1
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Webb KR, Hess KA, Shmidt A, Segner KD, Buchanan LE. Probing local changes to α-helical structures with 2D IR spectroscopy and isotope labeling. Biophys J 2023; 122:1491-1502. [PMID: 36906800 PMCID: PMC10147839 DOI: 10.1016/j.bpj.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/13/2022] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
α-Helical secondary structures impart specific mechanical and physiochemical properties to peptides and proteins, enabling them to perform a vast array of molecular tasks ranging from membrane insertion to molecular allostery. Loss of α-helical content in specific regions can inhibit native protein function or induce new, potentially toxic, biological activities. Thus, identifying specific residues that exhibit loss or gain of helicity is critical for understanding the molecular basis of function. Two-dimensional infrared (2D IR) spectroscopy coupled with isotope labeling is capable of capturing detailed structural changes in polypeptides. Yet, questions remain regarding the inherent sensitivity of isotope-labeled modes to local changes in α-helicity, such as terminal fraying; the origin of spectral shifts (hydrogen-bonding versus vibrational coupling); and the ability to definitively detect coupled isotopic signals in the presence of overlapping side chains. Here, we address each of these points individually by characterizing a short, model α-helix (DPAEAAKAAAGR-NH2) with 2D IR and isotope labeling. These results demonstrate that pairs of 13C18O probes placed three residues apart can detect subtle structural changes and variations along the length of the model peptide as the α-helicity is systematically tuned. Comparison of singly and doubly labeled peptides affirm that frequency shifts arise primarily from hydrogen-bonding, while vibrational coupling between paired isotopes leads to increased peak areas that can be clearly differentiated from underlying side-chain modes or uncoupled isotope labels not participating in helical structures. These results demonstrate that 2D IR in tandem with i,i+3 isotope-labeling schemes can capture residue-specific molecular interactions within a single turn of an α-helix.
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Affiliation(s)
| | - Kayla Anne Hess
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
| | - Alisa Shmidt
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee
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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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Beasley MA, Dunkelberger AD, Thum MD, Ryland ES, Fears KP, Grafton AB, Owrutsky JC, Lundin JG, So CR. Extremophilic behavior of catalytic amyloids sustained by backbone structuring. J Mater Chem B 2022; 10:9400-9412. [PMID: 36285764 DOI: 10.1039/d2tb01605b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Enzyme function relies on the placement of chemistry defined by solvent and self-associative hydrogen bonding displayed by the protein backbone. Amyloids, long-range multi-peptide and -protein materials, can mimic enzyme functions while having a high proportion of stable self-associative backbone hydrogen bonds. Though catalytic amyloid structures have exhibited a degree of temperature and solvent stability, defining their full extremophilic properties and the molecular basis for such extreme activity has yet to be realized. Here we demonstrate that, like thermophilic enzymes, catalytic amyloid activity persists across high temperatures with an optimum activity at 81 °C where they are 30-fold more active than at room temperature. Unlike thermophilic enzymes, catalytic amyloids retain both activity and structure well above 100 °C as well as in the presence of co-solvents. Changes in backbone vibrational states are resolved in situ using non-linear 2D infrared spectroscopy (2DIR) to reveal that activity is sustained by reorganized backbone hydrogen bonds in extreme environments, evidenced by an emergent vibrational mode centered at 1612 cm-1. Restructuring also occurs in organic solvents, and facilitates complete retention of hydrolysis activity in co-solvents of lesser polarity. We support these findings with molecular modeling, where the displacement of water by co-solvents leads to shorter, less competitive, bonding lifetimes that further stabilize self-associative backbone interactions. Our work defines amyloid properties that counter classical proteins, where extreme environments induce mechanisms of restructuring to support enzyme-like functions necessary for synthetic applications.
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Affiliation(s)
- Maryssa A Beasley
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6176, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Adam D Dunkelberger
- Chemistry Division, Code 6121, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Matthew D Thum
- ASEE Postdoctoral Associate Sited in Chemistry Division, Code 6124, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Elizabeth S Ryland
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6121, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Kenan P Fears
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA.
| | - Andrea B Grafton
- NRC Postdoctoral Associate Sited in Chemistry Division, Code 6121, U.S. Naval Research Laboratory, Washington, DC 20375-5342, USA
| | - Jeffrey C Owrutsky
- Chemistry Division, Code 6121, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Jeffrey G Lundin
- Chemistry Division, Code 6124, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA
| | - Christopher R So
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Ave, SW, Washington, DC 20375-5342, USA.
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4
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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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5
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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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6
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Biswas S, Mallik BS. Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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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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8
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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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9
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First JT, Novelli ET, Webb LJ. Beyond pKa: Experiments and Simulations of Nitrile Vibrational Probes in Staphylococcal Nuclease Show the Importance of Local Interactions. J Phys Chem B 2020; 124:3387-3399. [DOI: 10.1021/acs.jpcb.0c00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Elisa T. Novelli
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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10
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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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11
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Yu Y, Shi L. Vibrational solvatochromism of the ester carbonyl vibration of PCBM in organic solutions. J Chem Phys 2019. [DOI: 10.1063/1.5111046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Yue Yu
- School of Natural Sciences, University of California, Merced, California 95343, USA
| | - Liang Shi
- School of Natural Sciences, University of California, Merced, California 95343, USA
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12
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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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13
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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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14
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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
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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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15
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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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16
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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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17
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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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18
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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: 86] [Impact Index Per Article: 12.3] [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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19
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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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20
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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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21
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Błasiak B, Cho M. Vibrational solvatochromism. III. Rigorous treatment of the dispersion interaction contribution. J Chem Phys 2016; 143:164111. [PMID: 26520502 DOI: 10.1063/1.4934667] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A rigorous first principles theory of vibrational solvatochromism including the intermolecular dispersion interaction, which is based on the effective fragment potential method, is developed. The present theory is an extended version of our previous vibrational solvatochromism model that took into account the Coulomb, exchange-repulsion, and induction interactions. We show that the frequency shifts of the amide I mode of N-methylacetamide in H2O and CDCl3, when combined with molecular dynamics simulations, can be quantitatively reproduced by the theory, which indicates that the dispersion interaction contribution to the vibrational frequency shift is not always negligibly small. Nonetheless, the reason that the purely Coulombic interaction model for vibrational solvatochromism works well for describing amide I mode frequency shifts in polar solvents is because the electrostatic contribution is strong and highly sensitive to the relative orientation of surrounding solvent molecules, which is in stark contrast with polarization, dispersion, and exchange-repulsion contributions. It is believed that the theory presented and discussed here will be of great use in quantitatively describing vibrational solvatochromism and electrochromism of infrared probes in not just polar solvent environments but also in biopolymers such as proteins.
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Affiliation(s)
- Bartosz Błasiak
- Center of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), Seoul 136-701, South Korea and Department of Chemistry, Korea University, Seoul 136-701, South Korea
| | - Minhaeng Cho
- Center of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), Seoul 136-701, South Korea and Department of Chemistry, Korea University, Seoul 136-701, South Korea
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22
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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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23
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Lee C, Son H, Park S. Effect of Hydrogen Bonds on the Vibrational Relaxation and Orientational Relaxation Dynamics of HN3 and N3(-) in Solutions. J Phys Chem B 2016; 120:9723-31. [PMID: 27537433 DOI: 10.1021/acs.jpcb.6b06239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen bonds (H-bonds) play an important role in determining the structures and dynamics of molecular systems. In this work, we investigated the effect of H-bonds on the vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in methanol (CH3OH) and N,N-dimethyl sulfoxide (DMSO) using polarization-controlled infrared pump-probe spectroscopy and quantum chemical calculations. Our detailed analysis of experimental and computational results reveals that both vibrational population relaxation and orientational relaxation dynamics of HN3 and N3(-) in CH3OH and DMSO are substantially dependent on the strength of the H-bonds between the probing solute and its surrounding solvent. Especially in the case of N3(-) in CH3OH, the vibrational population relaxation of N3(-) is found to occur by a direct intermolecular vibrational energy transfer to CH3OH due to large vibrational coupling strength. The orientational relaxation dynamics of HN3 and N3(-), which are well fit by a biexponential function, are analyzed by the wobbling-in-a-cone model and extended Debye-Stokes-Einstein equation. Depending on the intermolecular interactions, the slow overall orientational relaxation occurs under slip, stick, and superstick boundary conditions. For HN3 and N3(-) in CH3OH and DMSO, the vibrational population relaxation becomes faster but the orientational relaxation becomes slower as the H-bond strength is increased. Our current results imply that H-bonds have significant effects on the vibrational population relaxation and orientational relaxation dynamics of a small solute whose size is comparable to the size of the solvent.
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Affiliation(s)
- Chiho Lee
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Hyewon Son
- Department of Chemistry, Korea University , Seoul 136-701, Korea
| | - Sungnam Park
- Department of Chemistry, Korea University , Seoul 136-701, Korea
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24
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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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25
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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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26
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Bondarenko AS, Jansen TLC. Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins. J Chem Phys 2016; 142:212437. [PMID: 26049457 DOI: 10.1063/1.4919716] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.
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Affiliation(s)
- Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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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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28
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Choi JH, Kim H, Kim S, Lim S, Chon B, Cho M. Ion aggregation in high salt solutions. III. Computational vibrational spectroscopy of HDO in aqueous salt solutions. J Chem Phys 2015; 142:204102. [DOI: 10.1063/1.4920972] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Seongheun Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Sohee Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Bonghwan Chon
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 136-713, South Korea
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
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Błasiak B, Cho M. Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method. J Chem Phys 2015; 140:164107. [PMID: 24784253 DOI: 10.1063/1.4872040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational solvatochromism is a solvation-induced effect on fundamental vibrational frequencies of molecules in solutions. Here we present a detailed first-principle coarse-grained theory of vibrational solvatochromism, which is an extension of our previous work [B. Błasiak, H. Lee, and M. Cho, J. Chem. Phys. 139(4), 044111 (2013)] by taking into account electrostatic, exchange-repulsion, polarization, and charge-transfer interactions. By applying our theory to the model N-methylacetamide-water clusters, solute-solvent interaction-induced effects on amide I vibrational frequency are fully elucidated at Hartree-Fock level. Although the electrostatic interaction between distributed multipole moments of solute and solvent molecules plays the dominant role, the contributions from exchange repulsion and induced dipole-electric field interactions are found to be of comparable importance in short distance range, whereas the charge-transfer effect is negligible. The overall frequency shifts calculated by taking into account the contributions of electrostatics, exchange-repulsion, and polarization terms are in quantitative agreement with ab initio results obtained at the Hartree-Fock level of theory.
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Affiliation(s)
- Bartosz Błasiak
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, South Korea
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Farag MH, Ruiz-López MF, Bastida A, Monard G, Ingrosso F. Hydration Effect on Amide I Infrared Bands in Water: An Interpretation Based on an Interaction Energy Decomposition Scheme. J Phys Chem B 2014; 119:9056-67. [PMID: 25233436 DOI: 10.1021/jp508675a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sensitivity of some infrared bands to the local environment can be exploited to shed light on the structure and the dynamics of biological systems. In particular, the amide I band, which is specifically related to vibrations within the peptide bonds, can give information on the ternary structure of proteins, and can be used as a probe of energy transfer. In this work, we propose a model to quantitatively interpret the frequency shift on the amide I band of a model peptide induced by the formation of hydrogen bonds in the first solvation shell. This method allows us to analyze to what extent the electrostatic interaction, electronic polarization and charge transfer affect the position of the amide I band. The impact of the anharmoniticy of the pontential energy surface on the hydration induced shift is elucidated as well.
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Affiliation(s)
- Marwa H Farag
- †Departamento de Química Física, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain
| | - Manuel F Ruiz-López
- ‡Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France.,§CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France
| | - Adolfo Bastida
- †Departamento de Química Física, Regional Campus of International Excellence "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain
| | - Gérald Monard
- ‡Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France.,§CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France
| | - Francesca Ingrosso
- ‡Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France.,§CNRS, SRSMC UMR 7565, Vandœuvre-lès-Nancy, F-54506, France
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Kim S, Kim H, Choi JH, Cho M. Ion aggregation in high salt solutions: Ion network versus ion cluster. J Chem Phys 2014; 141:124510. [DOI: 10.1063/1.4896227] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Seongheun Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Jun-Ho Choi
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, South Korea
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