Salt Effects on Peptide-Phosphate Co-Assemblies Open Access

Abstract

Short peptide chains have promiscuous binding abilities and unique assembly with themselves as well as phosphate template molecules, with one of the most known being DNA. Additionally, liquid-liquid phase separation helps give rise to nanostructures, such as nanotubes, specific to the templates that peptides are arrayed across. To further extend the knowledge around conditions that facilitate and promote the formation of nanotubes, we aimed to study the effects of various salt ions on the peptide-phosphate co-assemblies. Residual salts from synthesis and purification of peptides have been shown to be sufficient in destabilizing co-assembly nanotubes as observed as quick transitions to other nanostructures like ribbons, sheets, or fibers. Treatment of the salted peptide co-assemblies in increasingly concentrated NaCl solution also correlated with the transitions in the morphology away from nanotubes. In addition, examining the effects of the iodide and lithium ions in comparison to NaCl showed that co-assembly nanotubes were reduced in number and had generated thinner nanotube walls. Moreover, peptide co-assemblies with single-stranded DNA compared to double-stranded DNA under increased salt concentrations showed that greater β-sheet character is observed when the template is double-stranded DNA. Meanwhile, we observed that lithium ions can be capable of inducing a conformational DNA change from B to A form to create kinetically stabilized β-sheets observable through the ThT fluorescence assay. Uncovering the fundamentals behind co-assembly stabilization has applications in understanding the behavior of Nature’s biopolymers in the context of neurodegenerative diseases like Alzheimer’s disease and provides the basis for rational design of bio-inspired materials.

Table of Contents

Introduction....................................................................................................................................... 1

Results and Discussion....................................................................................................................... 4

Co-assembly with Trimetaphosphate................................................................................................ 4

Figure 1...................................................................................................................................... 4

Figure 2...................................................................................................................................... 5

Pep-KG:TMP Co-assembly Structural Stability.................................................................................... 5

Figure 2...................................................................................................................................... 5

Figure 3...................................................................................................................................... 6

Figure 4...................................................................................................................................... 7

Figure 5.................................................................................................................................... 10

Figure 6.................................................................................................................................... 12

Figure 7.................................................................................................................................... 13

Pep-KG: DNA-Salt Effects on DNA Conformation.............................................................................. 14

Figure 8.................................................................................................................................... 15

Figure 9.................................................................................................................................... 15

Figure 10................................................................................................................................... 16

Conclusion....................................................................................................................................... 17

Materials and Methods.................................................................................................................... 18

Peptide synthesis and purification.................................................................................................. 18

Desalting peptides......................................................................................................................... 19

Peptide assembly and peptide:phosphate co-assemblies.................................................................. 19

Transmission electron microscopy (TEM)......................................................................................... 19

Circular dichroism (CD).................................................................................................................. 20

Thioflavin (ThT) fluorescence assay................................................................................................. 20

About this Honors Thesis

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School	Emory College
Department	Chemistry
Degree	B.S.
Submission	Honors Thesis
Language	English
Research Field	Chemistry, Biochemistry
Keyword	Co-assemblies Salt effects Peptide
Committee Chair / Thesis Advisor	Lynn, David, Emory University
Committee Members	Saikawa, Eri , Emory University Nkomo, Simba , Emory University

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