Recent strategies for anticancer drug design have been focused on utilizing antibody as a drug or targeted moiety for targeted drug delivery. Antibody−drug conjugates (ADCs) have become a promising new class of targeted therapeutic agents for treatment of cancer. ADCs are designed to preferentially direct a cytotoxic drug to a cell-surface antigen recognized by an antibody. However, there are some challenges in developing ADCs, such as limited solid tumor penetration, high manufacturing costs and antibody-drug stoichiometry. Smaller molecules such as peptides have been shown to specifically bind to cancer related targets. These peptides can be used to form peptide-drug conjugates (PDCs) to overcome above-mentioned drawbacks presented by ADCs. In this study, it was hypothesized that novel synthesized PDCs can be a strategy for breast cancer therapy. HER2 specific binding peptides, MARAKE and MARSGL, were modified by addition of a cysteine at C-terminus. The modified peptides were coupled with monomethylauristatin E (MMAE) by using maleimidocaproyl (MC) as a non-cleavable linker to form peptide-drug conjugates (YW1, YW2) and maleimidocaproyl-valine-citrulline (MC-VC) as a cleavable linker to form peptide-drug conjugates (YW3 and YW4). The peptides, peptide-drug conjugates and MC-MMAE, MC-VC-MMAE were characterized using ESI-MS and purified by using high-performance liquid chromatography (HPLC). Cellular uptake study was performed to determine binding specificity and internalization of two HER2 specific peptides and cysteine-modified peptides (MARAKEC, MARSGLC). In vitro cell viability assay was conducted to assess the cytotoxicity and determine the targeting specificity as well as the potency of the peptide-drug conjugates. The purity of each compound was greater than 90%. Internalization of both HER2 specific binding peptides and cysteine-modified peptides were significantly higher than random peptides in HER2 over-expressed cell lines, MDA-MB361 and ZR75, while negligible uptake in HER2 negative cell line, HEK293. MC linked PDCs showed similar cytotoxicity as peptide in all cell lines; while MC-VC linked PDCs have higher cytotoxicity than MMAE in HER2 positive cell line and significant lower cytotoxicity than MMAE in normal cell line HEK293. However, PDCs with MC link do not show significant difference in cytotoxicity compared to the peptide in all cell lines. In conclusion, specificity of HER2 binding for both peptides was preserved after modification with cysteine. The derivation of MMAE to link drug and peptide played a crucial role in the anticancer activity. Peptide-MMAE conjugates with cleavable linker showed a promising targeting capability for delivery of MMAE to HER2 overexpressed cancer cells.

Because of the nutritious value of sodium glutamate and its meat-Like flavor, won 18 very pleasing to most people, and hence Its demand if it were properly promoted, and because of the abundance of protein in accessible form for its manufacture, it is only reasonable to assume that if too optimum continuous of protein hydrolysis were found, tho manufacturing metnous could be made a.highly successful enterprise.

6-aminonicotinamide (6-AN), an analogue and antagonist of nicotinamide, impairs cartilage formation and results in shortening of the limb when administered to chick embryos. 6-AN forms an abnormal NAD analogue (6-ANAD), which inhibits the activity of NAD-dependent enzymes associated with the production of ATP. The mechanism of action of 6-AN was studied by measuring the biosynthesis of protein and DNA, and the sulfation and glycosylation of chondroitin sulfate in control and 6-AN treated cartilage from 8-day chick embryos. The cartilage was also assayed for ATP levels. Incorporation of Na235SO4 was inhibited by 6 h treatment with 10 μg/ml 6-AN, whereas 3H-thymidine and 3H-amino acid incorporation were not inhibited until 12 h. 3H-glucosamine incorporation was not inhibited during any of the treatment times examined. Decrease in the level of ATP preceded inhibition of Na235SO4 incorporation. These results are consistent with the view that 6-AN inhibits chondroitin sulfate synthesis through a reduction in the level of ATP in chondrocytes.

In Caulobacter crescentus, progression through the cell cycle is regulated by the AAA+ protease ClpXP, and there are several classes of cell-cycle substrates that require adaptors in order to be degraded. CpdR, a single domain-response regulator, binds the N-terminal domain of ClpXP and primes the protease for degradation of downstream factors (Lau et al., 2015). The ability of CpdR to bind ClpX is regulated by its phosphorylation state. In the unphosphorylated state, CpdR binds ClpXP and guides its localization to the cell pole during the swarmer to stalked transition, where CpdR is mediates degradation of substrates such as PdeA. Phosphorylation of response regulator receiver domains requires magnesium as a cofactor to stabilize the phosphorylated aspartate and reciprocally, phosphorylated receiver domains bind magnesium more effectively. While it is understood that CpdR primers ClpX for substrate degradation, the mechanism by which it does so has remained unclear. Using CollabFold, we identified putative residues involved in CpdR-ClpX binding and validated them using a BACTH screening. In vitro, we characterized the role that magnesium plays in regulating CpdR binding to ClpX. In this work, we directly test the role of magnesium in CpdR priming of ClpXP to show that magnesium may play a regulatory role in CpdR-mediated degradation, and thus binding to ClpX. We identify residues in ClpX that seem to be important for CpdR binding, which prior to this work was not clear.

Translesion DNA Synthesis (TLS) is a mechanism that promotes DNA damage tolerance during DNA replication using an error-prone DNA polymerase complex. The complex is comprised of the ImuA, ImuB, and ImuC proteins that are found in approximately one-third of bacteria, including high priority antimicrobial resistant pathogens, such as Pseudomonas aeruginosa. Previous in vivo studies have shown that TLS increases beneficial bacterial mutations as the error-prone DNA polymerase, ImuC, lacks proof-reading activity. However, how ImuA and ImuB proteins contribute to the polymerase mechanism is unknown. Thus, the goal of this study is to characterize the TLS proteins in vitro to determine how ImuA and ImuB associate with ImuC to promote error- prone replication. ImuA and ImuBNΔ34 were successfully purified for biochemical characterization from the homolog Myxococcus xanthus. Using size-exclusion chromatography coupled to multi-angle light scattering, both ImuA and ImuBNΔ34 are trimers in solution. Each protein also binds DNA independently as assessed by fluorescence polarization. Interestingly, both proteins bind ssDNA and a 3’ overhang substrate mimicking the DNA replication intermediate with the highest affinity. DNA binding assays further confirm these proteins can form a DNA-ImuA-ImuBNΔ34 complex. Using bacterial two-hybrid assays, the ImuA- ImuB interaction occurs in the C-terminal region of both proteins. Overall, these results suggest that ImuA and ImuB may recruit and stabilize ImuC on DNA for replication past damaged DNA, providing the first insights into the ImuA and ImuB molecular mechanism. / Thesis / Master of Science (MSc)

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Cardiac arrest is a prevalent condition with a poor prognosis, attributable in part to persistent myocardial dysfunction following resuscitation. The molecular basis of this dysfunction remains unclear. We induced cardiac arrest in a porcine model of acute sudden death and assessed the impact of ischemia and reperfusion on the molecular function of isolated cardiac contractile proteins. Cardiac arrest was electrically induced, left untreated for 12 min, and followed by a resuscitation protocol. With successful resuscitations, the heart was reperfused for 2 h (IR2) and the muscle harvested. In failed resuscitations, tissue samples were taken following the failed efforts (IDNR). Actin filament velocity, using myosin isolated from IR2 or IDNR cardiac tissue, was nearly identical to myosin from the control tissue in a motility assay. However, both maximal velocity (25% faster than control) and Ca2+ sensitivity (pCa50 6.57 ± 0.04 IDNR vs. 6.34 ± 0.07 control) were significantly (p < 0.05) enhanced using native thin filaments (actin, troponin, and tropomyosin) from IDNR samples, suggesting that the enhanced velocity is mediated through an alteration in muscle regulatory proteins (troponin and tropomyosin). Mass spectrometry analysis showed that only samples from the IR2 had an increase in total phosphorylation levels of troponin (Tn) and tropomyosin (Tm), but both IR2 and IDNR samples demonstrated a significant shift from mono-phosphorylated to bis-phosphorylated forms of the inhibitory subunit of Tn (TnI) compared to control. This suggests that the shift to bis-phosphorylation of TnI is associated with the enhanced function in IDNR, but this effect may be attenuated when phosphorylation of Tm is increased in tandem, as was observed for IR2. There are likely many other molecular changes induced following cardiac arrest, but to our knowledge, these data provide the first evidence that this form cardiac arrest can alter the in vitro function of the cardiac contractile proteins.

Currently, human norovirus is the leading cause of acute gastroenteritis and accounts for most cases of foodborne illnesses in the United States each year. Due to its tissue culture inefficiency, studies of human norovirus have been crippled for more than forty years.Tulane virus (TV) stands out as a suitable surrogate of human norovirus given its high amino acid identity with human norovirus and its well-established cell culture system. It was first isolated from rhesus macaques (Macaca mulatta) in 2008 and identified as a novel Calicivirusrepresenting a new genus, Recovirus genus (Farkas et al., 2008). However, there are still unanswered questions about its infectious cycle and the essential factors for its infection. In this study, we have obtained a TV variant (the 9-6-17 strain) that has lost the binding ability to the B-type histo-blood group antigen (HBGA), which was proposed to be the receptor of both TV and human norovirus. In the first chapter, we outline how the sequence analysis,structural biology studies, and mutagenesis studies of the 9-6-17 TV strain have shed light on the interaction with its host cell receptor. To investigate the key residues for HBGA binding, we established the full-length infectious clone of the 9-6-17 TV strain. We present a highly selective transformation of serine 367, located in the predicted HBGA binding site, into a lysine residu e. Our results advance the understanding of genetic changes in TV required for adaptation to cell culture environments. Cryo-EM is an awarding winning technique that has been the greatest scientific breakthrough in recent years. It was awarded the Nobel Prize in Chemistry in 2017. Despite the technological advances of the direct electron detector and image processing software, several major roadblocks remain for high-resolution structure determination with cryo-EM. In the later chapters, we explored the most efficient way of using VPP to enhance image contrast, how to tackle the airwater interface problem by encapsulating target protein, how to reach a higher resolution by refining high order parameters, and the helical indexing problem in real space. These technical advances would benefit the whole cryo-EM community by providing convenient tools or insights for future directions.