Postdoctoral Associate

Postdoctoral Positions @Akbey Lab

Structural Biology Department, School of Medicine, University of Pittsburgh, PA, USA

akbey.structbio.pitt.edu

Structures and Molecular Mechanisms of Biofilm Forming Functional Amyloids by Solid-state NMR & Cryo-EM

The aim of Akbey Lab is to use modern solid-state NMR (ssNMR) spectroscopy to study functional amyloid fibrils involved in bacterial biofilm forming. We develop novel NMR methods to push the limits of the state of the art and apply these methods to understand molecular details and mechanisms of functional amyloids. Solid-state NMR has made a remarkable progress in the last decade to become a remarkably higher-resolution and -sensitivity method due to advances in sample preparation, hardware, and novel methods such as proton-detection and hyperpolarization (DNP). These allow studies of difficult insoluble proteins not only in-vitro but also in their complex in-vivo (or ex-vivo ) environment. We use recombinant protein expression and biophysical methods to produce and characterize isotope labeled protein samples and combine ssNMR with other exciting structural biology methodologies.

Profile of the candidates: We are looking for scientists who have solid background in the following research aread: biological ssNMR, Cryo-EM, biophysics, biochemistry, microbiology, and recombinant protein production/characterization. Expertise/interest in NMR/DNP method development will be highly appreciated. Interested candidates should send a cover letter, CV, and contact information of two scientists for recommendation letters to Ümit Akbey - [email protected]. More information on projects can be acquired per email and please don’t hesitate to contact. Employment will be for one year that can be extended up to several years. Career development options and support will be provided for the candidates. The starting date is asap.

Research Infrastructure: The Akbey Lab is funded via a startup package. We have full access to two dedicated modern solid state NMR instruments, 600 WB and 750 WB. A variety of conventional and fast MAS probes are available, including two unique low-temperature capable 1.3mm and 3.2mm MAS NMR probes. We have access to the NMR facility in the Structural Biology Department comprising state-of-the-art solution NMR instrumentation, including 900, 800, 700 and 2x600 MHz and several faculty with an emphasis in NMR are members of the department. The Akbey Lab is fully equipped for recombinant protein production and characterization, with a large wet lab space and space for data analysis. We have access to higher field ssNMR systems, ultra-fast MAS (0.7mm) and DNP via National & EU consortia.

In addition, excellent x-ray crystallography, Cryo-EM (Titan Krios, T12 & TF20), Cryo-Tomography, high-performance computation resources are available in the Department of Structural Biology. We collaborate with faculty who are experts in these structural biology methodologies. Graduate students are part of the Molecular Biophysics and Structural Biology Program.

University of Pittsburgh and the City of Pittsburgh: University of Pittsburgh is ranked #14 in best Medical Schools in Research in USA. The University of Pittsburgh Medical School is considered a top tier medical school with a focus in research ranking in the Top 10 recipients of NIH funding. The MBSB Graduate Program consists of more than 40 PIs and collects excellent scientists, research areas and a great environment for a scientist to be and develop from University of Pittsburgh and Carnegie Mellon University.

Pittsburgh has repeatedly been ranked among the nation's most livable cities. It's truly diverse and friendly place where higher education is valued and thriving, thanks to many great universities. It has a warm, friendly culture with so much history. A beautiful downtown, lively neighborhoods, a great art and music scene, and an influx of young professionals has made it a fantastic place to live. Despite all it offers, Pittsburgh is still a very affordable and easy to live city (~50% less compared to New York or California!). University provides comprehensive health insurance and other resources to its coworkers. City of Bridges : Pittsburgh's 440-plus bridges (more than even Venice can boast) span three major rivers and countless streams, creeks, valleys, and ravines. Pittsburgh airport makes it super easy to be connected to any large city in the States and World.

The University of Pittsburgh is an Affirmative Action/Equal Opportunity Employer and values equality of opportunity, human dignity and diversity. EOE, including disability/vets.

Selected recent publications related to the position: (orcid.org/0000-0003-3161-2969)

- Chang-Hyeock Byeon, Kasper Holst Hansen, Jasper Jeffrey, Maria Andreasen, Ümit Akbey. (2023) Initial Steps of Chaperone-Aided Fibrillation of Pseudomonas aeruginosa Biofilm Forming Functional Amyloid FapC. Biorxiv.

- Chang-Hyeock Byeon, Pang C. Wang, In-Ja L. Byeon, Ümit Akbey (2023) Solution-state NMR assignment and secondary structure propensity of the full length and minimalistic-truncated prefibrillar monomeric form of biofilm forming functional amyloid FapC from Pseudomonas aeruginosa. Biomolecular NMR Assignment.

- Ümit Akbey and Maria Andreasen (2022) Functional amyloids from bacterial biofilms – structural properties and interaction partners. Chemical Science: 13, 6457-6477

- Ümit Akbey (2022) Site-specific Protein Methyl Deuterium Quadrupolar Patterns by Proton detected 3D 2 H13 C1 H MAS NMR Spectroscopy. JBioNMR. 10.1007/s10858-021-00388-4

- Nelson Ferreira, Emil Gregersen, Zachary A. Sorrentino, Hjalte Gram, Cristine Betzer, Clara Perez-Gozalbo, Marjo Beltoja, Madhu Nagaraj, Jie Wang, Jan S. Nowak, Mingdong Dong, Daniel Otzen, Ümit Akbey, Sissel Schmidt, Morten Meyer, Marina Romero-Ramos, Benoit Giasson, Poul H. Jensen (2021) Multiple system atrophy-associated oligodendroglial protein p25 alpha stimulates formation of novel alpha-synuclein strain with enhanced neurodegenerative potential. Acta Neuropathologica 142, 1, 87-115

- Madhu Nagaraj; Mumdooh Ahmed; Jeppe Lyngso; Brian S. Vad; Andreas Bogglid; Anne Filipsen; Jan Skov Pederson; Daniel Otzen, Ümit Akbey (2020) Predicted Loop Regions Promote Aggregation: A Study of Amyloidogenic Domains in the Functional Amyloid FapC. JMB 432, 7, 2232-2252

- Anne Diehl, Yvette Roske, Linda Ball,  Anup Chowdhury, Mattias Hiller, Noel Moliere, Regina Kramer, Daniel Stöppler, Catherine L. Worth, Brigitte Schlegel, Martina Leidert, Nils Cremer, Natalja Erdmann, Daniel Lopez, Heike Stephanowitz, Eberhard Krause, Barth-Jan van Rossum, Peter Schmieder, Udo Heinemann, Kürşad Turgay, Ümit Akbey, Hartmut Oschkinat (2018) Structural changes of TasA in biofilm formation of Bacillus. PNAS 27, 115 (13), 3237-3242