Multiscale modeling in nanostructures : physical and biological systems
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Authors
Dearden, Albert Karcz
Issue Date
2014-08
Type
Electronic thesis
Thesis
Thesis
Language
ENG
Keywords
Physics
Alternative Title
Abstract
For the second half of this work, we move to a biological context in which we studied the effect of specific mutations in a protein. We find that in the context of the DnaE intein, mutations to the Thr69 residue can alter the conformational arrangement of the Gly-1 residue of the neighboring catalytic Cys1. We find that through hydrogen bonding, Gly-1 may adopt a distorted conformation which alters the splicing rate of the intein. We find that with the presence of Thr69 and the distorted Gly-1 conformation, the reaction barrier is less than that of the case with Thr69 mutated to Ala69 and a non-distorted conformation in Gly-1, which is supported by experimental data. Expanding our study on controlling the splicing mechanism, we examine the effect of metals on the N-S acyl shift. We find that by introducing even a single metallic ion near the reaction site of intein splicing, there are large differences in the reaction barriers. Furthermore, we find that due to a lack of π backbonding, certain metals such as platinum can in fact reduce the reaction barrier of the N-S acyl shift, thus accelerating the intein splicing process at the macroscopic scale.
Description
August 2014
School of Science
School of Science
Full Citation
Publisher
Rensselaer Polytechnic Institute, Troy, NY