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Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 2024; 7:1005. [PMID: 39152195 PMCID: PMC11329788 DOI: 10.1038/s42003-024-06690-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ziane Izri
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Oleg Dmytrenko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Patrick Fischer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Chase Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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Wehler P, Armbruster D, Günter A, Schleicher E, Di Ventura B, Öztürk MA. Experimental Characterization of In Silico Red-Shift-Predicted iLOV L470T/Q489K and iLOV V392K/F410V/A426S Mutants. ACS OMEGA 2022; 7:19555-19560. [PMID: 35722011 PMCID: PMC9202016 DOI: 10.1021/acsomega.2c01283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
iLOV is a flavin mononucleotide-binding fluorescent protein used for in vivo cellular imaging similar to the green fluorescent protein. To expand the range of applications of iLOV, spectrally tuned red-shifted variants are desirable to reduce phototoxicity and allow for better tissue penetration. In this report, we experimentally tested two iLOV mutants, iLOVL470T/Q489K and iLOVV392K/F410V/A426S, which were previously computationally proposed by (KhrenovaJ. Phys. Chem. B2017, 121 ( (43), ), pp 10018-10025) to have red-shifted excitation and emission spectra. While iLOVL470T/Q489K is about 20% brighter compared to the WT in vitro, it exhibits a blue shift in contrast to quantum mechanics/molecular mechanics (QM/MM) predictions. Additional optical characterization of an iLOVV392K mutant revealed that V392 is essential for cofactor binding and, accordingly, variants with V392K mutation are unable to bind to FMN. iLOVL470T/Q489K and iLOVV392K/F410V/A426S are expressed at low levels and have no detectable fluorescence in living cells, preventing their utilization in imaging applications.
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Affiliation(s)
- Pierre Wehler
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Daniel Armbruster
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Andreas Günter
- Institute
of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Erik Schleicher
- Institute
of Physical Chemistry, University of Freiburg, Albertstr. 21, 79104 Freiburg, Germany
| | - Barbara Di Ventura
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Mehmet Ali Öztürk
- Institute
of Biology II, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centers
for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
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Takada S, Yoshinaga N, Doi N, Fujiwara K. Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells. SCIENCE ADVANCES 2022; 8:eabm8460. [PMID: 35675408 PMCID: PMC9177070 DOI: 10.1126/sciadv.abm8460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Reaction-diffusion coupling (RDc) generates spatiotemporal patterns, including two dynamic wave modes: traveling and standing waves. Although mode selection plays a substantial role in the spatiotemporal organization of living cell molecules, the mechanism for selecting each wave mode remains elusive. Here, we investigated a wave mode selection mechanism using Min waves reconstituted in artificial cells, emerged by the RDc of MinD and MinE. Our experiments and theoretical analysis revealed that the balance of membrane binding and dissociation from the membrane of MinD determines the mode selection of the Min wave. We successfully demonstrated that the transition of the wave modes can be regulated by controlling this balance and found hysteresis characteristics in the wave mode transition. These findings highlight a previously unidentified role of the balance between activators and inhibitors as a determinant of the mode selection of waves by RDc and depict an unexplored mechanism in intracellular spatiotemporal pattern formations.
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Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 980-8577, Japan
- MathAM-OIL, AIST, Sendai 980-8577, Japan
- Corresponding author. (N.Y.); (K.F.)
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Corresponding author. (N.Y.); (K.F.)
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