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König I, Soranno A, Nettels D, Schuler B. Impact of In‐Cell and In‐Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Iwo König
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics Center for Science and Engineering of Living Systems (CSELS) Washington University in St. Louis St. Louis USA
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics University of Zurich Winterthurerstrasse 190 8057 Zürich Switzerland
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2
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König I, Soranno A, Nettels D, Schuler B. Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein. Angew Chem Int Ed Engl 2021; 60:10724-10729. [PMID: 33587794 DOI: 10.1002/anie.202016804] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/08/2021] [Indexed: 01/23/2023]
Abstract
The conformations and dynamics of proteins can be influenced by crowding from the large concentrations of macromolecules within cells. Intrinsically disordered proteins (IDPs) exhibit chain compaction in crowded solutions in vitro, but no such effects were observed in cultured mammalian cells. Here, to increase intracellular crowding, we reduced the cell volume by hyperosmotic stress and used an IDP as a crowding sensor for in-cell single-molecule spectroscopy. In these more crowded cells, the IDP exhibits compaction, slower chain dynamics, and much slower translational diffusion, indicating a pronounced concentration and length-scale dependence of crowding. In vitro, these effects cannot be reproduced with small but only with large polymeric crowders. The observations can be explained with polymer theory and depletion interactions and indicate that IDPs can diffuse much more efficiently through a crowded cytosol than a globular protein of similar dimensions.
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Affiliation(s)
- Iwo König
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, USA
| | - Daniel Nettels
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry and Department of Physics, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
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3
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Zhang W, Bertinetti L, Blank KG, Dimova R, Gao C, Schneck E, Fratzl P. Spatiotemporal Measurement of Osmotic Pressures by FRET Imaging. Angew Chem Int Ed Engl 2021; 60:6488-6495. [PMID: 33188706 PMCID: PMC7986915 DOI: 10.1002/anie.202011983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
Osmotic pressures (OPs) play essential roles in biological processes and numerous technological applications. However, the measurement of OP in situ with spatiotemporal resolution has not been achieved so far. Herein, we introduce a novel kind of OP sensor based on liposomes loaded with water-soluble fluorescent dyes exhibiting resonance energy transfer (FRET). The liposomes experience volume changes in response to OP due to water outflux. The FRET efficiency depends on the average distance between the entrapped dyes and thus provides a direct measure of the OP surrounding each liposome. The sensors exhibit high sensitivity to OP in the biologically relevant range of 0-0.3 MPa in aqueous solutions of salt, small organic molecules, and macromolecules. With the help of FRET microscopy, we demonstrate the feasibility of spatiotemporal OP imaging, which can be a promising new tool to investigate phenomena involving OPs and their dynamics in biology and technology.
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Affiliation(s)
- Wenbo Zhang
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Luca Bertinetti
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Kerstin G. Blank
- Mechano(bio)chemistryMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Rumiana Dimova
- Department of Theory & Bio-SystemsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and FunctionalizationDepartment of Polymer Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Emanuel Schneck
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
- Department of PhysicsTechnische Universität Darmstadt64289DarmstadtGermany
| | - Peter Fratzl
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
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4
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Zhang W, Bertinetti L, Blank KG, Dimova R, Gao C, Schneck E, Fratzl P. Spatiotemporal Measurement of Osmotic Pressures by FRET Imaging. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Wenbo Zhang
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Luca Bertinetti
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Kerstin G. Blank
- Mechano(bio)chemistry Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Rumiana Dimova
- Department of Theory & Bio-Systems Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization Department of Polymer Science and Engineering Zhejiang University Hangzhou 310027 China
| | - Emanuel Schneck
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
- Department of Physics Technische Universität Darmstadt 64289 Darmstadt Germany
| | - Peter Fratzl
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
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5
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Hämisch B, Pollak R, Ebbinghaus S, Huber K. Self-Assembly of Pseudo-Isocyanine Chloride as a Sensor for Macromolecular Crowding In Vitro and In Vivo. Chemistry 2020; 26:7041-7050. [PMID: 32154954 PMCID: PMC7317963 DOI: 10.1002/chem.202000113] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/20/2020] [Indexed: 11/21/2022]
Abstract
Pseudo‐isocyanine chloride (PIC) is a cationic dyestuff that exhibits self‐assembly in aqueous solution, promoted either by increasing the PIC concentration or by decreasing the temperature. PIC‐aggregates exhibit a characteristic and sharp absorption band as well as a fluorescence band at a wavelength of 573 nm making PIC an interesting candidate to analyze the self‐assembly process in various environments. The present work developed PIC‐based, synthetic model systems, suitable to investigate how macromolecular crowding influences self‐assembly processes. Four synthetic additives were used as potential crowders: Triethylene glycol (TEG), polyethylene glycol (PEG), Ficoll 400 as a highly branched polysaccharide, and sucrose corresponding to the monomeric unit of Ficoll. Combined UV/Vis spectroscopy and time‐resolved light scattering revealed a strong impact of crowding based on excluded volume effects only for Ficoll 400. Sucrose had hardly any influence on the self‐assembly of PIC and PEG and TEG impeded the PIC self‐assembly. Development of such a PIC based model system led over to in‐cell experiments. HeLa cells were infiltrated with PIC solutions well below the aggregation threshold in the infiltrating solution. In the cellular environment, PIC was exposed to a significant crowding and immediately started to aggregate. As was demonstrated by fluorescence imaging, the extent of aggregation can be modulated by exposing the cells to salt‐induced osmotic stress. The results suggest future use of such a system as a sensor for the analysis of in vitro and in vivo crowding effects on self‐assembly processes.
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Affiliation(s)
- Benjamin Hämisch
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
| | - Roland Pollak
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Simon Ebbinghaus
- Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany
| | - Klaus Huber
- Physical Chemistry, Paderborn University, 33098, Paderborn, Germany
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6
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Sikkema HR, Gaastra BF, Pols T, Poolman B. Cell Fuelling and Metabolic Energy Conservation in Synthetic Cells. Chembiochem 2019; 20:2581-2592. [PMID: 31381223 DOI: 10.1002/cbic.201900398] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Indexed: 12/14/2022]
Abstract
We are aiming for a blue print for synthesizing (moderately complex) subcellular systems from molecular components and ultimately for constructing life. However, without comprehensive instructions and design principles, we rely on simple reaction routes to operate the essential functions of life. The first forms of synthetic life will not make every building block for polymers de novo according to complex pathways, rather they will be fed with amino acids, fatty acids and nucleotides. Controlled energy supply is crucial for any synthetic cell, no matter how complex. Herein, we describe the simplest pathways for the efficient generation of ATP and electrochemical ion gradients. We have estimated the demand for ATP by polymer synthesis and maintenance processes in small cell-like systems, and we describe circuits to control the need for ATP. We also present fluorescence-based sensors for pH, ionic strength, excluded volume, ATP/ADP, and viscosity, which allow the major physicochemical conditions inside cells to be monitored and tuned.
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Affiliation(s)
- Hendrik R Sikkema
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Tjeerd Pols
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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7
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Xie S, Wong AYH, Chen S, Tang BZ. Fluorogenic Detection and Characterization of Proteins by Aggregation‐Induced Emission Methods. Chemistry 2019; 25:5824-5847. [DOI: 10.1002/chem.201805297] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Sheng Xie
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Alex Y. H. Wong
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Sijie Chen
- Ming Wai Lau Centre for Reparative MedicineKarolinska Institutet Hong Kong S.A.R. China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National, Engineering Research Center for Tissue Restoration and ReconstructionInstitute of Molecular Functional MaterialsState Key Laboratory of NeuroscienceDivision of Biomedical Engineering, and Division of Life Science, HKUST-Shenzhen Research InstituteThe Hong Kong University of Science and Technology, Kowloon Hong Kong S.A.R. China
- NSFC Center for Luminescence from Molecular AggregatesSCUT-HKUST Joint Research InstituteState Key Laboratory of Luminescent Materials and DevicesSouth China University of Technology Guangzhou 510640 P.R. China
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8
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Wangler A, Böttcher D, Hüser A, Sadowski G, Held C. Prediction and Experimental Validation of Co-Solvent Influence on Michaelis Constants: A Thermodynamic Activity-Based Approach. Chemistry 2018; 24:16418-16425. [DOI: 10.1002/chem.201803573] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Anton Wangler
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Dominik Böttcher
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Aline Hüser
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Gabriele Sadowski
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Christoph Held
- Department of Biochemical and Chemical Engineering; Laboratory of Thermodynamics; TU Dortmund University; Emil-Figge-Str. 70 44227 Dortmund Germany
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9
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Davis CM, Gruebele M. Non-Steric Interactions Predict the Trend and Steric Interactions the Offset of Protein Stability in Cells. Chemphyschem 2018; 19:2290-2294. [PMID: 29877016 DOI: 10.1002/cphc.201800534] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 01/15/2023]
Abstract
Although biomolecules evolved to function in the cell, most biochemical assays are carried out in vitro. In-cell studies highlight how steric and non-steric interactions modulate protein folding and interactions. VlsE and PGK present two extremes of chemical behavior in the cell: the extracellular protein VlsE is destabilized in eukaryotic cells, whereas the cytoplasmic protein PGK is stabilized. VlsE and PGK are benchmarks in a systematic series of solvation environments to distinguish contributions from non-steric and steric interactions to protein stability, compactness, and folding rate by comparing cell lysate, a crowding agent, ionic buffer and lysate buffer with in-cell results. As anticipated, crowding stabilizes proteins, causes compaction, and can speed folding. Protein flexibility determines its sensitivity to steric interactions or crowding. Non-steric interactions alone predict in-cell stability trends, while crowding provides an offset towards greater stabilization. We suggest that a simple combination of lysis buffer and Ficoll is an effective new in vitro mimic of the intracellular environment on protein folding and stability.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States.,Department of Chemistry and Department of Physics, University of Illinois at Urbana-Champaign Urbana, Illinois, 61801, United States
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10
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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11
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Gomez D, Klumpp S. Facilitated diffusion in the presence of obstacles on the DNA. Phys Chem Chem Phys 2017; 18:11184-92. [PMID: 27048915 DOI: 10.1039/c6cp00307a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Biological functions of DNA depend on the sequence-specific binding of DNA-binding proteins to their corresponding binding sites. Binding of these proteins to their binding sites occurs through a facilitated diffusion process that combines three-dimensional diffusion in the cytoplasm with one-dimensional diffusion (sliding) along the DNA. In this work, we use a lattice model of facilitated diffusion to study how the dynamics of binding of a protein to a specific site (e.g., binding of an RNA polymerase to a promoter or of a transcription factor to its operator site) is affected by the presence of other proteins bound to the DNA, which act as 'obstacles' in the sliding process. Different types of these obstacles with different dynamics are implemented. While all types impair facilitated diffusion, the extent of the hindrance depends on the type of obstacle. As a consequence of hindrance by obstacles, more excursions into the cytoplasm are required for optimal target binding compared to the case without obstacles.
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Affiliation(s)
- David Gomez
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany.
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany. and Institute for Nonlinear Dynamics, Georg-August University Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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12
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Heyden M, Ebbinghaus S, Winter R. Das Innere der Zelle: Ein komplexes Lösungsmittel. CHEM UNSERER ZEIT 2017. [DOI: 10.1002/ciuz.201700777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Schummel PH, Gao M, Winter R. Modulation of the Polymerization Kinetics of α/β-Tubulin by Osmolytes and Macromolecular Crowding. Chemphyschem 2016; 18:189-197. [DOI: 10.1002/cphc.201601032] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Paul Hendrik Schummel
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Mimi Gao
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Roland Winter
- Faculty of Chemistry and Chemical Biology, Physical Chemistry-Biophysical Chemistry; TU Dortmund University; Otto-Hahn-Str. 4a 44227 Dortmund Germany
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14
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Patra S, Erwin N, Winter R. Translational Dynamics of Lipidated Ras Proteins in the Presence of Crowding Agents and Compatible Osmolytes. Chemphyschem 2016; 17:2164-9. [PMID: 27028423 DOI: 10.1002/cphc.201600179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Indexed: 11/07/2022]
Abstract
Ras proteins are small GTPases and are involved in transmitting signals that control cell growth, differentiation, and proliferation. Since the cell cytoplasm is crowded with different macromolecules, understanding the translational dynamics of Ras proteins in crowded environments is crucial to yielding deeper insight into their reactivity and function. Herein, the translational dynamics of lipidated N-Ras and K-Ras4B is studied in the bulk and in the presence of a macromolecular crowder (Ficoll) and the compatible osmolyte and microcrowder sucrose by fluorescence correlation spectroscopy. The results reveal that N-Ras forms dimers due to the presence of its lipid moiety in the hypervariable region, whereas K-Ras4B remains in its monomeric form in the bulk. Addition of a macromolecular crowding agent gradually favors clustering of the Ras proteins. In 20 wt % Ficoll N-Ras forms trimers and K-Ras4B dimers. Concentrations of sucrose up to 10 wt % foster formation of N-Ras trimers and K-Ras dimers as well. The results can be rationalized in terms of the excluded-volume effect, which enhances the association of the proteins, and, for the higher concentrations, by limited-hydration conditions. The results of this study shed new light on the association state of these proteins in a crowded environment. This is of particular interest for the Ras proteins, because their solution state-monomeric or clustered-influences their membrane-partitioning behavior and their interplay with cytosolic interaction partners.
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Affiliation(s)
- Satyajit Patra
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Nelli Erwin
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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15
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. Faltung einer RNA-Haarnadel in der dicht gedrängten Zelle. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mimi Gao
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - David Gnutt
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Axel Orban
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Bettina Appel
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Francesco Righetti
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Roland Winter
- Lehrstuhl für Physikalische Chemie I; TU Dortmund; Otto-Hahn-Str. 4a 44227 Dortmund Deutschland
| | - Franz Narberhaus
- Biologie der Mikroorganismen; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
| | - Sabine Müller
- Institut für Biochemie; Ernst-Moritz-Arndt-Universität Greifswald; Felix-Hausdorff-Str. 4 17487 Greifswald Deutschland
| | - Simon Ebbinghaus
- Lehrstuhl für Physikalische Chemie II; Ruhr-Universität Bochum; Universitätsstr. 150 44801 Bochum Deutschland
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16
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Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. RNA Hairpin Folding in the Crowded Cell. Angew Chem Int Ed Engl 2016; 55:3224-8. [PMID: 26833452 PMCID: PMC4762321 DOI: 10.1002/anie.201510847] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Indexed: 12/02/2022]
Abstract
Precise secondary and tertiary structure formation is critically important for the cellular functionality of ribonucleic acids (RNAs). RNA folding studies were mainly conducted in vitro, without the possibility of validating these experiments inside cells. Here, we directly resolve the folding stability of a hairpin‐structured RNA inside live mammalian cells. We find that the stability inside the cell is comparable to that in dilute physiological buffer. On the contrary, the addition of in vitro artificial crowding agents, with the exception of high‐molecular‐weight PEG, leads to a destabilization of the hairpin structure through surface interactions and reduction in water activity. We further show that RNA stability is highly variable within cell populations as well as within subcellular regions of the cytosol and nucleus. We conclude that inside cells the RNA is subject to (localized) stabilizing and destabilizing effects that lead to an on average only marginal modulation compared to diluted buffer.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - David Gnutt
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Axel Orban
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Bettina Appel
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Francesco Righetti
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Roland Winter
- Physical Chemistry I, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Sabine Müller
- Institute for Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Simon Ebbinghaus
- Physical Chemistry II, Ruhr-Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
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17
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Gao M, Winter R. Kinetic Insights into the Elongation Reaction of Actin Filaments as a Function of Temperature, Pressure, and Macromolecular Crowding. Chemphyschem 2015; 16:3681-6. [PMID: 26420566 DOI: 10.1002/cphc.201500633] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Indexed: 11/08/2022]
Abstract
Actin polymerization is an essential process in eukaryotic cells that provides a driving force for motility and mechanical resistance for cell shape. By using preformed gelsolin-actin nuclei and applying stopped-flow methodology, we quantitatively studied the elongation kinetics of actin filaments as a function of temperature and pressure in the presence of synthetic and protein crowding agents. We show that the association of actin monomers to the pointed end of double-stranded helical actin filaments (F-actin) proceeds via a transition state that requires an activation energy of 56 kJ mol(-1) for conformational and hydration rearrangements, but exhibits a negligible activation volume, pointing to a compact transition state that is devoid of packing defects. Macromolecular crowding causes acceleration of the F-actin elongation rate and counteracts the deteriorating effect of pressure. The results shed new light on the combined effect of these parameters on the polymerization process of actin, and help us understand the temperature and pressure sensitivity of actin polymerization under extreme conditions.
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Affiliation(s)
- Mimi Gao
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227, Dortmund, Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology, Biophysical Chemistry, TU Dortmund University, Otto-Hahn-Str. 6, 44227, Dortmund, Germany.
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