Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity
We demonstrate how multimode 2D IR spectroscopy of the protein amide I′ and II′ vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I′−II′ 2D IR experiments on poly-l-lysine in the β-sheet, α-helix, and random coil conformations show that a combination of...
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| Format: | Article |
| Language: | en_US |
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American Chemical Society
2012
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| Online Access: | http://hdl.handle.net/1721.1/69554 |
| _version_ | 1811075270628605952 |
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| author | DeFlores, Lauren P. Ganim, Ziad Nicodemus, Rebecca A. Tokmakoff, Andrei |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry DeFlores, Lauren P. Ganim, Ziad Nicodemus, Rebecca A. Tokmakoff, Andrei |
| author_sort | DeFlores, Lauren P. |
| collection | MIT |
| description | We demonstrate how multimode 2D IR spectroscopy of the protein amide I′ and II′ vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I′−II′ 2D IR experiments on poly-l-lysine in the β-sheet, α-helix, and random coil conformations show that a combination of amide I′ and II′ diagonal and cross peaks can effectively distinguish between secondary structural content, where amide I′ infrared spectroscopy alone cannot. The enhanced sensitivity arises from frequency and amplitude correlations between amide II′ and amide I′ spectra that reflect the symmetry of secondary structures. 2D IR surfaces are used to parametrize an excitonic model for the amide I′−II′ manifold suitable to predict protein amide I′−II′ spectra. This model reveals that the dominant vibrational interaction contributing to this sensitivity is a combination of negative amide II′−II′ through-bond coupling and amide I′−II′ coupling within the peptide unit. The empirically determined amide II′−II′ couplings do not significantly vary with secondary structure: −8.5 cm−1 for the β sheet, −8.7 cm−1 for the α helix, and −5 cm−1 for the coil. |
| first_indexed | 2024-09-23T10:03:26Z |
| format | Article |
| id | mit-1721.1/69554 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:03:26Z |
| publishDate | 2012 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | mit-1721.1/695542022-09-26T15:25:25Z Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity DeFlores, Lauren P. Ganim, Ziad Nicodemus, Rebecca A. Tokmakoff, Andrei Massachusetts Institute of Technology. Department of Chemistry Tokmakoff, Andrei Tokmakoff, Andrei DeFlores, Lauren P. Ganim, Ziad Nicodemus, Rebecca A. We demonstrate how multimode 2D IR spectroscopy of the protein amide I′ and II′ vibrations can be used to distinguish protein secondary structure. Polarization-dependent amide I′−II′ 2D IR experiments on poly-l-lysine in the β-sheet, α-helix, and random coil conformations show that a combination of amide I′ and II′ diagonal and cross peaks can effectively distinguish between secondary structural content, where amide I′ infrared spectroscopy alone cannot. The enhanced sensitivity arises from frequency and amplitude correlations between amide II′ and amide I′ spectra that reflect the symmetry of secondary structures. 2D IR surfaces are used to parametrize an excitonic model for the amide I′−II′ manifold suitable to predict protein amide I′−II′ spectra. This model reveals that the dominant vibrational interaction contributing to this sensitivity is a combination of negative amide II′−II′ through-bond coupling and amide I′−II′ coupling within the peptide unit. The empirically determined amide II′−II′ couplings do not significantly vary with secondary structure: −8.5 cm−1 for the β sheet, −8.7 cm−1 for the α helix, and −5 cm−1 for the coil. National Science Foundation (U.S.) (CHE-0616575) United States. Dept. of Energy (DE-FG02-99ER14988) United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship) Petroleum Research Fund 2012-03-01T20:21:47Z 2012-03-01T20:21:47Z 2009-02 Article http://purl.org/eprint/type/JournalArticle 0002-7863 1520-5126 http://hdl.handle.net/1721.1/69554 DeFlores, Lauren P. et al. “Amide I′−II′ 2D IR Spectroscopy Provides Enhanced Protein Secondary Structural Sensitivity.” Journal of the American Chemical Society 131.9 (2009): 3385–3391. en_US http://dx.doi.org/10.1021/ja8094922 Journal of the American Chemical Society Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf American Chemical Society Prof. Tokmakoff via Erja Kajosalo |
| spellingShingle | DeFlores, Lauren P. Ganim, Ziad Nicodemus, Rebecca A. Tokmakoff, Andrei Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title | Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title_full | Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title_fullStr | Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title_full_unstemmed | Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title_short | Amide I’-II’ 2D IR spectroscopy provides enhanced protein secondary structural sensitivity |
| title_sort | amide i ii 2d ir spectroscopy provides enhanced protein secondary structural sensitivity |
| url | http://hdl.handle.net/1721.1/69554 |
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