Browsing by Subject "Proteins"
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Item Encapsulation of proteins and cells in silica nanoporous materials(2011-11) Reategui, EduardoMy dissertation presents fundamental and practical scientific contributions. I demonstrated the versatility of the sol-gel processing technology for the study of the basic science behind water and protein structure under confinement, and for the development of novel biotechnology and biomedical engineering applications based on cell encapsulation in nanoporous silica gels.For the basic science studies of my dissertation, silica nanoporous gels were used to investigate the kinetic and thermodynamic transitions of water under confinement. I demonstrated a direct correlation between the structure of confined water and the secondary structure of proteins in a wide range of temperatures (- 196C to 95C). I showed qualitatively that the incorporation of a highly hydrogen bonding osmolyte contributed to improve the thermal stability of encapsulated proteins by a mechanism based on prevention of adsorption at the surface of the nanoporous silica material. For the practical contributions of my dissertation, I developed two novel applications relevant to the biotechnology and biomedical engineering fields. These applications were based on the encapsulation of prokaryotic and eukaryotic cells in silica nanoporous gels. First, I developed a highly selective and efficient biodegradation platform for the removal of an herbicide, atrazine, from contaminated water. In the second application, I invented a cell capture and isolation methodology that was successfully tested as a cancer cell isolation tool from mixed populations of eukaryotic cells (normal and cancer cells). Miscellaneous applications were also investigated such as encapsulation as a means of cryopreservation of mammalian and algae cells, and were incorporated in the Appendices of this thesis.Item How proteins search for their targets on DNA.(2008-05) Hu, TaoIt is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smolu- chowski three-dimensional (3D) diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional (1D) search. We explicitly addressed the role of DNA conformation and the dispersion of nonspecific adsorption energies. We identified a wealth of new different scaling regimes and found that the maxi- mum on the rate-versus-ionic strength curve is asymmetric. We also studied the other facilitating mechanism termed intersegment trans- ferwhere proteins which have two DNA binding sites can transfer from one DNA segment to another without dissociation to water. We proposed a scaling the- ory which combines the effects of protein 3D diffusion, 1D sliding, intersegment transfer and DNA motion. A direct application of our work on target search problem is the kinetics of viral self-assembly. We show that due to the 1D sliding of capsid proteins on the unassembled chain of single-stranded RNA, the self-assembly is more than ten times faster than the case involving only three-dimensional diffusion. We further extended our theory to the macroscopic diffusion coefficient of proteins in a semi-dilute solution of DNA pieces and the effective conductivity of a composite made of well conducting nanowires suspended in some poor conducting medium.Item Protein Effects on Lipid Domain Formation in a Model Membrane(2014) Yusuf, Urji; Heikal, Ahmed A.Item Structure – Function Studies of Annexin A2 & A5(2014) Schramel, StephanieItem Structure – Function Studies of Annexin A2 & A5(2014) Schramel, Stephanie; Hinderliter, Anne