Feng, Liqi
(2014)
Molecular Dynamics Predicts The Solution Conformations of Poly-L-lysine in Salt Solutions.
Master's Thesis, University of Pittsburgh.
(Unpublished)
Abstract
Ultraviolet resonance Raman (UVRR) studies recently discovered that increasing concentrations of NaClO$_4$ increase the fraction of $\alpha$-helical conformations of poly-L-lysine (PLL) in water solutions. In contrast, this $\alpha$-helical content increase does not occur for NaCl solutions. We used enhanced sampling molecular dynamics to explore the conformational space of PLL and to examine the effect of ions on PLL conformation. The free-energy landscapes of PLL in solutions were determined using the simulation data. The simulation results were also used to develop a molecular picture of ion-PLL interactions as well as the impact of ions on peptide hydration. The examination of pair interaction energies reveals the mechanisms whereby ions stabilize PLL conformations. ClO$_4$$^-$ increases the $\alpha$-helix conformation by decreasing the hydration of the peptide backbone which stabilizes the $\alpha$-helical intramolecular hydrogen bonds (H-bonds). This occurs because of the relatively large ClO$_4$$^-$ size and its tetrahedral structure. In contrast, the smaller Cl$^-$ negligibly impacts the peptide backbone hydration and does not stabilize intramolecular H-bonds. In summary the results reported here support the experimental observations and provide a molecular picture of the role ions play in PLL conformations in aqueous salt solutions.
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Details
| Item Type: |
University of Pittsburgh ETD
|
| Status: |
Unpublished |
| Creators/Authors: |
|
| ETD Committee: |
| Title | Member | Email Address | Pitt Username | ORCID |
|---|
| Committee Chair | Asher, Sanford A. | asher@pitt.edu | ASHER | | | Committee Member | Madura, Jeffry D | | | | | Committee Member | Chong, Lillian T | | | |
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| Date: |
22 May 2014 |
| Date Type: |
Publication |
| Defense Date: |
16 April 2014 |
| Approval Date: |
22 May 2014 |
| Submission Date: |
16 April 2014 |
| Access Restriction: |
No restriction; Release the ETD for access worldwide immediately. |
| Number of Pages: |
45 |
| Institution: |
University of Pittsburgh |
| Schools and Programs: |
Dietrich School of Arts and Sciences > Chemistry |
| Degree: |
MS - Master of Science |
| Thesis Type: |
Master's Thesis |
| Refereed: |
Yes |
| Uncontrolled Keywords: |
Metadynamics, Specific-ion effect |
| Date Deposited: |
22 May 2014 19:09 |
| Last Modified: |
15 Nov 2016 14:19 |
| URI: |
http://d-scholarship.pitt.edu/id/eprint/21169 |
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