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N–H/N and C–H/O interactions in protein structure, assembly, and conformational dynamics: structural effects and probes of post-translational modification
Date
2025
Authors
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Journal ISSN
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Publisher
University of Delaware
Abstract
Noncovalent interactions allow for the relief of partial charge and excess electron density in protein structures. Noncovalent interactions within proteins are central to folding and function, facilitating life. Hydrogen bonding has been accepted for almost a century as the dominant force for protein folding interactions. Different types of noncovalent interactions and their energetic value for protein structure have been the subject of much debate recently. The stability of the polyproline II helix has been attributed to n→π* interactions. Hydrophobic interactions have also shown energetic value in proteins and serve critical roles in maintaining the stability of deoxyribonucleotide base pairs. ☐ The amino acid composition of a protein is a large determinant of the interactions it will form. These interactions produce the three-dimensional structure of proteins. The 20 canonical amino acids each have a different structure and can interact differently with the surrounding amino acids in a protein. These local interactions contribute to the overall structure of the protein and its stability. Proline is unique among the amino acids due to its cyclic structure. As a result, proline has a much greater propensity to form cis amide bonds. These amide bonds can undergo interconversion between isomers. The interconversion of proline amide isomers influences a wide number of biological processes. Noncovalent interactions have shown a key role in stabilizing individual proline amide isomers. We explored the potential roles of N–H/N and C–H/O interactions in proline amide cis-trans isomerism. ☐ The N–H/N interaction between consecutive amino acid residues has been observed in metal binding loop proteins but these interactions and their unusual geometries are poorly understood. We explored N–H/N interactions within protein structure and report unusual pyramidalization at the amide bonds engaged in N–N/N interactions. We also explored the role of N–H/N interactions in promoting proline cis-trans isomerism. During the course of these investigations, numerous C–H/O interaction were identified. These interactions were studied to understand how C–H/O interactions may influence protein structure. ☐ C–H/O interactions have been recently shown to stabilize the cis proline amide conformation in proteins. These C–H/O interactions may be more pronounced when the residue prior to proline is phosphorylated. Phosphorylation at amino acids prior to proline has been shown to reduce amide isomerism at proline. Furthermore, the removal of phosphate groups from residues prior to proline is usually cis or trans amide isomer-specific. We investigated this potential role of C–H/O interactions among a series of novel phosphoserine-proline derivatives in an effort to better understand how C–H/O interactions effect proline amide isomerism. ☐ Phosphorylation is a dynamic post-translational protein modification that changes the structure of proteins. High levels of phosphorylation of the microtubule associated tau protein have been shown to contribute to Alzheimer's disease. However, the specific structural consequences of phosphorylation are poorly understood We explored the effects of phosphorylation on these tau peptides, revealing novel autoproteolysis within the C-terminal domain. ☐ Certain phosphorylation sites on the tau protein compete with another post- translational modification, GlcNAcylation. GlcNAcylation in tau has been shown to prevent aggregation, contrary to phosphorylation. GlcNAcylation is accomplished by a single enzyme, OGT. As such, the specificity of this enzyme for protein sequences is crucial in the regulation of GlcNAcylation. However, the means to identify OGT activity within cellular lysates are currently limited due to labor and cost. Therefore, we explored a novel way to identify OGT activity from cellular lysates. This investigation also allowed for the simultaneous exploration of OGT substrate- specificity for the tau protein.
Description
"At the request of the author or degree granting institution, this graduate work is not available to view or purchase until August 27 2026."--ProQuest abstract/details page.
Keywords
Electron density, Protein structures, Amino acid composition