Sequence and Structure Based Protein Folding Studies With Implications

As the expression of the genetic blueprint, proteins are at the heart of all biological systems. The ever increasing set of available protein structures has taught us that diversity is the hallmark of their architecture, a fundamental characteristic that enables them to perform the vast array of functionality upon which all of life depends. This diversity, however, is central to one of the most challenging problems in molecular biology: how does a folding polypeptide chain navigate its way through all of the myriad of possible conformations to find its own particular biologically active form? With few overarching structural principles to draw upon that can be applied to all protein architecture, the search for a solution to the protein folding problem has yet to produce an algorithm that can explain and duplicate this fundamental biological process. In this thesis, we take a two-pronged approach for investigating the protein folding process. Our initial statistical studies of the distributions of hydrophobic and hydrophilic residues within α-helices and β-sheets suggest (i) that hydrophobicity plays a critical role in helix and sheet formation; and (ii) that the nucleation of these motifs may result in largely unidirectional growth. Most tellingly, from an examination of the amino acids found in the smallest β-sheets, we do not find any evidence of a β-nucleating code in the primary protein sequence. Complementing these statistical analyses, we have analyzed the structural environments of several ever-widening aspects of protein topology. Our examination of the gaps between strands in the smallest β-sheets reveals a common organizational principle underlying β-formation involving strands separated by large sequential gaps: with very few exceptions, these large gaps fold into single, compact structural modules, bringing the β-strands that are otherwise far apart in the sequence close together in space. We conclude, therefore, that β-nucleation in the smallest sheets results from the co-location of two strands that are either local in sequence, or local in space following prior folding events. A second study of larger β-sheets both corroborates and extends these findings: virtually all large sequential gaps between pairs of β-strands organize themselves into an hierarchical arrangement, creating a bread-crumb model of go-and-come-back structural organization that ultimately juxtaposes two strands of a parental β-structure that are far apart in the sequence in close spatial proximity. In a final study, we have formalized this go-and-come-back notion into the concept of anti-parallel double-strandedness (DS), and measure this property across protein architecture in general. With over 90% of all residues in a large, non-redundant set of protein structures classified as DS, we conclude that DS is a unifying structural principle that underpins all globular proteins. We postulate, moreover, that this one simple principle, anti-parallel double-strandedness, unites protein structure, protein folding and protein evolution.

Examination of body image among Canadian adolescents: Relations with physical activity and screen time

Background: Adolescence is a period of life associated with self-perceptions of negative body image. Physical activity levels are low and screen time levels are also high during this stage. These perceptions and behaviours are associated with poor health outcomes, making research on their determinants important. With adolescent populations, certain groups may be at higher risk of body dissatisfaction than others, and body dissatisfaction may influence individual physical activity and screen time levels. Objectives: The objectives of this thesis were to: 1) describe body image among young Canadians, examining possible health inequalities 2) estimate the strength and significance of associations between body satisfaction, physical activity and screen time, and 3) examine the potential etiological role of biological sex. Methods: Objective 1: The 2013/2014 Health Behaviour in School-aged Children study was employed. Sex-stratified Rao-Scott chi-square analyses were conducted to examine associations between socio-demographic factors and body satisfaction. Objective 2: The 2005/2006 and 2013/2014 cross-sectional and 2006 longitudinal HBSC data sets were used. Sex-stratified modified Poisson regressions were conducted and risk estimates and associated confidence intervals obtained. Results: Objective 1: Among males, being older, of East and Southeast Asian ethnicity, and reporting low SES all were associated with body dissatisfaction. Among females, being older, of Arab and West Asian or African ethnicity, being born in Canada, and reporting low SES were all associated with being body dissatisfied. Objective 2: Cross-sectionally, males who reported ‘too fat’ body dissatisfaction were more likely to be physically inactive. Adolescents of both sexes who reported ‘too fat’ body dissatisfaction were more likely to engage in high levels of screen time. Data from the longitudinal component supported the idea that male ‘too fat’ body dissatisfaction temporally leads to physical inactivity, but showed an inverse relationship between body dissatisfaction and screen time. Conclusions: Objective 1: Future prevention efforts in Canada should target subgroups to effectively help those at greatest risk of body dissatisfaction, and ameliorate potential inequalities at the population level. Objective 2: The presence of these relationships may inform future interventions as part of a multi-factorial etiology, in order to increase physical activity and decrease screen time among youth.

Kinome-wide CRISPR-Cas9 screen to identify kinases involved in Taxol resistance in breast cancer

Breast cancer is the most frequently diagnosed cancer in women, accounting for over 25% of cancer diagnoses and 13% of cancer-related deaths in Canadian women. There are many types of therapies for treatment or management of breast cancer, with chemotherapy being one of the most widely used. Taxol (paclitaxel) is one of the most extensively used chemotherapeutic agents for treating cancers of the breast and numerous other sites. Taxol stabilizes microtubules during mitosis, causing the cell cycle to arrest until eventually the cell undergoes apoptosis. Although Taxol has had significant benefits in many patients, response rates range from only 25-69%, and over half of Taxol-treated patients eventually acquire resistance to the drug. Drug resistance remains one of the greatest barriers to effective cancer treatment, yet little has been discerned regarding resistance to Taxol, despite its widespread clinical use. Kinases are known to be heavily involved in cancer development and progression, and several kinases have been linked to resistance of Taxol and other chemotherapeutic agents. However, a systematic screen for kinases regulating Taxol resistance is lacking. Thus, in this study, a set of kinome-wide screens was conducted to interrogate the involvement of kinases in the Taxol response. Positive-selection and negative-selection CRISPR-Cas9 screens were conducted, whereby a pooled library of 5070 sgRNAs targeted 507 kinase-encoding genes in MCF-7 breast cancer cells that were Taxol-sensitive (WT) or Taxol-resistant (TxR) which were then treated with Taxol. Next generation sequencing (NGS) was performed on cells that survived Taxol treatment, allowing identification and quantitation of sgRNAs. STK38, Blk, FASTK and Nek3 stand out as potentially critical kinases for Taxol-induced apoptosis to occur. Furthermore, kinases CDKL1 and FRK may have a role in Taxol resistance. Further validation of these candidate kinases will provide novel pre-clinical data about potential predictive biomarkers or therapeutic targets for breast cancer patients in the future.