2026-09-18T23:40:43Zhttps://dspace.mit.edu/server/oai/requestoai:dspace.mit.edu:1721.1/395412022-01-13T07:54:33Zcom_1721.1_7582com_1721.1_7581col_1721.1_131023
Bernhardt L. Trout.
Shinde, Chetan (Chetan Ulhas)
Massachusetts Institute of Technology. Dept. of Materials Science and Engineering.
Massachusetts Institute of Technology. Department of Materials Science and Engineering
2007-11-16T14:20:14Z
2007-11-16T14:20:14Z
2007
2007
http://hdl.handle.net/1721.1/39541
174042522
Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2007.
Includes bibliographical references (p. 61-62).
Rational design of protein additives has been limited by the understanding of mechanism of protein and additive interaction. In this work we have applied molecular dynamics with all atom potentials in order to study the thermodynamic effect of additives on proteins. The method is based on statistical mechanical model that characterizes the preferential binding of proteins to either water or additives. Extensive study was done on model systems comprising of additives urea, glycerol & arginine hydrochloride and proteins RNaseT1 and hen egg lysozyme. Trajectories in range 10-19 nanoseconds were analyzed in order to validate this method and compared with the experimental results. The method was found to agree with experimental results for the first 2 nanoseconds and the extended runs were studied further to narrow down the cause of deviations. Protein RNaseT1 was found to be very unstable and consequently showed very high deviations in preferential binding for longer runs. Constraining the protein using harmonic potential has resulted in better averages for RNase T1.
(cont.) Lysozyme has been found to be very stable and the calculations are in good agreement with experimental values. Local preferential binding calculations showed the importance of structure as well as sequence in prediction of preferential binding of protein.
by Chetan Shinde.
S.M.
62 p.
eng
Massachusetts Institute of Technology
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http://dspace.mit.edu/handle/1721.1/7582
Materials Science and Engineering.
Quantitative studies in effects of additives on protein aggregation
Thesis
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<Abstract>Rational design of protein additives has been limited by the understanding of mechanism of protein and additive interaction. In this work we have applied molecular dynamics with all atom potentials in order to study the thermodynamic effect of additives on proteins. The method is based on statistical mechanical model that characterizes the preferential binding of proteins to either water or additives. Extensive study was done on model systems comprising of additives urea, glycerol & arginine hydrochloride and proteins RNaseT1 and hen egg lysozyme. Trajectories in range 10-19 nanoseconds were analyzed in order to validate this method and compared with the experimental results. The method was found to agree with experimental results for the first 2 nanoseconds and the extended runs were studied further to narrow down the cause of deviations. Protein RNaseT1 was found to be very unstable and consequently showed very high deviations in preferential binding for longer runs. Constraining the protein using harmonic potential has resulted in better averages for RNase T1.</Abstract>
<Abstract>(cont.) Lysozyme has been found to be very stable and the calculations are in good agreement with experimental values. Local preferential binding calculations showed the importance of structure as well as sequence in prediction of preferential binding of protein.</Abstract>
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