The random-coil model has been dominant for unfolded proteins since the 1950’s; however, some experiments showed that the unfolded proteins were biased toward specific conformations in conflict with the random-coil model. Recently, residual dipolar couplings (RDCs) and paramagnetic relaxation enhancement (PRE) were applied to obtain a large amount of structural information on unfolded proteins. Typically, these data were interpreted in a framework of random-coil ensembles with a good agreement between experimental data and theoretical predictions. In this thesis, it was tested whether locally organized nonrandom ensembles could describe this agreement equally as well. Using a complete set of RDC and PRE data for denatured ubiquitin, it was revealed that there was no distinguishable difference between random-coil ensembles and ensembles containing 50% native structure. Thus, while it is important to measure as many RDCs or PRE as possible, even the best datasets may be insensitive to local organization in unfolded proteins.
| Identifer | oai:union.ndltd.org:MSSTATE/oai:scholarsjunction.msstate.edu:td-1747 |
| Date | 17 May 2014 |
| Creators | Zhang, Yue |
| Publisher | Scholars Junction |
| Source Sets | Mississippi State University |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | Theses and Dissertations |
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