University of Twente Student Theses


Revealing protein vibrational modes using plasmonic surfaces

Zaidouni, S. (2023) Revealing protein vibrational modes using plasmonic surfaces.

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Abstract:Proteins are essential components found in living organisms and play vital roles in various biological processes. Their significance is particularly evident in medical contexts, where the detection of proteins at extremely low concentrations, such as α-synuclein associated with diseases like Alzheimer’s and Parkinson’s, is crucial. Raman spectrum of proteins allows us to identify the chemical compounds based on their unique spectral fingerprint. However, the Raman effect is a relatively rare occurrence, making the detection of weak signals challenging. To overcome the low Raman intensity, researchers employ surface-enhanced Raman spectroscopy (SERS), which enhances the Raman signal and enables the analysis of proteins even at low concentrations. Nonetheless, SERS substrates often exhibit fluctuations in intensity across their surface, primarily due to nonuniform distribution of field enhancement in the sample. The objective of this research is to understand influence of the spatial intensity fluctuations on the Raman frequency, which is a measure of the protein conformation. In this project, we use a plasmonic nanostructure that includes an array of the nanoparticles on top of a gold mirror to probe multistate vibrational modes of proteins. Studying the vibrational modes of the protein on plasmonic surfaces is crucial to understand the possible conformations of proteins on such surfaces, which are widely used for sensing and biomedical diagnosis. In order to maintain stable bonding of the protein Bovine Serum Albumin (BSA) and ensure a consistent protein conformation on the surface, a self-assembled monolayer (SAM) surface is used as a mediator between the protein and gold surfaces. This SAM surface consists of regions with different characteristics, such as hydrophilic and hydrophobic properties, as well as neutral or charged traits. The research findings shows that a closed hotspot without any linking molecules provides the most effective intensity enhancement. Therefore, it is recommended to utilize an open hotspot when applying a self-assembled monolayer. Furthermore, the research demonstrates that α-helices remain intact only in coupled plasmonic nanocavities when neutral linking molecules are employed. In the case of both charged and neutral linking molecules, the surrounding environment exposes the side chains Tyr, Phe, and Trp. In case of particularly positive charged and neutral linking molecules, the α-helices are transformed into β-sheets.
Item Type:Essay (Bachelor)
Faculty:TNW: Science and Technology
Subject:33 physics, 42 biology
Programme:Biomedical Technology BSc (56226)
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