Masters Theses
Abstract
“The effect of (i) Methanol, (ii) Water and (iii) Glycerol on the stability and flexibility of (i) Polylysine, (ii) Polytryptophan and (iii) Ribonuclease A speptide was studied. Appropriate models for all the solvents were used to avoid unrealistic and abnormal behavior of the peptides solvated in them. GROMACS Software was used to perform all the simulations, generate the trajectory followed by the atoms and finally to analyze the results.
All the peptides were first equilibrated and simulated for about 500ps in vacuum and then in different solvents and solvent mixtures for about 350ps. The equilibration simulations were stopped when the potential energy oscillated about a mean value and when the charge was equally distributed across the box. Data was stored after every 0.2ps, for the last 50ps for analyzing both the solvent and the peptide structures. Hydrogen bonding, radial densities, correlation functions and Ramachandran plots are reported.
The simulation results indicate that the type of solvent largely affects the structure and flexibility of a peptide. The chemical nature of the polypeptide strongly affects its interaction with the solvent. Further work needs to be done to determine the effect of the presence of different solvents on the secondary structures by studying longer peptides”--Abstract, page iii.
Advisor(s)
Forciniti, Daniel
Committee Member(s)
Reed, X. B., Jr.
Erçal, Fikret
Department(s)
Chemical and Biochemical Engineering
Degree Name
M.S. in Chemical Engineering
Publisher
University of Missouri--Rolla
Publication Date
Fall 2000
Pagination
xi, 65 pages
Note about bibliography
Includes bibliographical references (pages 60-64).
Rights
© 2000 Rakesh Jayanthilal Jain, All rights reserved.
Document Type
Thesis - Restricted Access
File Type
text
Language
English
Thesis Number
T 7845
Print OCLC #
45902597
Recommended Citation
Jain, Rakesh Jayanthilal, "Effect of solvents on short peptides structure: A molecular dynamics study" (2000). Masters Theses. 1991.
https://scholarsmine.mst.edu/masters_theses/1991
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