Welcome to the KocerLab

We are an interdisciplinary group, which is interested in exploring the working mechanism of membrane proteins and in their potential applications to solve societal problems. Much of work focused on bacterial mechanosensitive ion channels.

financial support

Prof. Ben Feringa wins Nobel Prize 2016 in Chemistry! We wish him many more years of exciting science!

News from the lab

October 2016

  • Prof. A Kocer joined the Editorial Board of Frontiers in Oncology as a Review Editor in Cancer Imaging and Diagnosis.
  • Prof. Dame Carol Robinson is visiting University Medical Center Groningen, University of Groningen. In the second day of her visit to the Netherlands as “The Speaker of the Year 2016” of the Netherlands Society for Biochemistry and Biology (NVBMB), Prof. Robinson will be talking to principle investigators and giving a lecture.

September 2016

  • Our invited research paper  “In situ, Reversible Gating of a Mechanosensitive Ion Channel through Protein-Lipid Interactions ” is published in Frontiers in Physiology.(pdf)

August 2016

  • Claudio Tiecher started his five months collaborative project at the  Osaka University under the guidance of Prof. Yasushi Okamura and Dr. Akira Kawanabe. Claudio will be learning modifying ion channels with a genetically encoded environment-sensitive fluorescent probe. His visit is supported by JASSO Scholarship Program through the exchange program between the Graduate School of Medicine, Faculty of Medicine, Osaka University and University Medical Center Groningen, University of Groningen.

June 2016

  • Armagan Kocer organized a session “Ion channels of the nervous system in health and disease” for the Dutch Neuroscience Meeting. A Kocer gave a talk, Marloes Scholten, and Claudio Tiecher presented two posters.
  • Congratulations to Marloes Scholten for successfully defending her Master project on “Cloning and overexpression of Kv4.3-EGFP fusion protein in Pichia pastoris“. We wish her success and pleasure in her second project.
  • Claudio Tiecher presented his work on voltage-gated ion channel Kv4.3 at the European Neuroscience Conference for Doctoral Students

 April 2016

  • Armagan Kocer gave a lecture at “Biophysics of Protein-Lipid Interactions: From Model Systems to Cells” meeting in Bad Herrenalb, Germany. The joint meeting is organized by the Membrane Sections of the French and German Biophysical Societies.

December 2015

  • Marloes Scholten joined the Kocerlab to perform her master project. We wish her lots of success in her studies.
  • Congratulations to Dr. Mac Donald Jose for  successfully defending his Ph.D. thesis on 4th Dec 2015! We wish him  all the best and success in his academic position in his home country Malawi.
  • Dr. Armagan Kocer and Dr. Sebastien Balme (University of Montpellier/European Institute of Membrane) are awarded a Van Gogh travel grant from EP/NUFFIC. The PIs and their team members will initiate a collaborative work on hybrid nanopores mimicking biological ion channels.
  • Dr. Armagan Kocer is elected as one of the five board members of NVBMB (The Netherlands Society for Biochemistry and Molecular Biology)
  • Caludio Tiecher will present his work on Kv4.3 ion channels in a Pecha Kucha style at the TN2 Conference on 3rd December in Amsterdam in 6 minutes 40 seconds. We wish him lots of successes and a fruitful meeting.

November 2015

  • A. Kocer will give a pitch at the matchmaking event of NWO on “Building Blocks of Life“. This new research program aims at forming collaborations between public and private partners to improve the understanding of cellular systems based on the molecular building blocks of life.
  • Our invited review paper “Mechanisms of mechanosensing – Mechanosensitive channels, function and re-engineering” is published in Current Opinion In Chemical Biology (pdf). The review covers the exciting developments in the last two years, including force from the lipid principle of mechanosensation, new methods to study protein-lipid interactions, the role of water in mechanosensitive ion channel gating, and recent nanotechnology applications of these channels.

September 2015

  • Congratulations to Marwah Doestzade for successfully defending her Master thesis on 2nd Sep 2015! We wish her all the best and success in her further training in medicine and hope to see her back in the future.

July 2015

  • Our invited research paper “Study of light-induced MscL gating by EPR spectroscopy” is accepted for publication in European Biophysics Journal. The paper reports on the commanding at the gating of MscL to defined sub-open states by light and monitoring the resulting conformational changes by EPR spectrometry. The results showed that this approach can be employed to study the early conformational changes upon mechanosensing real time.

April 2015

  • A collaborative, invited research paper  “Top-down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment” is accepted for publication in Protein Science. This mass spectrometry work led by Frank Sobott reports on collision-induced dissociation (CID) of membrane proteins into highly charged monomers, to peptide fragments and their sequencing. Data showed the oligomeric state, mass, and the amino acid sequence of numerous membrane proteins including mechanosensitive channel of large conductance (MscL), a prokaryotic inwardly rectifying potassium channel (KirBac), and a Hepatitis C virus porin (P7) by employing  native mass spectrometry together with CID fragmentation  in a single experiment. 

March 2015

  • Our collaborative research paper  “Image Guided Drug Release From pH-sensitive Ion Channel-functionalized Stealth Liposomes into an in vivo Glioblastoma Modelis accepted for publication in Nanomedicine: Nanotechnology, Biology, and Medicine. The paper reports on a liposomal delivery system comprising of a chemically-modified pH-sensitive ion channel embedded in a stealth liposome, i.e. sterically-stabilised liposomes for prolonged circulation in the blood. Our data showed that, the engineered channel protein functions as a sensory valve in liposomes; can detect the mildly acidic pH of the tumor microenvironment with 0.2 pH unit precision and they release their intraluminal content into C6 glioma tumors selectively, in vivo. 
  • We welcome Claudio Tiecher to our group as a Ph.D. student. He will study  Kv4.3 ion channel. We wish Claudio lots of success in his “marriage” for 4 years.

January 2015

  • We welcome Marwah Doestzade to our group. She is graduated from Medicine at the end of 2014 and will perform her master studies with us. We wish Marwah lots of success and fun with her master thesis.

December 2014

  • Congratulations to Dr. Duygu Yilmaz for  successfully defending her Ph.D. thesis on 8th Dec 2014! We wish her  all the best and success in her new position as a scientist at ProQR Therapeutics NV.

October 2014

  • Our collaborative research paper on “Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry” is accepted for publication in Proc Natl Acad Sci USA (PNAS). The paper reports on direct observation of global conformation changes of an ion channel during its gating.

June 2014

  • Our paper titled “The activation mode of mechanosensitive ion channel MscL by
    lysophosphatidylcholine differs from tension-induced gating” is accepted for publication in the FASEB Journal. The paper reports on the molecular mechanism of lysophospholipid-induced activation of the mechanosensitive ion channel MscL. 
  • A new collaborative research paper on “Phytochemicals perturb membranes and promiscuously alter protein function” is accepted for publication in ACS Chemical Biology. A variety of phytochemicals that are consumed for their positive effects in our health have been found to change various cell functions. However, their action mechanism has not been well understood. In this collaborative work, by testing the effect of widely consumed phytochemicals on variety of ion channels we showed that, their effect is not specific to particular proteins. Many effects of phytochemicals are due to common, lipid bilayer-mediated mechanisms.

May 2014

  • Armagan Kocer will participate in the event organised at the ERC premises in Brussels by Science|Business on 3-4 July 2014. After a day of training with experts in communicating to investors, she will present her first ERC-Proof of concept  project  in the form of an elevator pitch to a group of leading innovators in industry and academia and some venture capitalists.  9 other ERC-PoC grantees will also participate in the event. You can find information about individual projects here.

April 2014

  • Congratulations to Dr. Nobina Mukherjee for  successfully defending her Ph.D. thesis on 28th Apr 2014! We wish her  all the best and success in her new position as a post doctoral fellow at Oxford.
  • Prof. Dr. Sebastian Cerdan is visiting Kocerlab. Prof. Cerdan will give a lecture on novel contrast agents for MRI, on 29 April at 13:00 in room 3215.0154 (UMCG, Groningen). He will be available for discussions before and after his lecture. If you are interested in talking to him, please send an email to a.kocer at umcg.nl.

February 2014

  • A new collaborative research paper with Prof. R. Tampé group on  ” Highly parallel transport recordings on a membrane-on-nanopore chip at single molecule resolution” is accepted for publication in Nano Letters. The paper reports on a silicon chip with 250,000 well-defined femtoliter cavities with an average of 100 nm in diameter openings as a platform to study ion channels and transporters in a multiplexed manner. Each cavity is individually accessible for fluorescence readout. Suspended lipid bilayers are formed in high yield by simply spreading large unilamellar proteoliposomes on the chip surface. A mechanosensitive ion channel MscL is used to demonstrate the functioning of the system.

January 2014

  • Our  paper  titled “Studying mechanosensitive ion channels with automated patch clamp” is accepted for publication in European Biophysics Journal. The research reports on the automated patch clamping of mechanosensitive ion channels. We patched the channels in their native environment using giant E. coli spheroplasts and in giant unilamellar liposomes using both conventional and automated patch clamp electrophysiology. The tension sensitivity and channel kinetics data obtained in an automated system were in good agreement with that obtained from conventional patch clamp. Ability to patch mechanosensitive ion channels on automated patch will pave the way to high throughput fundamental and drug screening studies on mechanosensitive ion channels. This work is done in collaboration with Nanion Technologies and Prof. Christian Wahl-Schott.

 

 

July 2013

  • An ERC-PoC grant  is awarded to Armagan Kocer for her project on sensors based on ion channels. The title of the project is “Ion ChANnel SENSors”.

May 2013

  • Congratulations to Nobina Mukherjee for winning the best poster prize in the biannual Zernike Vlieland meeting (26. – 28.05.2013). She presented  her PhD work on engineered ion channel-based liposomal carrier for targetted imaging/drug release to a tumor model in mice.

April 2013

  • A collaborative review paper with Prof. B.L. Feringa and Dr. W. Szymanski on “Bright ion channels and lipid bilayers” is accepted for publication in Accounts of Chemical Research (2 April 2013). The review focuses on approaches toward dynamic control of lipid bilayer assembly and channel function and in particular transport across the lipid bilayer-ion channel barrier of cells.
  • Research assistant Neeraj Kumar successfully completed his project on cloning of MscL in a GRAS organism, and preparation of three different liposomal formulations for immunological studies. We wish him all the best and success in his new position as a PhD student at the Center for Behaviour and Neurosciences.

January 2013

  • A new collaborative research paper with Prof. A. Månsson group on “Transportation of nanoscale cargoes by Myosin propelled actin filaments” has been published in PLoS ONE 8 (2):  p. e55931 (2013).

December 2012

  • Our new paper titled “Well Defined Micro-apertures for Ion Channel Biosensors” is accepted to be published in ANALYTICAL CHEMISTRY (21 December 2012). The research reports a new straightforward method for generating microfabricated small apertures on  Si/SiO2 chips and demonstration of its use for accommodating not only self-inserting pore-forming peptides but also bigger, selective, two-state (i.e. open/on and closed/off) gated ion channels.  Sensory chips with gated ion channels that can be engineered to sense different analytes could offer opportunities ranging from very early detection of disease markers to environmental control. This work is done in collaboration with Ir. Brian  Bilenberg and Ir. Tobias Hedegaard Bro from NIL Technology ApS (Denmark)

November 2012

  • Congratulations to Dr. Jan Peter Birkner for  successfully defending his PhD thesis on 23rd Nov 2012.

October 2012

  • Our new paper titled ” On the role of individual subunits in MscL gating: “All for one, one for all?” is accepted to be published in FASEB J (31 October 2012). The research reports that hydrophobic gating alone is not sufficient for full opening of the channel. This suggests the presence of supplementary mechanisms and/or insufficient expansion of the channel by hydrophobic gating in the absence of applied tension.
  • Congratulations to Nobina Mukherjee for winning the best talk prize in the 20th annual GBB Symposium.
  • Congratulations to Duygu Yilmaz for winning third poster prize in the 20th annual GBB Symposium.
  • Our new paper titled “Hydrophobic gating of mechanosensitive channel of large conductance evidenced by single-subunit resolution” has been published in Proc Natl Acad Sci USA. The research reports a method that allows single-subunit resolution for manipulating and monitoring of a homopentameric mechanosensitive channel protein.
  • A collaborative review paper with Prof. P. Déjardin group on “nanopore sensors: from hybrid to abiotic systems” has been publisjed in Biosensors & Bioelectronics. The review focuses on synthetic treck-etch pores in polymer foils and on biological nanopores.
  • A new collaborative research paper with Prof. P. Déjardin group titled “Phosphatidylcholine background surfaces for biosensors” has been published in Colloids and Surfaces B: Biointerfaces
  • Postdoc Martin Walko is leaving the Kocerlab where he worked for 2 years. He will be working at P. J. Safarik University in Kosice, Slovakia, as an Assist. Prof. We wish him all the best and success in his new position.
  • Bachelor student Martijn Zwama successfully completed his bachelor thesis on “Bilayer mediated modification of MscL function by phytochemicals”. We wish him lots of success in his Master studies.