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Over onsWaar vindt u onsprof. dr. A. (Armagan) Kocer
University Medical Center Groningen

prof. dr. A. Kocer

Tenure-Track Associate Professor

 RESEARCH INTERESTS

Functioning mechanism of ion channels, specifically, ion channels in neurodegenerative diseases, mechanosensitive ion channels, and viral ion channels

Synthetic biology tools for probing the structural changes of ion channels and controlling their function

Nanotechnology (Triggered drug delivery systems / Ion-channel-based biosensors)

FUNDING

  • 2014-2015 ERC Proof of Concept Grant on “Ion channel-based sensors    ICANSENSe” (PI) (€150,000)
  • 2014 In2LifeSciences on starting a collaborative work with Natural and Medical Sciences Institute (NMI) at the University of Tubingen 
  • 2013-2014 ERC Proof of Concept Grant on “Commercial feasibility of triggered liposomal drug delivery by means of modulated bacterial channels (MOCHA)” (PI) (€150,000)
  • 2009   Zernike Institute Grant on a joint project “Modulating protein channels and nanoporous” (Co-PI) (in kind, PhD                   student)
  • 2007-2014  ERC Starting Grant (PI) (€1,5000,000)
  • 2008-2011 European Union Seventh Research Framework Programme (FP7) on “Bio-inspired self-self-assembled                      nano-enabled surfaces (BISNES)”, NMP-Nanosciences, Nanotechnologies, Materials and new Production                            Technologies (Co-PI and Work Package leader) (€375,000)
  • 2008-2011 European Union Sixth Research Framework Programme (FP6) on “Targetted delivery of nanomedicine                    (MediTrans)”, NMP-Nanotechnologies and nanosciences, knowledge-based multifunctional materials and new   production processes and devices (Work Package leader) (€250,000)
  • 2007-2012 NWO Vidi Grant (PI) (€750,000)
  AWARDS
  • 2014         Runner-up in Science-Business Event in Brussels
  • 2009         New and Notable speaker, European Biophysical Societies Association (EBSA)
  • 2006         Young Investigator Award, International Liposomes Society (ILS), London, UK
  • 1994-1998 Graduate scholarship, The Scientific and Technical Research Council of Turkey (TUBITAK)
  • 1995-1997 Research assistantship, Middle East Technical University, Institute of Science, Ankara, Turkey
  • 1992          First rank graduate, B. Sc. in Biology, Middle East Technical University, Institute of Science, Ankara, Turkey
  • 1988-1992  Undergraduate Basic Science Scholarship, The Scientific and Technical Research Council of Turkey (TUBITAK). It is awarded to students who have chosen a basic science department and ranked in top 1% in a national university entrance exam.
WORK EXPERIENCE
  • 2016-present Tenure-track Associate Professor at UMCG, Department of Neurosciences
  • 2014-2016 Tenure-track Assistant Professor at UMCG, Department of Neurosciences
  • 2009-2014     Tenure-track Assistant Professor at University of Groningen, Department of Biochemistry
  • 2009-2007     Post-doc at University of Groningen, Department of Biochemistry
  • 2002-2007     Senior scientist at Biooragnic Materials and Devices (BiOMaDe), Groningen (non-academic)
  • 2001-2002     Research scientist at Biooragnic Materials and Devices (BiOMaDe), Groningen (non-academic)
PUBLICATIONS
(Kocerlab members are highlighted in bold)

2017

Calle, D. Yilmaz, S. Cerdan, A. Kocer “Drug delivery from engineered organisms and nanocarriers as monitored by multimodal imaging technologies”  AIMS Bioengineering 4(2):198- 222 (2017) (pdf)

N. Melo, C. Arnarez, H. Sikkema, N. Kumar, M. Walko, H. J. C. Berendsen, A. Kocer, S. J. Marrink and H. I. Ingólfsson “High-throughput simulations reveal membrane-mediated effects of alcohols on MscL gating”J. Am. Chem.Soc. 139: 2664-2671 DOI:10.1021/jacs.6b1109 (2017)

2016

A. Dimitrova, Walko, M. Hashemi Shabestari, P. Kumar, M. Huber, and A. Kocer  “In situ, Reversible Gating of a Mechanosensitive Ion Channel through Protein-Lipid Interactions” Frontiers in Physiology 7:Article 409 (2016)

2015

  •  A. Kocer “Mechanisms of mechanosensing - Mechanosensitive channels, function and re-engineering” Current Opinion in Chemical Biology 29: 120-127 (2015)
  • D. Yilmaz, A. Dimitrova, M. Walko, A. Kocer “Study of Light-induced MscL Gating by EPR Spectroscopy” European Biophysics Journal 44(7): 557-565 (2015) 
  • A. Konijnenberg, J B Gonzalez, L Bannwarth, D Yilmaz, A Kocer, C Venien-Bryan, N Zitzmann, F Sobott “Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment” Protein Science 24: 1292 - 1300 (Invited) (2015) 
  • J Pacheco-Torres#, N Mukherjee#, M Walko, P López-Larrubia, P Ballesteros, S Cerdan, A Kocer “Image Guided Drug Release From pH-sensitive Ion Channel-functionalized Stealth Liposomes into an in vivo Glioblastoma Model” Nanomedicine: Nanotechnology, Biology, and Medicine 11: 1345-1354 (2015) (#: equal contribution)
2014
  • A. Konijnenberg#, D Yilmaz#, H I Ingólfsson, A  Dimitrova, S J Marrink, Z. Lid, C. Vénien-Bryand, F. Sobott, A. Kocer “Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry” Proc Natl Acad Sci USA 111: 17170-17175 (2014) (#: equal contribution)
  • H Ingólfsson*, P. Thakur, K.  Herold, E.  Hobart, N.  Ramsey, X. Periole, D. de Jong, M. Zwama, D.  Yilmaz, K.  Hall, T.  Maretzky, H. Hemmings, C. Blobel, S. Marrink, A.  Kocer, J.  Sack, O. Andersen* "Phytochemicals perturb membranes and promiscuously alter protein function" ACS Chemical Biology  9: 1788-1798 (2014)
  • N Mukherjee, M. D. Jose, J. P. Birkner, M. Walko, H. I. Ingólfsson, A. Dimitrova , C. Arnarez, S. J. Marrink, A. Koçer “The activation mode of mechanosensitive ion channel MscL by lysophosphatidylcholine differs from tension-induced gating”  The FASEB Journal 28:4292-4302 (2014)
  • M Urban, A Kleefen, N Mukherjee, B Windschiegl, P Seelheim, M vor der Brüggen, A Koçer, R Tampé* “Semi-automated nanopore biochips for multiplexed parallel single transport recordings” Nano Letters 14:1674-1680 (2014)
  • M D F Jose#, M Barthmes#, J P Birkner, A Brüggemann, C Wahl-Schott, A Kocer “Studying mechanosensitive ion channels with automated patch clamp” European Biophysics Journal 43:97-104 (2014) (#: equal contribution).

2013

  • E Halzǎ, T Hedegaard Bro, B Bilenberg, A Kocer “Well-DefineDefined Microapertures for Ion Channel Biosensors” Anal. Chem. 85: 811−815 (2013)
  • J T Mika#, J P Birkner#, B. Poolman, A Koçer “On the role of individual subunits in MscL gating: “All for one, one for all?” FASEB J 27: 882-892, (2013) (#: equal contribution)
  • W Szymanski, D Yilmaz, A Kocer*, B L Feringa* “Bright ion channels and lipid bilayers” Accounts of Chemical Research 46: 2910-23, (2013) (AK and BLF are invited)
  • M Persson, M. Gullberg, C. Tolf, A. M. Lindberg, A. Månsson, A. Kocer “Transportation of nanoscale cargoes by Myosin propelled actin filaments” PLoS ONE 8 (2):  p. e55931 (2013)
  • L Tauk, T Thami, L Ferez, A Koçer, J M Janot, P Déjardin “Phosphatidylcholine background surfaces for biosensors” Colloids and Surfaces B: Biointerfaces 101 (1): 189-195 (2013)
2012
  • J P Birkner, B Poolman, A Koçer “Hydrophobic gating of Mechanosensitive channel of large conductance evidenced by single-subunit resolution”  Proc Natl Acad Sci USA 109 (32): 12944-12949 (2012)
  • A Kocer, L Tauk, P Dejardin “Nanopore sensors: from hybrid to abiotic systems” Biosensors and Bioelectronics 38(1): 1-10 (2012)

2011

  • I Kusters, N Mukherjee, M R de Jong, S Tans, A Koçer, A Driessen “Taming Membranes: Functional Immobilization of Biological Membranes in Hydrogels” PLoS ONE 6(5):e20435 (2011)
  • C E Price, A Koçer, S Kol, J P van der Berg, A J M Driessen “In vitro synthesis and oligomerization of the mechanosensitive channel of large conductance, MscL, into a functional ion channel” FEBS Letters 585: 249-254 (2011)
  • A D Cirac, G Moiset, J T Mika, A Koçer, P Salvador, B Poolman, S J Marrink, D Sengupta “The Molecular Basis for Antimicrobial Activity of Pore-Forming Cyclic Peptides” Biophysical Journal 100(10) pp. 2422 – 2431 (2011)

2008

  • A Dudia, A Koçer, V Subramaniam, H Kanger. “Biofunctionalized lipid-polymer hybrid nanocontainers with controlled permeability” Nano Letters 8 (4): 1105-1110, (2008)

2007

  • A Koçer “A Remote Controlled Valve in Liposomes for Triggered Liposomal Release” J Liposome Research 17 (3): 219 – 225, (2007) (invited)
  • A. Koçer*, M. Walko, B. L. Feringa*. “Synthesis and Utilization of reversible and irreversible light-activated nanovalves derived from the channel protein MscL” Nature Protocols 2(6): 1426- 1437, (2007)

2006

  • A. Koçer#, M. Walko#, E. Bulten, E. Halza, B. L. Feringa, W. Meijberg. ”Rationally Designed Chemical Modulators Convert a Bacterial Channel Protein into a pH-Sensory Valve” Angew. Chem. Int. Ed. 45: 3126-3130, (2006) (#: equal contribution)

2005

  • A. Koçer#, M. Walko#, W. Meijberg, B. L. Feringa. “A Light-Actuated Nanovalve Derived from a Channel Protein.” Science 309: 755-759, (2005) #: equal contribution)
Last modified:07 July 2017 12.02 p.m.