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.

Maternal and paternal growth regulatory factor expression in hybrid sunfish.

Unidirectional hybridization between bluegill (Lepomis macrochirus) and pumpkinseed (L. gibbosus) sunfish enables researchers to explore the relative expression of paternal and maternal alleles in hybrids. Past studies have found that the metabolic dysfunction in bluegill-pumpkinseed hybrids may be due to incompatibilities between nuclear and mitochondrial genomes. However, the consequences of hybridization on body size and muscle growth have not been examined. This topic is particularly interesting because hybrids grow larger than parentals despite the fact that they are often sired by smaller, precociously mature bluegills. In order to improve our understanding of growth dynamics in hybrid sunfish, I conducted real-time quantitative PCR using species-specific primers on the white muscle tissue of bluegills, pumpkinseeds, and hybrids collected from Lake Opinicon, ON. Five growth factors that have been linked to muscle growth and body size demonstrated similar expression for maternal and paternal alleles. While about half of the hybrids showed the same pattern with myogenin, about half showed very low levels of mRNA for the paternal (bluegill) gene. While this did not explain the heterosis seen in hybrids, it may explain the small body phenotype of the cuckholding bluegill males. I explored the upstream genetic structure of bluegill myogenin and established that four alleles exist within the population. Furthermore, I uncovered a relationship in hybrids between the proximal promoter/ 5’ UTR of myogenin and its transcript level. I found that the hybrids demonstrating low paternal myogenin expression unfailingly possessed A3 or A4 alleles, but future studies will be needed to reveal the molecular links between the genotype and the growth phenotype. A similar genotype-phenotype association was not obvious in parentals, even those that were homozygous for these alleles. Whether this relationship can provide insight into the genetic determinants of bluegill alternative mating strategies has yet to be determined.

The Effect of Foam Core Density on the Flexural and Axial Behaviour of Sandwich Panels of Varying Slenderness with Natural Flax-FRP and Glass-FRP Composite Skins

This study investigates the effect of foam core density and skin type on the behaviour of sandwich panels as structural beams tested in four-point bending and axially compressed columns of varying slenderness and skin thickness. Bio-composite unidirectional flax fibre-reinforced polymer (FFRP) is compared to conventional glass-FRP (GFRP) as the skin material used in conjunction with three polyisocyanurate (PIR) foam cores with densities of 32, 64 and 96 kg/m3. Eighteen 1000 mm long flexural specimens were fabricated and tested to failure comparing the effects of foam core density between three-layer FFRP skinned and single-layer GFRP skinned panels. A total of 132 columns with slenderness ratios (kLe/r) ranging from 22 to 62 were fabricated with single-layer GFRP skins, and one-, three-, and five-layer FFRP skins for each of the three foam core densities. The columns were tested to failure in concentric axial compression using pinned-end conditions to compare the effects of each material type and panel height. All specimens had a foam core cross-section of 100x50 mm with 100 mm wide skins of equal thickness. In both flexural and axial loading, panels with skins comprised of three FFRP layers showed equivalent strength to those with a single GFRP layer for all slenderness ratios and core densities examined. Doubling the core density from 32 to 64 kg/m3 and tripling the density to 96 kg/m3 led to flexural strength increases of 82 and 213%, respectively. Both FFRP and GFRP columns showed a similar variety of failure modes related to slenderness. Low slenderness of 22-25 failed largely due to localized single skin buckling, while those with high slenderness of 51-61 failed primarily by global buckling followed by secondary skin buckling. Columns with intermediate slenderness experienced both localized and global failure modes. High density foam cores more commonly exhibited core shear failure. Doubling the core density of the columns resulted in peak axial load increases, across all slenderness ratios, of 73, 56, 72 and 71% for skins with one, three and five FFRP layers, and one GFRP layer, respectively. Tripling the core density resulted in respective peak load increases of 116, 130, 176 and 170%.