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- All Subjects: Cyanovirin-N
- All Subjects: Organic Chemistry
- Creators: Ghirlanda, Giovanna
- Creators: Ackerman-Biegasiewicz, Laura
- Creators: Beerman, Eric Christopher
- Member of: Theses and Dissertations
- Status: Published
WW domains are small modules consisting of 32-40 amino acids that recognize proline-rich peptides and are found in many signaling pathways. We use WW domain sequences to explore protein folding by simulations using Zipping and Assembly Method. We identified five crucial contacts that enabled us to predict the folding of WW domain sequences based on those contacts. We then designed a folded WW domain peptide from an unfolded WW domain sequence by introducing native contacts at those critical positions.
This thesis is about how Fe catalysts can be degraded using photocatalysis and how Fe catalysts can degrade small molecules in conjunction with light. The goal of this paper is to look further into more sustainable methods of organic chemistry. Many current organic chemistry practices involve the use of precious metals. Iron is a more sustainable catalyst because it is abundant and inexpensive which is important for preserving the earth and making the organic chemistry more accessible. Along the same lines, light is a renewable energy source and has demonstrated its ability to aid in reactions. Overall, the goal of this paper is to explore the more sustainable alternatives to harsh and toxic organic chemistry practices through the use of Iron and light.
Non-canonical amino acids (NCAAs) can be used in protein chemistry to determine their structures. A common method for imaging proteins is cryo-electron microscopy (cryo-EM) which is ideal for imaging proteins that cannot be obtained in large quantities. Proteins with indistinguishable features are difficult to image using this method due to the large size requirements, therefore antibodies designed specifically for binding these proteins have been utilized to better identify the proteins. By using an existing antibody that binds to stilbene, NCAAs containing this molecule can be used as a linker between proteins and an antibody. Stilbene containing amino acids can be integrated into proteins to make this process more access able. In this paper, synthesis methods for various NCAAs containing stilbene were proposed. The resulting successfully synthesized NCAAs were E)-N6-(5-oxo-5-((4-styrylphenyl) amino) pentanoyl) lysine, (R,E)-2-amino-3-(5-oxo-5-((4-styrylphenyl)amino)pentanamido)propanoic acid, (E)-2-amino-5-(5-oxo-5-((4-styrylphenyl) amino) pentanamido) pentanoic acid. A synthesis for three more shorter amino acids, (R,E)-2-amino-3-(3-oxo-3-((4-styrylphenyl) amino) propanamido) propanoic acid, (E)-2-amino-5-(3-oxo-3-((4-styrylphenyl) amino) propanamido) pentanoic acid, and (E)-N6-(3-oxo-3-((4-styrylphenyl) amino) propanoyl) lysine, is also proposed.