Ümit Akbey
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Phone 412-383-9896
Fax 412-648-9008

University of Pittsburgh
2044 Biomedical Science Tower 3

 

Ümit Akbey
 
The aim of Akbey Lab is to use modern solid state NMR (ssNMR) spectroscopy to study biofilm forming functional amyloid 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 insoluble and non-crystalline proteins. Solid-state NMR has made a remarkable progress in the last decade to become a high-resolution and -sensitivity method due to advances in sample preparation, hardware, novel methods such as proton-detection and hyperpolarization (DNP). These allow studies of not only difficult proteins in-vitro but also in their complex in-vivo environment. We also like to combine ssNMR with other exciting structural biology tools. We use recombinant protein expression and biophysical methods to produce and characterize isotope labeled protein samples.
Our functional amyloid systems are a unique class of amyloid fibrils with specific biological functions in living organisms, in contrast to the pathological amyloids causing disease as neurodegenerative ones (aS or ab). A subgroup of these systems is forming bacterial biofilms (such as CsgA, FapC, TasA or PSMs), a major cause of persistent infections and an antimicrobial resistance (AMR) target. We focus on the NMR-based structural biology of these biofilm forming functional amyloids. We aim to determine atomic resolution structure and molecular dynamics information, for better understanding of amyloid formation, biofilms and their interactions. This will pave the way towards future treatments against bacterial infections and their antimicrobial resistance.
People working in the Akbey Lab get in-depth expertise in a variety of structural biology methods, mainly ssNMR based protein structure/dynamics determination, biophysics, biochemistry, recombinant protein expression and purification, physical chemistry and others. We are always looking for motivated scientists to work with us at any level, and please contact us for possibilities.
 

Visit Umit's lab website


Education & Training

Undergraduate

Bilkent University, Ankara, Turkey
B.Sc. in Chemistry, 1999-2005

Graduate

Max Planck Institute (MPIP), Mainz, Germany
Ph.D. in Solid-state NMR, 2005-2008 (with Prof. Hans W. Spiess) 

Postgraduate

Leibniz Institute for Molecular Pharmacology (FMP), Berlin, Germany
Postdoctoral Associate in Structural Biology, 2009-2015 (with Prof. Hartmut Oschkinat)

Aarhus University (iNano - AIAS), Aarhus, Denmark
Assistant Professor, 2015 - 2018

Forschung Zentrum Julich (FZJ), Julich, Germany
Senior Scientist, 2018-2019 (with Prof. Henrike Heise)

Weizmann Institute of Science, Rehovot, Israel
Senior Scientist, 2020-2021 (with Prof. Lucio Frydman)

Radboud University of Science, Nijmegen, The Netherlands
Senior Scientist, 2021 (with Prof. Arno Kentgens)



Representative Publications

Ümit Akbey. (2022) Site-specific Protein Methyl Deuterium Quadrupolar Patterns by Proton detected 3D 2H13C1H MAS NMR Spectroscopy. Journal of Biological NMR

 

Ümit Akbey. (2021) Dynamics of uniformly labelled solid proteins between 100 and 300 K: A 2D 2H13C MAS NMR approach. Journal of Magnetic Resonance, 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. Journal of Molecular Biology 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. Solid State NMR 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 Journal of Magnetic Resonance 269, 213-224

 

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

 

Ümit Akbey, Trant Franks, Arne Linden, Marcella Orwick Rydman, Sascha Lange, Hartmut Oschkinat. (2013) Dynamic Nuclear Polarization Enhanced Solid State NMR of Proteins. Topics in Current Chemistry

  

Full publication list