Mechanical Investigation of the AdeABC RND Efflux Pump
Ata Göktuğ Çim
Materials Science and Nano Engineering, MSc Thesis, 2026
Thesis Jury
Prof. Canan ATILGAN (Thesis Advisor)
Prof. Ali Rana ATILGAN (Thesis Co-Advisor)
Prof. Burç MISIRLIOĞLU
Asst. Prof. Onur VAROL
Assoc. Prof. Mehmet ÖZBİL
Date & Time: 13th July 2026 – 2:00 PM
Place: FENS G025
Keywords : Elastic Network Model, AdeABC Efflux Pump, Protein Mechanics, Force Propagation
Abstract
Proteins are complex molecular structures that move dynamically and organize the regions within themselves to communicate with each other. The nature of the communication network within protein complexes formed by the combination of more than one protein and the functions of the structure cannot be understood by analyzing the subunits individually, because the communication network and functional behavior can arise from mechanical, physical, or chemical couplings between different components. In this thesis, the mechanical organization of the tripartite Resistance-Nodulation-Division complex AdeABC efflux pump, which plays a role in multidrug resistance of Acinetobacter baumannii, was examined. The AdeABC protein complex consists of three parts: inner membrane carrier, periplasmic adapter, and outer membrane channel, and the protein extends from the inner membrane region of the Gram-negative bacterial cell to the outer membrane region. In this study, isolated subunits, binary partial complexes, and the ternary complete Ade-ABC complex were mechanistically analyzed using elastic network-based and linear response theory-based methods. The results show that AdeABC has a behavior that its subunits do not. Long-range force propagation occurs only at the ternary full complex level, indicating mechanical communication at the complex level. In addition, the fact that the regions of AdeB that direct apo transitions appear in different places in the isolated AdeB structure and in the AdeABC complex shows that the structure is organized differently from the subunits of the mechanical communication network. These findings demonstrate that the mechanical properties of AdeABC can only be understood within its fully complex architecture
