Category Archives: News

New Publication in Analytical Chemistry

The Arndt Group recently published in Analytical Chemistry on how to improve Laser-induced acoustic desorption (LIAD) for natural biochromophores. This methodology might enable us to use fragile biomolecules in Quantum-enhanced metrology experiments.

Link to Paper, look up other publications  or visit the Arndt Group Homepage.

Ugur Sezer, Lisa Wörner, Johannes Horak, Lukas Felix, Jens Tüxen, Christoph Götz, Alipasha Vaziri, Marcel Mayor, and Markus Arndt
Laser-induced acoustic desorption of natural and functionalized biochromophores
Anal. Chem., 2015, 87 (11), pp 5614–5619 (Download)

New publication in J. Phys. Chem. B

Together with our colleagues at the Institute for Biophysical Dynamics at the University of Chicago, we have developed a method using infrared spectroscopy and atomistic modeling that would allow to better understand the mechanism behind the extreme ion selectivity and transport properties in ion channels. Our findings have recently been published in The Journal of Physical Chemistry B.

Location of the potassium channel KcsA in the cell membrane of bacteria. The schematic illustration on the right shows the changes in strength and direction of vibrational coupling inside the filter depending on the ion species, as found by the study. @David S. Goodsell & RCSB Protein Data Bank
Location of the potassium channel KcsA in the cell membrane of bacteria. The schematic illustration on the right shows the changes in strength and direction of vibrational coupling inside the filter depending on the ion species, as found by the study. @David S. Goodsell & RCSB Protein Data Bank

Ion channels are essential structures of life.

Ion channels are specialized pores in the cell membrane and move charged atoms known as ions in and out of cells, thereby controlling a wide variety of biological processes including brain function and heartbeat. Ion channels are generally selective for certain ions, allowing specific types of ions to flow through at very high rates, while hindering the flow of others. On the basis of this selective permeability, ion channels are classified as potassium channels, sodium channels, etc.

The cell’s most ubiquitous gateways are potassium ion channels – the importance of this type of ion channels was underpinned in 2003 when Roderick MacKinnon received the Nobel Prize in Chemistry for resolving the first atomic structure of the bacterial KcsA potassium channel.

Despite a large body of work, the exact molecular details underlying ion selectivity and transport of the potassium channel remain unclear. Since conventional methods, such as X-ray crystallography, capture only averaged frozen structures, it is not possible to investigate how the dynamic of the protein could be involved in key aspects of their function.

New method to unravel the secret of ion channel selectivity

Our team, together with researchers at the Institute for Biophysical Dynamics (University of Chicago), have now used infrared (IR) spectroscopy coupled with molecular dynamic-based simulations of the obtained spectra to investigate the subtlest changes in the shape of the KcsA potassium channel that are induced by binding either potassium or the only 0.04 nanometers smaller sodium ion. This combination proved to be a powerful tool to disentangle convoluted IR spectra – which contain contributions from the whole protein – by assigning each part of the spectrum to the amino acids that contribute to it.

This new approach allows us to probe these mechanisms in a non-perturbative way, meaning without tedious and expensive isotope labeling strategies. Moreover, it opens the way to study the structure and dynamics of ion channels on their biologically relevant timescales by extending it to two-dimensional infrared spectroscopy.

The study shows for the first time that the combination of the two methods can be used to detect subtle conformational changes in large membrane proteins, such as the KcsA potassium channel. Furthermore, it opens the way to capture the dynamics of proteins in real time at atomic resolution, which has been impossible with standard techniques until now.

Read the publication, browse through other publications or visit the Vaziri Group Homepage.

Press releases about the topic by the MFPL and IMP.

Paul Stevenson, Christoph Götz, Carlos R. Baiz, Jasper Akerboom, Andrei Tokmakoff, and Alipasha Vaziri
Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
J. Phys. Chem. B 2015, 119 (18), pp 5824–5831 (Download)

Two New WWTF Grants for the Vaziri Lab

The Vaziri lab has successfully secured with colleagues at IMP and IMBA two grants in the WWTF’s Life Sciences Call 2014 – “IMAGING – Innovative Biological and Biomedical Applications of Novel Imaging Technologies”. The projects will be dedicated to building new super-resolution and high-speed whole-brain functional imaging techniques in behaving animals.
Congratulations!

A comment to a physical transduction model in magnetoreception

Here we expolore feasibility arguments considering the perturbation of retinal switching in rhodopsin by a local electric field from a nearby electric dipole. This work relates to a physical transduction mechanism of magnetoreception in migratory birds.

J. Espigulé-Pons, C. Götz, A. Vaziri and M. Arndt
Physical constraints for the Stoneham Model for Light-Dependent Magnetoreception
arXiv: 1412.7369 (2014)

For other papers published by the Qunabios Research Platform please visit our Publications Section.

Publication in J. Opt. Soc. Am. B

Here we discuss the role of wavefront effects on the nanometer scale to matter wave interferometry with pulsed photo-depletion gratings, illustrated with organic clusters.

Nadine Dörre, Philipp Haslinger, Jonas Rodewald, Philipp Geyer, Markus Arndt
Refined model for Talbot-Lau matter-wave optics with pulsed photodepletion gratings
JOSA B 32, 114–120 (2015)

For other papers published by the Qunabios Research Platform please visit our Publications Section.

 

Publication in Phys. Rev. Lett.

Photofragmentation gratings for Quantum Interferometry with Molecular Clusters of Vanillin, HFB and other organic molecules

N. Dörre, J. Rodewald, P. Geyer, B. von Issendorff, P. Haslinger, and M. Arndt,
Photofragmentation Beam Splitters for Matter-Wave Interferometry
Phys. Rev. Lett. 113, 233001 (2014),  highlighted as
PRL Editor’s Choice
Viewpoint in Physics 7, 122 (2014) by Gil Summy

These studies explore new coherent manipulation method for quantum interferometry in the time domain with organic van der Waals clusters that rather decompose than ionize upon absorption of a single photon.

 


VBC Art&Science Contest 2014 winner from the Vaziri lab

Friederike Schlumm and Christoph Götz from the Vaziri lab won together with Isabel Grießhammer (IMBA) the VBC Art&Science Contest with their video:

“Incubate over night”

Incubation is a widely used method in research. Nevertheless, the underlying mechanisms are not well understood. In this project we aimed to visualize this crucial process. We therefore applied the imaging technique “stop-motion” to study an overnight incubation. Our results reveal new insights into scientific experiments.

Four teams participated, with four terrific art pieces, which were exhibited in our Cafeteria, and the VBCers were voting for the best piece.

See the other great art pieces at: http://www.vbcphdprogramme.at/current-students/art-science-contest/