Protein Modeling C

[SWAnG]

Also, it states: "All protein topics used in the Science Olympiad Protein Modeling Event are from past Molecule of the Month articles. Teams are expected to study the articles related to this year's proteins." On the website but it seems like none of these are really related to our current proteins. Does this mean we are simply expected to know all of the MoMs from this year?

[SWAnG]

Anyone have a copy of the youtube videos that were removed from the CBM website? There were two on the Zinc Finger Nucleases and the Domains that are no longer available.

I am not exactly sure about which videos you are talking about since I am not doing this event, but did you try looking for it in the poster's Youtube channel?

If you go to http://cbm.msoe.edu/scienceOlympiad/participant2.php then scroll down to "designing Genome Editing Nucleases" then clicking on "the two domains of a finger nuclease protein" and "is 16 basepairs really a long enough sequence of DNA' the Youtube videos by Aron Geurts are no longer available.

[colorado mtn science]

So I got one of the on-site build practice kits (based on the 2012 State on-site) and the tuber they gave me was way too long. Did anyone else have this problem?

[1234alert]

We're given eight support posts in our pre-build model. Is there one particular way we have to use them? Or do we use them for the sake of keeping our protein rigid? Should they represent an interaction between amino acids? Also, is it ok if the 278 cm toober only has 139 amino acids when we're supposed to have 140? Thanks!

[colorado mtn science]

We're given eight support posts in our pre-build model. Is there one particular way we have to use them? Or do we use them for the sake of keeping our protein rigid? Should they represent an interaction between amino acids? Also, is it ok if the 278 cm toober only has 139 amino acids when we're supposed to have 140? Thanks!

They're used for keeping the protein rigid. If you want to show hydrogen or disulfide bonds, you can use some of your creative additions for that. In jmol, if you use the command "calculate struts," it shows the best position for your posts.

[ohmann]

Help!! This is my first time in protein modeling and I have no idea how to use the jmol or how to insert the sidechains into the jmol program. Thanks

[bernard]

Help!! This is my first time in protein modeling and I have no idea how to use the jmol or how to insert the sidechains into the jmol program. Thanks

Have you looked at the wiki for Protein Modeling? It has a lot of useful information about getting started on Jmol.

[Gearbox]

How does pH affect amino acids, and why is it important?

[bernard]

How does pH affect amino acids, and why is it important?

These resources answer your question pretty well:
Effect of pH on Structure of Amino Acids
How does pH affect the ionization of a amino acid?

[Nature_Girl]

I understand that endonuclease binds to DNA for transcription and genome editing purposes, but would a DNA molecule be reasonable to include in the pre-build? Also, besides the active sites, what other creative add-ons are available can we add to the model?