How to look at your protein’s functionality and concentration with Tycho.Cloud

May 27, 2020 Beate Kern

Magnifying Glasses

Whether you’re a Tycho.Cloud user or just hearing about it, the big vision for Tycho.Cloud and its current capabilities are focused on helping you get more out of your Tycho data and really understand the quality of your protein samples. Here are three more features that help you do that.

 

Be confident that your protein is functional

Have you checked to make sure your protein’s functional? Thermal shift assay (TSA) can be used to quickly test whether a ligand binds to a protein of interest. Often, this is done to find molecules that bind a target protein from a library of potential binders. At other times, a TSA is run with only one ligand against your protein of interest, a ligand that is already known to bind the protein. In such a situation, a TSA is a fast way of checking whether the interaction is still happening, and this is a useful way to test your protein’s quality – if it’s not binding (anymore), it‘s probably unfolded, and you’d definitely want to know that! Run this check after protein purification, or after you’ve stored your sample for a while, to see whether it’s still good.

The Tycho Binding Check app on Tycho.Cloud helps you decide whether there really is an interaction. The algorithms in the app are quite sophisticated, so they work even when there’s two proteins binding each other in the mix. Protein-protein interactions are commonly not analyzed via TSA because the interpretation of the resulting data can be complex, but thanks to Tycho.Cloud, it’s really fast and easy, just like running experiments on Tycho.

 

Look at protein concentration with Tycho


Tycho and Tycho.Cloud help you look at your protein’s concentration. Protein concentration is most commonly measured via absorbance, so people are often surprised to find out that it’s possible with fluorescence – and therefore with Tycho, too.

Fluorescence is a bit of a complex topic, but, in brief, it’s again about comparing the right samples (if you’re interested in how it all works, check out this FAQ). If you have a sample with known protein concentration available, you can use it as a reference to compare against other samples containing the same protein, similar to running a BSA standard curve for your Bradford assay. Except in the case of Tycho, one known concentration is enough and you don’t have to prepare a whole series of them. Tycho.Cloud then comes in when it’s time to analyze the data. It helps you do the calculations, and it plots your result in a way that’s easy to understand, so you don’t have to worry about making any mistakes.

 

Organize and manage your data effortlessly

 

Tycho data organization

 

At the end of the day, what good is data if you can’t easily work with and make sense of it. Part of that is having your data organized. Tycho.Cloud lets you upload and manage your own Tycho database (stay tuned for a future blog post on that!). You have the option to annotate your samples with some categories we suggest, like protein name or class, concentration, buffer and more. Alternatively, work with the annotations you provided earlier on Tycho itself, back when you ran the measurement. Then filter, sort and search your database pretty much any way you like – never again spend your time sorting through all those zip files!

 

Curious to learn more?

Learn more about Tycho.Cloud here or get access here. Anybody who has access to a Tycho is invited!

We’re sure there’s something in Tycho.Cloud for you too! If you have any ideas for great apps or additional features, tell us at nt.cloud@nanotempertech.com. It’s still in beta, so let us know what you think and help us build an awesome product.

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