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bioRxiv · 10.1101/2023.08.28.554951

Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles

Somarathne, R. P.·Misra, S. K.·Sharp, J. S.·Fitzkee, N. C.
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Abstract

In biological systems, proteins can bind to nanoparticles to form a "corona" of adsorbed molecules. The nanoparticle corona is of high interest because it impacts the organisms response to the nanomaterial. Understanding the corona requires knowledge of protein structure, orientation, and dynamics at the surface. Ultimately, a residue-level mapping of protein behavior on nanoparticle surfaces is needed, but this mapping is difficult to obtain with traditional approaches. Here, we have investigated the interaction between R2ab and polystyrene nanoparticles (PSNPs) at the level of individual residues. R2ab is a bacterial surface protein from Staphylococcus epidermidis and is known to interact strongly with polystyrene, leading to biofilm formation. We have used mass spectrometry after lysine methylation and hydrogen-deuterium exchange (HDX) NMR spectroscopy to understand how the R2ab protein interacts with PSNPs of different sizes. Through lysine methylation, we observe subtle but statistically significant changes in methylation patterns in the presence of PSNPs, indicating altered protein surface accessibility. HDX measurements reveal that certain regions of the R2ab protein undergo faster exchange rates in the presence of PSNPs, suggesting conformational changes upon binding. Both results support a recently proposed "adsorbotope" model, wherein adsorbed proteins consist of unfolded anchor points interspersed with regions of partial structure. Our data also highlight the challenges of characterizing complex protein-nanoparticle interactions using these techniques, such as fast exchange rates. While providing insights into how proteins respond to nanoparticle surfaces, this research emphasizes the need for advanced methods to comprehend these intricate interactions fully at the residue level. TOC Image O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/554951v2_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@19b8ac5org.highwire.dtl.DTLVardef@b3948aorg.highwire.dtl.DTLVardef@1dd2ef5org.highwire.dtl.DTLVardef@35e938_HPS_FORMAT_FIGEXP M_FIG C_FIG Lysine methylation and hydrogen-deuterium exchange can reveal useful structural details about protein adsorption to nanoparticle surfaces.

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Somarathne, R. P., Misra, S. K., Sharp, J. S., Fitzkee, N. C.. 2023-08-29. Exploring the Residue-Level Interactions between the R2ab Protein and Polystyrene Nanoparticles. https://doi.org/10.1101/2023.08.28.554951

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