Multi-mode two-dimensional infrared spectroscopy of peptides and proteins
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2008
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| Online Access: | http://hdl.handle.net/1721.1/43732 |
| _version_ | 1826188338055348224 |
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| author | DeFlores, Lauren P |
| author2 | Andrei Tokmakoff. |
| author_facet | Andrei Tokmakoff. DeFlores, Lauren P |
| author_sort | DeFlores, Lauren P |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. |
| first_indexed | 2024-09-23T07:58:08Z |
| format | Thesis |
| id | mit-1721.1/43732 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T07:58:08Z |
| publishDate | 2008 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/437322022-01-13T07:54:21Z Multi-mode two-dimensional infrared spectroscopy of peptides and proteins DeFlores, Lauren P Andrei Tokmakoff. Massachusetts Institute of Technology. Dept. of Chemistry. Massachusetts Institute of Technology. Department of Chemistry Chemistry. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2008. This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. Vita. Includes bibliographical references. In this thesis, a methodology for understanding structural stability of proteins through multi-mode two-dimensional infrared (2D IR) spectroscopy is developed. The experimental framework for generation of broadband infrared lasers and robust new approaches to 2D IR spectroscopy are demonstrated. Long-term phase stability is achieved through the development of a passively stabilized diffractive optic and wedge interferometer. A new approach for acquisition of 2D IR spectra in the pump-probe geometry reduces overall experimental complexity. These technological advances extend the capabilities of 2D IR to further resolve inter- and intramolecular couplings, relaxation pathways and structural kinetics in complex systems. Characterization of multi-mode spectra is first performed on model protein systems to reveal detailed information on the effects of solvation and structure on the amide vibrations. Differences in vibrational coupling, transition dipole angles and the anharmonic potential of the amide vibrations of isotopologues of N-methylacetamide arise from significant change in the local mode composition of the amide II band due to isotopic substitution of the peptide group. Extension of multi-mode 2D IR to study the amide I'-II' spectra of an ideal protein system, poly-L-lysine, provides direct evidence for the structural sensitivity of the amide II' vibration, particularly to the !-helix moiety. This structural sensitivity arises from through bond coupling and structure induced symmetry and orientation of adjacent residues. Integration of these tools with hydrogen exchange techniques allows for the protein structural kinetics and stability to be observed through protein-solvent interactions with enhanced structural sensitivity relative to amide I spectroscopy alone. The amide II' diagonal provides a measure of the degree of exchange and the cross peaks between the structurally sensitive amide I/I' vibration and the solvent exposure sensitive amide II and II' modes reveal the location of exchange. Partial exchange of the secondary structure of ubiquitin is revealed by correlation of the different amide signatures through analysis of cross peak line shapes, positions and amplitudes. Results provide direct evidence for a highly stable helix and labile "-sheet structure. by Lauren P. DeFlores. Ph.D. 2008-12-11T16:55:38Z 2008-12-11T16:55:38Z 2008 2008 Thesis http://hdl.handle.net/1721.1/43732 260486943 eng M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 238 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Chemistry. DeFlores, Lauren P Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title | Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title_full | Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title_fullStr | Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title_full_unstemmed | Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title_short | Multi-mode two-dimensional infrared spectroscopy of peptides and proteins |
| title_sort | multi mode two dimensional infrared spectroscopy of peptides and proteins |
| topic | Chemistry. |
| url | http://hdl.handle.net/1721.1/43732 |
| work_keys_str_mv | AT defloreslaurenp multimodetwodimensionalinfraredspectroscopyofpeptidesandproteins |