Žídek
- From the National Centre for Biomolecular Research, Faculty of Science, and .,the Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
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Louša P, Nedozrálová H, Župa E, Nováček J, Hritz J. Phosphorylation of the regulatory domain of human tyrosine hydroxylase 1 monitored using non-uniformly sampled NMR. Biophys Chem 2017; 223:25-29. [PMID: 28282625 DOI: 10.1016/j.bpc.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Human tyrosine hydroxylase 1 (hTH1) activity is regulated by phosphorylation of its regulatory domain (RD-hTH1) and by an interaction with the 14-3-3 protein. The RD-hTH1 is composed of a structured region (66-169) preceded by an intrinsically disordered protein region (IDP, hTH1_65) containing two phosphorylation sites (S19 and S40) which are highly relevant for its increase in activity. The NMR signals of the IDP region in the non-phosphorylated, singly phosphorylated (pS40) and doubly phosphorylated states (pS19_pS40) were assigned by non-uniformly sampled spectra with increased dimensionality (5D). The structural changes induced by phosphorylation were analyzed by means of secondary structure propensities. The phosphorylation kinetics of the S40 and S19 by kinases PKA and PRAK respectively were monitored by non-uniformly sampled time-resolved NMR spectroscopy followed by their quantitative analysis.
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Affiliation(s)
- Petr Louša
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Hana Nedozrálová
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Erik Župa
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jiří Nováček
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jozef Hritz
- CEITEC MU, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.
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Hritz J, Byeon IJL, Krzysiak T, Martinez A, Sklenar V, Gronenborn AM. Dissection of binding between a phosphorylated tyrosine hydroxylase peptide and 14-3-3zeta: A complex story elucidated by NMR. Biophys J 2015; 107:2185-94. [PMID: 25418103 DOI: 10.1016/j.bpj.2014.08.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022] Open
Abstract
Human tyrosine hydroxylase activity is regulated by phosphorylation of its N-terminus and by an interaction with the modulator 14-3-3 proteins. We investigated the binding of singly or doubly phosphorylated and thiophosphorylated peptides, comprising the first 50 amino acids of human tyrosine hydroxylase, isoform 1 (hTH1), that contain the critical interaction domain, to 14-3-3?, by (31)P NMR. Single phosphorylation at S19 generates a high affinity 14-3-3? binding epitope, whereas singly S40-phosphorylated peptide interacts with 14-3-3? one order-of-magnitude weaker than the S19-phosphorylated peptide. Analysis of the binding data revealed that the 14-3-3? dimer and the S19- and S40-doubly phosphorylated peptide interact in multiple ways, with three major complexes formed: 1), a single peptide bound to a 14-3-3? dimer via the S19 phosphate with the S40 phosphate occupying the other binding site; 2), a single peptide bound to a 14-3-3? dimer via the S19 phosphorous with the S40 free in solution; or 3), a 14-3-3? dimer with two peptides bound via the S19 phosphorous to each binding site. Our system and data provide information as to the possible mechanisms by which 14-3-3 can engage binding partners that possess two phosphorylation sites on flexible tails. Whether these will be realized in any particular interacting pair will naturally depend on the details of each system.
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Affiliation(s)
- Jozef Hritz
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; Department of Structural Biology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - In-Ja L Byeon
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania
| | - Aurora Martinez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Vladimir Sklenar
- Department of Structural Biology, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania.
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Mitra M, Singer D, Mano Y, Hritz J, Nam G, Gorelick RJ, Byeon IJL, Gronenborn AM, Iwatani Y, Levin JG. Sequence and structural determinants of human APOBEC3H deaminase and anti-HIV-1 activities. Retrovirology 2015; 12:3. [PMID: 25614027 PMCID: PMC4323217 DOI: 10.1186/s12977-014-0130-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/17/2014] [Indexed: 12/17/2022] Open
Abstract
Background Human APOBEC3H (A3H) belongs to the A3 family of host restriction factors, which are cytidine deaminases that catalyze conversion of deoxycytidine to deoxyuridine in single-stranded DNA. A3 proteins contain either one (A3A, A3C, A3H) or two (A3B, A3D, A3F, A3G) Zn-binding domains. A3H has seven haplotypes (I-VII) that exhibit diverse biological phenotypes and geographical distribution in the human population. Its single Zn-coordinating deaminase domain belongs to a phylogenetic cluster (Z3) that is different from the Z1- and Z2-type domains in other human A3 proteins. A3H HapII, unlike A3A or A3C, has potent activity against HIV-1. Here, we sought to identify the determinants of A3H HapII deaminase and antiviral activities, using site-directed sequence- and structure-guided mutagenesis together with cell-based, biochemical, and HIV-1 infectivity assays. Results We have constructed a homology model of A3H HapII, which is similar to the known structures of other A3 proteins. The model revealed a large cluster of basic residues (not present in A3A or A3C) that are likely to be involved in nucleic acid binding. Indeed, RNase A pretreatment of 293T cell lysates expressing A3H was shown to be required for detection of deaminase activity, indicating that interaction with cellular RNAs inhibits A3H catalytic function. Similar observations have been made with A3G. Analysis of A3H deaminase substrate specificity demonstrated that a 5′ T adjacent to the catalytic C is preferred. Changing the putative nucleic acid binding residues identified by the model resulted in reduction or abrogation of enzymatic activity, while substituting Z3-specific residues in A3H to the corresponding residues in other A3 proteins did not affect enzyme function. As shown for A3G and A3F, some A3H mutants were defective in catalysis, but retained antiviral activity against HIV-1vif (−) virions. Furthermore, endogenous reverse transcription assays demonstrated that the E56A catalytic mutant inhibits HIV-1 DNA synthesis, although not as efficiently as wild type. Conclusions The molecular and biological activities of A3H are more similar to those of the double-domain A3 proteins than to those of A3A or A3C. Importantly, A3H appears to use both deaminase-dependent and -independent mechanisms to target reverse transcription and restrict HIV-1 replication. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0130-8) contains supplementary material, which is available to authorized users.
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Gardner CL, Hritz J, Sun C, Vanlandingham DL, Song TY, Ghedin E, Higgs S, Klimstra WB, Ryman KD. Deliberate attenuation of chikungunya virus by adaptation to heparan sulfate-dependent infectivity: a model for rational arboviral vaccine design. PLoS Negl Trop Dis 2014; 8:e2719. [PMID: 24587470 PMCID: PMC3930508 DOI: 10.1371/journal.pntd.0002719] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/13/2014] [Indexed: 12/16/2022] Open
Abstract
Mosquito-borne chikungunya virus (CHIKV) is a positive-sense, single-stranded RNA virus from the genus Alphavirus, family Togaviridae, which causes fever, rash and severe persistent polyarthralgia in humans. Since there are currently no FDA licensed vaccines or antiviral therapies for CHIKV, the development of vaccine candidates is of critical importance. Historically, live-attenuated vaccines (LAVs) for protection against arthropod-borne viruses have been created by blind cell culture passage leading to attenuation of disease, while maintaining immunogenicity. Attenuation may occur via multiple mechanisms. However, all examined arbovirus LAVs have in common the acquisition of positively charged amino acid substitutions in cell-surface attachment proteins that render virus infection partially dependent upon heparan sulfate (HS), a ubiquitously expressed sulfated polysaccharide, and appear to attenuate by retarding dissemination of virus particles in vivo. We previously reported that, like other wild-type Old World alphaviruses, CHIKV strain, La Réunion, (CHIKV-LR), does not depend upon HS for infectivity. To deliberately identify CHIKV attachment protein mutations that could be combined with other attenuating processes in a LAV candidate, we passaged CHIKV-LR on evolutionarily divergent cell-types. A panel of single amino acid substitutions was identified in the E2 glycoprotein of passaged virus populations that were predicted to increase electrostatic potential. Each of these substitutions was made in the CHIKV-LR cDNA clone and comparisons of the mutant viruses revealed surface exposure of the mutated residue on the spike and sensitivity to competition with the HS analog, heparin, to be primary correlates of attenuation in vivo. Furthermore, we have identified a mutation at E2 position 79 as a promising candidate for inclusion in a CHIKV LAV. With the adaptation of chikungunya virus (CHIKV) to transmission by the Aedes albopictus mosquito, a pandemic has occurred resulting in four to six million human infections, and the virus continues to become endemic in new regions, most recently in the Caribbean. CHIKV can cause debilitating polyarthralgia, lasting for weeks to years, and there are currently no licensed vaccines or antiviral therapies available. While an investigational live-attenuated vaccine (LAV) exists, problems with reactogenicity have precluded its licensure. The purpose of the current study was to: i) devise an in vitro passage procedure that reliably generates a panel of CHIKV envelope glycoprotein mutations for screening as vaccine candidates; ii) determine the position of the mutations in the three-dimensional structure of the alphavirus spike complex and their effect on electrostatic potential; iii) determine the attenuation characteristics of each mutation in a murine model of CHIKV musculoskeletal disease; and iv) to identify in vitro assays examining the dependency of infection upon HS that correlate with attenuation and localization in the glycoprotein spike. This approach provides a paradigm for the rational design of future LAVs for CHIKV and other mosquito-borne viruses, by deliberately selecting and combining attenuating processes.
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Affiliation(s)
- Christina L. Gardner
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jozef Hritz
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Chengqun Sun
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dana L. Vanlandingham
- Department of Diagnostic Medicine & Pathobiology, Biosecurity Research Institute, Kansas State University, Manhattan, Kansas, United States of America
| | - Timothy Y. Song
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Elodie Ghedin
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Stephen Higgs
- Department of Diagnostic Medicine & Pathobiology, Biosecurity Research Institute, Kansas State University, Manhattan, Kansas, United States of America
| | - William B. Klimstra
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kate D. Ryman
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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26
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Lui VWY, Peyser ND, Ng PKS, Hritz J, Zeng Y, Lu Y, Li H, Wang L, Gilbert BR, General IJ, Bahar I, Ju Z, Wang Z, Pendleton KP, Xiao X, Du Y, Vries JK, Hammerman PS, Garraway LA, Mills GB, Johnson DE, Grandis JR. Frequent mutation of receptor protein tyrosine phosphatases provides a mechanism for STAT3 hyperactivation in head and neck cancer. Proc Natl Acad Sci U S A 2014; 111:1114-9. [PMID: 24395800 PMCID: PMC3903220 DOI: 10.1073/pnas.1319551111] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The underpinnings of STAT3 hyperphosphorylation resulting in enhanced signaling and cancer progression are incompletely understood. Loss-of-function mutations of enzymes that dephosphorylate STAT3, such as receptor protein tyrosine phosphatases, which are encoded by the PTPR gene family, represent a plausible mechanism of STAT3 hyperactivation. We analyzed whole exome sequencing (n = 374) and reverse-phase protein array data (n = 212) from head and neck squamous cell carcinomas (HNSCCs). PTPR mutations are most common and are associated with significantly increased phospho-STAT3 expression in HNSCC tumors. Expression of receptor-like protein tyrosine phosphatase T (PTPRT) mutant proteins induces STAT3 phosphorylation and cell survival, consistent with a "driver" phenotype. Computational modeling reveals functional consequences of PTPRT mutations on phospho-tyrosine-substrate interactions. A high mutation rate (30%) of PTPRs was found in HNSCC and 14 other solid tumors, suggesting that PTPR alterations, in particular PTPRT mutations, may define a subset of patients where STAT3 pathway inhibitors hold particular promise as effective therapeutic agents.
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Affiliation(s)
| | - Noah D. Peyser
- Departments of Otolaryngology
- Pharmacology and Chemical Biology
| | | | - Jozef Hritz
- Structural Biology, and
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | | | - Hua Li
- Departments of Otolaryngology
| | | | | | - Ignacio J. General
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Ivet Bahar
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Zhenlin Ju
- Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054
| | - Zhenghe Wang
- Department of Genetics and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106
| | | | | | - Yu Du
- Departments of Otolaryngology
| | - John K. Vries
- Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Peter S. Hammerman
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215; and
| | - Levi A. Garraway
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215; and
| | | | - Daniel E. Johnson
- Pharmacology and Chemical Biology
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh Cancer Institute and University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
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Oostenbrink C, de Ruiter A, Hritz J, Vermeulen N. Malleability and Versatility of Cytochrome P450 Active Sites Studied by Molecular Simulations. Curr Drug Metab 2012; 13:190-6. [DOI: 10.2174/138920012798918453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 03/28/2011] [Accepted: 04/29/2011] [Indexed: 11/22/2022]
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Hritz J, Läppchen T, Oostenbrink C. Fast and Efficient Calculations of Binding Affinities for C8-Substituted GTP Analogues to the FtsZ Protein. Biophys J 2011. [DOI: 10.1016/j.bpj.2010.12.1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Abstract
Active-site water molecules form an important component in biological systems, facilitating promiscuous binding or an increase in specificity and affinity. Taking water molecules into account in computational approaches to drug design or site-of-metabolism predictions is currently far from straightforward. In this study, the effects of including water molecules in molecular docking simulations of the important metabolic enzyme cytochrome P450 2D6 are investigated. The structure and dynamics of water molecules that are present in the active site simultaneously with a selected substrate are described, and based on this description, water molecules are selected to be included in docking experiments into multiple protein conformations. Apart from the parent substrate, 11 similar and 53 dissimilar substrates are included to investigate the transferability of active-site hydration sites between substrates. The role of water molecules appears to be highly dependent on the protein conformation and the substrate.
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Affiliation(s)
- Rita Santos
- Leiden-Amsterdam Center for Drug Research, Section of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Hritz J, Oostenbrink C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. J Phys Chem B 2009; 113:12711-20. [PMID: 19722597 DOI: 10.1021/jp902968m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such compounds. We present an enhanced sampling-one step perturbation method (ES-OS) to tackle this problem in a highly efficient way. A single molecular dynamics simulation of a judiciously chosen reference state (using two sets of soft-core interactions) is sufficient to determine conformational distributions of chemically similar compounds and the free energy differences between them. The ES-OS method is applied to a set of five biologically relevant 8-substituted GTP analogs having high energy barriers between the anti and the syn conformations of the base with respect to the ribose part. The reliability of ES-OS is verified by comparing the results to Hamiltonian replica exchange simulations of GTP and 8-Br-GTP and the experimentally determined 3J(C4,H1') coupling constant for GMP in water. Additional simulations in vacuum and octanol allow us to calculate differences in the solvation free energies and in lipophilicities (log P). Free energy contributions from individual conformational regions are also calculated, and their relationship with the overall free energy is derived leading to a set of multiconformational free energy formulas. These relationships are of general applicability and can be used in free energy calculations for a more diverse set of compounds.
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Affiliation(s)
- Jozef Hritz
- Leiden Amsterdam Center for Drug Research, Division of Molecular Toxicology, VU University Amsterdam, The Netherlands
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31
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Zoldák G, Aumüller T, Lücke C, Hritz J, Oostenbrink C, Fischer G, Schmid FX. A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases. Biochemistry 2009; 48:10423-36. [PMID: 19785464 DOI: 10.1021/bi9014242] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To fully explore the substrate specificities of prolyl isomerases, we synthesized a library of 20 tetrapeptides that are labeled with a 2-aminobenzoyl (Abz) group at the amino terminus and a p-nitroanilide (pNA) group at the carboxy terminus. In this peptide library of the general formula Abz-Ala-Xaa-Pro-Phe-pNA, the position Xaa before the proline is occupied by all 20 proteinogenic amino acids. A conformational analysis of the peptide by molecular dynamics simulations and by NMR spectroscopy showed that the mutual distance between the Abz and pNA moieties in the peptides depends on the isomeric state of the Xaa-Pro bond. In the cis, but not in the trans form, there are significant chemical shift changes of the Abz and pNA moieties, because their aromatic rings are close to each other. This proximity also leads to a strong quenching of Abz fluorescence, which, in combination with a solvent jump, was used to devise a sensitive assay for prolyl isomerases. Unlike the traditional assay, it is not coupled with peptide proteolysis and thus can be employed for protease-sensitive prolyl isomerases as well. The peptide library was used to provide a complete set of P1-site specificities for prototypic human members of the three prolyl isomerase families, FKBP12, cyclophilin 18, and parvulin 14. In a second application, the substrate specificity of SlyD, a protease-sensitive prolyl isomerase from Escherichia coli, was characterized and compared with that of human FKBP12 as well as with homologues from other bacteria.
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Affiliation(s)
- Gabriel Zoldák
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
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32
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Hritz J, de Ruiter A, Oostenbrink C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. J Med Chem 2009; 51:7469-77. [PMID: 18998665 DOI: 10.1021/jm801005m] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s (CYPs) exhibit a large plasticity and flexibility in the active site allowing for the binding of a large variety of substrates. The impact of plasticity and flexibility on ligand binding is investigated by docking 65 known CYP2D6 substrates to an ensemble of 2500 protein structures. The ensemble was generated by molecular dynamics simulations of CYP2D6 in complex with five representative substrates. The effect of induced fit, the conformation of Phe483, and thermal motion on the accuracy of site of metabolism (SOM) predictions is analyzed. For future predictions, the three most essential CYP2D6 structures were selected which are suitable for different kinds of ligands. We have developed a binary decision tree to decide which protein structure to dock the ligand into, such that each ligand needs to be docked only once, leading to successful SOM prediction in 80% of the substrates.
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Affiliation(s)
- Jozef Hritz
- Leiden-Amsterdam Center for Drug Research, Section of Molecular Toxicology, Department of Chemistry and Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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33
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Vasanthanathan P, Hritz J, Taboureau O, Olsen L, Jørgensen FS, Vermeulen NPE, Oostenbrink C. Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands. J Chem Inf Model 2009; 49:43-52. [PMID: 19099399 DOI: 10.1021/ci800371f] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the availability of an increasing number of high resolution 3D structures of human cytochrome P450 enzymes, structure-based modeling tools are more readily used. In this study we explore the possibilities of using docking and scoring experiments on cytochrome P450 1A2. Three different questions have been addressed: 1. Binding orientations and conformations were successfully predicted for various substrates. 2. A virtual screen was performed with satisfying enrichment rates. 3. A classification of individual compounds into active and inactive was performed. It was found that while docking can be used successfully to address the first two questions, it seems to be more difficult to perform the classification. Different scoring functions were included, and the well-characterized water molecule in the active site was included in various ways. Results are compared to experimental data and earlier classification data using machine learning methods. The possibilities and limitations of using structure-based drug design tools for cytochrome P450 1A2 come to light and are discussed.
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Affiliation(s)
- Poongavanam Vasanthanathan
- Leiden-Amsterdam Center for Drug Research, Section of Molecular Toxicology, Department of Chemistry and Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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34
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35
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Abstract
We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsecond time scale within a few minutes rather than the years, which would be required for real REMD. The speed of mimicked REMD makes it a useful tool for "testing" the efficiency of different settings for REMD and then to select those settings, that give the highest efficiency. We present an optimization approach with the example of Hamiltonian REMD using soft-core interactions on two model systems, GTP and 8-Br-GTP. The optimization process using REMD mimicking is very fast. Optimization of Hamiltonian-REMD settings of GTP in explicit water took us less than one week. In our study we focus not only on finding the optimal distances between neighboring replicas, but also on finding the proper placement of the highest level of softness. In addition we suggest different REMD simulation settings at this softness level. We allow several replicas to be simulated at the same Hamiltonian simultaneously and reduce the frequency of switching attempts between them. This approach allows for more efficient conversions from one stable conformation to the other.
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Affiliation(s)
- Jozef Hritz
- Leiden Amsterdam Center for Drug Research (LACDR), Division of Molecular Toxicology, Vrije Universiteit, Amsterdam, The Netherlands
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36
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Miskovsky P, Hritz J, Sanchez-Cortes S, Fabriciova G, Ulicny J, Chinsky L. Interaction of Hypericin with Serum Albumins: Surface-enhanced Raman Spectroscopy, Resonance Raman Spectroscopy and Molecular Modeling Study¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2001)0740172iohwsa2.0.co2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Abstract
NADH oxidase (NOX) from Thermus thermophilus is a member of a structurally homologous flavoprotein family of nitroreductases and flavin reductases. The importance of local conformational dynamics in the active site of NOX has been recently demonstrated. The enzyme activity was increased by 250% in the presence of 1 M urea with no apparent perturbation of the native structure of the protein. The present in silico results correlate with the in vitro data and suggest the possible explanation about the effect of urea on NOX activity at the molecular level. Both, X-ray structure and molecular dynamics (MD) simulations, show open conformation of the active site represented by approximately 0.9 nm distance between the indole ring of Trp47 and the isoalloxazine ring of FMN412. In this conformation, the substrate molecule can bind in the active site without sterical restraints. MD simulations also indicate more stable conformation of the active site called "closed" conformation. In this conformation, Trp47 and the isoalloxazine ring of FMN412 are so close to each other (approximately 0.5 nm) that the substrate molecule is unable to bind between them without perturbing this conformation. The open/close transition of the active site between Trp47 and the flavin ring is accompanied by release of the "tightly" bound water molecule from the active site--cofactor assisted gating mechanism. The presence of urea in aqueous solutions of NOX prohibits closing of the active site and even unlocks the closed active site because of the concomitant binding of a urea molecule in the active site cavity. The binding of urea in the active site is stabilized by formation of one/two persistent hydrogen bonds involving the carbonyl group of the urea molecule. Our report represents the first MD study of an enzyme from the novel flavoprotein family of nitroreductases and flavin reductases. The common occurrence of aromatic residues covering the active sites in homologous enzymes suggests the possibility of a general gating mechanism and the importance of local dynamics within this flavoprotein family.
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Affiliation(s)
- Jozef Hritz
- Department of Biochemistry, Faculty of Science P. J. Safárik University, Kosice, Slovakia
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38
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Kocanova S, Hornakova T, Hritz J, Jancura D, Chorvat D, Mateasik A, Ulicny J, Refregiers M, Maurizot JC, Miskovsky P. Characterization of the interaction of hypericin with protein kinase C in U-87 MG human glioma cells. Photochem Photobiol 2006; 82:720-8. [PMID: 16396605 DOI: 10.1562/2005-09-26-ra-696] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A fluorescence imaging technique was used to monitor intracellular localization of protein kinase C (PKC) in U-87 MG human glioma cells in the presence of hypericin (Hyp) and phorbol 12-myristate-13-acetate (PMA). It is shown that PKC localization, which reflects its activity, is influenced by Hyp and this influence is different from that observed for PMA which acts as PKC activator. Fluorescence binding experiments were used to determine the binding constants of Hyp to several isoforms of PKC. The obtained values of K(d)s (approximately 100 nM) suggest that Hyp binds with high affinity to PKC. Finally, molecular modeling was used to compare structural models of the interaction of C1B domain of PKC (PKC isoforms alpha, delta, gamma) with Hyp and our previously published model of the (C1B domain PKCgamma)/PMA complex. The influence of Hyp on PKC translocation in U-87 MG cells in comparison with PMA, colocalization fluorescence pattern of Hyp and PKC, the higher binding affinity of Hyp to PKC in comparison with known binding constants of phorbol esters, as well as the binding mode of Hyp and PMA to the C1B domain of PKC suggested by molecular modeling, support the idea that Hyp and PMA might competitively bind to the regulatory domain of PKC.
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Affiliation(s)
- Silvia Kocanova
- Department of Biophysics, University of PJ Safarik, Kosice, Slovak Republic
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39
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Hritz J, Ulicny J, Laaksonen A, Jancura D, Miskovsky P. Molecular Interaction Model for the C1B Domain of Protein Kinase C-γ in the Complex with Its Activator Phorbol-12-myristate-13-acetate in Water Solution and Lipid Bilayer. J Med Chem 2004; 47:6547-55. [PMID: 15588090 DOI: 10.1021/jm049786s] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detailed molecular models of the free C1B domain of protein kinase C-gamma (PKC-gamma) and the C1B domain with its activator phorbol-12-myristate-13-acetate (PMA) in water solution and in the presence of dipalmitoylphosphatidylcholine (DPPC) bilayer are presented. Molecular dynamics of the free C1B domain reveals hydrogen bonds, which are critical for the forming of the diacylglycerols/phorbol esters binding site, and indicates the important role of Gln27 for the geometry of this site. According to the model, PMA interacts with the C1B domain by hydrophobic interactions with Pro11 and Tyr22 and by three persistent hydrogen bonds between the C3 carbonyl group of PMA and Gly23 and between the C20 hydroxyl group of PMA and the Leu21 and Thr12 residues of the C1B domain. The C9 hydroxyl group of PMA does not interact with the C1B domain, but it is involved in the interaction with the DPPC bilayer. Two preferential orientations of the C1B-PMA complex toward the DPPC bilayer resulted from our molecular modeling study.
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Affiliation(s)
- Jozef Hritz
- Department of Biophysics, P. J. Safárik University, Jesenná 5, 041 54 Kosice, Slovak Republic
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40
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Becker T, Hritz J, Vogel M, Caliebe A, Bukau B, Soll J, Schleiff E. Toc12, a novel subunit of the intermembrane space preprotein translocon of chloroplasts. Mol Biol Cell 2004; 15:5130-44. [PMID: 15317846 PMCID: PMC524789 DOI: 10.1091/mbc.e04-05-0405] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Accepted: 08/09/2004] [Indexed: 11/11/2022] Open
Abstract
Translocation of proteins across membranes is essential for the biogenesis of each cell and is achieved by proteinaceous complexes. We analyzed the translocation complex of the intermembrane space from chloroplasts and identified a 12-kDa protein associated with the Toc machinery. Toc12 is an outer envelope protein exposing a soluble domain into the intermembrane space. Toc12 contains a J-domain and stimulates the ATPase activity of DnaK. The conformational stability and the ability to stimulate Hsp70 are dependent on a disulfide bridge within the loop region of the J-domain, suggesting a redox-regulated activation of the chaperone. Toc12 is associated with Toc64 and Tic22. Its J-domain recruits the Hsp70 of outer envelope membrane to the intermembrane space translocon and facilitates its interaction to the preprotein.
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Affiliation(s)
- Thomas Becker
- Botanisches Institut, LMU München, 80638 Munich, Germany
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41
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Hritz J, Kascakova S, Ulicny J, Miskovsky P. Influence of structure of human, rat, and bovine serum albumins on binding properties of photoactive drug hypericin. Biopolymers 2002; 67:251-4. [PMID: 12012440 DOI: 10.1002/bip.10110] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence binding measurements and molecular modeling were employed to study the interaction of hypericin (Hyp) with human (HSA), rat (RSA), and bovine (BSA) serum albumins. Fluorescence emission data show the solubility of Hyp increasing in the order BSA, HSA, and RSA. Molecular modeling was used to construct the detailed structural models of the complexes and to explain the differences in the binding properties of Hyp. It was shown that the structures of Hyp/HSA and Hyp/RSA complexes are more similar and in some aspects different from those found for the Hyp/BSA complex. The role of the amino acid sequence in the IIA subdomains of HSA, RSA, and BSA is discussed to explain the observed differences.
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Affiliation(s)
- Jozef Hritz
- Department of Biophysics, P. J. Safarik University, Jesenna 5, 041 54 Kosice, Slovak Republic
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42
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Miskovsky P, Hritz J, Sanchez-Cortes S, Fabriciova G, Ulicny J, Chinsky L. Interaction of hypericin with serum albumins: surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling study. Photochem Photobiol 2001. [PMID: 11547551 DOI: 10.1562/0031-8655(2001)0740172io] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling were employed to study the interaction of hypericin (Hyp) with human (HSA), rat (RSA) and bovine (BSA) serum albumins. The identification of the binding site of Hyp in serum albumins as well as the structural model for Hyp/HSA complex are presented. The interactions mainly reflect: (1) a change of the strength of H bonding at the N1-H site of Trp; (2) a change of the Trp side-chain conformation; (3) a change of the hydrophobicity of the Trp environment; and (4) a formation of an H-bond between the carbonyl group of Hyp and a proton donor in HSA and RSA which leads to a protonated-like carbonyl in Hyp. Our results indicate that Hyp is rigidly bound in IIA subdomain of HSA close to Trp214 (distance 5.12 A between the centers of masses). In the model presented the carbonyl group of Hyp is hydrogen bonded to Asn458. Two other candidates for hydrogen bonds have been identified between the bay-region hydroxyl group of Hyp and the carbonyl group of the Trp214 peptidic link and between the peri-region hydroxyl group of Hyp and the Asn458 carbonyl group. It is shown that the structures of the Hyp/HSA and Hyp/RSA complexes are similar to, and in some aspects different from, those found for the Hyp/BSA complex. The role of aminoacid sequence in the IIA subdomains of HSA, RSA and BSA is discussed to explain the observed differences.
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Affiliation(s)
- P Miskovsky
- Department of Biophysics, P. J. Safarik University, Jesenna, Kosice, Slovak Republic.
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43
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Miskovsky P, Hritz J, Sanchez-Cortes S, Fabriciova G, Ulicny J, Chinsky L. Interaction of hypericin with serum albumins: surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling study. Photochem Photobiol 2001; 74:172-83. [PMID: 11547551 DOI: 10.1562/0031-8655(2001)074<0172:iohwsa>2.0.co;2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Surface-enhanced Raman spectroscopy, resonance Raman spectroscopy and molecular modeling were employed to study the interaction of hypericin (Hyp) with human (HSA), rat (RSA) and bovine (BSA) serum albumins. The identification of the binding site of Hyp in serum albumins as well as the structural model for Hyp/HSA complex are presented. The interactions mainly reflect: (1) a change of the strength of H bonding at the N1-H site of Trp; (2) a change of the Trp side-chain conformation; (3) a change of the hydrophobicity of the Trp environment; and (4) a formation of an H-bond between the carbonyl group of Hyp and a proton donor in HSA and RSA which leads to a protonated-like carbonyl in Hyp. Our results indicate that Hyp is rigidly bound in IIA subdomain of HSA close to Trp214 (distance 5.12 A between the centers of masses). In the model presented the carbonyl group of Hyp is hydrogen bonded to Asn458. Two other candidates for hydrogen bonds have been identified between the bay-region hydroxyl group of Hyp and the carbonyl group of the Trp214 peptidic link and between the peri-region hydroxyl group of Hyp and the Asn458 carbonyl group. It is shown that the structures of the Hyp/HSA and Hyp/RSA complexes are similar to, and in some aspects different from, those found for the Hyp/BSA complex. The role of aminoacid sequence in the IIA subdomains of HSA, RSA and BSA is discussed to explain the observed differences.
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Affiliation(s)
- P Miskovsky
- Department of Biophysics, P. J. Safarik University, Jesenna, Kosice, Slovak Republic.
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