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Date of Award

Summer 8-15-2013

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Proteins can exhibit significant conformational heterogeneity either under denaturing conditions or in aqueous solutions. The latter is true for a class of proteins whose sequences predispose them to form heterogeneous ensembles of conformations. Characterization of conformational heterogeneity in a protein ensemble requires the quantification of the amplitudes of spontaneous fluctuations in conjunction with information regarding coarse grain measures that report on the average sizes, shapes, and densities. This often demands multiplexed experimental approaches whose readouts are interpreted or annotated using ensembles drawn from atomistic or coarse grain computational simulations. Efforts to characterize conformational heterogeneity contribute directly to our understanding of disorder-to-order transitions in protein folding and self-assembly. These efforts are also crucial to our understanding of the heterotypic interactions involving intrinsically disordered proteins and non-native states of well-folded proteins. These heterotypic interactions are important in signal transduction and the regulation of protein homeostasis. The onset and progression of several systemic and neurodegenerative "conformational diseases" are linked to the nature and degree of conformational heterogeneity in specific proteins or proteolytic products of proteins.

This thesis work focuses on the quantitative characterization of conformational heterogeneity in simulated ensembles of inducibly unfolded and intrinsically disordered proteins. Advances in nuclear magnetic resonance spectroscopy afford the possibility of detailed measurements of inter-residue distances and modulations to the relaxation dynamics of paramagnetic spins that are inserted as probes into a protein. These state-of-the-art measurements show interesting features within denatured state ensembles that cannot be explained using canonical random coil models. Here, we use computer simulations to generate plausible facsimiles of denatured state ensembles that reproduce experimental data and demonstrate that the ensembles that are consistent with the data are characterized by the presence of low-likelihood, long-range intra-chain contacts between hydrophobic groups. When placed in the context of sequence conservation information, it appears that these contacts act as gatekeepers that protect proteins from the deleterious consequences of protein aggregation by sequestering hydrophobic groups in an assortment of intra-chain long-range contacts. We also characterize the nature and degree of conformational heterogeneity in glutamine- and asparagine-rich containing systems. These efforts lead to insights regarding the role of conformational heterogeneity in mediating intermolecular associations that are implicated in aggregation and self-assembly of these systems. Analysis of results from atomistic simulations leads to a phenomenological model for the modulation of conformational heterogeneity and degeneracies of intermolecular interactions by naturally occurring sequences that flank polyglutamine domains.

Finally, we develop a formal order parameter to quantify the conformational heterogeneity in simulated ensembles of proteins. When combined with measures of density and fluctuations thereof, it can be used to provide a complete description of the degree and nature of conformational heterogeneity in different ensembles, thus affording the ability to compare different ensembles to each other while also providing a way to categorize conformational transitions.


English (en)

Chair and Committee

Rohit V. Pappu

Committee Members

Jan Bieschke, Anders E. Carlsson, James J. Havranek, Baranidharan Raman, Gary D. Stormo

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