Proteins often assemble into complexes to achieve a specific biological function. Obtaining high resolution atomistic structures of such complexes, however, is challenging. Software that can predict possible protein arrangements using available experimental data as guide can be exploited. The prediction of the structure of a protein assembly is however often difficult, because when interacting two binding partners may change conformation. Further challenges arise from difficulties in properly combining diverse (and possibly inconsistent) analytical data.
We are developing and applying methods to predict the flexible assembly of proteins into complexes. Our protein docking software, JabberDock, is currently among the best for de novo docking of protein in solution and in a membrane.
Representative articles for method development:
- L.S.P. Rudden & M.T. Degiacomi (2019), Protein docking using a single representation for protein surface, electrostatics and local dynamics, Journal of Chemical Theory and Computation.
- L.S.P. Rudden & M.T. Degiacomi (2021), Transmembrane protein docking with JabberDock, Journal of Chemical Information and Modelling
Representative articles for applications:
- A. Olerinyova, A. Sonn-Segev, J. Gault, C. Eichmann, J. Schimpf, A.H. Kopf, L.S.P. Rudden, D. Ashkinadze, R. Bomba, J. Greenwald, M.T. Degiacomi, J.A. Killian, T. Friedrich, R. Riek, W.B. Struwe, P. Kukura (2021). Mass Photometry of Membrane Proteins, Chem
- Santhanagopalan I., Degiacomi M.T., Shepherd D.A., Hochberg G.K.A., Benesch J.L.P., Vierling E., (2018). It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate, Journal of Biological Chemisty