# Protein Dynamics in F-like Bacterial Conjugation
## 7 Conclusions
\begin{table}
\begin{tabular}{c c c c c c c c} \hline \hline  & & & & & & & & \\ \hline \multirow{2}{*}{**Function**} & **Protein** & **Localization** & **Size (aa)** & **\% Disordered** & **Sequences** & **\% Identity** & **PDB** \\ \hline \multirow{2}{*}{Transcription Regulation} & FinO & Cytoplasm & 186 & 42\% & 33–184 & 100\% & 1 DVO \\  & TraJ & Cytoplasm & 229 & 21\% & 15–128 & 100\% & 4 KQD \\  & TraR & Cytoplasm & 73 & 19\% & 4–73 & 100\% & 5W1S \\ \hline \multirow{2}{*}{ProPilin Maturation} & TraA & IM, ECM & 70 & 20\% & 21–41 & 29\% & 2L8S \\  & TraQ & IM & 94 & 22\% & 32–64 & 46\% & 3 MP7 \\  & TraX & IM & 248 & 13\% & 28–37 & 24\% & 2 KP6 \\ \hline \multirow{2}{*}{T4 SS Core Proteins} & TraB & IM, & & & & & \\  & Periglasm & & 475 & 44\% & 203–412 & 14\% & 6 GYB \\  & TraK & OM, & & 242 & 34\% & 26–107 & 8\% & 6 GYB \\  & TraV & IM & 171 & 61\% & 25–36 & 42\% & 5V8K \\ \hline \multirow{6}{*}{Assembly/Extension} & TraP & IM & 196 & 24\% & 57–118 & 18\% & 2V4J \\  & TraE & IM & 188 & 11\% & 93–182 & 16\% & 5 KPE \\  & TraL & IM & 91 & 13\% & 18–47 & 30\% & 3 GEB \\  & TraC & Cytoplasm, & 875 & 15\% & 448–819 & 18\% & 4 AG5 \\  & TraW & Periplasm & 210 & 16\% & 100–171 & 20\% & 2 FU3 \\  & TrC & Periplasm & 212 & 29\% & 103–190 & 13\% & 1 HVU \\  & TraF & Periplasm & 247 & 17\% & 146–256 & 19\% & 6 GC1 \\  & TrbB & Periplasm & 181 & 31\% & 33–175 & 19\% & 2 HYX \\ \hline \multirow{2}{*}{Plus Retraction} & TraH & OM, & & & & & \\  & Periplasm & & 458 & 25\% & 90–144 & 24\% & 6S29 \\  & TrbI & IM, & & & & & \\  & TraN & & Periplasm & 128 & 23\% & 47–120 & 81\% & 1U2M \\ \hline \multirow{2}{*}{Mating Pair Stabilization} & TraN & OM, & & 602 & 25\% & 127–408 & 98\% & 4 XBM \\  & TraG & IM, & & & & & \\  & Periglasm & & 938 & 43\% & 774–930 & 93\% & 3 CWG \\  & TraU & Periplasm & 330 & 26\% & 31–39 & 26\% & 3 TOW \\ \hline \multirow{2}{*}{Relaxose Accuracy} & TraI & Cytoplasm & 1756 & 20\% & 1–1473 & 98\% & 5N8O \\ \hline \multirow{2}{*}{Relaxosome Accessory} & TraY & Cytoplasm & 131 & 25\% & 1–51 & 25\% & 1U9P \\  & TraM & Cytoplasm & 127 & 33\% & 2–121 & 39\% & 3 ON0 \\  & TraD & Cytoplasm, & 717 & 29\% & 145–574 & 30\% & 1E9R \\ \hline Surface Exclusion & TraT & OM, ECM & 244 & 34\% & 52–98 & 15\% & 3 BF2 \\ \hline Entry Exclusion & TraS & IM & 173 & 8\% & 22–35 & 38\% & 2M4V \\ \hline \hline \end{tabular}  
* Based on structural predictions in Phyre2 [20]. Shown is the percentage of disordered content based on secondary structure predictions and highest confidence models as determined through sequence homology of structures deposited in the PDB. Refer to Table S1 for further details regarding disordered sequences.  
\end{table} 
Table 1: Predicted Structural Dynamics of T4 SS Transfer Proteins of the F Plasmid *. ATPase TrwD from the R388 plasmid has been inhibited through the administration of unsaturated fatty acids (UFAs) such as linoleic acid, and 2-hexadecanoic acid; docking simulations have provided context for further optimization as the UFAs bind non-competitively [164]. TrwD is part of a superfamily of ATPases that include the Type II secretion, Type IV pilus and flagellar biogenesis machineries all of which have putative binding sites for similar UFAs [2]. It is possible that UFAs may be found that can target TraC from the F-like T4 SS (Section 3.2.3); a high-resolution structure of TraC would greatly aid in future in silico drug discovery processes. An increasingly promising drug target is the pilus itself; as mentioned previously, structural data exists for the polymerized pilus, and many functional studies have been performed on pili from a vast number of plasmids. Bacteriophages have high affinity for the bacterial pilus, and the M13 phage was shown to bind F-type pili using the coat protein g3p [165; 166]. This interaction allowed for the creation of a potential protein antibiotic, as addition of the soluble N-terminal domain of g3p to F-plasmid containing bacteria resulted in inhibition of conjugation [167].