Professor Ulrich Zachariae
Biological Chemistry and Drug Discovery, School of Life Sciences
Dr Ulrich Zachariae obtained his PhD in the structural biophysics lab of Wolfgang Baumeister at the Max Planck Institute for Biochemistry in Munich (2004).
Between 2005 and 2010, he worked as a Postdoc with Helmut Grubmüller and Bert de Groot at the Max Planck Institute for Biophysical Chemistry in Göttingen, Germany, and as a drug researcher for AstraZeneca in Alderley Park, focusing on computational and theoretical biophysics. From 2011—2013, Ulrich was an independent SUPA Advanced Fellow at the School of Physics at the University of Edinburgh, building up a team of researchers interested in membrane-protein simulations. He joined the University of Dundee as Reader in Physics and Life Sciences in May 2013.
- Membrane biophysics
- Ion channels: Gating mechanisms, permeation and selectivity
- Design of new antibacterial compounds
- Flexible protein scaffolds investigated by atomistic simulations with close links to experiments.
Atomistic & Coarse-Grained Simulations of Proteins and Membranes
Proteins form the machinery of biological cells. To perform their actions, they must undergo conformational changes, much like the motions of macroscopic machines. These can be followed and studied by molecular dynamics simulations, which allow us to gain insight into the mechanisms by which they work - and the underlying energetic principles.
We apply and develop simulation methods on a range of length and time scales, especially focusing on membrane proteins and ion channels. Membrane-bound proteins form a large part of the proteome and control many of the cell's fundamental functions. To investigate ion channels, we have developed CompEl, "computational electrophysiology", which allows the prediction of channel ion conductance and selectivity based on electrochemical gradients. Of special interest to us are potassium channels, membrane pores formed by antimicrobial peptides (e.g., dermcidin), and pores in the outer membrane of bacteria that are found to be mutated in strains resistant to antibiotics (e.g., Neisserial PorB).
Movies of ion conduction across KcsA (first video) and dermcidin (second video) are shown below. In KcsA, potassium ions are shown as purple and pink spheres, while the protein is shown in green and water in red and white. In the second movie on dermcidin, the peptide aggregate is coloured blue and orange, and chloride ions are shown in red. The grey spheres depict lipid membrane head groups. We also investigate the molecular basis for the impressive elasticity of solenoid proteins, such as importin-beta and CRM1, and we have developed methods to quantify pattern formation in many-particle systems.
- G Williamson, G Tamburrino, G Dias Mirandela, M Boeckstaens, M Bage, AV Pisliakov, CM Ives, E Terras, A Bizior, PA Hoskisson, AM Marini, U Zachariae*, A Javelle*: A two-lane mechanism for selective biological ammonium transport. *joint corresponding authors. eLife 9, e57183 (2020).
- S Llabrés, MI Tsenkov, SA MacGowan, GJ Barton, U Zachariae: Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) alpha-solenoid domain. J. Struct. Biol. 209, 107405 (2020).
- I Rodriguez-Espigares, et al.: GPCRmd uncovers the dynamics of the 3D-GPCRome. Nature Methods 17, 777-787 (2020).
- W Kopec, DA Köpfer, ON Vickery, A Bondarenko, TLC Jansen, BL de Groot, U Zachariae: Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 10, 813-820 (2018).
- ON Vickery, CA Carvalheda, S Zaidi, AV Pisliakov, V Katritch, U Zachariae: Intracellular transfer of Na+ in an active state G-protein coupled receptor. Structure 26, 171-180 (2018).
- AWP Fitzpatrick, S Llabrés, A Neuberger, D Brook, XC Bai, S Murakami, U Okada, H van Veen, U Zachariae, SHW Scheres*, BF Luisi*, D Du*: Structure of a tripartite ABC drug efflux pump. Nature Microbiology 2, 17070 (2017).
- C Kutzner, DA Köpfer, JP Machtens, BL de Groot, C Song, U Zachariae: Insights into the function of ion channels by Computational Electrophysiology simulations. Biochim. Biophys. Acta Biomembranes, 1858, 1741-1752 (2016).
- JP Machtens, C Lansche, D Kortzak, A Leinenweber, P Kilian, B Begemann, U Zachariae, D Ewers, BL de Groot, R Briones, C Fahlke: Mechanisms of anion conduction by coupled glutamate transporters. Cell 160, 542-553 (2015).
- DA Köpfer, C Song, T Gruene, GM Sheldrick, U Zachariae*, BL de Groot*: Ion permeation in K+ channels occurs by direct Coulomb knock-on. *joint corresponding authors. Science 346, 352-355 (2014).
- C Song, C Weichbrodt, ES Salnikov, M Dynowski, BO Forsberg, B Bechinger, C Steinem, BL de Groot, U Zachariae*, K Zeth*: Crystal structure and functional mechanism of a human antimicrobial membrane channel. *joint corresponding authors. Proc. Natl. Acad. Sci. USA 110, 4586-4591 (2013)
I am available for media commentary on my research.
Computational Biophysics and Drug Discovery
Contact Corporate Communications for media enquiries.
Areas of expertise
- Antimicrobial resistance
Programme leads have been appointed for two new taught postgraduate courses that will commence in the autumn.
Clues to the mechanism of yeast infections, which present risks to both humans and crops, have been identified.
Vacuum cleaners that unblock brain vessels, super normal design for extraordinary bodies, and the ways in which our medical data can aid the COVID-19 fight are just some of the topics to be explored at the University of Dundee next week.