# Protein Dynamics in F-like Bacterial Conjugation
## 3 Structures Involved in Pilin Processing, Pilus Extension, and Retraction
### Pilus Assembly and Extension Proteins
#### 3.2.2 T4 SS Core Proteins TraB, -K, and -V  
TraB from F-like plasmids range between 429 to 475 aa and share homology in their CTDs with TrbI from IncP plasmids (TrbI\({}_{\text{P}}\)), VirB10\({}_{\text{T}}\), and TraO\({}_{\text{I}}\)[14]. TraB from the F plasmid is 475 aa with asmall N-terminal IM-bound domain and the remaining protein extended into the periplasm where it forms an envelope-spanning complex with the mainly periplasmic TraK and TraV in the OM [80]. Utilizing yeast two-hybrid analysis, TraB residues Met138\(-\)Asp229 were shown to bind the region Thr6\(-\)Ala27 in TraK found in the periplasm, which interacts with the TraV residues Arg127\(-\)Asn171 in the OM using the domain Thr124\(-\)Arg237. It is hypothesized that TraK serves as a secretin to aid in creating an envelope structure spanning across the membrane allowing for pilus extension through the bacterial cell envelope [14]. The pED208 core complex solved by cryo-ET includes homologs of these proteins in the OM complex; despite the low resolution, three-dimensional classifications revealed the complex displays 13-fold symmetry (Figure 3A-C) [15]. TraB, -K, and -V are essential for F plasmid conjugation; therefore, the sequences of interaction between the proteins composing the core complex could be presented as useful targets for drug discovery.  
TraB is a predominantly hydrophilic protein anchored in the IM by Ile13-Leu33 [76]. The region in TraB predicted to be responsible for TraK interaction, Met138-Asp229, was found to be proline-rich at 23% of the residues in the segment [80]. Proline-rich segments are common in eukaryotic cell protein-protein interactions (PPIs); however, it is not known whether a proline-rich binding motif mediates the interaction between TraB and TraK. Structural predictions using Phyre2 show a high degree of disorder in the protein at 44%, but did not accurately estimate the location of the IM-bound region; highest confidence models were found in the periplasmic CTD exclusively [20].  
The TraK family of proteins are homologous to TrbG\({}_{\text{P}}\), VirB9\({}_{\text{T1}}\) and TraN\({}_{\text{I}}\) and range between 299-410 aa [37]. The TraK family shares similarities to secretin proteins, particularly the HrcC subgroup of the type III secretion system (T3 SS) encoded by _Pseudomonas syringae_[82]. The \(\beta\)-domain and S-domain of TraK is identical to the secretin PulD of _Klebsiella oxytoca_[83]. The \(\beta\)-domain is theorized to be embedded in the OM, and form a ring structure typical of most secretins. The S-domain consists of a 60 aa sequence that binds to a lipoprotein acting as a periplasmic chaperone [84]. The C-terminus interacts with TraV while the N-terminus interacts with TraB, and it is predicted that TraK could act as a chaperone for TraV [80]. Estimations of secondary structure characteristics by Phyre2 show the protein displays a mixed \(\alpha-\beta\) structure with a predicted disorder content of 34% [20].  
TraV is a lipoprotein with a conserved cysteine at the N-terminal signal sequence, with sizes ranging between 171 to 316 aa in the F-like plasmid family and is 171 aa in the F plasmid [80]. There are two conserved cysteines that appear to allow for multimerization and/or interaction with TraK [85]. TraV is predicted to be an OM anchor for the TraV\(-\)K\(-\)B complex [80]. Phyre2 predicts the structure of TraV to be highly disordered at 61% of the overall secondary structure; however, this value is likely caused by the lack of structural data on small TM proteins [20].