1
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Dicks M, Kock G, Kohl B, Zhong X, Pütz S, Heumann R, Erdmann KS, Stoll R. The binding affinity of PTPN13's tandem PDZ2/3 domain is allosterically modulated. BMC Mol Cell Biol 2019; 20:23. [PMID: 31286859 PMCID: PMC6615252 DOI: 10.1186/s12860-019-0203-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/02/2019] [Indexed: 11/24/2022] Open
Abstract
Background Protein tyrosine phosphatase PTPN13, also known as PTP-BL in mice, is a large multi-domain non-transmembrane scaffolding protein with a molecular mass of 270 kDa. It is involved in the regulation of several cellular processes such as cytokinesis and actin-cytoskeletal rearrangement. The modular structure of PTPN13 consists of an N-terminal KIND domain, a FERM domain, and five PDZ domains, followed by a C-terminal protein tyrosine phosphatase domain. PDZ domains are among the most abundant protein modules and they play a crucial role in signal transduction of protein networks. Results Here, we have analysed the binding characteristics of the isolated PDZ domains 2 and 3 from PTPN13 and compared them to the tandem domain PDZ2/3, which interacts with 12 C-terminal residues of the tumour suppressor protein of APC, using heteronuclear multidimensional NMR spectroscopy. Furthermore, we could show for the first time that PRK2 is a weak binding partner of PDZ2 and we demonstrate that the presence of PDZ3 alters the binding affinity of PDZ2 for APC, suggesting an allosteric effect and thereby modulating the binding characteristics of PDZ2. A HADDOCK-based molecular model of the PDZ2/3 tandem domain from PTPN13 supports these results. Conclusions Our study of tandem PDZ2/3 in complex with APC suggests that the interaction of PDZ3 with PDZ2 induces an allosteric modulation within PDZ2 emanating from the back of the domain to the ligand binding site. Thus, the modified binding preference of PDZ2 for APC could be explained by an allosteric effect and provides further evidence for the pivotal function of PDZ2 in the PDZ123 domain triplet within PTPN13.
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Affiliation(s)
- Markus Dicks
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Gerd Kock
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Bastian Kohl
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Xueyin Zhong
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Stefanie Pütz
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Rolf Heumann
- Biochemistry II, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany
| | - Kai S Erdmann
- Department of Biomedical Science, University of Sheffield, S10 2TN, Sheffield, UK
| | - Raphael Stoll
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany.
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2
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Carius AB, Rogne P, Duchoslav M, Wolf-Watz M, Samuelsson G, Shutova T. Dynamic pH-induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen. PHYSIOLOGIA PLANTARUM 2019; 166:288-299. [PMID: 30793329 DOI: 10.1111/ppl.12948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 06/09/2023]
Abstract
The PsbO protein is an essential extrinsic subunit of photosystem II, the pigment-protein complex responsible for light-driven water splitting. Water oxidation in photosystem II supplies electrons to the photosynthetic electron transfer chain and is accompanied by proton release and oxygen evolution. While the electron transfer steps in this process are well defined and characterized, the driving forces acting on the liberated protons, their dynamics and their destiny are all largely unknown. It was suggested that PsbO undergoes proton-induced conformational changes and forms hydrogen bond networks that ensure prompt proton removal from the catalytic site of water oxidation, i.e. the Mn4 CaO5 cluster. This work reports the purification and characterization of heterologously expressed PsbO from green algae Chlamydomonas reinhardtii and two isoforms from the higher plant Solanum tuberosum (PsbO1 and PsbO2). A comparison to the spinach PsbO reveals striking similarities in intrinsic protein fluorescence and CD spectra, reflecting the near-identical secondary structure of the proteins from algae and higher plants. Titration experiments using the hydrophobic fluorescence probe ANS revealed that eukaryotic PsbO proteins exhibit acid-base hysteresis. This hysteresis is a dynamic effect accompanied by changes in the accessibility of the protein's hydrophobic core and is not due to reversible oligomerization or unfolding of the PsbO protein. These results confirm the hypothesis that pH-dependent dynamic behavior at physiological pH ranges is a common feature of PsbO proteins and causes reversible opening and closing of their β-barrel domain in response to the fluctuating acidity of the thylakoid lumen.
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Affiliation(s)
- Anke B Carius
- Department of Plant Physiology, Umeå University, Umeå, SE-907 36, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - Miloš Duchoslav
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden
| | - Göran Samuelsson
- Department of Plant Physiology, Umeå University, Umeå, SE-907 36, Sweden
| | - Tatyana Shutova
- Department of Plant Physiology, Umeå University, Umeå, SE-907 36, Sweden
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3
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Kock G, Dicks M, Yip KT, Kohl B, Pütz S, Heumann R, Erdmann KS, Stoll R. Molecular Basis of Class III Ligand Recognition by PDZ3 in Murine Protein Tyrosine Phosphatase PTPN13. J Mol Biol 2018; 430:4275-4292. [PMID: 30189200 DOI: 10.1016/j.jmb.2018.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
Protein tyrosine phosphatase PTPN13, also known as PTP-BL in mice, represents a large multi-domain non-transmembrane scaffolding protein that contains five consecutive PDZ domains. Here, we report the solution structures of the extended murine PTPN13 PDZ3 domain in its apo form and in complex with its physiological ligand, the carboxy-terminus of protein kinase C-related kinase-2 (PRK2), determined by multidimensional NMR spectroscopy. Both in its ligand-free state and when complexed to PRK2, PDZ3 of PTPN13 adopts the classical compact, globular D/E fold. PDZ3 of PTPN13 binds five carboxy-terminal amino acids of PRK2 via a groove located between the EB-strand and the DB-helix. The PRK2 peptide resides in the canonical PDZ3 binding cleft in an elongated manner and the amino acid side chains in position P0 and P-2, cysteine and aspartate, of the ligand face the groove between EB-strand and DB-helix, whereas the PRK2 side chains of tryptophan and alanine located in position P-1 and P-3 point away from the binding cleft. These structures are rare examples of selective class III ligand recognition by a PDZ domain and now provide a basis for the detailed structural investigation of the promiscuous interaction between the PDZ domains of PTPN13 and their ligands. They will also lead to a better understanding of the proposed scaffolding function of these domains in multi-protein complexes assembled by PTPN13 and could ultimately contribute to low molecular weight antagonists that might even act on the PRK2 signaling pathway to modulate rearrangements of the actin cytoskeleton.
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Affiliation(s)
- Gerd Kock
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Markus Dicks
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - King Tuo Yip
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Bastian Kohl
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Stefanie Pütz
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Rolf Heumann
- Molecular Neurobiochemistry, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany
| | - Kai S Erdmann
- Department of Biomedical Science, University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Raphael Stoll
- Biomolecular NMR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, D-44780, Germany.
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4
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Lipiński PFJ, Garnuszek P, Maurin M, Stoll R, Metzler-Nolte N, Wodyński A, Dobrowolski JC, Dudek MK, Orzełowska M, Mikołajczak R. Structural studies on radiopharmaceutical DOTA-minigastrin analogue (CP04) complexes and their interaction with CCK2 receptor. EJNMMI Res 2018; 8:33. [PMID: 29663167 PMCID: PMC5902437 DOI: 10.1186/s13550-018-0387-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Background The cholecystokinin receptor subtype 2 (CCK-2R) is an important target for diagnostic imaging and targeted radionuclide therapy (TRNT) due to its overexpression in certain cancers (e.g., medullary thyroid carcinoma (MTC)), thus matching with a theranostic principle. Several peptide conjugates suitable for the TRNT of MTC have been synthesized, including a very promising minigastrin analogue DOTA-(DGlu)6-Ala-Tyr-Gly-Trp-Met-Asp-Phe-NH2 (CP04). In this contribution, we wanted to see whether CP04 binding affinity for CCK-2R is sensitive to the type of the complexed radiometal, as well as to get insights into the structure of CP04-CCK2R complex by molecular modeling. Results In vitro studies demonstrated that there is no significant difference in CCK-2R binding affinity and specific cellular uptake between the CP04 conjugates complexed with [68Ga]Ga3+ or [177Lu]Lu3+. In order to investigate the background of this observation, we proposed a binding model of CP04 with CCK-2R based on homology modeling and molecular docking. In this model, the C-terminal part of the molecule enters the cavity formed between the receptor helices, while the N-terminus (including DOTA and the metal) is located at the binding site outlet, exposed in large extent to the solvent. The radiometals do not influence the conformation of the molecule except for the direct neighborhood of the chelating moiety. Conclusions The model seems to be in agreement with much of structure-activity relationship (SAR) studies reported for cholecystokinin and for CCK-2R-targeting radiopharmaceuticals. It also explains relative insensitivity of CCK-2R affinity for the change of the metal. The proposed model partially fits the reported site-directed mutagenesis data.
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Affiliation(s)
- Piotr F J Lipiński
- Neuropeptides Department, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5 Str., 02-106, Warszawa, Poland.
| | - Piotr Garnuszek
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Michał Maurin
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Raphael Stoll
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Nils Metzler-Nolte
- Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, Universitätsstr. 150, 44780, Bochum, Germany
| | - Artur Wodyński
- Świerk Computing Centre, National Centre for Nuclear Research, A. Sołtana 7 Str., 05-400, Otwock, Poland.,Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, 10623, Berlin, Germany
| | - Jan Cz Dobrowolski
- Institute of Nuclear Chemistry and Technology, Dorodna 16 Street, 03-195, Warszawa, Poland.,National Medicines Institute, Chełmska 30/34 Str., 00-725, Warszawa, Poland
| | - Marta K Dudek
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Monika Orzełowska
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
| | - Renata Mikołajczak
- Radioisotope Centre POLATOM, National Centre for Nuclear Research, A. Sołtana 7 Str, 05-400, Otwock, Poland
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5
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Bommer M, Coates L, Dau H, Zouni A, Dobbek H. Protein crystallization and initial neutron diffraction studies of the photosystem II subunit PsbO. Acta Crystallogr F Struct Biol Commun 2017; 73:525-531. [PMID: 28876232 PMCID: PMC5619745 DOI: 10.1107/s2053230x17012171] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/22/2017] [Indexed: 11/10/2022] Open
Abstract
The PsbO protein of photosystem II stabilizes the active-site manganese cluster and is thought to act as a proton antenna. To enable neutron diffraction studies, crystals of the β-barrel core of PsbO were grown in capillaries. The crystals were optimized by screening additives in a counter-diffusion setup in which the protein and reservoir solutions were separated by a 1% agarose plug. Crystals were cross-linked with glutaraldehyde. Initial neutron diffraction data were collected from a 0.25 mm3 crystal at room temperature using the MaNDi single-crystal diffractometer at the Spallation Neutron Source, Oak Ridge National Laboratory.
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Affiliation(s)
- Martin Bommer
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Leighton Coates
- Biology and Soft Matter Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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6
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del Val C, Bondar AN. Charged groups at binding interfaces of the PsbO subunit of photosystem II: A combined bioinformatics and simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:432-441. [DOI: 10.1016/j.bbabio.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 01/20/2023]
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7
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Bommer M, Bondar AN, Zouni A, Dobbek H, Dau H. Crystallographic and Computational Analysis of the Barrel Part of the PsbO Protein of Photosystem II: Carboxylate–Water Clusters as Putative Proton Transfer Relays and Structural Switches. Biochemistry 2016; 55:4626-35. [DOI: 10.1021/acs.biochem.6b00441] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Martin Bommer
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Fachbereich
Physik, Theoretical Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Athina Zouni
- Institut
für Biologie, Biophysik der Photosynthese, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dobbek
- Institut
für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Holger Dau
- Fachbereich
Physik, Biophysics and Photosynthesis, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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8
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Lorch S, Capponi S, Pieront F, Bondar AN. Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. J Phys Chem B 2015; 119:12172-81. [DOI: 10.1021/acs.jpcb.5b06594] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastian Lorch
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Sara Capponi
- Department
of Physiology and Biophysics, University of California at Irvine, Medical Sciences I, Irvine, California 92697, United States
| | - Florian Pieront
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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9
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Rathner P, Rathner A, Horničáková M, Wohlschlager C, Chandra K, Kohoutová J, Ettrich R, Wimmer R, Müller N. Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants. Proteins 2015; 83:1677-86. [PMID: 26138376 PMCID: PMC4758407 DOI: 10.1002/prot.24853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 11/10/2022]
Abstract
The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found.
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Affiliation(s)
- Petr Rathner
- Institute of Organic Chemistry, Johannes Kepler University LinzLinz4040Austria,Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic
| | - Adriana Rathner
- Institute of Organic Chemistry, Johannes Kepler University LinzLinz4040Austria
| | - Michaela Horničáková
- Institute of Organic Chemistry, Johannes Kepler University LinzLinz4040Austria,Lohmann Animal HealthCuxhaven27472Germany
| | | | - Kousik Chandra
- Institute of Organic Chemistry, Johannes Kepler University LinzLinz4040Austria
| | - Jaroslava Kohoutová
- Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic,Center of Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech RepublicNové HradyCzech Republic
| | - Rüdiger Ettrich
- Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic,Center of Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech RepublicNové HradyCzech Republic
| | - Reinhard Wimmer
- Department of BiotechnologyChemistry and Environmental Engineering, Aalborg UniversityAalborg9220Denmark
| | - Norbert Müller
- Institute of Organic Chemistry, Johannes Kepler University LinzLinz4040Austria,Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic
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10
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Horničáková M, Kohoutová J, Schlagnitweit J, Wohlschlager C, Ettrich R, Fiala R, Schoefberger W, Müller N. Backbone assignment and secondary structure of the PsbQ protein from photosystem II. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:169-175. [PMID: 21259076 DOI: 10.1007/s12104-011-9293-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/07/2011] [Indexed: 05/30/2023]
Abstract
PsbQ is one of the extrinsic proteins situated on the lumenal surface of photosystem II (PSII) in the higher plants and green algae. Its three-dimensional structure was determined by X-ray crystallography with exception of the residues 14-33. To obtain further details about its structure and potentially its dynamics, we approached the problem by NMR. In this paper we report (1)H, (15)N, and (13)C NMR assignments for the PsbQ protein. The very challenging oligo-proline stretches could be assigned using (13)C-detected NMR experiments that enabled the assignments of twelve out of the thirteen proline residues of PsbQ. The identification of PsbQ secondary structure elements on the basis of our NMR data was accomplished with the programs TALOS+, web server CS23D and CS-Rosetta. To obtain additional secondary structure information, three-bond H(N)-H(α) J-coupling constants and deviation of experimental (13)C(α) and (13)C(β) chemical shifts from random coil values were determined. The resulting "consensus" secondary structure of PsbQ compares very well with the resolved regions of the published X-ray crystallographic structure and gives a first estimate of the structure of the "missing link" (i.e. residues 14-33), which will serve as the basis for the further investigation of the structure, dynamics and interactions.
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Affiliation(s)
- Michaela Horničáková
- Institute of Organic Chemistry, Johannes Kepler University, Altenbergerstraße 69, 4040, Linz, Austria
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11
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Aktas M, Gleichenhagen J, Stoll R, Narberhaus F. S-adenosylmethionine-binding properties of a bacterial phospholipid N-methyltransferase. J Bacteriol 2011; 193:3473-81. [PMID: 21602340 PMCID: PMC3133305 DOI: 10.1128/jb.01539-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 05/10/2011] [Indexed: 11/20/2022] Open
Abstract
The presence of the membrane lipid phosphatidylcholine (PC) in the bacterial membrane is critically important for many host-microbe interactions. The phospholipid N-methyltransferase PmtA from the plant pathogen Agrobacterium tumefaciens catalyzes the formation of PC by a three-step methylation of phosphatidylethanolamine via monomethylphosphatidylethanolamine and dimethylphosphatidylethanolamine. The methyl group is provided by S-adenosylmethionine (SAM), which is converted to S-adenosylhomocysteine (SAH) during transmethylation. Despite the biological importance of bacterial phospholipid N-methyltransferases, little is known about amino acids critical for binding to SAM or phospholipids and catalysis. Alanine substitutions in the predicted SAM-binding residues E58, G60, G62, and E84 in A. tumefaciens PmtA dramatically reduced SAM-binding and enzyme activity. Homology modeling of PmtA satisfactorily explained the mutational results. The enzyme is predicted to exhibit a consensus topology of the SAM-binding fold consistent with cofactor interaction as seen with most structurally characterized SAM-methyltransferases. Nuclear magnetic resonance (NMR) titration experiments and (14)C-SAM-binding studies revealed binding constants for SAM and SAH in the low micromolar range. Our study provides first insights into structural features and SAM binding of a bacterial phospholipid N-methyltransferase.
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Affiliation(s)
| | | | - Raphael Stoll
- Biomolecular NMR, Ruhr-Universität Bochum, Bochum, Germany
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12
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Karassek S, Berghaus C, Schwarten M, Goemans CG, Ohse N, Kock G, Jockers K, Neumann S, Gottfried S, Herrmann C, Heumann R, Stoll R. Ras homolog enriched in brain (Rheb) enhances apoptotic signaling. J Biol Chem 2010; 285:33979-91. [PMID: 20685651 PMCID: PMC2962498 DOI: 10.1074/jbc.m109.095968] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2009] [Revised: 07/19/2010] [Indexed: 12/18/2022] Open
Abstract
Rheb is a homolog of Ras GTPase that regulates cell growth, proliferation, and regeneration via mammalian target of rapamycin (mTOR). Because of the well established potential of activated Ras to promote survival, we sought to investigate the ability of Rheb signaling to phenocopy Ras. We found that overexpression of lipid-anchored Rheb enhanced the apoptotic effects induced by UV light, TNFα, or tunicamycin in an mTOR complex 1 (mTORC1)-dependent manner. Knocking down endogenous Rheb or applying rapamycin led to partial protection, identifying Rheb as a mediator of cell death. Ras and c-Raf kinase opposed the apoptotic effects induced by UV light or TNFα but did not prevent Rheb-mediated apoptosis. To gain structural insight into the signaling mechanisms, we determined the structure of Rheb-GDP by NMR. The complex adopts the typical canonical fold of RasGTPases and displays the characteristic GDP-dependent picosecond to nanosecond backbone dynamics of the switch I and switch II regions. NMR revealed Ras effector-like binding of activated Rheb to the c-Raf-Ras-binding domain (RBD), but the affinity was 1000-fold lower than the Ras/RBD interaction, suggesting a lack of functional interaction. shRNA-mediated knockdown of apoptosis signal-regulating kinase 1 (ASK-1) strongly reduced UV or TNFα-induced apoptosis and suppressed enhancement by Rheb overexpression. In conclusion, Rheb-mTOR activation not only promotes normal cell growth but also enhances apoptosis in response to diverse toxic stimuli via an ASK-1-mediated mechanism. Pharmacological regulation of the Rheb/mTORC1 pathway using rapamycin should take the presence of cellular stress into consideration, as this may have clinical implications.
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Affiliation(s)
| | | | | | | | - Nadine Ohse
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, 44780 Bochum, Germany
| | | | | | | | | | - Christian Herrmann
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr University of Bochum, 44780 Bochum, Germany
| | - Rolf Heumann
- From the Departments of Molecular Neurobiochemistry
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13
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Kock G, Dicks M, Heumann R, Erdmann KS, Stoll R. Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL. BIOMOLECULAR NMR ASSIGNMENTS 2010; 4:199-202. [PMID: 20563762 DOI: 10.1007/s12104-010-9242-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Accepted: 06/07/2010] [Indexed: 05/29/2023]
Abstract
Protein tyrosine phosphatase basophil-like (PTP-BL), also known as PTPN13, represents a large multi domain non-transmembrane scaffolding protein that contains five PDZ domains. Here we report the complete resonance assignments of the extended PDZ3 domain of PTP-BL. These assignments provide a basis for the detailed structural investigation of the interaction between the PDZ domains of PTP-BL as well as of their interaction with ligands. It will also lead to a better understanding of the proposed scaffolding function of these domains in multi-protein complexes assembled by PTB-BL.
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Affiliation(s)
- Gerd Kock
- Biomolecular NMR, Faculty of Chemistry and Biochemistry, Ruhr-University of Bochum, 44780, Bochum, Germany.
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14
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Nikitina J, Shutova T, Melnik B, Chernyshov S, Marchenkov V, Semisotnov G, Klimov V, Samuelsson G. Importance of a single disulfide bond for the PsbO protein of photosystem II: protein structure stability and soluble overexpression in Escherichia coli. PHOTOSYNTHESIS RESEARCH 2008; 98:391-403. [PMID: 18709441 DOI: 10.1007/s11120-008-9327-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 07/01/2008] [Indexed: 05/09/2023]
Abstract
PsbO protein is an important constituent of the water-oxidizing complex, located on the lumenal side of photosystem II. We report here the efficient expression of the spinach PsbO in E. coli where the solubility depends entirely on the formation of the disulfide bond. The PsbO protein purified from a pET32 system that includes thioredoxin fusion is properly folded and functionally active. Urea unfolding experiments imply that the reduction of the single disulfide bridge decreases stability of the protein. Analysis of inter-residue contact density through the PsbO molecule shows that Cys51 is located in a cluster with high contact density. Reduction of the Cys28-Cys51 bond is proposed to perturb the packing interactions in this cluster and destabilize the protein as a whole. Taken together, our results give evidence that PsbO exists in solution as a compact highly ordered structure, provided that the disulfide bridge is not reduced.
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Affiliation(s)
- Julia Nikitina
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87 Umea, Sweden
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15
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Williamson AK. Structural and functional aspects of the MSP (PsbO) and study of its differences in thermophilic versus mesophilic organisms. PHOTOSYNTHESIS RESEARCH 2008; 98:365-89. [PMID: 18780158 DOI: 10.1007/s11120-008-9353-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 08/06/2008] [Indexed: 05/16/2023]
Abstract
The Manganese Stabilizing Protein (MSP) of Photosystem II (PSII) is a so-called extrinsic subunit, which reversibly associates with the other membrane-bound PSII subunits. The MSP is essential for maximum rates of O(2) production under physiological conditions as stabilizes the catalytic [Mn(4)Ca] cluster, which is the site of water oxidation. The function of the MSP subunit in the PSII complex has been extensively studied in higher plants, and the structure of non-PSII associated MSP has been studied by low-resolution biophysical techniques. Recently, crystal structures of PSII from the thermophilic cyanobacterium Thermosynechococcus elongatus have resolved the MSP subunit in its PSII-associated state. However, neither any crystal structure is available yet for MSP from mesophilic organisms, higher plants or algae nor has the non-PSII associated form of MSP been crystallized. This article reviews the current understanding of the structure, dynamics, and function of MSP, with a particular focus on properties of the MSP from T. elongatus that may be attributable to the thermophilic ecology of this organism rather than being general features of MSP.
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Affiliation(s)
- Adele K Williamson
- Research School of Biological Sciences, the Australian National University, Canberra 0200, Australia.
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16
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Williamson AK, Liggins JR, Hillier W, Wydrzynski T. The importance of protein-protein interactions for optimising oxygen activity in photosystem II: reconstitution with a recombinant thioredoxin--manganese stabilising protein. PHOTOSYNTHESIS RESEARCH 2007; 92:305-14. [PMID: 17484036 DOI: 10.1007/s11120-007-9165-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Accepted: 03/29/2007] [Indexed: 05/15/2023]
Abstract
In this paper we describe how photosystem II (PSII) from higher plants, which have been depleted, of the extrinsic proteins can be reconstituted with a chimeric fusion protein comprising thioredoxin from Escherichia coli and the manganese stabilising protein from Thermosynechococcus elongatus. Surprisingly, even though E. coli thioredoxin is completely unrelated to PSII, the fusion protein restores higher rates of activity upon rebinding to PSII than either the native spinach MSP, or T. elongatus MSP. PSII reconstituted with the fusion protein also has a lower requirement for calcium than PSII with the small extrinsic proteins removed, or PSII reconstituted with spinach or T. elongatus MSP. The MSP portion of the fusion protein is less thermally stable compared to isolated MSP from T. elongatus, which could be the key to its superior activation capability through greater flexibility. This work reveals the importance of protein-protein interactions in the water splitting activity of PSII and suggests that conformational configurations, which increase flexibility in MSP, are essential to its function, even when these are induced by an unrelated protein.
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Affiliation(s)
- A K Williamson
- Research School of Biological Sciences, The Australian National University, Canberra 0200, Australia.
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17
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Shutova T, Klimov VV, Andersson B, Samuelsson G. A cluster of carboxylic groups in PsbO protein is involved in proton transfer from the water oxidizing complex of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:434-40. [PMID: 17336919 DOI: 10.1016/j.bbabio.2007.01.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Revised: 01/26/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
The hypothesis presented here for proton transfer away from the water oxidation complex of Photosystem II (PSII) is supported by biochemical experiments on the isolated PsbO protein in solution, theoretical analyses of better understood proton transfer systems like bacteriorhodopsin and cytochrome oxidase, and the recently published 3D structure of PS II (Pdb entry 1S5L). We propose that a cluster of conserved glutamic and aspartic acid residues in the PsbO protein acts as a buffering network providing efficient acceptors of protons derived from substrate water molecules. The charge delocalization of the cluster ensures readiness to promptly accept the protons liberated from substrate water. Therefore protons generated at the catalytic centre of PSII need not be released into the thylakoid lumen as generally thought. The cluster is the beginning of a localized, fast proton transfer conduit on the lumenal side of the thylakoid membrane. Proton-dependent conformational changes of PsbO may play a role in the regulation of both supply of substrate water to the water oxidizing complex and the resultant proton transfer.
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Affiliation(s)
- Tatiana Shutova
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden.
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18
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Lundin B, Thuswaldner S, Shutova T, Eshaghi S, Samuelsson G, Barber J, Andersson B, Spetea C. Subsequent events to GTP binding by the plant PsbO protein: structural changes, GTP hydrolysis and dissociation from the photosystem II complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1767:500-8. [PMID: 17223069 DOI: 10.1016/j.bbabio.2006.10.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/26/2006] [Accepted: 10/28/2006] [Indexed: 10/23/2022]
Abstract
Besides an essential role in optimizing water oxidation in photosystem II (PSII), it has been reported that the spinach PsbO protein binds GTP [C. Spetea, T. Hundal, B. Lundin, M. Heddad, I. Adamska, B. Andersson, Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 1409-1414]. Here we predict four GTP-binding domains in the structure of spinach PsbO, all localized in the beta-barrel domain of the protein, as judged from comparison with the 3D-structure of the cyanobacterial counterpart. These domains are not conserved in the sequences of the cyanobacterial or green algae PsbO proteins. MgGTP induces specific changes in the structure of the PsbO protein in solution, as detected by circular dichroism and intrinsic fluorescence spectroscopy. Spinach PsbO has a low intrinsic GTPase activity, which is enhanced fifteen-fold when the protein is associated with the PSII complex in its dimeric form. GTP stimulates the dissociation of PsbO from PSII under light conditions known to also release Mn(2+) and Ca(2+) ions from the oxygen-evolving complex and to induce degradation of the PSII reaction centre D1 protein. We propose the occurrence in higher plants of a PsbO-mediated GTPase activity associated with PSII, which has consequences for the function of the oxygen-evolving complex and D1 protein turnover.
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Affiliation(s)
- Björn Lundin
- Division of Cell Biology, Linköping University, SE-581 85 Linköping, Sweden
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19
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Wyman AJ, Yocum CF. Structure and activity of the photosystem II manganese-stabilizing protein: role of the conserved disulfide bond. PHOTOSYNTHESIS RESEARCH 2005; 85:359-72. [PMID: 16170637 DOI: 10.1007/s11120-005-7385-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Accepted: 05/13/2005] [Indexed: 05/04/2023]
Abstract
The 33-kDa manganese-stabilizing protein (MSP) of Photosystem II (PS II) maintains the functional stability of the Mn cluster in the enzyme's active site. This protein has been shown to possess characteristics similar to those of the intrinsically disordered, or natively unfolded proteins. Alternately it was proposed that MSP should be classified as a molten globule, based in part on the hypothesis that its lone disulfide bridge is necessary for structural stability and function in solution. A site-directed mutant MSP (C28A,C51A) that eliminates the disulfide bond reconstitutes O(2) evolution activity and binds to MSP-free PS II preparations at wild-type levels. This mutant was further characterized by incubation at 90 degrees C to determine the effect of loss of the disulfide bridge on MSP thermostability and solution structure. After heating at 90 degrees C for 20 min, C28A,C51A MSP was still able to bind to PS II preparations at molar stoichiometries similar to those of WT MSP and reconstitute O(2) evolution activity. A fraction of the protein aggregates upon heating, but after resolubilization, it regains the ability to bind to PS II and reconstitute O(2) evolution activity. Characterization of the solution structure of C28A,C51A MSP, using CD spectroscopy, UV absorption spectroscopy, and gel filtration chromatography, revealed that the mutant has a more disordered solution structure than WT MSP. The disulfide bond is therefore unnecessary for MSP function and the intrinsically disordered characteristics of MSP are not dependent on its presence. However, the disulfide bond does play a role in the solution structure of MSP in vivo, as evidenced by the lability of a C20S MSP mutation in Synechocystis 6803.
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Affiliation(s)
- Aaron J Wyman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA
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