Special stretches of sequence with low complexity, highly rich in one certain residue, such as glutamine, asparagines, glutamic acid and histidine, to fulfill certain unique functions, are defined as single-residue-rich sequence (SRRs). Increasing SRRs containing proteins have recently been characterized and some of them have been indentified to be associated with immune system diseases or neuro-degenerative. A systematic and comprehensive analysis on the relationship between the occurrence of histidine-rich motifs (HRMs) and the functions of corresponding proteins have been overlooked. In this thesis, proteome sequences of 675 prokaryotes including 50 archeae proteome sequences and 625 bacteria were examined and analyzed for HRMs. The HRMs are shown to be extensively distributed in prokaryotic proteomes and the majority (62%) of them is identified to be involved in metal homeostasis. Intriguingly, HRMs are essentially absent from obligate intracellular pathogenic species such as Rickettsiales, Chlamydiae and Tenericutes but are frequently found in the proteomes of Rhizobiales and Burkholderiales, both of which habitat in soils, indicative of environmental habitat-related occurrence of HRMs. Based on the primary sequence to explore the histidine-rich proteins, the present approach could be extended to apply for searching other single-residue-rich proteins, which may shed lights on gaining a further understanding about relationship between the proteins’ sequences and their functions. A novel group of globally histidine-rich proteins was discovered, among which a histidine-rich protein, bacterioferritin-associated ferredoxin ((BFD)-like [2Fe-2S]) protein from Rhodopseudomonas Palustris BisB18 (termed as BFD shortly) was digged out. The BFD protein consists of a Fe-S cluster domain (FeSD) at the N-terminus and an extremely histidine-rich domain (HRD) at the C-terminus. The intact protein BFD as well as its histidine-rich domain (HRD) was over-expressed, purified and characterized and the effects of metal binding on BFD and HRD were examined in this work. The intact protein BFD presents as a 20 mer whereas the HRD protein exists as a monomer in solution. However, the CD spectrum of BFD showed the presence of both α-helix and β-sheet in the structure of BFD. The CD spectrum of HRD demonstrated that an extremely large portion of the structure of HRD was random coils, which indicated that the most of the α-helix and β-sheet predominately were located in the Fe-S cluster domain (FeSD) of BFD. It also indicated that HRD adopted a very flexible conformation, which was in good agreement with the results that obtained from the 2D 1H-15N HSQC spectrum of HRD. Isothermal titration calorimetry and equilibrium dialysis revealed that HRD possessed a large binding capacity to divalent metal ions (up to 9 Ni2+, 5 Zn2+ and 4 Co2+ respectively). The E. coli cells over-expressed with the HRD protein showed a significantly evaluated metal resistance to the toxic Ni and Co ions. The amounts of meals in these cells were determined to be approximate 3-5 fold higher than those in the control groups. These results of HRD taken together suggest the characteristics of common globally histidine-rich proteins. / published_or_final_version / Chemistry / Doctoral / Doctor of Philosophy

Influenza A virus (IAV) is considered one of the main threats that causes contagious respiratory disease in humans. Each year it threatens the human population with epidemics and pandemics. Limited anti-Influenza drugs are available that target viral proteins. The Influenza virus can mutate rapidly and can quickly develop resistance against available drugs. Therefore, developing novel host-targeted therapeutics effective against different IAVs may be very beneficial. Influenza virus is an intracellular parasite that uses host cell system to favour its replication process and evade host cell defense system. The Influenza A viral nonstructural protein 1(NS1) is a multifunctional protein that is expressed to high levels in infected cells; thus, interacting proteins may be ideal targets for drug development. In this study nine broadly cross-reactive anti-NS1 monoclonal antibodies (mAbs) were generated, characterized and used to co-immunoprecipitate IAV NS1 and its interacting host proteins. 183 proteins were consistently identified in this NS1 interactome study. Importantly, most proteins clustered into different cellular pathways, biological processes and molecular functions, such as mRNA splicing, gene expression, processing of capped intron-containing pre-mRNA and nucleoside, nucleotide and nucleic acid metabolism. Among these, 124 proteins detected in my study represent novel NS1-interacting targets not previously identified. RNAi screening then identified 11 NS1-interacting host factors as vital for IAV replication. From RNAi screening two NS1-interacting candidates, NUMA1 and PRPF19 were chosen for further analysis. IAV production was dramatically reduced in NUMA1 knockdown (KD) cells. Although viral transcription and translation were not inhibited, transport of viral structural proteins to the cytoplasmic membrane was obstructed during maturation steps in NUMA1 KD cells. IAV maturation was also inhibited and new virion production was significantly reduced in PRPF19 KD cells. Overall, a list of novel NS1-interacting host factors were identified utilizing some broadly cross reactive anti-NS1 mAbs in my study, and 11 of them were required for IAV replication. Further research on these new proteins may discover new targets for anti-Influenza drug development. / May 2017

No description available.

A lot of things happen to proteins when Escherichia coli cells enter stationary phase, such as protein amount, post-translational modifications, conformation changes, and component of protein complex. Proteomics, which study the whole component of proteins, can be used to study the products of the genome and the physiology of Escherichia coli cells at different conditions. By comparing proteome from different growth phases, such as exponential and stationary phase, a lot of proteins with changes can be identified at the same time, which provides a pilot for further studies of mechanism. Current global proteomic studies have identified about 27% of the annotated proteins of E. coli, most of which are predicted to be abundance proteins. Subproteomics, the study of specific subsets of the proteome, can be used to study specific functional classes of proteins and low abundance proteins. In this dissertation, using non-denatured anion exchange column with 2D SDS-PAGE and tandem mass spectrometry, difference of E. coli cells between exponential and stationary phase were studied for whole soluble proteome. Also, using heparin column and mass spectrometry with tandem mass spectrometry, heparin-binding proteins were identified and analyzed for exponential growth and stationary phases. To manage and display the data generated by proteomics, a web-based database has been constructed for experiments in E. coli proteomics (EEP), which includes NonDeLC, Heparome, AIX/2D PAGE and other proteomic studies.

A lot of things happen to proteins when Escherichia coli cells enter stationary phase, such as protein amount, post-translational modifications, conformation changes, and component of protein complex. Proteomics, which study the whole component of proteins, can be used to study the products of the genome and the physiology of Escherichia coli cells at different conditions. By comparing proteome from different growth phases, such as exponential and stationary phase, a lot of proteins with changes can be identified at the same time, which provides a pilot for further studies of mechanism. Current global proteomic studies have identified about 27% of the annotated proteins of E. coli, most of which are predicted to be abundance proteins. Subproteomics, the study of specific subsets of the proteome, can be used to study specific functional classes of proteins and low abundance proteins. In this dissertation, using non-denatured anion exchange column with 2D SDS-PAGE and tandem mass spectrometry, difference of E. coli cells between exponential and stationary phase were studied for whole soluble proteome. Also, using heparin column and mass spectrometry with tandem mass spectrometry, heparin-binding proteins were identified and analyzed for exponential growth and stationary phases. To manage and display the data generated by proteomics, a web-based database has been constructed for experiments in E. coli proteomics (EEP), which includes NonDeLC, Heparome, AIX/2D PAGE and other proteomic studies.

Cells respond to their environment with programmed changes in gene expression. Cataloging these changes at the protein level is key towards understanding the physiology of an organism. Multi-subunit and multi-protein complexes are also important and pathogenic and physiologic processes. In order to identify expressed proteins and potential protein complexes, we utilized a combination of non-denaturing chromatography and peptide mass fingerprinting. This approach allows us to identify the components of protein mixtures, as well as information lost in traditional proteomics, such as subunit associations. Applying this methodology to cells at both mid-exponential and stationary phase growth conditions, we identified several thousand proteins from each cell-state of E. coli corresponding to hundreds of unique gene products. The copurification of proteins when fractionated at varying pHs could suggest the components of higher order complexes. This non-denaturing proteomic approach should provide physiological data unavailable by other means. The components of several known cellular complexes were also evident in this analysis. To characterize proteins associated with nucleic acid binding, we also performed proteome analysis on log and stationary phase cells grown in LB separated over heparin chromatography at neutral pH, which enriches for these proteins. The complete analysis of these identifications is discussed.

published_or_final_version / Medical Sciences / Master / Master of Medical Sciences

No description available.

Some of the most profound changes elicited by cell growth stimuli influence dramatic rewiring of metabolism. Intriguingly, rapidly dividing cells with aberrant growth factor signalling, such as cancer cells, tend to rely on glycolysis to generate an adequate supply of building blocks required for cell proliferation and invasion. In this study, we observed that in response to stimulation with insulin-like growth factor 1 (IGF-1), MCF-7 breast adenocarcinoma cells show increased levels of the key glycolysis proteins pyruvate kinase M2 and lactate dehydrogenase A. We then developed targeted multiple reaction monitoring (MRM) mass spectrometry assays to conduct quantitative analysis of glycolysis proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs), the latter implicated in pyruvate kinase splicing and many other aspects of cell proliferation. Application of the glycolysis MRM assay to examine IGF-1 stimulated MCF-7 cells revealed increased levels of all sequential proteins from phosphoglycerate mutase 1 to lactate dehydrogenase A in the glycolysis pathway. An extension of this study to cell lines of varying invasiveness, suggest a relation between glycolysis and metastasis. The clinical applicability of glycolysis MRM assay was also shown by its successful application to lung cancer biopsy analysis. Success with the targeted analysis of glycolysis proteins led to a similar approach for the hnRNP family. Our results showed evidence that a poorly characterized hnRNP (A/B) may be regulated by the c-Myc transcription factor but does not evidently influence pyruvate kinase splicing. Our approach using MRM to examine small subsets of proteins downstream of cellular growth signals is relatively novel. Our results demonstrate the potential for such targeted MS strategies because of their high selectivity and multiplexing capabilities. Further, the findings from our analyses provide novel insights into the downstream changes elicited by growth signals such as IGF-1 and c-Myc.

Thesis (Ph. D.)--University of Washington, 2008. / Vita. Includes bibliographical references (p. 89-97).