MOLECULAR MASS MANIPULATION ENABLED BY GRAPHENE BASED NANOSTRUCTURES

The surge of interest in graphene, as epitomized by the Nobel Prize in Physics in 2010, is attributed to its extraordinary properties. Graphene is ultrathin, mechanically tough, and has amendable surface chemistry. These features make graphene and graphene based nanostructure an ideal candidate for the use of molecular mass manipulation. The controllable and programmable molecular mass manipulation is crucial in enabling future graphene based applications, however is challenging to achieve. This dissertation studies several aspects in molecular mass manipulation including mass transportation, patterning and storage. For molecular mass transportation, two methods based on carbon nanoscroll are demonstrated to be effective. They are torsional buckling instability assisted transportation and surface energy induced radial shrinkage. To achieve a more controllable transportation, a fundamental law of direction transport of molecular mass by straining basal graphene is studied. For molecular mass patterning, we reveal a barrier effect of line defects in graphene, which can enable molecular confining and patterning in a domain of desirable geometry. Such a strategy makes controllable patterning feasible for various types of molecules. For molecular mass storage, we propose a novel partially hydrogenated bilayer graphene structure which has large capacity for mass uptake. Also the mass release can be achieved by simply stretching the structure. Therefore the mass uptake and release is reversible. This kind of structure is crucial in enabling hydrogen fuel based technology. Lastly, spontaneous nanofluidic channel formation enabled by patterned hydrogenation is studied. This novel strategy enables programmable channel formation with pre-defined complex geometry.

STRUCTURE AND FUNCTION OF THE GROUP III CHAPERONINS, A UNIQUE CLADE OF PROTEIN FOLDING NANOMACHINES

The survival and descent of cells is universally dependent on maintaining their proteins in a properly folded condition. It is widely accepted that the information for the folding of the nascent polypeptide chain into a native protein is encrypted in the amino acid sequence, and the Nobel Laureate Christian Anfinsen was the first to demonstrate that a protein could spontaneously refold after complete unfolding. However, it became clear that the observed folding rates for many proteins were much slower than rates estimated in vivo. This led to the recognition of required protein-protein interactions that promote proper folding. A unique group of proteins, the molecular chaperones, are responsible for maintaining protein homeostasis during normal growth as well as stress conditions. Chaperonins (CPNs) are ubiquitous and essential chaperones. They form ATP-dependent, hollow complexes that encapsulate polypeptides in two back-to-back stacked multisubunit rings, facilitating protein folding through highly cooperative allosteric articulation. CPNs are usually classified into Group I and Group II. Here, I report the characterization of a novel CPN belonging to a third Group, recently discovered in bacteria. Group III CPNs have close phylogenetic association to the Group II CPNs found in Archaea and Eukarya, and may be a relic of the Last Common Ancestor of the CPN family. The gene encoding the Group III CPN from Carboxydothermus hydrogenoformans and Candidatus Desulforudis audaxviator was cloned in E. coli and overexpressed in order to both characterize the protein and to demonstrate its ability to function as an ATPase chaperone. The opening and closing cycle of the Chy chaperonin was examined via site-directed mutations affecting the ATP binding site at R155. To relate the mutational analysis to the structure of the CPN, the crystal structure of both the AMP-PNP (an ATP analogue) and ADP bound forms were obtained in collaboration with Sun-Shin Cha in Seoul, South Korea. The ADP and ATP binding site substitutions resulted in frozen forms of the structures in open and closed conformations. From this, mutants were designed to validate hypotheses regarding key ATP interacting sites as well as important stabilizing interactions, and to observe the physical properties of the resulting complexes by calorimetry.