Two Postdoctoral Positions @Akbey Lab – Solid state NMR

Two Postdoctoral Positions @Akbey Lab
Structural Biology Department, School of Medicine, University of Pittsburgh, PA, USA

Research Topics: Structures and Molecular Mechanisms of Functional and Pathological amyloids, Solid state NMR, DNP, Functional Amyloid Fibrils in Biofilms
The aim of Akbey Lab is to use modern solid-state NMR (ssNMR) spectroscopy to study functional amyloid fibrils involved in bacterial biofilm forming, as well as pathological fibrils. 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 and pathological 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.
People working in the Akbey Lab will gain expertise in a variety of structural biology methods, mainly ssNMR based protein structure/dynamics determination combined with biophysical methods, as well as molecular biology and biochemistry techniques, among others. If you are interested in joining our team please contact me and I would be happy to talk to you more about the ongoing work.

Profile of the candidates:
We are looking for scientists who have background in biological ssNMR as well as in biophysics, biochemistry 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 per email and please don’t hesitate to contact. Initial employment will be for one year that can be extended. The starting date is as soon as possible with the application deadline on 15. May 2022.

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. 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.
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.

Selected publications related to these positions:
- 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 labelled 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
- Anna König, Daniel Schölzel, Boran Uluca, Thibault Viennet, Ümit Akbey, Henrike Heise (2019) Hyperpolarized MAS NMR of unfolded and misfolded proteins. SSNMR 98, 1-11
- 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
- Frederic Mentink-Vigier, Ümit Akbey, Akiva Feintuch, Shimon Vega, Hartmut Oschkinat. (2015) Theoretical Aspects of Magic Angle Spinning - Dynamic Nuclear Polarization. JMR. 258, 102-120
- Ümit Akbey, Andrew J. Nieuwkoop, Sebastian Wegner, Anja Voreck, Britta Kunert, Priyanga Bandara, Frank Engelke, Niels Chr. Nielsen, Hartmut Oschkinat (2014) Quadruple-Resonance MAS NMR Spectroscopy of Deuterated Solid Proteins. Angew. Chem. Int. Ed. 53, 2438-2442
- Sheetal K. Jain, Anders B. Nielsen, Anja Voreck, Matthias Hiller, Britta Kunert, Matthias Ernst, Hartmut Oschkinat, Ümit Akbey, Niels Chr. Nielsen (2014) Low-power polarization transfer between deuterons and spin-1/2 nuclei using adiabatic RESPI-RATION-CP in solid-state NMR. Phys. Chem. Chem. Phys. 16, 2827-2830

 

 

Asst. Prof. Ümit Akbey

Ph.D
Office: +1 412 383 9896
E-mail: umitakbey@pitt.edu

 

University of Pittsburgh
Department of Structural Biology
School of Medicine
3501 5th Ave.
2044 Biomedical Science Tower 3
Pittsburgh, PA, 15261, United States