1
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Frere GA, Hasabnis A, Francisco CB, Suleiman M, Alimowska O, Rahmatullah R, Gould J, Su CYC, Voznyy O, Gunning PT, Basso EA, Prosser RS. Next-Generation Tags for Fluorine Nuclear Magnetic Resonance: Designing Amplification of Chemical Shift Sensitivity. J Am Chem Soc 2024; 146:3052-3064. [PMID: 38279916 DOI: 10.1021/jacs.3c09730] [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: 01/29/2024]
Abstract
Fluorine NMR is a highly sensitive technique for delineating the conformational states of biomolecules and has shown great utility in drug screening and in understanding protein function. Current fluorinated protein tags leverage the intrinsic chemical shift sensitivity of the 19F nucleus to detect subtle changes in protein conformation and topology. This chemical shift sensitivity can be amplified by embedding the fluorine or trifluoromethyl reporter within a pyridone. Due to their polarizability and rapid tautomerization, pyridones exhibit a greater range of electron delocalization and correspondingly greater 19F NMR chemical shift dispersion. To assess the chemical shift sensitivity of these tautomeric probes to the local environment, 19F NMR spectra of all possible monofluorinated and trifluoromethyl-tagged versions of 2-pyridone were recorded in methanol/water mixtures ranging from 100% methanol to 100% water. 4-Fluoro-2-pyridone and 6-(trifluoromethyl)-2-pyridone (6-TFP) displayed the greatest sensitivity of the monofluorinated and trifluoromethylated pyridones, exceeding that of known conventional CF3 reporters. To evaluate the utility of tautomeric pyridone tags for 19F NMR of biomolecules, the alpha subunit of the stimulatory G protein (Gsα) and human serum albumin (HSA) were each labeled with a thiol-reactive derivative of 6-TFP and the spectra were recorded as a function of various adjuvants and drugs. The tautomeric tag outperformed the conventional tag, 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide through the improved resolution of several functional states.
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Affiliation(s)
- Geordon A Frere
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Advait Hasabnis
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Camila B Francisco
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
- Department of Chemistry, State University of Maringá, 5790, Maringá 87020-900, Brazil
| | - Motasem Suleiman
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Olga Alimowska
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Rima Rahmatullah
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Jerome Gould
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Celia Yi-Chia Su
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Oleksandr Voznyy
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Patrick T Gunning
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
| | - Ernani A Basso
- Department of Chemistry, State University of Maringá, 5790, Maringá 87020-900, Brazil
| | - Robert S Prosser
- Department of Chemistry, University of Toronto, CPS, UTM, 3359 Mississauga Rd, Mississauga, ON L5L 1C6, Canada
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2
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Huang Y, Reddy KD, Bracken C, Qiu B, Zhan W, Eliezer D, Boudker O. Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM. J Am Chem Soc 2023; 145:8583-8592. [PMID: 37023263 PMCID: PMC10119980 DOI: 10.1021/jacs.3c01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Indexed: 04/08/2023]
Abstract
Limited chemical shift dispersion represents a significant barrier to studying multistate equilibria of large membrane proteins by 19F NMR. We describe a novel monofluoroethyl 19F probe that dramatically increases the chemical shift dispersion. The improved conformational sensitivity and line shape enable the detection of previously unresolved states in one-dimensional (1D) 19F NMR spectra of a 134 kDa membrane transporter. Changes in the populations of these states in response to ligand binding, mutations, and temperature correlate with population changes of distinct conformations in structural ensembles determined by single-particle cryo-electron microscopy (cryo-EM). Thus, 19F NMR can guide sample preparation to discover and visualize novel conformational states and facilitate image analysis and three-dimensional (3D) classification.
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Affiliation(s)
- Yun Huang
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Krishna D. Reddy
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
| | - Clay Bracken
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Biao Qiu
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Wenhu Zhan
- Department
of Microbiology & Immunology, Weill
Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - David Eliezer
- Department
of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, New York 10021, United States
| | - Olga Boudker
- Department
of Physiology & Biophysics, Weill Cornell
Medicine, 1300 York Avenue, New York, New York 10021, United States
- Howard
Hughes Medical Institute, Chevy
Chase, Maryland 20815, United States
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3
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Huang B, Xu L, Zhao Z, Wang N, Zhao Y, Huang S. Simultaneous analysis of amino acids based on discriminative 19F NMR spectroscopy. Bioorg Chem 2022; 124:105818. [PMID: 35489271 DOI: 10.1016/j.bioorg.2022.105818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/02/2022]
Abstract
The simultaneous analysis of amino acids (AAs) is crucial for human health, diagnosis and treatment of disease, and nutritional quality evaluation in foodstuffs. Here, we establish an easy and rapid method for the simultaneous analysis of AAs using a single reagent 2-(trifluoromethyl)benzaldehyde (oTFMBA) based on spectral-separation-enabled 19F NMR spectroscopy. oTFMBA, a highly sensitive chemosensor, is capable of analyzing 19 proteinogenic AAs or non-amino acid amines (non-AAs) in a complex mixture by adjusting the pH in a toilless way. The 19F signals of oTFMBA-labeled AAs are distributed over a wide range of ∼ 0.7 ppm, demonstrating oTFMBA with higher resolution for simultaneous analysis of AAs compared to the o-phthaldialdehyde (OPA) method (<0.6 ppm). Additionally, 12 AAs were unambiguously identified in human urine, including Asp, Ser, Gly, Thr, Glu, Arg, Ala, Val, Ile, Tyr, His, and Phe. Furthermore, our method's detection limit for AAs is 5.83 μM, illustrating sensitivity with an ∼100-fold improvement over the OPA method. This work represents an approach to the analysis of AAs or non-AAs in a complicated mixture (even biofluid) using a 19F NMR probe with high sensitivity, which is of great significance for the simultaneous analysis of multiple analytes.
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Affiliation(s)
- Biling Huang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, PR China.
| | - Lihua Xu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China
| | - Zhao Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China
| | - Ning Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, PR China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, PR China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, and the Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, PR China; Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | - Shaohua Huang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, PR China; Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, Zhejiang, PR China.
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4
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Yang D, Gronenborn AM, Chong LT. Development and Validation of Fluorinated, Aromatic Amino Acid Parameters for Use with the AMBER ff15ipq Protein Force Field. J Phys Chem A 2022; 126:2286-2297. [PMID: 35352936 PMCID: PMC9014858 DOI: 10.1021/acs.jpca.2c00255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/15/2022] [Indexed: 12/27/2022]
Abstract
We developed force field parameters for fluorinated, aromatic amino acids enabling molecular dynamics (MD) simulations of fluorinated proteins. These parameters are tailored to the AMBER ff15ipq protein force field and enable the modeling of 4, 5, 6, and 7F-tryptophan, 3F- and 3,5F-tyrosine, and 4F- or 4-CF3-phenylalanine. The parameters include 181 unique atomic charges derived using the implicitly polarized charge (IPolQ) scheme in the presence of SPC/Eb explicit water molecules and 9 unique bond, angle, or torsion terms. Our simulations of benchmark peptides and proteins maintain expected conformational propensities on the μs time scale. In addition, we have developed an open-source Python program to calculate fluorine relaxation rates from MD simulations. The extracted relaxation rates from protein simulations are in good agreement with experimental values determined by 19F NMR. Collectively, our results illustrate the power and robustness of the IPolQ lineage of force fields for modeling the structure and dynamics of fluorine-containing proteins at the atomic level.
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Affiliation(s)
- Darian
T. Yang
- Molecular
Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania 15260, United States
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh
School of Medicine, Pittsburgh, Pennsylvania 15260, United States
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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5
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Jones JC, Banerjee R, Shi K, Semonis MM, Aihara H, Pomerantz WCK, Lipscomb JD. Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR. Biochemistry 2021; 60:1995-2010. [PMID: 34100595 PMCID: PMC8345336 DOI: 10.1021/acs.biochem.1c00293] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar KD values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.
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Affiliation(s)
- Jason C. Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Manny M. Semonis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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6
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Huang J, Byun JA, VanSchouwen B, Henning P, Herberg FW, Kim C, Melacini G. Dynamical Basis of Allosteric Activation for the Plasmodium falciparum Protein Kinase G. J Phys Chem B 2021; 125:6532-6542. [PMID: 34115498 DOI: 10.1021/acs.jpcb.1c03622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is required for the progression of the Plasmodium's life cycle and is therefore a promising malaria drug target. PfPKG includes four cGMP-binding domains (CBD-A to CBD-D). CBD-D plays a crucial role in PfPKG regulation as it is the primary determinant for the inhibition and cGMP-dependent activation of the catalytic domain. Hence, it is critical to understand how CBD-D is allosterically regulated by cGMP. Although the apo versus holo conformational changes of CBD-D have been reported, information on the intermediates of the activation pathway is currently lacking. Here, we employed molecular dynamics simulations to model four key states along the thermodynamic cycle for the cGMP-dependent activation of the PfPKG CBD-D domain. The simulations were compared to NMR data, and they revealed that the PfPKG CBD-D activation pathway samples a compact intermediate in which the N- and C-terminal helices approach the central β-barrel. In addition, by comparing the cGMP-bound active and inactive states, the essential binding interactions that differentiate these states were identified. The identification of structural and dynamical features unique to the cGMP-bound inactive state provides a promising basis to design PfPKG-selective allosteric inhibitors as a viable treatment for malaria.
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Affiliation(s)
- Jinfeng Huang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Jung Ah Byun
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Philipp Henning
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Friedrich W Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Choel Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030, United States.,Center for Drug Discovery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Giuseppe Melacini
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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7
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Rashid S, Lee BL, Wajda B, Spyracopoulos L. Nucleotide Binding and Active Site Gate Dynamics for the Hsp90 Chaperone ATPase Domain from Benchtop and High Field 19F NMR Spectroscopy. J Phys Chem B 2020; 124:2984-2993. [PMID: 32212608 DOI: 10.1021/acs.jpcb.0c00626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein turnover in cells is regulated by the ATP dependent activity of the Hsp90 chaperone. In concert with accessory proteins, ATP hydrolysis drives the obligate Hsp90 dimer through a cycle between open and closed states that is critical for assisting the folding and stability of hundreds of proteins. Cycling is initiated by ATP binding to the ATPase domain, with the chaperone and the active site gates in the dimer in open states. The chaperone then adopts a short-lived, ATP bound closed state with a closed active site gate. The structural and dynamic changes induced in the ATPase domain and active site gate upon nucleotide binding, and their impact on dimer closing are not well understood. We site-specifically 19F-labeled the ATPase domain at the active site gate to enable benchtop and high field 19F NMR spectroscopic studies. Combined with MD simulations, this allowed accurate characterization of pico- to nanosecond time scale motions of the active site gate, as well as slower micro- to millisecond time scale processes resulting from nucleotide binding. ATP binding induces increased flexibility at one of the hinges of the active site gate, a necessary prelude to release of the second hinge and eventual gate closure in the intact chaperone.
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Affiliation(s)
- Suad Rashid
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Brian L Lee
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Benjamin Wajda
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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8
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Hoffmann F, Mulder FAA, Schäfer LV. Predicting NMR relaxation of proteins from molecular dynamics simulations with accurate methyl rotation barriers. J Chem Phys 2020; 152:084102. [DOI: 10.1063/1.5135379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Falk Hoffmann
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
| | - Frans A. A. Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, D-44780 Bochum, Germany
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9
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Klein BA, Sykes BD. Feasibility of trifluoromethyl TROSY NMR at high magnetic fields. JOURNAL OF BIOMOLECULAR NMR 2019; 73:519-523. [PMID: 31267350 DOI: 10.1007/s10858-019-00266-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
Insights into the structure and dynamics of large biological systems has been greatly improved by two concurrent NMR approaches: the application of transverse relaxation-optimized spectroscopy (TROSY) techniques in multi-dimensional NMR, especially the methyl-TROSY, and the resurgence of 19F NMR using trifluoromethyl (CF3) probes. Herein we investigate the feasibility of combining these approaches into a trifluoromethyl-TROSY experiment. Using a CF3-labelled parvalbumin, we have evaluated the natural abundance 13C-19F correlation spectra and find no indication of a CF3 TROSY at high magnetic fields.
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Affiliation(s)
- Brittney A Klein
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada
| | - Brian D Sykes
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G2H7, Canada.
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