Click anywhere to go on to the next slide

What distribution of peptides result from digesting proteins with trypsin? This demonstration is best viewed as a slide show,enabling you to simulate a session and make changes in cursor position more obvious.To do this, click Slide Show on the top tool bar, then View show. Click anywhere to go on to the next slide

Teach BioBIKE how to be trypsin, a proteolytic enzyme that cuts proteins after lysine (K) and arginine (R).

Trypsin acts on proteins. To see it in action, we should give it the sequence of some protein to work with.

Perhaps something in our favorite cyanobacterium, ss120.

Here’s a protein in ss120: p-pro0047. Type it in the box and click “Execute” to evaluate the expression and see the sequence in the lower frame.

Ok. There it is, in all its glory. Or rather 200aa of its glory. But that is neither here nor there. We want to cut the sequence after "K" and "R". Select “Split” to begin thinking like an enzyme.

It looks like BioBIKE would appreciate a string here. Fair enough, let’s give it one…

Click in the SPLIT field.

Over in our sequence-calling node, select “Cut” to cut this function…

… and paste it into the SPLIT function.

Done and done. Let’s give SPLIT a little guidance by telling it where to cut the string. Trypsin cuts after "K" and "R".

Trypsin cuts after every "K" and "R".

Let's try "K" first. Enter "K" and execute your SPLIT command to see what it does.

But we need to tell BioBIKE two places to cut. A list may be of assistance here. Erase "K" by clicking the red x

“K” and “R.” Robot trypsin will cut after every Lysine and Arginine. Hit execute to see what this looks like.

Seems pretty variable… I wonder how long each fragment is? Choose “Surround with” and …

… LENGTHS-OF to evaluate the length of each fragment. Don’t forget we want the plural statement, and not the one directly above it.

Hit “Execute.”

And there they are. The length of each fragment of the protein p-pro0047 as digested by Trypsin. Do the numbers make sense? You can check by comparing these numbers with the peptides of the previous result. Do the lengths agree?

Now that we digested a single protein, let’s do all the proteins in an organism. Erase p-pro0047 and choose “PROTEINS-OF” from the GENOME menu.

Execute LENGTHS-OF again to display the lengths of all the proteins in ss120.

These numbers seem odd – much bigger than before! Check them by executing the SPLIT function, using Execute off of SPLIT's action menu.

The numbers and lengths don't agree at all! (31 31 75…) isn't (2 17 5)Why? One clue is double parentheses. If you scroll through your results, you'll find that the result is in the form ((…)(…)…). BioBIKE is actually returning the number of elements in each sublist.

We can take care of this headache with the SIMPLIFY-LIST function, which goes around your SPLIT node and combines all the sublists into a single list.

No more ((double parentheses))!Now execute it again, for real.

Again, there they are. Now do the numbers make sense?

Now that it works, we want to package the procedure so that we never have to think about it again. First we need to get more screen space. Select “collapse” from the SIMPLIFY-LIST node.

Add “DEFINE-FUNCTION.” It’s up in the DEFINITION menu.

Give it a catchy name. Then describe the function so you (and perhaps others) can get a basic idea of what it does…

…from a helpful summary

1 Give a descriptive name to the argument – the information the function acts on. TRYPSIN-DIGEST-OF will act on proteins.

2 The body of the function will be the procedure you just constructed. Copy it to paste into the body of the function.

3 Paste what you just copied into the body, using the menu obtained by clicking the box's green action icon.

Now that it's there, expand it to see what we got.

Whoops! We left it working on a specific case – all protein of ss120. We need to make it work on a general case, whatever the user provides as the argument, proteins. Delete the PROTEINS-OF node.

And type “proteins,” which is the variable we asked trypsin-digest-of to look for in the first place.

Executing DEFINE-FUNCTION adds our function to BioBIKE.

Check it out. No, seriously. Check it out.

Much less cluttered.

Click anywhere to go on to the next slide