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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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2
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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4
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Li Q, Wang X, Xiong X, Zhu S, Meng Z, Hong Y, Lin C, Liu X, Lin Y. Graphene-supported biomimetic catalysts with synergistic effect of adsorption and degradation for efficient dye capture and removal. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.04.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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5
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Kiefer LM, Kubarych KJ. Two-dimensional infrared spectroscopy of coordination complexes: From solvent dynamics to photocatalysis. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
Coherent two-dimensional (2D) optical spectroscopy has revolutionized our ability to probe many types of couplings and ultrafast dynamics in complex quantum systems. The dynamics and function of any quantum system strongly depend on couplings to the environment. Thus, studying coherent interactions for different environments remains a topic of tremendous interest. Here we introduce coherent 2D electronic mass spectrometry that allows 2D measurements on effusive molecular beams and thus on quantum systems with minimum system–bath interaction and employ this to identify the major ionization pathway of 3d Rydberg states in NO2. Furthermore, we present 2D spectra of multiphoton ionization, disclosing distinct differences in the nonlinear response functions leading to the ionization products. We also realize the equivalent of spectrally resolved transient-absorption measurements without the necessity for acquiring weak absorption changes. Using time-of-flight detection introduces cations as an observable, enabling the 2D spectroscopic study on isolated systems of photophysical and photochemical reactions. Multidimensional spectroscopy is a powerful tool in exploring photo-induced dynamics and electron coupling processes in molecules. Here the authors demonstrate coherent two-dimensional electronic mass spectrometry on molecular beams and its application to photoionization studies of the NO2 molecule.
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7
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Introduction to State-of-the-Art Multidimensional Time-Resolved Spectroscopy Methods. Top Curr Chem (Cham) 2018; 376:28. [DOI: 10.1007/s41061-018-0206-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
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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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9
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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10
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Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate Binding Primes Human Tryptophan 2,3-Dioxygenase for Ligand Binding. J Phys Chem B 2017; 121:7412-7420. [PMID: 28715185 DOI: 10.1021/acs.jpcb.7b03463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human heme enzyme tryptophan 2,3-dioxygenase (hTDO) catalyzes the insertion of dioxygen into its cognate substrate, l-tryptophan (l-Trp). Its active site structure is highly dynamic, and the mechanism of enzyme-substrate-ligand complex formation and the ensuing enzymatic reaction is not yet understood. Here we have studied complex formation in hTDO by using time-resolved optical and infrared spectroscopy with carbon monoxide (CO) as a ligand. We have observed that both substrate-free and substrate-bound hTDO coexist in two discrete conformations with greatly different ligand binding rates. In the fast rebinding hTDO conformation, there is facile ligand access to the heme iron, but it is greatly hindered in the slowly rebinding conformation. Spectroscopic evidence implicates active site solvation as playing a crucial role for the observed kinetic differences. Substrate binding shifts the conformational equilibrium markedly toward the fast species and thus primes the active site for subsequent ligand binding, ensuring that formation of the ternary complex occurs predominantly by first binding l-Trp and then the ligand. Consequently, the efficiency of catalysis is enhanced because O2 binding prior to substrate binding, resulting in nonproductive oxidation of the heme iron, is greatly suppressed.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Vincent Hahn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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11
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Nienhaus K, Nickel E, Nienhaus GU. Substrate binding in human indoleamine 2,3-dioxygenase 1: A spectroscopic analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:453-463. [DOI: 10.1016/j.bbapap.2017.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/22/2017] [Accepted: 02/07/2017] [Indexed: 11/27/2022]
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12
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Schubert A, Falvo C, Meier C. Mixed quantum-classical simulations of the vibrational relaxation of photolyzed carbon monoxide in a hemoprotein. J Chem Phys 2016; 145:054108. [DOI: 10.1063/1.4959859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Alexander Schubert
- Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse, France
| | - Cyril Falvo
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Christoph Meier
- Laboratoire Collisions Agrégats et Réactivité, IRSAMC, UMR CNRS 5589, Université Paul Sabatier, 31062 Toulouse, France
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13
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Soloviov M, Das AK, Meuwly M. Strukturelle Interpretation metastabiler Zustände in Myoglobin-NO. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Maksym Soloviov
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
| | - Akshaya K. Das
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
| | - Markus Meuwly
- Departement für Chemie; Universität Basel; Klingelbergstraße 80 4056 Basel Schweiz
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14
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Soloviov M, Das AK, Meuwly M. Structural Interpretation of Metastable States in Myoglobin-NO. Angew Chem Int Ed Engl 2016; 55:10126-30. [DOI: 10.1002/anie.201604552] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Maksym Soloviov
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Akshaya K. Das
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
| | - Markus Meuwly
- Department of Chemistry; University of Basel; Klingelbergstrasse 80 4056 Basel Switzerland
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15
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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16
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Ge C, Shen Y, Deng GH, Tian Y, Yu D, Yang X, Yuan K, Zheng J. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds. J Phys Chem B 2016; 120:3187-95. [DOI: 10.1021/acs.jpcb.5b12652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanqi Ge
- School
of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Yuneng Shen
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gang-Hua Deng
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Yuhuan Tian
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Dongqi Yu
- School
of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, China
| | - Xueming Yang
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Kaijun Yuan
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Junrong Zheng
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- College
of Chemistry and Molecular Engineering, Beijing National Laboratory
for Molecular Sciences, Peking University, Beijing 100871, China
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17
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Ghosh A, Serrano AL, Oudenhoven TA, Ostrander JS, Eklund EC, Blair AF, Zanni MT. Experimental implementations of 2D IR spectroscopy through a horizontal pulse shaper design and a focal plane array detector. OPTICS LETTERS 2016; 41:524-7. [PMID: 26907414 PMCID: PMC5301998 DOI: 10.1364/ol.41.000524] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Aided by advances in optical engineering, two-dimensional infrared spectroscopy (2D IR) has developed into a promising method for probing structural dynamics in biophysics and material science. We report two new advances for 2D IR spectrometers. First, we report a fully reflective and totally horizontal pulse shaper, which significantly simplifies alignment. Second, we demonstrate the applicability of mid-IR focal plane arrays (FPAs) as suitable detectors in 2D IR experiments. FPAs have more pixels than conventional linear arrays and can be used to multiplex optical detection. We simultaneously measure the spectra of a reference beam, which improves the signal-to-noise by a factor of 4; and two additional beams that are orthogonally polarized probe pulses for 2D IR anisotropy experiments.
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18
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Nuernberger P, Ruetzel S, Brixner T. Multidimensionale elektronische Spektroskopie photochemischer Reaktionen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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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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20
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Nuernberger P, Ruetzel S, Brixner T. Multidimensional Electronic Spectroscopy of Photochemical Reactions. Angew Chem Int Ed Engl 2015; 54:11368-86. [PMID: 26382095 DOI: 10.1002/anie.201502974] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/11/2022]
Abstract
Coherent multidimensional electronic spectroscopy can be employed to unravel various channels in molecular chemical reactions. This approach is thus not limited to analysis of energy transfer or charge transfer (i.e. processes from photophysics), but can also be employed in situations where the investigated system undergoes permanent structural changes (i.e. in photochemistry). Photochemical model reactions are discussed by using the example of merocyanine/spiropyran-based molecular switches, which show a rich variety of reaction channels, in particular ring opening and ring closing, cis-trans isomerization, coherent vibrational wave-packet motion, radical ion formation, and population relaxation. Using pump-probe, pump-repump-probe, coherent two-dimensional and three-dimensional, triggered-exchange 2D, and quantum-control spectroscopy, we gain intuitive pictures on which product emerges from which reactant and which reactive molecular modes are associated.
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Affiliation(s)
- Patrick Nuernberger
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, 44801 Bochum (Germany)
| | - Stefan Ruetzel
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg (Germany)
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg (Germany).
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21
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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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22
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Cyran JD, Nite JM, Krummel AT. Characterizing Anharmonic Vibrational Modes of Quinones with Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2015; 119:8917-25. [PMID: 25697689 DOI: 10.1021/jp506900n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two-dimensional infrared (2D IR) spectroscopy was used to study the vibrational modes of three quinones--benzoquinone, naphthoquinone, and anthraquinone. The vibrations of interest were in the spectral range of 1560-1710 cm(-1), corresponding to the in-plane carbonyl and ring stretching vibrations. Coupling between the vibrational modes is indicated by the cross peaks in the 2D IR spectra. The diagonal and off-diagonal anharmonicities range from 4.6 to 17.4 cm(-1) for the quinone series. In addition, there is significant vibrational coupling between the in-plane carbonyl and ring stretching vibrations. The diagonal anharmonicity, off-diagonal anharmonicity, and vibrational coupling constants are reported for benzoquinone, naphthoquinone, and anthraquinone.
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Affiliation(s)
- Jenée D Cyran
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Jacob M Nite
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Amber T Krummel
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
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23
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Koziol KL, Johnson PJM, Stucki-Buchli B, Waldauer SA, Hamm P. Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity. Curr Opin Struct Biol 2015; 34:1-6. [PMID: 25900180 DOI: 10.1016/j.sbi.2015.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 01/08/2023]
Abstract
2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.
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Affiliation(s)
- Klemens L Koziol
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Philip J M Johnson
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Steven A Waldauer
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
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24
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VIPER 2D-IR: Novel Pulse Sequence to Track Exchange Beyond the Vibrational Lifetime. SPRINGER PROCEEDINGS IN PHYSICS 2015. [DOI: 10.1007/978-3-319-13242-6_103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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25
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 DOI: 10.12688/f1000research.5836.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/27/2014] [Indexed: 03/23/2024] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany ; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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26
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Horn M, Nienhaus K, Nienhaus GU. Fourier transform infrared spectroscopy study of ligand photodissociation and migration in inducible nitric oxide synthase. F1000Res 2014; 3:290. [PMID: 25653844 PMCID: PMC4304226 DOI: 10.12688/f1000research.5836.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2014] [Indexed: 11/20/2022] Open
Abstract
Inducible nitric oxide synthase (iNOS) is a homodimeric heme enzyme that catalyzes the formation of nitric oxide (NO) from dioxygen and L-arginine (L-Arg) in a two-step process. The produced NO can either diffuse out of the heme pocket into the surroundings or it can rebind to the heme iron and inhibit enzyme action. Here we have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy at cryogenic temperatures, using the carbon monoxide (CO) and NO stretching bands as local probes of the active site of iNOS. Characteristic changes were observed in the spectra of the heme-bound ligands upon binding of the cofactors. Unlike photolyzed CO, which becomes trapped in well-defined orientations, as indicated by sharp photoproduct bands, photoproduct bands of NO photodissociated from the ferric heme iron were not visible, indicating that NO does not reside in the protein interior in a well-defined location or orientation. This may be favorable for NO release from the enzyme during catalysis because it reduces self-inhibition. Moreover, we used temperature derivative spectroscopy (TDS) with FTIR monitoring to explore the dynamics of NO and carbon monoxide (CO) inside iNOS after photodissociation at cryogenic temperatures. Only a single kinetic photoproduct state was revealed, but no secondary docking sites as in hemoglobins. Interestingly, we observed that intense illumination of six-coordinate ferrous iNOS oxy-NO ruptures the bond between the heme iron and the proximal thiolate to yield five-coordinate ferric iNOS oxy-NO, demonstrating the strong trans effect of the heme-bound NO.
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Affiliation(s)
- Michael Horn
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics, Karlsruhe, D-76131, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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27
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Jansen TLC. Linear absorption and two-dimensional infrared spectra of N-methylacetamide in chloroform revisited: polarizability and multipole effects. J Phys Chem B 2014; 118:8162-9. [PMID: 24666193 DOI: 10.1021/jp5012445] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of solvent polarizability and multipole effects on the amide I vibrational spectra of a peptide unit is investigated. Four molecular dynamics force fields of increasing complexity for the solvent are used to model both the linear absorption and two-dimensional infrared spectra. It is observed that, at least in chloroform solution, the predicted solvent shift is considerably improved when accounting for the polarizabiltiy and multipole effects. The latter are typically connected with halogen bonding. Significant deviations are still observed for more sensitive line shape parameters such as the spectral width and line skewness. However, the findings demonstrate that previously observed deviations have an origin in the force field treatment rather than in the electrostatic mapping procedure frequently employed to simulate linear absorption and two-dimensional infrared spectroscopy.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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28
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Oang KY, Kim JG, Yang C, Kim TW, Kim Y, Kim K, Kim J, Ihee H. Conformational Substates of Myoglobin Intermediate Resolved by Picosecond X-ray Solution Scattering. J Phys Chem Lett 2014; 5:804-808. [PMID: 24761190 PMCID: PMC3985870 DOI: 10.1021/jz4027425] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/11/2014] [Indexed: 05/04/2023]
Abstract
Conformational substates of proteins are generally considered to play important roles in regulating protein functions, but an understanding of how they influence the structural dynamics and functions of the proteins has been elusive. Here, we investigate the structural dynamics of sperm whale myoglobin associated with the conformational substates using picosecond X-ray solution scattering. By applying kinetic analysis considering all of the plausible candidate models, we establish a kinetic model for the entire cycle of the protein transition in a wide time range from 100 ps to 10 ms. Four structurally distinct intermediates are formed during the cycle, and most importantly, the transition from the first intermediate to the second one (B → C) occurs biphasically. We attribute the biphasic kinetics to the involvement of two conformational substates of the first intermediate, which are generated by the interplay between the distal histidine and the photodissociated CO.
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Affiliation(s)
- Key Young Oang
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Jong Goo Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Cheolhee Yang
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Tae Wu Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Youngmin Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Kyung
Hwan Kim
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
| | - Jeongho Kim
- Department
of Chemistry, Inha University, Incheon 402-751, Korea
| | - Hyotcherl Ihee
- Center for Nanomaterials
and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Korea
- Department
of Chemistry, Graduate School of Nanoscience
& Technology (WCU), Korea Advanced Institute of Science and Technology
(KAIST), Daejeon 305-701, Korea
- E-mail:
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29
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van Wilderen LJGW, Messmer AT, Bredenbeck J. Mixed IR/Vis Two-Dimensional Spectroscopy: Chemical Exchange beyond the Vibrational Lifetime and Sub-ensemble Selective Photochemistry. Angew Chem Int Ed Engl 2014; 53:2667-72. [DOI: 10.1002/anie.201305950] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/31/2013] [Indexed: 11/06/2022]
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30
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van Wilderen LJGW, Messmer AT, Bredenbeck J. Mixed IR/Vis Two-Dimensional Spectroscopy: Chemical Exchange beyond the Vibrational Lifetime and Sub-ensemble Selective Photochemistry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201305950] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Dunkelberger EB, Woys AM, Zanni MT. 2D IR cross peaks reveal hydrogen-deuterium exchange with single residue specificity. J Phys Chem B 2013; 117:15297-305. [PMID: 23659731 PMCID: PMC3812256 DOI: 10.1021/jp402942s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A form of chemical exchange, hydrogen-deuterium exchange (HDX), has long been used as a method for studying the secondary and tertiary structure of peptides and proteins using mass spectrometry and NMR spectroscopy. Using two-dimensional infrared (2D IR) spectroscopy, we resolve cross peaks between the amide II band and a (13)C(18)O isotope-labeled amide I band, which we show measures HDX with site-specific resolution. By rapidly scanning 2D IR spectra using mid-IR pulse shaping, we monitor the kinetics of HDX exchange on-the-fly. For the antimicrobial peptide ovispirin bound to membrane bilayers, we find that the amide II peak decays with a biexponential with rate constants of 0.54 ± 0.02 and 0.12 ± 0.01 min(-1), which is a measure of the overall HDX in the peptide. The cross peaks between Ile-10-labeled ovispirin and the amide II mode, which specifically monitor HDX kinetics at Ile-10, decay with a single rate constant of 0.36 ± 0.1 min(-1). Comparing this exchange rate to theoretically determined exchange rates of Ile-10 for ovispirin in a solution random coil configuration, the exchange rate at Ile-10 is at least 100 times slower, consistent with the known α-helix structure of ovispirin in bilayers. Because backbone isotope labels produce only a very small shift of the amide II band, site-specific HDX cannot be measured with FTIR spectroscopy, which is why 2D IR spectroscopy is needed for these measurements.
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Affiliation(s)
| | - Ann Marie Woys
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706-1396
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32
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Liang C, Jansen TLC. Simulation of Two-Dimensional Sum-Frequency Generation Response Functions: Application to Amide I in Proteins. J Phys Chem B 2013; 117:6937-45. [DOI: 10.1021/jp403111j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chungwen Liang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel,
Switzerland
| | - Thomas L. C. Jansen
- Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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33
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Ruetzel S, Kullmann M, Buback J, Nuernberger P, Brixner T. Tracing the steps of photoinduced chemical reactions in organic molecules by coherent two-dimensional electronic spectroscopy using triggered exchange. PHYSICAL REVIEW LETTERS 2013; 110:148305. [PMID: 25167047 DOI: 10.1103/physrevlett.110.148305] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Indexed: 06/03/2023]
Abstract
We establish coherent triggered-exchange two-dimensional (TE2D) electronic spectroscopy as an expansion of pump-repump-probe transient absorption spectroscopy and uniquely elucidate the role of higher-lying electronic states in ultrafast photochemistry. As an example, this is demonstrated for a molecular switch present in two ring-open conformations. The formation of a new species-the radical cation-is observed and its precursor state is identified via TE2D.
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Affiliation(s)
- Stefan Ruetzel
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Kullmann
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Johannes Buback
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Tobias Brixner
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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35
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Nienhaus K, Olson JS, Nienhaus GU. An engineered heme-copper center in myoglobin: CO migration and binding. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1824-31. [PMID: 23459127 DOI: 10.1016/j.bbapap.2013.02.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 02/19/2013] [Accepted: 02/20/2013] [Indexed: 11/19/2022]
Abstract
We have investigated CO migration and binding in CuBMb, a copper-binding myoglobin double mutant (L29H-F43H), by using Fourier transform infrared spectroscopy and flash photolysis over a wide temperature range. This mutant was originally engineered with the aim to mimic the catalytic site of heme-copper oxidases. Comparison of the wild-type protein Mb and CuBMb shows that the copper ion in the distal pocket gives rise to significant effects on ligand binding to the heme iron. In Mb and copper-free CuBMb, primary and secondary ligand docking sites are accessible upon photodissociation. In copper-bound CuBMb, ligands do not migrate to secondary docking sites but rather coordinate to the copper ion. Ligands entering the heme pocket from the outside normally would not be captured efficiently by the tight distal pocket housing the two additional large imidazole rings. Binding at the Cu ion, however, ensures efficient trapping in CuBMb. The Cu ion also restricts the motions of the His64 side chain, which is the entry/exit door for ligand movement into the active site, and this restriction results in enhanced geminate and slow bimolecular CO rebinding. These results support current mechanistic views of ligand binding in hemoglobins and the role of the CuB in the active of heme-copper oxidases. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Karlsruhe, Germany
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36
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Nienhaus K, Zosel F, Nienhaus GU. Ligand binding to heme proteins: a comparison of cytochrome c variants with globins. J Phys Chem B 2012; 116:12180-8. [PMID: 22978708 DOI: 10.1021/jp306775n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We have studied the binding of carbon monoxide (CO) in mutants of Cyt c having its methionine at position 80 replaced by alanine, aspartate, and arginine, so that the sixth coordination is available for ligand binding. We have employed Fourier transform infrared (FTIR) photolysis difference spectroscopy to examine interactions of the heme-bound and photolyzed CO (and also nitric oxide, NO) in the small heme pocket created by the mutations. By using FTIR temperature derivative spectroscopy (TDS) and nanosecond flash photolysis, the enthalpy barrier distributions for CO rebinding were determined. In flash photolysis experiments, the majority of ligands rebind to the heme iron on picosecond time scales so that only the high-barrier tail of the distributions is visible on the nanosecond scale. By continuous wave excitation prior to TDS characterization of the barriers, however, each Cyt c molecule is photoexcited multiple times and complete photodissociation can be achieved, which likely arises from a rotation of the CO within the heme pocket so that the oxygen faces the heme iron. Apparently, reorientation prior to rebinding constitutes an additional and significant contribution to the rebinding barrier. Our experiments reveal that the compact, rigid structure of Cyt c offers no alternative binding sites for photodissociated ligands in the protein matrix. A comparison of ligand binding in these Cyt c mutants and hemoglobins underscores the importance of internal ligand docking sites and ligand migration routes for conveying a ligand binding function to heme proteins.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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37
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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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38
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39
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Baiz CR, Peng CS, Reppert ME, Jones KC, Tokmakoff A. Coherent two-dimensional infrared spectroscopy: Quantitative analysis of protein secondary structure in solution. Analyst 2012; 137:1793-9. [DOI: 10.1039/c2an16031e] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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40
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Adamczyk K, Candelaresi M, Kania R, Robb K, Bellota-Antón C, Greetham GM, Pollard MR, Towrie M, Parker AW, Hoskisson PA, Tucker NP, Hunt NT. The effect of point mutation on the equilibrium structural fluctuations of ferric Myoglobin. Phys Chem Chem Phys 2012; 14:7411-9. [DOI: 10.1039/c2cp23568d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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41
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Nuernberger P, Lee KF, Bonvalet A, Bouzhir-Sima L, Lambry JC, Liebl U, Joffre M, Vos MH. Strong Ligand–Protein Interactions Revealed by Ultrafast Infrared Spectroscopy of CO in the Heme Pocket of the Oxygen Sensor FixL. J Am Chem Soc 2011; 133:17110-3. [DOI: 10.1021/ja204549n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Patrick Nuernberger
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
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Thielges MC, Axup JY, Wong D, Lee HS, Chung JK, Schultz PG, Fayer MD. Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand. J Phys Chem B 2011; 115:11294-304. [PMID: 21823631 PMCID: PMC3261801 DOI: 10.1021/jp206986v] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein dynamics and interactions in myoglobin (Mb) were characterized via two vibrational dynamics labels (VDLs): a genetically incorporated site-specific azide (Az) bearing unnatural amino acid (AzPhe43) and an active site CO ligand. The Az-labeled protein was studied using ultrafast two-dimensional infrared (2D IR) vibrational echo spectroscopy. CO bound at the active site of the heme serves as a second VDL located nearby. Therefore, it was possible to use Fourier transform infrared (FT-IR) and 2D IR spectroscopic experiments on the Az in unligated Mb and in Mb bound to CO (MbAzCO) and on the CO in MbCO and MbAzCO to investigate the environment and motions of different states of one protein from the perspective of two spectrally resolved VDLs. A very broad bandwidth 2D IR spectrum, encompassing both the Az and CO spectral regions, found no evidence of direct coupling between the two VDLs. In MbAzCO, both VDLs reported similar time scale motions: very fast homogeneous dynamics, fast, ∼1 ps dynamics, and dynamics on a much slower time scale. Therefore, each VDL reports independently on the protein dynamics and interactions, and the measured dynamics are reflective of the protein motions rather than intrinsic to the chemical nature of the VDL. The AzPhe VDL also permitted study of oxidized Mb dynamics, which could not be accessed previously with 2D IR spectroscopy. The experiments demonstrate that the combined application of 2D IR spectroscopy and site-specific incorporation of VDLs can provide information on dynamics, structure, and interactions at virtually any site throughout any protein.
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Affiliation(s)
- Megan C. Thielges
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jun Y. Axup
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Daryl Wong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, Seoul 121-742, Korea
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter G. Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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43
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Nienhaus K, Nickel E, Lu C, Yeh SR, Nienhaus GU. Ligand migration in human indoleamine-2,3 dioxygenase. IUBMB Life 2011; 63:153-9. [PMID: 21445845 DOI: 10.1002/iub.431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human indoleamine 2,3-dioxygenase (hIDO), a monomeric heme enzyme, catalyzes the oxidative degradation of L-tryptophan (L-Trp) and other indoleamine derivatives. Its activity follows typical Michaelis-Menten behavior only for L-Trp concentrations up to 50 μM; a further increase in the concentration of L-Trp causes a decrease in the activity. This substrate inhibition of hIDO is a result of the binding of a second L-Trp molecule in an inhibitory substrate binding site of the enzyme. The molecular details of the reaction and the inhibition are not yet known. In the following, we summarize the present knowledge about this heme enzyme.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe, Germany.
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44
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Remorino A, Korendovych IV, Wu Y, DeGrado WF, Hochstrasser RM. Residue-specific vibrational echoes yield 3D structures of a transmembrane helix dimer. Science 2011; 332:1206-9. [PMID: 21636774 PMCID: PMC3295544 DOI: 10.1126/science.1202997] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Two-dimensional (2D) vibrational echo spectroscopy has previously been applied to structural determination of small peptides. Here we extend the technique to a more complex, biologically important system: the homodimeric transmembrane dimer from the α chain of the integrin α(IIb)β(3). We prepared micelle suspensions of the pair of 30-residue chains that span the membrane in the native structure, with varying levels of heavy ((13)C=(18)O) isotopes substituted in the backbone of the central 10th through 20th positions. The constraints derived from vibrational coupling of the precisely spaced heavy residues led to determination of an optimized structure from a range of model candidates: Glycine residues at the 12th, 15th, and 16th positions form a tertiary contact in parallel right-handed helix dimers with crossing angles of -58° ± 9° and interhelical distances of 7.7 ± 0.5 angstroms. The frequency correlation established the dynamical model used in the analysis, and it indicated the absence of mobile water associated with labeled residues. Delocalization of vibrational excitations between the helices was also quantitatively established.
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Affiliation(s)
- Amanda Remorino
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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45
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Thielges MC, Chung JK, Fayer MD. Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy. J Am Chem Soc 2011; 133:3995-4004. [PMID: 21348488 PMCID: PMC3063108 DOI: 10.1021/ja109168h] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome (cyt) P450s hydroxylate a variety of substrates that can differ widely in their chemical structure. The importance of these enzymes in drug metabolism and other biological processes has motivated the study of the factors that enable their activity on diverse classes of molecules. Protein dynamics have been implicated in cyt P450 substrate specificity. Here, 2D IR vibrational echo spectroscopy is employed to measure the dynamics of cyt P450(cam) from Pseudomonas putida on fast time scales using CO bound at the active site as a vibrational probe. The substrate-free enzyme and the enzyme bound to both its natural substrate, camphor, and a series of related substrates are investigated to explicate the role of dynamics in molecular recognition in cyt P450(cam) and to delineate how the motions may contribute to hydroxylation specificity. In substrate-free cyt P450(cam), three conformational states are populated, and the structural fluctuations within a conformational state are relatively slow. Substrate binding selectively stabilizes one conformational state, and the dynamics become faster. Correlations in the observed dynamics with the specificity of hydroxylation of the substrates, the binding affinity, and the substrates' molecular volume suggest that motions on the hundreds of picosecond time scale contribute to the variation in activity of cyt P450(cam) toward different substrates.
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Affiliation(s)
| | - Jean K. Chung
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Michael D. Fayer
- Department of Chemistry, Stanford University, Stanford, CA 94305
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46
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Nienhaus K, Dominici P, Astegno A, Abbruzzetti S, Viappiani C, Nienhaus GU. Ligand migration and binding in nonsymbiotic hemoglobins of Arabidopsis thaliana. Biochemistry 2010; 49:7448-58. [PMID: 20666470 DOI: 10.1021/bi100768g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We have studied carbon monoxide (CO) migration and binding in the nonsymbiotic hemoglobins AHb1 and AHb2 of Arabidopsis thaliana using Fourier transform infrared (FTIR) spectroscopy combined with temperature derivative spectroscopy (TDS) at cryogenic temperatures. Both proteins have similar amino acid sequences but display pronounced differences in ligand binding properties, at both physiological and cryogenic temperatures. Near neutral pH, the distal HisE7 side chain is close to the heme-bound ligand in the majority of AHb1-CO molecules, as indicated by a low CO stretching frequency at 1921 cm(-1). In this fraction, two CO docking sites can be populated, the primary site B and the secondary site C. When the pH is lowered, a high-frequency stretching band at approximately 1964 cm(-1) grows at the expense of the low-frequency band, indicating that HisE7 protonates and, concomitantly, moves away from the bound ligand. Geminate rebinding barriers are markedly different for the two conformations, and docking site C is not accessible in the low-pH conformation. Rebinding of NO ligands was observed only from site B of AHb1, regardless of conformation. In AHb2, the HisE7 side chain is removed from the bound ligand; rebinding barriers are low, and CO molecules can populate only primary docking site B. These results are interpreted in terms of differences in the active site structures and physiological functions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
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47
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Pensack RD, Banyas KM, Asbury JB. Temperature-Independent Vibrational Dynamics in an Organic Photovoltaic Material. J Phys Chem B 2010; 114:12242-51. [DOI: 10.1021/jp105772y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan D. Pensack
- Department of Chemistry The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Kyle M. Banyas
- Department of Chemistry The Pennsylvania State University, University Park, Pennsylvania 16802
| | - John B. Asbury
- Department of Chemistry The Pennsylvania State University, University Park, Pennsylvania 16802
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48
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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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49
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Nienhaus K, Nienhaus GU. Ligand dynamics in heme proteins observed by Fourier transform infrared-temperature derivative spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:1030-41. [PMID: 20656073 DOI: 10.1016/j.bbapap.2010.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/14/2010] [Accepted: 07/15/2010] [Indexed: 11/29/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the investigation of protein-ligand interactions in heme proteins. Nitric oxide and carbon monoxide are attractive physiologically relevant ligands because their bond stretching vibrations give rise to strong mid-infrared absorption bands that can be measured with exquisite sensitivity and precision using photolysis difference spectroscopy at cryogenic temperatures. These stretching bands are fine-tuned by electrostatic interactions with the environment and, therefore, ligands can be utilized as local probes of structure and dynamics. Bound to the heme iron, the ligand stretching bands are susceptible to changes in the iron-ligand bond and the electric field at the active site. Upon photolysis, the vibrational bands display changes due to ligand relocation to docking sites within the protein, rotational motions of the ligand in these sites and protein conformational changes. Photolysis difference spectra taken over a wide temperature range (3-300K) using specific temperature protocols for sample photodissociation can provide detailed insights into both protein and ligand dynamics. Moreover, temperature-derivative spectroscopy (TDS) has proven to be a particularly powerful technique to study protein-ligand interactions. The FTIR-TDS technique has been extensively applied to studies of carbon monoxide binding to heme proteins, whereas measurements with nitric oxide are still scarce. Here we describe infrared cryo-spectroscopy and present a variety of applications to the study of protein-ligand interactions in heme proteins. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Karin Nienhaus
- Karlsruhe Institute of Technology (KIT), Institute of Applied Physics and Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1, D-76131 Karlsruhe, Germany
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50
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Zang C, Stevens JA, Link JJ, Guo L, Wang L, Zhong D. Ultrafast proteinquake dynamics in cytochrome c. J Am Chem Soc 2010; 131:2846-52. [PMID: 19203189 DOI: 10.1021/ja8057293] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report here our systematic studies of the heme dynamics and induced protein conformational relaxations in two redox states of ferric and ferrous cytochrome c upon femtosecond excitation. With a wide range of probing wavelengths from the visible to the UV and a site-directed mutation we unambiguously determined that the protein dynamics in the two states are drastically different. For the ferrous state the heme transforms from 6-fold to 5-fold coordination with ultrafast ligand dissociation in less than 100 fs, followed by vibrational cooling within several picoseconds, but then recombining back to its original 6-fold coordination in 7 ps. Such impulsive bond breaking and late rebinding generate proteinquakes and strongly perturb the local heme site and shake global protein conformation, which were found to completely recover in 13 and 42 ps, respectively. For the ferric state the heme however maintains its 6-fold coordination. The dynamics mainly occur at the local site, including ultrafast internal conversion in hundreds of femtoseconds, vibrational cooling on the similar picosecond time scale, and complete ground-state recovery in 10 ps, and no global conformation relaxation was observed.
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Affiliation(s)
- Chen Zang
- Department of Physics, Program of Biophysics, The Ohio State University, 191 West Woodruff Avenue, Columbus, Ohio, 43210, USA
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