Project Z04 – Computational models of structure, dynamics and evolution of GPCRs

This core unit provides a comprehensive computational analysis of all receptors of interest in the CRC. In an iterative loop, Z04 will construct computational models consistent with experimental data combining ROSETTA modeling, molecular dynamics simulation, and evolutionary analysis. From these models, we will derive testable hypothesis for the next iteration of experimental validation in the respective projects. Lastly, we will integrate information from these approaches into a holistic model that creates experimentally testable hypothesis. Given that a set of established computational protocols will need to be applied repetitively and timely to a large number of biological systems, this work is best conducted in a core unit.

Contact

Prof. Dr. Jens Meiler (Project Leader)

Leipzig University, Faculty of Medicine
Institute for Drug Development
Liebigstraße 19, D-04103 Leipzig

Phone +49 341 97 11801
E-Mail

Prof. Dr. Peter Stadler (Project Leader)

Leipzig University, Faculty of Mathematics and Computer Science
Institute of Computer Science
Härtelstraße 16 – 18, D-04107 Leipzig

Phone +49 341 97 16690
E-Mail

Prof. Dr. Peter Hildebrand (Project Leader)

Leipzig University, Faculty of Medicine
Institute of Medical Physics and Biophysics
Härtelstraße 16 – 18, D-04107 Leipzig

Phone +49 341 97 15705
E-Mail
Web biophysik.medizin.uni-leipzig.de/forschungresearch/prof-dr-peter-hildebrand/

N.N. (PostDoc)

Leipzig University, Faculty of Medicine
Institute of Medical Physics and Biophysics
Härtelstraße 16 – 18, 04107 Leipzig

Resources

We focus on: 

  1. Structural intermediates, complexes
  2. Combining MD simulations with evolutionary analysis
  3. Performing MD simulations of the membrane-embedded proteins
  4. Usage of paramagnetic restranst in structre determination

Techniques

  • computational models
  • MD Simulations: Classical Molecular Dynamics, QM/MM, QMD, DFT, Enhanced Sampling, AMBER, Gromacs, VMD
  • evolutionary analysis

Publications

Del Alamo D, Sala D, Mchaourab HS, Meiler J. Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife. 2022;11:e75751 DOI: 10.7554/eLife.75751.

Sala D, Del Alamo D, Mchaourab HS, Meiler J. Modeling of protein conformational changes with Rosetta guided by limited experimental data. Structure. 2022 May 12:S0969-2126(22)00140-X. doi: 10.1016/j.str.2022.04.013. Online ahead of print. PMID: 35597243.

Yang Y, Stensitzki T, Sauthof L, Schmidt A, Piwowarski P, Velazquez Escobar F, Michael N, Nguyen AD, Szczepek M, Brünig FN, Netz RR, Mroginski MA, Adam S, Bartl F, Schapiro I, Hildebrandt P, Scheerer P, Heyne K. Ultrafast proton-coupled isomerization in the phototransformation of phytochrome. Nat Chem. 2022 May 16. doi: 10.1038/s41557-022-00944-x. Online ahead of print. PMID: 35577919.

Rudolf S, Kaempf K, Vu O, Meiler J, Beck-Sickinger AG, Coin I. Binding of Natural Peptide Ligands to the Neuropeptide Y5 Receptor. Angew Chem Int Ed Engl. 2021 Nov 25. doi: 10.1002/anie.202108738 . PMID:34822209. 

Staritzbichler R, Ristic N, Goede A, Preissner R, Hildebrand PW. Voronoia 4-ever. Nucleic Acids Res. 2021 Jun 9:gkab466. doi: 10.1093/nar/gkab466. Epub ahead of print. PMID: 34107038.