Analysis of folding kinetics for simplified model proteins
| dc.contributor | Ph.D. Program in Chemical Engineering. | |
| dc.contributor.advisor | Bahar, Ivet. | |
| dc.contributor.author | Özkan, Ş. Banu. | |
| dc.date.accessioned | 2023-03-16T11:13:37Z | |
| dc.date.available | 2023-03-16T11:13:37Z | |
| dc.date.issued | 2001. | |
| dc.description.abstract | The conformational stochastics of simplified model chains that show an apparent two-state kinetics was explored.. A fundamental question addressed in the present analysis is to understand if the folding takes place through a continuum of paths, or if a preferred pathway involving subcooperative folding events can be discerned. To this aim, the complete sets of conformations for short model chains were generated as self-avoiding walks on a square lattice. Native-like contacts have been assigned attractive potentials, and transition rates have been assigned on the basis of native-like contacts and root-mean-square deviations between conformations. The time evolution of all conformational transitions has been analyzed starting from a uniform distribution of conformations, using a master equation formalism. A key conclusion is that: (i) The lack of intermediates that define two-state kinetics does not preclude folding through a specific sequence of events. (ii) F-value analysis, a measure of the stability and change in folding kinetics due to mutation reveals that non classical F-values can arise from parallel microscopic flow processes. Negative F values result when a mutation destabilizes a slow flow channel, causing an overflow into a faster flow channel. F-values greater than one occur when mutations redirect a fast flow into a slower channel. | |
| dc.format.extent | 30 cm. | |
| dc.format.pages | xiii, 87 leaves ; | |
| dc.identifier.other | CHE 2001 O85 PhD | |
| dc.identifier.uri | https://digitalarchive.library.bogazici.edu.tr/handle/123456789/14885 | |
| dc.publisher | Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2001. | |
| dc.subject.lcsh | Protein folding. | |
| dc.title | Analysis of folding kinetics for simplified model proteins |
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