Link to the University of Pittsburgh Homepage
Link to the University Library System Homepage Link to the Contact Us Form

Molecular Dynamics Predicts The Solution Conformations of Poly-L-lysine in Salt Solutions

Feng, Liqi (2014) Molecular Dynamics Predicts The Solution Conformations of Poly-L-lysine in Salt Solutions. Master's Thesis, University of Pittsburgh. (Unpublished)

Submitted Version

Download (5MB) | Preview


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.


Social Networking:
Share |


Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Feng, Liqilif25@pitt.eduLIF25
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Committee ChairAsher, Sanford A.asher@pitt.eduASHER
Committee MemberMadura, Jeffry D
Committee MemberChong, Lillian T
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


Monthly Views for the past 3 years

Plum Analytics

Actions (login required)

View Item View Item