Research


I am a Research Specialist in the Loogerlab. We work on the development of tools for neurobiology and imaging. I am interested in rationally designing and improving proteins to use as tools, structural biology, and solving fundamental questions in biology. We solved the structure of the calcium binding protein sensor GCaMP2 in several different oligomeric states. Using the structural information, we screened for better variants using the calcium release following acetylcholine agonization of HEK293 cells, resulting in GCaMP3 - the best calcium indicator for neurobiology to date. The GCaMP sensor is based on circularly permuted GFP, with attached to its new termini calmodulin and the M13 peptide. The sensor works like this: in the presence of calcium the calmodulin domain wraps around the M13 peptide and the bunghole in cpGFP is closed, resulting in an increase in fluorescence. We used targeted mutagenesis to force the protein to crystallize in its monomeric form. In addition, a calcium free structure was obtained by knocking out the calcium binding sites in the calmodulin domain of this protein. With the full panel of structural information in hand we were able to improve the sensor's signal change by directed mutagenesis. We did not stop here. Efforts to increase signal-to-noise, dynamic range, affinity and spectral variants resulted in a family of calcium indicators with different characteristics. Results on this will be published in the near future.


Calcium saturated GCaMP2 monomer. Circular permuted EGFP in green, Calmodulin in cyan, M13 peptide in purple, Calcium ions in orange.



I am also interested in fundamental and applied microbiology. We closely collaborate with researchers from Drs. John van der Oost, Stan Brouns and Fabian Blombach at Wageningen University. Using the by Dr. Jianyong Tang developed microscopy technique VVPalm we were able to localize Cas2, a protein molecule involved in the CRISPR-based immune system in bacteria and archaea, with high precision in three dimensions, and get detailed three dimensional information of a dendrite.



Recent Publications (current to 2008)

March, 2012
Akerboom J, Chen T, Wardill TJ, Tian L, Marvin JS, Mutlu S, Carreras Calderón N, Esposti F, Borghuis BG, Sun XR, Gordus A, Orger MB, Portugues R, Engert F, Macklin JJ, Filosa A, Aggarwal A, Kerr R, Takagi R, Kracun S, Shigetomi E, Khakh BS, Baier H, Lagnado L, Wang SSH, Bargmann CI, Kimmel BE, Jayaraman V, Svoboda K, Kim DS, Schreiter, ER and Looger L.
Optimization of a GCaMP calcium indicator for neural activity imaging
Submitted

January, 2012
Steven J. Husson, Wagner Steuer Costa, Sebastian Wabnig, Jeffrey N. Stirman, Joseph D. Watson, W. Clay Spencer, Jasper Akerboom, Loren L. Looger, Millet Treinin, David M. Miller, III, Hang Lu, and Alexander Gottschalk. Optogenetic analysis of a nociceptor neuron and network reveals modulatory ion channels acting downstream of nociceptive sensors.
Current Biology, In Press

November, 2011
Jasper Akerboom, Lin Tian, Jonathan S. Marvin, Loren L. Looger.
Engineering and Application of Genetically Encoded Calcium Indicators.
Springer Neuromethods 2012. In Press

September, 2011
Lin Tian, Jasper Akerboom, Eric R. Schreiter and Loren L. Looger.
Neural activity imaging with genetically encoded calcium indicators.
Progress in Brain Research 2012. In Press

May, 2010
Tang J, Akerboom J, Vaziri A, Looger LL and Shank, CV
Near-isotropic 3D optical nanoscopy with photon-limited chromophores.
PNAS (local) (supporting information) (supplemental movie 1) (supplemental movie 2) (supplemental movie 3)

December, 2009
Tian L, Hires SA, Mao T, Huber D, Chiappe ME, Chalasani SH, Petreanu L, Akerboom J, McKinney SA, Schreiter ER, Bargmann CI, Jayaraman V, Svoboda K, Looger LL
Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators.
Nature Methods (local) (supplementary materials) (supplemental movie 1) (supplemental movie 2) (supplemental movie 3)

August, 2009
R.K.P. Kuipers, H.J. Joosten, E. Verwiel, J. Paans, J. Akerboom, J. van der Oost, N.G.H Leferink, W.J.H. van Berkel, G. Vriend, P.J. Schaap.
Correlated mutation analyses on super-family alignments reveal functionally important residues
Proteins: Structure, Function, and Bioinformatics (local)

December, 2008
Akerboom J, Velez Rivera JD, Rodriguez Guilbe MM, Alfaro Malave EC, Hernandez HH, Tian L, Hires SA, Marvin JS, Looger LL, Schreiter ER.
Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.
Journal of Biological Chemistry, Dec 18, Epub (local) (supplementary figures) (supplementary tables)

July, 2008
Rodriguez Guilbe MM, Alfaro Malave EC, Akerboom J, Marvin JS, Looger LL, Schreiter ER.
Crystallization and preliminary X-ray characterization of the genetically encoded fluorescent calcium indicator protein GCaMP2.
Acta Crystallographica Section F. Volume 64, Part 7 (local)

May, 2008
Brouns SJ, Barends TR, Worm P, Akerboom J, Turnbull AP, Salmon L, van der Oost J.
Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily.
Journal of Molecular Biology. Volume 379, Issue 2, 29 May 2008, Pages 357-371 (local)