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Ramos S, Scott KJ, Horness RE, Le Sueur AL, Thielges MC. Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine. Phys Chem Chem Phys 2017; 19:10081-10086. [PMID: 28367555 PMCID: PMC6252261 DOI: 10.1039/c7cp00403f] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal intensity, it also dramatically increases the vibrational lifetime, enabling collection of 2D IR spectra for analysis of molecular dynamics on much longer timescales. Interestingly, we also find that the lifetime for CNSePhe shows increased sensitivity to the presence of hydrogen bonding interactions with the CN, suggesting that the probe should be useful for interpretation of CN spectra and possibly for the study of solvation.
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Affiliation(s)
- S. Ramos
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - K. J. Scott
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - R. E. Horness
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - A. L. Le Sueur
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
| | - M. C. Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA.
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52
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Jeon K, Yang M. Dimension of discrete variable representation for mixed quantum/classical computation of three lowest vibrational states of OH stretching in liquid water. J Chem Phys 2017; 146:054107. [PMID: 28178837 DOI: 10.1063/1.4974934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Three low-lying vibrational states of molecular systems are responsible for the signals of linear and third-order nonlinear vibrational spectroscopies. Theoretical studies based on mixed quantum/classical calculations provide a powerful way to analyze those experiments. A statistically meaningful result can be obtained from the calculations by solving the vibrational Schrödinger equation over many numbers of molecular configurations. The discrete variable representation (DVR) method is a useful technique to calculate vibrational eigenstates subject to an arbitrary anharmonic potential surface. Considering the large number of molecular configurations over which the DVR calculations are repeated, the calculations are desired to be optimized in balance between the cost and accuracy. We determine a dimension of the DVR method which appears to be optimum for the calculations of the three states of molecular vibrations with anharmonic strengths often found in realistic molecular systems. We apply the numerical technique to calculate the local OH stretching frequencies of liquid water, which are well known to be widely distributed due to the inhomogeneity in molecular configuration, and found that the frequencies of the 0-1 and 1-2 transitions are highly correlated. An empirical relation between the two frequencies is suggested and compared with the experimental data of nonlinear IR spectroscopies.
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Affiliation(s)
- Kiyoung Jeon
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
| | - Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, South Korea
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53
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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54
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Shen YN, Jiang B, Ge CQ, Deng GH, Chen HL, Yang XM, Yuan KJ, Zheng JR. Intermolecular Vibrational Energy Transfers in Melts and Solutions. CHINESE J CHEM PHYS 2016. [DOI: 10.1063/1674-0068/29/cjcp1602028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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55
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Schmitz AJ, Hogle DG, Gai XS, Fenlon EE, Brewer SH, Tucker MJ. Two-Dimensional Infrared Study of Vibrational Coupling between Azide and Nitrile Reporters in a RNA Nucleoside. J Phys Chem B 2016; 120:9387-94. [PMID: 27510724 DOI: 10.1021/acs.jpcb.6b07212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The vibrations in the azide, N3, asymmetric stretching region and nitrile, CN, symmetric stretching region of 2'-azido-5-cyano-2'-deoxyuridine (N3CNdU) are examined by two-dimensional infrared (2D IR) spectroscopy. At earlier waiting times, the 2D IR spectrum shows the presence of both vibrational transitions along the diagonal and off-diagonal cross peaks indicating vibrational coupling. The coupling strength is determined from the off-diagonal anharmonicity to be 66 cm(-1) for the intramolecular distance of ∼7.9 Å, based on a structural map generated for this model system. In addition, the frequency-frequency correlation decay is detected, monitoring the solvent dynamics around each individual probe position. Overall, these vibrational reporters can be utilized in tandem to simultaneously track global structural information and fast structural fluctuations.
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Affiliation(s)
- Andrew J Schmitz
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
| | - David G Hogle
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
| | - Xin Sonia Gai
- Department of Chemistry, Franklin & Marshall College , Lancaster, Pennsylvania 17604-3003, United States
| | - Edward E Fenlon
- Department of Chemistry, Franklin & Marshall College , Lancaster, Pennsylvania 17604-3003, United States
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College , Lancaster, Pennsylvania 17604-3003, United States
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada , Reno, Nevada 89557, United States
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56
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Ge C, Shen Y, Deng GH, Tian Y, Yu D, Yang X, Yuan K, Zheng J. Negligible Isotopic Effect on Dissociation of Hydrogen Bonds. J Phys Chem B 2016; 120:3187-95. [DOI: 10.1021/acs.jpcb.5b12652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanqi Ge
- School
of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Yuneng Shen
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Gang-Hua Deng
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Yuhuan Tian
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Dongqi Yu
- School
of Physics and Electronic Technology, Liaoning Normal University, Dalian 116029, China
| | - Xueming Yang
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Kaijun Yuan
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
| | - Junrong Zheng
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of
the Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China
- Department
of Chemistry, Rice University, Houston, Texas 77005, United States
- College
of Chemistry and Molecular Engineering, Beijing National Laboratory
for Molecular Sciences, Peking University, Beijing 100871, China
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57
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Dhayalan B, Fitzpatrick A, Mandal K, Whittaker J, Weiss MA, Tokmakoff A, Kent SBH. Efficient Total Chemical Synthesis of (13) C=(18) O Isotopomers of Human Insulin for Isotope-Edited FTIR. Chembiochem 2016; 17:415-20. [PMID: 26715336 DOI: 10.1002/cbic.201500601] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/08/2022]
Abstract
Isotope-edited two-dimensional Fourier transform infrared spectroscopy (2 D FTIR) can potentially provide a unique probe of protein structure and dynamics. However, general methods for the site-specific incorporation of stable (13) C=(18) O labels into the polypeptide backbone of the protein molecule have not yet been established. Here we describe, as a prototype for the incorporation of specific arrays of isotope labels, the total chemical synthesis-via a key ester insulin intermediate-of 97 % enriched [(1-(13) C=(18) O)Phe(B24) ] human insulin: stable-isotope labeled at a single backbone amide carbonyl. The amino acid sequence as well as the positions of the disulfide bonds and the correctly folded structure were unambiguously confirmed by the X-ray crystal structure of the synthetic protein molecule. In vitro assays of the isotope labeled [(1-(13) C=(18) O)Phe(B24) ] human insulin showed that it had full insulin receptor binding activity. Linear and 2 D IR spectra revealed a distinct red-shifted amide I carbonyl band peak at 1595 cm(-1) resulting from the (1-(13) C=(18) O)Phe(B24) backbone label. This work illustrates the utility of chemical synthesis to enable the application of advanced physical methods for the elucidation of the molecular basis of protein function.
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Affiliation(s)
- Balamurugan Dhayalan
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Ann Fitzpatrick
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.,The James Frank Institute, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Kalyaneswar Mandal
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA
| | - Jonathan Whittaker
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Michael A Weiss
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Andrei Tokmakoff
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA. .,The James Frank Institute, University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
| | - Stephen B H Kent
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL, 60637, USA.
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