Submitted to the faculty of the Bioinformatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, Indiana University August 2005 / Protein regions which lack a fixed structure are called ‘disordered’. These intrinsically disordered regions are not only very common in many proteins, they are also crucial to the function of many proteins, especially proteins involved in signaling and regulation. The goal of this work was to identify the prevalence, characteristics, and functions of conserved disordered regions within protein domains and families. A database was created to store the amino acid sequences of nearly one million proteins and their domain matches from the InterPro database, a resource integrating eight different protein family and domain databases. Disorder prediction was performed on these protein sequences. Regions of sequence corresponding to domains were aligned using a multiple sequence alignment tool. From this initial information, regions of conserved predicted disorder were found within the domains. The methodology for this search consisted of finding regions of consecutive positions in the multiple sequence alignments in which a 90% or more of the sequences were predicted to be disordered. This procedure was constrained to find such regions of conserved disorder prediction that were at least 20 amino acids in length. The results of this work were 3,653 regions of conserved disorder prediction, found within 2,898 distinct InterPro entries. Most regions of conserved predicted disorder detected were short, with less than 10% of those found exceeding 30 residues in length. Regions of conserved disorder prediction were found in protein domains from all available InterPro member databases, although with varying frequency. Regions of conserved disorder prediction were found in proteins from all kingdoms of life, including viruses. However, domains found in eukaryotes and viruses contained a higher proportion of long regions of conserved disorder than did domains found in bacteria and archaea. In both this work and previous work, eukaryotes had on the order of ten times more proteins containing long disordered regions than did archaea and bacteria. Sequence conservation in regions of conserved disorder varied, but was on average slightly lower than in regions of conserved order. Both this work and previous work indicate that in some cases, disordered regions evolve faster, in others they evolve slower, and in the rest they evolve at roughly the same rate. A variety of functions were found to be associated with domains containing conserved disorder. The most common were DNA/RNA binding, and protein binding. Many ribosomal protein families also were found to contain conserved disordered regions. Other functions identified included membrane translocation and amino acid storage for germination. Due to limitations of current knowledge as well as the methodology used for this work, it was not determined whether or not these functions were directly associated with the predicted disordered region. However, the functions associated with conserved disorder in this work are in agreement with the functions found in other studies to correlate to disordered regions. This work has shown that intrinsic disorder may be more common in bacterial and archaeal proteins than previously thought, but this disorder is likely to be used for different purposes than in eukaryotic proteins, as well as occurring in shorter stretches of protein. Regions of predicted disorder were found to be conserved within a large number of protein families and domains. Although many think of such conserved domains as being ordered, in fact a significant number of them contain regions of disorder that are likely to be crucial to their function.

Submitted to the faculty of Indiana University in partial fulfillment of the requirements for the degree Master of Science in the Department of Bioinformatics in the School of Informatics of, Indiana University December, 2004 / Electrostatic modeling was done with Delphi of insight II to explain and predict protein aggregation, measured here for β-lactoglobulin and insulin using turbidimetry and stopped flow spectrophotometry. The initial rate of aggregation of β-Lactoglobulin was studied between pH 3.8 and 5.2 in 4.5mM NaCl; and for ionic strengths from 4.5 to 500mM NaCl at pH 5.0. The initial slope of the turbidity vs. time curve was used to define the initial rate of aggregation. The highest initial rate was observed near pH < pI i.e., 4.6 (< 5.2). The decrease in aggregation rate when the pH was increased from 4.8 to 5.0 was large compared to its decrease when the pH was reduced from 4.4 to 4.2; i.e., the dependence of initial rate on pH was highly asymmetric. The initial rate of aggregation at pH 5.0 increased linearly with the reciprocal of ionic strength in the range I = 0.5 to 0.0045M. Protein electrostatic potential distributions are used to understand the pH and ionic strength dependence of the initial rate of aggregation. Similar studies were done with insulin. In contrast to BLG, the highest initial aggregation rate for insulin was observed at pH = pI. Electrostatic computer modeling shows that these differences arise from the distinctly different surface charge distributions of insulin and BLG.

Submitted to the faculty of the Bioinformatics Graduate Program in partial fulfillment of the requirements for the degree Master of Science in the School of Informatics, Indiana University December 2005 / The last decade has witnessed numerous proteomic studies which have predicted and successfully confirmed the existence of extended structurally flexible regions in protein molecules. Parallel to these advancements, the last five years of structural bioinformatics has also experienced an explosion of results on molecular recognition and its importance in protein-protein interactions. This work provides an extension to past and ongoing research efforts by looking specifically at the “flexibility and disorder†found in protein sequences involved in molecular recognition processes and known as, Molecular Recognition Elements or Molecular Recognition Features (MoREs or MoRFs, as we call them). MoRFs are relatively short in length (10 – 70 residues length); loosely structured protein regions within longer sequences that are largely disordered in nature. Interestingly, upon binding to other proteins, these MoRFs are able to undergo disorder-to-order transition. Thus, in our interpretation, MoRFs could serve as potential binding sites, and that this binding to another protein lends a functional advantage to the whole protein complex by enabling interaction with their physiological partner. There are at least three basic types of MoRFs: those that form α-helical structures upon binding, those that form β-strands (in which the peptide forms a β-sheet with additional β-strands provided by the protein partner), and those that form irregular structures when bound. Our proposed names for these structures are α-MoRF (also known as α-MoRE, alpha helical molecular recognition feature/element), β-MoRF (beta sheet molecular recognition feature/element), and I-MoRF (Irregular molecular recognition feature/element), respectively. The results presented in this work suggest that functionally significant residual structure can exist in MoRF regions prior to the actual binding event. We also demonstrate profound conformational preferences within MoRF regions for α-helices. We believe that the results from this study would subsequently improve our understanding of protein-protein interactions especially those related to the molecular recognition, and may pave way for future work on the development of protein binding site predictions. We hope that via the conclusions of this work, we would have demonstrated that within only a few of years of its conception, intrinsic protein disorder has gained wide-scale importance in the field of protein-protein interactions and can be strongly associated with molecular recognition.

Modification of cellular proteins with molecules of ubiquitin is an important process that regulates the activity of cellular proteins. Cullin RING ligases (CRLs) are multi-subunit complexes that act in concert with E2 enzymes to attach molecules of ubiquitin to protein substrates. There are seven CRLs in mammalian cells (Cul1, Cul2, Cul3, Cul4A, Cul4B, Cul5, and Cul7) that are highly homologous in sequence and structure. CRLs possess a highly conserved C- terminal domain that interacts with E2 enzymes, and a more variable N- terminal domain which recruits substrates through distinct substrate adapter molecules. Despite the structural similarity, these CRLs recognize distinct substrates and carry out unique functions in cells. In order to characterize the functional domains of cullins that are responsible for their unique activity, we generated cullin chimeras for expression and analysis in mammalian cells. These chimeras are Cul3 mutants in which the C- terminal domain or N- terminal domain of Cul3 has been replaced by that of Cul1 or Cul2, respectively. These chimeras were cloned into a mammalian expression vector for the purpose of experimentation in cultured cells. The chimeric cullin constructs provided a valuable tool for investigating how different functional domains of CRLs contribute to their specific functions in cells. In this study, we first investigated if the chimeras that we engineered were able to interact with their respective substrate adapters. We performed co- immunoprecipitation experiments in which we tested the ability of wild type, chimeric, or mutant cullin proteins to bind to three different substrate adapter proteins. We found that the chimera possessing the C- terminus of Cul1 and the N- terminus of Cul3 retains the ability to interact with the BTB substrate adapters Ctb57 and KLHL3. We also found that the chimera that possesses the C- terminus of Cul3 and the N- terminus of Cul1 was unable to interact with BTB proteins. Lastly, we found that the Cul1 adapter Skp1 was able to bind to Cul1, but did not bind to Cul3 or either chimera. We concluded that the chimera possessing the N- terminus of Cul3 likely retains the functional binding abilities of Cul3 at the N- terminus and would therefore be useful for conducting experiments. In this study, we also used the cullin chimeras to investigate the binding interactions between E2 enzymes and cullin RING ligases. We performed co- immunoprecipitation assays to examine the interactions between E2 enzymes and wild type, mutant or chimeric cullin proteins. We found that E2 enzyme UbE2E1 selectively binds to Cul3 and not to Cull. Notably, the BTB binding region at the N- terminus of Cul3 is required for binding to UbE2E1. Furthermore, we found that UbE2E1 also binds to Cul3 substrate adapter protein Ctb57. These experiments revealed a novel interaction between and E2 enzyme and the N- terminus of Cul3, as well as with a Cul3 substrate adapter protein. In conclusion, the chimeras generated in this study have provided valuable information regarding what regions of CRLs are important for interactions with other proteins, and will continue to be a useful tool for investigating CRL structure and function.

Indiana University-Purdue University Indianapolis (IUPUI) / Studies performed by our lab have investigated the potential radioprotective effect of rDEK protein. Although roles played by DEK in cell differentiation, DNA repair, DNA binding, chromatin regulating and different malignancies have been investigated previously in different cell types, the prospect of DEK being used as a potential radioprotective agent for HSCs has not yet been explored. In this study, using primary cells isolated from bone marrow of C57BL/6 mice in vitro, our data indicated that rDEK has the ability to act as potential radioprotector of HSC. Moreover, a significant decrease in percentages of caspase-3 and caspase-9 protease enzymes was observed after irradiation in presence of rDEK. Taken, together the data suggests that DEK imparts its effect as a potential radioprotective agent, via inhibiting the caspase-dependent intrinsic apoptosis pathway. We found no evidence that DEK could act as a radiomitigator but this was not tested in primary cells as well as in animals.

Philosophiae Doctor - PhD / Mycotoxins attract worldwide attention because of the significant economic losses associated with their impact on human health, animal productivity, domestic and international trade. Over 300 mycotoxins have been discovered, of which a few are of serious concern (Smith and Moss 1985; Rheeder et al., 1994). Exposure to these mycotoxins can produce both acute and chronic effects ranging from death to effects upon the central nervous, cardiovascular, pulmonary systems and upon the alimentary tract. Mycotoxins may be carcinogenic, mutagenic, teratogenic and immunosuppressive (Ferrante et al., 2002). Mycotoxins are currently considered as a major problem in developing countries (Miller, 1994).

Proteins and organothiols are known for their high binding affinity to noble metal surface including gold nanoparticles (AuNPs). Numerous reports have been dedicated to AuNP interaction with protein or organothiol alone. Competitive protein and organothiol (OT) interaction is, however, mostly an unexplored area. The research reported here focused on developing a fundamental understanding of sequential and simultaneous protein and organothiol interaction with AuNPs in which protein and OT are added either simultaneously or sequentially into the colloidal AuNP solutions. In studies of OT interactions with bovine serum albumin (BSA) stabilized AuNPs, we found that the protein coating layer is highly porous and permeable for small molecules such as mercaptobenzimidazole (MBI), cysteine (Cys), homocysteine (Hcy), and glutathione (GSH). Based on the amounts of MBI adsorbed and the kinetics of MBI adsorption onto BSA stabilized AuNPs, we were able to get an insight into protein conformational changes on the AuNPs. The competitive and sequential studies of protein and OT interactions with AuNPs involving eight model organothiols showed that the protein and OT cosorption onto AuNPs is a kinetically controlled process. The AuNP stability against ligandsorption-induced AuNP aggregation differed significantly among the AuNP/OT and AuNP/BSA/OT mixtures where the AuNP stability order increased from (AuNP/OT)/BSA to AuNP/(BSA/OT), and finally (AuNP/BSA)/OT samples (the two components inside the parenthesis are mixed first followed by the addition of the third component). The studies on the role of cysteine in protein-AuNP interactions found that the cysteine has no significant effect on the kinetics of protein adsorption onto AuNPs. However the stability of the protein-AuNP complex against the organothiolsorption induced AuNP aggregation increased as the number of cysteine residues increased from zero to two. Besides providing new insights on protein interaction with AuNPs, this research is important for AuNP biological/biomedical applications because AuNPs in biofuids encounter a mixture of proteins and OTs in addition to other molecular species.

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