title: Computational Molecular Physics of FKBPs and FRB-domain containing proteins
Creators: name: Mayer, Benjamin Eugen
Publisher: name: UNSPECIFIED
Year: 2025

description: Protein-protein interactions (PPIs) are fine-tuned dynamics essential to cells and their life cycles. In cancer,
deviations of these dynamics occur, leading to uncontrollable cell growth. The process of DNA repair is
particularly important here to preserve the genetic information inside our cells and to correct mutations that can lead to changes in cell dynamics.
DNA repair is a biological pathway often controlled by large proteins that recruit other proteins. This recruitment leads to a complex construct of molecules (protein complex) that performs the actual DNA repair.
The areas within the protein complex where proteins interact with each other are called protein-protein interfaces. Understanding these interfaces at the molecular level may enable us to develop new inhibitors that interfere with DNA repair processes in a controlled manner. Since it is assumed that increased resistance to radiation and chemotherapy can be explained by the increased DNA repair ability of tumors, such inhibitors would enable the treatment of previously resistant tumors.
For the prediction of the structure of protein complexes, both classical algorithms (docking) and state-of-the-art machine learning-based methods were used in this work. The generated complexes are used as input for molecular dynamics simulations (MD simulations) to gain a time-resolved insight into the molecular biophysics of these protein-protein interfaces.
The central recruiting proteins of DNA repair form a class of protein kinases that all contain a so-called FKBP Rapamycin Binding region (FRB region). In this context, FKBP stands for FK506 binding protein, a class of proteins defined by the binding of the small molecule FK506. The FRB region is a structural subunit of a protein to which FKBPs or Rapamycin binds.
The common feature of FKBPs is the existence of a structural region binding FK506. This region can also bind numerous other proteins instead of FK506. FKBPs are therefore associated with a variety of diseases and various inhibitors interfering with these proteins’ binding capabilities are being investigated as potential drugs.
This common feature is also one of the reasons why FKBPs can fulfill various functions in our body.
This thesis examines a series of protein complexes, each containing either a single FKBP or a protein with an FRB region. Additionally, complexes in which binding occurs between both proteins are also analyzed.
The central protein kinase of the non-homologous end joining (NHEJ) DNA repair pathway was chosen as a representative for a protein containing an FRB region without a linked FKBP: DNA-dependent protein kinase, catalytic subunit (DNA-PKcs). A series of protein complexes with DNA-PKcs were modeled in collaboration with experimenters. The modeling indicates the existence of a previously unknown protein complex consisting of, among others, two DNA-PKcs molecules, which explains previously published laboratory results.
Furthermore, the protein structure of the DNA-PKcs was resolved with AlphaFold v2 (AF2) for the first time.
Based on the resolved structure, the biophysics of the binding between DNA and DNA-PKcs were investigated in the context of the NHEJ repair mechanism.

Similar studies were carried out for an FKBP of L. pneumophila. This protein is associated with the virulence of the bacterium. Several experimentally proven protein complexes containing this FKBP were modeled. This fundamental research in collaboration with the Steinert group at the TU Braunschweig provides new insight
into how the virulence of L. pneumophila can be explained.