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.
 

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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



 


 



Stella Sun
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Phone 412-383-5907
Fax 412-648-9008

University of Pittsburgh
2050 Biomedical Science Tower 3

 

Stella Sun

 
Stella Y. Sun’s research is focused on addressing important scientific and biomedical problems, particularly in pathogen-host interaction from structural and molecular cell biology perspectives. My lab is dedicated to the experimental and computational application of cryo-ET for structural determination of biological macromolecules or biological machinery in single-celled parasites that cause important human diseases. I am particularly interested in understanding the molecules transportation, organelle biogenesis and their regulations in the invasion process of the malaria parasites (or related apicomplexan parasites) and the migration of Trypanosoma brucei that causes African sleeping sickness in humans and Nagano in cattle. Our research is to visualize the organization of cellular structures and their coordination in 3D spatial organization through a multi-scale imaging platform ranging from microns to sub-nanometers, to elucidate the molecular and structure functions that drive cell migration or invasion. Crucially, the novel cryo-ET analysis developed will also broadly enable the study of molecular machines in other complex biological contexts.  

Visit Stella's lab website


Education & Training

Undergraduate

Wuhan University, Wuhan, China
B.S. Life Sciences, 2004-2008

Postgraduate

Stanford University, Stanford, California, United States
Research Scientist 2017-2021

Baylor College of Medicine, Houston, Texas, United States
Postdoc Associate 2016-2017

Mechanobiology Institute, Singapore
Research Fellow 2014-2016

National University of Singapore, Singapore
Ph.D., in Biological Sciences 2008-2014



Selected Awards and Honors


2020 Stanford ChEM-H Seed Grant
2014 Young Scientist Travel Award, Kuo Symposium on 3D Cryo-EM Molecular Imaging
2011 Blackwell Poster Awards, 22nd Annual Molecular Parasitology Meeting



Representative Publications


Sun SY, Segev-Zarko L-A, Chen M, Pintilie GD, Schmid MF, Ludtke SJ, Boothroyd JC, Chiu W. Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures [Internet]. Proceedings of the National Academy of Sciences. 2022. Available from: http://dx.doi.org/10.1073/pnas.2111661119 

 

Tierney W, Vicino I, Sun S, Chiu W, Engel E, Taylor M, Hogue I. Methods and Applications of Campenot Trichamber Neuronal Cultures for the Study of Neuroinvasive Viruses [Internet]. 2021. Available from: http://dx.doi.org/10.20944/preprints202105.0098.v1 

 

Chen M, Bell JM, Shi X, Sun SY, Wang Z, Ludtke SJ. A complete data processing workflow for cryo-ET and subtomogram averaging. Nat Methods. 2019 Nov;16(11):1161–1168. PMCID: PMC6858567 

 

Sun SY, Kaelber JT, Chen M, Dong X, Nematbakhsh Y, Shi J, Dougherty M, Lim CT, Schmid MF, Chiu W, He CY. Flagellum couples cell shape to motility in. Proc Natl Acad Sci U S A. 2018 Jun 26;115(26):E5916–E5925. PMCID: PMC6042131 

 

Jin J, Galaz-Montoya JG, Sherman MB, Sun SY, Goldsmith CS, O’Toole ET, Ackerman L, Carlson L-A, Weaver SC, Chiu W, Simmons G. Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane. Cell Host Microbe. 2018 Sep 12;24(3):417–428.e5. PMCID: PMC6137268 

 

Chen M, Dai W, Sun SY, Jonasch D, He CY, Schmid MF, Chiu W, Ludtke SJ. Convolutional neural networks for automated annotation of cellular cryo-electron tomograms. Nat Methods. 2017 Oct;14(10):983–985. PMCID: PMC5623144

 

Luengo I, Darrow MC, Spink MC, Sun Y, Dai W, He CY, Chiu W, Pridmore T, Ashton AW, Duke EMH, Basham M, French AP. SuRVoS: Super-Region Volume Segmentation workbench. J Struct Biol. 2017 Apr;198(1):43–53. PMCID: PMC5405849

 

Li C, Zhang Y, Yang Q, Ye F, Sun SY, Chen ES, Liou Y-C. NuSAP modulates the dynamics of kinetochore microtubules by attenuating MCAK depolymerisation activity. Sci Rep. 2016 Jan 6;6:18773. PMCID: PMC4702128

 

Sun SY, Wang C, Yuan YA, He CY. An intracellular membrane junction consisting of flagellum adhesion glycoproteins links flagellum biogenesis to cell morphogenesis in Trypanosoma brucei. J Cell Sci. 2013 Jan 15;126(Pt 2):520–531. PMID: 23178943

 

Li F-J, Shen Q, Wang C, Sun Y, Yuan AY, He CY. A role of autophagy in Trypanosoma brucei cell death. Cell Microbiol. 2012 Aug;14(8):1242–1256. PMID: 22463696

 

Zhou Q, Liu B, Sun Y, He CY. A coiled-coil- and C2-domain-containing protein is required for FAZ assembly and cell morphology in Trypanosoma brucei. J Cell Sci. 2011 Nov 15;124(Pt 22):3848–3858. PMID: 22114307

  

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Jonathan Coleman
This email address is being protected from spambots. You need JavaScript enabled to view it. 
Phone (412) 648-8077
Fax (412) 648-9008

University of Pittsburgh
1050 Biomedical Science Tower 3

 

Jonathan Coleman

 
The aim of my research is to elucidate the molecular function, architecture, and high-affinity drug binding sites of synaptic vesicle transporters in neurons by studying their function using biochemical techniques and determining their structures using single particle cryo-EM. I am particularly interested in understanding the conformational changes and mechanism associated with transport. I have developed methods for large-scale expression, stabilization by drugs, and for the production of antibodies which recognize these transporters. The use of transporter-antibody complexes is essential in order to provide mass and molecular features to assist in cryo-EM reconstructions because these transporters are small membrane proteins which are largely ensconced within membrane. Atomic structures of transporters in complex with therapeutic drugs are essential for the design of better small-molecule therapeutics with higher specificity and fewer side-effects and will also advance efforts toward understanding the function of these transporters.  

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Education & Training

Undergraduate

University of British Columbia
Hon. B.Sc. Biochemistry, 2002-2007

Postgraduate

Aarhus University, Department of Physiology
Visiting student in lab of Dr. Jens Peter Anderson, 2010

University of British Columbia, Department of Biochemistry and Molecular Biology
Ph.D. in lab of Dr. Robert Molday, 2007-2013

Oregon Health & Science University, Vollum Institute
Postdoctoral training in lab of Dr. Eric Gouaux, 2013-2020


Selected Awards and Honors


2018 OHSU School of Medicine Paper of the Month
2016 Finalist for OHSU Postdoctoral Paper of the Year
2014-2016 Banting Postdoctoral Fellowship


Representative Publications


Coleman, J.A.*, Navratna, V.*, Antermite D., Yang, D, Bull, J.A., Gouaux, E. (2020). Chemical and structural investigation of the paroxetine-human serotonin transporter complex. eLife, 9:e56427

 

Coleman, J.A.*, Yang, D.*, Zhao, Z., Wen, P., Yoshioka, C., Tajkhorshid, E., Gouaux, E. (2019). Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport. Nature 569, 141-145.

 

Coleman, J. A., Gouaux, E. (2018). Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Nat. Struct. Mol. Biol. 25, 170-175.

 

Coleman, J. A., Green, E. M., Gouaux, E. (2016). Thermostabilization, Expression, Purification, and Crystallization of the Human Serotonin Transporter Bound to S-citalopram. J. Vis. Exp., e54792, doi:10.3791/54792.

 

Coleman J.A., Green E.M., Gouaux E. (2016). X-ray structures and mechanism of the human serotonin transporter. Nature 532 (7599), 334-339.

 

Green E.M., Coleman J.A., Gouaux E. (2015). Thermostabilization of the human serotonin transporter in an antidepressant-bound conformation. PloS One 10 (12), e0145688.

 

Vestergaard A.L., Coleman J.A., Lemmin T., Mikkelsen S.A., Molday L.L., Vilsen B., Molday R.S., Dal Peraro M., Peter Andersen J. (2014). Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2. Pro. Natl. Acad. Sci. 111 (14), E1334-E1343.

 

Coleman J.A.*, Zhu X.*, Djajadi H.R., Molday L.L, Smith R.S., Libby R.T., John S.W.M., Molday R.S. (2014). Phospholipid flippase ATP8A2 is required for normal visual and auditory function and photoreceptor and spiral ganglion cell survival. J. Cell. Sci. 127 (5), 1138-1149.

 

Coleman J.A., Quazi F., Molday R.S. (2013). Mammalian P(4)-ATPases and ABC transporters and their role in phospholipid transport. Biochim. Biophys. Acta. 1831, 555-74.

 

Coleman J.A., Vestergaard A.L., Molday R.S., Vilsen B., Peter Andersen J. (2012). Critical role of a transmembrane lysine in aminophospholipid transport by mammalian photoreceptor P4-ATPase ATP8A2. Proc. Natl. Acad. Sci. 109, 1449-54.

 

Coleman J.A., Molday RS. (2011). Critical role of the beta-subunit CDC50A in the stable expression, assembly, subcellular localization, and lipid transport activity of the P4-ATPase ATP8A2. J. Biol. Chem. 286, 17205-16.

 

Coleman J.A., Kwok M.C., Molday R.S. (2009). Localization, purification, and functional reconstitution of the P4-ATPase Atp8a2, a phosphatidylserine flippase in photoreceptor disc membranes. J. Biol. Chem. 284, 32670-9. 

  

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(*equal contribution)


 


 



Rieko Ishima
This email address is being protected from spambots. You need JavaScript enabled to view it.
Phone (412) 648-9056
Fax (412) 648-9008

University of Pittsburgh
1037 Biomedical Science Tower 3

 

Rieko Ishima

Associate Professor


The major objective of our research has been to determine protein structure and dynamics using nuclear magnetic resonance (NMR); spectroscopy, in order to elucidate protein function particularly relating to protein-ligand interactions.



Visit Ishima lab website


Education & Training

Graduate

Kyoto University, Kyoto, Japan
Ph.D., 1992 in Chemistry, Supervisor:  Dr. Kazuyuki Akasaka

Postgraduate

Ontario Cancer Institute
Postdoctoral Fellow 1995 – 1997


Representative Publications


Webb, C., Upadhyay, A., Giuntini, F., Eggleston, I., Furutani-Seiki, M., Ishima, R. & Bagby, S. (2011) Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway. Biochemistry, 50, 3300-9.

Myint, W., Cai, Y., Schiffer, C., Ishima, R. (2012) Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes. J Biomol NMR, 53, 13-23.

Cai, Y., Yilmaz, N.K., Myint, W., Ishima, R., Schiffer, C. (2012) Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput. 8, 3452-62.

Liriano,  M.A., Varney, K.M., Wright, N.T., Hoffman, C.L.,  Toth, E.A., Ishima, R., and Weber, D.J. (2012) Target binding to S100B reduces dynamic properties and increases

Christen, M.T., Menon, L., Myshakina, N.A., Ahn, J., Parniak, M.A. & Ishima, R. (2012) Structural Basis of the Allosteric Inhibitor Interaction on the HIV-1 Reverse Transcriptase RNase H domain. Chemical Biology & Drug Design, 80, 706-16.



Active Grants


Conformational dynamics and inhibitor responses of HIV-1 RT RNase H in solution
10/01/13 – 08/31/17
National Institutes of Health
R01

Pittsburgh Center for HIV Protein Interactions (PCHPI)
09/30/12 – 07/31/17
National Institutes of Health
P50