Fast folding dynamics of proteins and peptides

Whynes, Renee Fast folding dynamics of proteins and peptides. Doctor of Philosophy thesis, University of Liverpool.

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Abstract

The dynamics of protein folding has become a major area of research interest today, particularly in biophysical chemistry. The first steps of protein folding have been reported to occur on the 100-ns time scale, made possible by with the development of several experimental techniques. For this research, laser induced temperature jumps coupled to infrared spectroscopy were used for observing the fast folding dynamics of a small protein and a peptide on the nanosecond time scale by probing changes in the amide I band, which is sensitive to secondary structure. This research project also describes the development and demonstration of a new photochemical triggering technique for protein folding. Peptide and poly-ethylene glycol-capped gold nanoparticles were tested and used as heat transducers for inducing temperature jumps in protein and peptide samples. The results demonstrate that, for the typical concentration used in our temperature jump measurements, the nanoparticles do not affect the helix-coil transition of proteins and peptides. We also describe a new method for subtracting the pressure relief artifact observed after a ns-temperature jump. Application of this method allows us to identify a hidden phase on the nanosecond time scale in the temperature jump induced dynamics of a small protein. The effect of pD and temperature on the fast folding dynamics of a small protein (BBL) was studied. The results show, for the first time, that the protein exhibits three distinct phases; two nanosecond phases and a microsecond phase. However, we found that the nanosecond components are not easily distinguished due to similarities in the time constants. Finally, this research project also describes the development of a new photo-triggering method which is based on a photocleavage reaction that generates the desired functional group from an inactive caged one upon photolysis, namely the photocleavage reaction of a peptide that is covalently bonded to 4,5-dimethoxy-2-nitrobenzyl. Our experimental results show, that cleavage of the backbone peptide is very fast, so that the photo-triggering technique is valid for observing the fast dynamics of peptides and proteins on the nanosecond/microsecond timescale.

Item Type:	Thesis (Doctor of Philosophy)
Additional Information:	Date: 2010-09-29 (completed)
Uncontrolled Keywords:	Protein Folding, Nanoparticles, Heat Transducers, Photocleavage Reaction
Subjects:	?? QD ??
Divisions:	Faculty of Science and Engineering > School of Physical Sciences
Depositing User:	Symplectic Admin
Date Deposited:	01 Dec 2011 11:51
Last Modified:	16 Dec 2022 04:35
DOI:	10.17638/00003013
Supervisors:	Volk, Martin
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3013