1
|
Berner F, Kovermann M. Including the Ensemble of Unstructured Conformations in the Analysis of Protein's Native State by High-Pressure NMR Spectroscopy. Angew Chem Int Ed Engl 2024:e202401343. [PMID: 38656763 DOI: 10.1002/anie.202401343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
The analysis of pressure induced changes in the chemical shift of proteins allows statements on structural fluctuations proteins exhibit at ambient pressure. The inherent issue of separating general pressure effects from structural related effects on the pressure dependence of chemical shifts has so far been addressed by considering the characteristics of random coil peptides on increasing pressure. In this work, chemically and pressure denatured states of the cold shock protein B from Bacillus subtilis (BsCspB) have been assigned in 2D 1H-15N HSQC NMR spectra and their dependence on increasing hydrostatic pressure has been evaluated. The pressure denatured polypeptide chain has been used to separate general from structural related effects on 1H and 15N chemical shifts of native BsCspB and the implications on the interpretation of pressure induced changes in the chemical shift regarding the structure of BsCspB are discussed. It has been found that the ensemble of unstructured conformations of BsCspB shows different responses to increasing pressure than random coil peptides do. Thus, the approach used for considering the general effects that arise when hydrostatic pressure increases changes the structural conclusions that are drawn from high pressure NMR spectroscopic experiments that rely on the analysis of chemical shifts.
Collapse
Affiliation(s)
| | - Michael Kovermann
- Universitat Konstanz, Chemie, Universitaetsstraße 10, 78457, Konstanz, GERMANY
| |
Collapse
|
2
|
Immler F, Schneider T, Kovermann M. Targeted Preparation and NMR Spectroscopic Characterization of Lys11-Linked Ubiquitin Trimers. Chembiochem 2024; 25:e202300670. [PMID: 37983597 DOI: 10.1002/cbic.202300670] [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: 09/29/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/22/2023]
Abstract
Ubiquitylation refers to the attachment of mono- or poly-ubiquitin molecules to a substrate protein. To shield ubiquitin chains against potential hydrolysis, a facile, click-chemistry based approach was recently established for the generation of site-specifically conjugated ubiquitin dimers relying on triazole-linkage. Here, the preparation of such ubiquitin chains was advanced by the generation of homotypic Lys11-linked ubiquitin trimers considering an isotopic labeling scheme in a moiety-wise manner. The structural and dynamical impact on the ubiquitin unit at proximal, central, or distal position that is potentially invoked by the respective other two moieties was systematically probed by heteronuclear high-resolution NMR spectroscopic approaches. As a result, conjugating a third ubiquitin moiety to the proximal or distal site of a ubiquitin dimer does not alter structural and dynamical characteristics as it has been seen for ubiquitin dimers. This observation suggests that recognition of a homotypically assembled ubiquitin chain by a potential substrate is primarily done by screening the length of a ubiquitin chain rather than relying on subtle changes in structure or dynamic properties of single ubiquitin moieties composing the chain.
Collapse
Affiliation(s)
- Fabian Immler
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Department of Chemistry and Graduate School of Chemical Biology (KoRS-CB), Universitätsstraße 10, 78457, Konstanz, Germany
| |
Collapse
|
3
|
Schneider T, Sawade K, Berner F, Peter C, Kovermann M. Specifying conformational heterogeneity of multi-domain proteins at atomic resolution. Structure 2023; 31:1259-1274.e10. [PMID: 37557171 DOI: 10.1016/j.str.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/02/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
The conformational landscape of multi-domain proteins is inherently linked to their specific functions. This also holds for polyubiquitin chains that are assembled by two or more ubiquitin domains connected by a flexible linker thus showing a large interdomain mobility. However, molecular recognition and signal transduction are associated with particular conformational substates that are populated in solution. Here, we apply high-resolution NMR spectroscopy in combination with dual-scale MD simulations to explore the conformational space of K6-, K29-, and K33-linked diubiquitin molecules. The conformational ensembles are evaluated utilizing a paramagnetic cosolute reporting on solvent exposure plus a set of complementary NMR parameters. This approach unravels a conformational heterogeneity of diubiquitins and explains the diversity of structural models that have been determined for K6-, K29-, and K33-linked diubiquitins in free and ligand-bound states so far. We propose a general application of the approach developed here to demystify multi-domain proteins occurring in nature.
Collapse
Affiliation(s)
- Tobias Schneider
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Kevin Sawade
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Graduate School Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Frederic Berner
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany.
| |
Collapse
|
4
|
Kovermann M, Stefan A, Palazzetti C, Immler F, Dal Piaz F, Bernardi L, Cimone V, Bellone ML, Hochkoeppler A. The Mycobacterium tuberculosis protein tyrosine phosphatase MptpA features a pH dependent activity overlapping the bacterium sensitivity to acidic conditions. Biochimie 2023; 213:66-81. [PMID: 37201648 DOI: 10.1016/j.biochi.2023.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023]
Abstract
The Mycobacterium tuberculosis low-molecular weight protein tyrosine phosphatase (MptpA) is responsible for the inhibition of phagosome-lysosome fusion and is essential for the bacterium pathogenicity. This inhibition implies that M. tuberculosis is not exposed to a strongly acidic environment in vivo, enabling successful propagation in host cells. Remarkably, MptpA has been previously structurally and functionally investigated, with special emphasis devoted to the enzyme properties at pH 8.0. Considering that the virulence of M. tuberculosis is strictly dependent on the avoidance of acidic conditions in vivo, we analysed the pH-dependence of the structural and catalytic properties of MptpA. Here we show that this enzyme undergoes pronounced conformational rearrangements when exposed to acidic pH conditions, inducing a severe decrease of the enzymatic catalytic efficiency at the expense of phosphotyrosine (pTyr). In particular, a mild decrease of pH from 6.5 to 6.0 triggers a significant increase of K0.5 of MptpA for phosphotyrosine, the phosphate group of which we determined to feature a pKa2 equal to 5.7. Surface plasmon resonance experiments confirmed that MptpA binds poorly to pTyr at pH values < 6.5. Notably, the effectiveness of the MptpA competitive inhibitor L335-M34 at pH 6 does largely outperform the inhibition exerted at neutral or alkaline pH values. Overall, our observations indicate a pronounced sensitivity of MptpA to acidic pH conditions, and suggest the search for competitive inhibitors bearing a negatively charged group featuring pKa values lower than that of the substrate phosphate group.
Collapse
Affiliation(s)
- Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätstraße 10, 78464, Konstanz, Germany
| | - Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy
| | - Chiara Palazzetti
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Fabian Immler
- Department of Chemistry, University of Konstanz, Universitätstraße 10, 78464, Konstanz, Germany
| | - Fabrizio Dal Piaz
- Department of Medicine, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Luca Bernardi
- Department of Industrial Chemistry "Toson Montanaro", University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Valentina Cimone
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Maria Laura Bellone
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy.
| |
Collapse
|
5
|
Horvath I, Welte H, Schmit JD, Kovermann M, Wittung-Stafshede P. Distinct growth regimes of α-synuclein amyloid elongation. Biophys J 2023; 122:2556-2563. [PMID: 37170496 PMCID: PMC10323017 DOI: 10.1016/j.bpj.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
Addition of amyloid seeds to aggregation-prone monomers allows for amyloid fiber growth (elongation) omitting slow nucleation. We here combine Thioflavin T fluorescence (probing formation of amyloids) and solution-state NMR spectroscopy (probing disappearance of monomers) to assess elongation kinetics of the amyloidogenic protein, α-synuclein, for which aggregation is linked to Parkinson's disease. We found that both spectroscopic detection methods give similar kinetic results, which can be fitted by applying double exponential decay functions. When the origin of the two-phase behavior was analyzed by mathematical modeling, parallel paths as well as stop-and-go behavior were excluded as possible explanations. Instead, supported by previous theory, the experimental elongation data reveal distinct kinetic regimes that depend on instantaneous monomer concentration. At low monomer concentrations (toward end of experiments), amyloid growth is limited by conformational changes resulting in β-strand alignments. At the higher monomer concentrations (initial time points of experiments), growth occurs rapidly by incorporating monomers that have not successfully completed the conformational search. The presence of a fast disordered elongation regime at high monomer concentrations agrees with coarse-grained simulations and theory but has not been detected experimentally before. Our results may be related to the wide range of amyloid folds observed.
Collapse
Affiliation(s)
- Istvan Horvath
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Hannah Welte
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, Kansas.
| | | | | |
Collapse
|
6
|
Vogel K, Bläske T, Nagel MK, Globisch C, Maguire S, Mattes L, Gude C, Kovermann M, Hauser K, Peter C, Isono E. Lipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking. Nat Commun 2022; 13:6897. [PMID: 36371501 PMCID: PMC9653390 DOI: 10.1038/s41467-022-34637-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
The abundance of plasma membrane-resident receptors and transporters has to be tightly regulated by ubiquitin-mediated endosomal degradation for the proper coordination of environmental stimuli and intracellular signaling. Arabidopsis OVARIAN TUMOR PROTEASE (OTU) 11 and OTU12 are plasma membrane-localized deubiquitylating enzymes (DUBs) that bind to phospholipids through a polybasic motif in the OTU domain. Here we show that the DUB activity of OTU11 and OTU12 towards K63-linked ubiquitin is stimulated by binding to lipid membranes containing anionic lipids. In addition, we show that the DUB activity of OTU11 against K6- and K11-linkages is also stimulated by anionic lipids, and that OTU11 and OTU12 can modulate the endosomal degradation of a model cargo and the auxin efflux transporter PIN2-GFP in vivo. Our results suggest that the catalytic activity of OTU11 and OTU12 is tightly connected to their ability to bind membranes and that OTU11 and OTU12 are involved in the fine-tuning of plasma membrane proteins in Arabidopsis.
Collapse
Affiliation(s)
- Karin Vogel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Tobias Bläske
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Marie-Kristin Nagel
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Christoph Globisch
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Shane Maguire
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Lorenz Mattes
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christian Gude
- grid.6936.a0000000123222966School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Kovermann
- grid.9811.10000 0001 0658 7699NMR, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Karin Hauser
- grid.9811.10000 0001 0658 7699Biophysical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, D-78464 Konstanz, Germany
| | - Christine Peter
- grid.9811.10000 0001 0658 7699Computational and Theoretical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Erika Isono
- grid.9811.10000 0001 0658 7699Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| |
Collapse
|
7
|
Abstract
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His3-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pKa of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
Collapse
Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| |
Collapse
|
8
|
Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
A combinatorial approach toward novel functional WW domains based on coiled-coil-mediated reconstitution of split WW domains is presented. As such, an ATP-binding WW domain was found from a 4-by-6 library of N- and C-terminal WW domain fragments.
Collapse
Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Florian R. Häge
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| |
Collapse
|
9
|
Kovermann M, Weininger U, Löw C. Completing the family of human EH domains: Solution structure of the internal EH domain of γ-synergin. Protein Sci 2021; 31:811-821. [PMID: 34967068 PMCID: PMC8927860 DOI: 10.1002/pro.4269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/11/2021] [Accepted: 12/24/2021] [Indexed: 11/05/2022]
Abstract
Eps15 homology (EH) domains are universal interaction domains to establish networks of protein-protein interactions in the cell. These networks mainly coordinate cellular functions including endocytosis, actin remodeling and other intracellular signaling pathways. They are well characterized in structural terms, except for the internal EH domain from human γ-synergin (EHγ). Here, we complete the family of EH domain structures by determining the solution structure of the EHγ domain. The structural ensemble follows the canonical EH domain fold and the identified binding site is similar to other known EH domains. But EHγ differs significantly in the N- and C-terminal regions. The N-terminal α-helix is shortened compared to known homologs, while the C-terminal one is fully formed. A significant proportion of the remaining N- and C-terminal regions are well structured, a feature not seen in other EH domains. Single mutations in both the N-terminal and the C-terminal structured extensions lead to the loss of the distinct three-dimensional fold and turn EHγ into a molten globule like state. Therefore, we propose that the structural extensions in EHγ function as a clamp and are undoubtedly required to maintain its tertiary fold. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, D-22607 Hamburg, Germany Molecular Biology Laboratory (EMBL), Hamburg Unit c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| |
Collapse
|
10
|
Welte H, Sinn P, Kovermann M. Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate. Chembiochem 2021; 22:2973-2980. [PMID: 34390111 PMCID: PMC8596521 DOI: 10.1002/cbic.202100304] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/30/2021] [Indexed: 11/12/2022]
Abstract
The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.
Collapse
Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Pia Sinn
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| |
Collapse
|
11
|
Stuber K, Schneider T, Werner J, Kovermann M, Marx A, Scheffner M. Structural and functional consequences of NEDD8 phosphorylation. Nat Commun 2021; 12:5939. [PMID: 34642328 PMCID: PMC9020517 DOI: 10.1038/s41467-021-26189-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/21/2021] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin (Ub) and Ub-like proteins (Ubls) such as NEDD8 are best known for their function as covalent modifiers of other proteins but they are also themselves subject to post-translational modifications including phosphorylation. While functions of phosphorylated Ub (pUb) have been characterized, the consequences of Ubl phosphorylation remain unclear. Here we report that NEDD8 can be phosphorylated at S65 - the same site as Ub - and that S65 phosphorylation affects the structural dynamics of NEDD8 and Ub in a similar manner. While both pUb and phosphorylated NEDD8 (pNEDD8) can allosterically activate the Ub ligase Parkin, they have different protein interactomes that in turn are distinct from those of unmodified Ub and NEDD8. Among the preferential pNEDD8 interactors are HSP70 family members and we show that pNEDD8 stimulates HSP70 ATPase activity more pronouncedly than unmodified NEDD8. Our findings highlight the general importance of Ub/NEDD8 phosphorylation and support the notion that the function of pUb/pNEDD8 does not require their covalent attachment to other proteins. Both ubiquitin and NEDD8 can be phosphorylated, but the biological role of NEDD8 phosphorylation remains unclear. Here, the authors identify similarities and differences of ubiquitin and NEDD8 phosphorylation, showing that phosphorylated NEDD8 has a distinct interactome and regulates HSP70 proteins.
Collapse
Affiliation(s)
- Katrin Stuber
- Dept. of Biology, University of Konstanz, Konstanz, Germany.,Dept. of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Tobias Schneider
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jill Werner
- Dept. of Biology, University of Konstanz, Konstanz, Germany.,Dept. of Chemistry, University of Konstanz, Konstanz, Germany
| | - Michael Kovermann
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Andreas Marx
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Martin Scheffner
- Dept. of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| |
Collapse
|
12
|
Köhn B, Schwarz P, Wittung-Stafshede P, Kovermann M. Impact of crowded environments on binding between protein and single-stranded DNA. Sci Rep 2021; 11:17682. [PMID: 34480058 PMCID: PMC8417293 DOI: 10.1038/s41598-021-97219-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/20/2021] [Indexed: 11/09/2022] Open
Abstract
The concept of Molecular Crowding depicts the high density of diverse molecules present in the cellular interior. Here, we determine the impact of low molecular weight and larger molecules on binding capacity of single-stranded DNA (ssDNA) to the cold shock protein B (CspB). Whereas structural features of ssDNA-bound CspB are fully conserved in crowded environments as probed by high-resolution NMR spectroscopy, intrinsic fluorescence quenching experiments reveal subtle changes in equilibrium affinity. Kinetic stopped-flow data showed that DNA-to-protein association is significantly retarded independent of choice of the molecule that is added to the solution, but dissociation depends in a nontrivial way on its size and chemical characteristics. Thus, for this DNA-protein interaction, excluded volume effect does not play the dominant role but instead observed effects are dictated by the chemical properties of the crowder. We propose that surrounding molecules are capable of specific modification of the protein's hydration shell via soft interactions that, in turn, tune protein-ligand binding dynamics and affinity.
Collapse
Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Patricia Schwarz
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296, Gothenburg, Sweden
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany. .,Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.
| |
Collapse
|
13
|
Zhou T, Fleming JR, Lange S, Hessel AL, Bogomolovas J, Stronczek C, Grundei D, Ghassemian M, Biju A, Börgeson E, Bullard B, Linke WA, Chen J, Kovermann M, Mayans O. Molecular Characterisation of Titin N2A and Its Binding of CARP Reveals a Titin/Actin Cross-linking Mechanism. J Mol Biol 2021; 433:166901. [PMID: 33647290 PMCID: PMC8052292 DOI: 10.1016/j.jmb.2021.166901] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 12/10/2020] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 12/16/2022]
Abstract
Striated muscle responds to mechanical overload by rapidly up-regulating the expression of the cardiac ankyrin repeat protein, CARP, which then targets the sarcomere by binding to titin N2A in the I-band region. To date, the role of this interaction in the stress response of muscle remains poorly understood. Here, we characterise the molecular structure of the CARP-receptor site in titin (UN2A) and its binding of CARP. We find that titin UN2A contains a central three-helix bundle fold (ca 45 residues in length) that is joined to N- and C-terminal flanking immunoglobulin domains by long, flexible linkers with partial helical content. CARP binds titin by engaging an α-hairpin in the three-helix fold of UN2A, the C-terminal linker sequence, and the BC loop in Ig81, which jointly form a broad binding interface. Mutagenesis showed that the CARP/N2A association withstands sequence variations in titin N2A and we use this information to evaluate 85 human single nucleotide variants. In addition, actin co-sedimentation, co-transfection in C2C12 cells, proteomics on heart lysates, and the mechanical response of CARP-soaked myofibrils imply that CARP induces the cross-linking of titin and actin myofilaments, thereby increasing myofibril stiffness. We conclude that CARP acts as a regulator of force output in the sarcomere that preserves muscle mechanical performance upon overload stress.
Collapse
Affiliation(s)
- Tiankun Zhou
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | - Stephan Lange
- Division of Cardiology, School of Medicine, University of California, San Diego 92093 CA, USA;,Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Anthony L. Hessel
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Julius Bogomolovas
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA;,Department of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Chiara Stronczek
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - David Grundei
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Majid Ghassemian
- Department of Chemistry and Biochemistry, University of California, San Diego 92093 CA, USA
| | - Andrea Biju
- Division of Cardiology, School of Medicine, University of California, San Diego 92093 CA, USA
| | - Emma Börgeson
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Belinda Bullard
- Department of Biology, University of York, York YO10 5DD, UK
| | - Wolfgang A Linke
- Institute of Physiology II, University Hospital Münster, Münster, Germany
| | - Ju Chen
- School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.,Correspondence: Prof. Olga Mayans, Tel: +49 7531 882212, ; Dr. Michael Kovermann, Tel: +49 7531 883801,
| | - Olga Mayans
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany;,Correspondence: Prof. Olga Mayans, Tel: +49 7531 882212, ; Dr. Michael Kovermann, Tel: +49 7531 883801,
| |
Collapse
|
14
|
Abstract
In living organisms, protein folding and function take place in an inhomogeneous, highly crowded environment possessing a concentration of diverse macromolecules of up to 400 g/L. It has been shown that the intracellular environment has a pronounced effect on the stability, dynamics and function of the protein under study, and has for this reason to be considered. However, most protein studies neglect the presence of these macromolecules. Consequently, we probe here the overall thermodynamic stability of cold shock protein B from Bacillus subtilis (BsCspB) in cell lysate. We found that an increase in cell lysate concentration causes a monotonic increase in the thermodynamic stability of BsCspB. This result strongly underlines the importance of considering the biological environment when inherent protein parameters are quantitatively determined. Moreover, we demonstrate that targeted application of 19 F NMR spectroscopy operates as an ideal tool for protein studies performed in complex cellular surroundings.
Collapse
Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity KonstanzResearch School Chemical Biology (KoRS-CB)Universitätsstrasse 1078457KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity KonstanzResearch School Chemical Biology (KoRS-CB)Universitätsstrasse 1078457KonstanzGermany
| |
Collapse
|
15
|
Keßler S, González-Rubio G, Reinalter ER, Kovermann M, Cölfen H. Synthesis of nickel hexacyanoferrate nanocubes with tuneable dimensions via temperature-controlled Ni 2+-citrate complexation. Chem Commun (Camb) 2020; 56:14439-14442. [PMID: 33146182 DOI: 10.1039/d0cc04628k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The citrate-assisted growth of nickel hexacyanoferrate (NiHCF) nanocubes was investigated. Control over the complexation of Ni2+ ions with citrate at different temperatures enabled fine tuning of the nanocrystal (NC) dimensions and their self-assembly into mesocrystals. Our results introduce new concepts towards the synthesis of NiHCF NCs, potentially applicable to other members of the Prussian blue analogues family.
Collapse
Affiliation(s)
- Sascha Keßler
- Physical Chemistry, Department of Chemistry, University of Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany.
| | | | | | | | | |
Collapse
|
16
|
Abstract
The high density of macromolecules affecting proteins due to volume exclusion has been discussed in theory but numerous in vivo experiments cannot be sufficiently understood taking only pure entropic stabilization into account. Here, we show that the thermodynamic stability of a beta barrel protein increases equally at all atomic levels comparing crowded environments with dilute conditions by applying multidimensional high-resolution NMR spectroscopy in a systematic manner. Different crowding agents evoke a pure stabilization cooperatively and do not disturb the surface or integrity of the protein fold. The here developed methodology provides a solid base that can be easily expanded to incorporate e.g. binding partners to recognize functional consequences of crowded conditions. Our results are relevant to research projects targeting soluble proteins in vivo as it can be anticipated that their thermodynamic stability increase comparably and has consequently to be taken into account to coherently understand intracellular processes.
Collapse
Affiliation(s)
- Birgit Köhn
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
- Konstanz Research School Chemical Biology KoRS-CB, University of Konstanz, Universitätsstrasse. 10, 78457, Konstanz, Germany.
| |
Collapse
|
17
|
Siu HW, Heck B, Kovermann M, Hauser K. Template-assisted design of monomeric polyQ models to unravel the unique role of glutamine side chains in disease-related aggregation. Chem Sci 2020; 12:412-426. [PMID: 33552461 PMCID: PMC7863018 DOI: 10.1039/d0sc05299j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 09/24/2020] [Accepted: 10/28/2020] [Indexed: 01/28/2023] Open
Abstract
PolyQ model peptides reveal the effect of individual glutamine side chains on fibril formation.
Expanded polyglutamine (polyQ) sequences cause numerous neurodegenerative diseases which are accompanied by the formation of polyQ fibrils. The unique role of glutamines in the aggregation onset is undoubtedly accepted and a lot structural data of the fibrils have been acquired, however side-chain specific structural dynamics inducing oligomerization are not well understood yet. To analyze spectroscopically the nucleation process, we designed various template-assisted glutamine-rich β-hairpin monomers mimicking the structural motif of a polyQ fibril. In a top-down strategy, we use a template which forms a well-defined stable hairpin in solution, insert polyQ-rich sequences into each strand and monitor the effects of individual glutamines by NMR, CD and IR spectroscopic approaches. The design was further advanced by alternating glutamines with other amino acids (T, W, E, K), thereby enhancing the solubility and increasing the number of cross-strand interacting glutamine side chains. Our spectroscopic studies reveal a decreasing hairpin stability with increased glutamine content and demonstrate the enormous impact of only a few glutamines – far below the disease threshold – to destabilize structure. Furthermore, we could access sub-ms conformational dynamics of monomeric polyQ-rich peptides by laser-excited temperature-jump IR spectroscopy. Both, the increased number of interacting glutamines and higher concentrations are key parameters to induce oligomerization. Concentration-dependent time-resolved IR measurements indicate an additional slower kinetic phase upon oligomer formation. The here presented peptide models enable spectroscopic molecular analyses to distinguish between monomer and oligomer dynamics in the early steps of polyQ fibril formation and in a side-chain specific manner.
Collapse
Affiliation(s)
- Ho-Wah Siu
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Benjamin Heck
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Michael Kovermann
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| | - Karin Hauser
- Department of Chemistry , University of Konstanz , 78457 Konstanz , Germany . ;
| |
Collapse
|
18
|
Welte H, Zhou T, Mihajlenko X, Mayans O, Kovermann M. What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein. Sci Rep 2020; 10:2640. [PMID: 32060391 PMCID: PMC7021800 DOI: 10.1038/s41598-020-59446-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/29/2020] [Indexed: 11/21/2022] Open
Abstract
Fluorine labelling represents one promising approach to study proteins in their native environment due to efficient suppressing of background signals. Here, we systematically probe inherent thermodynamic and structural characteristics of the Cold shock protein B from Bacillus subtilis (BsCspB) upon fluorine labelling. A sophisticated combination of fluorescence and NMR experiments has been applied to elucidate potential perturbations due to insertion of fluorine into the protein. We show that single fluorine labelling of phenylalanine or tryptophan residues has neither significant impact on thermodynamic stability nor on folding kinetics compared to wild type BsCspB. Structure determination of fluorinated phenylalanine and tryptophan labelled BsCspB using X-ray crystallography reveals no displacements even for the orientation of fluorinated aromatic side chains in comparison to wild type BsCspB. Hence we propose that single fluorinated phenylalanine and tryptophan residues used for protein labelling may serve as ideal probes to reliably characterize inherent features of proteins that are present in a highly biological context like the cell.
Collapse
Affiliation(s)
- Hannah Welte
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Tiankun Zhou
- Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Xenia Mihajlenko
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Olga Mayans
- Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.,Department of Biology, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany
| | - Michael Kovermann
- Department of Chemistry, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Graduate School Chemical Biology KoRS-CB, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany. .,Zukunftskolleg, Universitätsstrasse 10, Universität Konstanz, DE-78457, Konstanz, Germany.
| |
Collapse
|
19
|
Schneider T, Berg A, Peter C, Kovermann M. Exploring Artificially Conjugated Ubiquitin Dimers by Means of NMR Spectroscopy and MD Simulations. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
20
|
Wiedenbeck E, Kovermann M, Gebauer D, Cölfen H. Flüssige metastabile Vorstufen von Ibuprofen als Zwischenprodukt der Nukleation in wässriger Lösung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910986] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Eduard Wiedenbeck
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Michael Kovermann
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Denis Gebauer
- Leibniz University of Hannover, Institut für Anorganische Chemie Callinstraße 9 30167 Hannover Deutschland
| | - Helmut Cölfen
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| |
Collapse
|
21
|
Wiedenbeck E, Kovermann M, Gebauer D, Cölfen H. Liquid Metastable Precursors of Ibuprofen as Aqueous Nucleation Intermediates. Angew Chem Int Ed Engl 2019; 58:19103-19109. [PMID: 31556970 PMCID: PMC6972611 DOI: 10.1002/anie.201910986] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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: 08/28/2019] [Indexed: 01/25/2023]
Abstract
The nucleation mechanism of crystals of small organic molecules, postulated based on computer simulations, still lacks experimental evidence. In this study we designed an experimental approach to monitor the early stages of the crystallization of ibuprofen as a model system for small organic molecules. Ibuprofen undergoes liquid–liquid phase separation prior to nucleation. The binodal and spinodal limits of the corresponding liquid–liquid miscibility gap were analyzed and confirmed. An increase in viscosity sustains the kinetic stability of the dense liquid intermediate. Since the distances between ibuprofen molecules within the dense liquid phase are similar to those in the crystal forms, this dense liquid phase is identified as a precursor phase in the nucleation of ibuprofen, in which densification is followed by generation of structural order. This discovery may make it possible to enrich poorly soluble pharmaceuticals beyond classical solubility limitations in aqueous environments.
Collapse
Affiliation(s)
- Eduard Wiedenbeck
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Denis Gebauer
- Leibniz University of Hannover, Institute of Inorganic Chemistry, Callinstraße 9, 30167, Hannover, Germany
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| |
Collapse
|
22
|
Zhao X, Mißun M, Schneider T, Müller F, Lutz J, Scheffner M, Marx A, Kovermann M. Artificially Linked Ubiquitin Dimers Characterised Structurally and Dynamically by NMR Spectroscopy. Chembiochem 2019; 20:1772-1777. [PMID: 30920720 PMCID: PMC6771822 DOI: 10.1002/cbic.201900146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/05/2019] [Indexed: 12/23/2022]
Abstract
As one of the most prevalent post‐translational modifications in eukaryotic cells, ubiquitylation plays vital roles in many cellular processes, such as protein degradation, DNA metabolism, and cell differentiation. Substrate proteins can be tagged by distinct types of polymeric ubiquitin (Ub) chains, which determine the eventual fate of the modified protein. A facile, click chemistry based approach for the efficient generation of linkage‐defined Ub chains, including Ub dimers, was recently established. Within these chains, individual Ub moieties are connected through a triazole linkage, rather than the natural isopeptide bond. Herein, it is reported that the conformation of an artificially K48‐linked Ub dimer resembles that of the natively linked dimer, with respect to structural and dynamic characteristics, as demonstrated by means of high‐resolution NMR spectroscopy. Thus, it is proposed that artificially linked Ub dimers, as generated by this approach, represent potent tools for studying the inherently different properties and functions of distinct Ub chains.
Collapse
Affiliation(s)
- Xiaohui Zhao
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Maite Mißun
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Tobias Schneider
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Franziska Müller
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Joachim Lutz
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Martin Scheffner
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Universität Konstanz, Chemie, Universitätsstrasse 10, 78457, Konstanz, Germany
| |
Collapse
|
23
|
Welte H, Kovermann M. Targeted expression and purification of fluorine labelled cold shock protein B by using an auxotrophic strategy. Protein Expr Purif 2019; 157:86-91. [DOI: 10.1016/j.pep.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/05/2019] [Accepted: 02/05/2019] [Indexed: 01/14/2023]
|
24
|
Zegarra FC, Homouz D, Gasic AG, Babel L, Kovermann M, Wittung-Stafshede P, Cheung MS. Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico. J Phys Chem B 2019; 123:3607-3617. [PMID: 30963769 DOI: 10.1021/acs.jpcb.9b00782] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
Collapse
Affiliation(s)
- Fabio C Zegarra
- Department of Physics , University of Houston , Houston 77204 , United States
| | - Dirar Homouz
- Department of Physics , University of Houston , Houston 77204 , United States.,Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Andrei G Gasic
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| | - Lucas Babel
- Department of Physics , University of Houston , Houston 77204 , United States
| | | | | | - Margaret S Cheung
- Department of Physics , University of Houston , Houston 77204 , United States.,Center for Theoretical Biological Physics , Rice University , Houston 77005 , United States
| |
Collapse
|
25
|
Kovermann M, Stefan A, Castaldo A, Caramia S, Hochkoeppler A. Structural and catalytic insights into HoLaMa, a derivative of Klenow DNA polymerase lacking the proofreading domain. PLoS One 2019; 14:e0215411. [PMID: 30970012 PMCID: PMC6457538 DOI: 10.1371/journal.pone.0215411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/01/2019] [Accepted: 04/01/2019] [Indexed: 11/18/2022] Open
Abstract
We report here on the stability and catalytic properties of the HoLaMa DNA polymerase, a Klenow sub-fragment lacking the 3’-5’ exonuclease domain. HoLaMa was overexpressed in Escherichia coli, and the enzyme was purified by means of standard chromatographic techniques. High-resolution NMR experiments revealed that HoLaMa is properly folded at pH 8.0 and 20°C. In addition, urea induced a cooperative folding to unfolding transition of HoLaMa, possessing an overall thermodynamic stability and a transition midpoint featuring ΔG and CM equal to (15.7 ± 1.9) kJ/mol and (3.5 ± 0.6) M, respectively. When the catalytic performances of HoLaMa were compared to those featured by the Klenow enzyme, we did observe a 10-fold lower catalytic efficiency by the HoLaMa enzyme. Surprisingly, HoLaMa and Klenow DNA polymerases possess markedly different sensitivities in competitive inhibition assays performed to test the effect of single dNTPs.
Collapse
Affiliation(s)
- Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätstraße, Konstanz, Germany
| | - Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- CSGI, University of Firenze, Sesto Fiorentino (Firenze), Italy
| | - Anna Castaldo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sara Caramia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- CSGI, University of Firenze, Sesto Fiorentino (Firenze), Italy
- * E-mail:
| |
Collapse
|
26
|
Abstract
In all intracellular processes, protein structure and dynamics are subject to the influence of macromolecular crowding (MC). Here, the impact of MC agents of different types and sizes on the model protein Bacillus subtilis Cold shock protein B (BsCspB) during both thermal and chemical denaturation have been comprehensively investigated. We consistently reveal a distinct stabilization of BsCspB in a manner dependent on the MC concentration but not on viscosity, polarity, or size of the MC agent used. This general stabilization has been decoded by use of NMR spectroscopy, through monitoring of chemical shift (CS) perturbations and the intramolecular hydrogen‐bonding networks, as well as local protection of amide protons against exchange with solvent protons. Whereas CSs and hydrogen‐bonding networks are not systematically affected in the presence of MC, we detected a pronounced reduction in exchange in loop regions of BsCspB. We conclude that this reduced accessibility of solvent protons is a key parameter for the increases in protein stability seen under MC.
Collapse
Affiliation(s)
- Birgit Köhn
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Research School Chemical Biology (KoRS-CB), Universität Konstanz, Universitätsstrassee 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Research School Chemical Biology (KoRS-CB), Universität Konstanz, Universitätsstrassee 10, 78457, Konstanz, Germany
| |
Collapse
|
27
|
Geitner AJ, Weininger U, Paulsen H, Balbach J, Kovermann M. Structure-Based Insights into the Dynamics and Function of Two-Domain SlpA from Escherichia coli. Biochemistry 2017; 56:6533-6543. [PMID: 29155566 DOI: 10.1021/acs.biochem.7b00786] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SlpA (SlyD-like protein A) comprises two domains, a FK506 binding domain (FKBP fold) of moderate prolyl cis/trans-isomerase activity and an inserted in flap (IF) domain that hosts its chaperone activity. Here we present the nuclear magnetic resonance (NMR) solution structure of apo Escherichia coli SlpA determined by NMR that mirrors the structural properties seen for various SlyD homologues. Crucial structural differences in side-chain orientation arise for F37, which points directly into the hydrophobic core of the active site. It forms a prominent aromatic stacking with F15, one of the key residues for PPIase activity, thus giving a possible explanation for the inherently low PPIase activity of SlpA. The IF domain reveals the highest stability within the FKBP-IF protein family, most likely arising from an aromatic cluster formed by four phenylalanine residues. Both the thermodynamic stability and the PPIase and chaperone activity let us speculate that SlpA is a backup system for homologous bacterial systems under unfavorable conditions.
Collapse
Affiliation(s)
| | - Ulrich Weininger
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany
| | - Hauke Paulsen
- Institut für Physik, Universität Lübeck , Ratzeburger Allee 160, D-23562 Lübeck, Germany
| | - Jochen Balbach
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg , D-06099 Halle (Saale), Germany.,Universität Konstanz , Fachbereich Chemie, Universitätsstraße 10, D-78457 Konstanz, Germany
| |
Collapse
|
28
|
Kahra D, Kovermann M, Wittung-Stafshede P. The C-Terminus of Human Copper Importer Ctr1 Acts as a Binding Site and Transfers Copper to Atox1. Biophys J 2016; 110:95-102. [PMID: 26745413 PMCID: PMC4805863 DOI: 10.1016/j.bpj.2015.11.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 08/26/2015] [Revised: 11/10/2015] [Accepted: 11/10/2015] [Indexed: 11/19/2022] Open
Abstract
Uptake of copper (Cu) ions into human cells is mediated by the plasma membrane protein Ctr1 and is followed by Cu transfer to cytoplasmic Cu chaperones for delivery to Cu-dependent enzymes. The C-terminal cytoplasmic tail of Ctr1 is a 13-residue peptide harboring an HCH motif that is thought to interact with Cu. We here employ biophysical experiments under anaerobic conditions in peptide models of the Ctr1 C-terminus to deduce Cu-binding residues, Cu affinity, and the ability to release Cu to the cytoplasmic Cu chaperone Atox1. Based on NMR assignments and bicinchoninic acid competition experiments, we demonstrate that Cu interacts in a 1:1 stoichiometry with the HCH motif with an affinity, KD, of ∼10(-14) M. Removing either the Cys residue or the two His residues lowers the Cu-peptide affinity, but site specificity is retained. The C-terminal peptide and Atox1 do not interact in solution in the absence of Cu. However, as directly demonstrated at the residue level via NMR spectroscopy, Atox1 readily acquires Cu from the Cu-loaded peptide. We propose that Cu binding to the Ctr1 C-terminal tail regulates Cu transport into the cytoplasm such that the metal ion is only released to high-affinity Cu chaperones.
Collapse
Affiliation(s)
- Dana Kahra
- Chemistry Department, Umeå University, Umeå, Sweden
| | - Michael Kovermann
- Chemistry Department, Umeå University, Umeå, Sweden; Chemistry Department, University of Konstanz, Konstanz, Germany.
| | - Pernilla Wittung-Stafshede
- Chemistry Department, Umeå University, Umeå, Sweden; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
29
|
Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M. Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis. PLoS One 2016; 11:e0163115. [PMID: 27642758 PMCID: PMC5028032 DOI: 10.1371/journal.pone.0163115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/03/2016] [Indexed: 01/08/2023] Open
Abstract
Enzymes have evolved with highly specific values of their catalytic parameters kcat and KM. This poses fundamental biological questions about the selection pressures responsible for evolutionary tuning of these parameters. Here we are address these questions for the enzyme adenylate kinase (Adk) in eukaryotic yeast cells. A plasmid shuffling system was developed to allow quantification of relative fitness (calculated from growth rates) of yeast in response to perturbations of Adk activity introduced through mutations. Biophysical characterization verified that all variants studied were properly folded and that the mutations did not cause any substantial differences to thermal stability. We found that cytosolic Adk is essential for yeast viability in our strain background and that viability could not be restored with a catalytically dead, although properly folded Adk variant. There exist a massive overcapacity of Adk catalytic activity and only 12% of the wild type kcat is required for optimal growth at the stress condition 20°C. In summary, the approach developed here has provided new insights into the evolutionary tuning of kcat for Adk in a eukaryotic organism. The developed methodology may also become useful for uncovering new aspects of active site dynamics and also in enzyme design since a large library of enzyme variants can be screened rapidly by identifying viable colonies.
Collapse
Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | | | - Anders Byström
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
| |
Collapse
|
30
|
Zimmermann S, Pfennig S, Neumann P, Yonus H, Weininger U, Kovermann M, Balbach J, Stubbs MT. High-resolution structures of the D-alanyl carrier protein (Dcp) DltC from Bacillus subtilis reveal equivalent conformations of apo- and holo-forms. FEBS Lett 2015; 589:2283-9. [PMID: 26193422 DOI: 10.1016/j.febslet.2015.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 05/04/2015] [Revised: 07/02/2015] [Accepted: 07/07/2015] [Indexed: 12/18/2022]
Abstract
D-Alanylation of lipoteichoic acids plays an important role in modulating the properties of Gram-positive bacteria cell walls. The D-alanyl carrier protein DltC from Bacillus subtilis has been solved in apo- and two cofactor-modified holo-forms, whereby the entire phosphopantetheine moiety is defined in one. The atomic resolution of the apo-structure allows delineation of alternative conformations within the hydrophobic core of the 78 residue four helix bundle. In contrast to previous reports for a peptidyl carrier protein from a non-ribosomal peptide synthetase, no obvious structural differences between apo- and holo-DltC forms are observed. Solution NMR spectroscopy confirms these findings and demonstrates in addition that the two forms exhibit similar backbone dynamics on the ps-ns and ms timescales.
Collapse
Affiliation(s)
- Stephan Zimmermann
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Sabrina Pfennig
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Piotr Neumann
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Huma Yonus
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany
| | - Ulrich Weininger
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße 7, D-06120 Halle/Saale, Germany
| | - Michael Kovermann
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße 7, D-06120 Halle/Saale, Germany
| | - Jochen Balbach
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Straße 7, D-06120 Halle/Saale, Germany
| | - Milton T Stubbs
- Institut für Biochemie und Biotechnologie, Martin-Luther Universität Halle-Wittenberg, Kurt-Mothes Strasse 3, D-06120 Halle/Saale, Germany.
| |
Collapse
|
31
|
Hoffmann A, Kovermann M, Oberwinkler T, Siedler F, Cortina NS, Balbach J, Oesterhelt D. Novel sulfated phosphoglycolipids from Natronomonas moolapensis. Chem Phys Lipids 2015; 191:8-15. [PMID: 26134137 DOI: 10.1016/j.chemphyslip.2015.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 10/30/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 01/09/2023]
Abstract
Polar lipid pattern determination is often used for the taxonomic classification of halophilic Archaea in addition to a genomic characterization. During the analysis of polar lipid extracts from the recently described haloarchaeon Natrononomonas moolapensis, an unknown glycolipid was detected. Fragmentation patterns observed from preliminary mass spectrometric analysis initially suggested the presence of a sulfo-hexosyl-phosphatidylglycerol. However, by NMR spectroscopy and enzymatic assays the existence of two isomeric molecules with different hexoses (1-(6-sulfo-d-glcp/galf-β1,2-glycero)-phospho-2,3-diphytanylglycerol) could be shown. The structural origin from phosphatidylglycerol distinguishes these glycolipids within Archaea, because all other characterized haloarchaeal glycolipids consist of diphytanylglycerol directly linked to an oligoglycosyl moiety. Now the door is open to investigate the physical and functional consequences of these architectural differences of the head groups.
Collapse
Affiliation(s)
- Andreas Hoffmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Michael Kovermann
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120 Halle, Germany; Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Tanja Oberwinkler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Frank Siedler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Niña Socorro Cortina
- Institute of Organic Chemistry and Chemical Biology, Goethe University, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Jochen Balbach
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120 Halle, Germany
| | - Dieter Oesterhelt
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| |
Collapse
|
32
|
Dinesh DC, Kovermann M, Gopalswamy M, Hellmuth A, Calderón Villalobos LIA, Lilie H, Balbach J, Abel S. Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response. Proc Natl Acad Sci U S A 2015; 112:6230-5. [PMID: 25918389 PMCID: PMC4434759 DOI: 10.1073/pnas.1424077112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The plant hormone auxin activates primary response genes by facilitating proteolytic removal of auxin/indole-3-acetic acid (AUX/IAA)-inducible repressors, which directly bind to transcriptional auxin response factors (ARF). Most AUX/IAA and ARF proteins share highly conserved C-termini mediating homotypic and heterotypic interactions within and between both protein families. The high-resolution NMR structure of C-terminal domains III and IV of the AUX/IAA protein PsIAA4 from pea (Pisum sativum) revealed a globular ubiquitin-like β-grasp fold with homologies to the Phox and Bem1p (PB1) domain. The PB1 domain of wild-type PsIAA4 features two distinct surface patches of oppositely charged amino acid residues, mediating front-to-back multimerization via electrostatic interactions. Mutations of conserved basic or acidic residues on either face suppressed PsIAA4 PB1 homo-oligomerization in vitro and confirmed directional interaction of full-length PsIAA4 in vivo (yeast two-hybrid system). Mixing of oppositely mutated PsIAA4 PB1 monomers enabled NMR mapping of the negatively charged interface of the reconstituted PsIAA4 PB1 homodimer variant, whose stoichiometry (1:1) and equilibrium binding constant (KD ∼ 6.4 μM) were determined by isothermal titration calorimetry. In silico protein-protein docking studies based on NMR and yeast interaction data derived a model of the PsIAA4 PB1 homodimer, which is comparable with other PB1 domain dimers, but indicated considerable differences between the homodimeric interfaces of AUX/IAA and ARF PB1 domains. Our study provides an impetus for elucidating the molecular determinants that confer specificity to complex protein-protein interaction circuits between members of the two central families of transcription factors important to the regulation of auxin-responsive gene expression.
Collapse
Affiliation(s)
| | - Michael Kovermann
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine
| | - Mohanraj Gopalswamy
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine
| | - Antje Hellmuth
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, D-06120 Halle, Germany
| | | | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany; and
| | - Jochen Balbach
- Institute of Physics, Biophysics and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine;
| | - Steffen Abel
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, D-06120 Halle, Germany; Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle, Germany; and Department of Plant Sciences, University of California, Davis, CA 95616
| |
Collapse
|
33
|
Reich S, Kovermann M, Lilie H, Knick P, Geissler R, Golbik RP, Balbach J, Behrens SE. Initiation of RNA synthesis by the hepatitis C virus RNA-dependent RNA polymerase is affected by the structure of the RNA template. Biochemistry 2014; 53:7002-12. [PMID: 25310724 PMCID: PMC4230328 DOI: 10.1021/bi5006656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The
hepatitis C virus (HCV) RNA-dependent RNA polymerase NS5B is
a central enzyme of the intracellular replication of the viral (+)RNA
genome. Here, we studied the individual steps of NS5B-catalyzed RNA
synthesis by a combination of biophysical methods, including real-time
1D 1H NMR spectroscopy. NS5B was found to bind to a nonstructured
and a structured RNA template in different modes. Following NTP binding
and conversion to the catalysis-competent ternary complex, the polymerase
revealed an improved affinity for the template. By monitoring the
folding/unfolding of 3′(−)SL by 1H NMR, the
base pair at the stem’s edge was identified as the most stable
component of the structure. 1H NMR real-time analysis of
NS5B-catalyzed RNA synthesis on 3′(−)SL showed that
a pronounced lag phase preceded the processive polymerization reaction.
The presence of the double-stranded stem with the edge base pair acting
as the main energy barrier impaired RNA synthesis catalyzed by NS5B.
Our observations suggest a crucial role of RNA-modulating factors
in the HCV replication process.
Collapse
Affiliation(s)
- Stefan Reich
- Institute of Biochemistry and Biotechnology, Section of Microbial Biotechnology, ‡Institute of Physics, Section of Biophysics, §Institute of Biochemistry and Biotechnology, Section of Technical Biochemistry, Martin Luther University Halle-Wittenberg , D-06120 Halle/Saale, Germany
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Löw C, Quistgaard EM, Kovermann M, Anandapadamanaban M, Balbach J, Nordlund P. Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A. Biol Chem 2014; 395:881-9. [DOI: 10.1515/hsz-2014-0106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 05/20/2014] [Indexed: 01/04/2023]
Abstract
Abstract
Protein phosphatase 2A (PP2A) is a highly abundant heterotrimeric Ser/Thr phosphatase involved in the regulation of a variety of signaling pathways. The PP2A phosphatase activator (PTPA) is an ATP-dependent activation chaperone, which plays a key role in the biogenesis of active PP2A. The C-terminal tail of the catalytic subunit of PP2A is highly conserved and can undergo a number of posttranslational modifications that serve to regulate the function of PP2A. Here we have studied structurally the interaction of PTPA with the conserved C-terminal tail of the catalytic subunit carrying different posttranslational modifications. We have identified an additional interaction site for the invariant C-terminal tail of the catalytic subunit on PTPA, which can be modulated via posttranslational modifications. We show that phosphorylation of Tyr307PP2A-C or carboxymethylation of Leu309PP2A-C abrogates or diminishes binding of the C-terminal tail, whereas phosphorylation of Thr304PP2A-C is of no consequence. We suggest that the invariant C-terminal residues of the catalytic subunit can act as affinity enhancer for different PP2A interaction partners, including PTPA, and a different ‘code’ of posttranslational modifications can favour interactions to one subunit over others.
Collapse
|
35
|
Kovermann M, Schmid FX, Balbach J. Molecular function of the prolyl cis/trans isomerase and metallochaperone SlyD. Biol Chem 2014; 394:965-75. [PMID: 23585180 DOI: 10.1515/hsz-2013-0137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 03/26/2013] [Indexed: 11/15/2022]
Abstract
SlyD is a bacterial two-domain protein that functions as a molecular chaperone, a prolyl cis/trans isomerase, and a nickel-binding protein. This review summarizes recent findings about the molecular enzyme mechanism of SlyD. The chaperone function located in one domain of SlyD is involved in twin-arginine translocation and increases the catalytic efficiency of the prolyl cis/trans isomerase domain in protein folding by two orders of magnitude. The C-terminal tail of SlyD binds Ni2+ ions and supplies them for the maturation of [NiFe] hydrogenases. A combined biochemical and biophysical analysis revealed the molecular basis of the delicate interplay of the different domains of SlyD for optimal function.
Collapse
Affiliation(s)
- Michael Kovermann
- Institut für Physik, Biophysik, und Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine MZP, Martin-Luther Universität Halle-Wittenberg, D-06120 Halle, Germany
| | | | | |
Collapse
|
36
|
Kovermann M, Balbach J. Dynamic control of the prolyl isomerase function of the dual-domain SlyD protein. Biophys Chem 2013; 171:16-23. [DOI: 10.1016/j.bpc.2012.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/22/2012] [Accepted: 11/22/2012] [Indexed: 12/13/2022]
|
37
|
Kovermann M, Saalwächter K, Chassé W. Real-Time Observation of Polymer Network Formation by Liquid- and Solid-State NMR Revealing Multistage Reaction Kinetics. J Phys Chem B 2012; 116:7566-74. [DOI: 10.1021/jp302745a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Kovermann
- Institut für Physik—Biophysik, Martin-Luther-Universität Halle-Wittenberg,
Betty-Heimann-Str. 7, D-06120 Halle, Germany
| | - Kay Saalwächter
- Institut für Physik—NMR, Martin-Luther-Universität Halle-Wittenberg,
Betty-Heimann-Str. 7, D-06120 Halle, Germany
| | - Walter Chassé
- Institut für Physik—NMR, Martin-Luther-Universität Halle-Wittenberg,
Betty-Heimann-Str. 7, D-06120 Halle, Germany
| |
Collapse
|
38
|
Löw C, Jegerschöld C, Kovermann M, Moberg P, Nordlund P. Optimisation of over-expression in E. coli and biophysical characterisation of human membrane protein synaptogyrin 1. PLoS One 2012; 7:e38244. [PMID: 22675529 PMCID: PMC3365889 DOI: 10.1371/journal.pone.0038244] [Citation(s) in RCA: 19] [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: 01/17/2012] [Accepted: 05/02/2012] [Indexed: 11/25/2022] Open
Abstract
Progress in functional and structural studies of integral membrane proteins (IMPs) is lacking behind their soluble counterparts due to the great challenge in producing stable and homogeneous IMPs. Low natural abundance, toxicity when over-expressed and potential lipid requirements of IMPs are only a few reasons for the limited progress. Here, we describe an optimised workflow for the recombinant over-expression of the human tetraspan vesicle protein (TVP) synaptogyrin in Escherichia coli and its biophysical characterisation. TVPs are ubiquitous and abundant components of vesicles. They are believed to be involved in various aspects of the synaptic vesicle cycle, including vesicle biogenesis, exocytosis and endocytotic recycling. Even though TVPs are found in most cell types, high-resolution structural information for this class of membrane proteins is still missing. The optimisation of the N-terminal sequence of the gene together with the usage of the recently developed Lemo21(DE3) strain which allows the balancing of the translation with the membrane insertion rate led to a 50-fold increased expression rate compared to the classical BL21(DE3) strain. The protein was soluble and stable in a variety of mild detergents and multiple biophysical methods confirmed the folded state of the protein. Crosslinking experiments suggest an oligomeric architecture of at least four subunits. The protein stability is significantly improved in the presence of cholesteryl hemisuccinate as judged by differential light scattering. The approach described here can easily be adapted to other eukaryotic IMPs.
Collapse
Affiliation(s)
- Christian Löw
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (CL); (PN)
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michael Kovermann
- Institut für Physik, Biophysik, Martin-Luther-Universität Halle-Wittenberg, Saale, Germany
| | - Per Moberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (CL); (PN)
| |
Collapse
|
39
|
Haupt C, Weininger U, Kovermann M, Balbach J. Local and Coupled Thermodynamic Stability of the Two-Domain and Bifunctional Enzyme SlyD from Escherichia coli. Biochemistry 2011; 50:7321-9. [DOI: 10.1021/bi2000627] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Caroline Haupt
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Ulrich Weininger
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Jochen Balbach
- Institut für Physik,
Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
- Mitteldeutsches Zentrum für
Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| |
Collapse
|
40
|
Kovermann M, Zierold R, Haupt C, Löw C, Balbach J. NMR relaxation unravels interdomain crosstalk of the two domain prolyl isomerase and chaperone SlyD. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2011; 1814:873-81. [DOI: 10.1016/j.bbapap.2011.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/18/2011] [Accepted: 03/25/2011] [Indexed: 11/26/2022]
|
41
|
Haupt C, Patzschke R, Weininger U, Gröger S, Kovermann M, Balbach J. Transient Enzyme–Substrate Recognition Monitored by Real-Time NMR. J Am Chem Soc 2011; 133:11154-62. [DOI: 10.1021/ja2010048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Caroline Haupt
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Rica Patzschke
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Ulrich Weininger
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Stefan Gröger
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Michael Kovermann
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Jochen Balbach
- Institut für Physik, Biophysik and ‡Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
| |
Collapse
|
42
|
Kahra D, Kovermann M, Löw C, Hirschfeld V, Haupt C, Balbach J, Hübner CG. Conformational plasticity and dynamics in the generic protein folding catalyst SlyD unraveled by single-molecule FRET. J Mol Biol 2011; 411:781-90. [PMID: 21596048 DOI: 10.1016/j.jmb.2011.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Revised: 04/29/2011] [Accepted: 05/02/2011] [Indexed: 11/15/2022]
Abstract
The relation between conformational dynamics and chemistry in enzyme catalysis recently has received increasing attention. While, in the past, the mechanochemical coupling was mainly attributed to molecular motors, nowadays, it seems that this linkage is far more general. Single-molecule fluorescence methods are perfectly suited to directly evidence conformational flexibility and dynamics. By labeling the enzyme SlyD, a member of peptidyl-prolyl cis-trans isomerases of the FK506 binding protein type with an inserted chaperone domain, with donor and acceptor fluorophores for single-molecule fluorescence resonance energy transfer, we directly monitor conformational flexibility and conformational dynamics between the chaperone domain and the FK506 binding protein domain. We find a broad distribution of distances between the labels with two main maxima, which we attribute to an open conformation and to a closed conformation of the enzyme. Correlation analysis demonstrates that the conformations exchange on a rate in the 100 Hz range. With the aid from Monte Carlo simulations, we show that there must be conformational flexibility beyond the two main conformational states. Interestingly, neither the conformational distribution nor the dynamics is significantly altered upon binding of substrates or other known binding partners. Based on these experimental findings, we propose a model where the conformational dynamics is used to search the conformation enabling the chemical step, which also explains the remarkable substrate promiscuity connected with a high efficiency of this class of peptidyl-prolyl cis-trans isomerases.
Collapse
Affiliation(s)
- Dana Kahra
- Institut für Physik, Universität zu Lübeck, Ratzeburger Allee 160, D-23564 Lübeck, Germany
| | | | | | | | | | | | | |
Collapse
|
43
|
Dahse K, Garvey M, Kovermann M, Vogel A, Balbach J, Fändrich M, Fahr A. DHPC strongly affects the structure and oligomerization propensity of Alzheimer's Aβ(1-40) peptide. J Mol Biol 2010; 403:643-59. [PMID: 20851128 DOI: 10.1016/j.jmb.2010.09.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/01/2010] [Accepted: 09/08/2010] [Indexed: 02/03/2023]
Abstract
Alzheimer's disease (AD) is thought to depend on the deleterious action of amyloid fibrils or oligomers derived from β-amyloid (Aβ) peptide. Out of various known Aβ alloforms, the 40-residue peptide Aβ(1-40) occurs at highest concentrations inside the brains of AD patients. Its aggregation properties critically depend on lipids, and it was thus proposed that lipids could play a major role in AD. To better understand their possible effects on the structure of Aβ and on the ability of this peptide to form potentially detrimental amyloid structures, we here analyze the interactions between Aβ(1-40) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC). DHPC has served, due to its controlled properties, as a major model system for studying general lipid properties. Here, we show that DHPC concentrations of 8 mM or higher exert dramatic effects on the conformation of soluble Aβ(1-40) peptide and induce the formation of β-sheet structure at high levels. By contrast, we find that DHPC concentrations well below the critical micelle concentration present no discernible effect on the conformation of soluble Aβ, although they substantially affect the peptide's oligomerization and fibrillation kinetics. These data imply that subtle lipid-peptide interactions suffice in controlling the overall aggregation properties and drastically accelerate, or delay, the fibrillation kinetics of Aβ peptide in near-physiological buffer solutions.
Collapse
Affiliation(s)
- Kirsten Dahse
- Department of Pharmaceutical Technology, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | | | | | | | | | | | | |
Collapse
|
44
|
Weininger U, Jakob RP, Kovermann M, Balbach J, Schmid FX. The prolyl isomerase domain of PpiD from Escherichia coli shows a parvulin fold but is devoid of catalytic activity. Protein Sci 2010; 19:6-18. [PMID: 19866485 DOI: 10.1002/pro.277] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PpiD is a periplasmic folding helper protein of Escherichia coli. It consists of an N-terminal helix that anchors PpiD in the inner membrane near the SecYEG translocon, followed by three periplasmic domains. The second domain (residues 264-357) shows homology to parvulin-like prolyl isomerases. This domain is a well folded, stable protein and follows a simple two-state folding mechanism. In its solution structure, as determined by NMR spectroscopy, it resembles most closely the first parvulin domain of the SurA protein, which resides in the periplasm of E. coli as well. A previously reported prolyl isomerase activity of PpiD could not be reproduced when using improved protease-free peptide assays or assays with refolding proteins as substrates. The parvulin domain of PpiD interacts, however, with a proline-containing tetrapeptide, and the binding site, as identified by NMR resonance shift analysis, colocalized with the catalytic sites of other parvulins. In its structure, the parvulin domain of PpiD resembles most closely the inactive first parvulin domain of SurA, which is part of the chaperone unit of this protein and presumably involved in substrate recognition.
Collapse
Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Biophysik, and Mitteldeutsches Zentrum für Struktur und Dynamik der Proteine (MZP), Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle(Saale), Germany
| | | | | | | | | |
Collapse
|
45
|
Weininger U, Haupt C, Schweimer K, Graubner W, Kovermann M, Brüser T, Scholz C, Schaarschmidt P, Zoldak G, Schmid FX, Balbach J. NMR solution structure of SlyD from Escherichia coli: spatial separation of prolyl isomerase and chaperone function. J Mol Biol 2009; 387:295-305. [PMID: 19356587 DOI: 10.1016/j.jmb.2009.01.034] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 10/21/2022]
Abstract
SlyD (sensitive to lysis D) is a putative folding helper from the bacterial cytosol and harbors prolyl isomerase and chaperone activities. We determined the solution NMR structure of a truncated version of SlyD (1-165) from Escherichia coli (SlyD*) that lacks the presumably unstructured C-terminal tail. SlyD* consists of two well-separated domains: the FKBP domain, which harbors the prolyl isomerase activity, and the insert-in-flap (IF) domain, which harbors the chaperone activity. The IF domain is inserted into a loop of the FKBP domain near the prolyl isomerase active site. The NMR structure of SlyD* showed no distinct orientation of the two domains relative to each other. In the FKBP domain, Tyr68 points into the active site, which might explain the lowered intrinsic prolyl isomerase activity and the much lower FK506 binding affinity of the protein compared with archetype human FKBP12 (human FK506 binding protein with 12 kDa). The thermodynamics and kinetics of substrate binding by SlyD* were quantified by fluorescence resonance energy transfer. NMR titration experiments revealed that the IF domain recognizes and binds unfolded or partially folded proteins and peptides. Insulin aggregation is markedly slowed by SlyD* as evidenced by two-dimensional NMR spectroscopy in real time, probably due to SlyD* binding to denatured insulin. The capacity of the IF domain to establish an initial encounter-collision complex, together with the flexible orientation of the two interacting domains, makes SlyD* a very powerful catalyst of protein folding.
Collapse
Affiliation(s)
- Ulrich Weininger
- Institut für Physik, Fachgruppe Biophysik, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle (Saale), Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Pornsuriyasak P, Vetter C, Kaeothip S, Kovermann M, Balbach J, Steinborn D, Demchenko AV. Coordination chemistry approach to the long-standing challenge of stereocontrolled chemical glycosylation. Chem Commun (Camb) 2009:6379-81. [DOI: 10.1039/b903942b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
47
|
Reichert D, Kovermann M, Hunter N, Hughes D, Pascui O, Belton P. Slow dynamics in glassy methyl α-l-rhamnopyranoside studied by 1D NMR exchange experiments. Phys Chem Chem Phys 2008; 10:542-9. [DOI: 10.1039/b711113d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|