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Therefore, ion channels are present in the cell membrane to transport them in and outside of the cell. They are porous in nature and are specific for specific types of charged atoms. Some are symporter (transporting two types of ions in the same direction) while some are antiporter (transporting two ions in the opposite direction to each other). Some are also conjugated with the transport of other bio-molecules like glucose (glucose transporter involved in transporting glucose and Na ion in opposite direction).
Ion channels are most important in certain cells like nerve cells where they are involved in maintaining electrical charges. These electrical charges are necessary to generate electrical gradient necessary for the signal transmission from one nerve cell to another one. Based on the selective permeability of the ion channels, they are classified as the potassium channel, sodium channel, chloride channel, calcium channel, etc.
The most common and ubiquitous ion channels are potassium ion channels. The importance of which first came into light when Roderick MacKinnon received the Nobel Prize in Chemistry for his work to resolve the first atomic structure of the bacterial LcsA potassium channel in 2003. Despite the elucidation of the atomic structure of the potassium channel, the exact molecular basis of the selectivity and the transport of the potassium ion channel remained unclear.
Alipasha Vaziri is a physicist and the head of the Research Platform “Quantum Phenomena and Nanoscale Biological System of the University of the Vienna. He together with his group of researchers at the Max F. Perutz Laboratory and the Institute of Molecular Pathology, explained that using a conventional method like X-ray crystallography, it was not possible to investigate the dynamics of the potassium channel that involves a key aspect of their function.
To elucidate the dynamics and the ion channel specificity, Vaziri together with his team and researchers of the Institute for Biophysical Dynamics at University of Chicago, have used infrared (IR) spectroscopy in combination with molecular dynamic-based simulations of the obtained spectra to carry out the investigation in changes in the shape of the KcsA potassium channel when bound to either potassium or to the only 0.04 nanometer-sized sodium ion.
The combination of IR-spectroscopy and molecular dynamics provided a powerful tool to solve the convoluted IR spectra that contain contributions from the whole protein by assigning each part of the spectrum to the amino acids.
This approach has now allowed us to probe these mechanisms in an easy way that is not tedious and requires less expensive isotope labeling strategies. It also opens a way to study the structure and the dynamics of ion channels in their own biological time scale by extending it to the 2D infrared spectroscopy. This approach can also be used to detect the conformational changes in the large membrane proteins in real time at atomic resolution, which were not possible using standard techniques until now.
Reference: The Journal of Physical Chemistry (Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling)
Article doi: 10.1021/acs.jpcb.5b02223