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On the role of entropy in the protein folding process
Please use this identifier to cite or link to this item:
http://hdl.handle.net/1860/3488
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| Title: | On the role of entropy in the protein folding process |
| Authors: | Hoppe, Travis |
| Keywords: | Physics
Ising model
Protein folding |
| Issue Date: | 20-May-2011 |
| Abstract: | A protein's ultimate function and activity is determined by the unique three-dimensional structure taken by the folding process. Protein malfunction due to misfolding is the culprit of many clinical disorders, such as abnormal protein aggregations. This leads to neurodegenerative disorders like
Huntington's and Alzheimer's disease. We focus on a subset of the folding problem, exploring the role and effects of entropy on the process of protein folding. Four major concepts and models are developed and each pertains to a specfic aspect of the folding process: entropic forces, conformational
states under crowding, aggregation, and macrostate kinetics from microstate trajectories.
The exclusive focus on entropy is well-suited for crowding studies, as many interactions are nonspecific. We show how a stabilizing entropic force can arise purely from the motion of crowders in solution. In addition we are able to make a a quantitative prediction of the crowding effect with an
implicit crowding approximation using an aspherical scaled-particle theory.
In order to investigate the effects of aggregation, we derive a new operator expansion method to solve the Ising/Potts model with external fields over an arbitrary graph. Here the external fields are representative of the entropic forces. We show that this method reduces the problem of calculating the partition function to the solution of recursion relations.
Many of the methods employed are coarse-grained approximations. As such, it is useful to have a viable method for extracting macrostate information from time series data. We develop a method to cluster the microstates into physically meaningful macrostates by grouping similar relaxation times from a transition matrix.
Overall, the studied topics allow us to understand deeper the complicated process involving proteins. |
| URI: | http://hdl.handle.net/1860/3488 |
| Appears in Collections: | Drexel Theses and Dissertations
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