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.

TILTED COLUMNAR THIN FILM COATINGS WITH ANISOTROPIC LIGHT SCATTERING PROPERTIES FOR SOLAR ENERGY APPLICATIONS

The main goal of this thesis is to show the versatility of glancing angle deposition (GLAD) thin films in applications. This research is first focused on studying the effect of select deposition variables in GLAD thin films and secondly, to demonstrate the flexibility of GLAD films to be incorporated in two different applications: (1) as a reflective coating in low-level concentration photovoltaic systems, and (2) as an anode structure in dye-sensitized solar cells (DSSC). A particular type of microstructure composed of tilted micro-columns of titanium is fabricated by GLAD. The microstructures form elongated and fan-like tilted micro-columns that demonstrate anisotropic scattering. The thin films texture changes from fiber texture to tilted fiber texture by increasing the vapor incidence angle. At very large deposition angles, biaxial texture forms. The morphology of the thin films deposited under extreme shadowing condition and at high temperature (below recrystallization zone) shows a porous and inclined micro-columnar morphology, resulting from the dominance of shadowing over adatom surface diffusion. The anisotropic scattering behavior of the tilted Ti thin film coatings is quantified by bidirectional reflectance distribution function (BRDF) measurements and is found to be consistent with reflectance from the microstructure acting as an array of inclined micro-mirrors that redirect the incident light in a non-specular reflection. A silver-coating of the surface of the tilted-Ti micro-columns is performed to enhance the total reflectance of the Ti-thin films while keeping the anisotropic scattering behavior. By using such coating is as a booster reflector in a laboratory-scale low-level concentration photovoltaic system, the short-circuit current of the reference silicon solar cell by 25%. Finally, based on the scattering properties of the tilted microcolumnar microstructure, its scattering effect is studied as a part of titanium dioxide microstructure for the anode in DSSCs. GLAD-fabricated TiO2 microstructures for the anode in a DSSC, consisting of vertical micro-columns, and combined vertical topped with tilted micro-columns are compared. The solar cell with the two-part microstructure shows the highest monochromatic incident photon to current efficiency with 20% improvement compared to the vertical microstructure, and the efficiency of the cell increases from 1.5% to 2% due to employing the scattering layer.