How Do Biological Nanomachines Work?
Functional Mechanisms of Biomolecular Complexes

Fatty acid synthases and polyketide synthases catalyse the synthesis of complex organic compounds through the interplay of a multitude of catalytic sites contained within multi-enzyme complexes. We pursued a stochastic kinetic simulation approach to represent the reaction network of yeast typ I FAS, a synthetic megacomplex.
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Eukaryotic microtubules (MTs) are cellular filaments that form the mitotic spindle, define the shape of axons and dendrites in neurons, and provide tracks for intracellular transport. MTs undergo stochastic switching between phases of growth and shrinkage. Elucidating the detailed mechanism of assembly and disassembly is core of this research project.
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The ribosome is a large biomolecular complex composed of ribonucleic acids and proteins. Ribosomes translate the genetic code (mRNA) into proteins and are therefore essential in all kingdoms of life. The aim of this project is to understand functional mechanisms of the ribosome at an atomic level using molecular dynamics (MD) simulations.
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The FOF1 ATP Synthase is a complex nanomotor that synthesizes nearly 90% of the ATP made during cellular respiration. It consists of an integral membrane complex (FO) and an enzymatic complex that converts ADP and inorganic phosphate to ATP (F1). We study the conformational changes upon ADP and phosphate binding and the release of ATP.
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Bacteriophage Φ 29 infects the bacterium Bacillus subtilis. During infection the newly synthesized DNA has to be translocated into an empty viral capsid. For this purpose the virus produces a packaging machine, consisting of a terminase enzyme and a head-tail connector. We study the packaging mechanism and the particular role of the connector.
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The discovery of green fluorescent protein (GFP) in the early 1960s ultimately heralded a new era in cell biology. GFP can be tagged to subcellular structures to monitor cellular processes in living organisms. Collaborating with other groups, we were able to elucidate the photo-switching mechanism in the fluorescent protein asFP595 at the atomic level.
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The transport of proteins and RNA through the nuclear pore complex is a key process in eukaryotic cells. It is mainly mediated by the superfamily of β-karyopherins, to which the exportin CAS (whose yeast homolog is Cse1p) belongs. We studied the substantial conformational changes that appear during the transport cycle using MD simulations.
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Insulin aggregation critically depends on pH. However, the underlying energetic and structural determinants are unknown. Applying combined mass spectrometry, atomic force spectroscopy, and molecular dynamics (MD) simulations, we have obtained structural information of putative aggregation rate-determining transition states.
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