One postdoctoral position is available in Dr. Ümit Akbey’s lab (https://akbey.structbio.pitt.edu/) in the Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA. We are seeking an enthusiastic postdoctoral fellow to work on “biofilm forming functional amyloid” Structural biology. This research field is an interdisciplinary research avenue, comprising protein biophysics, structural biology, NMR spectroscopy, microbiology, electron-microscopy, bacterial biofilms, antimicrobial resistance, and others. 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 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. We also benefit from the established cryo-EM facility at the department and use the cryo-EM symbiotically combined with NMR to understand the structural details of our systems.

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, and 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.

Profile of the candidates: We are looking for an open-minded, motivated, driven scientist who has a background in biological ssNMR as well as in 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 - umitakbey@pitt.edu. More information on projects can be acquired via email and please don’t hesitate to contact us. Employment will be for one year and can be extended up to several years. Career development options and support will be provided for the candidates. The starting date is as soon as possible. The position will involve 1) producing high-quality homogeneous amyloid fibrillar functional amyloid proteins, characterizing them in detail, determining biophysical properties thoroughly and reproducibly, and characterizing them by advanced structural biology tools, mainly NMR bur also EM. We are particularly looking for an independent and motivated person, who will take the lead and expand the project.

Duties or Responsibilities

·         Ability to design and perform experiments

·         Ability to analyze and interpret experimental results

·         Ability to use a collaborative approach to formulate alternative and creative solutions to problems

·         Present research projects to internal and external meetings or workshops

·         Engage in writing of publications and reports

·         Engage in writing of research proposals and help acquire funding

·         Assist with graduate students. Student and technician training

·         Good communication with group leaders and members

Expectations or Standards

·         Ph.D. or equivalent in biochemistry, microbiology, structural biology, biophysics, cell biology, biomedical engineering, or related fields. This position is subject to the University's background check policy.

·         Interested applicants should send their application package (a full CV, a cover letter of their research interest, and the contact information of 3 referees) to Dr. Ümit Akbey, umitakbey@pitt.edu with the subject.

Opportunities Available

·         Attendance of workshops, symposiums, and conferences will be supported

·         Postdoctoral independent funding applications will be encouraged

·         Postdoctoral Career Development and Progress Assessment Process (https://www.oacd.health.pitt.edu/postdocs/postdoctoral-career-development-progress-assessment-process )

·         Pittsburgh has great central locations, scenic views, and award-winning restaurants, offering a variety of events and things to do (https://www.visitpittsburgh.com/)

Selected publications related to these positions:

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 (2023) Site-specific protein backbone deuterium 2Hα quadrupolar patterns by proton-detected quadruple-resonance 3D 2HαcαNH MAS NMR spectroscopy. Journal of Magnetic Resonance, 125, 1010861.

- 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 2H13C1H MAS NMR Spectroscopy. JBioNMR. 10.1007/s10858-021-00388-4

- Ümit Akbey (2021) Dynamics of uniformly labeled solid proteins between 100 and 300 K: A 2D 2H13C MAS NMR approach. JMR 327, 106974

- 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

- Ümit Akbey and Hartmut Oschkinat (2016) Structural Biology Applications of Solid State MAS DNP NMR. JMR 269, 213-224 

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