PhD in the field of amyloid and bio-condensate structural biology by NMR spectroscopy

The Reif group at the Bavarian NMR Center (BNMRZ) at the TU Munich is looking for a PhD student to work on the characterization of amyloid fibrils, protein condensates and liquid liquid phase separation (LLPS) using a combination of solution- and MAS solid-state NMR spectroscopy. The position is available immediately.

Membraneless organelles (such as nucleoli, nuclear speckles, stress granules etc.) are vital for living organisms. These biomolecular condensates are formed by multi-domain proteins that are involved in multi-valent interactions. Condensate formation implies both protein-protein and protein-RNA interactions, involving prion-like low complexity regions and RNA binding domains. The delicate balance between liquid-liquid phase separation (LLPS) and amyloid fibril formation requires tight regulation. This can be achieved by chaperones, posttranslational modifications, small molecules and/or metals that affect this balance and either yield disintegration or rigidification of protein liquid droplets into β-strand rich protein fibrils. It is the aim of the PhD project to better understand the mechanisms that modulate the equilibrium between amyloid fibril and granule formation in the cell on a structural basis.

Protein systems under investigation involve stress granule (SG) associated factors, the Alzheimer’s disease Aβ peptide, the diabetes type II related human islet amyloid polypeptide (hIAPP/amylin), light chain antibody domains involved in AL-amyloidosis and serum amyloid A (SAA) involved in AA-amyloidosis. We employ solution- and MAS solid-state NMR to characterize these systems. In addition, we use low resolution biophysical methods such as fluorescence microscopy, ThT aggregation assays, CD spectroscopy, electron microscopy and dynamic light scattering (DLS).

Interested candidates should have a background in biochemistry and biophysical methods to characterize protein misfolding.

References
– Pradhan T, Sarkar R, Meighen-Berger KM, Feige MJ, Zacharias M, Reif B (2023) Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain protein FOR005. Nature Comm. 14:e3755; doi: 10.1038/s41467-023-39280-0.
– Rodina N, Hornung S, Sarkar R, Suladze S, Peters C, Schmid PWN, Niu Z, Haslbeck M, Buchner J, Kapurniotu A, Reif B (2024) Modulation of Alzheimer’s Disease Aβ40 Fibril Polymorphism by the Small Heat Shock Protein αB-Crystallin. J.Am. Chem. Soc. 146, 19077; doi: 10.1021/jacs.4c03504
– Suladze S, Sarkar R, Rodina N, Bokvist K, Krewinkel M, Scheps D, Nagel N, Bardiaux B, Reif B (2024) Atomic resolution structure of full-length human insulin fibrils. Proc. Natl. Acad. Sci. USA 121, e2401458121; doi: 10.1073/pnas.2401458121
– Suladze S, Sustay Martinez C, Rodriguez Camargo DC, Engler J, Rodina N, Sarkar R, Zacharias M, Reif B (2024) Structural Insights into Seeding Mechanisms of hIAPP Fibril Formation. J.Am. Chem. Soc. 146, 13783; doi: 10.1021/jacs.3c14233

General Information
For further information, please see our web page: https://www.bio.nat.tum.de/ocb/home/. Our group is integrated into the Bavarian NMR Center (www.bnmrz.org) at the Technical University Munich and is associated with the Institute of Structural Biology (www.helmholtz-munich.de/en/stb) at the Helmholtz-Zentrum München (HMGU). Labs are located in the Bavarian NMR Center at Campus Garching, and are used together with the groups of Profs. Michael Sattler, Franz Hagn and Steffen Glaser. In addition to a high-end NMR facility, our group has direct access on campus to an X-ray crystallography facility, as well as to a cryo-EM platform equipped with a Selectrix X imaging filter and a modern Falcon 4i direct electron detector enabling cutting-edge single-particle analysis and in situ cryo-electron tomography. While working at BNMRZ, you participate in the scientific seminars organized by the BNMRZ, and the STB. Membraneless organelles (such as nucleoli, nuclear speckles, stress granules

,

etc.) are essential for living organisms. These biomolecular condensates are formed by multi-domain proteins involved in multivalent interactions. Condensation formation relies on both protein-protein and protein-RNA interactions, involving prion-like regions of low complexity as well as RNA-binding domains. The delicate balance between liquid-liquid phase separation (LLPS) and amyloid fibril formation requires precise regulation. This can be achieved by chaperones, post-translational modifications, small molecules, and/or metals that influence this balance, leading either to the disintegration or solidification of liquid protein droplets into β-strand-rich protein fibrils. The aim of this doctoral project is to gain a better structural understanding of the mechanisms that modulate the balance between the formation of amyloid fibrils and granules in cells. The

protein systems under investigation include factors associated with stress granules (SG), the Aβ peptide (Alzheimer’s disease), the human islet amyloid polypeptide (hIAPP/amylin) associated with type 2 diabetes, antibody light chain domains (involved in AL amyloidosis), and serum amyloid A (SAA; involved in AA amyloidosis). We use solution-based and MAS solid-state NMR spectroscopy to characterize these systems. In addition, we employ lower-resolution biophysical methods such as fluorescence microscopy, ThT aggregation assays, CD spectroscopy, electron microscopy, and dynamic light scattering (DLS).

Interested candidates should have knowledge of biochemistry and biophysical methods for characterizing protein misfolding.

References
– Pradhan T, Sarkar R, Meighen-Berger KM, Feige MJ, Zacharias M, Reif B (2023) Mechanistic insights into the aggregation pathway of the patient-derived immunoglobulin light chain protein FOR005. Nature Comm. 14:e3755; doi: 10.1038/s41467-023-39280-0. – Rodina N, Hornung S, Sarkar R, Suladze S, Peters C, Schmid PWN, Niu Z, Haslbeck M, Buchner J, Kapurniotu A, Reif B (2024) Modulation of Alzheimer’s Disease Aβ40 Fibril Polymorphism by the Small Heat Shock Protein αB-Crystallin. J.Am. Chem. Soc. 146, 19077; doi: 10.1021/jacs.4c03504
– Suladze S, Sarkar R, Rodina N, Bokvist K, Krewinkel M, Scheps D, Nagel N, Bardiaux B, Reif B (2024) Atomic resolution structure of full-length human insulin fibrils. Proc. Natl. Acad. Sci. USA 121, e2401458121; doi: 10.1073/pnas.2401458121
– Suladze S, Sustay Martinez C, Rodriguez Camargo DC, Engler J, Rodina N, Sarkar R, Zacharias M, Reif B (2024) Structural Insights into Seeding Mechanisms of hIAPP Fibril Formation. J.Am. Chem. Soc. 146, 13783; doi: 10.1021/jacs.3c14233

General Information
Further information can be found on our website: https://www.bio.nat.tum.de/ocb/home/. Our research group is integrated into the Bavarian NMR Center (www.bnmrz.org) at the Technical University of Munich and associated with the Institute of Structural Biology (www.helmholtz-munich.de/en/stb) at the Helmholtz Center Munich (HMGU). The laboratories are located in the Bavarian NMR Center on the Garching campus and are shared with the research groups of Professors Michael Sattler, Franz Hagn, and Steffen Glaser. In addition to a state-of-the-art NMR facility, our group has direct access on campus to an X-ray diffractometry system and a cryo-EM platform equipped with a Selectrix X image filter and a modern Falcon 4i direct electron detector, thus enabling cutting-edge performance in single-particle analysis and in-situ cryo-electron tomography. During your work at the BNMRZ, you will participate in the scientific seminars organized by the BNMRZ and the STB.

The position is suitable for disabled persons. Disabled applicants will be given preference in case of generally equivalent suitability, aptitude and professional performance.

Data Protection Information:
When you apply for a position at the Technical University of Munich (TUM), you are submitting personal information. With regard to this personal information, please note the data protection information pursuant to Article 13 of the General Data Protection Regulation (GDPR) concerning the collection and processing of personal data in connection with your application. By submitting your application, you confirm that you have acknowledged the above data protection information of TUM.

Contact: Interested candidates send an email with a copy of your CV and certificates to Prof. Dr. Bernd Reif, email: reif@tum.de