1
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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2
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You M, Gao Z, Zhou L, Guo C, Guo Q. Investigation of the Vibrational Characteristics of 6-Isocyano-1-Methyl-1H-Indole: Utilizing the Isonitrile Group as an Infrared Probe. Molecules 2023; 28:6939. [PMID: 37836782 PMCID: PMC10574170 DOI: 10.3390/molecules28196939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Indole derivatives have garnered considerable attention in the realm of biochemistry due to their multifaceted properties. In this study, we undertake a systematic investigation of the vibrational characteristics of a model indole derivative, 6-isocyano-1-methyl-1H-indole (6ICMI), by employing a combination of FTIR, IR pump-probe spectroscopy, and theoretical calculations. Our findings demonstrate a strong dependence of the isonitrile stretching frequency of 6ICMI on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when the isonitrile group is bonded to aromatic groups. Both experimental and theoretical analyses unveil a significant correlation between the isonitrile stretch vibration of 6ICMI and the solvent acceptor number of alcohols. Furthermore, the polarization-controlled infrared pump-probe conducted on 6ICMI in dimethyl sulfoxide provides additional support for the potential use of the isonitrile stretching mode of 6ICMI as an effective infrared probe for local environments.
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Affiliation(s)
- Min You
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Zilin Gao
- School of Computer Science and Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing 404100, China
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China;
| | - Changyuan Guo
- Key Laboratory of Intelligent Air-Ground Cooperative Control for Universities in Chongqing, College of Automation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Qiang Guo
- Shanxi Province Key Laboratory of Higee-Oriented Chemical Engineering, School of Chemistry and Chemical Engineering, North University of China, Taiyuan 030051, China
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3
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Haldar T, Chatterjee S, Alam MN, Maity P, Bagchi S. Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules. J Phys Chem B 2022; 126:10732-10740. [PMID: 36511763 DOI: 10.1021/acs.jpcb.2c05848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cyano-tryptophan is an unnatural fluorescent amino acid that emits in the visible region. Along with the structural similarity with tryptophan, the unique photophysical properties of this fluorophore make it an ideal probe for biophysical research. Herein, combining fluorescence spectroscopy, infrared spectroscopy, and molecular dynamics simulations, we show that the cyano-tryptophan's emission energy quantifies the underlying bond-specific noncovalent interactions in terms of the electric field. We further report the use of fluorophore's emission energy to predict its hydrogen bond characteristics. We demonstrate that combining experiments with molecular dynamics simulations can provide the hydrogen bonding status of the nitrile moiety. In addition, we report a method to differentiate between aqueous and nonaqueous hydrogen-bonding partners. Using a phenomenological approach, we demonstrate that the presence of the cyano-indole moiety is responsible for the distinct correlations between the fluorophore's emission and the electrostatic forces on the nitrile bond. As indole is a privileged scaffold for both native amino acids and nucleobases, cyano-indoles will have many multifaceted applications.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Md Nirshad Alam
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Pradip Maity
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
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4
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Micikas R, Acharyya A, Gai F, Smith AB. A Scalable Synthesis of the Blue Fluorescent Amino Acid 4-Cyanotryptophan and the Fmoc Derivative: Utility Demonstrated with the Influenza M2 Peptide Tetramer. Org Lett 2021; 23:1247-1250. [DOI: 10.1021/acs.orglett.0c04055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Micikas
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34th St, Philadelphia, Pennsylvania 19104, United States
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5
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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6
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Konstantinidi A, Chountoulesi M, Naziris N, Sartori B, Amenitsch H, Mali G, Čendak T, Plakantonaki M, Triantafyllakou I, Tselios T, Demetzos C, Busath DD, Mavromoustakos T, Kolocouris A. The boundary lipid around DMPC-spanning influenza A M2 transmembrane domain channels: Its structure and potential for drug accommodation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183156. [PMID: 31846647 DOI: 10.1016/j.bbamem.2019.183156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
We have investigated the perturbation of influenza A M2TM in DMPC bilayers. We have shown that (a) DSC and SAXS detect changes in membrane organization caused by small changes (micromolar) in M2TM or aminoadamantane concentration and aminoadamantane structure, by comparison of amantadine and spiro[pyrrolidine-2,2'-adamantane] (AK13), (b) that WAXS and MD can suggest details of ligand topology. DSC and SAXS show that at a low M2TM micromolar concentration in DPMC bilayers, two lipid domains are observed, which likely correspond to M2TM boundary lipids and bulk-like lipids. At higher M2TM concentrations, one domain only is identified, which constitutes essentially all of the lipid molecules behaving as boundary lipids. According to SAXS, WAXS, and DSC in the absence of M2TM, both aminoadamantane drugs exert a similar perturbing effect on the bilayer at low concentrations. At the same concentrations of the drug when M2TM is present, amantadine and, to a lesser extent, AK13 cause, according to WAXS, a significant disordering of chain-stacking, which also leads to the formation of two lipid domains. This effect is likely due, according to MD simulations, to the preference of the more lipophilic AK13 to locate closer to the lateral surfaces of M2TM when compared to amantadine, which forms stronger ionic interactions with phosphate groups. The preference of AK13 to concentrate inside the lipid bilayer close to the exterior of the hydrophobic M2TM helices may contribute to its higher binding affinity compared to amantadine.
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Affiliation(s)
- Athina Konstantinidi
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Nikolaos Naziris
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, A-8010 Graz, Austria
| | - Gregor Mali
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Tomaž Čendak
- Department of Inorganic Chemistry and Technology, National Institute of Chemistry, Ljubljana SI-1001, Slovenia
| | - Maria Plakantonaki
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Iro Triantafyllakou
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Theodore Tselios
- Department of Chemistry, School of Natural Sciences, University of Patras, Rion, Patras 26500, Greece
| | - Costas Demetzos
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece
| | - David D Busath
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, UT 84602, USA
| | - Thomas Mavromoustakos
- Section of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece.
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens 15771, Greece.
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7
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To J, Torres J. Viroporins in the Influenza Virus. Cells 2019; 8:cells8070654. [PMID: 31261944 PMCID: PMC6679168 DOI: 10.3390/cells8070654] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/21/2019] [Accepted: 06/27/2019] [Indexed: 12/28/2022] Open
Abstract
Influenza is a highly contagious virus that causes seasonal epidemics and unpredictable pandemics. Four influenza virus types have been identified to date: A, B, C and D, with only A–C known to infect humans. Influenza A and B viruses are responsible for seasonal influenza epidemics in humans and are responsible for up to a billion flu infections annually. The M2 protein is present in all influenza types and belongs to the class of viroporins, i.e., small proteins that form ion channels that increase membrane permeability in virus-infected cells. In influenza A and B, AM2 and BM2 are predominantly proton channels, although they also show some permeability to monovalent cations. By contrast, M2 proteins in influenza C and D, CM2 and DM2, appear to be especially selective for chloride ions, with possibly some permeability to protons. These differences point to different biological roles for M2 in types A and B versus C and D, which is also reflected in their sequences. AM2 is by far the best characterized viroporin, where mechanistic details and rationale of its acid activation, proton selectivity, unidirectionality, and relative low conductance are beginning to be understood. The present review summarizes the biochemical and structural aspects of influenza viroporins and discusses the most relevant aspects of function, inhibition, and interaction with the host.
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Affiliation(s)
- Janet To
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jaume Torres
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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8
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You M, Zhou L, Huang X, Wang Y, Zhang W. Isonitrile-Derivatized Indole as an Infrared Probe for Hydrogen-Bonding Environments. Molecules 2019; 24:molecules24071379. [PMID: 30965674 PMCID: PMC6480494 DOI: 10.3390/molecules24071379] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/24/2019] [Accepted: 03/30/2019] [Indexed: 11/18/2022] Open
Abstract
The isonitrile (NC) group has been shown to be a promising infrared probe for studying the structure and dynamics of biomolecules. However, there have been no systematic studies performed on the NC group as an infrared probe, when it is bonded to an indole ring. Here, we systematically study the NC stretching mode of two model compounds, 5-isocyano-1H-indole (5ICI) and 5-isocyano-1-methyl-1H-indole (NM5ICI), using Fourier transform infrared (FTIR) spectroscopy. The NC stretching frequency is shown to be strongly dependent on the polarizability of protic solvents and the density of hydrogen-bond donor groups in the solvent when NC is bonded to an indole ring. Infrared pump–probe studies of 5ICI in DMSO and in EtOH further support that the NC stretching mode could be used as a site-specific infrared probe for local environments when NC is bonded to an indole ring.
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Affiliation(s)
- Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Liang Zhou
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Xinyue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
| | - Yang Wang
- Department of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China.
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9
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Huang XY, You M, Ran GL, Fan HR, Zhang WK. Ester-Derivatized indoles as fluorescent and infrared probes for hydration environments. CHINESE J CHEM PHYS 2018. [DOI: 10.1063/1674-0068/31/cjcp1805118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Xin-yue Huang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Min You
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Guang-liu Ran
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
| | - Hao-ran Fan
- Department of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wen-kai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, China
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10
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Chalyavi F, Gilmartin PH, Schmitz AJ, Fennie MW, Tucker MJ. Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018; 57:7528-7532. [PMID: 29710418 PMCID: PMC6002807 DOI: 10.1002/anie.201803849] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Indexed: 12/20/2022]
Abstract
A concise synthesis of protected 5-cyano-l-tryptophan (Trp5CN ) has been developed for 2D IR spectroscopic investigations within either peptides or proteins. To assess the potential of differently substituted cyano-tryptophans, several model cyano-indole systems were characterized using IR spectroscopy. Upon assessment of their spectroscopic properties, Trp5CN was integrated into a model peptide sequence, Trp5CN -Gly-Phe4CN , to elucidate its structure. This peptide demonstrates the capability of this probe to capture structural information by 2D IR spectroscopy. The 2D IR spectrum of the peptide in water was simulated to reveal a unique spectral signature resulting from the presence of dipolar coupling. The coupling strength between cyano labels was determined to be 1.4 cm-1 by matching the slopes along the max contour for the simulated and experimental spectrum. Using transition dipole coupling, a distance between the two probes of 13 Å was calculated.
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Affiliation(s)
- Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Philip H Gilmartin
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
| | - Michael W Fennie
- Department of Chemistry, University of Scranton, 204 Monroe Ave., Scranton, PA, 18510, USA
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, 1664 N. Virginia Street, Reno, NV, 89557, USA
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11
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Synthesis of 5-Cyano-Tryptophan as a Two-Dimensional Infrared Spectroscopic Reporter of Structure. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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12
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Wang J. Ultrafast two-dimensional infrared spectroscopy for molecular structures and dynamics with expanding wavelength range and increasing sensitivities: from experimental and computational perspectives. INT REV PHYS CHEM 2017. [DOI: 10.1080/0144235x.2017.1321856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, The Chinese Academy of Sciences, Beijing, P.R. China
- College of Chemistry, University of Chinese Academy of Sciences, Beijing, P.R. China
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13
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Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017; 56:5283-5287. [PMID: 28374543 PMCID: PMC5543805 DOI: 10.1002/anie.201701874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/17/2022]
Abstract
Because of its importance in viral replication, the M2 proton channel of the influenza A virus has been the focus of many studies. Although we now know a great deal about the structural architecture underlying its proton conduction function, we know little about its conformational dynamics, especially those controlling the rate of this action. Herein, we employ a single-molecule fluorescence method to assess the dynamics of the inter-helical channel motion of both full-length M2 and the transmembrane domain of M2. The rate of this motion depends not only on the identity of the channel and membrane composition but also on the pH in a sigmoidal manner. For the full-length M2 channel, the rate is increased from approximately 190 μs-1 at high pH to approximately 80 μs-1 at low pH, with a transition midpoint at pH 6.1. Because the latter value is within the range reported for the conducting pKa value of the His37 tetrad, we believe that this inter-helical motion accompanies proton conduction.
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Affiliation(s)
- Chun-Wei Lin
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - Marta Barniol-Xicota
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, San Francisco, CA, 94158-2517, USA
| | - Feng Gai
- Ultrafast Optical Processes Laboratory, Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, 231 S. 34th Street, Philadelphia, PA, 19104, USA
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14
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Lin CW, Mensa B, Barniol-Xicota M, DeGrado WF, Gai F. Activation pH and Gating Dynamics of Influenza A M2 Proton Channel Revealed by Single-Molecule Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chun-Wei Lin
- Ultrafast Optical Processes Laboratory; Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - Marta Barniol-Xicota
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry; University of California San Francisco; 600 16th Street San Francisco CA 94158-2517 USA
| | - Feng Gai
- Ultrafast Optical Processes Laboratory; Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
- Department of Chemistry; University of Pennsylvania, Philadelphia; 231 S. 34th Street Philadelphia PA 19104 USA
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15
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Abaskharon RM, Brown SP, Zhang W, Chen J, Smith AB, Gai F. Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein. Chem Phys Lett 2017; 683:193-198. [PMID: 29033461 DOI: 10.1016/j.cplett.2017.03.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Applicability of this site-specific vibrational probe is demonstrated by using it to assess the dynamics of an aspartate ion buried inside a small protein via two-dimensional infrared spectroscopy.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Stephen P Brown
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Jianxin Chen
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.,Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
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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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