Forschungsschwerpunkt BioComp

BioComp-2.0-Projekt #9

A refined quantitative model of APP processing


Stefan Kins – Christoph Garth – Sandro Keller – Jan Hauth


Intramembrane proteolysis has been recognized within the last two decades as a ubiquitous process occurring in all forms of life, ranging from prokaryotes to plants and animals. Such cleavage events are involved in numerous biological processes and regulate many different functions, including signaling, membrane remodeling, protein quality control, cell adhesion, and communication (1). One of the best analyzed processes in this context is the sequential cleavage of the Amyloid Precursor Protein (APP) by α-,β-, and γ-secretases, leading to generation of Aβ peptides, which accumulate in Alzheimer’s Disease brains (2). Accordingly, a first mathematical model of this process has been suggested (3). Contrary to previous hypotheses, this study came to the conclusion that secretases represent allosteric enzymes that require cooperativity by APP dimerization for efficient processing. Notably, however, the authors did not validate their model with the aid of experimental data by determining APP dimerization and processing characteristics, and surprisingly they did not include Aβ generation into the model.



A) Extension of the existing model by incorporation of Aβ generation.

B) Establishment of a multiple-compartment model that implements knowledge of subcellular localization of substrates and enzymes.

C) Extension of the existing model by visual tools for modeling protein kinetics networks, allowing implementation of different data sets (for other enzymes and substrates).

D) Purification and incorporation of APP in native nanodiscs to allow biophysical characterization of its dimerization properties (9-11), thus extending a previous collaboration aiming at analyzing APP extracellular domain dimerization (8). In the future, this system shall also be used to study APP–secretase interactions.

E) Refinement of the parameters describing the kinetics of APP processing based on experimental data gained with secretase inhibitors, the above APP dimerization data, and a previously established inducible dimerization system for APP (4-7).



1. Erez, E., Fass, D., and Bibi, E. (2009) How intramembrane proteases bury hydrolytic reactions in the membrane. Nature 459, 371-378

2. Brunholz, S., Sisodia, S., Lorenzo, A., Deyts, C., Kins, S., and Morfini, G. (2012) Axonal transport of APP and the spatial regulation of APP cleavage and function in neuronal cells. Exp Brain Res 217, 353‐364

3. Schmidt, V., Baum, K., Lao, A., Rateitschak, K., Schmitz, Y., Teichmann, A., Wiesner, B., Petersen, C. M., Nykjaer, A., Wolf, J., Wolkenhauer, O., and Willnow, T. E. (2012) Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease. EMBO J 31, 187-200

4. Stahl, R., Schilling, S., Soba, P., Rupp, C., Hartmann, T., Wagner, K., Merdes, G., Eggert, S., and Kins, S. (2014) Shedding of APP limits its synaptogenic activity and cell adhesion properties. Front Cell Neurosci 8, 410

5. Soba, P., Eggert, S., Wagner, K., Zentgraf, H., Siehl, K., Kreger, S., Lower, A., Langer, A., Merdes, G., Paro, R., Masters, C. L., Muller, U., Kins, S., and Beyreuther, K. (2005) Homo and heterodimerization of APP family members promotes intercellular adhesion. EMBO J 24, 3624-3634

6. Isbert, S., Wagner, K., Eggert, S., Schweitzer, A., Multhaup, G., Weggen, S., Kins, S., and Pietrzik, C. U. (2012) APP dimer formation is initiated in the endoplasmic reticulum and differs between APP isoforms. Cell Mol Life Sci 69, 1353-1375

7. Eggert, S., Midthune, B., Cottrell, B., and Koo, E. H. (2009) Induced dimerization of the amyloid precursor protein leads to decreased amyloid-­‐beta protein production. J Biol Chem 284, 28943-28952

8. Baumkotter, F., Schmidt, N., Vargas, C., Schilling, S., Weber, R., Wagner, K., Fiedler, S., Klug, W., Radzimanowski, J., Nickolaus, S., Keller, S., Eggert, S., Wild, K., and Kins, S. (2014) Amyloid precursor protein dimerization and synaptogenic function depend on copper binding to the growth factor-like domain. J Neurosci 34, 11159-11172

9. Lee SC, Knowles TJ, Postis VL, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR. (2016) A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 11, 1149‐1162

10. Vargas C, Cuevas Arenas R, Frotscher E, Keller S. (2015) Nanoparticle self-assembly in mixtures of phospholipids with styrene/maleic acid copolymers or fluorinated surfactants. Nanoscale 7, 2068-20696

11. Cuevas Arenas R, Klingler J, Vargas C, Keller S. (2016) Influence of lipid bilayer properties on nanodisc formation mediated by styrene/maleic acid copolymers. Nanoscale 8, 15016-15026

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