Ahmed, Zeeshan
(2009)
UV-Resonance Raman Studies of Small Peptides and Proteins.
Doctoral Dissertation, University of Pittsburgh.
(Unpublished)
Abstract
An understanding of protein folding and how it impacts the structure and function of proteins will have a major impact on our understanding of the molecular underpinings of life. In particular, a robust understanding of protein folding will provide a molecular insight into misfolded protein diseases such as Alzheimer's disease. Currently, our understanding of protein folding is limited by the available tool-set, necessitating the development of novel spectroscopic tools for protein structure elucidation. This work is a continuation of our ongoing efforts to develop UV-resonance Raman spectroscopy (UVRR) as a powerful tool for protein structure determination. We utilize UVRR to determine changes in the conformation distribution of various model systems, such as the mini-protein Trp-cage and the therapeutically relevant gp41659-671 peptide. Utilizing deep UV-excitation we quantitatively track temperature induced conformation changes in these peptides. Similarly we utilized UVRR and circular dichroism to determine the conformation distribution of elastin-like peptides and demarcated the role of val, pro and gly peptide bonds in the elastin's hydrophobic collapse peptides. Our results indicate that conformation changes leading to elastin's inverse temperature transition are localized at the gly and pro peptide bonds. We utilized UVRR and DFT calculations to demonstrate that the AmII'p frequency is sensitive to Ψ-conformation changes. We correlate a 7 cm-1 downshift in the AmII'p frequency of polyproline to temperature-induced conformation changes from Ψ = 145º to Ψ = 100º. The latter high temperature compact conformation shows a ~26% decrease in its solvent accessible surface area, indicating a temperature induced hydrophobic collapse. We utilized steady-state and time-resolved UVRR spectroscopy to determine the molecular mechanism of poly-(N-isopropylacrylamide)'s (PNIPAM) temperature-induced hydrophobic collapse. Our results indicate that the hydrophobic collapse results in the loss of a C=O-water hydrogen bond at the carbonyl site. The N-H-water remains unperturbed by PNIPAM's collapse. The collapse rate (106 s-1) indicates a persistence length of n~10. We postulate that at elevated temperature PNIPAM forms hydrophobic nano-pockets when the (i, i +3) groups make hydrophobic contacts. A persistence length of n~10 suggests a cooperative collapse where hydrophobic interactions between adjacent hydrophobic pockets stabilize the collapsed PNIPAM.
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Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
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| ETD Committee: |
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| Date: |
22 January 2009 |
| Date Type: |
Completion |
| Defense Date: |
13 October 2008 |
| Approval Date: |
22 January 2009 |
| Submission Date: |
5 November 2008 |
| Access Restriction: |
5 year -- Restrict access to University of Pittsburgh for a period of 5 years. |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Chemistry |
| Degree: |
PhD - Doctor of Philosophy |
| Thesis Type: |
Doctoral Dissertation |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
310-helix; a-helix; amide; dehydration; density functional theory; elastin; hydrophobic collapse; inverse temperature transition; nipam; peptide bond; Protein folding; rough energy landscape; Trp-cage; vibrational spectra; volume phase transition; proline; UV-Resonance Raman |
| Other ID: |
http://etd.library.pitt.edu/ETD/available/etd-11052008-140423/, etd-11052008-140423 |
| Date Deposited: |
10 Nov 2011 20:04 |
| Last Modified: |
15 Nov 2016 13:51 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/9578 |
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