1
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Chenchiliyan M, Kübel J, Ooi SA, Salvadori G, Mennucci B, Westenhoff S, Maj M. Ground-state heterogeneity and vibrational energy redistribution in bacterial phytochrome observed with femtosecond 2D IR spectroscopy. J Chem Phys 2023; 158:085103. [PMID: 36859103 DOI: 10.1063/5.0135268] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Phytochromes belong to a group of photoreceptor proteins containing a covalently bound biliverdin chromophore that inter-converts between two isomeric forms upon photoexcitation. The existence and stability of the photocycle products are largely determined by the protein sequence and the presence of conserved hydrogen-bonding interactions in the vicinity of the chromophore. The vibrational signatures of biliverdin, however, are often weak and obscured under more intense protein bands, limiting spectroscopic studies of its non-transient signals. In this study, we apply isotope-labeling techniques to isolate the vibrational bands from the protein-bound chromophore of the bacterial phytochrome from Deinococcus radiodurans. We elucidate the structure and ultrafast dynamics of the chromophore with 2D infra-red (IR) spectroscopy and molecular dynamics simulations. The carbonyl stretch vibrations of the pyrrole rings show the heterogeneous distribution of hydrogen-bonding structures, which exhibit distinct ultrafast relaxation dynamics. Moreover, we resolve a previously undetected 1678 cm-1 band that is strongly coupled to the A- and D-ring of biliverdin and demonstrate the presence of complex vibrational redistribution pathways between the biliverdin modes with relaxation-assisted measurements of 2D IR cross peaks. In summary, we expect 2D IR spectroscopy to be useful in explaining how point mutations in the protein sequence affect the hydrogen-bonding structure around the chromophore and consequently its ability to photoisomerize to the light-activated states.
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Affiliation(s)
- Manoop Chenchiliyan
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Joachim Kübel
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Saik Ann Ooi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56126 Pisa, Italy
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden
| | - Michał Maj
- Department of Chemistry-Ångström Laboratory, Uppsala University, SE-75120 Uppsala, Sweden
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2
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Romei M, von Krusenstiern EV, Ridings ST, King RN, Fortier JC, McKeon CA, Nichols KM, Charkoudian LK, Londergan CH. Frequency Changes in Terminal Alkynes Provide Strong, Sensitive, and Solvatochromic Raman Probes of Biochemical Environments. J Phys Chem B 2023; 127:85-94. [PMID: 36538691 PMCID: PMC9841980 DOI: 10.1021/acs.jpcb.2c06176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/19/2022] [Indexed: 12/24/2022]
Abstract
The C≡C stretching frequencies of terminal alkynes appear in the "clear" window of vibrational spectra, so they are attractive and increasingly popular as site-specific probes in complicated biological systems like proteins, cells, and tissues. In this work, we collected infrared (IR) absorption and Raman scattering spectra of model compounds, artificial amino acids, and model proteins that contain terminal alkyne groups, and we used our results to draw conclusions about the signal strength and sensitivity to the local environment of both aliphatic and aromatic terminal alkyne C≡C stretching bands. While the IR bands of alkynyl model compounds displayed surprisingly broad solvatochromism, their absorptions were weak enough that alkynes can be ruled out as effective IR probes. The same solvatochromism was observed in model compounds' Raman spectra, and comparisons to published empirical solvent scales (including a linear regression against four meta-aggregated solvent parameters) suggested that the alkyne C≡C stretching frequency mainly reports on local electronic interactions (i.e., short-range electron donor-acceptor interactions) with solvent molecules and neighboring functional groups. The strong solvatochromism observed here for alkyne stretching bands introduces an important consideration for Raman imaging studies based on these signals. Raman signals for alkynes (especially those that are π-conjugated) can be exceptionally strong and should permit alkynyl Raman signals to function as probes at very low concentrations, as compared to other widely used vibrational probe groups like azides and nitriles. We incorporated homopropargyl glycine into a transmembrane helical peptide via peptide synthesis, and we installed p-ethynylphenylalanine into the interior of the Escherichia coli fatty acid acyl carrier protein using a genetic code expansion technique. The Raman spectra from each of these test systems indicate that alkynyl C≡C bands can act as effective and unique probes of their local biomolecular environments. We provide guidance for the best possible future uses of alkynes as solvatochromic Raman probes, and while empirical explanations of the alkyne solvatochromism are offered, open questions about its physical basis are enunciated.
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Affiliation(s)
- Matthew
G. Romei
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Eliana V. von Krusenstiern
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Stephen T. Ridings
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Renee N. King
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Julia C. Fortier
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Caroline A. McKeon
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Krysta M. Nichols
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
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3
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Kwac K, Freedman H, Cho M. Machine Learning Approach for Describing Water OH Stretch Vibrations. J Chem Theory Comput 2021; 17:6353-6365. [PMID: 34498885 DOI: 10.1021/acs.jctc.1c00540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A machine learning approach employing neural networks is developed to calculate the vibrational frequency shifts and transition dipole moments of the symmetric and antisymmetric OH stretch vibrations of a water molecule surrounded by water molecules. We employed the atom-centered symmetry functions (ACSFs), polynomial functions, and Gaussian-type orbital-based density vectors as descriptor functions and compared their performances in predicting vibrational frequency shifts using the trained neural networks. The ACSFs perform best in modeling the frequency shifts of the OH stretch vibration of water among the types of descriptor functions considered in this paper. However, the differences in performance among these three descriptors are not significant. We also tried a feature selection method called CUR matrix decomposition to assess the importance and leverage of the individual functions in the set of selected descriptor functions. We found that a significant number of those functions included in the set of descriptor functions give redundant information in describing the configuration of the water system. We here show that the predicted vibrational frequency shifts by trained neural networks successfully describe the solvent-solute interaction-induced fluctuations of OH stretch frequencies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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4
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Błasiak B, Bartkowiak W, Góra RW. An effective potential for Frenkel excitons. Phys Chem Chem Phys 2021; 23:1923-1935. [PMID: 33459313 DOI: 10.1039/d0cp04636a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Excitation energy transfer (EET) is a ubiquitous process in life and materials sciences. Here, a new and computationally efficient method of evaluating the electronic EET couplings between interacting chromophores is introduced that is valid in a wide range of intermolecular distances. The proposed approach is based on the effective elimination of electron repulsion integrals from the excitonic Hamiltonian matrix elements via the density-fitting approach and distributed multipole approximation. The excitonic Hamiltonian represented in a basis including charge transfer (CT) states is re-cast in terms of the effective one-electron potential functions (EOPs) and adapted into the effective fragment parameter (EFP) framework. Calculations for model systems indicate that the speedup of at least three orders of magnitude, as compared to the state-of-the-art methods, can be achieved while maintaining the accuracy of the EET couplings even at short intermolecular distances.
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Affiliation(s)
- Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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5
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Cho M, Fleming GR. Two-Dimensional Electronic–Vibrational Spectroscopy Reveals Cross-Correlation between Solvation Dynamics and Vibrational Spectral Diffusion. J Phys Chem B 2020; 124:11222-11235. [DOI: 10.1021/acs.jpcb.0c08959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoSciences Institute at Berkeley, Berkeley, California 94720, United States
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6
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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: 171] [Impact Index Per Article: 42.8] [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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7
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Kwac K, Cho M. Machine learning approach for describing vibrational solvatochromism. J Chem Phys 2020; 152:174101. [DOI: 10.1063/5.0005591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea
- Department of Chemistry, Korea University, 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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8
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Kwac K, Cho M. Differential evolution algorithm approach for describing vibrational solvatochromism. J Chem Phys 2019; 151:134112. [PMID: 31594319 DOI: 10.1063/1.5120777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.
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Affiliation(s)
- Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, South Korea and Department of Chemistry, Korea University, Seoul 02841, South Korea
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9
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Cai K, Zheng X, Liu J, Du F, Yan G, Zhuang D, Yan S. Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:391-400. [PMID: 31059891 DOI: 10.1016/j.saa.2019.04.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid β-peptide fragment (Aβ25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aβ25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming β-sheet and random coil structure for Aβ25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China; Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Guiyang Yan
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Siyi Yan
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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10
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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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11
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Dalton SR, Vienneau AR, Burstein SR, Xu RJ, Linse S, Londergan CH. Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation. Biochemistry 2018; 57:3702-3712. [PMID: 29787228 PMCID: PMC6034165 DOI: 10.1021/acs.biochem.8b00283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
To investigate the
cyanylated cysteine vibrational probe group’s
ability to report on binding-induced changes along a protein–protein
interface, the probe group was incorporated at several sites in a
peptide of the calmodulin (CaM)-binding domain of skeletal muscle
myosin light chain kinase. Isothermal titration calorimetry was used
to determine the binding thermodynamics between calmodulin and each
peptide. For all probe positions, the binding affinity was nearly
identical to that of the unlabeled peptide. The CN stretching infrared
band was collected for each peptide free in solution and bound to
calmodulin. Binding-induced shifts in the IR spectral frequencies
were correlated with estimated solvent accessibility based on molecular
dynamics simulations. This work generally suggests (1) that site-specific
incorporation of this vibrational probe group does not cause major
perturbations to its local structural environment and (2) that this
small probe group might be used quite broadly to map dynamic protein-binding
interfaces. However, site-specific perturbations due to artificial
labeling groups can be somewhat unpredictable and should be evaluated
on a site-by-site basis through complementary measurements. A fully
quantitative, simulation-based interpretation of the rich probe IR
spectra is still needed but appears to be possible given recent advances
in simulation techniques.
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Affiliation(s)
- Shannon R Dalton
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Alice R Vienneau
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Shana R Burstein
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Sara Linse
- Department of Chemistry and Biochemistry , Lund University , Kemicentrum, Box 118 , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
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12
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Xu RJ, Blasiak B, Cho M, Layfield JP, Londergan CH. A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes. J Phys Chem Lett 2018; 9:2560-2567. [PMID: 29697984 DOI: 10.1021/acs.jpclett.8b00969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
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Affiliation(s)
- Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
| | - Bartosz Blasiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Joshua P Layfield
- Department of Chemistry , St. Thomas University , Minneapolis , Minnesota , United States
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
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13
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Kelly KL, Dalton SR, Wai RB, Ramchandani K, Xu RJ, Linse S, Londergan CH. Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups. J Phys Chem A 2018; 122:2947-2955. [PMID: 29400461 PMCID: PMC5867645 DOI: 10.1021/acs.jpca.8b00475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Seven native residues on the regulatory
protein calmodulin, including
three key methionine residues, were replaced (one by one) by the vibrational
probe amino acid cyanylated cysteine, which has a unique CN stretching
vibration that reports on its local environment. Almost no perturbation
was caused by this probe at any of the seven sites, as reported by
CD spectra of calcium-bound and apo calmodulin and
binding thermodynamics for the formation of a complex between calmodulin
and a canonical target peptide from skeletal muscle myosin light chain
kinase measured by isothermal titration. The surprising lack of perturbation
suggests that this probe group could be applied directly in many protein–protein
binding interfaces. The infrared absorption bands for the probe groups
reported many dramatic changes in the probes’ local environments
as CaM went from apo- to calcium-saturated to target
peptide-bound conditions, including large frequency shifts and a variety
of line shapes from narrow (interpreted as a rigid and invariant local
environment) to symmetric to broad and asymmetric (likely from multiple
coexisting and dynamically exchanging structures). The fast intrinsic
time scale of infrared spectroscopy means that the line shapes report
directly on site-specific details of calmodulin’s variable
structural distribution. Though quantitative interpretation of the
probe line shapes depends on a direct connection between simulated
ensembles and experimental data that does not yet exist, formation
of such a connection to data such as that reported here would provide
a new way to evaluate conformational ensembles from data that directly
contains the structural distribution. The calmodulin probe sites developed
here will also be useful in evaluating the binding mode of calmodulin
with many uncharacterized regulatory targets.
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Affiliation(s)
- Kristen L Kelly
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Shannon R Dalton
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rebecca B Wai
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Kanika Ramchandani
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund University , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
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14
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Van Hoozen BL, Petersen PB. A combined electronic structure and molecular dynamics approach to computing the OH vibrational feature of strongly hydrogen-bonded carboxylic acids. J Chem Phys 2017; 147:224304. [DOI: 10.1063/1.5000341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Brian L. Van Hoozen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Poul B. Petersen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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15
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Cai K, Zheng X, Du F. Electrostatic frequency maps for amide-I mode of β-peptide: Comparison of molecular mechanics force field and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:150-157. [PMID: 28448953 DOI: 10.1016/j.saa.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/09/2017] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
The spectroscopy of amide-I vibrations has been widely utilized for the understanding of dynamical structure of polypeptides. For the modeling of amide-I spectra, two frequency maps were built for β-peptide analogue (N-ethylpropionamide, NEPA) in a number of solvents within different schemes (molecular mechanics force field based, GM map; DFT calculation based, GD map), respectively. The electrostatic potentials on the amide unit that originated from solvents and peptide backbone were correlated to the amide-I frequency shift from gas phase to solution phase during map parameterization. GM map is easier to construct with negligible computational cost since the frequency calculations for the samples are purely based on force field, while GD map utilizes sophisticated DFT calculations on the representative solute-solvent clusters and brings insight into the electronic structures of solvated NEPA and its chemical environments. The results show that the maps' predicted amide-I frequencies present solvation environmental sensitivities and exhibit their specific characters with respect to the map protocols, and the obtained vibrational parameters are in satisfactory agreement with experimental amide-I spectra of NEPA in solution phase. Although different theoretical schemes based maps have their advantages and disadvantages, the present maps show their potentials in interpreting the amide-I spectra for β-peptides, respectively.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China.
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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16
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Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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17
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Błasiak B, Londergan CH, Webb LJ, Cho M. Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems. Acc Chem Res 2017; 50:968-976. [PMID: 28345879 DOI: 10.1021/acs.accounts.7b00002] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as vibrational Stark effect theory has been considered to be quite appealing and, even in some cases, e.g., carbonyl stretch modes in amide, ester, ketone, and carbonate compounds or proteins, it works quantitatively well, which makes it highly useful in determining the strength of local electric field around the IR chromophore. However, noting that the vibrational frequency shift results from changes of solute-solvent intermolecular interaction potential along its normal coordinate, Pauli exclusion repulsion, polarization, charge transfer, and dispersion interactions, in addition to the electrostatic interaction between distributed charges of both vibrational chromophore and solvent molecules, are to be properly included in the theoretical description of vibrational solvatochromism. Since the electrostatic and nonelectrostatic intermolecular interaction components have distinctively different distance and orientation dependences, they affect the solvatochromic vibrational properties in a completely different manner. Over the past few years, we have developed a systematic approach to simulating vibrational solvatochromic data based on the effective fragment potential approach, one of the most accurate and rigorous theories on intermolecular interactions. We have further elucidated the interplay of local electric field with the general vibrational solvatochromism of small IR probes in either solvents or complicated biological systems, with emphasis on contributions from non-Coulombic intermolecular interactions to vibrational frequency shifts and fluctuations. With its rigorous foundation and close relation to quantitative interpretation of experimental data, this and related theoretical approaches and experiments will be of use in studying and quantifying the structure and dynamics of biomolecules with unprecedented time and spatial resolution when combined with time-resolved vibrational spectroscopy and chemically sensitive vibrational imaging techniques.
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Affiliation(s)
- Bartosz Błasiak
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Casey H. Londergan
- Department
of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Lauren J. Webb
- Department
of Chemistry, Center for Nano- and Molecular Science and Technology,
and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105
E. 24th Street, STOP A5300, Austin, Texas 78712, United States
| | - Minhaeng Cho
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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18
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Schneider SH, Kratochvil HT, Zanni MT, Boxer SG. Solvent-Independent Anharmonicity for Carbonyl Oscillators. J Phys Chem B 2017; 121:2331-2338. [PMID: 28225620 DOI: 10.1021/acs.jpcb.7b00537] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The physical origins of vibrational frequency shifts have been extensively studied in order to understand noncovalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arise predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures. Here we test these hypotheses using vibrational solvatochromism as measured using 2D IR to assess the solvent dependence of the bond anharmonicity. These results indicate that the carbonyl bond's anharmonicity is independent of solvent as tested using hexanes, DMSO, and D2O and is supported by simulated 2D spectra. In support of the linear vibrational Stark effect, these 2D IR measurements are consistent with the assertion that the Stark tuning rate is unperturbed by the electric field generated by both hydrogen and non-hydrogen bonding environments and further extends the general applicability of carbonyl probes for studying intermolecular interactions.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Huong T Kratochvil
- 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
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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19
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Daly CA, Berquist EJ, Brinzer T, Garrett-Roe S, Lambrecht DS, Corcelli SA. Modeling Carbon Dioxide Vibrational Frequencies in Ionic Liquids: II. Spectroscopic Map. J Phys Chem B 2016; 120:12633-12642. [DOI: 10.1021/acs.jpcb.6b09509] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Clyde A. Daly
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
| | - Eric J. Berquist
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Thomas Brinzer
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Sean Garrett-Roe
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Daniel S. Lambrecht
- Department
of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
- Pittsburgh
Quantum Institute, University of Pittsburgh, 3943 O’Hara Street, Pittsburgh, Pennsylvania 15260, United States
| | - Steven A. Corcelli
- Department
of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46656, United States
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20
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Fingerhut BP, Costard R, Elsaesser T. Predominance of short range Coulomb forces in phosphate-water interactions—a theoretical analysis. J Chem Phys 2016. [DOI: 10.1063/1.4962755] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Benjamin P. Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Rene Costard
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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21
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Schneider SH, Boxer SG. Vibrational Stark Effects of Carbonyl Probes Applied to Reinterpret IR and Raman Data for Enzyme Inhibitors in Terms of Electric Fields at the Active Site. J Phys Chem B 2016; 120:9672-84. [PMID: 27541577 DOI: 10.1021/acs.jpcb.6b08133] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases. These results demonstrate that the vibrational Stark effect provides a general framework for estimating the electrostatic contribution to the catalytic rate and may provide a metric for the design or modification of enzymes. Opportunities and limitations of the approach are also described.
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Affiliation(s)
- Samuel H Schneider
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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22
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Maj M, Ahn C, Błasiak B, Kwak K, Han H, Cho M. Isonitrile as an Ultrasensitive Infrared Reporter of Hydrogen-Bonding Structure and Dynamics. J Phys Chem B 2016; 120:10167-10180. [DOI: 10.1021/acs.jpcb.6b04319] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Changwoo Ahn
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Bartosz Błasiak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hogyu Han
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
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23
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Pan X, Schwartz SD. Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models. J Phys Chem B 2016; 120:6612-20. [PMID: 27347759 DOI: 10.1021/acs.jpcb.6b05119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate. Recent isotope-edited IR spectroscopy suggests that conformational heterogeneity exists within the Michaelis complex of LDH, and this heterogeneity affects the propensity toward the on-enzyme chemical step for each Michaelis substate. By combining molecular dynamics simulations with Markov and hidden Markov models, we obtained a detailed kinetic network of the substates of the Michaelis complex of LDH. The ensemble-average electric fields exerted onto the vibrational probe were calculated to provide a direct comparison with the vibrational spectroscopy. Structural features of the Michaelis substates were also analyzed on atomistic scales. Our work not only clearly demonstrates the conformational heterogeneity in the Michaelis complex of LDH and its coupling to the reactivities of the substates, but it also suggests a methodology to simultaneously resolve kinetics and structures on atomistic scales, which can be directly compared with the vibrational spectroscopy.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Steven D Schwartz
- Department of Chemistry and Biochemistry, University of Arizona , 1306 East University Boulevard, Tucson, Arizona 85721, United States
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24
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Basom EJ, Maj M, Cho M, Thielges MC. Site-Specific Characterization of Cytochrome P450cam Conformations by Infrared Spectroscopy. Anal Chem 2016; 88:6598-606. [PMID: 27185328 DOI: 10.1021/acs.analchem.6b01520] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Conformational changes are central to protein function but challenging to characterize with both high spatial and temporal precision. The inherently fast time scale and small chromophores of infrared (IR) spectroscopy are well-suited for characterization of potentially rapidly fluctuating environments, and when frequency-resolved probes are incorporated to overcome spectral congestion, enable characterization of specific sites in proteins. We selectively incorporated p-cyanophenylalanine (CNF) as a vibrational probe at five distinct locations in the enzyme cytochrome P450cam and used IR spectroscopy to characterize the environments in substrate and/or ligand complexes reflecting those in the catalytic cycle. Molecular dynamics (MD) simulations were performed to provide a structural basis for spectral interpretation. Together the experimental and simulation data suggest that the CN frequencies are sensitive to both long-range influences, resulting from the particular location of a residue within the enzyme, as well as short-range influences from hydrogen bonding and packing interactions. The IR spectra demonstrate that the environments and effects of substrate and/or ligand binding are different at each position probed and also provide evidence that a single site can experience multiple environments. This study illustrates how IR spectroscopy, when combined with the spectral decongestion and spatial selectivity afforded by CNF incorporation, provides detailed information about protein structural changes that underlie function.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
| | - Michał Maj
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Republic of Korea.,Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood, Bloomington, Indiana 47405, United States
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25
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Ravi Kumar V, Verma C, Umapathy S. Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone. J Chem Phys 2016; 144:064302. [DOI: 10.1063/1.4941058] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Cai K, Du F, Zheng X, Liu J, Zheng R, Zhao J, Wang J. General Applicable Frequency Map for the Amide-I Mode in β-Peptides. J Phys Chem B 2016; 120:1069-79. [PMID: 26824578 DOI: 10.1021/acs.jpcb.5b11643] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In this work, a general applicable amide-I vibrational frequency map (GA map) for β-peptides in a number of common solvents was constructed, based on a peptide derivative, N-ethylpropionamide (NEPA). The map utilizes force fields at the ab initio computational level to accurately describe molecular structure and solute-solvent interactions, and also force fields at the molecular mechanics level to take into account long-range solute-solvent interactions. The results indicate that the GA map works reasonably for mapping the vibrational frequencies of the amide-I local-modes for β-peptides, holding promises for understanding the complicated infrared spectra of the amide-I mode in β-polypeptides.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Fenfen Du
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Xuan Zheng
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Jia Liu
- College of Chemistry and Chemical Engineering, Fujian Normal University , Fuzhou, Fujian 350007, P. R. China.,Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry , Xiamen, Fujian 361005, P. R. China
| | - Renhui Zheng
- Beijing National Laboratory for Molecular Sciences, Structural Chemistry of Unstable and Stable Species Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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27
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Błasiak B, Ritchie AW, Webb LJ, Cho M. Vibrational solvatochromism of nitrile infrared probes: beyond the vibrational Stark dipole approach. Phys Chem Chem Phys 2016; 18:18094-111. [DOI: 10.1039/c6cp01578f] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Systematic probing of local environments around biopolymers is important for understanding their functions.
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Affiliation(s)
- Bartosz Błasiak
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
| | - Andrew W. Ritchie
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Lauren J. Webb
- Department of Chemistry
- Center for Nano- and Molecular Science and Technology, and Institute for Cell and Molecular Biology
- The University of Texas at Austin
- Austin
- USA
| | - Minhaeng Cho
- Center of Molecular Spectroscopy and Dynamics
- Institute of Basic Science (IBS)
- Seoul 02841
- Republic of Korea
- Department of Chemistry
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