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Jöhr R, Bauer MS, Schendel LC, Kluger C, Gaub HE. Dronpa: A Light-Switchable Fluorescent Protein for Opto-Biomechanics. NANO LETTERS 2019; 19:3176-3181. [PMID: 30912662 DOI: 10.1021/acs.nanolett.9b00639] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Since the development of the green fluorescent protein, fluorescent proteins (FP) are indispensable tools in molecular biology. Some FPs change their structure under illumination, which affects their interaction with other biomolecules or proteins. In particular, FPs that are able to form switchable dimers became an important tool in the field of optogenetics. They are widely used for the investigation of signaling pathways, the control of surface recruitment, as well as enzyme and gene regulation. However, optogenetics did not yet develop tools for the investigation of biomechanical processes. This could be leveraged if one could find a light-switchable FP dimer that is able to withstand sufficiently high forces. In this work, we measure the rupture force of the switchable interface in pdDronpa1.2 dimers using atomic force microscopy-based single molecule force spectroscopy. The most probable dimer rupture force amounts to around 80 pN at a pulling speed of 1600 nm/s. After switching of the dimer using illumination at 488 nm, there are hardly any measurable interface interactions, which indicates the successful dissociation of the dimers. Hence this Dronpa dimer could expand the current toolbox in optogenetics with new opto-biomechanical applications like the control of tension in adhesion processes.
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Affiliation(s)
- Res Jöhr
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , Munich 80799 , Germany
| | - Magnus S Bauer
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , Munich 80799 , Germany
| | - Leonard C Schendel
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , Munich 80799 , Germany
| | - Carleen Kluger
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , Munich 80799 , Germany
| | - Hermann E Gaub
- Lehrstuhl für Angewandte Physik and Center for Nanoscience , Ludwig-Maximilians-Universität , Munich 80799 , Germany
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Exploring the Sulfatase 1 Catch Bond Free Energy Landscape using Jarzynski's Equality. Sci Rep 2018; 8:16849. [PMID: 30442949 PMCID: PMC6237999 DOI: 10.1038/s41598-018-35120-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/25/2018] [Indexed: 01/29/2023] Open
Abstract
In non-covalent biological adhesion, molecular bonds commonly exhibit a monotonously decreasing life time when subjected to tensile forces (slip bonds). In contrast, catch bonds behave counter intuitively, as they show an increased life time within a certain force interval. To date only a hand full of catch bond displaying systems have been identified. In order to unveil their nature, a number of structural and phenomenological models have been introduced. Regardless of the individual causes for catch bond behavior, it appears evident that the free energy landscapes of these interactions bear more than one binding state. Here, we investigated the catch bond interaction between the hydrophilic domain of the human cell surface sulfatase 1 (Sulf1HD) and its physiological substrate heparan sulfate (HS) by atomic force microscopy based single molecule force spectroscopy (AFM-SMFS). Using Jarzynski’s equality, we estimated the associated Gibbs free energy and provide a comprehensive thermodynamic and kinetic characterization of Sulf1HD/HS interaction. Interestingly, the binding potential landscape exhibits two distinct potential wells which confirms the recently suggested two state binding. Even though structural data of Sulf1HD is lacking, our results allow to draft a detailed picture of the directed and processive desulfation of HS.
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Harder A, Möller AK, Milz F, Neuhaus P, Walhorn V, Dierks T, Anselmetti D. Catch bond interaction between cell-surface sulfatase Sulf1 and glycosaminoglycans. Biophys J 2016; 108:1709-1717. [PMID: 25863062 DOI: 10.1016/j.bpj.2015.02.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 02/18/2015] [Accepted: 02/27/2015] [Indexed: 02/06/2023] Open
Abstract
In biological adhesion, the biophysical mechanism of specific biomolecular interaction can be divided in slip and catch bonds, respectively. Conceptually, slip bonds exhibit a reduced bond lifetime under increased external force and catch bonds, in contrast, exhibit an increased lifetime (for a certain force interval). Since 2003, a handful of biological systems have been identified to display catch bond properties. Upon investigating the specific interaction between the unique hydrophilic domain (HD) of the human cell-surface sulfatase Sulf1 against its physiological glycosaminoglycan (GAG) target heparan sulfate (HS) by single molecule force spectroscopy (SMFS), we found clear evidence of catch bond behavior in this system. The HD, ∼320 amino acids long with dominant positive charge, and its interaction with sulfated GAG-polymers were quantitatively investigated using atomic force microscopy (AFM) based force clamp spectroscopy (FCS) and dynamic force spectroscopy (DFS). In FCS experiments, we found that the catch bond character of HD against GAGs could be attributed to the GAG 6-O-sulfation site whereas only slip bond interaction can be observed in a GAG system where this site is explicitly lacking. We interpreted the binding data within the theoretical framework of a two state two path model, where two slip bonds are coupled forming a double-well interaction potential with an energy difference of ΔE ≈ 9 kBT and a compliance length of Δx ≈ 3.2 nm. Additional DFS experiments support this assumption and allow identification of these two coupled slip-bond states that behave consistently within the Kramers-Bell-Evans model of force-mediated dissociation.
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Affiliation(s)
- Alexander Harder
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Ann-Kristin Möller
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
| | - Fabian Milz
- Biochemistry I, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Phillipp Neuhaus
- Biochemistry I, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Volker Walhorn
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany.
| | - Thomas Dierks
- Biochemistry I, Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Dario Anselmetti
- Experimental Biophysics, Physics Faculty, Bielefeld University, Bielefeld, Germany
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Gensler M, Eidamshaus C, Taszarek M, Reissig HU, Rabe JP. Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy. Beilstein J Org Chem 2015; 11:817-27. [PMID: 26124883 PMCID: PMC4464087 DOI: 10.3762/bjoc.11.91] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/06/2015] [Indexed: 12/19/2022] Open
Abstract
Multivalent biomolecular interactions allow for a balanced interplay of mechanical stability and malleability, and nature makes widely use of it. For instance, systems of similar thermal stability may have very different rupture forces. Thus it is of paramount interest to study and understand the mechanical properties of multivalent systems through well-characterized model systems. We analyzed the rupture behavior of three different bivalent pyridine coordination complexes with Cu2+ in aqueous environment by single-molecule force spectroscopy. Those complexes share the same supramolecular interaction leading to similar thermal off-rates in the range of 0.09 and 0.36 s−1, compared to 1.7 s−1 for the monovalent complex. On the other hand, the backbones exhibit different flexibility, and we determined a broad range of rupture lengths between 0.3 and 1.1 nm, with higher most-probable rupture forces for the stiffer backbones. Interestingly, the medium-flexible connection has the highest rupture forces, whereas the ligands with highest and lowest rigidity seem to be prone to consecutive bond rupture. The presented approach allows separating bond and backbone effects in multivalent model systems.
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Affiliation(s)
- Manuel Gensler
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
| | - Christian Eidamshaus
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Maurice Taszarek
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Hans-Ulrich Reissig
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, D-14195 Berlin, Germany
| | - Jürgen P Rabe
- Department of Physics & IRIS Adlershof, Humboldt-Universität zu Berlin, Newtonstr. 15, D-12489 Berlin, Germany
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Cheng B, Wu S, Liu S, Rodriguez-Aliaga P, Yu J, Cui S. Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases. NANOSCALE 2015; 7:2970-2977. [PMID: 25597693 DOI: 10.1039/c4nr07140a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Most proteins are typically folded into predetermined three-dimensional structures in the aqueous cellular environment. However, proteins can be exposed to a nonpolar environment under certain conditions, such as inside the central cavity of chaperones and unfoldases during protein degradation. It remains unclear how folded proteins behave when moved from an aqueous solvent to a nonpolar one. Here, we employed single-molecule atomic force microscopy and molecular dynamics (MD) simulations to investigate the structural and mechanical variations of a polyprotein, I278, during the change from a polar to a nonpolar environment. We found that the polyprotein was unfolded into an unstructured polypeptide spontaneously when pulled into nonpolar solvents. This finding was corroborated by MD simulations where I27 was dragged from water into a nonpolar solvent, revealing details of the unfolding process at the water/nonpolar solvent interface. These results highlight the importance of water in maintaining folding stability, and provide insights into the response of folded proteins to local hydrophobic environments.
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Affiliation(s)
- Bo Cheng
- Key Lab of Advanced Technologies of Materials, Ministry of Education of China, Southwest Jiaotong University, Chengdu 610031, China.
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Nakahara Y, Mitani H, Kado S, Kimura K. Single-molecule force spectroscopic study on chiral recognition of cysteine derivatives immobilized on a gold substrate by using AFM tips chemically modified with optically active crown ethers. RSC Adv 2014. [DOI: 10.1039/c4ra10553b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The chiral recognition of cysteine derivatives on a gold substrate was investigated using AFM tips modified with optically active crown ethers.
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Affiliation(s)
- Yoshio Nakahara
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Hitoshi Mitani
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Shinpei Kado
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
| | - Keiichi Kimura
- Department of Applied Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama 640-8510, Japan
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Liang CK, Dubacheva GV, Buffeteau T, Cavagnat D, Hapiot P, Fabre B, Tucker JHR, Bassani DM. Reversible control over molecular recognition in surface-bound photoswitchable hydrogen-bonding receptors: towards read-write-erase molecular printboards. Chemistry 2013; 19:12748-58. [PMID: 23929495 DOI: 10.1002/chem.201301613] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/12/2013] [Indexed: 01/27/2023]
Abstract
The synthesis of an anthracene-bearing photoactive barbituric acid receptor and its subsequent grafting onto azide-terminated alkanethiol/Au self-assembled monolayers by using an Cu(I) -catalyzed azide-alkyne reaction is reported. Monolayer characterization using contact-angle measurements, electrochemistry, and spectroscopic ellipsometry indicate that the monolayer conversion is fast and complete. Irradiation of the receptor leads to photodimerization of the anthracenes, which induces the open-to-closed gating of the receptor by blocking access to the binding site. The process is thermally reversible, and polarization-modulated IR reflection-absorption spectroscopy indicates that photochemical closure and thermal opening of the surface-bound receptors occur in 70 and 100 % conversion, respectively. Affinity of the open and closed surface-bound receptor was characterized by using force spectroscopy with a barbituric-acid-modified atomic force microscope tip.
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Affiliation(s)
- Chih-Kai Liang
- Institut des Sciences Moléculaires CNRS UMR5255, Univ. Bordeaux 1, 351, Cours de la Libération, 33400 Talence (France), Fax: (+33) 5-4000-6158
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Jiang F, Wang J, Li J, Wang N, Bao X, Wang T, Yang Y, Lan Z, Yang R. Supramolecular Assemblies with Symmetrical Octahedral Structures - Synthesis, Characterization, and Electrochemical Properties. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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