Observing the unfolding transition of [beta]-hairpin peptides with nonlinear infrared spectroscopy

The biological function of a protein is in large measure determined by its three-dimensional structure. To date, however, the transition of the protein between the native and non-native conformations is not well-understood. Part of the difficulty is the large conformational space available to a poly-peptide chain, and a general lack of experimental probes that can access local structural information on the time scale of the transition. Single domain peptides are excellent model systems that reduce the size and complexity of the problem, while maintaining the essential physical interactions. In this thesis, P-hairpin peptides are used as model systems for studying P-sheet secondary structure. Hairpin folding has been studied for a number of years, but there is still debate in the literature about the relative importance of the cross-strand hydrogen bonds, tertiary side chain contacts, and p-turn in the folding pathway. In addition, the denatured state is very poorly understood, which complicates any attempt to describe the folding pathway. In this work, amide I vibrational spectroscopy is used to resolve the secondary structure of P-hairpin peptides during thermal denaturation. Spectroscopic modeling is presented to describe the amide I band of 0-hairpins and relate it to structural features. Three spectroscopic methods are used to probe the amide I band: Fourier transform infrared (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and dispersed vibrational echo (DVE) spectroscopy. 2D IR and DVE spectroscopy are 3rd order-nonlinear methods that interrogate the system with a series of ultrafast (100 fs) laser pulses. 2D IR spectra reveal vibrational couplings and measure spectral dynamics on a picosecond time scale. .

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemistry.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2008

Author dc:creator

• Smith, Adam Wilcox, 1977-

Advisor dc:contributor.advisor

• Andrei Tokmakoff.

• Chemistry.

Statement dc:rights

• 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.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/43772

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/43772