Determinants of cis-trans isomerism of the aromatic-prolyl amide bond and design of lathanide-binding peptides
| Author(s) | Meng, Hai Yun | |
| Date Accessioned | 2020-09-15T11:50:45Z | |
| Date Available | 2020-09-15T11:50:45Z | |
| Publication Date | 2006 | |
| Abstract | Cis-trans isomerization of amide bonds plays critical roles in protein molecular recognition, protein folding, protein misfolding and disease. Aromatic-proline sequences are particularly prone to exhibit cis amide bonds. The roles of residues adjacent to a tyrosine-proline residue pair on cis-trans isomerism were examined. A series of peptides XYPN was synthesized and the following effects were observed: (a) aromatic residues immediately preceding Tyr-Pro disfavor cis amide bonds; (b) proline residues preceding Tyr-Pro lead to multiple species; and (c) other residues exhibit similar values of Ktrans/cis. In addition, the effect of the i+3 residue was examined in a limited series of peptides TYPZ. NMR data indicated that aromatic residues, Pro, Asn, Ala and Val at the i+3 residue all favor cis amide bonds. ☐ The zinc finger is a compact metal-binding motif, consisting of an N-terminal β-hairpin and a C-terminal α-helix connected by a loop. A new, general lanthanidebinding motif inspired by zinc fingers was designed, which involved optimization of nearly all residues of the protein. A series of peptides was synthesized and analyzed by circular dichroism, and the dissociation constants were determined for each peptide. The optimized peptide design, LF4, bound Terbium (III) with a dissociation constant of 6.8 μM and adopted a metal-bound structure similar to a zinc finger. ☐ Many human proteins exhibit function which is dependent on phosphorylation. We are trying to understand the effects of protein phosphorylation on protein structure within native proteins by the design of proteins whose structures are dependent on their phosphorylation state. Nine peptides were synthesized and the fluorescence analyzed in the non-phosphorylated and phosphorylated states. In addition, the dissociation constants were determined for both phosphorylated and nonphosphorylated forms, and the rate of phosphorylation by Protein Kinase A (PKA) analyzed. Two peptides were developed that are rapidly phosphorylated by PKA and that show a significant increase in fluorescence on phosphorylation, enabling their use as genetically encoded protein kinase sensors. | en_US |
| Advisor | Zondlo, Neal J. | |
| Degree | M.S. | |
| Department | University of Delaware, Department of Chemistry and Biochemistry | |
| Unique Identifier | 82143468 | |
| URL | https://udspace.udel.edu/handle/19716/27518 | |
| Publisher | University of Delaware | en_US |
| URI | https://login.udel.idm.oclc.org/login?url=https://www.proquest.com/docview/305324656?accountid=10457 | |
| dc.subject.lcsh | Protein folding | |
| dc.subject.lcsh | Peptides -- Synthesis | |
| dc.subject.lcsh | Isomerization | |
| dc.subject.lcsh | Molecular association | |
| Title | Determinants of cis-trans isomerism of the aromatic-prolyl amide bond and design of lathanide-binding peptides | en_US |
| Type | Thesis | en_US |