Graduation Year
2016
Document Type
Thesis
Degree
Ph.D.
Degree Name
Doctor of Philosophy (Ph.D.)
Degree Granting Department
Medicine
Major Professor
Vladimir Uversky, Ph.D.
Committee Member
Yu Chen, Ph.D.
Committee Member
Robert Deschenes, Ph.D.
Committee Member
Sandy Westerheide, Ph.D.
Committee Member
Bin Xue, Ph.D.
Keywords
intrinsically disordered protein, x-ray crystallography, structural biology, enzyme function
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) exist as interconverting conformational ensembles, without a single fixed three-dimensional structure in vivo. The focus in the literature up to this point has been primarily on IDPs that are mostly or entirely disordered. Therefore, we have an incomplete understanding of the incidence and functional relevance of IDPRs in proteins that have regions of both order and disorder. This work explores these populations, by examining IDPRs in the Protein Data Bank (PDB) and in enzymes. By applying disorder prediction methods combined with an analysis of missing regions in crystal structure data, this work shows that enzymes have a similar incidence and length of IDPRs as do non-enzymes, and that these IDPRs are correlated with functions related to macromolecular metabolism, signaling, and regulation. Furthermore, extensive analyses of missing regions with conflicting information between multiple structures in the PDB show that, rather than experimental artifacts, this ambiguity most likely arises due to partially or conditionally disordered regions. This work documents the first proteome level study of protein intrinsic disorder in enzyme populations and demonstrates a novel way of analyzing missing regions in the PDB. Furthermore, an extensive literature search as part of this work provides information for 1127 IDPs with experimental evidence documented in the literature, 96 of which are enzymes. The results contained herein present a new model of the protein universe, where disorder is directed by evolution in both non-enzymes and enzymes to make the most of limited proteomes in complex organisms through complicated signaling networks and tightly controlled regulation.
Scholar Commons Citation
Deforte, Shelly, "Intrinsic Disorder Where You Least Expect It: The Incidence and Functional Relevance of Intrinsic Disorder in Enzymes and the Protein Data Bank" (2016). USF Tampa Graduate Theses and Dissertations.
https://digitalcommons.usf.edu/etd/6219
