Multiscale modeling in nanostructures : physical and biological systems

Dearden, Albert Karcz
Thumbnail Image
Other Contributors
Nayak, Saroj K.
Wang, G.-C. (Gwo-Ching), 1946-
Korniss, Gyorgy
Belfort, Marlene
Issue Date
Terms of Use
This electronic version is a licensed copy owned by Rensselaer Polytechnic Institute, Troy, NY. Copyright of original work retained by author.
Full Citation
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.
August 2014
School of Science
Dept. of Physics, Applied Physics, and Astronomy
Rensselaer Polytechnic Institute, Troy, NY
Rensselaer Theses and Dissertations Online Collection
Restricted to current Rensselaer faculty, staff and students. Access inquiries may be directed to the Rensselaer Libraries.