1
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Zhao Z, Rudman NA, Dmochowski IJ. A Site-Specific Cross-Linker for Visible-Light Control of Proteins. ACS OMEGA 2024; 9:29331-29338. [PMID: 39005769 PMCID: PMC11238208 DOI: 10.1021/acsomega.4c00968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 07/16/2024]
Abstract
There is a need for photochemical tools that allow precise control of protein structure and function with visible light. We focus here on the s-tetrazine moiety, which can be installed at a specific protein site via the reaction between dichlorotetrazine and two adjacent sulfhydryl groups. Tetrazine's compact size enables structural mimicry of native amino acid linkages, such as an intramolecular salt bridge or disulfide bond. In this study, we investigated tetrazine installation in three different proteins, where it was confirmed that the cross-linking reaction is highly efficient in aqueous conditions and site-specific when two cysteines are located proximally: the S-S distance was 4-10 Å. As shown in maltose binding protein, the tetrazine cross-linker can replace an interdomain salt bridge crucial for xenon binding and serve as a visible-light photoswitch to modulate 129Xe NMR contrast. This work highlights the ease of aqueous tetrazine bioconjugation and its applications for protein photoregulation.
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Affiliation(s)
- Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
| | - Nathan A Rudman
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S. 34th St., Philadelphia, Pennsylvania 19104, United States
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2
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Zhang X, Yang Y, Yuan Y, Yue S, Zhao X, Yue Q, Zeng Q, Guo Q, Zhou X. Hyperpolarized 129Xe Atoms Sense the Presence of Drug Molecules in Nanohosts Revealed by Magnetic Resonance Imaging. Anal Chem 2024; 96:10152-10160. [PMID: 38818902 DOI: 10.1021/acs.analchem.3c05573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Assessing the effectiveness of nanomedicines involves evaluating the drug content at the target site. Currently, most research focuses on monitoring the signal responses from loaded drugs, neglecting the changes caused by the nanohosts. Here, we propose a strategy to quantitatively evaluate the content of loaded drugs by detecting the signal variations resulting from the alterations in the microenvironment of the nanohosts. Specifically, hyperpolarized (HP) 129Xe atoms are employed as probes to sense the nanohosts' environment and generate a specific magnetic resonance (MR) signal that indicates their accessibility. The introduction of drugs reduces the available space in the nanohosts, leading to a crowded microenvironment that hinders the access of the 129Xe atoms. By employing 129Xe atoms as a signal source to detect the alterations in the microenvironment, we constructed a three-dimensional (3D) map that indicated the concentration of the nanohosts and established a linear relationship to quantitatively measure the drug content within the nanohosts based on the corresponding MR signals. Using the developed strategy, we successfully quantified the uptake of the nanohosts and drugs in living cells through HP 129Xe MR imaging. Overall, the proposed HP 129Xe atom-sensing approach can be used to monitor alterations in the microenvironment of nanohosts induced by loaded drugs and provides a new perspective for the quantitative evaluation of drug presence in various nanomedicines.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuqi Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaping Yuan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
| | - Sen Yue
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuchao Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
| | - Quer Yue
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
| | - Qingbin Zeng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
| | - Qianni Guo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Barskiy DA. Molecules, Up Your Spins! Molecules 2024; 29:1821. [PMID: 38675641 PMCID: PMC11052189 DOI: 10.3390/molecules29081821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) are indispensable tools in science and medicine, offering insights into the functions of biological processes [...].
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Affiliation(s)
- Danila A. Barskiy
- Institut für Physik, Johannes-Gutenberg-Universität Mainz, 55128 Mainz, Germany;
- Helmholtz Institut Mainz, 55128 Mainz, Germany
- GSI Helmholtzzentrum für Schwerionenforschung, 64291 Darmstadt, Germany
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4
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He J, Dmochowski IJ. Local Xenon-Protein Interaction Produces Global Conformational Change and Allosteric Inhibition in Lysozyme. Biochemistry 2023; 62:1659-1669. [PMID: 37192381 PMCID: PMC10821772 DOI: 10.1021/acs.biochem.3c00046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Noble gases have well-established biological effects, yet their molecular mechanisms remain poorly understood. Here, we investigated, both experimentally and computationally, the molecular modes of xenon (Xe) action in bacteriophage T4 lysozyme (T4L). By combining indirect gassing methods with a colorimetric lysozyme activity assay, a reversible, Xe-specific (20 ± 3)% inhibition effect was observed. Accelerated molecular dynamic simulations revealed that Xe exerts allosteric inhibition on the protein by expanding a C-terminal hydrophobic cavity. Xe-induced cavity expansion results in global conformational changes, with long-range transduction distorting the active site where peptidoglycan binds. Interestingly, the peptide substrate binding site that enables lysozyme specificity does not change conformation. Two T4L mutants designed to reshape the C-terminal Xe cavity established a correlation between cavity expansion and enzyme inhibition. This work also highlights the use of Xe flooding simulations to identify new cryptic binding pockets. These results enrich our understanding of Xe-protein interactions at the molecular level and inspire further biochemical investigations with noble gases.
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Affiliation(s)
- Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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5
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Zhao Z, Rudman NA, He J, Dmochowski IJ. Programming xenon diffusion in maltose-binding protein. Biophys J 2022; 121:4635-4643. [PMID: 36271622 PMCID: PMC9748359 DOI: 10.1016/j.bpj.2022.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 12/15/2022] Open
Abstract
Protein interiors contain void space that can bind small gas molecules. Determination of gas pathways and kinetics in proteins has been an intriguing and challenging task. Here, we combined computational methods and the hyperpolarized xenon-129 chemical exchange saturation transfer (hyper-CEST) NMR technique to investigate xenon (Xe) exchange kinetics in maltose-binding protein (MBP). A salt bridge ∼9 Å from the Xe-binding site formed upon maltose binding and slowed the Xe exchange rate, leading to a hyper-CEST 129Xe signal from maltose-bound MBP. Xe dissociation occurred faster than dissociation of the salt bridge, as shown by 13C NMR spectroscopy and variable-B1 hyper-CEST experiments. "Xe flooding" molecular dynamics simulations identified a surface hydrophobic site, V23, that has good Xe binding affinity. Mutations at this site confirmed its role as a secondary exchange pathway in modulating Xe diffusion. This shows the possibility for site-specifically controlling xenon protein-solvent exchange. Analysis of the available MBP structures suggests a biological role of MBP's large hydrophobic cavity to accommodate structural changes associated with ligand binding and protein-protein interactions.
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Affiliation(s)
- Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nathan A Rudman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jiayi He
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania.
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6
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Abstract
The use of magnetic resonance imaging (MRI) and spectroscopy (MRS) in the clinical setting enables the acquisition of valuable anatomical information in a rapid, non-invasive fashion. However, MRI applications for identifying disease-related biomarkers are limited due to low sensitivity at clinical magnetic field strengths. The development of hyperpolarized (hp) 129Xe MRI/MRS techniques as complements to traditional 1H-based imaging has been a burgeoning area of research over the past two decades. Pioneering experiments have shown that hp 129Xe can be encapsulated within host molecules to generate ultrasensitive biosensors. In particular, xenon has high affinity for cryptophanes, which are small organic cages that can be functionalized with affinity tags, fluorophores, solubilizing groups, and other moieties to identify biomedically relevant analytes. Cryptophane sensors designed for proteins, metal ions, nucleic acids, pH, and temperature have achieved nanomolar-to-femtomolar limits of detection via a combination of 129Xe hyperpolarization and chemical exchange saturation transfer (CEST) techniques. This review aims to summarize the development of cryptophane biosensors for 129Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of 129Xe MRI. This review aims to summarize the development of cryptophane biosensors for 129Xe MRI applications, while highlighting innovative biosensor designs and the consequent enhancements in detection sensitivity, which will be invaluable in expanding the scope of 129Xe MRI.![]()
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Affiliation(s)
- Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323, USA
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 South 34 St., Philadelphia, PA 19104-6323, USA
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7
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Jiang W, Guo Q, Luo Q, Zhang X, Yuan Y, Li H, Zhou X. Molecular Concentration Determination Using Long-Interval Chemical Exchange Inversion Transfer (CEIT) NMR Spectroscopy. J Phys Chem Lett 2021; 12:8652-8657. [PMID: 34472873 DOI: 10.1021/acs.jpclett.1c02239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Functionalized hyperpolarized xenon "cage" molecules have often been used for ultrasensitive detection of biomolecules and microenvironment properties. However, the rapid and accurate measurement of molecule concentration is still a challenge. Here, we report a molecule concentration measurement method using long-interval chemical exchange inversion transfer (CEIT) NMR spectroscopy. The molecule concentration can be quantitatively measured with only 2 scans, which shortens the acquisition time by about 10 times compared to conventional Hyper-CEST (chemical exchange saturation transfer) z-spectrum method. Moreover, we found that the accuracy of concentration determination would be the best when the CEIT effect is 1-1/e or close to it, and a relative deviation of CrA-(COOH)6 less than ±1% has been achieved by only a one-step optimization of the number of cycles. The proposed method enables efficient and accurate determination of molecule concentration, which provides a potential way for rapid quantitative molecular imaging applications.
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Affiliation(s)
- Weiping Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Qianni Guo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Qing Luo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
| | - Xiaoxiao Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
| | - Yaping Yuan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Haidong Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Wuhan 430071, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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8
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Kunth M, Witte C, Schröder L. Mapping of Absolute Host Concentration and Exchange Kinetics of Xenon Hyper-CEST MRI Agents. Pharmaceuticals (Basel) 2021; 14:79. [PMID: 33494166 PMCID: PMC7909792 DOI: 10.3390/ph14020079] [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: 12/03/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 12/14/2022] Open
Abstract
Xenon magnetic resonance imaging (MRI) provides excellent sensitivity through the combination of spin hyperpolarization and chemical exchange saturation transfer (CEST). To this end, molecular hosts such as cryptophane-A or cucurbit[n]urils provide unique opportunities to design switchable MRI reporters. The concentration determination of such xenon binding sites in samples of unknown dilution remains, however, challenging. Contrary to 1H CEST agents, an internal reference of a certain host (in this case, cryptophane-A) at micromolar concentration is already sufficient to resolve the entire exchange kinetics information, including an unknown host concentration and the xenon spin exchange rate. Fast echo planar imaging (EPI)-based Hyper-CEST MRI in combination with Bloch-McConnell analysis thus allows quantitative insights to compare the performance of different emerging ultra-sensitive MRI reporters.
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Affiliation(s)
- Martin Kunth
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, 13125 Berlin, Germany;
| | - Christopher Witte
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, 13125 Berlin, Germany;
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Str. 10, 13125 Berlin, Germany;
- Translational Molecular Imaging, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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9
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Shapiro MG. Reporter Genes for Ultrasound and MRI. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00051-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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10
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Kunth M, Schröder L. Binding site exchange kinetics revealed through efficient spin-spin dephasing of hyperpolarized 129Xe. Chem Sci 2020; 12:158-169. [PMID: 34163587 PMCID: PMC8178811 DOI: 10.1039/d0sc04835f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Spin exchange between different chemical environments is an important observable for characterizing chemical exchange kinetics in various contexts, including protein folding, chelation chemistry, and host-guest interactions. Such spins experience effective spin-spin relaxation rate, R 2,eff, that typically shows a dispersive behavior which requires detailed analysis. Here, we describe a class of highly simplified R 2,eff behavior by relying on hyperpolarized 129Xe as a freely exchanging ligand reporter. It provides large chemical shift separations that yield reduced expressions of both the Swift-Connick and the Carver-Richards treatment of exchange-induced relaxation. Despite observing a diamagnetic system, R 2,eff is dominated by large Larmor frequency jumps and thus allows detection of otherwise inaccessible analyte concentrations with a single spin echo train (only 0.01% of the overall hyperpolarized spins need to be transiently bound to the molecule). The two Xe hosts cryptophane-A monoacid (CrA-ma) and cucurbit[6]uril (CB6) represent two exemplary families of container molecules (the latter one also serving as drug delivery vehicles) that act as highly efficient phase shifters for which we observed unprecedented exchange-induced relaxivity r 2 (up to 866 s-1 mM-1). By including methods of spatial encoding, multiple data points can be collected simultaneously to isolate the exchange contribution and determine the effective exchange rate in partially occupied binding sites with a single delivery of hyperpolarized nuclei. The relaxivity is directly related to the guest turnover in these systems and temperature-dependent measurements yield an activation energy of E A = 41 kJ mol-1 for Xe@CrA-ma from simple relaxometry analysis. The concept is transferable to many applications where Xe is known to exhibit large chemical shifts.
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Affiliation(s)
- Martin Kunth
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch, Robert-Roessle-Str. 10 13125 Berlin Germany +49 30 94793 121
| | - Leif Schröder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP) Campus Berlin-Buch, Robert-Roessle-Str. 10 13125 Berlin Germany +49 30 94793 121
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11
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Jayapaul J, Schröder L. Molecular Sensing with Host Systems for Hyperpolarized 129Xe. Molecules 2020; 25:E4627. [PMID: 33050669 PMCID: PMC7587211 DOI: 10.3390/molecules25204627] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/27/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Hyperpolarized noble gases have been used early on in applications for sensitivity enhanced NMR. 129Xe has been explored for various applications because it can be used beyond the gas-driven examination of void spaces. Its solubility in aqueous solutions and its affinity for hydrophobic binding pockets allows "functionalization" through combination with host structures that bind one or multiple gas atoms. Moreover, the transient nature of gas binding in such hosts allows the combination with another signal enhancement technique, namely chemical exchange saturation transfer (CEST). Different systems have been investigated for implementing various types of so-called Xe biosensors where the gas binds to a targeted host to address molecular markers or to sense biophysical parameters. This review summarizes developments in biosensor design and synthesis for achieving molecular sensing with NMR at unprecedented sensitivity. Aspects regarding Xe exchange kinetics and chemical engineering of various classes of hosts for an efficient build-up of the CEST effect will also be discussed as well as the cavity design of host molecules to identify a pool of bound Xe. The concept is presented in the broader context of reporter design with insights from other modalities that are helpful for advancing the field of Xe biosensors.
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Affiliation(s)
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany;
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12
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Zemerov SD, Roose BW, Farenhem KL, Zhao Z, Stringer MA, Goldman AR, Speicher DW, Dmochowski IJ. 129Xe NMR-Protein Sensor Reveals Cellular Ribose Concentration. Anal Chem 2020; 92:12817-12824. [PMID: 32897053 PMCID: PMC7649717 DOI: 10.1021/acs.analchem.0c00967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Dysregulation of cellular ribose uptake can be indicative of metabolic abnormalities or tumorigenesis. However, analytical methods are currently limited for quantifying ribose concentration in complex biological samples. Here, we utilize the highly specific recognition of ribose by ribose-binding protein (RBP) to develop a single-protein ribose sensor detectable via a sensitive NMR technique known as hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST). We demonstrate that RBP, with a tunable ribose-binding site and further engineered to bind xenon, enables the quantitation of ribose over a wide concentration range (nM to mM). Ribose binding induces the RBP "closed" conformation, which slows Xe exchange to a rate detectable by hyper-CEST. Such detection is remarkably specific for ribose, with the minimal background signal from endogenous sugars of similar size and structure, for example, glucose or ribose-6-phosphate. Ribose concentration was measured for mammalian cell lysate and serum, which led to estimates of low-mM ribose in a HeLa cell line. This highlights the potential for using genetically encoded periplasmic binding proteins such as RBP to measure metabolites in different biological fluids, tissues, and physiologic states.
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Affiliation(s)
- Serge D. Zemerov
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Benjamin W. Roose
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Kelsey L. Farenhem
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Madison A. Stringer
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
| | - Aaron R. Goldman
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
| | - David W. Speicher
- Proteomics and Metabolomics Facility, The Wistar Institute,
Philadelphia, PA 19104, USA
- Molecular and Cellular Oncogenesis Program, The Wistar
Institute, Philadelphia, PA 19104, USA
| | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania,
Philadelphia, PA 19104, USA
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13
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Du K, Zemerov SD, Hurtado Parra S, Kikkawa JM, Dmochowski IJ. Paramagnetic Organocobalt Capsule Revealing Xenon Host-Guest Chemistry. Inorg Chem 2020; 59:13831-13844. [PMID: 32207611 PMCID: PMC7672707 DOI: 10.1021/acs.inorgchem.9b03634] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We investigated Xe binding in a previously reported paramagnetic metal-organic tetrahedral capsule, [Co4L6]4-, where L2- = 4,4'-bis[(2-pyridinylmethylene)amino][1,1'-biphenyl]-2,2'-disulfonate. The Xe-inclusion complex, [XeCo4L6]4-, was confirmed by 1H NMR spectroscopy to be the dominant species in aqueous solution saturated with Xe gas. The measured Xe dissociation rate in [XeCo4L6]4-, koff = 4.45(5) × 102 s-1, was at least 40 times greater than that in the analogous [XeFe4L6]4- complex, highlighting the capability of metal-ligand interactions to tune the capsule size and guest permeability. The rapid exchange of 129Xe nuclei in [XeCo4L6]4- produced significant hyperpolarized 129Xe chemical exchange saturation transfer (hyper-CEST) NMR signal at 298 K, detected at a concentration of [XeCo4L6]4- as low as 100 pM, with presaturation at -89 ppm, which was referenced to solvated 129Xe in H2O. The saturation offset was highly temperature-dependent with a slope of -0.41(3) ppm/K, which is attributed to hyperfine interactions between the encapsulated 129Xe nucleus and electron spins on the four CoII centers. As such, [XeCo4L6]4- represents the first example of a paramagnetic hyper-CEST (paraHYPERCEST) sensor. Remarkably, the hyper-CEST 129Xe NMR resonance for [XeCo4L6]4- (δ = -89 ppm) was shifted 105 ppm upfield from the diamagnetic analogue [XeFe4L6]4- (δ = +16 ppm). The Xe inclusion complex was further characterized in the crystal structure of (C(NH2)3)4[Xe0.7Co4L6]·75 H2O (1). Hydrogen bonding between capsule-linker sulfonate groups and exogenous guanidinium cations, (C(NH2)3)+, stabilized capsule-capsule interactions in the solid state and also assisted in trapping a Xe atom (∼42 Å3) in the large (135 Å3) cavity of 1. Magnetic susceptibility measurements confirmed the presence of four noninteracting, magnetically anisotropic high-spin CoII centers in 1. Furthermore, [Co4L6]4- was found to be stable toward aggregation and oxidation, and the CEST performance of [XeCo4L6]4- was unaffected by biological macromolecules in H2O. These results recommend metal-organic capsules for fundamental investigations of Xe host-guest chemistry as well as applications with highly sensitive 129Xe-based sensors.
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14
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Zhao Z, Roose BW, Zemerov SD, Stringer MA, Dmochowski IJ. Detecting protein-protein interactions by Xe-129 NMR. Chem Commun (Camb) 2020; 56:11122-11125. [PMID: 32814938 PMCID: PMC7511426 DOI: 10.1039/d0cc02988b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Detection of protein-protein interactions (PPIs) is limited by current bioanalytical methods. A protein complementation assay (PCA), split TEM-1 β-lactamase, interacts with xenon at the interface of the TEM-1 fragments. Reconstitution of TEM-1-promoted here by cFos/cJun leucine zipper interaction-gives rise to sensitive 129Xe NMR signal in bacterial cells.
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Affiliation(s)
- Zhuangyu Zhao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Benjamin W Roose
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Madison A Stringer
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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15
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Du K, Zemerov SD, Carroll PJ, Dmochowski IJ. Paramagnetic Shifts and Guest Exchange Kinetics in Co nFe 4-n Metal-Organic Capsules. Inorg Chem 2020; 59:12758-12767. [PMID: 32851844 DOI: 10.1021/acs.inorgchem.0c01816] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the magnetic resonance properties and exchange kinetics of guest molecules in a series of hetero-bimetallic capsules, [ConFe4-nL6]4- (n = 1-3), where L2- = 4,4'-bis[(2-pyridinylmethylene)amino]-[1,1'-biphenyl]-2,2'-disulfonate. H bond networks between capsule sulfonates and guanidinium cations promote the crystallization of [ConFe4-nL6]4-. The following four isostructural crystals are reported: two guest-free forms, (C(NH2)3)4[Co1.8Fe2.2L6]·69H2O (1) and (C(NH2)3)4[Co2.7Fe1.3L6]·73H2O (2), and two Xe- and CFCl3-encapsulated forms, (C(NH2)3)4[(Xe)0.8Co1.8Fe2.2L6]·69H2O (3) and (C(NH2)3)4[(CFCl3)Co2.0Fe2.0L6]·73H2O (4), respectively. Structural analyses reveal that Xe induces negligible structural changes in 3, while the angles between neighboring phenyl groups expand by ca. 3° to accommodate the much larger guest, CFCl3, in 4. These guest-encapsulated [ConFe4-nL6]4- molecules reveal 129Xe and 19F chemical shift changes of ca. -22 and -10 ppm at 298 K, respectively, per substitution of low-spin FeII by high-spin CoII. Likewise, the temperature dependence of the 129Xe and 19F NMR resonances increases by 0.1 and 0.06 ppm/K, respectively, with each additional paramagnetic CoII center. The optimal temperature for hyperpolarized (hp) 129Xe chemical exchange saturation transfer (hyper-CEST) with [ConFe4-nL6]4- capsules was found to be inversely proportional to the number of CoII centers, n, which is consistent with the Xe chemical exchange accelerating as the portals expand. The systematic study was facilitated by the tunability of the [M4L6]4- capsules, further highlighting these metal-organic systems for developing responsive sensors with highly shifted 129Xe resonances.
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Affiliation(s)
- Kang Du
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Patrick J Carroll
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States
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16
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Jayapaul J, Schröder L. Nanoparticle-Based Contrast Agents for 129Xe HyperCEST NMR and MRI Applications. CONTRAST MEDIA & MOLECULAR IMAGING 2019; 2019:9498173. [PMID: 31819739 PMCID: PMC6893250 DOI: 10.1155/2019/9498173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/15/2019] [Indexed: 02/06/2023]
Abstract
Spin hyperpolarization techniques have enabled important advancements in preclinical and clinical MRI applications to overcome the intrinsic low sensitivity of nuclear magnetic resonance. Functionalized xenon biosensors represent one of these approaches. They combine two amplification strategies, namely, spin exchange optical pumping (SEOP) and chemical exchange saturation transfer (CEST). The latter one requires host structures that reversibly bind the hyperpolarized noble gas. Different nanoparticle approaches have been implemented and have enabled molecular MRI with 129Xe at unprecedented sensitivity. This review gives an overview of the Xe biosensor concept, particularly how different nanoparticles address various critical aspects of gas binding and exchange, spectral dispersion for multiplexing, and targeted reporter delivery. As this concept is emerging into preclinical applications, comprehensive sensor design will be indispensable in translating the outstanding sensitivity potential into biomedical molecular imaging applications.
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Affiliation(s)
- Jabadurai Jayapaul
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
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17
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Truxal AE, Cao L, Isaacs L, Wemmer DE, Pines A. Directly Functionalized Cucurbit[7]uril as a Biosensor for the Selective Detection of Protein Interactions by 129 Xe hyperCEST NMR. Chemistry 2019; 25:6108-6112. [PMID: 30868660 DOI: 10.1002/chem.201900610] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Indexed: 12/14/2022]
Abstract
Advancement of hyperpolarized 129 Xe MRI technology toward clinical settings demonstrates the considerable interest in this modality for diagnostic imaging. The number of contrast agents, termed biosensors, for 129 Xe MRI that respond to specific biological targets, has grown and diversified. Directly functionalized xenon-carrying macrocycles, such as the large family of cryptophane-based biosensors, are good for localization-based imaging and provide contrast before and after binding events occur. Noncovalently functionalized constructs, such as cucurbituril- and cyclodextrin-based biosensors, benefit from commercial availability and optimal exchange dynamics for CEST imaging. In this work, we report the first directly functionalized cucurbituril used as a xenon biosensor. Biotinylated cucurbit[7]uril (btCB7) gives rise to a 129 Xe hyperCEST response at the unusual shift of δ=28 ppm when bound to its protein target with substantial CEST contrast. We posit that the observed chemical shift is due to the deformation of btCB7 upon binding to avidin, caused by proximity to the protein surface. Conformational searches and molecular dynamics (MD) simulations support this hypothesis. This construct combines the strengths of both families of biosensors, enables a multitude of biological targets through avidin conjugation, and demonstrates the advantages of functionalized cucurbituril-based biosensors.
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Affiliation(s)
| | - Liping Cao
- Northwest University, College of Chemistry and Materials Science, Xi'an, China
| | - Lyle Isaacs
- University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, USA
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18
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Kunth M, Lu GJ, Witte C, Shapiro MG, Schröder L. Protein Nanostructures Produce Self-Adjusting Hyperpolarized Magnetic Resonance Imaging Contrast through Physical Gas Partitioning. ACS NANO 2018; 12:10939-10948. [PMID: 30204404 DOI: 10.1021/acsnano.8b04222] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Signal amplification strategies are critical for overcoming the intrinsically poor sensitivity of nuclear magnetic resonance (NMR) reporters in noninvasive molecular detection. A mechanism widely used for signal enhancement is chemical exchange saturation transfer (CEST) of nuclei between a dilute sensing pool and an abundant detection pool. However, the dependence of CEST amplification on the relative size of these spin pools confounds quantitative molecular detection with a larger detection pool typically making saturation transfer less efficient. Here we show that a recently discovered class of genetically encoded nanoscale reporters for 129Xe magnetic resonance overcomes this fundamental limitation through an elastic binding capacity for NMR-active nuclei. This approach pairs high signal amplification from hyperpolarized spins with ideal, self-adjusting saturation transfer behavior as the overall spin ensemble changes in size. These reporters are based on gas vesicles, i.e., microbe-derived, gas-filled protein nanostructures. We show that the xenon fraction that partitions into gas vesicles follows the ideal gas law, allowing the signal transfer under hyperpolarized xenon chemical exchange saturation transfer (Hyper-CEST) imaging to scale linearly with the total xenon ensemble. This conceptually distinct elastic response allows the production of quantitative signal contrast that is robust to variability in the concentration of xenon, enabling virtually unlimited improvement in absolute contrast with increased xenon delivery, and establishing a unique principle of operation for contrast agent development in emerging biochemical and in vivo applications of hyperpolarized NMR and magnetic resonance imaging.
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Affiliation(s)
- Martin Kunth
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
| | - George J Lu
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
| | - Christopher Witte
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
| | - Mikhail G Shapiro
- California Institute of Technology , Division of Chemistry and Chemical Engineering , Pasadena , California 91125 , United States
| | - Leif Schröder
- Leibniz-Forschungsinstitut für Molekulare Pharmarkologie (FMP) , 13125 Berlin , Germany
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19
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Roose BW, Zemerov SD, Wang Y, Kasimova MA, Carnevale V, Dmochowski IJ. A Structural Basis for 129 Xe Hyper-CEST Signal in TEM-1 β-Lactamase. Chemphyschem 2018; 20:260-267. [PMID: 30151973 DOI: 10.1002/cphc.201800624] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Indexed: 11/10/2022]
Abstract
Genetically encoded (GE) contrast agents detectable by magnetic resonance imaging (MRI) enable non-invasive visualization of gene expression and cell proliferation at virtually unlimited penetration depths. Using hyperpolarized 129 Xe in combination with chemical exchange saturation transfer, an MR contrast approach known as hyper-CEST, enables ultrasensitive protein detection and biomolecular imaging. GE MRI contrast agents developed to date include nanoscale proteinaceous gas vesicles as well as the monomeric bacterial proteins TEM-1 β-lactamase (bla) and maltose binding protein (MBP). To improve understanding of hyper-CEST NMR with proteins, structural and computational studies were performed to further characterize the Xe-bla interaction. X-ray crystallography validated the location of a high-occupancy Xe binding site predicted by MD simulations, and mutagenesis experiments confirmed this Xe site as the origin of the observed CEST contrast. Structural studies and MD simulations with representative bla mutants offered additional insight regarding the relationship between local protein structure and CEST contrast.
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Affiliation(s)
- Benjamin W Roose
- Department of Chemistry, University of Pennsylvania, 231 S 34th St, Philadelphia, PA 19104
| | - Serge D Zemerov
- Department of Chemistry, University of Pennsylvania, 231 S 34th St, Philadelphia, PA 19104
| | - Yanfei Wang
- Harvard Medical School, 300 Longwood Ave, Boston, MA 02115
| | - Marina A Kasimova
- Science for Life Laboratory Department of Theoretical Physics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science College of Science and Technology, Temple University, 1925 N 12th St, Philadelphia, PA 19122
| | - Ivan J Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S 34th St, Philadelphia, PA 19104
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20
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Schnurr M, Joseph R, Naugolny-Keisar A, Kaizerman-Kane D, Bogdanoff N, Schuenke P, Cohen Y, Schröder L. High Exchange Rate Complexes of 129 Xe with Water-Soluble Pillar[5]arenes for Adjustable Magnetization Transfer MRI. Chemphyschem 2018; 20:246-251. [PMID: 30079552 DOI: 10.1002/cphc.201800618] [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: 06/28/2018] [Indexed: 01/16/2023]
Abstract
Macrocyclic host structures for generating transiently bound 129 Xe have been used in various ultra-sensitive NMR and MRI applications for molecular sensing of biochemical analytes. They are based on hyperpolarized nuclei chemical exchange saturation transfer (Hyper-CEST). Here, we tested a set of water-soluble pillar[5]arenes with different counterions in order to compare their potential contrast agent abilities with that of cryptophane-A (CrA), the most widely used host for such purposes. The exchange of Xe with such compounds was found to be sensitive to the type of ions present in solution and can be used for switchable magnetization transfer (MT) contrast that arises from off-resonant pre-saturation. We demonstrate that the adjustable MT magnitude depends on the interplay of saturation parameters and found that the optimum MT contrast surpasses the CrA CEST performance at moderate saturation power. Since modification of such water-soluble pillar[5]arenes is straightforward, these compounds can be considered a promising platform for designing various sensors that may complement the field of Xe HyperCEST-based biosensing MRI.
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Affiliation(s)
- Matthias Schnurr
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Roymon Joseph
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Alissa Naugolny-Keisar
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Dana Kaizerman-Kane
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Nils Bogdanoff
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Patrick Schuenke
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Yoram Cohen
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Leif Schröder
- Molecular Imaging, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
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21
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Farhadi A, Ho G, Kunth M, Ling B, Lakshmanan A, Lu GJ, Bourdeau RW, Schröder L, Shapiro MG. Recombinantly Expressed Gas Vesicles as Nanoscale Contrast Agents for Ultrasound and Hyperpolarized MRI. AIChE J 2018; 64:2927-2933. [PMID: 30555168 DOI: 10.1002/aic.16138] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. However, the need to produce these nanostructures via expression in specialized cultures of cyanobacteria or haloarchaea limits their broader adoption by other laboratories and hinders genetic engineering of their properties. Here, we describe recombinant expression and purification of Bacillus megaterium gas vesicles using a common laboratory strain of Escherichia coli, and characterize the physical, acoustic and magnetic resonance properties of these nanostructures. Recombinantly expressed gas vesicles produce ultrasound and hyperpolarized 129Xe MRI contrast at sub-nanomolar concentrations, thus validating a simple platform for their production and engineering.
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Affiliation(s)
- Arash Farhadi
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - Gabrielle Ho
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Martin Kunth
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Bill Ling
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Anupama Lakshmanan
- Division of Biology and Biological Engineering; California Institute of Technology; Pasadena CA 91125
| | - George J Lu
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Raymond W. Bourdeau
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
| | - Leif Schröder
- Dept. of Structural Biology, Molecular Imaging; Leibniz-Forschungsinstitute für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering; California Institute of Technology; Pasadena CA 91125
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22
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Lu GJ, Farhadi A, Mukherjee A, Shapiro MG. Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging. Curr Opin Chem Biol 2018; 45:57-63. [PMID: 29549770 PMCID: PMC6076850 DOI: 10.1016/j.cbpa.2018.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 12/31/2022]
Abstract
A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound were available, and most genetically encoded reporters for MRI were limited by metal availability or relatively low sensitivity. Here we review how these limitations are being addressed by recently introduced reporter genes based on air-filled and water-transporting biomolecules. We focus on gas-filled protein nanostructures adapted from buoyant microbes, which scatter sound waves, perturb magnetic fields and interact with hyperpolarized nuclei, as well as transmembrane water channels that alter the effective diffusivity of water in tissue.
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Affiliation(s)
- George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arash Farhadi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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23
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Zemerov SD, Roose BW, Greenberg ML, Wang Y, Dmochowski IJ. Cryptophane Nanoscale Assemblies Expand 129Xe NMR Biosensing. Anal Chem 2018; 90:7730-7738. [PMID: 29782149 PMCID: PMC6050516 DOI: 10.1021/acs.analchem.8b01630] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cryptophane-based biosensors are promising agents for the ultrasensitive detection of biomedically relevant targets via 129Xe NMR. Dynamic light scattering revealed that cryptophanes form water-soluble aggregates tens to hundreds of nanometers in size. Acridine orange fluorescence quenching assays allowed quantitation of the aggregation state, with critical concentrations ranging from 200 nM to 600 nM, depending on the cryptophane species in solution. The addition of excess carbonic anhydrase (CA) protein target to a benzenesulfonamide-functionalized cryptophane biosensor (C8B) led to C8B disaggregation and produced the expected 1:1 C8B-CA complex. C8B showed higher affinity at 298 K for the cytoplasmic isozyme CAII than the extracellular CAXII isozyme, which is a biomarker of cancer. Using hyper-CEST NMR, we explored the role of stoichiometry in detecting these two isozymes. Under CA-saturating conditions, we observed that isozyme CAII produces a larger 129Xe NMR chemical shift change (δ = 5.9 ppm, relative to free biosensor) than CAXII (δ = 2.7 ppm), which indicates the strong potential for isozyme-specific detection. However, stoichiometry-dependent chemical shift data indicated that biosensor disaggregation contributes to the observed 129Xe NMR chemical shift change that is normally assigned to biosensor-target binding. Finally, we determined that monomeric cryptophane solutions improve hyper-CEST saturation contrast, which enables ultrasensitive detection of biosensor-protein complexes. These insights into cryptophane-solution behavior support further development of xenon biosensors, but will require reinterpretation of the data previously obtained for many water-soluble cryptophanes.
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Affiliation(s)
- Serge D. Zemerov
- Department of Chemistry, University of Pennsylvania, 231 S 34 St., Philadelphia, PA 19104
| | - Benjamin W. Roose
- Department of Chemistry, University of Pennsylvania, 231 S 34 St., Philadelphia, PA 19104
| | | | | | - Ivan J. Dmochowski
- Department of Chemistry, University of Pennsylvania, 231 S 34 St., Philadelphia, PA 19104
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24
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Roose BW, Zemerov SD, Dmochowski IJ. Xenon-Protein Interactions: Characterization by X-Ray Crystallography and Hyper-CEST NMR. Methods Enzymol 2018; 602:249-272. [PMID: 29588032 DOI: 10.1016/bs.mie.2018.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The physiological activity of xenon has long been recognized, though the exact nature of its interactions with biomolecules remains poorly understood. Xe is an inert noble gas, but can act as a general anesthetic, most likely by binding internal hydrophobic cavities within proteins. Understanding Xe-protein interactions, therefore, can provide crucial insight regarding the mechanism of Xe anesthesia and potentially other general anesthetic agents. Historically, Xe-protein interactions have been studied primarily through X-ray crystallography and nuclear magnetic resonance (NMR). In this chapter, we first describe our methods for preparing Xe derivatives of protein crystals and identifying Xe-binding sites. Second, we detail our procedure for 129Xe hyper-CEST NMR spectroscopy, a versatile NMR technique well suited for characterizing the weak, transient nature of Xe-protein interactions.
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