Bianka Farkas1,2, Hedvig Tordai1, Rita Padányi1,3, János Gera4, Gábor Paragi4, Tamás Hegedűs1,3
1 Department of Biophysics and Radiation Biology, Semmelweis University, Budapest
2 Faculty of Information Technology and Bionics, PPKE, Budapest
3 MTA-SE Molecular Biophysics Research Group, HAS, Budapest
4 Department of Medical Chemistry, University of Szeged, Szeged
Introduction: Cystic fibrosis (CF) is a severe, monogenic disease caused by mutant forms of the CFTR/ABCC7 chloride channel, a member of the ATP Binding Cassette (ABC) protein superfamily. There are small drug molecules to correct the protein folding and restore the function, but their therapeutic effect is small. In order to understand protein function and to develop more efficient drug molecules, a high-resolution protein structure is required.
Aims: Even though the recently published zebrafish cryo-EM CFTR structure (PDBID:5W81) is solved in the active (ATP-bound, phosphorylated) conformation, it lacks an open channel for chloride permeation. Our goal is to characterize the CFTR structure and dynamics based on both experimental and homology models, using in silico methods. We aim to analyze the potential chloride pathways using molecular dynamics simulations.
Method: In order to generate a conformational ensemble of the protein, we performed extensive molecular dynamics simulations. Channel detecting algorithms were applied to identify conformations with open channel and the possible pathways were characterized. Since chloride ions entered the pathway in our equilibrium simulations without traversing the bottleneck region, we performed metadynamics simulations to describe the passage through this region.
Results: Our simulations indicate two intracellular pores, where chloride can enter the protein. The in silico identified amino acids in the bottleneck region are in good agreement with experiments. Metadynamics simulations revealed two possible exits at the extracellular side, one including hydrophobic lipid tails that could explain the lipid-dependency of CFTR function.
Conclusion: We described the chloride pathway of CFTR at atomic resolution. Our results suggest that several intra- and extracellular entry sites exist, no large conformational changes of the closed structures are required for opening, and lipids may directly influence the channel path. Our study and methodology will lead to understand the gating mechanism of the wild type and mutant CFTR proteins.
Doctoral School: Roska Tamás Doctoral School of Sciences and Technology
Program: PhD in Biological Sciences, Bionics
Supervisor: Tamás Hegedűs
E-mail address: firstname.lastname@example.org
Support: NKFIH-111678, NKFI-127961, CFF HEGEDU18I0, KIFÜ HPC, MTA Wigner GPU Laboratory, NVIDIA Corporation, and Semmelweis Science and Innovation Fund.