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Lu J, Dreyer I, Dickinson MS, Panzer S, Jaślan D, Navarro-Retamal C, Geiger D, Terpitz U, Becker D, Stroud RM, Marten I, Hedrich R. Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels. eLife 2023; 12:e86384. [PMID: 37991833 PMCID: PMC10665017 DOI: 10.7554/elife.86384] [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: 01/23/2023] [Accepted: 10/12/2023] [Indexed: 11/23/2023] Open
Abstract
To fire action-potential-like electrical signals, the vacuole membrane requires the two-pore channel TPC1, formerly called SV channel. The TPC1/SV channel functions as a depolarization-stimulated, non-selective cation channel that is inhibited by luminal Ca2+. In our search for species-dependent functional TPC1 channel variants with different luminal Ca2+ sensitivity, we found in total three acidic residues present in Ca2+ sensor sites 2 and 3 of the Ca2+-sensitive AtTPC1 channel from Arabidopsis thaliana that were neutral in its Vicia faba ortholog and also in those of many other Fabaceae. When expressed in the Arabidopsis AtTPC1-loss-of-function background, wild-type VfTPC1 was hypersensitive to vacuole depolarization and only weakly sensitive to blocking luminal Ca2+. When AtTPC1 was mutated for these VfTPC1-homologous polymorphic residues, two neutral substitutions in Ca2+ sensor site 3 alone were already sufficient for the Arabidopsis At-VfTPC1 channel mutant to gain VfTPC1-like voltage and luminal Ca2+ sensitivity that together rendered vacuoles hyperexcitable. Thus, natural TPC1 channel variants exist in plant families which may fine-tune vacuole excitability and adapt it to environmental settings of the particular ecological niche.
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Affiliation(s)
- Jinping Lu
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
- School of Life Sciences, Zhengzhou UniversityZhengzhouChina
| | - Ingo Dreyer
- Universidad de Talca, Faculty of Engineering, Center of Bioinformatics, Simulation and ModelingTalcaChile
| | - Miles Sasha Dickinson
- University of California San Francisco, Department of Biochemistry and BiophysicsSan FranciscoUnited States
| | - Sabine Panzer
- Julius-Maximilians-Universität (JMU), Biocenter, Theodor-Boveri-Institute, Department of Biotechnology and BiophysicsWürzburgGermany
| | - Dawid Jaślan
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
- Ludwig Maximilians-Universität, Faculty of Medicine, Walther Straub Institute of Pharmacology and ToxicologyMunichGermany
| | - Carlos Navarro-Retamal
- Universidad de Talca, Faculty of Engineering, Center of Bioinformatics, Simulation and ModelingTalcaChile
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkUnited States
| | - Dietmar Geiger
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Ulrich Terpitz
- Julius-Maximilians-Universität (JMU), Biocenter, Theodor-Boveri-Institute, Department of Biotechnology and BiophysicsWürzburgGermany
| | - Dirk Becker
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Robert M Stroud
- University of California San Francisco, Department of Biochemistry and BiophysicsSan FranciscoUnited States
| | - Irene Marten
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
| | - Rainer Hedrich
- Julius-Maximilians-Universität (JMU), Biocenter, Department of Molecular Plant Physiology and BiophysicsWürzburgGermany
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Simon AA, Navarro-Retamal C, Feijó JA. Merging Signaling with Structure: Functions and Mechanisms of Plant Glutamate Receptor Ion Channels. Annu Rev Plant Biol 2023; 74:415-452. [PMID: 36854472 DOI: 10.1146/annurev-arplant-070522-033255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant glutamate receptor-like (GLR) genes encode ion channels with demonstrated roles in electrical and calcium (Ca2+) signaling. The expansion of the GLR family along the lineage of land plants, culminating in the appearance of a multiclade system among flowering plants, has been a topic of interest since their discovery nearly 25 years ago. GLRs are involved in many physiological processes, from wound signaling to transcriptional regulation to sexual reproduction. Emerging evidence supports the notion that their fundamental functions are conserved among different groups of plants as well. In this review, we update the physiological and genetic evidence for GLRs, establishing their role in signaling and cell-cell communication. Special emphasis is given to the recent discussion of GLRs' atomic structures. Along with functional assays, a structural view of GLRs' molecular organization presents a window for novel hypotheses regarding the molecular mechanisms underpinning signaling associated with the ionic fluxes that GLRs regulate. Newly uncovered transcriptional regulations associated with GLRs-which propose the involvement of genes from all clades ofArabidopsis thaliana in ways not previously observed-are discussed in the context of the broader impacts of GLR activity. We posit that the functions of GLRs in plant biology are probably much broader than anticipated, but describing their widespread involvement will only be possible with (a) a comprehensive understanding of the channel's properties at the molecular and structural levels, including protein-protein interactions, and (b) the design of new genetic approaches to explore stress and pathogen responses where precise transcriptional control may result in more precise testable hypotheses to overcome their apparent functional redundancies.
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Affiliation(s)
- Alexander A Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA;
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA;
| | - Carlos Navarro-Retamal
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA;
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA;
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3
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Dreyer I, Vergara-Valladares F, Mérida-Quesada F, Rubio-Meléndez ME, Hernández-Rojas N, Riedelsberger J, Astola-Mariscal SZ, Heitmüller C, Yanez-Chávez M, Arrey-Salas O, San Martín-Davison A, Navarro-Retamal C, Michard E. The Surprising Dynamics of Electrochemical Coupling at Membrane Sandwiches in Plants. Plants (Basel) 2023; 12:204. [PMID: 36616332 PMCID: PMC9824766 DOI: 10.3390/plants12010204] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Transport processes across membranes play central roles in any biological system. They are essential for homeostasis, cell nutrition, and signaling. Fluxes across membranes are governed by fundamental thermodynamic rules and are influenced by electrical potentials and concentration gradients. Transmembrane transport processes have been largely studied on single membranes. However, several important cellular or subcellular structures consist of two closely spaced membranes that form a membrane sandwich. Such a dual membrane structure results in remarkable properties for the transport processes that are not present in isolated membranes. At the core of membrane sandwich properties, a small intermembrane volume is responsible for efficient coupling between the transport systems at the two otherwise independent membranes. Here, we present the physicochemical principles of transport coupling at two adjacent membranes and illustrate this concept with three examples. In the supplementary material, we provide animated PowerPoint presentations that visualize the relationships. They could be used for teaching purposes, as has already been completed successfully at the University of Talca.
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Affiliation(s)
- Ingo Dreyer
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Fernando Vergara-Valladares
- Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Franko Mérida-Quesada
- Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - María Eugenia Rubio-Meléndez
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Naomí Hernández-Rojas
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Janin Riedelsberger
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Sadith Zobeida Astola-Mariscal
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Charlotte Heitmüller
- Electrical Signaling in Plants (ESP) Laboratory, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mónica Yanez-Chávez
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca 3460000, Chile
| | - Oscar Arrey-Salas
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca 3460000, Chile
| | - Alex San Martín-Davison
- Instituto de Investigación Interdisciplinaria, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile
| | - Carlos Navarro-Retamal
- Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742–5815, USA
| | - Erwan Michard
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca 3460000, Chile
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Mérida-Quesada F, Vergara-Valladares F, Rubio-Meléndez ME, Hernández-Rojas N, González-González A, Michard E, Navarro-Retamal C, Dreyer I. TPC1-Type Channels in Physcomitrium patens: Interaction between EF-Hands and Ca 2. Plants (Basel) 2022; 11:plants11243527. [PMID: 36559639 PMCID: PMC9783492 DOI: 10.3390/plants11243527] [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] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 05/26/2023]
Abstract
Two-pore channels (TPCs) are members of the superfamily of ligand-gated and voltage-sensitive ion channels in the membranes of intracellular organelles of eukaryotic cells. The evolution of ordinary plant TPC1 essentially followed a very conservative pattern, with no changes in the characteristic structural footprints of these channels, such as the cytosolic and luminal regions involved in Ca2+ sensing. In contrast, the genomes of mosses and liverworts encode also TPC1-like channels with larger variations at these sites (TPC1b channels). In the genome of the model plant Physcomitrium patens we identified nine non-redundant sequences belonging to the TPC1 channel family, two ordinary TPC1-type, and seven TPC1b-type channels. The latter show variations in critical amino acids in their EF-hands essential for Ca2+ sensing. To investigate the impact of these differences between TPC1 and TPC1b channels, we generated structural models of the EF-hands of PpTPC1 and PpTPC1b channels. These models were used in molecular dynamics simulations to determine the frequency with which calcium ions were present in a coordination site and also to estimate the average distance of the ions from the center of this site. Our analyses indicate that the EF-hand domains of PpTPC1b-type channels have a lower capacity to coordinate calcium ions compared with those of common TPC1-like channels.
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Affiliation(s)
- Franko Mérida-Quesada
- Programa de Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Fernando Vergara-Valladares
- Programa de Doctorado en Ciencias mención Modelado de Sistemas Químicos y Biológicos, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - María Eugenia Rubio-Meléndez
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Naomí Hernández-Rojas
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
| | - Angélica González-González
- Programa de Doctorado en Ciencias mención Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
| | - Erwan Michard
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
| | - Carlos Navarro-Retamal
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Avenida Lircay, Talca CL-3460000, Chile
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742-5815, USA
| | - Ingo Dreyer
- Electrical Signaling in Plants (ESP) Laboratory–Centro de Bioinformática y Simulación Molecular (CBSM), Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Talca CL-3460000, Chile
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5
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Ríos D, Valderrama JA, Quiroga G, Michea J, Salas F, Duarte EÁ, Venegas-Casanova EA, Jara-Aguilar R, Navarro-Retamal C, Calderon PB, Benites J. Antifungal Activity and In Silico Studies on 2-Acylated Benzo- and Naphthohydroquinones. Molecules 2022; 27:3035. [PMID: 35566386 PMCID: PMC9103303 DOI: 10.3390/molecules27093035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 03/26/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
The high rates of morbidity and mortality due to fungal infections are associated with a limited antifungal arsenal and the high toxicity of drugs. Therefore, the identification of novel drug targets is challenging due to the several resemblances between fungal and human cells. Here, we report the in vitro antifungal evaluation of two acylphenols series, namely 2-acyl-1,4-benzo- and 2-acyl-1,4-naphthohydroquinones. The antifungal properties were assessed on diverse Candida and filamentous fungi strains through the halo of inhibition (HOI) and minimal inhibitory concentration (MIC). The antifungal activities of 2-acyl-1,4-benzohydroquinone derivatives were higher than those of the 2-acyl-1,4-naphthohydroquinone analogues. The evaluation indicates that 2-octanoylbenzohydroquinone 4 is the most active member of the 2-acylbenzohydroquinone series, with MIC values ranging from 2 to 16 μg/mL. In some fungal strains (i.e., Candida krusei and Rhizopus oryzae), such MIC values of compound 4 (2 and 4 μg/mL) were comparable to that obtained by amphotericin B (1 μg/mL). The compound 4 was evaluated for its antioxidant activity by means of FRAP, ABTS and DPPH assays, showing moderate activity as compared to standard antioxidants. Molecular docking studies of compound 4 and ADMET predictions make this compound a potential candidate for topical pharmacological use. The results obtained using the most active acylbenzohydroquinones are promising because some evaluated Candida strains are known to have decreased sensitivity to standard antifungal treatments.
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Affiliation(s)
- David Ríos
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
| | - Jaime A. Valderrama
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
| | - Gonzalo Quiroga
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
| | - Jonathan Michea
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
| | - Felipe Salas
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
| | - Eduardo Álvarez Duarte
- Unidad de Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Av. Independencia 1027, Santiago 8380453, Chile;
| | - Edmundo A. Venegas-Casanova
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (E.A.V.-C.); (R.J.-A.)
| | - Rafael Jara-Aguilar
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (E.A.V.-C.); (R.J.-A.)
| | - Carlos Navarro-Retamal
- Instituto de Ciencias Biológicas, Universidad de Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Pedro Buc Calderon
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
- Research Group in Metabolism and Nutrition, Louvain Drug Research Institute, Université Catholique de Louvain, 73 Avenue E. Mounier, 1200 Brussels, Belgium
| | - Julio Benites
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile; (D.R.); (J.A.V.); (G.Q.); (J.M.); (F.S.); (P.B.C.)
- Facultad de Farmacia y Bioquímica, Universidad Nacional de Trujillo, Trujillo 13011, Peru; (E.A.V.-C.); (R.J.-A.)
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6
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Navarro-Retamal C, Schott-Verdugo S, Gohlke H, Dreyer I. Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway. Int J Mol Sci 2021; 22:ijms221910345. [PMID: 34638686 PMCID: PMC8508871 DOI: 10.3390/ijms221910345] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/05/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Two Pore Channels (TPCs) are cation-selective voltage- and ligand-gated ion channels in membranes of intracellular organelles of eukaryotic cells. In plants, the TPC1 subtype forms the slowly activating vacuolar (SV) channel, the most dominant ion channel in the vacuolar membrane. Controversial reports about the permeability properties of plant SV channels fueled speculations about the physiological roles of this channel type. TPC1 is thought to have high Ca2+ permeability, a conclusion derived from relative permeability analyses using the Goldman–Hodgkin–Katz (GHK) equation. Here, we investigated in computational analyses the properties of the permeation pathway of TPC1 from Arabidopsis thaliana. Using the crystal structure of AtTPC1, protein modeling, molecular dynamics (MD) simulations, and free energy calculations, we identified a free energy minimum for Ca2+, but not for K+, at the luminal side next to the selectivity filter. Residues D269 and E637 coordinate in particular Ca2+ as demonstrated in in silico mutagenesis experiments. Such a Ca2+-specific coordination site in the pore explains contradicting data for the relative Ca2+/K+ permeability and strongly suggests that the Ca2+ permeability of SV channels is largely overestimated from relative permeability analyses. This conclusion was further supported by in silico electrophysiological studies showing a remarkable permeation of K+ but not Ca2+ through the open channel.
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Affiliation(s)
- Carlos Navarro-Retamal
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Campus Talca, Universidad de Talca, Talca 346000, Chile
- Correspondence: (C.N.-R.); (H.G.); (I.D.)
| | - Stephan Schott-Verdugo
- John von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany;
- Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Biological Information Processing (IBI-7: Structural Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Correspondence: (C.N.-R.); (H.G.); (I.D.)
| | - Ingo Dreyer
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Campus Talca, Universidad de Talca, Talca 346000, Chile
- Correspondence: (C.N.-R.); (H.G.); (I.D.)
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7
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Lehmann J, Jørgensen ME, Fratz S, Müller HM, Kusch J, Scherzer S, Navarro-Retamal C, Mayer D, Böhm J, Konrad KR, Terpitz U, Dreyer I, Mueller TD, Sauer M, Hedrich R, Geiger D, Maierhofer T. Acidosis-induced activation of anion channel SLAH3 in the flooding-related stress response of Arabidopsis. Curr Biol 2021; 31:3575-3585.e9. [PMID: 34233161 DOI: 10.1016/j.cub.2021.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 11/20/2020] [Revised: 02/03/2021] [Accepted: 06/08/2021] [Indexed: 10/20/2022]
Abstract
Plants, as sessile organisms, gained the ability to sense and respond to biotic and abiotic stressors to survive severe changes in their environments. The change in our climate comes with extreme dry periods but also episodes of flooding. The latter stress condition causes anaerobiosis-triggered cytosolic acidosis and impairs plant function. The molecular mechanism that enables plant cells to sense acidity and convey this signal via membrane depolarization was previously unknown. Here, we show that acidosis-induced anion efflux from Arabidopsis (Arabidopsis thaliana) roots is dependent on the S-type anion channel AtSLAH3. Heterologous expression of SLAH3 in Xenopus oocytes revealed that the anion channel is directly activated by a small, physiological drop in cytosolic pH. Acidosis-triggered activation of SLAH3 is mediated by protonation of histidine 330 and 454. Super-resolution microscopy analysis showed that the increase in cellular proton concentration switches SLAH3 from an electrically silent channel dimer into its active monomeric form. Our results show that, upon acidification, protons directly switch SLAH3 to its open configuration, bypassing kinase-dependent activation. Moreover, under flooding conditions, the stress response of Arabidopsis wild-type (WT) plants was significantly higher compared to SLAH3 loss-of-function mutants. Our genetic evidence of SLAH3 pH sensor function may guide the development of crop varieties with improved stress tolerance.
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Affiliation(s)
- Julian Lehmann
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany; Department of Biotechnology and Biophysics, University of Würzburg, Biocenter -Am Hubland, Würzburg 97074, Germany
| | - Morten E Jørgensen
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Stefanie Fratz
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Heike M Müller
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Jana Kusch
- University Hospital Jena, Institute of Physiologie II, Kollegiengasse 9, Jena 07743, Germany
| | - Sönke Scherzer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Carlos Navarro-Retamal
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Dominik Mayer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Jennifer Böhm
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Kai R Konrad
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter -Am Hubland, Würzburg 97074, Germany
| | - Ingo Dreyer
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Universidad de Talca, 2 Norte 685, Talca, Chile
| | - Thomas D Mueller
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, University of Würzburg, Biocenter -Am Hubland, Würzburg 97074, Germany
| | - Rainer Hedrich
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany.
| | - Dietmar Geiger
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany
| | - Tobias Maierhofer
- Institute for Molecular Plant Physiology and Biophysics, University of Würzburg, Julius-von-Sachs Institute, Würzburg 97082, Germany.
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Alfaro S, Navarro-Retamal C, Caballero J. Transforming Non-Selective Angiotensin-Converting Enzyme Inhibitors in C- and N-domain Selective Inhibitors by Using Computational Tools. Mini Rev Med Chem 2020; 20:1436-1446. [DOI: 10.2174/1389557520666191224113830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 01/01/2023]
Abstract
The two-domain dipeptidylcarboxypeptidase Angiotensin-I-converting enzyme (EC
3.4.15.1; ACE) plays an important physiological role in blood pressure regulation via the reninangiotensin
and kallikrein-kinin systems by converting angiotensin I to the potent vasoconstrictor angiotensin
II, and by cleaving a number of other substrates including the vasodilator bradykinin and the
anti-inflammatory peptide N-acetyl-SDKP. Therefore, the design of ACE inhibitors is within the priorities
of modern medical sciences for treating hypertension, heart failures, myocardial infarction, and
other related diseases. Despite the success of ACE inhibitors for the treatment of hypertension and
congestive heart failure, they have some adverse effects, which could be attenuated by selective domain
inhibition. Crystal structures of both ACE domains (nACE and cACE) reported over the last decades
could facilitate the rational drug design of selective inhibitors. In this review, we refer to the history
of the discovery of ACE inhibitors, which has been strongly related to the development of molecular
modeling methods. We stated that the design of novel selective ACE inhibitors is a challenge
for current researchers which requires a thorough understanding of the structure of both ACE domains
and the help of molecular modeling methodologies. Finally, we performed a theoretical design of potential
selective derivatives of trandolaprilat, a drug approved to treat critical conditions of hypertension,
to illustrate how to use molecular modeling methods such as de novo design, docking, Molecular
Dynamics (MD) simulations, and free energy calculations for creating novel potential drugs with specific
interactions inside nACE and cACE binding sites.
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Affiliation(s)
- Sergio Alfaro
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformatica y Simulacion Molecular, Facultad de Ingenieria, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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9
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Velázquez-Libera JL, Rossino G, Navarro-Retamal C, Collina S, Caballero J. Docking, Interaction Fingerprint, and Three-Dimensional Quantitative Structure-Activity Relationship (3D-QSAR) of Sigma1 Receptor Ligands, Analogs of the Neuroprotective Agent RC-33. Front Chem 2019; 7:496. [PMID: 31355187 PMCID: PMC6637851 DOI: 10.3389/fchem.2019.00496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/27/2019] [Indexed: 01/25/2023] Open
Abstract
The human Sigma1 receptor (S1R), which has been identified as a target with an important role in neuropsychological disorders, was first crystallized 3 years ago. Since S1R structure has no relation with another previous crystallized structures, the presence of the new crystal is an important hallmark for the design of agonists and antagonists against this important target. Some years ago, our group identified RC-33, a potent and selective S1R agonist, endowed with neuroprotective properties. In this work, drawing on new structural information, we studied the interactions of RC-33 and its analogs with the S1R binding site by using computational methods such as docking, interaction fingerprints, and receptor-guided alignment three dimensional quantitative structure–activity relationship (3D-QSAR). We found that RC-33 and its analogs adopted similar orientations within S1R binding site, with high similitude with orientations of the crystallized ligands; such information was used for identifying the residues involved in chemical interactions with ligands. Furthermore, the structure-activity relationship of the studied ligands was adequately described considering classical QSAR tests. All relevant aspects of the interactions between the studied compounds and S1R were covered here, through descriptions of orientations, binding interactions, and features that influence differential affinities. In this sense, the present results could be useful in the future design of novel S1R modulators.
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Affiliation(s)
- José Luis Velázquez-Libera
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Giacomo Rossino
- Pharmaceutical and Medicinal Chemistry Section, Drug Sciences Department, Università di Pavia, Pavia, Italy
| | - Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Simona Collina
- Pharmaceutical and Medicinal Chemistry Section, Drug Sciences Department, Università di Pavia, Pavia, Italy
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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10
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Thalhammer A, Bremer A, Knox-Brown P, Navarro-Retamal C, González W, Bryant G, Hincha DK. Lea proteins – from understanding the basics to tailoring for improved functionality. Cryobiology 2018. [DOI: 10.1016/j.cryobiol.2018.10.074] [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: 11/25/2022]
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11
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Caballero J, Morales-Bayuelo A, Navarro-Retamal C. Mycobacterium tuberculosis serine/threonine protein kinases: structural information for the design of their specific ATP-competitive inhibitors. J Comput Aided Mol Des 2018; 32:1315-1336. [PMID: 30367309 DOI: 10.1007/s10822-018-0173-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/20/2018] [Indexed: 12/17/2022]
Abstract
In the last decades, human protein kinases (PKs) have been relevant as targets in the development of novel therapies against many diseases, but the study of Mycobacterium tuberculosis PKs (MTPKs) involved in tuberculosis pathogenesis began much later and has not yet reached an advanced stage of development. To increase knowledge of these enzymes, in this work we studied the structural features of MTPKs, with focus on their ATP-binding sites and their interactions with inhibitors. PknA, PknB, and PknG are the most studied MTPKs, which were previously crystallized; ATP-competitive inhibitors have been designed against them in the last decade. In the current work, reported PknA, PknB, and PknG inhibitors were extracted from literature and their orientations inside the ATP-binding site were proposed by using docking method. With this information, interaction fingerprints were elaborated, which reveal the more relevant residues for establishing chemical interactions with inhibitors. The non-crystallized MTPKs PknD, PknF, PknH, PknJ, PknK, and PknL were also studied; their three-dimensional structural models were developed by using homology modeling. The main characteristics of MTPK ATP-binding sites (the non-crystallized and crystallized MTPKs, including PknE and PknI) were accounted; schemes of the main polar and nonpolar groups inside their ATP-binding sites were constructed, which are suitable for a major understanding of these proteins as antituberculotic targets. These schemes could be used for establishing comparisons between MTPKs and human PKs in order to increase selectivity of MTPK inhibitors. As a key tool for guiding medicinal chemists interested in the design of novel MTPK inhibitors, our work provides a map of the structural elements relevant for the design of more selective ATP-competitive MTPK inhibitors.
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Affiliation(s)
- Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile.
| | - Alejandro Morales-Bayuelo
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
| | - Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca, Chile
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12
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Navarro-Retamal C, Bremer A, Ingólfsson HI, Alzate-Morales J, Caballero J, Thalhammer A, González W, Hincha DK. Folding and Lipid Composition Determine Membrane Interaction of the Disordered Protein COR15A. Biophys J 2018; 115:968-980. [PMID: 30195939 DOI: 10.1016/j.bpj.2018.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/27/2018] [Accepted: 08/13/2018] [Indexed: 01/02/2023] Open
Abstract
Plants from temperate climates, such as the model plant Arabidopsis thaliana, are challenged with seasonal low temperatures that lead to increased freezing tolerance in fall in a process termed cold acclimation. Among other adaptations, this involves the accumulation of cold-regulated (COR) proteins, such as the intrinsically disordered chloroplast-localized protein COR15A. Together with its close homolog COR15B, it stabilizes chloroplast membranes during freezing. COR15A folds into amphipathic α-helices in the presence of high concentrations of low-molecular-mass crowders or upon dehydration. Under these conditions, the (partially) folded protein binds peripherally to membranes. In our study, we have used coarse-grained molecular dynamics simulations to elucidate the details of COR15A-membrane binding and its effects on membrane structure and dynamics. Simulation results indicate that at least partial folding of COR15A and the presence of highly unsaturated galactolipids in the membranes are necessary for efficient membrane binding. The bound protein is stabilized on the membrane by interactions of charged and polar amino acids with galactolipid headgroups and by interactions of hydrophobic amino acids with the upper part of the fatty acyl chains. Experimentally, the presence of liposomes made from a mixture of lipids mimicking chloroplast membranes induces additional folding in COR15A under conditions of partial dehydration, in agreement with the simulation results.
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Affiliation(s)
- Carlos Navarro-Retamal
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Anne Bremer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, The Netherlands
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Anja Thalhammer
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Casilla, Talca, Chile
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany.
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13
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Navarro-Retamal C, Caballero J. Energetic differences between non-domain-swapped and domain-swapped chain connectivities in the K2P potassium channel TRAAK. RSC Adv 2018; 8:26610-26618. [PMID: 35541058 PMCID: PMC9083029 DOI: 10.1039/c8ra04159h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/16/2018] [Accepted: 07/19/2018] [Indexed: 01/15/2023] Open
Abstract
Two-pore domain (K2P) channels are twofold symmetric K+ channels which control cell excitability by enabling the leak of potassium ions from cells in response to physicochemical stimuli. Crystallization of K2P channels revealed the presence of several structural features, which include an external cap. In the available crystallographic structures, the cap is present as non-domain-swapped (NDS) and domain-swapped (DS) chain conformations, where DS chain conformation exchanges two opposing outer helices 180° around the channel. In this work, energy differences between the residues located at the highest point of the cap in NDS and DS conformations were evaluated for TRAAK, a K2P channel that was crystallized in both conformations. Results indicated a preference for DS conformation, but this result is not extensible to TASK K2P channels. In the available crystallographic structures of K2P channels, the cap is present as non-domain-swapped (NDS) and domain-swapped (DS) chain conformations.![]()
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Affiliation(s)
- Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular
- Facultad de Ingeniería
- Universidad de Talca
- Talca
- Chile
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14
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Reissig F, Mamat C, Steinbach J, Pietzsch HJ, Freudenberg R, Navarro-Retamal C, Caballero J, Kotzerke J, Wunderlich G. Direct and Auger Electron-Induced, Single- and Double-Strand Breaks on Plasmid DNA Caused by 99mTc-Labeled Pyrene Derivatives and the Effect of Bonding Distance. PLoS One 2016; 11:e0161973. [PMID: 27583677 PMCID: PMC5008623 DOI: 10.1371/journal.pone.0161973] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/15/2016] [Indexed: 11/29/2022] Open
Abstract
It is evident that 99mTc causes radical-mediated DNA damage due to Auger electrons, which were emitted simultaneously with the known γ-emission of 99mTc. We have synthesized a series of new 99mTc-labeled pyrene derivatives with varied distances between the pyrene moiety and the radionuclide. The pyrene motif is a common DNA intercalator and allowed us to test the influence of the radionuclide distance on damages of the DNA helix. In general, pUC 19 plasmid DNA enables the investigation of the unprotected interactions between the radiotracers and DNA that results in single-strand breaks (SSB) or double-strand breaks (DSB). The resulting DNA fragments were separated by gel electrophoresis and quantified by fluorescent staining. Direct DNA damage and radical-induced indirect DNA damage by radiolysis products of water were evaluated in the presence or absence of the radical scavenger DMSO. We demonstrated that Auger electrons directly induced both SSB and DSB in high efficiency when 99mTc was tightly bound to the plasmid DNA and this damage could not be completely prevented by DMSO, a free radical scavenger. For the first time, we were able to minimize this effect by increasing the carbon chain lengths between the pyrene moiety and the 99mTc nuclide. However, a critical distance between the 99mTc atom and the DNA helix could not be determined due to the significantly lowered DSB generation resulting from the interaction which is dependent on the type of the 99mTc binding motif. The effect of variable DNA damage caused by the different chain length between the pyrene residue and the Tc-core as well as the possible conformations of the applied Tc-complexes was supplemented with molecular dynamics (MD) calculations. The effectiveness of the DNA-binding 99mTc-labeled pyrene derivatives was demonstrated by comparison to non-DNA-binding 99mTcO4–, since nearly all DNA damage caused by 99mTcO4– was prevented by incubating with DMSO.
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Affiliation(s)
- Falco Reissig
- University Hospital/ Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Department of Nuclear Medicine, Dresden, Germany
- * E-mail: (GW); (FR)
| | - Constantin Mamat
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Joerg Steinbach
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Hans-Juergen Pietzsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Dresden, Germany
| | - Robert Freudenberg
- University Hospital/ Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Department of Nuclear Medicine, Dresden, Germany
| | - Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Joerg Kotzerke
- University Hospital/ Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Department of Nuclear Medicine, Dresden, Germany
| | - Gerd Wunderlich
- University Hospital/ Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Department of Nuclear Medicine, Dresden, Germany
- * E-mail: (GW); (FR)
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15
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Navarro-Retamal C, Caballero J. Flavonoids as CDK1 Inhibitors: Insights in Their Binding Orientations and Structure-Activity Relationship. PLoS One 2016; 11:e0161111. [PMID: 27517610 PMCID: PMC4982677 DOI: 10.1371/journal.pone.0161111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/29/2016] [Indexed: 01/20/2023] Open
Abstract
In the last years, the interactions of flavonoids with protein kinases (PKs) have been described by using crystallographic experiments. Interestingly, different orientations have been found for one flavonoid inside different PKs and different chemical substitutions lead to different orientations of the flavonoid scaffold inside one PK. Accordingly, orientation predictions of novel analogues could help to the design of flavonoids with high PK inhibitory activities. With this in mind, we studied the binding modes of 37 flavonoids (flavones and chalcones) inside the cyclin-dependent PK CDK1 using docking experiments. We found that the compounds under study adopted two different orientations into the active site of CDK1 (orientations I and II in the manuscript). In addition, quantitative structure-activity relationship (QSAR) models using CoMFA and CoMSIA methodologies were constructed to explain the trend of the CDK1 inhibitory activities for the studied flavonoids. Template-based and docking-based alignments were used. Models developed starting from docking-based alignment were applied for describing the whole dataset and compounds with orientation I. Adequate R2 and Q2 values were obtained by each method; interestingly, only hydrophobic and hydrogen bond donor fields describe the differential potency of the flavonoids as CDK1 inhibitors for both defined alignments and subsets. Our current application of docking and QSAR together reveals important elements to be drawn for the design of novel flavonoids with increased PK inhibitory activities.
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Affiliation(s)
- Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
- * E-mail:
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16
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Navarro-Retamal C, Bremer A, Alzate-Morales J, Caballero J, Hincha DK, González W, Thalhammer A. Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana. Phys Chem Chem Phys 2016; 18:25806-16. [PMID: 27255148 DOI: 10.1039/c6cp02272c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The LEA (late embryogenesis abundant) proteins COR15A and COR15B from Arabidopsis thaliana are intrinsically disordered under fully hydrated conditions, but obtain α-helical structure during dehydration, which is reversible upon rehydration. To understand this unusual structural transition, both proteins were investigated by circular dichroism (CD) and molecular dynamics (MD) approaches. MD simulations showed unfolding of the proteins in water, in agreement with CD data obtained with both HIS-tagged and untagged recombinant proteins. Mainly intramolecular hydrogen bonds (H-bonds) formed by the protein backbone were replaced by H-bonds with water molecules. As COR15 proteins function in vivo as protectants in leaves partially dehydrated by freezing, unfolding was further assessed under crowded conditions. Glycerol reduced (40%) or prevented (100%) unfolding during MD simulations, in agreement with CD spectroscopy results. H-bonding analysis indicated that preferential exclusion of glycerol from the protein backbone increased stability of the folded state.
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Affiliation(s)
- Carlos Navarro-Retamal
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile. (Wendy González, for correspondence relating to protein modelling)
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17
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Navarro-Retamal C, Gaete-Eastman C, Herrera R, Caballero J, Alzate-Morales JH. Structural and Affinity Determinants in the Interaction between Alcohol Acyltransferase from F. x ananassa and Several Alcohol Substrates: A Computational Study. PLoS One 2016; 11:e0153057. [PMID: 27078149 PMCID: PMC4831670 DOI: 10.1371/journal.pone.0153057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/23/2016] [Indexed: 11/26/2022] Open
Abstract
Aroma and flavor are important factors of fruit quality and consumer preference. The specific pattern of aroma is generated during ripening by the accumulation of volatiles compounds, which are mainly esters. Alcohol acyltransferase (AAT) (EC 2.3.1.84) catalyzes the esterification reaction of aliphatic and aromatic alcohols and acyl-CoA into esters in fruits and flowers. In Fragaria x ananassa, there are different volatiles compounds that are obtained from different alcohol precursors, where octanol and hexanol are the most abundant during fruit ripening. At present, there is not structural evidence about the mechanism used by the AAT to synthesize esters. Experimental data attribute the kinetic role of this enzyme to 2 amino acidic residues in a highly conserved motif (HXXXD) that is located in the middle of the protein. With the aim to understand the molecular and energetic aspects of volatiles compound production from F. x ananassa, we first studied the binding modes of a series of alcohols, and also different acyl-CoA substrates, in a molecular model of alcohol acyltransferase from Fragaria x ananassa (SAAT) using molecular docking. Afterwards, the dynamical behavior of both substrates, docked within the SAAT binding site, was studied using routine molecular dynamics (MD) simulations. In addition, in order to correlate the experimental and theoretical data obtained in our laboratories, binding free energy calculations were performed; which previous results suggested that octanol, followed by hexanol, presented the best affinity for SAAT. Finally, and concerning the SAAT molecular reaction mechanism, it is suggested from molecular dynamics simulations that the reaction mechanism may proceed through the formation of a ternary complex, in where the Histidine residue at the HXXXD motif deprotonates the alcohol substrates. Then, a nucleophilic attack occurs from alcohol charged oxygen atom to the carbon atom at carbonyl group of the acyl CoA. This mechanism is in agreement with previous results, obtained in our group, in alcohol acyltransferase from Vasconcellea pubescens (VpAAT1).
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Affiliation(s)
- Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Carlos Gaete-Eastman
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile
- * E-mail: (JAM); (RH)
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
- * E-mail: (JAM); (RH)
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Valdés C, Alzate-Morales J, Osorio E, Villaseñor J, Navarro-Retamal C. A characterization of the two-step reaction mechanism of phenol decomposition by a Fenton reaction. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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