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Qin H, Miao Y, Cross TA, Fu R. Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance. J Phys Chem B 2017; 121:4799-4809. [PMID: 28425709 DOI: 10.1021/acs.jpcb.7b02468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In terms of structural biology, solid-state NMR experiments and strategies have been well established for resonance assignments, leading to the determination of three-dimensional structures of insoluble membrane proteins in their native-like environment. It is also known that NMR has the unique capabilities to characterize structure-function relationships of membrane-bound biological systems beyond structural biology. Here, we report on solid-state NMR experiments and strategies for extracting functional activities on a sub-millisecond time scale. Specifically, we use the His37-labeled full length M2 (M2FL) protein of the Influenza A virus embedded in synthetic lipid bilayers as an example to characterize the proton conduction mechanism and kinetics. The integral membrane M2 protein assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Our results present convincing evidence for the formation of imidazolium-imidazole hydrogen bonds in the His37 tetrad at low pH and that these hydrogen bonds have a low barrier that facilitates the proton conduction mechanism in the M2FL protein. Moreover, it has been possible to measure hydronium ion exchange between water and the protons in the His37 NH bonds based on chemical exchange spectroscopy with minimized spin diffusion. The results identify an exchange rate constant of ∼4000 s-1 for pH 5.8 at -10 °C.
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Affiliation(s)
- Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University , Tallahassee, Florida 32306, United States.,National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Riqiang Fu
- National High Magnet Field Lab , 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
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Qiu W, Wei Z, Ding N, Yang Y, Ye Q, Lin Y, Chen Z. Partial-Homogeneity-Based Two-Dimensional High-Resolution Nuclear Magnetic Resonance Spectroscopy under Inhomogeneous Magnetic Fields. Chemphyschem 2016; 17:1493-9. [DOI: 10.1002/cphc.201501207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 02/10/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Wenqi Qiu
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
| | - Zhiliang Wei
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
| | - Nan Ding
- Department of Mechanical and Electrical Engineering; Xiamen University; Xiamen 361005 China
| | - Yu Yang
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
| | - Qimiao Ye
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
| | - Yulan Lin
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
| | - Zhong Chen
- Department of Electronic Science; Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance; State Key Laboratory for the Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen 361005 China
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Cai H, Lin L, Ding S, Cui X, Chen Z. Fast quantification of fatty acid profile of intact fish by intermolecular double-quantum coherence1H-NMR spectroscopy. EUR J LIPID SCI TECH 2015. [DOI: 10.1002/ejlt.201500309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Honghao Cai
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen P. R. China
- Department of Chemistry; National Sun Yat-sen University; Kaohsiung Taiwan
| | - Liangjie Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen P. R. China
| | - Shangwu Ding
- Department of Chemistry; National Sun Yat-sen University; Kaohsiung Taiwan
| | - Xiaohong Cui
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen P. R. China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces; Xiamen University; Xiamen P. R. China
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Jin Y, Cai H, Lin Y, Cui X, Chen Z. Usage of the ultrafast intermolecular single-quantum coherence (UF iSQC) sequence for NMR spectroscopy of ex vivo tissue. Food Res Int 2015. [DOI: 10.1016/j.foodres.2015.08.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Miao Y, Fu R, Zhou HX, Cross TA. Dynamic Short Hydrogen Bonds in Histidine Tetrad of Full-Length M2 Proton Channel Reveal Tetrameric Structural Heterogeneity and Functional Mechanism. Structure 2015; 23:2300-2308. [PMID: 26526851 DOI: 10.1016/j.str.2015.09.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 12/25/2022]
Abstract
The tetrameric M2 protein from influenza A conducts protons into the virus upon acid activation of its His37 tetrad and is a proven drug target. Here, in studies of full-length M2 protein solubilized in native-like liquid-crystalline lipid bilayers, a pH titration monitored by solid-state nuclear magnetic resonance revealed a clustering of the first three His37 pKas (6.3, 6.3, and 5.5). When the +2 state of the tetrad accepts a third proton from the externally exposed portion of the channel pore and releases a proton to the internally exposed pore, successful proton conductance is achieved, but more frequently the tetrad accepts and returns the proton to the externally exposed pore, resulting in a futile cycle. Both dynamics and conformational heterogeneity of the His37 tetrad featuring short hydrogen bonds between imidazolium-imidazole pairs are characterized, and the heterogeneity appears to reflect oligomeric helix packing and the extent of transmembrane helical bending around Gly34.
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Affiliation(s)
- Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Huan-Xiang Zhou
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Timothy A Cross
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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Hansen SK, Bertelsen K, Paaske B, Nielsen NC, Vosegaard T. Solid-state NMR methods for oriented membrane proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2015; 88-89:48-85. [PMID: 26282196 DOI: 10.1016/j.pnmrs.2015.05.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Oriented-sample solid-state NMR represents one of few experimental methods capable of characterising the membrane-bound conformation of proteins in the cell membrane. Since the technique was developed 25 years ago, the technique has been applied to study the structure of helix bundle membrane proteins and antimicrobial peptides, characterise protein-lipid interactions, and derive information on dynamics of the membrane anchoring of membrane proteins. We will review the major developments in various aspects of oriented-sample solid-state NMR, including sample-preparation methods, pulse sequences, theory required to interpret the experiments, perspectives for and guidelines to new experiments, and a number of representative applications.
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Affiliation(s)
- Sara K Hansen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Kresten Bertelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Berit Paaske
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Thomas Vosegaard
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark.
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Wei Z, Yang J, Chen Y, Lin Y, Chen Z. Line broadening interference for high-resolution nuclear magnetic resonance spectra under inhomogeneous magnetic fields. J Chem Phys 2015; 142:134202. [DOI: 10.1063/1.4916520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Zhiliang Wei
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Jian Yang
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Youhe Chen
- Department of Electronic Engineering, Xiamen University, Xiamen 361005, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory of Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
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Wang C, Zhang L, Wei Z, Lin L, Lin Y, Chen Z. High-resolution NMR spectroscopy via simultaneous acquisitions of intermolecular zero- and double-quantum coherence signals in inhomogeneous magnetic fields. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Wang T, Williams JK, Schmidt-Rohr K, Hong M. Relaxation-compensated difference spin diffusion NMR for detecting 13C-13C long-range correlations in proteins and polysaccharides. JOURNAL OF BIOMOLECULAR NMR 2015; 61:97-107. [PMID: 25510834 PMCID: PMC4522165 DOI: 10.1007/s10858-014-9889-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 12/03/2014] [Indexed: 05/04/2023]
Abstract
The measurement of long-range distances remains a challenge in solid-state NMR structure determination of biological macromolecules. In 2D and 3D correlation spectra of uniformly (13)C-labeled biomolecules, inter-residue, inter-segmental, and intermolecular (13)C-(13)C cross peaks that provide important long-range distance constraints for three-dimensional structures often overlap with short-range cross peaks that only reflect the covalent structure of the molecule. It is therefore desirable to develop new approaches to obtain spectra containing only long-range cross peaks. Here we show that a relaxation-compensated modification of the commonly used 2D (1)H-driven spin diffusion (PDSD) experiment allows the clean detection of such long-range cross peaks. By adding a z-filter to keep the total z-period of the experiment constant, we compensate for (13)C T1 relaxation. As a result, the difference spectrum between a long- and a scaled short-mixing time spectrum show only long-range correlation signals. We show that one- and two-bond cross peaks equalize within a few tens of milliseconds. Within ~200 ms, the intensity equilibrates within an amino acid residue and a monosaccharide to a value that reflects the number of spins in the local network. With T1 relaxation compensation, at longer mixing times, inter-residue and inter-segmental cross peaks increase in intensity whereas intra-segmental cross-peak intensities remain unchanged relative to each other and can all be subtracted out. Without relaxation compensation, the difference 2D spectra exhibit both negative and positive intensities due to heterogeneous T1 relaxation in most biomolecules, which can cause peak cancellation. We demonstrate this relaxation-compensated difference PDSD approach on amino acids, monosaccharides, a crystalline model peptide, a membrane-bound peptide and a plant cell wall sample. The resulting difference spectra yield clean multi-bond, inter-residue and intermolecular correlation peaks, which are often difficult to resolve in the parent 2D spectra.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Jonathan K. Williams
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
| | - Klaus Schmidt-Rohr
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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Lin L, Wei Z, Lin Y, Chen Z. A single-scan method for NMR 2D J-resolved spectroscopy. Chem Commun (Camb) 2015; 51:1234-6. [DOI: 10.1039/c4cc07751b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A single-scan NMR 2D J-resolved method is proposed for obtaining decoupled proton spectra and fine scalar-coupling splitting patterns.
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Affiliation(s)
- Liangjie Lin
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Zhiliang Wei
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Yanqin Lin
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
| | - Zhong Chen
- Department of Electronic Science
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance
- State Key Laboratory for Physical Chemistry of Solid Surfaces
- Xiamen University
- Xiamen
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Cai HH, Chen H, Lin YL, Feng JH, Cui XH, Chen Z. Feasibility of Ultrafast Intermolecular Single-Quantum Coherence Spectroscopy in Analysis of Viscous-Liquid Foods. FOOD ANAL METHOD 2014. [DOI: 10.1007/s12161-014-0046-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Cross TA, Ekanayake V, Paulino J, Wright A. Solid state NMR: The essential technology for helical membrane protein structural characterization. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 239:100-9. [PMID: 24412099 PMCID: PMC3957465 DOI: 10.1016/j.jmr.2013.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/21/2023]
Abstract
NMR spectroscopy of helical membrane proteins has been very challenging on multiple fronts. The expression and purification of these proteins while maintaining functionality has consumed countless graduate student hours. Sample preparations have depended on whether solution or solid-state NMR spectroscopy was to be performed - neither have been easy. In recent years it has become increasingly apparent that membrane mimic environments influence the structural result. Indeed, in these recent years we have rediscovered that Nobel laureate, Christian Anfinsen, did not say that protein structure was exclusively dictated by the amino acid sequence, but rather by the sequence in a given environment (Anfinsen, 1973) [106]. The environment matters, molecular interactions with the membrane environment are significant and many examples of distorted, non-native membrane protein structures have recently been documented in the literature. However, solid-state NMR structures of helical membrane proteins in proteoliposomes and bilayers are proving to be native structures that permit a high resolution characterization of their functional states. Indeed, solid-state NMR is uniquely able to characterize helical membrane protein structures in lipid environments without detergents. Recent progress in expression, purification, reconstitution, sample preparation and in the solid-state NMR spectroscopy of both oriented samples and magic angle spinning samples has demonstrated that helical membrane protein structures can be achieved in a timely fashion. Indeed, this is a spectacular opportunity for the NMR community to have a major impact on biomedical research through the solid-state NMR spectroscopy of these proteins.
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Affiliation(s)
- Timothy A Cross
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
| | - Vindana Ekanayake
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Anna Wright
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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Miao Y, Cross TA. Solid state NMR and protein-protein interactions in membranes. Curr Opin Struct Biol 2013; 23:919-28. [PMID: 24034903 DOI: 10.1016/j.sbi.2013.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/17/2013] [Accepted: 08/12/2013] [Indexed: 11/17/2022]
Abstract
Solid state NMR spectroscopy has evolved rapidly in recent years into an excellent tool for the characterization of membrane proteins and their complexes. In the past few years it has also become clear that the structure of membrane proteins, especially helical membrane proteins is determined, in part, by the membrane environment. Therefore, the modeling of this environment by a liquid crystalline lipid bilayer for solid state NMR has generated a unique tool for the characterization of native conformational states, local and global dynamics, and high-resolution structure for these proteins. Protein-protein interactions can also benefit from this solid state NMR capability to characterize membrane proteins in a native-like environment. These complexes take the form of oligomeric structures and hetero-protein interactions both with water-soluble proteins and other membrane proteins.
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Affiliation(s)
- Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, United States; National High Magnetic Field Lab, 1800 E. Paul Dirac Dr., Florida State University, Tallahassee, FL 32310, United States
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