Post-translational modifications are chemical changes that occur to proteins after their synthesis, which are essential to their function and regulation. Ubiquitination is a post translation modification that serves key roles in the regulation of proteins. USP7 is a deubiquitinase that has several critical substrates important for human health and disease, including the cancer relevant proteins PTEN, p53, MDM2 and DMNT1. Most of these substrates have been identified by cell biology or proteomics experiments, but a detailed biochemical and structural analysis is lacking, likely due to the challenge of generating site-specific and stoichiometrically ubiquitinated proteins. Therefore, we leveraged our expertise in protein semi-synthesis to generate these ubiquitinated substrates to study USP7’s ability to recognize and hydrolyze the ubiquitin, which will reveal key details on how USP7 selects its substrates. In our investigation, we generated several mono-ubiquitinated peptides, that could be functionalized later to install on the protein, and assayed USP7’s ability to hydrolyze the ubiquitin. / 2026-03-06T00:00:00Z

In the process of translation, ribosomes, a type of macromolecules, read the genetic code on a messenger RNA template (mRNA) and assemble amino acids into a polypeptide chain which folds into a functioning protein product. The ribosomes perform discrete directed motion that is well modeled by a totally asymmetric simple exclusion process (TASEP) with open boundaries. We incorporate the essential components of the translation process: Ribosomes, cognate tRNA concentrations, and mRNA templates correspond to particles (covering ell > 1 sites), hopping rates, and the underlying lattice, respectively. As the hopping rates in an mRNA are given by its sequence (in the unit of codons), we are especially interested in the effects of a finite number of slow codons to the overall stationary current. To study this matter systematically, we first explore the effects of local inhomogeneities, i.e., one or two slow sites of hopping rate q<1 in TASEP for particles of size ell > 1(in the unit of lattice site) using Monte Carlo simulation. We compare the results of ell =1 and ell >1 and notice that the existence of local defects has qualitatively similar effects to the steady state. We focus on the stationary current as well as the density profiles. If there is only a single slow site in the system, we observe a significant dependence of the current on the location of the slow site for both ell =1 and ell >1 cases. In particular, we notice a novel "edge" effect, i.e., the interaction of a single slow codon with the system boundary. When two slow sites are introduced, more intriguing phenomena such as dramatic decreases in the current when the two are close together emerge. We analyze the simulation results using several different levels of mean-field theory. A finite-segment mean-field approximation is especially successful in understanding the "edge effect." If we consider the systems with finite defects as "contrived mRNA's", the real mRNA's are of more biological significance. Inspired by the previous results, we study several mRNA sequences from Escherichia coli. We argue that an effective translation rate including the context of each codon needs to be taken into consideration when seeking an efficient strategy to optimize the protein production. / Ph. D.

Specific AA have been demonstrated to activate signaling pathways that regulate<br />translation initiation and to stimulate protein synthesis in mammary tissue. The<br />objectives of this research were to determine the response to Ile, Leu, Met, and Thr in<br />cellular signaling and "-S1 casein fractional synthesis rates (CFSR). An experiment was<br />developed as a composite design. The experiment was replicated in tissue corresponding<br />to 5 cows. Mammary tissue slices (0.12 ± 0.02 g) from lactating dairy cows were<br />incubated 4 h in treatment media enriched with 2H5 Phe. Following incubation, slices<br />were homogenized in lysis buffer and caseins were precipitated by acidification to pH<br />4.6. An aliquot of the pellet was trypsinized and 2H5 Phe enrichment in the 34-<br />NLLRFFVAPFPE-45 peptide of "-S1 casein was measured by MALDI TOF-MS and<br />used to determine CFSR (%/h). Western immunoblotting was performed to identify total<br />and site-specific phosphorylated mammalian target of rapamycin (mTOR, Ser2448),<br />eukaryotic elongation factor (eEF) 2 (Thr56), ribosomal protein (rp) S6 (Ser235/236),<br />and eukaryotic initiation factor (eIF) 2" (Ser51). Addition of Ile, Leu, Met, or Thr had<br />no effect on eIF2" phosphorylation. Isoleucine positively affected mTOR, and rpS6, and<br />negatively affected eEF2 phosphorylation. Leu had a similar effect on eEF2, but not on<br />mTOR or rpS6, and these two AA inhibited each other. Thr negatively interacted with<br />Ile on mTOR and rpS6, and with Leu on eEF2. Increasing concentrations of Ile, Leu,<br />Met, and Thr caused curvilinear increases in CFSR. The maximum response to Ile, Leu,<br />iii<br />Met, and Thr was at 71, 49, 60, and 65% of DMEM concentrations, respectively. All<br />maximums were above plasma AA concentrations observed in lactating cows fed to meet<br />NRC requirements. The CFSR estimated at those maximums were similar between AA<br />(3.6 ± 0.6 %/h). Individual AA effects on CFSR did not correlate with mTOR signaling.<br />Independent CFSR responses to individual essential AA observed in this study contradict<br />the single-limiting AA theory assumed in current requirement systems. The saturable<br />responses of CFSR to these 4 AA also demonstrate the deficiencies of a fixed postabsorptive<br />AA efficiency approach for determining AA requirements for milk protein<br />synthesis. / Ph. D.

Dairy cows inefficiently convert dietary protein to milk protein causing economic and environmental costs. Amino acids (AA), insulin, and glucose significantly enhance muscle protein synthesis efficiencies. The objectives of this research project were 1) to investigate the regulatory effects of essential AA (EAA) and their interactions with insulin, glucose and acetate on mammary protein synthesis rates, 2) to investigate whether branched chain amino acids (BCAA): leucine , isoleucine , and valine , become limiting for milk protein synthesis when Met and Lys supply were not limiting, and 3) to develop a mathematical representation for the EAA and insulin effects on cellular signals for protein synthesis. MAC-T cells were treated with EAA, insulin, glucose, and acetate to observe their individual and interactive effects on phosphorylation of mTOR, rpS6, S6K1, 4EBP1, eEF2, eIF2α, Akt, and AMPK. These signaling effects on protein synthesis rates were examined with mammary tissue slices. A mathematical representation of the insulin and EAA effects was developed. The effects of supplementing BCAA on milk protein synthesis were investigated using nine Holstein cows, assigned to 7 d continuous jugular infusions of saline, Met and Lys, and Met and Lys plus BCAA. Multiple essential amino acids, Leu, Ile, Met, and Thr were able to substantially regulate protein synthesis rates in bovine mammary cells by increasing (P < 0.05) phosphorylation of mTOR, S6k1, 4EBP1, and decreasing (P < 0.10) eEF2 phosphorylation. Insulin considerably (P < 0.10) exerted similar signaling effects in MAC-T cells, independent of EAA. Supplementation of only acetate increased (P = 0.09) mammary cell energy status as indicated by reduced AMPK phosphorylation in MAC-T cells. Neither acetate nor glucose had substantial regulatory effects on mammary protein synthesis rates. Although Met and Lys supplementation increased (P < 0.01) milk protein yields and protein efficiencies, there were no apparent benefits of BCAA supplementation under the feeding circumstances of our study. The developed mathematical model adequately represented the regulatory effects of EAA and insulin. Such mathematical representations of regulatory effects of EAA and their interaction with other nutrients may improve our current AA requirement models to predict AA requirements of dairy cows with increased accuracy. / Ph. D.

<p>Aerobic exercise can stimulate mixed muscle protein synthesis (MPS) acutely post-exercise; however, the types of proteins synthesized as a result of aerobic exercise are not known by studying changes in mixed MPS. We aimed to study the effect of aerobic exercise intensity on the 4 and 24 h post-exercise fractional synthesis rate (FSR) of myofibrillar proteins. Using a within-subject design, eight males (21 ± 1 years, VO_{2 peak}: 46.7 ± 2.0 mL kg^-1 min^-1) underwent 2 trials with a primed constant infusion of L-[<em>ring</em>-¹³C₆]phenylalanine in the fasted state for each work-matched exercise intensity (LOW: cycling for 60 min at 30% W_max and HIGH: 30 min at 60% W_max). Muscle biopsies were obtained to determine resting, 4 and 24 h post-exercise myofibrillar FSR. We also studied the phosphorylation of signaling proteins involved in protein synthesis at each time point using immunoblotting methods. Phospho-p38^{Thr180/Tyr182} was greater at 4.5 h after exercise compared to 0.5, 24 and 28 h post-exercise (<em>p</em> < 0.05). Additionally, a strong trend was present for phospho-mTOR^Ser2448 (<em>p</em> = 0.056) with 0.5 h post-exercise phosphorylation significantly higher after HIGH than after LOW exercise (<em>p </em>< 0.05). Myofibrillar protein synthesis was stimulated 1.5–fold 0.5 – 4 h post-exercise (<em>p</em> < 0.05), returning to rest in the LOW condition 24 h post-exercise, while 6 out of 8 subjects maintained increased myofibrillar FSR 24 h post HIGH exercise (<em>p</em> < 0.05). The increase in myofibrillar FSR 0.5 – 4 h post-exercise was correlated with phospho-mTOR^Ser2448 0.5 h post-exercise (r = 0.698, <em>p</em> < 0.01), indicating the role of this signaling pathway in myofibrillar protein synthesis. It is concluded that aerobic exercise has an effect on myofibrillar protein synthesis and intensity may play a role in the duration of this response.</p> / Master of Science in Kinesiology

Skeletal muscle protein synthesis is regulated by the mammalian target of rapamycin (mTOR) signaling pathway. The first objective was to optimize the methodological procedures for assessing mTOR signaling in horses. The response of mTOR signaling (P-Akt Ser473, P-S6K1 Thr389, P-rpS6 Ser235/26 & 240/244, and P-4EBP1 Thr37/46 by Western blotting techniques) to meal consumption was determined at three gluteal muscle biopsy depths (6, 8, and 10 cm), and the repeatability of the contralateral side at 8 cm during 5 days of repeated biopsies. There was no effect (P > 0.05) of sampling side or biopsy depth on mTOR signaling in mature horses. During repeated biopsies there was an increase (P < 0.05) in downstream (P-S6K1 Thr389, P-rpS6 Ser235/236 & 240/244 and P-4EBP1 Thr389) mTOR signaling in response to feeding. The second objective was to characterize alterations in mTOR signaling throughout the equid lifespan. Adolescent horses (yearlings and two year olds) studied in the postprandial had a lowered (P < 0.05) activation of downstream mTOR signaling with aging. There was a lower (P < 0.05) abundance of P-S6K1 Thr389 in aged horses (23.5 years old) than in mature horses (11 years old) during the post-absorptive state. The final objective was to assess mTOR signaling during acute and chronic inflammation. Acute inflammation occurred during 5 days of repeated biopsies, and chronic inflammation is characteristic of the aged. During acute inflammation, characterized by increased muscle mRNA expression of inflammatory cytokines, there was an increase (P < 0.05) in downstream mTOR signaling. Chronic inflammation resulted in a decrease (P < 0.05) in the abundance of P-S6K1 Thr389. Phenylbutazone was administered to reduce (P < 0.05) acute and chronic inflammation in muscle. Phenylbutazone administration during acute inflammation reduced (P < 0.05) the activation of downstream mTOR signaling and trended to increase (P = 0.09) P-S6K1 Thr389 abundance during chronic inflammation. Whole-body protein synthesis determined using isotope infusion techniques increased (P < 0.05) when chronic inflammation was reduced due to phenylbutazone administration. This research provides new standards for muscle biopsy collection when examining mTOR signaling, and insight into management and feeding practices for adolescent and aging horses.

Antibiotics that target the bacterial ribosome make up about half of all clinically used antibiotics. We have studied two ribosome targeting drugs: Fusidic acid and Viomycin. Fusidic acid inhibits bacterial protein synthesis by binding to elongation factor G (EF-G) on the ribosome, thereby inhibiting translocation of the bacterial ribosome. Viomycin binds directly to the ribosome and inhibits both the fidelity of mRNA decoding and translocation. We found that the mechanisms of inhibition of these two antibiotics were unexpectedly complex. Fusidic acid can bind to EF-G on the ribosome during three separate stages of translocation. Binding of the drug to the first and most sensitive state does not lead to stalling of the ribosome. Rather the ribosome continues unhindered to a downstream state where it stalls for around 8 seconds. Dissociation of fusidic acid from this state allows the ribosome to continue translocating but it soon reaches yet another fusidic acid sensitive state where it can be stalled again, this time for 6 seconds. Viomycin inhibits translocation by binding to the pre-translocation ribosome in competition with EF-G. If viomycin binds before EF-G it stalls the ribosome for 44 seconds, much longer than a normal elongation cycle. Both viomycin and fusidic acid probably cause long queues of ribosomes to build up on the mRNA when they bind. Viomycin inhibits translational fidelity by binding to the ribosome during initial selection. We found that the concentration of viomycin required to bind to the ribosome with a given probability during decoding is proportional to the accuracy of the codon∙anticodon pair being decoded. This demonstrated that long standing models about ribosomal accuracy cannot be correct. Finally, we demonstrated that a common viomycin resistance mutation increases the drug binding rate and decreases its dissociation rate. Our results demonstrate that ribosome targeting drugs have unexpectedly complex mechanisms of action. Both fusidic acid and viomycin preferentially bind to conformations of the ribosome other than those that they stabilize. This suggests that determining the structures of stable drug-bound states may not give sufficient information for drug design.

A proteína colibistina (CB), uma Rho GEF neuro-especifica, apresenta papel importante na formação e funcionamento das sinapses inibitórias do sistema nervoso central por interagir com a proteína scaffold gefirina e com receptores GABAA e promover o agrupamento e transporte dessas proteínas para a membrana pós-sináptica. Recentemente, nosso grupo de pesquisa identificou interação de CB com um complexo proteico que controla o início da tradução em eucariotos (complexo eIF3), o que sugeriu pela primeira vez que essa proteína pode estar envolvida também na regulação da tradução em células neurais. Ainda, já havia sido descrito que gefirina, parceira funcional de CB, interage com mTOR, uma quinase que desempenha papel fundamental no controle do início da tradução. Contudo, até o momento não havia estudos adicionais investigando o papel de CB neste cenário. Assim sendo, o presente trabalho teve como objetivo investigar o envolvimento da proteína CB no controle do início da síntese proteica mediada pela via de sinalização mTORC1. Foram utilizados dois modelos experimentais: i) um sistema de expressão heteróloga - superexpressão de CB em células HEK293T, e ii) um modelo endógeno de expressão - células neuroprogenitoras derivadas de células-tronco pluripotentes induzidas (iNPCs) provenientes de indivíduos controles e de um paciente com deleção no gene da CB. Por meio de experimentos de coimunoprecipação nós verificamos que CB interage fisicamente com mTOR nos dois modelos experimentais utilizados. Ainda, nossos resultados mostraram que CB parece modular a atividade da via mTORC1, e nas iNPCs derivadas do paciente a ausência de CB leva a um aumento na ativação desta via de sinalização. Em concordância com esses resultados, nós observamos aumento em neo-síntese proteica nas iNPCs provenientes do paciente, o que pode ser um mecanismo patofisiológico contribuindo para as alterações cognitivas e comportamentais observadas no paciente. Embora estudos adicionais sejam necessários para melhor entender os mecanismos moleculares deste controle de início de tradução mediado por CB, nós sugerimos um modelo no qual CB, por interagir fisicamente com mTOR e eIF3, sequestra estas proteínas e impede que mTOR ative seus alvos e desencadeie a formação do complexo de inicio de tradução. Em conclusão, nossos resultados oferecem novas evidências do envolvimento de CB no controle da síntese proteica / Collybistin (CB), a neural specific RhoGEF, plays key roles in inhibitory synapse formation and function that cluster and localize the scaffold protein gephyrin and GABAA receptors to the neural postsynaptic membrane. We have recently reported that CB interacts with a protein complex that controls translation initiation in eukaryotic cells (eIF3 complex), which suggested for the first time that this protein may also act as regulator of protein synthesis in neural cells. Moreover, it has been previously described that gephyrin, the CB functional partner, interacts with mTOR, a kinase that plays a pivotal role in the control of translation initiation. However, until now there were no further studies investigating the role of CB in this scenario. The purpose of this study was to investigate if CB is involved in the control of translational initiation mediated by the mTORC1 signaling pathway. Two experimental models were used: i) a heterologous expression system - overexpression of CB in HEK293T cells, and ii) an endogenous expression model - neural progenitor cells derived from induced pluripotent stem cells (iNPCs) from control individuals and a patient with a deletion of the entire CB gene. We performed coimmunoprecipitation experiments and verified that CB physically interacts with mTOR both in 293T cells and in control iNPCs. In addition, our results show that CB appears to modulate the activity of mTORC1 pathway, and the absence of CB leads to increased mTORC1 signaling activation in patient\' iNPCs. In agreement with these results, we observed increased de novo cap-dependent translation in patient cells, which could be a pathophysiological mechanism contributing to cognitive and behavioral abnormalities observed in the patient. Although further studies are needed to better understand the molecular details of CB-mediated translational control, we suggest a model whereby CB, by physically interacting with mTOR and eIF3, sequesters these proteins, thereby preventing both the ability of mTOR to activate its targets and the formation of the translational initiation complex. In conclusion, our results offer new insights into the role of CB in protein synthesis control

<p>Insulin as well as glucagon are important hormones in maintaining glucose homeostasis and regulating the metabolism in the body. Insulin receptors (IR) are transmembrane receptors that promote a signal transduction when activated by insulin. This can for example cause an increased influx of glucose into the cell performed by so called glucose transporters (GLUTs). These membrane proteins facilitate the transport of glucose from the blood into the cells, so the cell always has a constant supply of energy. Peroxisome proliferator-activated receptors (PPAR) are nuclear fatty acid receptors. They are activated by lipids and regulate fatty acid transcription. PPARδ/β is located in skeletal muscle and can promote fatty acid catabolism as well as cause a switch in fuel preference from glucose to fatty acids. It has been suggested that ligands for PPARδ could act as insulin sensitizers. The PPARγ coactivator-1α can increase mitochondrial content in skeletal muscle if over expressed. The same is true for endurance exercise.</p><p>Hormones released from adipose tissue can cause hyperphagia<strong> </strong>and obesity if over- or under expressed. They can also work in the opposite way by decreasing appetite with weight loss as an effect. Impaired signalling or dysfunctional receptor can cause insulin resistance, obesity and diabetes. Lipolysis occurs in adipose tissues and is conducted by three enzymes, namely adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL) and monoglyceride lipase (MGL). There are some factors that can increase lipolysis such as caffeine, a low glycemic index, high protein intake and training.</p><p>The enzyme PEPCK is involved in the gluconeogensis in the liver and kidney cortex, and also in the glyceroneogenesis in the liver, as well as in brown and white adipose tissue. When overexpressed in skeletal muscle the enzyme increases the muscle activity. The overexpression of the enzyme did promote the β-oxidation as energy source for the muscles during exercise, instead of muscle glycogen as fuel.</p><p>The processes of protein synthesis and breakdown are together called protein turnover. Muscle grows when synthesis is greater than breakdown, and withers if breakdown exceeds the level of synthesis. Acute effects of training is catabolic, but long time exercise causes however an increased protein synthesis. Leucine, an essential amino acid, has an important role in the initiation phase of translation. Glutamine is probably important in the regulation of muscle protein synthesis and breakdown. Together with glutamate, aspartate and asparagine, these are responsible for the amino acid metabolism that occurs in the muscles. Protein synthesis reaches its maximum in the recovery phase after intense training.</p>

Molecular functions of eukaryotic initiation factor 3 (eIF3) in translation are manifold, encompassing events from initiation complex assembly to translation termination. The contribution of the individual subunits of eIF3 to its multiple activities is quite unclear. It has been hypothesized that several of its 13 subunits contribute to mRNA specific regulation. Prior research had established that the h subunit of eIF3 in Arabidopsis was required for translation of specific mRNAs as well as for organ formation and meristem development. This study aims towards understanding the functions of individual subunits of eIF3 in the context of plant development and to further define the role of eIF3h at the molecular level. This dissertation describes an effort to identify mutations affecting each of the 13 eIF3 subunits. Using a panel of pollen-specific fluorescent marker genes, eIF3 subunits e, h and i1 were demonstrated to be essential for normal male gametophyte development. Furthermore, subunits b and c proved to be essential for embryo development. In contrast, a mutation in eIF3k revealed no phenotypic abnormalities. This work represents a systematic effort to attribute functions to many of the eIF3 subunits in growth and development in a multicellular eukaryote. The h subunit of eIF3 is necessary for the efficient translation of specific mRNAs in Arabidopsis. In particular, eIF3h fosters the translation of those mRNAs that harbor multiple upstream open reading frames (uORFs) in their 5’ leader. The specific molecular activity of eIF3h was investigated by structure-function analysis of the 5' leader of the Arabidopsis AtbZip11 mRNA, which harbors a set of four uORFs that is evolutionarily conserved. By pairing extensive mutagenesis of the AtbZip11 5' leader with gene expression analysis in Arabidopsis seedlings, it was revealed that eIF3h helps the ribosome to retain its reinitiation competence during uORF translation. These data establish a function for the h subunit of eIF3 in a special case of translation initiation, reinitiation. Finally, the molecular events during translation reinitiation were investigated further for a functional cooperation between eIF3h and the large subunit of the ribosome, given that the large ribosomal subunit had been implicated in reinitiation in other biological contexts. Reinitiation profiling using the AtbZip11 leader demonstrated that a protein of the large ribosomal subunit, RPL24B, bolsters reinitiation similar to eIF3h. Taken together, there exists a functional cooperation between the large ribosomal subunit and eIF3 that helps ribosomes to reinitiate after translation of uORFs.