NACHRDB: Solving the puzzle of ion channel functioning


Can you recognize this famous painting?


Can you tell me how many pieces, if any, are missing? I know it is next to impossible!





Interestingly, we faced quite a similar problem in our research. And, at first, we also thought that it is next to impossible. We were wrong.


But, first things first, as our research is heavily related to the nervous system, let us start from there.




The nervous system regulates every single process in the body.


The nerve cell (or neuron) is the building block of the nervous system. Billions of neurons are “talking” to each other, transferring vast amounts of information over long distances with enormous speed.


The nerve impulse (we biologists call it “action potential”) travels across the neuron-like this: wzzzzzzuh, bump – and once it reaches the end of the cell, having no clear idea how to cross the space – separating it from another cell, some magic happens.





Magic happens outside the comfort zone. Neuronal transmission is no exception

(Source: Reworked from https://www.khanacademy.org/science/biology/human-biology/neuron-nervous-system/a/the-synapse and icons made by Freepick from www.flaticon.com)




The key to the whole process lies in this very gap between two cells.

In biology, magic often ends up as some rather dull biochemistry! 

This is precisely the case.




Nicotinic acetylcholine receptor – a cornerstone of the nervous system


At the very beginning of the 20th century, Sir Henry Dale and Otto Loewi shed some light on what is going on in this magical void. They shared a Nobel Prize for their discovery.

It turned out that tiny organic molecules of acetylcholine are released in this gap by one cell and received by another cell (a process called chemical signaling).


It is very similar to sending text messages to your friend using a cell phone: first, the message is released, then it reaches your friend's device, and then your friend reads it. Both processes can be called signaling.

Analogous to the post-synaptic cell’s global system for mobile communication (GSM) module, which makes it possible to receive a chemical signal, is a receptor.


In this particular case, it is the nicotinic acetylcholine receptor (as it responds to nicotine as well), or nAChR - a protein transferring chemical signals across the nervous system, allowing us to think, feel and move.




Nerve cells communicate with each other almost as we do with our cell phones

(Source: Reworked from icons made by Freepick from www.flaticon.com)



Simple and clear?


Far from it!


For example, how does the chemical signal transform back into an action potential, allowing the nerve impulse to travel further to the next cell?



Riddles of the nAChR


In 1970, we learned that nAChRs are ion channels that receive a chemical signal (e.g., acetylcholine) and open the channel allowing the ions to move in and out of the cell, thus explaining the action potential.


Though invaluable, this is a very crude description that does not tell when and how the channel opens. What have we learned, standing here nearly 50 years after the discovery?


Important information we all gathered is that structure, or “shape” and composition of the molecule, defines what you can and cannot do.



     As in biology, we say, “structure determines function.”



But here lies a problem.


Although the general role of nAChRs was recognized, the regulation of nAChR function and dysfunction (resulting in some disorders and diseases) remained mostly unclear. We lacked the know-how, how the molecular pieces of nAChR come and work together.


Revealing the detailed 3D structure of nAChRs provided a few answers but raised many more questions.


There are ~2500 amino acid residues in each nAChR molecule. If you change one, it may dramatically disturb the entire structure; and at the same time, changing many might not have any effect at all.


To solve this riddle, many studies focused on specific chunks (groups of residues) of the molecule that seemed relevant. However, it is challenging to study even individual pieces of this molecule because of nAChR’s complicated structure and function.



Why are nAChRs important?


This complexity comes from many different sources.


First, nAChRs or very similar molecules, but with diverse 3D structures, are found in all multicellular animals (from worms and snails to fish, frogs, elephants, and, of course, humans).


NAChRs (or very similar receptors) can be found in almost all of our related bilateral species

(Source: Reworked based on freely available images from www.unsplash.com and www.pixabay.com)



Second, nAChR subunits are found in most tissues, but in various quantities. The diversity of nAChR receptor types in the brain is impressive (16 vs. 1 in muscles).


Humans have 17 different nAChR genes producing 17 different nAChR subunits.


To make a functional nAChR, you need only 5 subunits, which is evident for a massive number of possible permutations to yield these 17 nAChR receptor types.


All those different nAChR receptor types possess distinct electrophysiological and pharmacological properties.


Third, all those nAChRs are involved in many physiological processes and disorders.


Fourth, there is a wide range of small molecules (or drugs) that can bind at numerous locations (or binding sites) across the nAChR molecule, affecting its functioning.


Thus, this overwhelming knowledge is not systematically accessible, which makes it hard to define contemporary challenges in the field of study and apply the available knowledge to promote further discoveries.



“We chose it because we deal with huge amounts of data. Besides, it sounds really cool” © Larry Page



How to solve this issue?


Well, like Google’s co-founder Larry Page, we thought a database would be an excellent way to overcome the complexity of the current knowledge on nAChRs.


Our database is rooted on three pillars: 3D models, sequence alignment, and residue-level functional annotations.


NACHRDB , a webserver, facilitates data interpretation by integrating the residue-level functional annotations (i.e., what each residue is responsible for) with interactive visualization of the 3D structure.


It can help scientists in all the stages of the research process, and it is freely available online (https://crocodile.ncbr.muni.cz/Apps/NAChRDB/).



Now, it is high time to go back to our puzzle exercise!


Here is it (on the right). Still no clues, huh?





Our web service comes in handy here.


NACHRDB helps us to track how the pieces (functionality of individual residues) come together, and which pieces (residues with the unknown role) are missing so that new lessons can be learned, and relevant experiments can be designed to obtain a big picture of nAChR biology in all its beauty.    



Imagine this work of art (Courtesy to Rembrandt), which is now unveiled for you, as an assembled nAChR molecule.



         


Do you see the captain and the lieutenant in the center? Their role is to lead the company.


The ensign carries the company's colors for recognition.


The drummer helps the whole company to march in the same step with his rhythmic drumbeats.


The musketeer loads a gun, and the pike-man holds his pike to repel any cavalry and so on.



They all act as a whole, performing complex tasks beyond one man's capacity.



The same held true for the NAChR: its complex functioning is based on the orchestrated multitude of various small functions performed by individual residues (one governs the channel opening, another one binds some drug, etc.).


NACHRDB helps you to easily explore residues' functionality, not only putting the scattered literature data in one place but also visualizing it and placing it into a structural context to give you a better idea of the functional importance of certain nAChR regions and how they are related to each other.

           

    

In case you are interested to learn more about the NACHRDB, you are welcome to read our scientific article’s preprint, freely available online: https://www.biorxiv.org/content/10.1101/2020.01.08.898171v1


P.S. NACHRDB is a part of a broader web-based platform of bioinformatic tools, called CrocoTools (http://crocodile.ncbr.muni.cz). CrocoTools focuses on providing user-friendly, scalable, and computationally efficient software and web-services. Though these tools were designed for scientists, we tried to make them as easy to use as possible. We warmly encourage you to try out one of them and provide suggestions!




Written by Aliaksei Chareshneu

Edited by Somsuvro Basu and Markus Dettenhofer


Publication date: 23.01.2020