## 3 Results and Discussion
### Binding Interactions with PHF Tau  
To explore the interactions between the CCR2 domain and paired helical tau filament (PHF) (PBD ID: 503L), we utilized ClusPro. The results from the highest ranked model were used, which revealed a 23-amino-acid segment (SKAWVCDGDNDCEDNSDEENCES) that appeared to be primarily involved in the interaction of PHF tau and the homology modeled structure of LRP1. In particular, the LRP1 CR9 in the CCR2 subunit (1128-1138, DNDCEDNSDEE) showed optimal interactions, suggesting that this region is implicated in LRP1-tau interaction, as seen in Figure 2. To further validate the binding site of LRP1 with PHF tau, we used PrankWeb to determine if the 23-amino-acid LRP1 sequence was in fact binding to the binding site of the PHF tau with the highest pocket score. The results obtained confirm the binding interactions, as shown in Figure 3 and in Table 1. These results further suggest that the LRP1 23-amino-acid segment binds to the highest pocket probability of PHF tau.  
Figure 1: Phyre2 model generated for CR3–10 region of CCR2 subunit of LRP1 receptor (**a**) before cleavage of the beta-propeller region (black); (**b**) after cleavage of beta-propeller region.  
Figure 2: Results from ClusPro modeling showing the interaction between PHF tau and LRP1 Cluster 2 (CCR2) domain. The 23-amino-acid segment SKAWVCDGDNDCEDNSDEENCES is shown in green.  
The LRP1 binding pocket identified from this model is outlined in pink. (**a**) Shows the interactions with the entire CCR2 domain with PHF Tau. (**b**) Close-up image showing residues of the binding pocket (in pink).  
Several studies have shown that short peptide sequences often have critical molecular properties that can influence cellular pathways and binding abilities. Thus, short peptides are being widely studied not only to determine mechanistic details, but also for the development of novel peptide-based therapeutics due to their targeting abilities, among others [89; 90; 91]. Based on the results obtained from ClusPro and PrankWeb, we derived fourteen short peptide sequences by creating 10-amino-acid sections from the 23-amino-acid sequence binding region of LRP1. The goal in doing so was to explore the binding ability of each of these short peptide sequences toward PHF Tau and thereby competitively reduce LRP1-mediated tau internalization. In previous work, it has been shown that peptides derived from the extracellular domain of receptors can selectively inhibit the internalization ability of its own ligands [92]. The sequences designed are shown in Table 2.  
\begin{table}
\begin{tabular}{c c c c} \hline
**Pockets** & **Rank** & **Score** & **Probability** \\ \hline Pocket 1 & 1 & 83.27 & 0.993 \\ Pocket 2 & 2 & 82.55 & 0.993 \\ Pocket 3 & 3 & 28.54 & 0.908 \\ \hline \end{tabular}
\end{table}
Table 1: Binding pocket scores for the LRP1 sequence obtained from PrankWeb.  
\begin{table}
\begin{tabular}{c c} \hline
**Sequence Abbreviation** & **Sequence Designed** \\ \hline TauRP1-1 & SKAWVCDGDN \\ TauRP1-2 & KAWVCDGDND \\ TauRP1-3 & AWVCDGDNDC \\ TauRP1-4 & WVCDGDNDCE \\ TauRP1-5 & VCDGDNDCED \\ TauRP1-6 & CDGDNDCEDN \\ TauRP1-7 & DGDNDCEDNS \\ TauRP1-8 & GDNDCEDNDSD \\ \hline \end{tabular}
\end{table}
Table 2: Short peptide sequences designed derived from the 23-amino-acid sequence of the LPR1 binding segment.  
Figure 3: PHF Tau structure with spheres representing the different binding pockets. Green spheres show pocket 1, red spheres represent pocket 2 and yellow spheres show pocket 3.