Information Content in Ribonuclease A: An Investigation of Protein Structure and Identification of New Qsars
type: CreativeWork
description: The research of this dissertation presents a newly identified quantitative relationship between statistical information expressed by protein structure and the resulting enzymatic function. All molecules contain information in their atom/covalent bond structure. It is this structural information that confers the physical and chemical properties of the molecule. It was the goal of this project to formulate a method for quantifying structural information of protein molecules. A computational model was developed for this quantification. Ribonuclease A (RNase A) was used as a model system of investigation. In solution, molecules are subjected to numerous collisions powered by the thermal energy of Brownian motion. It is upon each Brownian collision that structural information is momentarily trapped and therefore communicated between molecules. In most cases, the result of a collision is not a reaction. However, the sequences of collisions resulting in no chemical reaction are the ones that communicate details of molecular structure. In a liquid environment, every molecule, enzyme or otherwise, offers a complex set of collision possibilities, which differentiates its chemical nature. The computational model of this investigation is one that mimics collisions between a folded protein and an inert colliding random walker. Every instance of collision between the random walker and protein molecule results in expression of information about a small fraction of the protein structure. The deviations from randomness in the random walk are imposed by the molecular lattice of the protein molecule. The model tracks the path of the random walker as it traverses the structure of a folded protein. The structural data expressed by the protein molecule at each collision is documented and recorded. The collision sequences are then probed for Shannon and mutual information quantities. This model is one that is not expensive in computational time or power. In fact, all of the programs imple…
abstract: The research of this dissertation presents a newly identified quantitative relationship between statistical information expressed by protein structure and the resulting enzymatic function. All molecules contain information in their atom/covalent bond structure. It is this structural information that confers the physical and chemical properties of the molecule. It was the goal of this project to formulate a method for quantifying structural information of protein molecules. A computational model was developed for this quantification. Ribonuclease A (RNase A) was used as a model system of investigation. In solution, molecules are subjected to numerous collisions powered by the thermal energy of Brownian motion. It is upon each Brownian collision that structural information is momentarily trapped and therefore communicated between molecules. In most cases, the result of a collision is not a reaction. However, the sequences of collisions resulting in no chemical reaction are the ones that communicate details of molecular structure. In a liquid environment, every molecule, enzyme or otherwise, offers a complex set of collision possibilities, which differentiates its chemical nature. The computational model of this investigation is one that mimics collisions between a folded protein and an inert colliding random walker. Every instance of collision between the random walker and protein molecule results in expression of information about a small fraction of the protein structure. The deviations from randomness in the random walk are imposed by the molecular lattice of the protein molecule. The model tracks the path of the random walker as it traverses the structure of a folded protein. The structural data expressed by the protein molecule at each collision is documented and recorded. The collision sequences are then probed for Shannon and mutual information quantities. This model is one that is not expensive in computational time or power. In fact, all of the programs imple…
author: Greminger, Jessica L.
keywords: Information Theory, Protein Structure, Ribonuclease, Chemistry
date published: 2009-01-01T08:00:00Z
date modified: 2026-07-24T02:55:23Z
provider: Loyola University Chicago
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: Loyola University Chicago