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Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
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2
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Muhammad P, Hanif S, Yan J, Rehman FU, Wang J, Khan M, Chung R, Lee A, Zheng M, Wang Y, Shi B. SERS-based nanostrategy for rapid anemia diagnosis. NANOSCALE 2020; 12:1948-1957. [PMID: 31907500 DOI: 10.1039/c9nr09152a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Iron detection is one of the critical markers to diagnose multiple blood-related disorders that correspond to various biological dysfunctions. The currently available anemia detection approach can be used only for pre-treated blood samples that interfere with the actual iron level in blood. Real-time detection approaches with higher sensitivity and specificity are certainly needed to cope with the commercial level clinical analyses. Herein, we presented a novel strategy to determine the blood iron that can be easily practiced at commercial levels. The blend of well-known iron-cyanide chemistry with nanotechnology is advantageous with ultrahigh sensitivity in whole blood analysis without any pre-treatments. This approach is a combined detection system of the conventional assay (UV-visible spectroscopy) with surface-enhanced Raman scattering (SERS). Organic cyanide modified silver nanoparticles (cAgNPs) can selectively respond to Fe3+ ions and Hb protein with a detection limit of 10 fM and 0.46 μg mL-1, respectively, without being affected by matrix interfering species in the complex biological fluid. We confirmed the clinical potential of our new cAgNPs by assessing iron-status in multiple anemia patients and normal controls. Our SERS-based iron quantitation approach is highly affordable for bulk-samples, cheap, quick, flexible, and useful for real-time clinical assays. Such a method for metal-chelation has extendable features of therapeutics molecular tracking within more complex living systems at cellular levels.
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Affiliation(s)
- Pir Muhammad
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences Henan University Kaifeng, Henan 475004, China.
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Kossowska D, Park K, Park JY, Lim C, Kwak K, Cho M. Rational Design of an Acetylenic Infrared Probe with Enhanced Dipole Strength and Increased Vibrational Lifetime. J Phys Chem B 2019; 123:6274-6281. [DOI: 10.1021/acs.jpcb.9b04925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Chaiho Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
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Kossowska D, Lee G, Han H, Kwak K, Cho M. Simultaneous enhancement of transition dipole strength and vibrational lifetime of an alkyne IR probe via π-d backbonding and vibrational decoupling. Phys Chem Chem Phys 2019; 21:24919-24925. [DOI: 10.1039/c9cp04356j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alkyne IR probes 1–6 with Si and S (or Se) atoms incorporated into the CC bond were synthesized, and the vibrational properties of their CC stretch mode were studied using FTIR and femtosecond IR PP spectroscopies and quantum chemical calculations.
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Affiliation(s)
- Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
| | - Giseong Lee
- Department of Chemistry
- Korea University
- Seoul 02841
- Korea
| | - Hogyu Han
- Department of Chemistry
- Korea University
- Seoul 02841
- Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 02841
- Korea
- Department of Chemistry
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Eckert PA, Kubarych KJ. Solvent Quality Controls Macromolecular Structural Dynamics of a Dendrimeric Hydrogenase Model. J Phys Chem B 2018; 122:12154-12163. [PMID: 30427195 DOI: 10.1021/acs.jpcb.8b07259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We report a spectroscopic investigation of the ultrafast dynamics of the second-generation poly(aryl ether) dendritic hydrogenase model using two-dimensional infrared (2D-IR) spectroscopy to probe the metal carbonyl vibrations of the dendrimer and a reference small molecule, [Fe(μ-S)(CO)3]2. We find that the structural dynamics of the dendrimer are reflected in a slow phase of the spectral diffusion, which is absent from [Fe(μ-S)(CO)3]2, and we relate the slow phase to the quality of the solvent for poly(aryl ether) dendrimers. We observe a solvent-dependent modulation of the initial phase of vibrational relaxation of the carbonyl groups, which we attribute to an inhibition of solvent assistance in the intramolecular vibrational redistribution process for the dendrimer. There is also a clear solvent dependence of the vibrational frequencies of both the dendrimer and [Fe(μ-S)(CO)3]2. Our data represent the first 2D-IR study of a dendritic complex and provide insight into the solvent dependence of molecular conformation in solution and the ultrafast dynamics of moderately sized, conformationally mobile compounds.
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Affiliation(s)
- Peter A Eckert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
| | - Kevin J Kubarych
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 49109 , United States
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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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Lee G, Kossowska D, Lim J, Kim S, Han H, Kwak K, Cho M. Cyanamide as an Infrared Reporter: Comparison of Vibrational Properties between Nitriles Bonded to N and C Atoms. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00887] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giseong Lee
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Joonhyung Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Soobin Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
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Hoffman DJ, Fayer MD. Discontinuity in Fast Dynamics at the Glass Transition of ortho-Terphenyl. J Phys Chem B 2017; 121:10417-10428. [PMID: 29039665 DOI: 10.1021/acs.jpcb.7b08301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of the molecular glass former ortho-terphenyl through the glass transition were observed with two-dimensional infrared vibrational spectroscopy measurements of spectral diffusion using the small probe molecule phenylselenocyanate. Although the slow diffusive motions were not visible on the experimental time scale, a picosecond-scale exponential relaxation was observed at temperatures from above to well below the glass transition temperature. The characteristic time scale has a smooth temperature dependence from the liquid into the glass phase, but the range of vibrational frequencies the probe samples displayed a discontinuity at the glass transition temperature. Complementary pump-probe experiments associate the observed motion with density fluctuations. The key features of the dynamics are reproduced with a simple corrugated well potential energy surface model. In addition, the temperature dependence of the homogeneous vibrational dephasing was found to have a T2 functional form, where T is the absolute temperature.
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Affiliation(s)
- David J Hoffman
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Michael D Fayer
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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Hoffman DJ, Sokolowsky KP, Fayer MD. Direct observation of dynamic crossover in fragile molecular glass formers with 2D IR vibrational echo spectroscopy. J Chem Phys 2017; 146:124505. [DOI: 10.1063/1.4978852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- David J. Hoffman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Falvo C. A new interpretation of the meaning of the center of line slope from a two-dimensional infrared spectrum. J Chem Phys 2016; 144:234103. [PMID: 27334150 DOI: 10.1063/1.4953848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
This article presents a new approximation to understand the connection between the center of line slope from a single peak of a two-dimensional (2D) infrared spectrum and the frequency-frequency correlation function. This approximation which goes beyond the short-time approximation includes explicitly pure dephasing mechanisms by introducing a time parameter that separates the fast fluctuations and slow fluctuations. While in the short-time approximation, the center of line slope is given by the normalized frequency fluctuations auto-correlation function, I show using this new approximation that the center of line slope measures on long time scales a shifted and scaled correlation function. The results present a new interpretation of the meaning of the center of line slope that allows for a better understanding of what 2D experiments can measure. To illustrate these findings, I compare this approximation with the short-time approximation for several examples of frequency-frequency correlation functions. I also give an estimate of the value of the time separation parameter for a correlation function with a simple exponential decay.
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Affiliation(s)
- Cyril Falvo
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
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Kundu A, Kwak K, Cho M. Water Structure at the Lipid Multibilayer Surface: Anionic Versus Cationic Head Group Effects. J Phys Chem B 2016; 120:5002-7. [PMID: 27171689 DOI: 10.1021/acs.jpcb.6b02340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Membrane water interface is a potential reaction site for many biochemical reactions. Therefore, a molecular level understanding of water structure and dynamics that strongly depend on the chemical structure of lipid is prerequisite for elucidating the role of water in biological reactions on membrane surface. Recently, we carried out femtosecond infrared pump-probe studies of water structure and dynamics at multibilayer surfaces of zwitterionic phosphatidylcholine-analogue lipid ( J. Phys. Chem. Lett. 2016 , 7 , 741 ). Here, to further elucidate the anionic and cationic headgroup effects on water, we study vibrational dynamics of water on lipid multibilayers formed by anionic phospho-glycerol lipid molecules as well as by cationic choline-derivatized lipid molecules. We observed two significantly different vibrational lifetime components (very fast 0.5 ps and slow 1.9 ps) of the OD stretch mode of HOD molecules at the negatively charged phospho-lipid multibilayer whereas only one vibrational lifetime component (1.6 ps) was observed at the positively charged choline-derivatized lipid multibilayer. From the detailed analyses about the vibrational energy and rotational relaxations of HOD molecules in lipid multibilayers composed of anionic lipid with phosphate and cationic lipid without phosphate, the role of phosphate group in structuring water molecules at phospholipid membrane interface is revealed.
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Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
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