2 PhD projects offered in the IPP winter call 2020/2021
Many physiological processes are regulated in a day-time dependent (circadian) manner. Circadian clocks allow organisms to synchronize themselves to the environmental light-dark cycle. Disruption of circadian cycles due to mutations, jet-lag or shift-work can severely compromise physiology and human health. Circadian rhythms are generated by cell-autonomous ~ 24h transcription-translation feedback loops. In mammals, the BMAL1/CLOCK transcription factor complex regulates three period (PER1,2,3) and two cryptochrome (CRY1,2) clock genes as well as many clock controlled genes. Mammalian TIMELESS (TIM) plays a minor role in the clock, but (together with TIPIN) plays diverse roles in genome maintenance. Our goal is to acquire an atomic resolution picture and quantitative mechanistic understanding of the molecular processes governing circadian gene regulation and epigenetics, light synchronization of the clock as well as the link of the circadian clock to genome maintenance. To this end we are using a highly interdisciplinary structural biology approach.
To elucidate the molecular mechanisms underlying circadian regulation, the PhD student will apply a wide range of techniques including 3D-structural analyses (e.g. X-ray crystallography, Cryo-EM, SAXS, Crosslink-MS), biochemical and biophysical protein interaction studies as well as UV/VIS- and CD spectroscopy. To produce highly pure proteins and protein complexes for these applications, she/he will perform cloning, recombinant protein expression and protein purification using FPLC systems. Within collaborations, she/he will also analyze clock protein interactions and protein functions in cell-based approaches. Candidates with a strong interest in structural biology, protein biochemistry, protein structure-function relationship and a significant previous exposure to these research areas during their master education are encouraged to apply.
Publications relevant to this project
Wolf E and Kramer A (2020) Circadian Regulation: from Molecules to Physiology. JMB, 432:3223-3425.
Garg A, Orru R, Ye W, Distler U, Chojnacki JE, Köhn M, Tenzer S, Sönnichsen C and Wolf E (2019) Structural and mechanistic insights into the interaction of the circadian transcription factor BMAL1 with the KIX domain of the CREB-binding protein. JBC, 294:16604–16619.
Witosch J, Wolf E and Mizuno N (2014) Architecture and ssDNA interaction of the Timeless- Tipin-RPA Complex. Nucleic Acids Res., 42:12912-27.
Schmalen I, Reischl S, Wallach T, Klemz R, Grudziecki A, Prabu JR, Benda C, Kramer A and Wolf E (2014) Interaction of circadian clock proteins CRY1 and PER2 is modulated by zinc binding and disulfide bond formation. Cell, 157(5):1203–1215.
Czarna A, Berndt A, Singh HR, Grudziecki A, Ladurner A, Timinszky G, Kramer A and Wolf E (2013) Structures of Drosophila Cryptochrome and mouse Cryptochrome1 provide insight into circadian function. Cell, 153(6):1394-405.
Kucera N, Schmalen I, Hennig S, Öllinger R, Strauss HM, Grudziecki A, Wieczorek C, Kramer A and Wolf E (2012) Unwinding the Differences of the Mammalian PERIOD Clock Proteins from Crystal Structure to Cellular Function. PNAS, 109(9):3311-6.