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.

An integrative case study of positive youth development in a recreational community sport program

Participation in organized activities is associated with many markers of positive youth development (PYD) such as improved self-esteem, social competence, and academic achievement (Mahoney et al., 2009). Sport is an extra-curricular activity that is particularly popular among youth, as nearly three quarters of Canadian children and adolescents are engaged in organized sport or physical activity (CFLRI, 2012). Much of the research in this area has examined sport programs which are explicitly structured to promote life skills or PYD outcomes; however, the sustainability of such programs has recently been called into question (Turnnidge, Hancock, & Côté, 2014). The purpose of this program of research was to conduct an in-depth case study of a successful, sustainable community youth basketball league. Study 1 was a qualitative descriptive exploration of coaches’ perceptions of the basketball league. This study provided a general overview of the structure and perceived benefits of the league, from the perspective of current coaches. Coaches highlighted the unique emphasis that the league places on fun and positive immediate sport experiences. Study 2 expanded on selected themes from Study 1, namely, the salience of the league’s culture and tendency for former players to return to the league as volunteers. This study used an ethnographic approach wherein the first author volunteered as an assistant coach on a basketball team over the course of a six-month season. This approach enabled him to gain considerable first hand insight into the organizational culture of the basketball league. The third and final study adopted a quantitative approach using both systematic observation and questionnaires to investigate the relationship between PYD outcomes and observed athlete behaviour during basketball games. A cluster analysis revealed the presence of two distinct groups of athletes characterized by relatively high and low perceptions of PYD outcomes, which were also associated with varying behavioural characteristics during competition. The results of these three studies provide a detailed blueprint of a successful youth sport program that has been sustained over 60 years. While not without limitations, many characteristics of the league should prove useful in structuring youth sport programs in other contexts.