Multiscale modeling in nanostructures : physical and biological systems

Loading...
Thumbnail Image
Authors
Dearden, Albert Karcz
Issue Date
2014-08
Type
Electronic thesis
Thesis
Language
ENG
Keywords
Physics
Research Projects
Organizational Units
Journal Issue
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
Full Citation
Publisher
Rensselaer Polytechnic Institute, Troy, NY
Terms of Use
Journal
Volume
Issue
PubMed ID
DOI
ISSN
EISSN