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Kwon HJ, Gwak S, Park JY, Cho M, Han H. TfNN 15N: A γ- 15N-Labeled Diazo-Transfer Reagent for the Synthesis of β- 15N-Labeled Azides. ACS OMEGA 2022; 7:293-298. [PMID: 35036700 PMCID: PMC8757338 DOI: 10.1021/acsomega.1c04679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Azides are infrared (IR) probes that are important for structure and dynamics studies of proteins. However, they often display complex IR spectra owing to Fermi resonances and multiple conformers. Isotopic substitution of azides weakens the Fermi resonance, allowing more accurate IR spectral analysis. Site-specifically 15N-labeled aromatic azides, but not aliphatic azides, are synthesized through nitrosation. Both 15N-labeled aromatic and aliphatic azides are synthesized through nucleophilic substitution or diazo-transfer reaction but as an isotopomeric mixture. We present the synthesis of TfNN15N, a γ-15N-labeled diazo-transfer reagent, and its use to prepare β-15N-labeled aliphatic as well as aromatic azides.
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Affiliation(s)
- Hyeok-Jun Kwon
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Sungduk Gwak
- Department
of Chemistry, Korea University, Seoul 02841, Korea
| | - Jun Young Park
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 02841, Korea
- Center
for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department
of Chemistry, Korea University, Seoul 02841, Korea
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2
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Zhang J, Wang L, Zhang J, Zhu J, Pan X, Cui Z, Wang J, Fang W, Li Y. Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine. J Phys Chem B 2018; 122:8122-8133. [DOI: 10.1021/acs.jpcb.8b03887] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Li Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jin Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xin Pan
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Zhifeng Cui
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Weihai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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3
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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Adhikary R, Zimmermann J, Liu J, Dawson PE, Romesberg FE. Experimental characterization of electrostatic and conformational heterogeneity in an SH3 domain. J Phys Chem B 2013; 117:13082-9. [PMID: 23834285 DOI: 10.1021/jp402772x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electrostatic and conformational heterogeneity make central contributions to protein function, but their experimental characterization requires a combination of spatial and temporal resolution that is challenging to achieve. Src homology 3 (SH3) domains mediate protein-protein interactions, and NMR studies have demonstrated that most possess conformational heterogeneity, which could be critical for their function. Here, we use the IR absorptions of carbon-deuterium (C-D) bonds site-selectively incorporated throughout the N-terminal SH3 domain from the murine adapter protein Crk-II to characterize its different microenvironments with high spatial and temporal resolution. The C-D absorptions are only differentiated in the folded state of the protein where they show evidence of significant environmental heterogeneity. However, the spectra of the folded state are independent of temperature, and upon thermal denaturation the protein undergoes a single, global unfolding transition. While some evidence of conformational heterogeneity is found within the peptide backbone, the majority of the environmental heterogeneity appears to result from electrostatics.
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Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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5
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Hickert AS, Durgan AC, Patton DA, Blake SA, Cremeens ME. A B3LYP investigation of the conformational and environmental sensitivity of carbon–deuterium frequencies of aryl-perdeuterated phenylalanine and tryptophan. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1050-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Haldar S, Chaudhuri A, Chattopadhyay A. Organization and dynamics of membrane probes and proteins utilizing the red edge excitation shift. J Phys Chem B 2011; 115:5693-706. [PMID: 21428321 DOI: 10.1021/jp200255e] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamics of confined water has interesting implications in the organization and function of molecular assemblies such as membranes. A direct consequence of this type of organization is the restriction imposed on the mobility of the constituent structural units. Interestingly, this restriction (confinement) of mobility couples the motion of solvent (water) molecules with the slow moving molecules in the assembly. It is in this context that the red edge excitation shift (REES) represents a sensitive approach to monitor the environment and dynamics around a fluorophore in such organized assemblies. A shift in the wavelength of maximum fluorescence emission toward higher wavelengths, caused by a shift in the excitation wavelength toward the red edge of the absorption band, is termed REES. REES relies on slow solvent reorientation in the excited state of a fluorophore that can be used to monitor the environment and dynamics around a fluorophore in a host assembly. In this article, we focus on the application of REES to monitor organization and dynamics of membrane probes and proteins.
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Affiliation(s)
- Sourav Haldar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007 India
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7
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Miller CS, Ploetz EA, Cremeens ME, Corcelli SA. Carbon-deuterium vibrational probes of peptide conformation: alanine dipeptide and glycine dipeptide. J Chem Phys 2009; 130:125103. [PMID: 19334896 DOI: 10.1063/1.3100185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The utility of alpha-carbon deuterium-labeled bonds (C(alpha)-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C(alpha)-D labeled alanine dipeptide (Adp-d(1)) and C(alpha)-D(2) labeled glycine dipeptide (Gdp-d(2)). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d(1) and Gdp-d(2), we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of phi and psi, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5 degrees spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C(alpha)-D and C(alpha)-D(2) stretch transition frequencies for each structure. For Adp-d(1) the C(alpha)-D stretch frequency exhibited a maximum variability of 39.4 cm(-1) between the six stable structures identified in the gas phase. The C(alpha)-D(2) frequencies of Gdp-d(2) show an even more substantial difference between its three stable conformations: there is a 40.7 cm(-1) maximum difference in the symmetric C(alpha)-D(2) stretch frequencies and an 81.3 cm(-1) maximum difference in the asymmetric C(alpha)-D(2) stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C(alpha)-D(2) stretch frequencies of Gdp-d(2) is remarkably sensitive to its conformation.
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Affiliation(s)
- C S Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Zimmermann J, Gundogdu K, Cremeens ME, Bandaria JN, Hwang GT, Thielges MC, Cheatum CM, Romesberg FE. Efforts toward developing probes of protein dynamics: vibrational dephasing and relaxation of carbon-deuterium stretching modes in deuterated leucine. J Phys Chem B 2009; 113:7991-4. [PMID: 19441845 DOI: 10.1021/jp900516c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The spectral position of C-D stretching absorptions in the so-called "transparent window" of protein absorption (1800-2300 cm(-1)) makes them well suited as probes of protein dynamics with high temporal and structural resolution. We have previously incorporated single deuterated amino acids into proteins to site-selectively follow protein folding and ligand binding by steady-state FT IR spectroscopy. Ultimately, our goal is to use C-D bonds as probes in time-resolved IR spectroscopy to study dynamics and intramolecular vibrational energy redistribution (IVR) in proteins. As a step toward this goal, we now present the first time-resolved experiments characterizing the population and dephasing dynamics of selectively excited C-D bonds in a deuterated amino acid. Three differently deuterated, Boc-protected leucines were selected to systematically alter the number of additional C-D bonds that may mediate IVR out of the initially populated bright C-D stretching mode. Three-pulse photon echo experiments show that the steady-state C-D absorption linewidths are broadened by both homogeneous and inhomogeneous effects, and transient grating experiments reveal that IVR occurs on a subpicosecond time scale and is nonstatistical. The results have important implications for the interpretation of steady-state C-D spectra and demonstrate the potential utility of C-D bonds as probes of dynamics and IVR within a protein.
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Miller CS, Corcelli SA. Carbon−Deuterium Vibrational Probes of Amino Acid Protonation State. J Phys Chem B 2009; 113:8218-21. [DOI: 10.1021/jp903520s] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C. S. Miller
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - S. A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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10
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Lindquist BA, Furse KE, Corcelli SA. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys Chem Chem Phys 2009; 11:8119-32. [DOI: 10.1039/b908588b] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Lindquist BA, Haws RT, Corcelli SA. Optimized Quantum Mechanics/Molecular Mechanics Strategies for Nitrile Vibrational Probes: Acetonitrile and para-Tolunitrile in Water and Tetrahydrofuran. J Phys Chem B 2008; 112:13991-4001. [DOI: 10.1021/jp804900u] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beth A. Lindquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Ryan T. Haws
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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12
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Lindquist BA, Corcelli SA. Nitrile Groups as Vibrational Probes: Calculations of the C≡N Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran. J Phys Chem B 2008; 112:6301-3. [DOI: 10.1021/jp802039e] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Beth A. Lindquist
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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13
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Raczyńska ED, Kosińska W, Ośmiałowski B, Gawinecki R. Tautomeric Equilibria in Relation to Pi-Electron Delocalization. Chem Rev 2005; 105:3561-612. [PMID: 16218561 DOI: 10.1021/cr030087h] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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