1
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Fan X, Wu J, Zhang T, Liu J. Electrochemical/Electrochemiluminescence Sensors Based on Vertically-Ordered Mesoporous Silica Films for Biomedical Analytical Applications. Chembiochem 2024:e202400320. [PMID: 38874487 DOI: 10.1002/cbic.202400320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/04/2024] [Accepted: 06/14/2024] [Indexed: 06/15/2024]
Abstract
Vertically-ordered mesoporous silica films (VMSF, also named as silica isoporous membranes) have shown tremendous potential in the field of electroanalytical sensors due to their unique features in terms of controllable and ultrasmall nanopores, high molecular selectivity and permeability, and mechanical stability. This review will present the recent progress on the biomedical analytical applications of VMSF, focusing on the small biomolecules, diseases-related biomarkers, drugs and cancer cells. Finally, conclusions with recent developments and future perspective of VMSF in the relevant fields will be envisioned.
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Affiliation(s)
- Xue Fan
- Department of Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jiayi Wu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Tongtong Zhang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Department of Hepatobiliary and Pancreatic Surgery, Hangzhou First People's Hospital, Hangzhou, 310006, China
| | - Jiyang Liu
- Department of Chemistry, School of Chemistry and Chemical Engineering, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China
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2
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Soenarjo AL, Lan Z, Sazanovich IV, Chan YS, Ringholm M, Jha A, Klug DR. The Transition from Unfolded to Folded G-Quadruplex DNA Analyzed and Interpreted by Two-Dimensional Infrared Spectroscopy. J Am Chem Soc 2023; 145:19622-19632. [PMID: 37647128 PMCID: PMC10510320 DOI: 10.1021/jacs.3c04044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 09/01/2023]
Abstract
A class of DNA folds/structures known collectively as G-quadruplexes (G4) commonly forms in guanine-rich areas of genomes. G4-DNA is thought to have a functional role in the regulation of gene transcription and telomerase-mediated telomere maintenance and, therefore, is a target for drugs. The details of the molecular interactions that cause stacking of the guanine-tetrads are not well-understood, which limits a rational approach to the drugability of G4 sequences. To explore these interactions, we employed electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectroscopy to measure extended vibrational coupling spectra for a parallel-stranded G4-DNA formed by the Myc2345 nucleotide sequence. We also tracked the structural changes associated with G4-folding as a function of K+-ion concentration. To classify the structural elements that the folding process generates in terms of vibrational coupling characteristics, we used quantum-chemical calculations utilizing density functional theory to predict the coupling spectra associated with given structures, which are compared against the experimental data. Overall, 102 coupling peaks are experimentally identified and followed during the folding process. Several phenomena are noted and associated with formation of the folded form. This includes frequency shifting, changes in cross-peak intensity, and the appearance of new coupling peaks. We used these observations to propose a folding sequence for this particular type of G4 under our experimental conditions. Overall, the combination of experimental 2DIR data and DFT calculations suggests that guanine-quartets may already be present before the addition of K+-ions, but that these quartets are unstacked until K+-ions are added, at which point the full G4 structure is formed.
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Affiliation(s)
- A. Larasati Soenarjo
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Zhihao Lan
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton
Laboratory, Harwell, Oxfordshire OX11 0QX, United Kingdom
| | - Yee San Chan
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
| | - Magnus Ringholm
- Hylleraas
Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Ajay Jha
- Rosalind
Franklin Institute, Harwell, Oxfordshire OX11 0QX, United Kingdom
- Department
of Pharmacology, University of Oxford, Oxford, OX1 3QT, United Kingdom
| | - David R. Klug
- Department
of Chemistry, Imperial College London, White City Campus, London W12 0BZ, United Kingdom
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3
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Long F, Xie H, Zhuang W. Identification of Trans- and Cis-2-Methylcyclopropanecarboxylic acid using EVV 2DIR spectroscopy: A theoretical study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Dicke SS, Alperstein AM, Schueler KL, Stapleton DS, Simonett SP, Fields CR, Chalyavi F, Keller MP, Attie AD, Zanni MT. Application of 2D IR Bioimaging: Hyperspectral Images of Formalin-Fixed Pancreatic Tissues and Observation of Slow Protein Degradation. J Phys Chem B 2021; 125:9517-9525. [PMID: 34396779 PMCID: PMC8769495 DOI: 10.1021/acs.jpcb.1c05554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used two-dimensional IR bioimaging to study the structural heterogeneity of formalin-fixed mouse pancreas. Images were generated from the hyperspectral data sets by plotting quantities associated with the amide I vibrational mode, which is created by the backbone carbonyl stretch. Images that measure the fundamental vibrational frequencies, cross peaks, and anharmonic shifts are presented. Histograms are generated for each quantity, providing averaged values and distributions around the mean that serve as metrics for protein structures. Images were generated from tissue that had been stored in a formalin fixation for 3, 8, and 48 weeks. Over this period, all three metrics show that that the β-sheet content of the samples increased, consistent with protein aggregation. Our results indicate that formalin fixation does not entirely arrest the degradation of a protein structure in pancreas tissue.
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Affiliation(s)
- Sidney S Dicke
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Ariel M Alperstein
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Shane P Simonett
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Caitlyn R Fields
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Farzaneh Chalyavi
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, Wisconsin 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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5
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Thielges MC. Transparent window 2D IR spectroscopy of proteins. J Chem Phys 2021; 155:040903. [PMID: 34340394 PMCID: PMC8302233 DOI: 10.1063/5.0052628] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Indiana University, Bloomington,
Indiana 47405, USA
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6
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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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7
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Donaldson PM. Photon echoes and two dimensional spectra of the amide I band of proteins measured by femtosecond IR - Raman spectroscopy. Chem Sci 2020; 11:8862-8874. [PMID: 34123140 PMCID: PMC8163424 DOI: 10.1039/d0sc02978e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infrared (IR) and Raman spectroscopy are fundamental techniques in chemistry, allowing the convenient determination of bond specific chemical composition and structure. Over the last decades, ultrafast multidimensional IR approaches using sequences of femtosecond IR pulses have begun to provide a new means of gaining additional information on molecular vibrational couplings, distributions of molecular structures and ultrafast molecular structural dynamics. In this contribution, new approaches to measuring multidimensional spectra involving IR and Raman processes are presented and applied to the study of the amide I band of proteins. Rephasing of the amide I band is observed using dispersed IR-Raman photon echoes and frequency domain 2D-IR-Raman spectra are measured by use of a mid-IR pulse shaper or over a broader spectral range using a tuneable picosecond laser. A simple pulse shaping approach to performing heterodyned time-domain Fourier Transform 2D-IR-Raman spectroscopy is introduced, revealing that the 2D-IR-Raman spectra distinguish homogeneous and inhomogeneous broadening in the same way as the well-established methods of 2D-IR spectroscopy. Across all datasets, the unique dependence of the amide I data on the IR and Raman strengths, vibrational anharmonicities and inhomogeneous broadening provides a fascinating spectroscopic view of the amide I band. New ultrafast 2D-IR-Raman photon echo spectroscopy techniques are introduced and applied to the structural analysis of proteins.![]()
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Affiliation(s)
- Paul M Donaldson
- Central Laser Facility, RCaH, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus Didcot OX11 0QX UK
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8
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Sowley H, Liu Z, Davies J, Peach R, Guo R, Sim S, Long F, Holdgate G, Willison K, Zhuang W, Klug DR. Detection of Drug Binding to a Target Protein Using EVV 2DIR Spectroscopy. J Phys Chem B 2019; 123:3598-3606. [PMID: 30848913 DOI: 10.1021/acs.jpcb.9b00501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We demonstrate that electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) can be used to detect the binding of a drug to a target protein-active site. The EVV 2DIR spectrum of the FGFR1 kinase target protein is found to have ∼200 detectable cross-peaks in the spectral region 1250-1750 cm-1/2600-3400 cm-1, with additional 63 peaks caused by the addition of a drug, SU5402. Of these 63 new peaks, it is shown that only six are due to protein-drug interactions, with the other 57 being due to vibrational coupling within the drug itself. Quantum mechanical calculations employing density functional theory are used to support assignment of the six binding-dependent peaks, with one being assigned to a known interaction between the drug and a backbone carbonyl group which forms part of the binding site. None of the 57 intramolecular coupling peaks associated with the drug molecule change substantially in either intensity or frequency when the drug binds to the target protein. This strongly suggests that the structure of the drug in the target binding site is essentially identical to that when it is not bound.
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Affiliation(s)
| | - ZhiQiang Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
| | | | | | | | | | - FengQin Long
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
| | - Geoffrey Holdgate
- Hit Discovery, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Macclesfield SK10 2NA , U.K
| | | | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on Structure of Matters , CAS , Fuzhou 350002 , P. R. China
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9
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Jansen TLC, Saito S, Jeon J, Cho M. Theory of coherent two-dimensional vibrational spectroscopy. J Chem Phys 2019; 150:100901. [DOI: 10.1063/1.5083966] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Thomas la Cour Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shinji Saito
- Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan and The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Jonggu Jeon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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10
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Handali JD, Sunden KF, Thompson BJ, Neff-Mallon NA, Kaufman EM, Brunold TC, Wright JC. Three Dimensional Triply Resonant Sum Frequency Spectroscopy Revealing Vibronic Coupling in Cobalamins: Toward a Probe of Reaction Coordinates. J Phys Chem A 2018; 122:9031-9042. [PMID: 30365322 DOI: 10.1021/acs.jpca.8b07678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triply resonant sum frequency (TRSF) spectroscopy is a fully coherent mixed vibrational-electronic spectroscopic technique that is ideally suited for probing the vibrational-electronic couplings that become important in driving reactions. We have used cyanocobalamin (CNCbl) and deuterated aquacobalamin (D2OCbl+) as model systems for demonstrating the feasibility of using the selectivity of coherent multidimensional spectroscopy to resolve electronic states within the broad absorption spectra of transition metal complexes and identify the nature of the vibrational and electronic state couplings. We resolve three short and long axis vibrational modes in the vibrationally congested 1400-1750 cm-1 region that are individually coupled to different electronic states in the 18 000-21 000 cm-1 region but have minimal coupling to each other. Double resonance with the individual vibrational fundamentals and their overtones selectively enhances the corresponding electronic resonances and resolves features within the broad absorption spectrum. This work demonstrates the feasibility of identifying coupling between different pairs of vibrational states with different electronic states that together form the reaction coordinate surface of transition metal enzymes.
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Affiliation(s)
- Jonathan D Handali
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Kyle F Sunden
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Blaise J Thompson
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Nathan A Neff-Mallon
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Emily M Kaufman
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - Thomas C Brunold
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
| | - John C Wright
- Department of Chemistry , University of Wisconsin-Madison , Madison Wisconsin 53706 , United States
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11
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Kern-Michler D, Neumann C, Mielke N, van Wilderen LJGW, Reinfelds M, von Cosel J, Santoro F, Heckel A, Burghardt I, Bredenbeck J. Controlling Photochemistry via Isotopomers and IR Pre-excitation. J Am Chem Soc 2018; 140:926-931. [PMID: 29182322 DOI: 10.1021/jacs.7b08723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is a photochemist's dream to be able to photoinduce a reaction of a specific molecular species in an ensemble of similar but not identical ones. The problem is that similar molecules often exhibit nearly identical UV-Vis absorption spectra, making them difficult or impossible to distinguish or to select spectroscopically. The ultrafast VIPER (VIbrationally Promoted Electronic Resonance) pulse sequence allows to pick a single species for electronic excitation based on its infrared spectrum. The latter usually shows more features, allowing the discrimination between species than the UV-Vis spectrum. Here, we show that it is possible to induce and monitor species-selective photochemistry even for molecules with virtually identical UV-Vis spectra, which is the case for isotopomers. Next to isotope-selective photochemistry in solution, applications to orthogonal photo-uncaging and species-selective spectroscopy and photochemistry in mixtures are within reach.
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Affiliation(s)
- Daniela Kern-Michler
- Institute of Biophysics, Goethe University Frankfurt , Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Carsten Neumann
- Institute of Biophysics, Goethe University Frankfurt , Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Nicole Mielke
- Institute of Biophysics, Goethe University Frankfurt , Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Luuk J G W van Wilderen
- Institute of Biophysics, Goethe University Frankfurt , Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Matiss Reinfelds
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jan von Cosel
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR) , UOS di Pisa, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Irene Burghardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , Max-von-Laue Str. 7, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt , Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
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12
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Ghosh A, Ostrander JS, Zanni MT. Watching Proteins Wiggle: Mapping Structures with Two-Dimensional Infrared Spectroscopy. Chem Rev 2017; 117:10726-10759. [PMID: 28060489 PMCID: PMC5500453 DOI: 10.1021/acs.chemrev.6b00582] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proteins exhibit structural fluctuations over decades of time scales. From the picosecond side chain motions to aggregates that form over the course of minutes, characterizing protein structure over these vast lengths of time is important to understanding their function. In the past 15 years, two-dimensional infrared spectroscopy (2D IR) has been established as a versatile tool that can uniquely probe proteins structures on many time scales. In this review, we present some of the basic principles behind 2D IR and show how they have, and can, impact the field of protein biophysics. We highlight experiments in which 2D IR spectroscopy has provided structural and dynamical data that would be difficult to obtain with more standard structural biology techniques. We also highlight technological developments in 2D IR that continue to expand the scope of scientific problems that can be accessed in the biomedical sciences.
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Affiliation(s)
| | - Joshua S. Ostrander
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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13
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Wright JC. Applications of the New Family of Coherent Multidimensional Spectroscopies for Analytical Chemistry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:45-70. [PMID: 28375700 DOI: 10.1146/annurev-anchem-061516-045349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new family of vibrational and electronic spectroscopies has emerged, comprising the coherent analogs of traditional analytical methods. These methods are also analogs of coherent multidimensional nuclear magnetic resonance (NMR) spectroscopy. This new family is based on creating the same quantum mechanical superposition states called multiple quantum coherences (MQCs). NMR MQCs are mixtures of nuclear spin states that retain their quantum mechanical phase information for milliseconds. The MQCs in this new family are mixtures of vibrational and electronic states that retain their phases for picoseconds or shorter times. Ultrafast, high-intensity coherent beams rapidly excite multiple states. The excited MQCs then emit bright beams while they retain their phases. Time-domain methods measure the frequencies of the MQCs by resolving their phase oscillations, whereas frequency-domain methods measure the resonance enhancements of the output beam while scanning the excitation frequencies. The resulting spectra provide multidimensional spectral signatures that increase the spectroscopic selectivity required for analyzing complex samples.
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Affiliation(s)
- John C Wright
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706;
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14
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Chen PC. An Introduction to Coherent Multidimensional Spectroscopy. APPLIED SPECTROSCOPY 2016; 70:1937-1951. [PMID: 27940533 DOI: 10.1177/0003702816669730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/05/2016] [Indexed: 06/06/2023]
Abstract
Coherent multidimensional spectroscopy is a field that has drawn much attention as an optical analogue to multidimensional nuclear magnetic resonance imaging. Coherent multidimensional spectroscopic techniques produce spectra that show the magnitude of an optical signal as a function of two or more pulsed laser frequencies. Spectra can be collected in either the frequency or the time domain. In addition to improving resolution and overcoming spectral congestion, coherent multidimensional spectroscopy provides the ability to investigate and conduct studies based upon the relationship between different peaks. The purpose of this paper is to provide a general introduction to the area of coherent multidimensional spectroscopy, to provide a brief overview of current experimental approaches, and to discuss some emerging developments in this relatively young field.
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15
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Deng J, Wang L, Ni J, Beretov J, Wasinger V, Wu D, Duan W, Graham P, Li Y. Proteomics discovery of chemoresistant biomarkers for ovarian cancer therapy. Expert Rev Proteomics 2016; 13:905-915. [DOI: 10.1080/14789450.2016.1233065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Junli Deng
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
- Department of Gynecological Oncology, Henan Cancer Hospital, Zhengzhou, China
- Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Department of Gynecological Oncology, Henan Cancer Hospital, Zhengzhou, China
- Zhengzhou University, Zhengzhou, China
| | - Jie Ni
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
| | - Julia Beretov
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
| | - Valerie Wasinger
- Mark Wainwright Analytical Centre, Bioanalytical Mass Spectrometry Facility, University of New South Wales (UNSW), Kensington, Australia
- School of Medical Sciences, University of New South Wales (UNSW), Kensington, Australia
| | - Duojia Wu
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
| | - Wei Duan
- School of Medicine, Deakin University, Waurn Ponds, Australia
| | - Peter Graham
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
| | - Yong Li
- Cancer Care Centre, St George Hospital, Kogarah, Australia
- St George and Sutherland Clinical School, University of New South Wales (UNSW), Kensington, Australia
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16
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Ostrander JS, Serrano AL, Ghosh A, Zanni MT. Spatially Resolved Two-Dimensional Infrared Spectroscopy via Wide-Field Microscopy. ACS PHOTONICS 2016; 3:1315-1323. [PMID: 27517058 PMCID: PMC4976945 DOI: 10.1021/acsphotonics.6b00297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report the first wide-field microscope for measuring two-dimensional infrared (2D IR) spectroscopic images. We concurrently collect more than 16 000 2D IR spectra, made possible by a new focal plane array detector and mid-IR pulse shaping, to generate hyperspectral images with multiple frequency dimensions and diffraction-limited spatial resolution. Both frequency axes of the spectra are collected in the time domain by scanning two pairs of femtosecond pulses using a dual acousto-optic modulator pulse shaper. The technique is demonstrated by imaging a mixture of metal carbonyl absorbed polystyrene beads. The differences in image formation between FTIR and 2D IR microscopy are also explored by imaging a patterned USAF test target. We find that our 2D IR microscope has diffraction-limited spatial resolution and enhanced contrast compared to FTIR microscopy because of the nonlinear scaling of the 2D IR signal to the absorptivity coefficient for the vibrational modes. Images generated using off-diagonal peaks, created from vibrational anharmonicities, improve the molecular discrimination and eliminate noise. Two-dimensional wide-field IR microscopy provides information on vibrational lifetimes, molecular couplings, transition dipole orientations, and many other quantities that can be used for creating image contrast to help disentangle and interpret complex and heterogeneous samples. Such experiments made possible could include the study of amyloid proteins in tissues, protein folding in heterogeneous environments, and structural dynamics in devices employing mid-IR materials.
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van Wilderen LJGW, Bredenbeck J. Von ultraschnellen Strukturbestimmungen bis zum Steuern von Reaktionen: mehrdimensionale gemischte IR/nicht-IR-Schwingungsspektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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van Wilderen LJGW, Bredenbeck J. From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies. Angew Chem Int Ed Engl 2015; 54:11624-40. [PMID: 26394274 DOI: 10.1002/anie.201503155] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/27/2022]
Abstract
Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.
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Affiliation(s)
| | - Jens Bredenbeck
- Institute of Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main (Germany).
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19
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Abstract
Two-dimensional infrared (2D IR) spectroscopy has recently emerged as a powerful tool with applications in many areas of scientific research. The inherent high time resolution coupled with bond-specific spatial resolution of IR spectroscopy enable direct characterization of rapidly interconverting species and fast processes, even in complex systems found in chemistry and biology. In this minireview, we briefly outline the fundamental principles and experimental procedures of 2D IR spectroscopy. Using illustrative example studies, we explain the important features of 2D IR spectra and their capability to elucidate molecular structure and dynamics. Primarily, this minireview aims to convey the scope and potential of 2D IR spectroscopy by highlighting select examples of recent applications including the use of innate or introduced vibrational probes for the study of nucleic acids, peptides/proteins, and materials.
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Affiliation(s)
- Amanda L Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana, 47405, USA.
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Luo L, Dong LY, Yan QG, Cao SJ, Wen XT, Huang Y, Huang XB, Wu R, Ma XP. Research progress in applying proteomics technology to explore early diagnosis biomarkers of breast cancer, lung cancer and ovarian cancer. Asian Pac J Cancer Prev 2015; 15:8529-38. [PMID: 25374164 DOI: 10.7314/apjcp.2014.15.20.8529] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
According to the China tumor registry 2013 annual report , breast cancer, lung cancer, and ovarian cancer are three common cancers in China nowadays, with high mortality due to the absence of early diagnosis technology. However, proteomics has been widespreadly implanted into every field of life science and medicine as an important part of post-genomics era research. The development of theory and technology in proteomics has provided new ideas and research fields for cancer research. Proteomics can be used not only for elucidating the mechanisms of carcinogenesis focussing on whole proteins of the tissue or cell, but also seeking the biomarkers for diagnosis and therapy of cancer. In this review, we introduce proteomics principles, covering current technology used in exploring early diagnosis biomarkers of breast cancer, lung cancer and ovarian cancer.
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Affiliation(s)
- Lu Luo
- College of Veterinary Medicine, Sichuan Agricultural University, Yaan, Sichuan, China E-mail :
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21
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Huerta-Viga A, Amirjalayer S, Domingos SR, Meuzelaar H, Rupenyan A, Woutersen S. The structure of salt bridges between Arg+ and Glu− in peptides investigated with 2D-IR spectroscopy: Evidence for two distinct hydrogen-bond geometries. J Chem Phys 2015; 142:212444. [DOI: 10.1063/1.4921064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Adriana Huerta-Viga
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Saeed Amirjalayer
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Sérgio R. Domingos
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Heleen Meuzelaar
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Alisa Rupenyan
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Sander Woutersen
- Van ’t Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
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22
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Rezende Valim L, Davies JA, Tveen Jensen K, Guo R, Willison KR, Spickett CM, Pitt AR, Klug DR. Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy. J Phys Chem B 2014; 118:12855-64. [PMID: 25347525 DOI: 10.1021/jp509053q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy.
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23
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Chapman HN. Disruptive photon technologies for chemical dynamics. Faraday Discuss 2014; 171:525-43. [DOI: 10.1039/c4fd00156g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A perspective of new and emerging technologies for chemical dynamics is given, with an emphasis on the use of X-ray sources that generate sub-picosecond pulses. The two classes of experimental techniques used for time-resolved measurements of chemical processes and their effects are spectroscopy and imaging, where the latter includes microscopy, diffractive imaging, and crystallography. X-Ray free-electron lasers have brought new impetus to the field, allowing not only temporal and spatial resolution at atomic time and length scales, but also bringing a new way to overcome limitations due to perturbation of the sample by the X-ray probe by out-running radiation damage. Associated instrumentation and methods are being developed to take advantage of the new opportunities of these sources. Once these methods of observational science have been mastered it should be possible to use the new tools to directly control those chemical processes.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science
- DESY
- 22607 Hamburg, Germany
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24
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Zhao W, He A, Xu Y. Second hyperpolarizability of C-H, C-D, and C≡N stretch vibrations determined from computational Raman activities and a comparison with experiments. J Phys Chem B 2013; 117:15812-8. [PMID: 24020330 DOI: 10.1021/jp4073119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have recently demonstrated that the second hyperpolarizability γ of a selected vibrational mode of a molecule can be determined by using the computational Raman activity against an internal standard with a known Raman γ value. This approach provides a convenient way for prediction of the γ magnitude of DOVE four wave mixing spectroscopy, an optical analogue to two-dimensional (2D) NMR. Here, by using the Hartree-Fock (HF) method, the density functional theory (DFT) method, and the second-order Møller-Plesset perturbation theory (MP2) method, we extend our early work from the less anharmonic region <2000 cm(-1) into the more anharmonic region >2000 cm(-1) covering C-H, C-D, and C≡N stretching modes of benzene, deuterated benzene, acetonitrile, deuterated acetonitrile, and tetrahydrofuran. The computed Raman γ values of these vibrational modes have been determined by using either the 992 cm(-1) Raman band of benzene or the compound's own Raman band (C-C stretch) around 800-1000 cm(-1) as an internal standard. In this more anharmonic region, the HF method with a larger basis set provides the best outputs and the predicted Raman γ values agree well with experimental values for most of the vibrational modes studied. By choosing a suitable method and basis set, this facile approach could be applied to a broader spectral range for Raman γ estimation of various materials.
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Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock , 2801 South University Avenue, Little Rock, Arkansas 72204, United States
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Zhao W, He A, Xu Y. Raman second hyperpolarizability determination using computational Raman activities and a comparison with experiments. J Phys Chem A 2013; 117:6217-23. [PMID: 23683174 DOI: 10.1021/jp400447a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Doubly vibrationally enhanced (DOVE) four-wave mixing spectroscopy, an optical analogue to 2D NMR, involves two infrared transitions and a Raman transition. The magnitude of the DOVE second hyperpolarizability γ (or third-order susceptibility χ((3))) can be theoretically estimated if the values of the dipolar moments of the two infrared transitions and the γ of the Raman transition are known. The Raman γ can be measured by using the four-wave mixing interferometric method or conventional Raman spectroscopy in the presence of an internal standard. In this work, we examine if one can use the Raman activity computed from density functional theory calculation to determine the Raman γ of selected vibrational modes of several samples including deuterated benzene, acetonitrile, tetrahydrofuran, and sodium benzoate aqueous solution. The 992 cm(-1) Raman band of benzene serves as an internal standard for organic solvents, and the 880 cm(-1) Raman band of hydrogen peroxide is for the aqueous solution sample with known γ values. We have found that the predicted Raman γ values from the computational Raman activities match experimental data reasonably well, suggesting a facile approach to predict the Raman γ of interested systems.
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Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock, 2801 South University Avenue, Little Rock, Arkansas 72204, USA.
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27
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Guo R, Mukamel S, Klug DR. Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method. Phys Chem Chem Phys 2012; 14:14023-33. [PMID: 22990297 DOI: 10.1039/c2cp42593a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate the use of a new vibrational transition density cube (VTDC) method for determining the geometry of complexes in a molecular liquid mixture from electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectra. The VTDC method was used to calculate the electrically-mediated intermolecular vibrational coupling and thereby the EVV 2DIR spectra. Using the 1:1 benzonitrile-phenylacetylene (BN-PA) liquid mixture as a test case, the new method leads to a distance of 3.60 Å between the interacting BN-PA pair, a much more accurate value than the distance previously obtained using a dipolar approximation for the electrical coupling. We also show that molecular dynamics simulations of the liquid mixture predict a modal geometry of complexation which agrees well with the geometry determined from the 2DIR data via VTDC analysis. We therefore conclude the combination of VTDC and EVV 2DIR data is a useful approach for the determination of the geometry of molecular complexes in the condensed phase.
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Affiliation(s)
- Rui Guo
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, London SW7 2AZ, UK
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28
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Goyder MS, Willison KR, Klug DR, Demello AJ, Ces O. Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins. BMB Rep 2012; 45:233-8. [PMID: 22531133 DOI: 10.5483/bmbrep.2012.45.4.233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a top down separation platform for yeast ribosomal proteins using affinity chromatography and capillary electrophoresis which is designed to allow deposition of proteins onto a substrate. FLAG tagged ribosomes were affinity purified, and rRNA acid precipitation was performed on the ribosomes followed by capillary electrophoresis to separate the ribosomal proteins. Over 26 peaks were detected with excellent reproducibility (<0.5% RSD migration time). This is the first reported separation of eukaryotic ribosomal proteins using capillary electrophoresis. The two stages in this workflow, affinity chromatography and capillary electrophoresis, share the advantages that they are fast, flexible and have small sample requirements in comparison to more commonly used techniques. This method is a remarkably quick route from cell to separation that has the potential to be coupled to high throughput readout platforms for studies of the ribosomal proteome.
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Affiliation(s)
- Miriam S Goyder
- The Single Cell Proteomics Group, Institute of Chemical Biology, Department of Chemistry, Imperial College London, South Kensington, London, UK
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29
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Anna JM, Baiz CR, Ross MR, McCanne R, Kubarych KJ. Ultrafast equilibrium and non-equilibrium chemical reaction dynamics probed with multidimensional infrared spectroscopy. INT REV PHYS CHEM 2012. [DOI: 10.1080/0144235x.2012.716610] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Christiansen O. Selected new developments in vibrational structure theory: potential construction and vibrational wave function calculations. Phys Chem Chem Phys 2012; 14:6672-87. [DOI: 10.1039/c2cp40090a] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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32
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An overview of human protein databases and their application to functional proteomics in health and disease. SCIENCE CHINA-LIFE SCIENCES 2011; 54:988-98. [PMID: 22173304 DOI: 10.1007/s11427-011-4247-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Accepted: 11/23/2011] [Indexed: 02/02/2023]
Abstract
Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs. In recent years, a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery. In addition to being used to annotate the proteome, these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease. Here, we present a comprehensive review of the major human protein bioinformatics databases. We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.
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33
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Zhao W. Measurement of Raman χ(3) and theoretical estimation of DOVE four wave mixing of hydrogen peroxide. J Phys Chem A 2011; 115:6525-30. [PMID: 21591714 DOI: 10.1021/jp202977v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hydrogen peroxide has strong infrared (IR) transitions ν(6) and its combination band ν(2)+ν(6), which may provide a unique opportunity to implement doubly vibrationally enhanced (DOVE) four wave mixing (FWM) for directly measuring hydrogen peroxide in spectrally overcrowded mixtures. In this work, the magnitude of the DOVE third-order susceptibility χ(3) was theoretically estimated. By using a FWM interferometric method, one of the strongest Raman bands, O-O stretch ν(3) Raman χ(3) of 30 wt % H(2)O(2), was first measured to be 1.2 × 10(-14) esu. The Raman χ(3) of ν(2) was then determined to be 5.3 × 10(-15) esu based on their relative Raman intensities. The resulting Raman χ(3) of ν(2) was used to calculate the DOVE χ(3) of (ν(6), ν(2)+ν(6)), together with the dipolar moments of the two IR transitions determined from IR absorption measurement. The calculated value of DOVE-IR χ(3) was 1.1 × 10(-13) esu for pure H(2)O(2), about 1.5 times larger than that of the strong ring breathing Raman band of benzene. The large DOVE χ(3) suggests the feasibility of direct measurement of hydrogen peroxide in an aqueous environment using DOVE four wave mixing.
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Affiliation(s)
- Wei Zhao
- Department of Chemistry, University of Arkansas at Little Rock, 2801 South University Avenue, Little Rock, Arkansas 72204, United States.
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34
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Affiliation(s)
- John C. Wright
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706;
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35
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Ye S, Wei F. An approach to compatible multiple nonlinear vibrational spectroscopy measurements using a commercial sum frequency generation system. Analyst 2011; 136:2489-94. [DOI: 10.1039/c1an15032d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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36
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Guo R, Miele M, Gardner EM, Fournier F, Kornau KM, Gould IR, Klug DR. Potential for the detection of molecular complexes and determination of interaction geometry by 2DIR: Application to protein sciences. Faraday Discuss 2011; 150:161-74; discussion 257-92. [PMID: 22457947 DOI: 10.1039/c1fd00007a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Rui Guo
- Institute of Chemical Biology, Imperial College London, London SW7 2AZ, United Kingdom
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37
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Lee KK, Park KH, Park S, Jeon SJ, Cho M. Polarization-Angle-Scanning 2DIR Spectroscopy of Coupled Anharmonic Oscillators: A Polarization Null Angle Method. J Phys Chem B 2010; 115:5456-64. [DOI: 10.1021/jp1102274] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Kyung-Koo Lee
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
| | - Kwang-Hee Park
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
| | - Seung-Joon Jeon
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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38
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Choi JH, Cho M. Communication: Polarization-angle-scanning two-dimensional infrared spectroscopy of antiparallel β-sheet polypeptide: Additional dimensions in two-dimensional optical spectroscopy. J Chem Phys 2010; 133:241102. [DOI: 10.1063/1.3522765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Kramer MA, Andrews B, Hugar DL, Jaitli A, Larsen SB, Kline BP, McEllen KN, Agrawal N, Su SM, Dammu SA, Kammeyer RM, Ivanisevic A. Characterization of conformational adsorbate changes on a tissue-derived substrate using Fourier transform infrared spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18083-18088. [PMID: 21067159 DOI: 10.1021/la1038766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Fourier transform infrared (FT-IR) spectroscopy is utilized to observe adsorbate interactions with a tissue-derived collagen scaffold extracted from the Bruch's membrane of pig eyes. The characterization includes conformational changes in isoleucine, polyisoleucine, collagen-binding peptide, RGD-tagged collagen-binding peptide, and laminin after adsorption onto the substrate. Isotopically labeled isoleucine is further utilized to understand changes in the biomolecular structure upon binding to a tissue-derived surface. The adsorbates associated with the collagen scaffold predominately through hydrophobic interactions and hydrogen bonding. The results of this study can be used to improve our understanding of surface chemistry changes during the engineering of biomimetic scaffolds before and after biomolecule adsorption.
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Affiliation(s)
- Marcus A Kramer
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States
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40
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Donaldson PM, Willison KR, Klug DR. Generation of simplified protein Raman spectra using three-color picosecond coherent anti-stokes Raman spectroscopy. J Phys Chem B 2010; 114:12175-81. [PMID: 20804132 DOI: 10.1021/jp1061607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The well-known and prominent marker bands of aromatic amino acids in Raman spectra of protein and peptide films are revisited in the frequency and time domains using three-color picosecond coherent anti-Stokes Raman spectroscopy (CARS). We show here that control of the probe delay allows the narrow width/long lifetime states to be observed free not only from nonresonant background and fluorescence contamination but also free from the spectral congestion that arises from the complex background of spectrally broader (shorter lifetime) vibrational modes. The reasonable limits of detection obtained indicate that such CARS methods may be useful for quantitative analysis of protein composition.
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Affiliation(s)
- Paul M Donaldson
- The Single Cell Proteomics Group, Chemical Biology Centre, Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, United Kingdom
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41
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Baiz CR, McCanne R, Kubarych KJ. Transient vibrational echo versus transient absorption spectroscopy: a direct experimental and theoretical comparison. APPLIED SPECTROSCOPY 2010; 64:1037-1044. [PMID: 20828441 DOI: 10.1366/000370210792434369] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Transient dispersed vibrational echo (DVE) spectroscopy is a practical alternative to transient-absorption spectroscopy because it affords increased sensitivity as well as greater signal-to-noise ratio without the need to detect a reference spectrum. However, as a third-order nonlinear probe, the extraction of kinetic information from transient-DVE is somewhat cumbersome compared to transient absorption. This article provides a direct experimental and theoretical comparison between transient-absorption and transient-DVE measurements and presents a framework for analyzing kinetic measurements while exploring the implications of making some simplifying assumptions in the data analysis. The equations for computing the signal-to-noise ratios under different experimental conditions are derived and used in the analysis of the experimental data. The results, obtained under the same experimental conditions, show that for a relatively strong terminal carbonyl stretching mode, signal-to-noise ratios in transient-DVE spectroscopy are approximately 2.5 times greater than transient absorption. The experimental results along with the theoretical models indicate that transient-DVE could become an attractive alternative to transient-absorption spectroscopy for measuring the kinetics of light-induced processes.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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Abstract
Advances in the generation and interpretation of proteomics data have spurred a transition from focusing on protein identification to functional analysis. Here we review recent proteomics results that have elucidated new aspects of the roles and regulation of signal transduction pathways in cancer using the epidermal growth factor receptor (EGFR), ERK and breakpoint cluster region (BCR)-ABL1 networks as examples. The emerging theme is to understand cancer signalling as networks of multiprotein machines which process information in a highly dynamic environment that is shaped by changing protein interactions and post-translational modifications (PTMs). Cancerous genetic mutations derange these protein networks in complex ways that are tractable by proteomics.
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Affiliation(s)
- Walter Kolch
- Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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